title: Beta-blockers disrupt mitochondrial bioenergetics and increase radiotherapy efficacy independently of beta-adrenergic receptors in medulloblastoma.

city: Marseille

first: MANON

last: CARRE

address: 27 boulevard Jean Moulin

department: Faculté de Pharmacie

institute: CRCM

summary: Our study showed that propranolol, carvedilol and nebivolol inhibited medulloblastoma cell proliferation and invasion by affecting energy metabolism pathways (OXPHOS and glycolysis) and by triggering a metabolic catastrophe that deprived tumor cells of their adaptive bioenergetics capacities. To better understand the importance of bioenergetics in response to treatment, we generated β-blocker-resistant ONS-76 cells by exposing them to increasing concentrations of propranolol, carvedilol or nebivolol for 16 weeks. The resulting cell lines i.e., ONS-76 RP, ONS-76 RC and ONS-76 RN, displayed a higher mitochondrial OCR and ATP production than the sensitive parental ONS-76 WT cells.  By qRT-PCR, we showed that the expression of β-blockers canonical targets (β-ARs) was not altered in these resistant cells. Sequencing of total RNA from the four meduloblastoma cell models further indicated that cell resistance could not be explained by the down-regulation of key proteins of the β-AR downstream signaling, including the adenylate cyclase or their transcriptional targets. Our data also showed that the efficacy of propranolol, carvedilol and nebivolol was not impacted by β-AR silencing, further supporting the idea that β-blockers trigger an alternative signaling pathway in medulloblastoma cells.

overall_design: RNAseq from ONS-76 medulloblastoma parental cells and three derived cell lines resistant to beta-blockers.

first: Celine

last: Keime

first: Mailys

last: Rossi

first: Manon

last: Carre


title: Mechanistic basis for maintenance of CHG methylation in plants

status: Public on May 30 2022

city: St Louis

first: Xuehua

last: Zhong

state: MO

address: One Brookings Drive

department: Biology

country: USA

institute: Washington University in St. Louis

type: Methylation profiling by high throughput sequencing

summary: This study investigated the regulatory mechanism of CMT3 mediated CHG methylation in A. thaliana.

overall_design: Whole-genome bisulfite sequencing of CMT3 and CMT3 mutants to determine genome-wide levels of CHG methylation and the effect on DNA methylation of making point mutations to CMT3.

first: Sarah

last: Leichter

first: Jianjun

last: Jiang


title: Endothelial cell activation driven by CD4+ memory T cells produced soluble factors

status: Public on May 29 2022

city: Amsterdam

first: Kim

last: Jeucken

address: Meibergdreef 9

country: Netherlands

institute: Amsterdam UMC

type: Expression profiling by high throughput sequencing

summary: In this project we analyzed whole transcriptome changes in endothelial cells (ECs) in response to stimulation with activated CD4+ memory T cells produced factors. Given the central role of NF-κB signaling in EC activation we treated cells with inhibitors for canonical NF-κB signaling (IKKβ inhibitor, iIKKβ) and non-canonical NF-κB signaling (NF-κB inducting kinase (NIK) inhibitor, iNIK). Cells were stimulated 72h with conditioned medium (hereafter called Tm sup = 50% culture supernatant from aCD3/aCD28 activated CD4+ memory T cells; 50% RMPI supplemented with 10% FCS) and treated with iIKKβ, iNIK or DMSO as a control. Other controls taken along were unstimulated DMSO treated ECs and unstimulated untreated ECs.

overall_design: Examination of whole transcriptome changes in primary human umbilical cord ECs (HUVEC) stimulated with Tm sup and treated with iIKKβ or iNIK.

last: M Jeucken

first: Charlotte

middle: C

last: van Rooijen

first: Yik

middle: Y

last: Kan

first: Lotte

middle: A

last: Kocken

first: Aldo

last: Jongejan

first: Abraham

last: I van Steen

first: Jaap

middle: D

last: van Buul

first: Jan

middle: P

last: van Hamburg

first: Sander

middle: W

last: Tas


title: 3D landscape of Hepatitis B virus interactions with human chromatins [3C-HTGTS]

status: Public on May 31 2022

city: Beijing

first: Xiong

last: Ji

address: Yiheyuan Road

department: School of life science

country: China

institute: Peking University

summary: We employed a highly sensitive technology, 3C-HTGTS (3C-high-throughput genome-wide sequencing), to globally identify HBV DNA-host DNA contacts in cellular models of HBV infection.  We found that HBV cccDNA does not randomly position in host genome, but instead preferentially establishes contacts with the host DNA at active chromatin regions.  In contrast, the organization of integrated HBV DNA is largely regulated by the local genome epigenetic environment, which particularly forms chromosome loop with host genome where gene promoters together with active histone modifications are enriched. Our study provides a high throughput 3D landscape for the spatial organizations of cccDNA and integrated HBV DNA within the human genome, and provides a foundation to further understand the mechanisms of HBV modulation of liver disease development and progression in the future.

overall_design:
Examination of 2 different HBV DNAs in 2 HBV cell models using two different primer.
Expressing human NTCP in human hepatoma HepG2 cells (HepG2-NTCP) renders these cells susceptible for HBV infection.
HepAD38 replicates human hepatitis B virus (HBV) under conditions that can be regulated with tetracycline.

first: Bo

last: Yang

first: Boyuan

last: Li


title: The dsRBP Staufen2 governs RNP assembly of neuronal Argonaute proteins

city: Martinsried

first: Michael

last: Kiebler

address: Großhaderner Str. 9

department: BioMedical Center

country: Germany

institute: Ludwig-Maximilians University Munich

type: Non-coding RNA profiling by high throughput sequencing

summary: Here, we have characterized the role of the RNA-binding protein Staufen2, a potential Ago interactor, in RNP assembly. Staufen2 depletion resulted in the upregulation of Ago1/2 and the RISC effector proteins Ddx6 and Dcp1a. This upregulation was accompanied by the displacement of Ago2 from processing bodies, large RNPs implicated in RNA storage, and subsequent association of Ago2 with translating polysomes. Analysis of miRNA expression levels did not reveal changes of global miRNA abundance. In parallel, Staufen2 deficiency yielded decreased global translation. As the observed phenotype can be rescued by Ago1/2 knockdown, we propose a working model in which both Staufen2 and Ago proteins critically depend on each other and contribute to neuronal homeostasis.

overall_design: 12 samples, including 4 biological replicates, were analyzed for miRNA expression levels in cortical neurons deficient for Stau2 or Pum2, the non-targeting control samples (shNTC) served as reference and shPum2 as additional control for shRNA-induced background changes.

first: Janina

last: Ehses

first: Sophia

last: Derdak

first: Martin

last: Bilban


title: Whole transcriptome sequencing of peripheral blood from opioid use disorder [miRNA-seq]

city: Wuhan

first: Yong

last: Wu

address: Gongnongbing road 89#

institute: Wuhan Mental Health Center

summary: 7 male OUD patients and 7 male health controls with demographic and clinical data matched were enrolled in this study. rRNA removed library and small RNA library were constructed using peripheral blood RNA. RNA-seq was used to investigate the peripheral transcriptomic changes between the two groups.

overall_design: transcriptome profile of 7 male OUD patients and 7 male health controls

first: Shan-Shan

last: Pu

first: Xiao-Bo

last: Liu

first: Yi


title: Normalisation-free Gene Expression Survival Classification for Melanoma

city: Camperdown

first: Dario

last: Strbenac

state: NSW

address: City Road

department: School of Mathematics and Statistics

country: Australia

institute: University of Sydney

summary: Early-stage melanoma gene expression analysis measuring 192 genes and relationship to recurrence-free survival using NanoString nCounter.

overall_design: 94 patients and 105 samples (11 patients have a replicate assay).

first: Graham

middle: H

last: Mann

first: Gulietta

last: Pupo

first: Varsha

last: Tembe


title: Single cell RNAseq of small intestinal stromal cells

city: Lausanne

first: Rachel

last: Jeitziner Marcone

address: Rue du Bugnon 25a

country: Switzerland

institute: Swiss Institute of Bioinformatics

summary: We used scRNAseq approaches (Smartseq2 and 10X Genomics) to investigate the diversity of small intestinal stromal cells.

overall_design: Small intestines from adult C57Bl/6 mice were harvested and digested with Liberase TL. Single, live, CD45neg, EpCAMneg, CD31neg, gp38+ cells were either sorted into 384-well plates (Smartseq2) or captured in an oil emulsion (10X Genomics). RNA was amplified, barcoded and sequenced.

first: Jeremiah

last: Berner-Latmani

last: Marcone

first: Mauro

last: Delorenzi

first: Tatiana

middle: V

last: Petrova


title: Human lungs show limited permissiveness for SARS-CoV-2 due to scarce ACE2 levels but virus-induced expansion of inflammatory macrophages

city: Berlin

first: Benedikt

last: Obermayer

address: Chariteplatz 1

department: Core Unit Bioinformatics

institute: Berlin Institute of Health

summary: Scarce ACE2 expression limits alveolar SARS-CoV-2 permissiveness and related tissue damage. Instead, non-productive virus uptake by alveolar macrophages leads to a specific pulmonary immune activation. COVID-19 ARDS is most likely caused by immunopathogenesis rather than alveolar viral damage.

overall_design:
Spectral microscopy, single-cell/-nucleus RNA sequencing or ACE2 ‘gain-of-function’ experiments were applied on infected human lung explants and adult stem cell-derived human lung organoids to correlate ACE2 and related host factors with SARS-CoV-2 tropism, propagation, virulence and immune activation compared to SARS-CoV, influenza and MERS-CoV. COVID-19 autopsy material was used to validate ex vivo results.

>>>Submitter states that raw data are not available due to patient privacy concerns<<<

first: Andreas

last: Hocke

first: Katja

last: Hönzke

first: Morris

last: Baumgardt

first: Emanuel

last: Wyler

first: Stefan

last: Hippenstiel

first: Christin

last: Mache


title: Ep300 sequestration to functionally distinct glucocorticoid receptor binding loci underlie rapid gene activation and repression

city: Ramat Gan

first: Ofir

last: Hakim

address: Bar-Ilan University

country: Israel

institute: Bar-Ilan University

summary: The transcription factor glucocorticoid receptor (GR) is a key mediator of stress response and a broad range of physiological processes. How can GR rapidly activate the expression of some genes while repress others, remains an open question due to the challenge to associate GR binding sites (GBSs) to their distant gene targets. Mapping the 3D scope of GR-responsive promoters using high-resolution 4C-seq unravelled spatial separation between chromatin interaction networks of GR-activated and repressed genes. The spatial compartments of GR-activated and GR-repressed genes vary in the types and configuration of their residing regulatory elements. GR binding to chromatin sequester the co-activator Ep300 from non-GR regulatory loci in GR-activated and repressed gene compartments. While this allows rapid gene repression, effective Ep300 recruitment to GR binding sites positioned within the activated compartments provide the basis for gene induction.  Moreover, focused analysis on GBS together with other regulatory loci that cluster in the GR activated compartments identifies ROR, Rev-erb, and Klf4 transcription factors as co-regulators for GR-mediated gene expression. Thus spatial crosstalk between various regulatory loci in GR-responsive compartments provides the basis for precise transcriptional response

overall_design: RNA seq of GFP/EP300 over expression before and after 1h of DEX treatment

first: Avital

last: Sarusi Portuguez


title: 3D landscape of Hepatitis B virus interactions with human chromatins

first: Xiong

last: Ji

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

overall_design: Refer to individual Series


title: Characterization of the ALDH1B1-dependent transcriptome in SW480 cells by RNA-seq

status: Public on Jun 01 2022

city: Stanford

first: James

middle: K

last: Chen

state: CA

address: 269 Campus Dr., CCSR 3150

department: Chemical and Systems Biology

institute: Stanford University

summary: The mitochondrial enzyme ALDH1B1 is upregulated in colorectal and pancreatic adenocarcinomas and promotes tumor growth. Using both genetic and chemical perturbations, we have characterized the ALDH1B1-regulated transcriptome in a colorectal cancer cell line. Genes induced by ALDH1B1 include those related to mitochondrial metabolism, stemness, and ribosomal function. These findings implicate ALDH1B1 in cancer metabolism and cancer stem cell maintenance, and they underscore the potential of ALDH1B1 as a therapeutic target.

overall_design: Four experimental conditions were analyzed, each with three biological replicates. In all conditions, SW480 cells were cultured in RPMI-1640 medium containing 10% FBS and 100 U/mL penicillin-streptomycin. The first two conditions compared an ALDH1B1 knockout SW480 clone expressing EGFP and the same clone expressing ALDH1B1. The other two conditions compared the parental SW480 line treated with either DMSO or an ALDH1B1-selective inhibitor for 24 hours.

first: Zhiping

last: Feng

first: Yuchao

last: Gu


type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: ChIP seq of EP300 after 1h of Et or DEX treatment


sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: ID2 and HIF-1α Collaborate to Protect Quiescent Hematopoietic Stem Cells from Activation, Differentiation and Exhaustion

city: Frederick

first: Kristbjorn

middle: Orri

last: Gudmundsson

state: MD

address: 1050 Boyles St.

department: MCGP

institute: NCI

sample_organism:
Mus
Mus musculus

platform_organism:
Mus
Mus musculus


title: Cell-Free Fat Extract Improves Ovarian Function and Fertility in Mice with Advanced Age

status: Public on May 27 2022

city: Shanghai

first: Mengyu

last: Liu

state: Shanghai

address: 197 Ruijin 2nd Road

department: Department of Obstetrics and Gynecology

institute: Ruijin Hospital, Shanghai Jiao Tong University School of Medicine

summary:
Purpose: To assess changes in gene expression profiles of mouse ovarian gruanlosa cells from normal control mice, 11-month mice and 11-month mice treated with CEFFE.
Methods:The control group comprised 8-week-old female mice, and the 10-month-old female mice were equally divided into two groups, Aged and Aged +CF groups. The mice from Aged +CF group were treated with 200 μL CEFFE (protein concentration: 3 μg/μL) via tail vein every two days for 2 weeks. At the same time, mice from Control and Aged group were injected with the same volume of saline. Then at the forth week ,ovaries were collected. Furthermore, the mRNA-Seq of mouse ovaries were performed to explore underlying mechanism of CEFFE.
Results: 1302 genes were significantly increased and 1425 genes were significantly decreased in expression level between Aged vs Ctrl gorup.154 genes were significantly increased and 167 genes were significantly decreased in expression level between Aged+CF vs Aged gorup.

overall_design: total RNA was isolated and sequenced from the mouse ovaries from normal control mice, Aged mice and Aged mice treated with CEFFE in triplicate using an Illumina high-seq 2500. Raw data was analyzed using TopHat. Genes were considered changed which demonstrated fold-change>=1.5, and p value <=0.05.

first: Wenzhu

last: Li

first: Xiaowei

last: Zhou

first: Mingjuan

first: Wenjie

last: Zhang

first: Qiang

first: Aijun

first: Bufang

last: Xu


title: Toxicotranscriptomics of single cell RNA-Seq and conventional RNA-Seq in TCDD-exposed testicular tissue

status: Public on May 28 2022

city: Gainesville

first: Tracie

middle: R

last: Baker

state: FL

institute: University of Florida

summary: Spermatogenesis is a dynamic, tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) is believed to be a cause of idiopathic male infertility. To understand TCDD-induced disruption of spermatogenesis at the single cell level, we profiled adult zebrafish testes with and without early-life exposure to TCDD. Secondly, to investigate the potential for technical artifacts in scRNA-seq, we compared bulk-sequenced and scRNA-seq-paired samples from control and TCDD-exposed samples, and included an intact control fish to account for dissociation-induced artifacts. We found scRNA-seq and bulk-seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA-seq, we found TCDD exposure induces mid-late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk-seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA-seq and bulk-seq, with scRNA-seq biased towards detecting longer and more abundant transcripts, but this was not mediated by TCDD exposure.

overall_design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA-seq, remained intact for bulk-seq, or were dissociated for bulk-seq.

first: Alex

last: Haimbaugh

first: Katherine

last: Gurdziel

first: Danielle

last: Meyer

first: Camille

last: Akemann


title: Epigenomic analysis reveals a dynamic and context-specific macrophage enhancer landscape associated with innate immune activation and tolerance

city: Oxford

first: Ping

address: Roosevelt Drive

department: Wellcome Centre for Human Genetics

country: United Kingdom

institute: University of Oxford

summary:
Background
Chromatin states and enhancers associate gene expression, cell identity and disease. Here we systematically delineate the acute innate immune response to endotoxin in terms of human macrophage enhancer activity and contrast with endotoxin tolerance, profiling the coding and non-coding transcriptome, chromatin accessibility and epigenetic modifications.
Results
We describe the spectrum of enhancers under acute and tolerance conditions, and the regulatory networks between these enhancers and biological processes including gene expression, splicing regulation, transcription factor binding and enhancer RNA signatures. We demonstrate that the vast majority of differentially regulated enhancers on acute stimulation are subject to tolerance, and that expression quantitative trait loci, disease-risk variants and eRNAs are enriched in these regulatory regions and related to context-specific gene expression. We find enrichment for context-specific eQTL involving endotoxin response and specific infections, and delineate specific differential regions informative for GWAS variants in inflammatory bowel disease and multiple sclerosis, together with a context-specific enhancer involving a bacterial infection eQTL for KLF4. We show enrichment in differential enhancers for tolerance involving transcription factors NFκB-p65, STATs and IRFs, and prioritise putative causal genes directly linking to genetic variants and disease risk enhancers. We further delineate similarities and differences in epigenetic landscape between stem cell-derived macrophages and primary cells, and characterise the context-specific enhancer activities for key innate immune response genes KLF4, SLAMF1 and IL2RA.
Conclusions
Our study demonstrates the importance of context-specific macrophage enhancers in gene regulation and utility for interpreting disease associations, providing a roadmap to link genetic variants with molecular and cellular functions.

overall_design: Analysis of transcriptome, chromatin accessibility and epigenetic modifications in human macrophages derived from primary monocytes and induced pluripotent stem cells.

first: Harindra

last: Amarasinghe

first: Andrew

last: Brown

first: Julian

last: Knight


title: FOXM1 variant contributes to gefitinib resistance via activating wnt/β-catenin signal pathway in non-small cell lung cancer patients

status: Public on May 25 2022

city: Guangzhou

first: Shaoxing

last: Guan

address: 132# Waihuan Dong Road,Guangzhou University

institute: sun yat-sen university

summary: To further explore the functional role of rs3742076 in the regulation of gefitinib response, stable overexpression FOXM1 rs3742076_A and _G were established in PC9 cells in which FOXM1 knock-out by CRISPR/Cas9.

overall_design:
Differentially expressed genes were identified from transcriptome analysis between FOXM1 rs3742076_A and rs3742076_G cells
Comparative gene expression profiling analysis of RNA-seq data for FOXM1 rs3742076_A cells and rs3742076_G cells.

first: Min

last: Huang

first: Xueding

last: Wang


title: Umbilical cord blood methylome analysis of IVF neonates that underwent embryo culture in G5 or HTF medium

status: Public on May 26 2022

city: Maastricht

first: Rebekka

middle: Maria

last: Koeck

address: Maastricht UMC+

department: Clinical Genetics

institute: Maastricht University Medical Centre

type: Methylation profiling by genome tiling array

summary:
Follow-up study of IVF neonates who underwent embryo culture in G5 (Vitrolife) or HTF (Lonza) medium.
Genome-wide DNA methylation profiling of IVF neonates (umbilical cord blood samples) who had undergone embryo culture in G5 medium (Vitrolife) or HTF medium (Lonza). The EPIC array was used to profile the methylome at approximately 850,000 CpG sites across the human genome.

overall_design: Bisulphite converted DNA from umbilical cord blood samples from IVF neonates that had undergone embryo culture in G5 (n = 59 ) or HTF (n = 47) culture medium, were hybridized to the Illumina EPIC array. Data processing was conducted in R using the RnBeads package. Processing consisted of SWAN normalization, and site/sample removal based on greedycut (detection p-value threshold 0.05), SNP proximity, position on the sex chromosomes, missing values in >5% of samples and sites not in a CpG context.

middle: M

first: Florence

last: Busato

first: Jorg

last: Tost

first: Dimitri

last: Consten

first: Jannie

last: van Echten-Arends

first: Sebastiaan

last: Mastenbroek

first: Yvonne

last: Wurth

first: Sylvie

last: Remy

first: Sabine

last: Langie

first: Tim

middle: S

last: Nawrot

first: Michelle

last: Plusquin

first: Rossella

last: Alfano

first: Esmée

last: Bijnens

first: Marij

last: Gielen

first: Ron

last: van Golde

first: John

last: Dumoulin

first: Han

last: Brunner

first: Aafke

last: van Montfoort

first: Masoud

last: Zamani Esteki


title: Whole transcriptome sequencing of peripheral blood from opioid use disorder

first: Yong

last: Wu


title: Chromatin accessibility analysis of MIAT sufficient and MIAT deficient Th17 cells by ATAC-seq

city: Turku

first: Riitta

last: Lahesmaa

address: Tykistökatu 6A

department: Turku Bioscience

country: Finland

institute: University of Turku

summary: T helper 17 (Th17) cells protect against fungal and bacterial infections and are implicated in autoimmunity. Several long intergenic noncoding RNAs (lincRNA) are induced during Th17 differentiation, however, their contribution to Th17 differentiation is poorly understood. We discovered a lincRNA myocardial infarction associated transcript (MIAT) to be upregulated early after induction of human Th17 cell differentiation along with an increase in the chromatin accessibility at the gene locus. We found that MIAT deficiency leads to chromatin accessibility at several loci including IL17A promoter.

overall_design: CD4 T cells were isolated using magnetic bead-based positive selection kit from Dynal. Cells were nucleofected with the two antisense locked nuelceic acid (LNAs) targeting the lincRNA MIAT or non targeting control LNAs (NC). After 48 hours of rest, cells were differentiated to Th17 for 24 hours or 72 hours. There were three biological replicates. Three LNAs * two time points* three replicates =18 samples.

first: Mohd

last: Khan

first: Meraj

first: Ubaid

middle: U

last: Kalim

first: Omid

last: Rasool

first: Sini

last: Junttila

first: Niklas

last: Paulin

first: Laura

last: Elo


title: Single Cell RNA-Seq of normal and AMD eyes

city: Philadelphia

first: Dwight

middle: Edward

last: Stambolian

state: PA

address: 422 Curie Blvd.

department: Opthalmalogy

institute: University of Pennsylvania

overall_design: Normal and Age-related macular degeneration


title: Long Intergenic Noncoding RNA MIAT Contributes to Human Th17 Cell Differentiation

summary: T helper 17 (Th17) cells protect against fungal and bacterial infections and are implicated in autoimmunity. Several long intergenic noncoding RNAs (lincRNA) are induced during Th17 differentiation, however, their contribution to Th17 differentiation is poorly understood. We discovered a lincRNA myocardial infarction associated transcript (MIAT) to be upregulated early after induction of human Th17 cell differentiation along with an increase in the chromatin accessibility at the gene locus. RNA-seq analysis identified genes implicated in Th17 differentiation and functions as MIAT targets. Our data suggests that MIAT contributes to human Th17 differentiation by upregulating several genes implicated in Th17 differentiation.

overall_design: CD4 T cells were isolated using magnetic bead-based positive selection kit from Dynal. Cells were nucleofected with the three antisense locked nuelceic acid (LNAs) targeting the lincRNA MIAT or non targeting control LNAs (NC). After 48 hours of rest, cells were differentiated to Th17 for 24 hours or 72 hours. There were three biological replicates. Four LNAs * two time points* three replicates =24 samples.

first: Lingjia

last: Kong


title: The lncRNA RUS shapes gene expression program towards neurogenesis

status: Public on May 24 2022

city: Planegg-Martinsried

first: Marius

middle: Frederik

last: Schneider

state: Bayern

department: molecular biology

institute: Biomedical center munich - LMU


title: Analysis of mRNA and EZH2 binding in TGF-B-treated A549 cells

city: Granada

first: Jordi

last: Martorell-Marugan

address: Avenida de la Ilustración 114

department: Bioinformatics Unit

country: Spain

institute: GENyO

summary: mRNA-seq of A549 cells carrying out EMT-MET in the absence or presence of the EZH2 inhibitor GSK126. In addition, we carried out ChIP-seq of EZH2 in A549 cells upon TGF-B treatment.

overall_design: mRNA-seq of A549 cells during EMT-MET in the presence of the EZH2 inhibitor GSK126 (McCabe, MT et al. Nature. 2012). ChIP-seq of EZH2 samples in A549 cells treated with TGF-B for six days.

first: Amador

last: Gallardo

first: Helena

first: Pedro

last: Carmona-Saez

first: David

last: Landeira


title: Next Generation Sequencing and Analysis of the Transcriptomes of Wild-type and Alkbh5-/- Neutrophils

city: Beijing

first: Yang

last: Liu

address: Dongdan Santiao 5

department: Immunology

institute: Peking Union Medical College&Chinese Academy of Medical Sciences

summary: By performing transcriptome-wide RNA sequencing (RNA-seq) analysis on the peritoneal neutrophils from Alkbh5-deficient mice (Alkbh5-/-) and Wild-type littermates (Alkbh5+/+) at 12h or 36h after mild cecal ligation and puncture (CLP), respectively, we want to identify potential targets of ALKBH5 and characterize the transcriptional landscape in neutrophils during antibacterial innate defense. Gene Ontology biological processes enrichment analysis of the significantly differentially expressed genes (DEGs) showed that neutrophil migration made up the most significantly enriched biological processes with annotations of neutrophil association upon loss of ALKBH5 in neutrophils, at both 12h and 36h after CLP. Many significantly DEGs also encompassed transcriptional signatures related to neutrophils, specifically to neutrophil influx into the infection site, including chemotaxis, response to chemokine, extravasation, ERK1 and ERK2 cascade, homeostasis of neutrophils. ALKBH5 deletion led to significantly decreased transcript expression of neutrophil migration-promoting Cxcr2 and Nlrp12; while increased transcript expression of neutrophil migration-suppressive Ptger4, Tnc, and Wnk1. These results demonstrated that ALKBH5 imprints migration-promoting transcriptional landscape in neutrophils to enable their migration into the site of infection for antibacterial innate defense.

overall_design: Transcriptomes profiles of gene expression changes in peritoneal neutrophils from Alkbh5-deficient mice (Alkbh5-/-) and Wild-type littermates (Alkbh5+/+) at 12h or 36h after mild CLP, respectively. Four biological replicates.


title: Identification of dysregulated transcripts in apob-1(RNAi);apob-2(RNAi) planarians

city: Oklahoma

middle: J

last: Forsthoefel

state: OK

address: 825 NE 13th St

department: Genes and Human Disease Research Program

institute: Oklahoma Medical Research Foundation

summary: ApoB-1 and ApoB-2 are intestine-enriched regulators of lipoprotein secretion in planarians. The goal of this study was to identify differentially expressed transcripts in uninjured apob-1(RNAi);apob-2(RNAi) double knockdown planarians relative to egfp(RNAi) control animals.

overall_design: Total RNA was isolated from uninjured egfp(RNAi) (control), apob-1(RNAi);apob-2(RNAi) (mild phenotype - "apob-M"), and apob-1(RNAi);apob-2(RNAi) (severe phenotype - "apob-S") planarians (fed three times, 4-6 biological replicates each). Library generation (NEB NEXT ULTRA) and RNA sequencing (2x150bp paired-end, Illumina HiSeq 4000) were conducted by Genewiz. Bioinformatic analysis was conducted using BBDuk, Bowtie2, and edgeR.

first: Lily

middle: L

last: Wong

first: Christina

middle: G

last: Bruxvoort

first: Nicholas

middle: I

last: Cejda

first: Matthew

last: Delaney

first: Jannette

last: Rodriguez Otero


title: Host CLIC4 is essential for breast cancer metastatic competence

city: Bethesda

first: Howard

last: Yang

address: 37 CONVENT DR, Room 5120

department: CCR

summary: Chloride Intracellular Channel 4 (CLIC4) expression is elevated in the stroma of many cancers. We show that  CLIC4 expression is higher in  breast cancers from younger women and  early stage metastatic disease, portends poor prognosis,  and is linked to  TGF-β expression. Two murine breast cancer models with lung metastases revealed that ablation of host Clic4 nearly eliminated lung metastases without reducing primary tumor size while Clic4 null tumor cells retained metastatic capability. Thus, CLIC4 is required for host metastatic competence. Deficiencies in circulating pro-metastatic soluble factors were detected in CLIC4 deficient hosts bearing primary tumors. Necrosis and vascular abnormalities were more abundant in primary tumors from CLIC4 deficient hosts than from CLIC4 proficient control hosts. Transcriptional profiles of lungs and primary tumors prior to the onset of metastases indicated that loss of host CLIC4 enhances an inflammatory microenvironment.  Thus, CLIC4 expression in human breast cancers may serve as a prognostic biomarker, and targeting host CLIC4 could reduce metastatic competence.

overall_design:
Transcriptional profiles of lungs and primary tumors prior to the onset of metastases.
The 6DT1 mouse mammary tumor explant cell line was injected orthotopically into the fourth mammary fat pad of wildtype or CLIC4 knockout syngeneic FVB/N mice.
Lung tissue was isolated from wildtype and CLIC4 knockout mice at baseline or 14 days after orthografting. Primary tumor tissue was isolated at 14 days after orthografting.

first: Vanesa

last: Sanchez

first: Brandi

last: Carofino

first: Stuart

last: Yuspa


title: WT and fhy3 mutant in constant red light

status: Public on May 23 2022

city: Egham

first: Paul

last: Devlin

state: Surrey

address: Egham Hill

department: Biological Sciences

institute: Department of Biological Sciences, Royal Holloway University of London

summary: The red-light regulated transcription factors FHY3 and FAR1 form a key point of light input to the plant circadian clock in positively regulating expression of genes within the central clock. However, the fhy3 mutant shows an additional red light-specific disruption of rhythmicity which is inconsistent with this role. Here we demonstrate that only fhy3 and not far1 mutants show this red specific disruption of rhythmicity. We examined the differences in rhythmic transcriptome in red versus white light and reveal differences in patterns of rhythmicity among the central clock proteins suggestive of a change in emphasis withing the central mechanism of the clock, changes which underlie the red specificity of the fhy3 mutant. In particular, changes in enrichment of promoter elements were consistent with a key role for the HY5 transcription factor, a known integrator of the ratio of red to blue light in regulation of the clock. Examination of differences in the rhythmic transcriptome in the fhy3 mutant in red light which identified specific disruption of the CCA1-regulated ELF3 and LUX central clock genes, while the CCA1 target TBS element, TGGGCC, was enriched among genes that became arrhythmic. Coupled with the known interaction of FHY3 but not FAR1 with CCA1 we propose that the red-specific circadian phenotype of fhy3 may involve disruption of the previously-demonstrated moderation of CCA1 activity by FHY3 rather than a disruption of its own transcriptional regulatory activity. Together, this evidence suggests a conditional redundancy between FHY3 and HY5 in the integration of red and blue light input to the clock in order to enable a plasticity in response to light and optimise plant adaptation. Furthermore, our evidence also suggests changes in CCA1 activity between red and white light transcriptomes. This, together with the documented interaction of HY5 with CCA1, leads us to propose a model whereby this integration of red and blue signals may at least partly occur via direct FHY3 and HY5 interaction with CCA1 leading to moderation of CCA1 activity.

overall_design: The data consist of 8 samples. Four wild type (No-0) and four fhy3-4. Samples were entrained for 7 days in 12 h/12 h white light/dark cycles then released into constant red light. WT and mutant samples were collected at 24, 32, 40 and 48 h after transfer to constant red light.

middle: F


title: Multi-dimensional histone modifications for coordinated regulation of gene expression under hypoxia or clioquinol (CQ) treatment [gene expression]

city: Daegu

first: Sehyun

last: Chae

address: 61, Cheomdan-ro

department: Neurovascular Unit Research Group

country: South Korea

institute: Korea Brain Research Institute

summary: Clioquinol (CQ) has been identified as a hypoxic mimicker to activate hypoxia-inducible factor-1α (HIF-1α) by inhibiting HIF-1a specific asparaginyl hypoxylase (Factor inhibiting HIF-1, FIH-1).  We previously showed that hypoxia  coordinately regulate induction or repression of hypoxia-responsive genes  by altering  different types of methylations (H3K4me3, H3K9me3, and H3K27me3) at gene level. Here, we investigated CQ-mediated regulation of the expression of hypoxia-responsive genes and whether CQ had a similar effect on histone methylation and transcription of target genes under hypoxia.

overall_design: To examine target genes of CQ, we performed gene expression profiling of adipocyte-derived stem cells (hADSCs) under normoxia (N) and hypoxia (H) or with CQ treatment (CQ).

first: Yunwon

last: Moon

first: Daehee

last: Hwang

first: Hyunsung

last: Park


title: Identification of dysregulated transcripts in planarians

overall_design: Refer to individual Series


title: Identification of transcripts directly bound to U1A (iCLIP data) and the cell transcriptome after U1A knockdown

city: San Sebastian

first: Lorea

last: Blazquez

address: Dr Begiristain

institute: Biogipuzkoa Health Research Institute


title: The Atlas of Immune Infiltrates in Islet Cell Allo-transplantation

city: Shenzhen

first: Lisha

last: Mou

state: Guangdong

address: Room 604, Building 1, Yinxingzhijie 1 Qi Guanlan, Longhua District

institute: Shenzhen Second People's Hospital

summary: Islet transplantation to treat the late stage of T1DM patients has made some inspiring success recently in clinical trials. However, most of patients underwent a decline of islet cell graft in one to three years due to chronic immune rejection. Although the mechanisms of immune cells including macrophages, dendritic cells (DCs), neutrophils, natural killer cells (NKs), B cells, T cells that mediate immune rejection have been investigated, the overall characteristics of immune infiltrates in islet allografts remain unclear. Single-cell RNA sequencing (scRNA-seq) has provided us with new opportunities to study the molecular characteristics of the immune microenvironment in islet transplants. In the present study, we used scRNA-seq to comprehensively analyze the immune heterogeneity in islet graft, and compared the variances regarding to transcriptomal profiling and immune atlas between syngeneic islet transplantation and allograft.

overall_design: We performed single-cell RNA sequencing (scRNA-seq) on islet cell allograft (Balb/c islets to C57bl/6 recipients) and syngeneic graft (C57bl/6 islets to C57bl/6 recipients) to identify the comprehensive cell components and variations that are related to graft rejection. 7 days after transplantation, the grafts were harvested and subjected to 10X Genomics pipeline barcoding, library preparation, and sequencing.

first: Pengfei

last: Chen

first: Ying

last: Lu

first: Yuanzheng

last: Peng


title: Unravelling the sex-specific diversity and functions of adrenal gland macrophages

city: Saint-Petersburg

first: Maria

last: Firulyova

address: Kronverksky Pr. 49

department: Department of Computer Technologies

country: Russia

institute: Information Technologies, Mechanics, and Optics University


title: Schlafen 5 Suppresses Human Immunodeficiency Virus Type 1 Transcription by Commandeering Cellular Epigenetic Machinery

first: Jiwei

last: Ding

address: Nanwei Rd 2#

department: Institute of Medicinal Biotechnology

institute: Chinese Academy of Medical Sciences & Peking Union Medical College

summary: Schlafen-5 (SLFN5) is an interferon-induced protein of the Schlafen family which are involved in immune responses and oncogenesis. To date, little is known regarding its anti-HIV-1 function. Here, the authors report that overexpression of SLFN5 inhibits HIV-1 replication and reduces viral mRNA levels, whereas depletion of endogenous SLFN5 promotes HIV-1 replication. Moreover, they show that SLFN5 markedly decreases the transcriptional activity of HIV-1 long terminal repeat (LTR) via binding to two sequences in the U5-R region, which consequently represses the recruitment of RNA polymerase Ⅱ to the transcription initiation site. Mutagenesis studies show the importance of nuclear localization and the N-terminal 1-570 amino acids fragment in the inhibition of HIV-1. Further mechanistic studies demonstrate that SLFN5 interacts with components of the PRC2 complex, G9a and Histone H3, thereby promoting H3K27me2 and H3K27me3 modification leading to silencing HIV-1 transcription. In concert with this, they find that SLFN5 blocks the activation of latent HIV-1. Altogether, their findings demonstrate that SLFN5 is a transcriptional repressor of HIV-1 through epigenetic modulation and a potential determinant of HIV-1 latency.

overall_design: mRNA profile of  SupT1 cells to determine the binding sites of SLFN5 throughout the human genome and whether the binding sites is modified by H3K27me2 or H3K27me3.

first: Shujie

last: Wang

first: Xiaoyu

last: Li

first: Shan

last: Cen


title: The lncRNA RUS shapes gene expression program towards neurogenesis [RNA-Seq ]

first: Marius

last: Schneider

address: Großhaderner Str. 9

summary: The evolution of brain complexity correlates with an increased expression of long, non-coding (lnc) RNAs in neuronal tissues. Although prominent examples illustrate the potential of lncRNAs to scaffold and target epigenetic regulators to chromatin loci, only few cases have been described to function during neurogenesis.  We present a first functional characterization of the lncRNA LINC01322, which we term RUS for ‘RNA upstream of Slitrk3’. The RUS gene is well conserved in mammals by sequence and synteny next to the neurodevelopmental gene Slitrk3. RUS is exclusively expressed in neural cells and its expression increases along with neuronal markers during neuronal differentiation of mouse embryonic cortical neural stem cells. Depletion of RUS locks neuronal precursors in an intermediate state towards neuronal differentiation, with arrested cell cycle and increased apoptosis. RUS associates with chromatin in the vicinity of genes involved in neurogenesis, most of which change their expression upon RUS depletion. The identification of a range of epigenetic regulators as specific RUS interactors suggests that the lncRNA may mediate gene activation and repression in a highly context-dependent manner.

overall_design: Transcriptome profiling of neural stem cells (NSC) at two different timepoints after ctrl and  RUS KD ( 4 experiments per condition).

first: Veronika

last: Müller

first: Stephan

first: Stefan

last: Lichtenthaler

first: Johanna

last: Scheuermann

first: Peter

middle: B

last: Becker


title: Multi-dimensional histone modifications for coordinated regulation of gene expression under hypoxia or clioquinol (CQ) treatment.

first: Sehyun

last: Chae

summary: Clioquinol (CQ) has been identified as a hypoxic mimicker to activate hypoxia-inducible factor-1α (HIF-1α) by inhibiting HIF-1a specific asparaginyl hypoxylase (Factor inhibiting HIF-1, FIH-1).  We previously showed that hypoxia  coordinately regulate induction or repression of hypoxia-responsive genes  by altering  different types of methylations (H3K4me3, H3K9me3, and H3K27me3) at gene level. Here, we investigated CQ-mediated regulation of the three histone methylations and whether CQ had a similar effect on histone methylation and transcription of target genes under hypoxia.

overall_design: To examine the genome-wide landscape of methylated histones affected by CQ, we performed ChIP-seq for H3K4me3, H3K9me3, and H3K27me3 in adipocyte-derived stem cells (hADSCs) under normoxia (N) and hypoxia (H) or with CQ treatment (CQ).

first: Yunwon

last: Moon

first: Daehee

last: Hwang

first: Hyunsung


title: The lncRNA RUS shapes gene expression program towards neurogenesis [ChIRP-seq]

summary: The evolution of brain complexity correlates with an increased expression of long, non-coding (lnc) RNAs in neuronal tissues. Although prominent examples illustrate the potential of lncRNAs to scaffold and target epigenetic regulators to chromatin loci, only few cases have been described to function during neurogenesis.  We present a first functional characterization of the lncRNA LINC01322, which we term RUS for 'RNA upstream of Slitrk3'. The RUS gene is well conserved in mammals by sequence and synteny next to the neurodevelopmental gene Slitrk3. RUS is exclusively expressed in neural cells and its expression increases along with neuronal markers during neuronal differentiation of mouse embryonic cortical neural stem cells. Depletion of RUS locks neuronal precursors in an intermediate state towards neuronal differentiation, with arrested cell cycle and increased apoptosis. RUS associates with chromatin in the vicinity of genes involved in neurogenesis, most of which change their expression upon RUS depletion. The identification of a range of epigenetic regulators as specific RUS interactors suggests that the lncRNA may mediate gene activation and repression in a highly context-dependent manner.

overall_design: Chromatin Isolation by RNA Purification (ChIRP) of RUS bound chromatin binding sites using two independent probe sets (odd & even) and an input control (3 replicates per condition).


title: Unravelling the sex-specific diversity and functions of adrenal gland macrophages (RNA-Seq).

summary: Despite the ubiquitous function of macrophages across the body, the diversity, origin, and function of adrenal gland macrophages remain largely unknown. We defined the heterogeneity of adrenal gland immune cells using single-cell RNA sequencing and used genetic models to explore the developmental mechanisms yielding to macrophage diversity. We defined populations of monocyte-derived and embryonically seeded adrenal gland macrophages and identified a female-specific subset with low MHC-II expression. In adulthood, monocyte recruitment dominated adrenal gland macrophage maintenance in female mice, while self-proliferation was more important in males. Adrenal gland macrophage sub-tissular distribution followed a sex-dimorphic pattern, with MHC-IIlow macrophages located at the border between the cortex and the medulla. Macrophage sex dimorphism depended on the presence of the cortical Xzone. Forcing X-zone maintenance in males, or its degradation in females, directly impacted the presence of MHC-IIlow macrophages. Adrenal gland macrophage depletion resulted in altered tissue homeostasis, modulated lipid- metabolism and decreased local aldosterone production during stress exposure. Overall, these data explain the heterogeneity of adrenal gland macrophages and point toward sexrestricted distribution and functions of these cells.

overall_design: Adrenal gland from isotype control treated and a-CD115-treated male and female C57bl/6J were collected at seven week old  and total RNAs were extracted in RNase-free water.

first: Stoyan

last: Ivanov

first: Bastien

last: Dolf

first: Alexandre

last: Gallerand

last: Merlin

first: Adélie

last: Dumont

first: Alexia

last: Castiglione

first: Nathalie

last: Vaillant

first: Sandrine

last: Quemener

first: Stunault

last: Marion

first: Patricia

last: Schrank

first: Yingzheng

last: Xu

first: Seung

last: Kim

first: Jie

first: Jerome

last: Gilleron

first: Virginie

last: Magnone

first: Pascal

last: Barbry

first: David

last: Dombrowicz

first: Christophe

last: Duranton

first: Abdelilah

last: Wakkach

first: Claudine

last: Blin-Wakkach

first: Burkhard

last: Becher

first: Sophie

last: Pagnotta

first: Konstantin

last: Zaitsev

first: Ki-Wook

first: Laurent

last: Yvan-Charvet

first: Rodolphe

last: Guinamard

first: Jesse

middle: W

last: Williams


title: Identification of dysregulated transcripts in nkx2.2(RNAi) planarians.

last: Forsthoefel

summary: Nkx2.2 is an intestine-enriched transcription factor required for regeneration in planarians. The goal of this study was to identify differentially expressed transcripts in uninjured nkx2.2(RNAi) planarians.

overall_design: Total RNA was isolated from uninjured egfp(RNAi) (control) and nkx2.2(RNAi) planarians (fed one time, three biological replicates each). Library generation (IIllumina TruSeq Stranded mRNA Prep Kit) and RNA sequencing (2x150bp paired-end, Illumina NovaSeq 6000) were conducted by the OMRF Clinical Genomics Core. Bioinformatic analysis was conducted using BBDuk, Bowtie2, and edgeR.

first: Lily

last: Wong

first: Christina

last: Bruxvoort

first: Nicholas

last: Cejda

first: Matthew

last: Delaney

first: Jannette

last: Rodriguez Otero


title: The human milk oligosaccharide 2’-fucosyllactose alleviates liver steatosis and associated gut permeability, ER stress and insulin resistance by reducing hepatic diacylglycerols in obese Ldlr-/-.Leiden mice

city: Rijswijk

first: Eveline

last: Gart

state: Zuid-Holland

address: Van vredenburchweg 659

institute: TNO

summary: Abstract:   - Non-alcoholic fatty liver disease (NAFLD) is a complex multifactorial disorder that is associated with gut dysbiosis, enhanced gut permeability, adiposity and insulin resistance. Prebiotics such as human milk oligosaccharide 2’-fucosyllactose are thought to primarily improve gut health and it is uncertain whether they would affect more distant organs. This study investigates whether 2’-fucosyllactose can alleviate NAFLD development in manifest obesity.  Obese hyperinsulinemic Ldlr-/-.Leiden mice, after an 8 week run-in on HFD,  were treated with 2’-fucosyllactose by oral gavage until week 28 and compared to HFD-vehicle controls. 2’-fucosyllactose did not affect food intake, body weight, total fat mass or plasma lipids. 2’-fucosyllactose altered the fecal microbiota composition which was paralleled by a suppression of HFD-induced gut permeability at t=12 weeks. 2’-fucosyllactose significantly attenuated the development of NAFLD by reducing microvesicular steatosis. These hepatoprotective effects were supported by functional transcriptome analyses showing that 2’-fucosyllactose activated ACOX1 (involved in lipid catabolism), while deactivating SREBF1 (involved in lipogenesis). Furthermore, 2’-fucosyllactose suppressed ATF4, ATF6, ERN1, and NUPR1 all of which participate in ER stress. 2’-fucosyllactose reduced fasting insulin concentrations and HOMA-IR, which was corroborated by decreased intrahepatic diacylglycerols.  - In conclusion, long-term prebiotic treatment with 2’-fucosyllactose can counteract the detrimental effects of HFD on gut dysbiosis and gut permeability and attenuates the development of liver steatosis. The observed reduction in intrahepatic diacylglycerols provides a mechanistic rationale for the improvement of hyperinsulinemia and supports the use of 2’-fucosyllactose to correct dysmetabolism and insulin resistance.

overall_design: After a run-in of 8 weeks on HFD, obese hyperinsulinemic mice were treated with 2-fucosyllactose (2’-FL) by oral gavage twice daily (750 mg/kg/day) until week 28, and compared with vehicle control mice receiving saline (n=15/group). Mice on standard rodent chow were used as a reference.

first: Kanita

last: Salic

first: Martine

middle: C

last: Morrison

first: Martin

last: Giera

first: Joline

last: Attema

first: Christa

last: de Ruiter

first: Martien

last: Caspers

first: Frank

last: Schuren

first: Ivana

last: Bobeldijk-Pastorova

first: Yan

last: Qin

first: Marianne

last: Heer

first: Robert

last: Kleemann


title: Unravelling the sex-specific diversity and functions of adrenal gland macrophages (scRNA-Seq).

first: Maria

last: Firulyova

overall_design: Males and females seven week old adrenal glands of C57BL/6 J were collected and digested. Cells suspension were stained using viability dye (DAPI) and CD45 antibody and all the alive CD45 cells were analysed using SCRNA-seq.

first: Stoyan

last: Ivanov

first: Bastien

last: Dolf

first: Alexandre

last: Gallerand

first: Johanna

last: Merlin

first: Adélie

last: Dumont

first: Alexia

last: Castiglione

first: Nathalie

last: Vaillant

first: Sandrine

last: Quemener

first: Stunault

last: Marion

first: Patricia

last: Schrank

first: Yingzheng

last: Xu

first: Seung

last: Kim

first: Jie

last: Ding

first: Jerome

last: Gilleron

first: Virginie

last: Magnone

first: Pascal

last: Barbry

first: David

last: Dombrowicz

first: Christophe

last: Duranton

first: Abdelilah

last: Wakkach

first: Claudine

last: Blin-Wakkach

first: Burkhard

last: Becher

first: Sophie

last: Pagnotta

first: Konstantin

last: Zaitsev

first: Ki-Wook

first: Laurent

last: Yvan-Charvet

first: Rodolphe

last: Guinamard

first: Jesse

last: Williams


title: Genome-wide chromatin occupancy of transcription factor TBX2 in luminal breast cancer cells

city: Belfast

first: Paul

last: Mullan

address: 97 Lisburn Road

department: PGJCCR

institute: Queen's University Belfast

summary: Here we demonstrate a previously unknown mechanism of TBX2-mediated gene repression in breast tumours, whereby TBX2 physically interacts with CoREST-associated proteins LSD1, HDAC1 and the ZNF217 oncogene. Through Chromatin Immunoprecipitation sequencing (ChIP-seq) we find that while over 80% of TBX2 binding sites are concentrated at promoters, these regions show remarkably no enrichment for the T-box element; rather TBX2-bound regions are biased toward a small number of non-T-box motifs, with the most abundant being Specificity Protein 1 (Sp1), EGR1 and Nuclear Transcription Factor Y (NF-Y). Furthermore, we uncover that Sp1 is crucial for recruitment of TBX2 to the NDRG1 promoter and subsequent repression of this gene. We also observe that ZNF217 cooccupies approximately 30% of TBX2-bound sites, a number of which contain RCOR1 and exhibit upregulation of the associated transcripts following disruption of TBX2/CoREST function. Overall these data highlight a novel potential therapeutic opportunity whereby poor-prognosis, TBX2 overexpressing breast tumours may be pharmacologically exploited by targeting the CoREST-dependent gene repression network, to recover normal growth control.

overall_design: Examination of TBX2 genome-wide occupancy in MCF-7 cells by ChIP-seq

first: Alexander

last: McIntyre

first: James

last: Smith


title: AnxA1 inhibits pathological bone resorption

city: Sapporo

first: Mohamad Alaa

last: Terkawi

state: Hokkaido

address: Kita-15, Nish-7, Kita-ku

department: Department of Orthopedic Surgery

country: Japan

institute: Hokkaido University

summary: We explored the functional role of AnxA1 in osteoclastogenesis and pathological bone loss associated with inflammatory osteolysis.

overall_design: RNA-seq for macrophages stimulated by macrophage colony-stimulating factor, receptor activator of nuclear factor kappa-b ligand and AnxA1

first: Gen

last: Matsumae

first: Shimizu

last: Tomohiro

first: Alaa

first: Norimasa

last: Iwasaki


title: A human breast transcriptome atlas

city: Boston

first: Joan

middle: S.

last: Brugge

state: MA

address: 240 Longwood Avenue

department: Department of Cell Biology

institute: Harvard Medical School

summary: The breast is a dynamic organ whose response to physiological and pathophysiological conditions alters its disease susceptibility, yet the specific effects of these clinical variables on cell state remain poorly annotated. We present a unified, high-resolution breast atlas by integrating single-cell RNA-seq, mass cytometry, and cyclic immunofluorescence, encompassing a myriad of states. We define cell subtypes within the alveolar, hormone-sensing, and basal epithelial lineages, delineating associations of several subtypes with cancer risk factors, including age, parity, and BRCA2 germline mutation. Of particular interest is a subset of alveolar cells termed basal-luminal (BL) cells, which exhibit poor transcriptional lineage fidelity, accumulate with age, and carry a gene signature associated with basal-like breast cancer. We further utilize a medium-depletion approach to identify molecular factors regulating cell-subtype proportion in organoids. Together, these data are a rich resource to elucidate diverse mammary cell states.

overall_design: A total of 16 breast samples were assayed (4 samples from reductive mammoplasties and 12 from prophylactic mastectomies).

first: Carman

last: Li

first: Laura

last: Selfors


title: Lipolysis regulates major transcriptional programs in brown adipocytes [hBA]

status: Public on May 21 2022

city: Odense M

first: Lasse Kruse

last: Markussen

address: Campusvej 55

department: BMB

country: Denmark

institute: University of Southern Denmark

summary: β-Adrenergic signaling is a core regulator of brown adipocyte function stimulating both lipolysis and transcription of thermogenic genes, thereby expanding the capacity for oxidative metabolism. Here we have used pharmacological inhibitors and a novel direct activator of lipolysis to acutely modulate the activity of lipases, thereby enabling us to uncover lipolysis-dependent signaling pathways downstream of β-adrenergic signaling in brown adipocytes. We show that induction of lipolysis leads to acute induction of several gene programs and is required for transcriptional regulation by β-adrenergic signals. Using machine-learning algorithms to infer causal transcription factors, we show that PPARs are key mediators of lipolysis-induced activation of genes involved in lipid metabolism and thermogenesis. Importantly, lipolysis also activates the unfolded protein response and regulates the core circadian transcriptional machinery independently of PPARs. Our results demonstrate that lipolysis generates important metabolic signals that exert profound pleiotropic effects on brown adipocyte transcription and function.

overall_design: Immortalized human brown adipocytes (D12) treated +/- 10uM SR-3420 for 3hrs.

first: Lasse

middle: K

first: Susanne

last: Mandrup


title: Gardnerella exposures alter bladder gene expression and augment uropathogenic Escherichia coli urinary tract infection in mice.

status: Public on May 20 2022

city: St. Louis

first: Nicole

last: Gilbert

address: 425 S Euclid Ave

institute: Washington University School of Medicine

summary: The anaerobic actinobacterium Gardnerella was first isolated from the bladder by suprapubic aspiration more than fifty years ago. Since then, Gardnerella has been increasingly recognized as a common and often abundant member of the female urinary microbiome (urobiome). Some studies even suggest that the presence of Gardnerella is associated with urological disorders in women. We recently reported that inoculation of Gardnerella into the bladders of mice results in urothelial exfoliation. Here we performed whole bladder RNA-seq in our mouse model to identify additional host pathways involved in the response to Gardnerella bladder exposure.  The transcriptional response to Gardnerella reflected the urothelial turnover that is a consequence of exfoliation, while also illustrating the activation pathways involved in inflammation and immunity. Additional timed exposure experiments in mice provided further evidence of a potentially clinically relevant consequence of bladder exposures to Gardnerella -- increased susceptibility to subsequent UTI caused by uropathogenic Escherichia coli. Together these data provide a broader picture of the bladder response to Gardnerella and lay the groundwork for future studies examining the impact of Gardnerella on bladder health.

overall_design: A total of 9 mouse bladders were analyzed. 4 bladders from 12 hours  (h) after 2 PBS exposures given 12h apart (PBS), and 5 bladders from 12h after 2 G. vaginalis exposures given 12h apart (Gard)

first: Valerie

middle: P

last: O'Brien

first: Amanda

last: Lewis


title: Transcriptional response to carbapenem treatment in Acinetobacter baumannii

city: Richardson

first: Joseph

middle: Michael

last: Boll

state: TX

address: 800 W Campbell

institute: University of Texas at Dallas

summary: We report transcriptome sequencing analysis on A. baumannii strain ATCC 17978 cultures treated with or without meropnem at 0.5, 3 and 9 h, in triplicate.

overall_design: Differential gene expression of genes in A. baumannii strain ATCC 17978 with meropnem treatment.

first: Nowrosh

last: Islam

first: Misha

last: Kazi

first: Katie

middle: N

last: Kang

first: Tobias

last: Dörr


title: Brain tissue of mice:sham group, the 3d after MCAO group, the 7d after MCAO group

first: Li

last: Yudi

address: No. 1098 Xueyuan Avenue, 518060 Shenzhen, Guangdong, China.

institute: Shenzhen Hospital, Southern Medical University

summary: This study is the first to show changes of m6A abundance in circRNAs in cerebral infarction by Methylated RNA immunoprecipitation (MeRIP) and circRNA microarray. The bioinformatics analysis predicted the possible functions and related pathways of m6A modified circRNAs in secondary injury and the repair of cerebral infarction. Our results provide new insights into the molecular mechanism of infarct stroke.

overall_design: Two-condition experiment, stroke vs sham. Biological replicates: 3 control replicates, 3 Experimental  replicates.

last: Ling

first: Fangming


title: RPB1 ChIP-Seq of adrenal glands tissue from Wild Type (WT) and Armc5 knockout mice

city: Montreal

first: Jiangping

last: Wu

address: 900 Rue Saint Denis

country: Canada

summary: RPB1-specific ubiquitin ligase (E3) controls the degradation of this largest subunit of Pol II and consequently the Pol II pool size. Although several RPB1-specific E3s have been documented, their function is only revealed in cells with massive DNA damage. We demonstrated that ARMC5 physically interacted with cullin3 (CUL3) and RPB1. ARMC5 is an armadillo domain-containing protein with unknown mechanisms of action. ARMC5 deletion caused significant RPB1 accumulation in all the major organs under a physiological condition in the absence of artificially induced DNA damage. This is accompanied by reduced RPB1 ubiquitination. In vitro ubiquitination assay proved that ARMC5, CUL3, and RBX1 formed an effective E3 for RPB1. RPB1 was confirmed as being highly accumulated in the adrenal gland nodules from PBMAH patients with mutations in the ARMC5 coding sequence. Surprisingly, the compromised RPB1 degradation did not lead to increased Pol II stalling according to ChIP-Seq, or a general decrease of gene transcription according to RNA-seq. On the contrary, among 1486 differentially expressed genes in the KO adrenal glands, 93.5% of them were upregulated, probably due to the enlarged Pol II pool size. Our results showed that the ARMC3-CUL3 E3 was the dominant E3 in normal cells and organs and controlled Pol II pool size. The abnormally large Pol II pool size due to ARMC5 mutation dysregulated a large number of genes that in turn led to many phenotypes, including PBMAH in humans.

overall_design: ChIP-Seq profiles of RPB1(NTD)-specific antibody for adrenal glands tissue from WT and Armc5(-/-) mice

first: Linjiang

last: Lao

first: Hongyu

last: Luo


title: Characterizing a role for HNRNPA2B1 during normal myogenesis

status: Public on May 22 2022

city: Aurora

first: Aaron

middle: M

last: Johnson

state: CO

address: 12801 E 17th Ave Research 1 South L18-10402G

department: Biochemistry and Molecular Genetics

institute: University of Colorado Denver

summary: The RNA localization mechanisms in muscle are incompletely known however numerous RNA binding proteins and RNA aggregate into higher order amyloid-like assemblies in degenerative muscle disease. Here we assign a role for the RNA binding protein hnRNPA2B1, heterogeneous RNA binding protein A2/B1, in normal myogenesis. Loss of hnRNPA2/B1 impairs muscle differentiation in vitro. hnRNPA2B1 binds to the 3’UTR of select myogeneic transcripts distinct from other RNA-binding proteins during muscle differentiation. hnRNPA2B1 associated RNPs are capable of assembling into higher order microtubule associated RNP assemblies and redistribute from the nucleus into the cytoplasm during muscle differentiation both in vitro and in vivo. Together, our results contribute to a broader theme in RNA localization during myogenesis and may provide additional insights into the origins of pathological cytoplasmic RNP aggregation.

overall_design: eCLIP-seq in mouse C2C12 cells

first: Eric

middle: D

last: Nguyen

first: Joshua

middle: R

last: Wheeler

first: Thomas

middle: O

last: Vogler


title: Genome-wide expression analysis of C. elegans nematodes engineered to stably express a Cas9-derived synthetic transcription factor, fed HT115 scrambled bacteria

status: Public on May 19 2022

city: Berlin

first: Michael

last: Ristow

state: CH

address: Charitéplatz 1

department: Inst. Exp. Endocrinology

institute: Charite Berlin

summary: We report identification of possible differentially regulated genes in C. elegans, by analyzing changes in overall transcriptome following stable overexpression of this transcription factor.

overall_design:
In total six samples (independent biological replicates) were analysed. Three samples were derived from wild-type N2 nematodes and three from a strain engineered to stably express a Cas9-derived synthetic transcription factor
contributor: Functional Genomics Center Zurich (FGCZ)

first: Christoph

last: Benner

first: Giovanna

last: Grigolon

first: Fabian

last: Fischer


title: Expression data from Arabidopsis thaliana depleted of HYPK or NAA10

city: Mannheim

first: Carolina

last: Delatorre

address: Theodor-Kutzer-Ufer 1-3

institute: University Heidelberg

summary:
N-alpha terminal acetylation is an abundant protein modification in eukaryotes. The NatA (N-alpha acetyltransferase A) complex is responsible for N-terminal acetylation of majority of the cytosolic proteins and its core is composed of NAA10 and NAA15 subunit. HYPK has been shown to interact with NatA core complex in human and fungus, modulating its activity. Here we address the in vivo function of the plant HYPK protein.
A transcriptomics approach was applied to compare transcriptional reprogramming induced by depletion of NAA10 or HYPK mutants in plants.

overall_design: 6-week-old plants grown on soil under short-day conditions were used for RNA extraction and hybridization of RNA to Affymetrix arrays. 4 samples of each WT (control), NAA10 knock-down line (amiNaa10) and HYPK knockout lines (hypk-1, hypk-3) were chosen.

first: Pavlína

last: Miklánková

last: de la Torre

first: Markus

last: Wirtz


title: Effect of genom-wide depletion on gene expression during treatment with the JAK2 inhibitor Ruxolitinib of JAK2 mutated HEL erythroleukemia cells [CRISPR]

status: Public on May 18 2022

city: Jena

first: Philipp

last: Ernst

address: Am Klinikum 1

institute: Jena University Hospital

summary: In order to confirm the functional dependency on KDM4C under treatment conditions with the JAK-inhibitor ruxolitinib (RUX), we applied a genome-wide CRISPR-Cas9 screen in the human JAK2-mutated cell line HEL by CRISPR/Cas9.

overall_design: Comparative gene expression profiling analysis of library-seq data for HEL cells with Genome-wide CRISPR/Cas9 knockout under treatment with Ruxolitinib or control (DMSO).

first: Tina

last: Schnöder

first: Nicolas

last: Huber

first: Florian

last: Perner

middle: H

last: Heidel


title: RNA-Seq of adrenal glands tissue from Wild Type (WT) and Armc5 knockout mice

first: Jiangping

last: Wu

overall_design: Adrenal glands mRNA profiles of WT and Armc5(-/-) mice

first: Linjiang

last: Lao


title: Epigenetic DNA Methylation Signatures Associated with the Severity of  Paget’s disease of bone

city: Doha

first: Omar

middle: M E

last: Albagha

address: Qatar Foundation

department: College of Health and Life Sciences

country: Qatar

institute: Hamad Bin Khalifa University

summary: This pioneering study investigated associations between DNA methylation levels and PDB severity. 100 methylation sites associated with PDB disease severity were identified, while important molecular pathways associated with disease progression were also disclosed. Importantly, DNA methylation markers to predict disease severity with high accuracy were also identified but require further validations.

overall_design: The study was conducted in 232 cases with clinical and radiological evidence of PDB. DNA methylation profiling was determined using Illumina Infinium 450k Human Methylation array. The severity of PDB disease was defined as a composite score and a multivariate predictor of severity of PDB was devised  based on the identification of a panel of differentially methylated loci in PDB patients.

first: Ilhame

last: Diboun


title: Pseudomonas aeruginosa gene regulation by Staphylococcus aureus supernatant or added secreted products

city: Bethesda

first: Anupama

last: Khare

address: 37 Convent Drive

institute: National Cancer Institute

summary: Pseudomonas aeruginosa and Staphylococcus aureus are often co-isolated in persistent infections. The goal of this study was to determine how secreted products that were identified in S. aureus supernatant affect gene expression in P. aeruginosa. Therefore, media control, the indicated products in media, or S. aureus supernatant was added to P. aeruginosa cultures at 25% total volume and gene expression was measured at 20 min and 2 h using RNA-seq. The individual products induced distinct pathways in P. aeruginosa. The products in combination recapitulated much of the differential gene expression seen in P. aeruginosa in response to S. aureus supernatant.

overall_design: We prepared RNA-seq samples from P. aeruginosa cultures at the time of treatment, and 20 minutes and 2 hours after the addition of 25% (v/v) media control, S. aureus supernatant, or the following concentrations of additives either together or separately in media: 80 µM staphylopine, mix of 1000 µM diethylene triamine pentaacetic acid (DTPA) with 500 µM deferoxamine, 150 µM citrate, or 150 µM acetoin. RNAprotect (Qiagen) was added to each sample before purification using the Total RNA Purification Plus Kit (Norgen). Genomic DNA was removed using Turbo DNase (Invitrogen) and rRNA was removed using riboPOOLs (siTOOLs Biotech). The cDNA libraries were generated using NEBNext Ultra II Directional Library Kit and amplified with NEBNext index primers (New England Biolabs). Sequencing was performed at the National Cancer Institute Center for Cancer Research Genomics Core.

first: Tiffany

last: Zarrella


title: Effect of depletion of KDM4C on gene expression of JAK2-mutated HEL erythroleukemia cells [RNA-seq]

summary: To investigate the function of KDM4C in progression of leukemia, we established HEL-Cas9 cell lines in which the target gene has been knocked out by CRISPR/Cas9. We then performed transcriptome analysis using data obtained from RNA-seq of control or KDM4C depletd cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for HEL cells with KDM4C knockout and KDM4C wildtype.


title: The snoGloBe interaction predictor reveals a broad spectrum of C/D snoRNA RNA targets

city: Montréal

first: Gabrielle

last: Deschamps-Francoeur

address: 110 Avenue des Pins, Ouest

institute: Institut de Recherches Cliniques de Montréal

summary: Box C/D small nucleolar RNAs (snoRNAs) are a conserved class of RNA known for their role in guiding ribosomal RNA 2’-O-ribose methylation through base pairing with targeted sequences. Recently, C/D snoRNAs were also implicated in regulating the expression of non-ribosomal genes through different modes of binding. Large scale RNA-RNA interaction datasets detect many snoRNAs binding messenger RNA. However, these studies provide a narrow portrait of snoRNA targets forming under specific experimental conditions. To enable a more comprehensive study of C/D snoRNA interactions, we created snoGloBe, a human C/D snoRNA machine learning interaction predictor based on a gradient boosting classifier. SnoGloBe considers the target type, and position and sequence of the interactions, enabling it to outperform existing predictors. Interestingly, for specific snoRNAs, snoGloBe identifies strong enrichment of interactions near gene expression regulatory elements including splice sites. Abundance and splicing of predicted targets were altered upon the knockdown of their associated snoRNA. Strikingly, the predicted snoRNA interactions often overlap with the binding sites of functionally related RNA binding proteins, reinforcing their role in gene expression regulation. The interactions of snoRNAs are not randomly distributed but often accumulate in functionally related transcripts sharing common regulatory elements suggesting coordinated regulatory function. The wide scope of snoGloBe makes it an excellent tool for discovering viral RNA targets, which is evident from its capacity to identify snoRNAs targeting SARS-CoV-2 RNA, known to be heavily methylated. Overall, snoGloBe is capable of identifying experimentally validated binding sites and predicting novel sites with shared regulatory function.

overall_design: PolyA libraries were generated from SNORD126 knockdown HepG2 cells, using 2 ASO against SNORD126 and 1 control ASO with two replicates at two concentrations each, totaling 4 samples per ASO.

first: Michelle

middle: S

last: Scott


title: The lactate-NAD axis activate cancer associated fibroblasts by downregulating p62 [Lactate ATAC-seq]

status: Public on May 16 2022

city: New York

first: Jorge

last: Moscat

state: NY

address: 1188 York Avenue

department: Pathology and Laboratory Medicine

institute: WEILL CORNELL MEDICINE

summary: Reduced p62 levels are associated with the induction of the cancer-associated fibroblast (CAF) phenotype, which promotes tumorigenesis in vitro and in vivo through inflammation and metabolic reprogramming. However, how p62 is downregulated in the stroma fibroblasts by tumor cells to drive CAF activation is an unresolved central issue in the field. Here we show that tumor-secreted lactate downregulate p62 transcriptionally through a mechanism involving reduction of the NAD+/NADH ratio, which impaired poly(ADP-Ribose)-polymerase 1 (PARP1) activity. PARP1 inhibition blocked the poly(ADP-ribosyl)ation of the AP1 transcription factors, c-FOS and c-JUN, which is an obligate step for p62 downregulation. Importantly, restoring p62 levels in CAFs by NAD+ rendered CAFs less active. PARP inhibitors, such as Olaparib, mimicked lactate in the reduction of stromal p62 levels, as well as the subsequent stromal activation both in vitro and in vivo, which suggests that therapies utilizing Olaparib would benefit from strategies aimed at inhibiting CAF activity.

overall_design: ATACseq samples from WPMY-1 cells treated or not with Lactate 24 mM for 48 h

first: Juan

last: Linares

first: Tania

last: Cid-Diaz

first: Angeles

last: Duran

first: Anxo

last: Martinez-Ordoñez

first: Miguel

last: Reina-Campos

first: Thekla

last: Cordes

first: Timothy

last: Thompson

first: Christian

last: Metallo

first: Maria

middle: T

last: Diaz-Meco


title: The lactate-NAD axis activate cancer associated fibroblasts by downregulating p62 [OLA ATAC-seq]

overall_design: ATACseq samples from WPMY-1 cells treated or not with olaparib for 4 days

middle: F


title: Lipolysis regulates major transcriptional programs in brown adipocytes [3Dcultured_eWAs_RNA-seq]

status: Public on May 15 2022

first: Lasse Kruse

last: Markussen

overall_design: Isolated epididymal white adipocytes with ISO for 3 hrs in the presence and absence of lipase inhibitors and determined the effect on the transcriptome by RNA-seq analysis. Subsequently, we stimulated the mature brown adipocytes with SR-3420 for 3hrs and harvsted for RNA for RNAsequencing.

first: Lasse

last: Kruse Markussen

first: Susanne

last: Mandrup


title: The lactate-NAD axis activate cancer associated fibroblasts by downregulating p62 [RNA-seq]

overall_design: RNA samples from WPMY-1 cells, treated or not with 24 mM Lactate for 48h, were profiled in three biological replicates.


title: Exploring comparative and transcriptomic analyses to unveil mechanisms of resistance to azoles dependent and independent of CgPdr1 in Candida glabrata clinical isolates

city: Aveiro

first: Ana

last: Soares

address: Campus de Santiago

country: Portugal

institute: University of Aveiro

summary: The pathogenic yeast species Candida glabrata has an intrinsically high resilience to azoles and a rapid capability of acquiring resistance. Azole-resistant clinical strains derive mostly from them encoding hyperactive mutants of the CgPdr1 regulator, however, strains encoding wild-type CgPdr1 variants were identified suggesting a role for CgPdr1-independent mechanisms in acquisition of resistance in vivo. Seven azole-resistant C. glabrata isolates were found to encode CgPdr1 gain-of-function variants, two, I392M and I803T, being herein described for the first time. OMICS profile of the sole azole-resistant strain encoding a wild-type CgPDR1 allele revealed that these cells over-express several genes described for providing protection against azoles, while down-regulating genes described to increase sensitivity to these drugs. Over-expression of genes required for metabolism and transport of sterols to compensate the azole-induced inhibition of Erg11 and a more active calcineurin pathway are other mechanisms suggested to underlie azole resistance in ISTB218.

overall_design: The Candida isolates were cultivated in RPMI medium (with 20 g/L as the carbon source) until mid-exponential phase after which they were harvested by centrifugation and immediately frozen until further processing for mRNA extraction and hybridisation in the microarray.

first: Sara

middle: B

last: Salazar

first: Nuno

last: Mira

first: M Joana

last: Pinheiro


title: Dynamic Enlargement and Mobilization of Lipid Droplets in Pluripotent Cells Coordinate Morphogenesis during Mouse Peri-implantation Development

city: London

first: Veronique

last: Azuara

state: London

address: Institute of Reproductive and Developmental Biology, Hammersmith Hospital Campus

department: Metabolism, Digestion and Reproduction

institute: Imperial College London

summary: ESCs grown in Growth Factor-reduced Matrigel can recapitulate in vitro the morphogenesis of the epiblast tissue during peri-implantation development. We performed RNA-sequencing on wild-type (WT) and Cidea knockout (KO) mouse R1-ESCs grown under self-renewing (serum/LIF) conditions and in 3D culture conditions (i.e., 3D spheroids ) at different time-points of differentiation (24h and 48h post-induction) to help us understand the role of the lipid droplet associated factor CIDEA (Cell Death Inducing DFFA Like Effector A) in ESC biology and during the process of morphogenesis.

overall_design: Cidea KO ESCs were generated from CRISPR-Cas9 deletion of the whole locus (Cidea). Subclone (19.7) of the KO cells and parental WT R1-ESCs, along with 3D spheroids (differentiating in Growth Factor-reduced Matrigel) formed from both cell lines, were sequenced for gene expression comparison.

first: King Hang

last: Mau

first: Roshni

middle: A

last: de Souza


title: The lactate-NAD axis activate cancer associated fibroblasts by downregulating p62 [Quantseq]

first: Jorge

last: Moscat

country: USA

overall_design: RNA samples from WPMY-1 cells grown in normal conditions or in androgen deprivation (ADT), and treated or not with Olaparib for four days, were profiled in three biological replicates.

first: Juan

last: Linares

first: Tania

last: Cid-Diaz

first: Angeles

last: Duran

middle: C


title: PqsE expands and differentially modulates the RhlR quorum sensing regulon in Pseudomonas aeruginosa

status: Public on May 17 2022

city: Rome

first: Morgana

last: Letizia

address: Viale Guglielmo Marconi, 446

country: Italy

institute: Roma Tre University

summary:
While it is known that PqsE can stimulate the ability of RhlR to control some virulence factors, no data are available allowing clear discrimination of the PqsE and RhlR regulons.
In this study, a P. aeruginosa PAO1 mutant strain with deletion of multiple QS elements and inducible expression of PqsE and/or RhlR has been generated and validated.
RNA-seq performed in this genetic background allowed to unambiguously define the regulons controlled by PqsE and RhlR when produced alone or in combination
Data produced in this study demonstrate that PqsE mainly impacts on the P. aeruginosa transcriptome via an RhlR-dependent pathway, and splits the RhlR-regulon in PqsE-dependent and PqsE-independent sub-regulons.

overall_design: 12 samples of Pseudomonas aeruginosa PAO1 gathered in 4 different groups consisting of 3 biological replicates. Group A: mutant strain (baseline). Group B: mutant strain expressing PqsE. Group C: mutant expressing RhlR. Group D: mutant expressing both PqsE and RhlR.

first: Marta

last: Mellini

first: Alessandra

last: Fortuna

first: Paolo

last: Visca

first: Francesco

last: Imperi

first: Livia

last: Leoni

first: Giordano

last: Rampioni


title: RNF31 inhibition sensitizes tumors to bystander killing by innate and adaptive immune cells

status: Public on May 14 2022

city: Suzhou

first: Zhengkui

last: Zhang

address: No. 199, Renai Road, Suzhou Industrial Park

department: Institutes of Biology and Medical Science

country: China

institute: Soochow University

summary: We evaluated whether there are transcriptional differences between RNF31-proficient immune-resistant and RNF31-deficient immune-sensitive tumor cells. We stimulated sensitive (sgRNF31- or HOIPIN-8-treated) and resistant (sgCtl, vehicle) BLM tumor cells with TNF for 0 or 6 hours and performed RNA sequencing analysis. Tumor cells sensitized by RNF31 inhibition show a reduced canonical NF-kB and increased pro-death signature upon TNF challenge.

overall_design: 1×10E6 BLM sgCtl or sgRNF31 BLM human melanoma cells were pretreated with vehicle (DMSO) or HOIPIN-8 (10 µM) for 16 h, followed by TNF stimulation (100 ng/ml) for 0 or 6 hours. Two replicates for each sample were performed.

first: Zhnegkui

first: Daniel

last: Peeper


title: GoPeaks: histone modification peak calling for CUT&Tag

city: Portland

first: Theodore

last: Braun

state: Oregon

address: 2720 S Moody Ave

institute: Oregon Health and Science University

summary: Peak calling tool for CUT&Tag histone modifications.

overall_design:
CUT&Tag H3K27Ac and IgG performed in replicates.
Bulk ATAC-seq performed in triplicate.

first: William

last: Yashar

first: Garth

last: Kong

first: Jake

last: VanCampen

first: Brittany

last: Curtiss


title: Lipolysis regulates major transcriptional programs in brown adipocytes

city: Odense M

first: Lasse Kruse

last: Markussen

address: Campusvej 55

institute: University of Southern Denmark

summary: β-Adrenergic signaling is a core regulator of brown adipocyte function stimulating both lipolysis and transcription of thermogenic genes, thereby expanding the capacity for oxidative metabolism. Here we have used pharmacological inhibitors and a novel direct activator of lipolysis to acutely modulate the activity of lipases, thereby enabling us to uncover lipolysis-dependent signaling pathways downstream of β-adrenergic signaling in brown adipocytes. We show that induction of lipolysis leads to acute induction of several gene programs and is required for transcriptional regulation by β-adrenergic signals. Using machine-learning algorithms to infer causal transcription factors, we show that PPARs are key mediators of lipolysis-induced activation of genes involved in lipid metabolism and thermogenesis. Importantly, lipolysis also activates the unfolded protein response and regulates the core circadian transcriptional machinery independently of PPARs. Our results demonstrate that lipolysis generates important metabolic signals that exert profound pleiotropic effects on brown adipocyte transcription and function.

overall_design: Refer to individual Series

first: Lasse

last: Kruse Markussen

first: Susanne

last: Mandrup


title: An Engineered Multicellular Stem Cell Niche for the 3D Derivation of Human Myogenic Progenitors from iPSCs

status: Public on May 13 2022

city: Lausanne

first: Omid

last: Mashinchian

state: Vaud

address: EPFL INNOVATION PARK, BUILDING H

institute: Nestlé Institute of Health Science, Nestlé Research

summary: Fate decisions in the embryo are controlled by a plethora of microenvironmental interactions in a three-dimensional niche. To investigate whether aspects of this microenvironmental complexity can be engineered to direct myogenic human induced pluripotent stem cell (hiPSC) differentiation, we screened cell types present in the developmental or adult stem cell niche in heterotypic suspension embryoids. We identified embryonic endothelial cells and fibroblasts as highly permissive for myogenic specification of hiPSCs. After two weeks of consecutive Wnt and FGF pathway induction, three-component embryoids (iTCEs) containing these cell types yielded between 40-50% human Pax7 positive embryonic-like myogenic progenitors (eMPs). In a secondary screen we identified cell surface markers allowing for flow cytometric isolation of >99% of the Pax7 positive eMP population from iTCEs. Myogenic differentiation of hiPSCs in iTCEs relies on a specialized structural microenvironment and activates the MAPK, PI3K/AKT, and Notch pathways. After transplantation in a mouse model Duchenne muscular dystrophy, eMPs repopulate the stem cell niche, reactivate after repeated injury and, compared to adult human myoblasts, display enhanced fusion and lead to stronger muscles. Altogether, we provide a highly efficient and scalable suspension-based protocol for 3D derivation of Pax7 positive myogenic progenitors from hiPSCs within a two-week time window.

overall_design: 2D cultured human induced pluripotent stem cells (hiPSCs) (day 0) and of 7 and 13 day 3D-hiPSC organoids analyzed using scRNAseq.

first: Filippo

last: De Franceschi

first: Sina

last: Nassiri

first: Joris

last: Michaud

first: Eugenia

last: Migliavacca

first: Patrick

last: Aouad

first: Sylviane

last: Metairon

first: Solenn

last: Pruvost

first: Sonia

last: Karaz

first: Paul

last: Fabre

first: Thomas

last: Molina

first: Pascal

last: Stuelsatz

first: Nagabhooshan

last: Hegde

first: Emmeran

last: Le Moal

first: Gabriele

last: Dammone

first: Nicolas

last: Dumont

first: Matthias

last: Lutolf

first: Jerome

last: Feige

first: C

last: Bentzinger


title: bulk RNA-seq data analysis of primary human mesenchymal stem cells of Multiple Myeloma patients compared to control patients

city: Muenster

first: Klara

middle: Maria

last: Möllers

address: Albert-Schweitzer-Campus 1

department: Medical Department A

country: Germany

institute: University Hospital Muenster

summary:
Purpose: In this study we compared bone marrow-derived mesenchymal stem cells (MSC) of 6 Multiple Myeloma patients (MM-MSC) with MSC of 5 control donors with other (non) malignant diseases (CTR-MSC) to detect transciptomic alterations in RNA sequencing and to identify altered gene expression patterns.
Methods: MSC were obtained from bone marrow, cultivated, analyzed by flow cytometry and underwent quality control using the 4200 TapeStation (Agilent, California, USA). Following the TrueSeq stranded protocol (Illumina, California, USA) we sequenced the RNA in a 100 bp paired-end run on the HiSeq 4000 (Illumina).
Results: We detected 2174 significant DEGs (adjusted p<0.05) between MM-MSC and CTR-MSC, among which 967 were up-regulated in MM-MSC. 18 out of 50 MSigDB Hallmark gene sets were significantly enriched in MM-Act-MSC compared to CTR-MSC (FDR<0.05) including PI3K-AKT-mTOR signaling, as well as NOTCH, MYC and Inflammatory response.
Conclusion: Our data provides a deeper insight into the molecular signature and function of MSC associated MM-cells and show that targeting PI3K-AKT-mTOR signaling in MSC may represent an additional therapeutic pathway in the treatment of MM-patients.

overall_design: bulk-RNA sequencing data analysis of Multiple Myeloma MSC compared to control MSC

first: Lanying

last: Wei

first: Anja

last: Baumann

first: Alexandra

last: Poos

first: Marc

last: Raab


title: Triiodothyronine (T3) promotes brown fat hyperplasia via thyroid hormone receptor α mediated adipocyte progenitor cell proliferation

city: Shanghai

first: Siyi

last: Shen

address: 320 Yueyang Road

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

summary: The thyroid hormone (TH)-controlled recruitment process of brown adipose tissue (BAT) is not fully understood. Here, we show that long-term treatment of T3, the active form of TH, increases the recruitment of thermogenic capacity in interscapular BAT  of male mice through hyperplasia by promoting the TH receptor α-mediated adipocyte progenitor cell proliferation. Our single-cell analysis reveals the heterogeneous nature and hierarchical trajectory within adipocyte progenitor cellsof interscapular BAT. Further analyses suggest that T3 facilitates cell state transition from a more stem-like state towards a more committed adipogenic state and promotes cell cycle progression towards a mitotic state in adipocyte progenitor cells, through mechanisms involving the action of Myc on glycolysis. Our findings elucidate the mechanisms underlying the TH action in adipocyte progenitors residing in BAT and provide a framework for better understanding of the TH effects on hyperplastic growth and adaptive thermogenesis in BAT depot at a single-cell level.

overall_design: To explore the role of T3 in APCs of iBAT, we performed scRNA-seq on APCs of iBAT from MMI mice with and without long-term T3 treatment.

first: Hao

last: Ying

first: Jingjing

last: Jiang

first: Shengnan

last: Liu


title: Y RNAs are conserved endogenous RIG-I ligands across RNA virus infection and are targeted by HIV-1

city: New York City

last: Vabret

address: 1470 Madison Avenue, Hess 5th floor

department: Hematology/Oncology

institute: ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI

summary: Pattern recognition receptors (PRRs) protect against microbial invasion by detecting specific molecular patterns found in pathogens and initiating an immune response. While microbial-derived PRR ligands have been extensively characterized, the contribution and relevance of endogenous ligands to PRR activation remains overlooked. Here, we characterize the landscape of endogenous ligands that engage RIG-I-like receptors (RLRs) upon infection by different RNA viruses. In each infection, several RNAs transcribed by RNA polymerase III (Pol3) specifically engaged RLRs, particularly the family of Y RNAs. Sensing of Y RNAs was dependent on their mimicking of viral secondary structure and their 5’-triphosphate extremity. Further, we found that HIV-1 triggered a VPR-dependent downregulation of RNA triphosphatase DUSP11 in vitro and in vivo, inducing a transcriptome-wide change of cellular RNA 5’-triphosphorylation that licenses Y RNA immunogenicity. Overall, our work uncovers the contribution of endogenous RNAs to antiviral immunity and demonstrates the importance of this pathway in HIV-1 infection.

overall_design: We performed 5'-PPP RNAseq on A549 WT or DUSP11KO; Jurkat WT or DUSP11KO; Jurkat Non infected, infectd with HIV-1 NL4.3 GFP WT or infected with HIV-1 NL4.3 GFP delta VPR. Everycondition was done in triplicate

first: Alexander

last: Solovyov


title: R-spondin driven NF-κB signaling shapes the gastric gland base cell compartment and enables rapid inflammation upon infection of stem cells

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

institute: Max-Planck-Institute for Infection Biology

summary: Mechanisms by which mucosal surfaces discriminate between harmless bacteria and pathogens are not well understood. Gastric gland base colonization by Helicobacter pylori, in contrast to surface colonization causes inflammation and gastric pathology. This compartment contains stem cells, that are controlled by stromal R-spondin 3. Here, we asked how R-spondin 3 and its receptors Lgr4 and Lgr5 control inflammatory responses to H. pylori. We find that epithelial responses to infection are mediated by Rspodnin 3 mainly via Lgr4, causing NF-κB signaling and pro-inflammatory chemokine production. R-spondin 3 signaling induces a baseline NF-κB activity exclusively in the gland base, enabling rapid nuclear translocation of p65 upon infection, triggering inflammtion. Intriguingly, knockout mice that lack NF-κB signaling display an almost complete loss of gland base cells. Our data reveal that gland base cells are primed to act as central proinflammatory mediators, enabling rapid and selective mucosal responses to infections.

overall_design: Microarray experiments were performed as dual-color hybridizations on Agilent whole mouse catalog 4x44K (Agilent-014868) arrays. To compensate for dye-specific effects, a dye-reversal color-swap was applied. We here investigated the function of Lgr4 and Lgr5,  R-spondin 3 receptors, by using conditional mouse models that enable manipulation of Lgr4 and Lgr5 gene expression in gastric Axin2+ cells. The effect and the physiological function of Lgr4 was analzyed in the antrum with Lgr4 gene knock-out mice (Lgr4fl/fl/Axin2CreErt2). These mice were infected for 2 month with Helicobacter pylori. In addition the effect and physiological function of Lgr4 and Lgr5 was analyzed in the antrum with Lgr4 and Lgr5 gene knock-out mice (Lgr4fl/flLgr5fl/flAxin2CreErt2).

first: Michael

last: Sigal

first: Jonas

last: Wizenty

first: Manqiang

last: Lin

first: Julian

last: Heuberger

first: Frank

last: Tacke

first: Hilmar

last: Berger


title: The lactate-NAD axis activate cancer associated fibroblasts by downregulating p62.

first: Jorge

last: Moscat

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


title: Effects of Lactobacillus curvatus HY7601 and Lactobacillus plantarum KY1032 on Overweight and Gut Microbiota in Human: Randomized, Double-Blinded, Placebo-Controlled Clinical Trial

status: Public on May 12 2022

city: Yongin-si

first: Sungjoon

last: Mo

address: 22, Giheungdanji-ro 24beon-gil

institute: hy R&BD center

summary: Obesity and overweight are closely related to diet, and gut microbiota play an important role in body weight and human health. The aim of this study was to explore how Lactobacillus curvatus HY7601 and Lactobacillus plantarum KY1032 supplementation alleviate obesity by modulating the human gut microbiome. A randomized, double-blind, placebo-controlled study was conducted on 72 overweight individuals. Over a 12-week period, probiotic groups consumed 5×10^9 colony-forming units of HY7601 and KY1032), whereas the placebo group consumed the same product without probiotics. After treatment, the probiotic group displayed a reduction in body weight (p <0.001), visceral fat mass (p <0.025), and waist circumference (p <0.007), and an increase in adiponectin (p <0.046), compared with the placebo group. Additionally, HY7601 and KY1032 supplementation modulated bacterial gut microbiota characteristics and beta diversity by increasing Bifidobacteriaceae and Akkermansiaceae, and decreasing Prevotellaceae and Selenomonadaceae. In summary, HY7601 and KY1032 probiotics exert anti-obesity effects by regulating the gut microbiota; hence, they have therapeutic potential for preventing or alleviating obesity and overweight.

overall_design:
Fecal samples were collected from each human and metagenomic analysis was conducted.

Sample group (indicated in the sample characteristics field):
BPRO, Before probiotics;
BPLA, Before placebo;
APRO, After probiotics;
APLA, After placebo.

first: Kippeum

last: Lee


title: Pseudomonas aeruginosa gene regulation by Staphylococcus aureus exoproducts

first: Anupama

last: Khare

state: MD

summary: Pseudomonas aeruginosa and Staphylococcus aureus are often co-isolated in persistent infections. The goal of this study was to determine how secreted products from S. aureus affect gene expression in P. aeruginosa. Therefore, media control or S. aureus supernatant was added to P. aeruginosa cultures at 25% total volume and gene expression was measured at 20 min, 1 h, and 2 h using RNA-seq. Overall, after addition of S. aureus supernatant, there was an upregulation in genes involved in metal deprivation and intermediate metabolite uptake.

overall_design: We prepared RNA-seq samples from P. aeruginosa cultures at the time of treatment, and 20 minutes, 1 hour, and 2 hours after the addition of 25% (v/v) media control or S. aureus supernatant. RNAprotect (Qiagen) was added to each sample before purification using the Total RNA Purification Plus Kit (Norgen). Genomic DNA was removed using Turbo DNase (Invitrogen) and rRNA was removed using Ribo-Zero (Epicentre). The cDNA libraries were generated using NEBNext Ultra II Directional Library Kit and amplified with NEBNext index primers (New England Biolabs). Sequencing was performed at the National Cancer Institute Center for Cancer Research Genomics Core.

first: Tiffany

last: Zarrella


title: Molecular subtyping of “double negative” MIBC

city: Frankfurt

first: Florestan

middle: Johannes

last: Koll

address: Theodor-Stern-Kai 7

department: Department of Urology

institute: University Hospital Frankfurt, Goethe University

summary: Identifying patients that benefit from cisplatin-based adjuvant chemotherapy is a major issue in the management of muscle-invasive bladder cancer (MIBC). The purpose of this study is to correlate “luminal” and “basal” type protein expression with histological subtypes, to investigate the prognostic impact on survival after adjuvant chemotherapy and to define molecular subtypes of “double negative” patients (i.e. without expression of CK5/6 or GATA3).

overall_design: 10 IHC-double negative cases were analyzed with the HTG transcriptome panel with 19398 mRNA targets. Molecular consensus classification was determined according to Kamoun et al. (Euro Urol, 2019)

first: Claudia

last: Döring

middle: J


title: iBAT total RNA profiles of wild type C57BL/6N mice exposed to cold and high fat diet

city: Odense

first: Jan

middle: Wilhelm

last: Kornfeld

address: Campusbej 50

department: Biochemistry and Molecular Biology

summary: Cold and nutrient activated brown adipose tissue (BAT) is capable of increasing systemic energy expenditure via uncoupled respiration and secretion of endocrine factors thereby protecting mice against diet-induced obesity and improving insulin response and glucose tolerance in men. Long non-coding RNAs (lncRNAs) have recently been identified as fine tuning regulators of cellular function. While certain lncRNAs have been functionally characterised in adipose tissue, their overall contribution in the activation of BAT remains elusive. We identified lncRNAs correlating to inter- scapular brown adipose tissue (iBAT) function in high fat diet (HFD) and cold stressed mice. We focused on Gm15551 which has an adipose tissue specific expression profile, is highly upregulated during adipogenesis and downregulated by β-adrenergic activation in mature adipocytes. Albeit we performed comprehensive transcriptional and adipocyte physiology profiling in vitro and in vivo, we could not detect an effect of gain or loss of function of Gm15551.

overall_design: Inguinal brown adipose tissue (iBAT) total RNA profiles of 20-week old  C57BL/6N mice on high fat diet for 12 weeks and cold treated for 24 h at 4°C were generated by deep sequencing in triplicate.

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