title: Disease modeling of pulmonary fibrosis using human iPS cell-derived alveolar organoids (fibroblasts)

city: Kyoto

first: Shimpei

last: Gotoh

address: 53 Kawaharacho, Shogoin, Sakyo-ku

department: Center for iPS cell Research and Application

institute: Kyoto University

summary: We developed an in vitro model of pulmonary fibrosis using alveolar organoids, consisting of human induced pluripotent stem cell-derived alveolar epithelial cells and human lung fibroblasts. In this model, fibroblasts were activated by bleomysin (BLM) treatment in an epithelial cell-dependent manner simillar to the pathogenic mechanism of pulmonary fibrosis.

overall_design: CPMhigh progenitor cells were differentiated from iPSCs. CPMhigh progenitor cells and human fetal lung fibroblasts (HFLF) were cocultured to generate SPC+cells. SPC+ cell-derived alveolar organoids passaged 3 times were treated with DMSO or 3 μg/mL BLM from day 11 to day14, then washed out of BLM, and incubated for another 3 days. Co-cultured fibroblasts were isolated by negative selection of EpCAM+ cells from alveolar organoids. In fibroblast only culture, the cells were treated as in alveolar organoids and all cells were collected.

first: Takahiro

last: Suezawa


title: Disease modeling of pulmonary fibrosis using human iPS cell-derived alveolar organoids

status: Public on Nov 19 2021

country: Japan

type: Expression profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: A neuronal transcription factor is required in the prefrontal cortex for transcriptional and behavioral adaptation to chronic stress

city: Old Westbury

first: Ying-Tao

last: Zhao

state: NY

address: Riland building, Room 024 Northern Boulevard, P.O. Box 8000

department: Biomedical Sciences

country: USA

institute: New York Institute of Technology

summary: Stressful life events increase risk for depression, yet the molecular mechanisms by which stress is encoded in the brain to induce maladaptive behaviors are not well understood. Emerging evidence has shown that stress dysregulates gene expression in the brain, yet the cellular origin of these gene expression alterations has yet to be determined.  To address this question, we used a chronic unpredictable stress (CUS) paradigm that drives depressive- and anxiety-like behaviors in male and female mice and single-nucleus transcriptomics to identify cell type-specific gene expression changes in the cortex. We find that neocortical excitatory neurons are particularly vulnerable to chronic stress exposure, and that CUS reprograms these cells to decrease transcription of synaptic genes involved in glutamatergic neurotransmission. We identify the ubiquitously expressed factor, Yin Yang 1 (YY1), as a key driver of the transcriptional reprogramming observed in excitatory neurons isolated from CUS mice. Selective depletion of YY1 in excitatory neurons of the prefrontal cortex (PFC) increases the stress sensitivity of mice, inducing depressive- and anxiety-related behaviors following an abbreviated stress exposure and deregulating expression of key stress-related genes in the PFC. Importantly, we find that YY1 functions in both males and females to facilitate stress coping. This work establishes a novel mechanism underlying chronic stress-induced behavior, in which epigenetic responses to stress in PFC excitatory neurons are mediated by stress-dependent YY1 activity. Our findings demonstrate how post-mitotic neurons adapt to stress experience and identify a novel molecular target that is generalizable to males and females for therapeutic treatment of stress-related neuropsychiatric disorders.

overall_design: Examine gene expression profiles in stressed mice

first: Deborah

middle: Y

last: Kwon

first: Peng

last: Hu

first: Jennifer

middle: E

last: Phillips-Cremins

first: Hao

last: Wu

first: Zhaolan

last: Zhou


title: EPDR1 inhibits proliferation and matastasis of ovarian cancer through PI3K/AKT pathway

status: Public on Nov 18 2021

city: Jinan

first: dan

middle: zhen

state: Shandong Province

address: 107 Wenhua West Road

department: Department of Gynecology and Obstetrics

country: China

institute: Shandong University

summary: Epithelial ovarian cancer (EOC) is the main subtype of ovarian cancer. In this study, we found that Ependymin-related 1 (EPDR1) was significantly downregulated in EOC tissues and low EPDR1 expression was associated with International Federation of Gynecology and Obstetrics (FIGO) stage, metastasis and poor prognosis. We confirmed that EPDR1 overexpression dramatically inhibited EOC cells proliferation, migration and invasion in vitro and in vivo. Mechanistically, EPDR1 suppressed EOC tumorigenesis and progression, at least in part, through inhibiting PI3K/AKT pathway. Furthermore, the expression and function were regulated by miR-429, as demonstrated by luciferase reporter assays and rescue experiments. In conclusion, our study demonstrated that EPDR1, negatively regulated by miR-429, played an important role in EOC development via PI3K/AKT pathway. The miR-429/EPDR1 axis might provide promising therapeutic targets for individualized treatment of EOC patients in future.

overall_design: Significantly changed genes in EPDR1 ovexpression A2780 cells compared to the control HCT116 cells

first: Zhendan

first: Yingwei

last: Li

first: Zhiling

last: Wang

first: Pengling

first: Xingsheng

last: Yang


title: Cortical diurnal rhythms remain intact with microglial depletion

city: Irvine

first: Kim

last: Green

state: CA

address: 3208 Biological Sciences 3

department: Neurobiology and Behavior

institute: University of California, Irvine

summary: This dataset allows for the exploration of cortical genes at across different timepoints (ZT2, ZT6, ZT10, ZT14, ZT 18, ZT22) in control C57BL/6J mice compared to microglia-depleted C57BL/6J mice (10 day PLX5622 treatment).

overall_design: C57BL/6J mice were fed either control diet or diet containing the CSF1R inhibitor PLX5622 (1200 ppm) for 10 days. Following treatment, brains were harvested at Zeitgeber times (ZT): ZT2, ZT6, ZT10, ZT14, ZT18, and ZT22. Brains were microdissected for bulk-tissue RNA sequencing (RNAseq) of the cortex. N=4 per group except for control ZT14 which has N=3.

middle: N

first: Rocio

middle: A

last: Barahona


title: Disease modeling of pulmonary fibrosis using human iPS cell-derived alveolar organoids (SPC+ cells)

summary: We developed an in vitro model of pulmonary fibrosis using alveolar organoids, consisting of human induced pluripotent stem cell-derived alveolar epithelial cells and human lung fibroblasts. In this model, fibroblasts were activated by bleomysin (BLM) treatment in an epithelial cell-dependent manner simillar to the pathogenic mechanism observed in pulmonary fibrosis.

overall_design: CPMhigh progenitor cells were differentiated from iPSCs. CPMhigh progenitor cells and human fetal lung fibroblasts were cocultured to generate SPC+cells. SPC+ cell-derived alveolar organoids passaged 3 times were treated with DMSO or 3 μg/mL BLM from day 11 to day14. Then each reagent was washed out and the organoids were incubated for another 3 days. SPC+ cells in each condition were isolated from alveolar organoids on day17.


title: Chronic IL-1 Exposed AR+ PCa Cell Lines Show Conserved Loss of IL-1 Sensitivity and Evolve Both Conserved and Unique Differential Gene Expression Profiles

city: Richardson

first: Nikki

last: Delk

address: 800 West Campbell Road

department: Biological Sciences

institute: University of Texas at Dallas

summary: AR+ PCa cell lines show conserved activation of canonical IL-1 intracellular signaling cascades, including repression of androgen receptor mRNA levels, in response to acute IL-1 treatment and show conserved loss of sensitivity to prolonged (chronic) IL-1 intracelluar signaling, including the restoration of the androgen receptor.  Thus, chronic IL-1 exposure selects for cells that have a growth advantage against cytotoxic/static inflammation, including restoration of constitutive AR expression.

overall_design: MDA-PCa-2b cells were chronically cultured in 0.5 ng/ml IL-1 alpha or IL-1 beta (in HPC1 + 20% FBS) for 4 months. IL-1 is cytotoxic/static, so the viable, proliferating colonies that emerged after 4 months in IL-1 alpha or IL-1 beta were expanded to generate the IL-1a subline (MDA-αs1) and the IL-1b subline (MDA-βs1). MDA-PCa-2b parental cells were cultured in vehicle (0.1% BSA in 1xPBS) in HPC1 + 20% FBS. For basal expression and acute IL-1 treatment expression studies, MDA-PCa-2b parental, MDA-αs1 and MDA-βs1 cells were cultured in vehicle (0.1% BSA in 1xPBS) in HPC1 + 20% FBS for 3 days and the MDA-PCa-2b parental cells were treated with 25 ng/ml IL-1 alpha or IL-1 beta in HPC1 + 20% FBS for 3 days.  Total RNA was isolated from 3 biological replicates for RNA sequencing.

first: Shayna

last: Thomas-Jardin

first: Mohammed

last: Kanchwala

first: Haley

last: Dahl

first: Vivian

last: Liu

first: Rohan

last: Ahuja

first: Reshma

last: Soundharrajan

first: Nicole

last: Roos

first: Chao

last: Xing


title: Bioinformatic analysis of Protein Disulfide Isomerase A1  (PDIA1)-associated pathways towards developing stratified  breast cancer therapies

city: Kuwait City

first: Rashed

last: Alhammad

address: Safat 13110 - Kuwait

department: Department of Pharmacology & Toxicology, Faculty of Medicine, Health Sciences Centre

country: Kuwait

institute: Kuwait University

summary: The oxidoreductase protein disulfide isomerase A1 (PDIA1) functions as a cofactor for  many transcription factors including the estrogen receptor alpha (ERα), the NF-κΒ, the nuclear  factor erythroid 2-like 2 (NRF2) and regulates the protein stability of the tumor suppressor p53.  Taking this into account we hypothesized that PDIA1, by differentially modulating the gene  expression of diverse subsets of genes in the ERα positive versus the ERα negative breast cancer  cells, modifies dissimilar pathways in the two types of breast cancer. This hypothesis was  investigated using RNA-seq data from PDIA1-silenced MCF-7 (ERα+) and MDA-MB-231 (ERα-)  breast cancer cells treated with either interferon gamma (IFN-γ) or etoposide (ETO) and the  obtained data were further analyzed using a variety of bioinformatic tools alongside clinical  relevance assessment via Kaplan-Meier patient survival curves. The results highlighted the dual  role of PDIA1 in suppressing carcinogenesis in the ERα+ breast cancer patients by negatively  regulating the response to reactive oxygen species and promoting carcinogenesis by inducing cell  cycle progression. In the ERα- breast cancer patients PDIA1 prevents tumor development by  regulating the NF-kappa B and p53 by modulating cell migration and inducing breast cancer  progression through control of cytokine signaling and the immune response. The findings  reported in this study shed light on the differential pathways regulating carcinogenesis in the  ERα+ and ERα- breast cancer patients and could help identify therapeutic targets selectively  effective in the ERα+ versus the ERα- patients.

overall_design: RNA-sequencing study. 24 samples. Two cell lines. Three replicates per condition. Cells were treated with either etoposide (ETOP) or Interferon-Gamma (INF/IFN) and either with scramble siRNA or siRNA against P4HB (PDIA1).

first: Emyr

last: Bakker

first: Masayuki

last: Fujii

first: Marija

last: Krstic-Demonacos

first: Constantinos

last: Demonacos


title: Identification of small molecule inhibitors of the Pathogen Box against Vibrio cholerae

city: Calgary

first: Haeun

last: Kim

state: AB

address: 3330 Hospital Drive N.W.  HSC-B045

country: Canada

institute: University of Calgary

summary: Antimicrobial resistance (AMR) has become a serious public and economic threat. The rate of bacteria acquiring AMR surpasses the rate of new antibiotics discovery, projecting more deadly AMR infections in the future. The Pathogen Box is an open-source library of drug-like compounds that can be screened for antibiotic activity. We have screened molecules of the Pathogen Box against Vibrio cholerae, the cholera-causing pathogen, and successfully identified two compounds, MMV687807 and MMV675968, that inhibit growth. RNA-seq analyses of V. cholerae after incubation with each compound revealed that both compounds affect cellular functions on multiple levels including carbon metabolism, iron homeostasis, and biofilm formation. In addition, whole-genome sequencing analysis of spontaneous resistance mutants identified an efflux system that confers resistance to MMV687807. We also identified that the dihydrofolate reductase is the likely target of MMV675968 suggesting it acts as an analog of trimethoprim but with a minimum inhibitory concentration (MIC) 14-fold lower than trimethoprim in molar concentration. In summary, these two compounds that effectively inhibit V. cholerae and other bacteria may lead to the development of new antibiotics for better treatment of the cholera disease.

overall_design: 9 samples: 3 replicates of control and each treatment (2.5 μM MMV687807, 10 nM MMV675968)

first: Brianne

middle: J

last: Burkinshaw

first: Linh

middle: G

last: Lam

first: Kevin

last: Manera

first: Tao

last: Dong


title: N4-acetyldeoxycytosine DNA modification marks euchromatin regions in Arabidopsis thaliana.

city: Fuzhou

first: mao

last: fei

state: Fujian

address: Shangxiadianlu NO.15

department: National Engineering Research Center of JUNCAO

institute: Fujian Agriculture and Forestry University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We report the application of Next-generation sequencing (NGS) for high-throughput profiling of N4-acetylcytosine (4acC) DNA modification in Arabidopsis thaliana. We find  that 4acC  peaks mostly distribute in the euchromatin regions and are present in nearly half of the protein-coding genes in Arabidopsis.  4acC mainly locates around transcription start sites (TSSs) of protein-coding genes and positively correlates with gene expression level . Compared to non-4acC marked genes, 4acC marked genes display a higher methylation level of 5mC in the CG context within coding regions, but a lower methylation level of 5mC in the CHG and CHH contexts. In addition, 4acC peaks showed higher overlaps with active histone modification marks than by chance, but similar overlaps with repressive histone modification marks.  We observed complex cooperative interactions among 4acC, 5mC, and histone modifications on gene transcription.  4acC containing genes with low level of mCG, or active histone modification marks displayed a higher expression. In sum, we have uncovered 4acC as a hitherto unknown epigenetic DNA mark that is associated with gene expression in Arabidopsis, and suggest potential cross-talks  among epigenetic marks for gene expression.

sample_organism:
Arabidopsis thaliana
Zea mays

platform_organism:
Arabidopsis thaliana
Zea mays

overall_design: Examination of 4acC DNA modification in Arabidopsis thaliana.

first: Shuai

last: Wang

first: Hairong

last: Xie

first: Fei

last: Mao

first: Haiyan

first: Shu

first: Zhenglin

last: Chen

first: Yuxia

last: Zhang

first: Zhihui

last: Xu

first: Jinming

first: Zhaokang

last: Cui

first: Xiquan

last: Gao

first: Hongmei

last: Jin

first: Jian

last: Hua

first: Bo

last: Xiong

first: Yufeng

last: Wu


title: Genome-wide maps of double strand breaks after siRNA knockdown of DDX41 in HCT116 cells

status: Public on Nov 17 2021

city: Mainz

first: Petra

last: Beli

address: Ackermannweg 4

country: Germany

institute: Institute of Molecular Biology (IMB)

summary: We report the first genome-wide mapping of fragility hotspots after siRNA-mediated knockdown of the DEAD-box helicase DDX41 in HCT116 cells using sBLISS. DDX41 defficient cells display elevated levels of genomic instability. sBLISS analysis revealed that hotspots for genomic instability in the absence of DDX41 are located around the transcription start site of transcribed genes.

overall_design: Genome-wide mapping of DNA double-strand breaks by sBLISS upon siRNA-mediated knockdown of DDX41 was performed in human adenocarcinoma HCT116 cells. Non-targeting siRNA was used as a control. The experiment was carried out in biological replicates.

first: Gabriel

middle: M

last: Longo

first: Vassilis

last: Roukos

first: Giuseppe

last: Petrosino


title: Growth Differentiation Factor 1-Induced Tumour Plasticity Provides A Therapeutic Window for Immunotherapy in Hepatocellular Carcinoma

city: Guangzhou

first: Wei

last: Cheng

state: Guangdong

address: Xinzao, Panyu District

institute: Guangzhou Medical University

summary: Poorly differentiated hepatocellular carcinoma (HCC) is an aggressive disease with poor prognosis. Here the authors show that GDF1, a member of the TGF-β superfamily, is highly expressed in high-grade poorly differentiated HCC and is associated with tumor plasticity, and that GDF1-induced re-expression of cancer testis antigens could render tumors sensitive to immune checkpoint inhibition.

overall_design: RNA sequencing was performed in PLC-8024-CTR and PLC-8024-GDF1 cells at Shanghai Shenggong Biotech Co., Ltd. RNA samples were analyzed by RNA sequencing based on the manufacturer’s protocols. Briefly, Illumina HiSeq platform was used to sequence the RNA samples for the subsequent generation of raw data. R package was utilized to select genes with significantly differential expression. In order to obtain the significant differential genes, the screening conditions were set as follows: q-value <0.05 and difference multiple log2FoldChange >1. GSEA enrichment analysis were used for functional pathway analysis.

first: Ming

last: Liu


title: Analysis of differentiating 3T3L1 mouse pre-adipocytes with knock-down of Tmem120a and Tmem120b

city: Edinburgh

first: Jose

middle: Ignacio

last: de las Heras

address: Max Born Crescent

department: Wellcome Trust Centre

country: United Kingdom

institute: University of Edinburgh


title: A Novel Non-Classical Monocyte-derived Macrophage Subset That Provides A Splenic Replication Niche For Intracellular Salmonella [Bulk RNA-Seq II]

status: Public on Nov 16 2021

city: Rehoboth

first: Dotan

last: Hoffman

address: Herzel St 234, Biological regulation

department: Biological regulation

country: Israel

institute: Weizmann institute of science

summary: Interactions between intracellular bacteria and mononuclear phagocytes give rise to diverse cellular phenotypes that may determine the outcome of infection. Recent advances in single-cell RNA-seq (scRNA-seq) have identified multiple subsets within the mononuclear population, but implications to their function during infection remain unknown. Here, we applied microscopy, flow cytometry and scRNA-seq to survey the mononuclear niche of intracellular Salmonella Typhimurium (S.Tm) during early systemic infection in mice. We describe eclipse-like growth kinetics in the spleen, with a first phase of bacterial control mediated by tissue-resident red-pulp macrophages. A second phase involved extensive bacterial replication within a newly identified macrophage population characterized by CD9 expression. Using Nr4a1e2-/- mice we established that CD9+ macrophages originated from non-classical monocytes (NCM), and NCM-depleted mice were more resistant to S.Tm infection. Our study defines a novel host-pathogen interface, with macrophage subset-specific interactions that determines early infection dynamics and the infection outcome of the entire organism.

overall_design: Splenocytes were isolated from 6 mice 24 hours post infection with Salmonella enterica serovar Typhimurium. RNA was extracted from CD9 Mf and iNOS Mf

first: Yaara

last: Tevet

first: Sebastien

last: Trzebanski

first: Gili

last: Rosenberg

first: Leia

last: Vainman

first: Aryeh

last: Solomon

first: Noa

middle: B

last: Ben-Moshe

first: Shelly

last: Hen-Avivi

first: Roi

last: Avraham


title: Genome wide mapping of native R-loops using a targeted nuclease approach in HCT116 cells after DDX41 siRNA knockdown (MapR)

summary:
Purpose: Investigation of genome-wide changes in R-loop levels after knockdown of DDX41 HCT116 cells in comparison to a control knockdown.
Method: Concanavalin A-coated beads were activated in Binding Buffer (20 mM Hepes-KOH pH 7.9, 10 mM KCl, 1mM CaCl2, 1 mM MnCl2). 1*10^6HCT116 cells were washed twice with Wash Buffer (Hepes-NaOH pH7.5, 150 mM NaCl, 0.5 mM Spermidine, 1 mM protease inhibitor) at room temperature and afterwards immobilized on the activated beads in 50 µl Wash Buffer containing 0.05% Digitonin. Either pA-MNase or RHΔ-MNase were added to the cells overnight at 4°C on a rotating wheel. After three washes with Wash Buffer containing 0.05% Digitonin, samples resuspended in 100 µl Dig-Wash-Buffer were equilibrated on ice. Activity of the MNase was triggered by adding 2mM CaCl2 to the samples for 30 minutes. 2x Stop Buffer (68 µl 5M NaCl, 40 µl 0.5 M EDTA, 20 µl 0.2 M EGTA, 10 µl 5% digitonin, 5 µl 10mg/ml RnaseA, 20 pg/ml spike-in Drosophila DNA (Active Motif)) was mixed with the samples to stop the reaction. Chromatin fragments were released by incubating the samples for 20 minutes at 37°C and centrifugation at 16.000×g for 10 minutes at 4°C. Supernatants were incubated at 70°C in the presence of 0.1% SDS and 5 µg proteinase K. Before library preparation, the DNA was recovered by phenol-chloroform extraction
Results: We were able to map R-loop dynamics genome-wide in HCT116 cells in biological triplicates. MapR signal was significantly increased around the transcription start site in the absence of DDX41

overall_design: R-loop mapping using MapR after 48h knockdown with a control siRNA or a DDX41 siRNA

first: Thorsten

last: Mosler

first: Nastasja

last: Kreim


title: Robust differentiation of human enteroendocrine cells from intestinal stem cells

city: Boston

first: Ivan

last: Zanoni

state: MA

address: 300 Longwood Ave

institute: Boston Children's Hospital

summary: Enteroendocrine (EE) cells are the most abundant hormone-producing cells in humans and are critical regulators of energy homeostasis and gastrointestinal function. Challenges in converting human intestinal stem cells (ISCs) into functional EE cells, ex vivo, have limited progress in elucidating their role in disease pathogenesis and in harnessing their therapeutic potential. To address this, we employed small molecule targeting of key transcriptional regulators, GATA4, JNK and FOXO1, known to mediate endodermal development and hormone production, together with directed differentiation of human ISCs from the duodenum and rectum. We observed marked induction of EE cell differentiation and gut-derived expression and secretion of SST, 5HT, GIP, GLP-1 and PYY upon treatment with various combinations of three small molecules: rimonabant, SP600125 and AS1842856. Robust differentiation strategies capable of driving human EE cell differentiation is a critical step towards understanding these essential cells and the development of cell-based therapeutics.

overall_design: mRNA isolated from enteroids exposed to three different conditions, G2D12, AS and RSP, from three different enteroid lines (9 samples total, detailed in the 'metadata_9samples.txt' including the hashtag sequences for each sample). Samples were mixed using hashtagged antibodies prior to scRNA-Seq

first: Daniel

last: Zeve

first: Joshua

last: de Sousa Casal

last: Ordovas-Montanes

first: David

last: Breault


title: Arabidopsis spliceosome factor SmD3-b modulates immunity to Pseudomonas syringae infection

city: Warsaw

first: Michal

last: Krzyszton

address: Pawinskiego 5a

country: Poland

institute: Institute of Biochemistry and Biophysics, Polish Academy of Sciences

summary: SmD3 is a core protein of small nuclear ribonucleoproteins essential for pre-mRNA splicing. To assess the role of Arabidopsis SmD3-b in response to biotic stress we investigated sensitivity of the smd3-b mutant to Pseudomonas syringae pv. tomato DC3000 infection and its pathogenesis effectors flg22, elf18 and coronatine. We show that the mutant exhibits enhanced susceptibility to Pst accompanied with marked changes in the expression of key pathogenesis markers. mRNA levels of major biotic stress response factors were also altered upon treatment with Pseudomonas effectors. Our genome-wide transcriptome analysis of smd3-b mutant infected with Pst confirmed that lack of SmD3 protein deregulates defense to Pst DC3000 infection on the transcriptional level, including defects in splicing and altered pattern of alternative splicing. In addition, callose deposition, which is another marker of plant immunity, was strongly induced by elf18 and flg22 in the mutant, whereas production of reactive oxygen species triggered by flg22 was reduced. Finally, detection of phosphorylated forms of MPK3, MPK6 and MPK4/11 revealed higher activation of all MAPKs in the smd3-b mutant. All our data indicate that SmD3 contributes to plant immune response possibly via regulation of mRNA splicing of the key pathogenesis factors.

overall_design: Transcriptome profiles of Col-0 and smd3-b mutant plants after pathogen or control treatment using RNA-seq (three biological replicates).

first: Anna

last: Golisz

first: Monika

last: Stepien

first: Jakub

last: Dolata

first: Justyna

last: Piotrowska

first: Zofia

last: Szweykowska-Kulinska

first: Artur

last: Jarmolowski

first: Joanna

last: Kufel


title: LaminB1-DamID analysis of differentiating 3T3L1 mouse pre-adipocytes with knock-down of Tmem120a and Tmem120b

first: Jose

last: de las Heras

summary: Maps of genomic regions in proximity to the nuclear lamina were determined in undifferentiated 3T3L1 preadipocytes and 9 day differentiated (wild type, and under Tmem120a or Tmem120a/b knockdown) adipocytes using DamID with a Dam-Lamin B1-encoding lentivirus.

overall_design: Examination of Lamin B1-chromatin contacts in 3T3L1 derived adipocytes, and the effect of Tmem120a/b knock-down

first: Dzmitri

last: Batrakou

middle: I

first: Eric

middle: C

last: Schirmer


title: Micro-array analysis of SARS-CoV2 treated Calu3 and A549-ACE2 cells

city: Heidelberg

first: Florian

last: Heigwer

address: Im Neuenheimer Feld 580

department: Signaling and Functional genomics

institute: Deutsches Krebsforschungszentrum (DKFZ)

summary: To determine the effects of SARS-CoV-2 infection on the host transcriptional profile, total RNA was isolated from infected cells and analyzed by microarray. For these studies, we took into account that the SARS-CoV-2 replication cycle in cell culture is 6-16 h, followed by death of infected cells 28. Therefore, to evaluate the direct effects of virus infection and avoid the analysis of secondary infection events or cell death effects, we did not extend our analysis beyond 24 h post infection. Analysis of significantly differentially expressed genes showed substantial transcriptomic changes in Calu-3 cells with a total of 3215 differentially expressed genes (FDR< 10%).

overall_design: 2 cell lines (A549-ACE2 and Calu3, 4 time point 4,8,12,24 hours, mock treated vs SARS-CoV2-infected

first: Christopher

last: Neufeldt


title: ADNP suppresses R-loops at its binding sites

status: Public on Nov 15 2021

city: Philadelphia

first: Phillip

last: Wulfridge

state: Pennsylvania

address: 3601 Spruce St

institute: The Wistar Institute

summary: We have identified ADNP as an R-loop regulator using a proximity-dependent labeling system. We find that ADNP is necessary to suppress R-loops at its binding sites, and that deletion of the ADNP homeodomain reduces ADNP binding to chromatin and results in R-loop accumulation.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: CUT&RUN, MapR, and RNA-Seq was performed on E14 mouse embryonic stem cells and human induced pluripotent stem cells. MNase-normalized tracks were generated for MapR samples by subtracting GST-MNase signal (negative control) from GST-RHΔ-Mnase signal.

first: Qingqing

last: Yan

first: John

last: Doherty

middle: L

last: Fernandez-Luna

first: Pedro

last: Real

first: Hsin

last: Tang

first: Kavitha

last: Sarma


title: HIF-1-regulated expression of calreticulin promotes breast   tumorigenesis and progression through Wnt/β-catenin   pathway activation

city: wuhan

first: dong

last: chen

state: Hubei

address: GaoXin 2nd Road

institute: ablife

summary: Calreticulin (CALR) is a multi-functional protein that participates in various cellular processes, which include calcium homeostasis, cell adhesion, protein folding and cancer progression. However, the role of CALR in breast cancer is unclear. Here we report that CALR is overexpressed in breast cancer compared with normal tissue, and its expression is correlated with patient mortality and stemness indices. CALR expression was increased in mammosphere cultures, CD24-CD44+ subsets and ALDH+ subsets, which are enriched for breast cancer stem cells (BCSCs). Additionally, CALR knockdown led to BCSC depletion, which impaired tumor initiation and metastasis, and enhanced chemosensitivity in vivo. Chromatinimmunoprecipitation and reporter assays revealed that hypoxia-inducible factor 1 (HIF-1) directly activated CALR transcription in hypoxic breast cancer cells. CALR expression was correlated with Wnt/β-catenin pathway activation and an activator of Wnt/β-catenin signaling abrogated the inhibitory effect of CALR knockdown on mammosphere formation. Taken together, our results demonstrate that CALRfacilitates breast cancer progression by promoting the BCSC phenotype through Wnt/β-catenin signaling in a HIF-1-dependent manner, and suggest that CALR may represent a novel target for breast cancer therapy.

overall_design: In this study, we demonstrate that CALR expression is activated by HIF-1 when human BC cells are exposed to hypoxia. Knockdown of CALR expression decreased the number of BCSCs and impaired Wnt/β-catenin pathway activation. CALR expression in human BC biopsies was correlated with patient mortality.

first: Huimin

last: Zhang

first: Jianjun

last: He

first: Gregg

last: Semenza


title: Pluripotent stem cells related to embryonic disc exhibit common self-renewal requirements in diverse livestock species

city: Exeter

first: Daniel

last: Spindlow

state: Devon

address: Stocker Road

department: Living Systems Institute

institute: University of Exeter

summary: Despite four decades of effort, robust propagation of pluripotent stem cells from livestock animals remains challenging. The requirements for self-renewal are unclear and the relationship of cultured stem cells to pluripotent cells resident in the embryo uncertain. Here we avoided feeder cells or serum factors to provide a defined culture microenvironment. We show that the combination of Activin A, Fibroblast growth factor, and Wnt inhibitor XAV939 (AFX), supports establishment and continuous expansion of pluripotent stem cell lines from porcine, ovine and bovine embryos. Germ layer differentiation was evident in teratomas and readily induced in vitro. Global transcriptome analyses highlighted commonality in transcription factor expression across the three species, while global comparison with porcine embryo stages showed proximity to bilaminar disc epiblast. Clonal genetic manipulation and gene targeting were exemplified in porcine stem cells. We further demonstrated that genetically modified AFX stem cells gave rise to cloned porcine foetuses by nuclear transfer. In summary, for major livestock mammals pluripotent stem cells related to the formative embryonic disc are reliably established using a common and defined signaling environment.

sample_organism:
Sus scrofa
Bos taurus
Ovis aries

platform_organism:
Sus scrofa
Bos taurus
Ovis aries

overall_design: RNA-seq analysis of EDSCs established from pig, sheep and cow embryos

first: Masaki

last: Kinoshita

first: Susanne

last: Bornelöv

first: Giuliano

last: Stirparo

first: Austin

last: Smith


title: RNA Expression Profiling Of Normal Mouse Live Across a Reproductive Cycle

city: Portland

first: Zheng

last: Xia

state: Oregon

address: 3181 SW Sam Jackson Park Rd

department: Department of Biomedical Engineering

institute: Oregon Health & Science University

summary:
Purpose: To perform RNA-Seq expression profiling of the normal rodent liver at nulliparous, lactation, and involution day 6 reproductive stages.
Methods:  RNA was extracted and isolated from flash frozen murine liver using the Direct-zol RNA MiniPrep kit. An input of 100ng of RNA was used for library preparation. Library construction was performed by Novogene using a NEBNext® Ultra RNA Library Prep Kit for Illumina. Qualified libraries were sequenced on an Illumina Novaseq6000 Platform using a paired-end 150 run.
Results: We identified gene pathway differences bile acid production and FGFR4 signaling between different reproductive stages with upregulation of these pathways during lactation. Additionally, individual genes involved with promoting bile acid synthesis were elevated at lactation whereas genes associated with inhibiting bile acid synthesis were reduced during lactation and elevated during involution.

overall_design: Mouse liver derived mRNA from 7 nulliparous mice, 6 lactation stage mice, and 6 involution day 6 mice generated by 150-cycle paired-end sequencing using the  Illumina Novaseq6000 Platform. Fastq files were aligned to mm10 mouse reference genome (GRCm38.89) and per-gene counts quantified by RSEM (version 1.3.1) based on the gene annotation Mus_musculus.GRCm38.89.chr.gtf. Differential gene expression analysis was performed using DESeq2 (version 1.22.2).

first: Pepper

last: Schedin


title: The histologic phenotype of lung cancers is associated with transcriptomic features rather than genomic characteristics

status: Public on Nov 13 2021

city: Houston

first: Shawna

middle: Marie

last: Hubert

state: Texas

address: 1515 Holcombe Blvd

department: Thoracic/Head and Neck Medical Oncology

institute: University of Texas MD Anderson Cancer Center

summary:
Histology plays an essential role in therapeutic decision-making for lung cancer patients. However, the molecular determinants of lung cancer histology are largely unknown. We conducted whole-exome sequencing (WES) and microarray profiling on 19 micro-dissected tumor regions of different histologic subtypes from 9 patients with lung cancers of mixed histology. A median of 68.9% of point mutations and 83% of copy number aberrations were shared between different histologic components within the same tumors. Furthermore, different histologic components within the tumors demonstrated similar subclonal architecture. On the other hand, transcriptomic profiling revealed shared pathways between the same histologic subtypes from different patients, which was supported by the analyses of the transcriptomic data from 141 cell lines and 343 lung cancers of different histologic subtypes. These data derived from mixed histologic subtypes in the setting of identical genetic background and exposure history support that the histologic fate of lung cancer cells is associated with transcriptomic features rather than the genomic profiles.
The in-house clariom.s.human microarray data were analyzed using Bioconductor packages Oligo, pd.clariom.s.human, and limma following standard workflow.  Gene set enrichment analysis using Hallmark dataset was carried out using fgsea Bioconductor package and the genes are pre-ranked by (signed log2FoldChange) * -log10(p-value) for all the public datasets. For the in-house microarray data, we computed the fold change between distinct histologies within the same patient and rank the genes by the fold change.

overall_design: 19 different tumor tissues, from 9 patients, including 6 LUAD, 6 LCNEC, 3 SCLC, 3 LUSC, and one poorly differentiated NSCLC-NOS were subjected to WES and microarray RNA profiling. The in-house clariom.s.human microarray data were analyzed using Bioconductor packages Oligo, pd.clariom.s.human, and limma62 following standard workflow.

first: Ming

first: Hussein

last: Abbas

first: Marcelo

middle: V

last: Negrao

first: Maheshwari

last: Ramineni

first: Xin

last: Hu

first: Junya

last: Fujimoto

first: Alexandre

last: Reuben

first: Susan

last: Varghese

first: Jianhua

first: Jun

last: Li

first: Chi-Wan

last: Chow

first: Xizeng

last: Mao

first: Xingzhi

last: Song

first: Won-Chul

last: Lee

first: Jia

last: Wu

first: Latasha

last: Little

first: Curtis

last: Gumbs

first: Carmen

last: Behrens

first: Cesar

last: Moran

first: Annikka

last: Weissferdt

first: J

first: Boris

last: Sepesi

first: Stephen

last: Swisher

first: Chao

last: Cheng

first: Jonathan

last: Kurie

first: Don

last: Gibbons

last: Heymach

first: Ignacio

last: Wistuba

first: P

last: Futreal

first: Neda

last: Kalhor


title: Single Cell RNA Profiles of a Human Triple Negative Breast Cancer

city: Winston-Salem

first: Jeff

last: Chou

state: NC

address: Medical Center Blvd

institute: Atrium Health Wake Forest Baptist

summary: To investigate the transcriptional dynamics of the breast tumor microenvironment, remnant surgical tissue from an AJCC stage III triple negative invasive ductal carcinoma resected at Wake Forest Baptist Medical Center (WFBMC) in Winston Salem, NC, was accessed via Wake Forest University Health Sciences Institutional Review Board protocol IRB00048977 and expression profiled by single cell RNA sequencing. Approximately 770 high-quality cell expression profiles were identified.

overall_design: A single fresh surgical specimen of primary breast tumor tissue was enzymatically dissociated to form a single cell suspension. The cells were processed on a 10X Genomics Chromium controller to generate a cDNA library, and the library was sequenced on an Illumina NextSeq 500.

first: Lance

middle: D

last: Miller

middle: W


title: A chromosomal loop anchor mediates bacterial genome organization

status: Public on Nov 14 2021

city: Amsterdam

first: Gaurav

last: Dugar

address: Science Park 904

department: Bacterial Cell Biology

country: Netherlands

institute: University of Amsterdam

summary: Nucleoprotein complexes play an integral role in genome organization of both eukaryotes and prokaryotes. Apart from their role in locally structuring and compacting DNA, several complexes are known to influence global organization by mediating long-range anchored chromosomal loop formation leading to spatial segregation of large sections of DNA. Such megabase (Mb) range interactions are ubiquitous in eukaryotes, but have not been demonstrated in prokaryotes. Here, using a novel genome-wide sedimentation based approach, we found that a transcription factor, Rok, forms large nucleoprotein complexes in the bacterium Bacillus subtilis. Using chromosome conformation capture (Hi-C) and live-imaging of DNA loci, we show that these complexes robustly interact with each other over large distances. Importantly, these Rok dependent long-range interactions lead to anchored chromosomal loop formation, thereby spatially isolating large sections of DNA, as previously observed for insulator proteins in eukaryotes.

overall_design: RNA-seq, sedimentation assay, and Hi-C performed on wild type B. subtilis and rok mutant strains. We used sedimentation based DNA coverage to identify large chromosomal complexes. Briefly, in this assay cell lysates are mildly treated with DNase and then separated using untracentrifugation on sucrose steps. The top and dense fraction is then analysed for loss or gain of DNA coverage to identify large DNA-protein complexes.

first: Andreas

last: Hofmann

first: Dieter

last: Heermann

first: Leendert

last: Hamoen


title: The transcription factor EGR2 is indispensable for tissue-specific imprinting of alveolar macrophages in health and tissue repair [myeloid cells]

first: Calum

last: Bain

address: 47 Little France Crescent

department: Centre for Inflammation Research

summary: We profile the transcriptomes of over 3,000 mouse single  myeloid cells from mouse lung to define the transcriptional profiles of monocytes and subsets of dendritic cells and macrophages. We perform differential gene expression analysis to determine the transcriptional regulators unique to each cluster.

overall_design: We present single-cell transcriptomic data on myeloid cells isolated from the lung of a healthy Rag1-deficient (Tgfbr1-fl/fl) mouse.

first: Jack

last: McCowan

first: Frederic

last: Fercoq

first: Phoebe

last: Kirkwood

first: Wouter

last: T'Jonck

first: Lizi

last: Hegarty

first: Connar

last: Mawer

first: Richard

last: Cunningham

first: Ananda

middle: S

last: Mirchandani

first: Duncan

last: Humpheries

first: Anna

last: Hoy

first: Gareth-Rhys

last: Jones

first: Carsten

last: Hansen

first: Nik

last: Hirani

last: Jenkins

first: Sandrine

last: Henri

first: Bernard

last: Malissen

first: Sarah

middle: R

last: Walmsley

first: David

middle: H

last: Dockrell

first: Philippa

middle: T

last: Saunders

first: Leo

last: Carlin


title: CLINICOPATHOLOGIC AND MOLECULAR ANALYSIS OF A BCOR-CCNB3+ UNDIFFERENTIATED SARCOMA OF THE KIDNEY REVEALS SIGNIFICANT EPI-GENETIC ALTERATION [RNA-seq]

status: Public on Nov 12 2021

city: BUFFALO

first: Eduardo

last: Cortes

address: ELM AND CARLTON STREETS

department: Biostatistics and Bioinformatics

institute: ROSWELL PARK CANCER INSTITUTE

summary: Undifferentiated soft tissue sarcomas (UDSTS ) are a group of mesenchymal tumors that remain a diagnostic challenge due to their morphologic heterogeneity and unclear histologic origin (Pe-ters et al. 2015b). In this case report, we present the first multi-omics molecular signature for BCOR-CCNB3 sarcomas (BCS) that includes mutation analysis, gene expression, DNA methyla-tion, and mi-RNA expression. We identify a paucity of additonal mutations in this tumor and de-tail that there is significant dysregulation of gene expression of epigeneic remodeling agents in-cluding key members of the PRC, Sin3A/3b, NuRD, and NcoR/SMRT complexes and the DNA methyltransferases DNMT1, DNMT3a, and DNMT3b. This is accompanied by significant DNA methylation changes and dysregulation of multiple miRNA with known links to tumorigenesis. This study significantly increases our understanding of the BCOR effects on fusion positive un-differentiated sarcomas at both the genomic and epigenomic level, and suggests that as better-tailored and more refined treatment algorithms continue to evolve, epigenetic modifying agents should be further evaluated for their efficacy against these tumors.

overall_design: Single,paired,tumor-control,sample

first: Tamara

last: Hagoel

first: Ajay

last: Gupta

first: Clare

last: Twist

first: Rafal

last: Kozielski

first: Jeffrey

last: Martin

first: Lingui

last: Gao

first: Joseph

last: Kuechle

first: Prashant

middle: K

last: Singh

first: Miranda

last: Lynch

first: Lei

last: Wei

first: Song

last: Liu

first: Jianmin

last: Wang

first: Joyce

middle: E

last: Ohm


title: CLINICOPATHOLOGIC AND MOLECULAR ANALYSIS OF A BCOR-CCNB3+ UNDIFFERENTIATED SARCOMA OF THE KIDNEY REVEALS SIGNIFICANT EPI-GENETIC ALTERATION

type: Non-coding RNA profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: CLINICOPATHOLOGIC AND MOLECULAR ANALYSIS OF A BCOR-CCNB3+ UNDIFFERENTIATED SARCOMA OF THE KIDNEY REVEALS SIGNIFICANT EPI-GENETIC ALTERATION [miRNA-seq]

overall_design: Single paired tumor-control sample

middle: J


title: Next-generation sequencing facilitates quantitative analysis of the transcriptome in normal lung tissue and in lung tissue with LPS-induced acute lung injury

city: shenyang

first: wei

last: xu

state: Liaoning province

address: NO.36  of sanhao street

department: Department of Pediatrics

institute: shengjing hospital of China medical university

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways and the function of all RNAs in a certain functional state of a specific cell was studied, mainly including non-coding RNAs.The aim of this study was to compare lung tissue transcriptome analysis (RNA-SEQ) with microarray and quantitative reverse transcription polymerase chain reaction (QRT-PCR) methods for LPS-induced acute lung injury and to evaluate the optimal high-throughput data analysis protocol.
Methods: LncRNA profiles of normal lung tissue and LPS-induced acute lung injury after 24h in mice were generated by deep sequencing, in triplicate, using Illumina HiSeq 4000
Results: A total of 8,610 lncRNAs were identified in the normal and LPS groups.
Conclusions: Our study represents detailed analysis of lung tissue transcriptomes, withh biological replicates, generated by RNA-seq technology. Novel ideas are presented to expand our knowledge on the regulation mechanisms of lncRNA-related ceRNAs in the pathogenesis of ALI.

first: Xianxian

last: Jia

first: Wei

last: Xu


title: Transcriptome analysis of differentiating 3T3L1 mouse pre-adipocytes with knock-down of Tmem120a and Tmem120b

first: Jose

last: de las Heras

summary: The nuclear envelope transmembrane proteins (NETs) NET29a/Tmem120a and NET29b/Tmem120b are expressed or localise preferentially to the nuclear envelope in adipocytes. We knocked these proteins down using specific shRNAs and studied their effect in the diffentiation of the mouse 3T3L1 preadipocyte cell line.

overall_design: Total RNA was isolated from 3T3L1 cells at d0 (confluent preadipocytes) and d6 post induction of differentiation using medium supplemented with 0.5uM insulin, 1uM dexamethasone, 1uM rosiglitazone and 0.5mM IBMX, replacing the medium every 48h up to 9 days post-induction with medium supplemented with insulin and rosiglitazone only. Tmem120a/b knock-downs were generated by transduction of shRNA-encoding lentiviruses as described in Batrakou et al. (2015) PLoS ONE 10(05): e0127712.

first: Dzmitri

middle: G

last: Batrakou

first: Eric

last: Schirmer


title: Deletions in VANGL1 are a novel risk factor for antibody mediated kidney disease

status: Public on Nov 11 2021

city: Smithfield

first: Matt

last: Field

address: 14-88 Macgregor Road

country: Australia

institute: James Cook University

summary: Kidney involvement is one of the most devastating manifestations of systemic lupus erythematosus. Approximately half of all SLE patients develop kidney involvement yet the mechanisms predisposing to nephritis are unelucidated.  Genetic variance is a potent risk factor for development of SLE, yet limited evidence of the contribution to specific organ involvement exists. Using an Affymetrix SNP array and qPCR we identified a recurrent intronic copy number variation (CNV) in intron 8 of Van Gogh Like 1 (VANGL1) which associated with nephritis. To model the effect of VANGL1 deficiency we obtained Vangl1 deficient mice. Kidneys from Vangl1+/- mice were cryopreserved and sections stained for immunoglobulin. Vangl1+/- developed spontaneous IgA and IgG deposition within the glomerular mesangium with no evidence of proteinuria or inflammation. Vangl1+/- had normal lymphocyte populations by flow cytometry and were ANA negative. Serum transfer into a B cell deficient Vangl1+/- mice resulted in IgG deposition, but not in B cell deficient Vangl1+/+ mice suggesting that immunoglobulin deposition occurs in a kidney intrinsic fashion. We have identified a recurrent copy number variation in VANGL1 which associates with the development of nephritis in SLE, but not SLE in general. Examination of Vangl1 deficient mice demonstrates a kidney-intrinsic role in the development of nephritis. This represents the first known copy number variant which predisposes to the development of nephritis in SLE in a kidney-intrinsic method.

overall_design: RNASeq analysis of samples with homozygous and heterozygous deletions  in VANGL1

middle: A

first: Simon

last: Jiang


title: Induction of Rosette-to-Lumen stage embryoids using reprogramming paradigms in ESCs

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

summary: Blastocyst-derived stem cell lines were shown to self-organize into embryo-like structures in 3D cell culture environments. Here, we provide evidence that embryo-like structures can be generated solely based on transcription factor-mediated reprogramming of embryonic stem cells in a simple 3D co-culture system. Embryonic stem cells in these cultures self-organize into elongated, compartmentalized embryo-like structures reflecting aspects of the inner regions of the early post-implantation embryo. Single-cell RNA-seq reveals transcriptional profiles resembling epiblast, primitive-/visceral endoderm, and extraembryonic ectoderm of early murine embryos around E4.5–E5.5. In this stem cell-based embryo model, progression from rosette formation to lumenogenesis accompanied by progression from naïve- to primed pluripotency was observed within Epi-like cells. Additionally, lineage specification of primordial germ cells and distal/anterior visceral endoderm-like cells was observed in epiblast- or visceral endoderm-like compartments, respectively. The system presented in this study allows for fast and reproducible generation of embryo-like structures, providing an additional tool to study aspects of early embryogenesis.

overall_design: Examination of 1149 3D Rosette-to-Lumen embryoid cells, 317 2D 2i/LIF Embryonic stem cells (2D 2i/LIF ESCs), 283 2D induced trophoblast stem cells (2D iTSCs) and 182 2D induced extraembryonic endoderm stem cells (2D iXEN)

first: Jan

last: Langkabel

first: Arik

last: Horne

first: Thomas

last: Ulas

first: Matthias

last: Becker

last: Schulze

first: Hubert

last: Schorle


title: MAFB surrogates the glucocorticoid receptor ability to induce tolerogenesis in dendritic cells [CHIP_SEQ]

city: Badalona, Barcelona

first: Esteban

last: Ballestar

state: N/A = Not Applicable

address: Ctra de Can Ruti, Camí de les Escoles s/n

country: Spain

institute: Josep Carreras Research Institute (IJC)

summary: Glucocorticoids (GCs) exert potent anti-inflammatory effects in immune cells through the glucocorticoid receptor (GR). Dendritic cells (DCs), central actors for coordinating immune responses, acquire tolerogenic properties in response to GCs. Tolerogenic DCs (tolDCs) have emerged as a potential treatment for different inflammatory diseases. To date, the underlying cell type-specific regulatory mechanisms orchestrating GC-mediated acquisition of immunosuppressive properties remain poorly understood. In this study, we investigated the transcriptomic and epigenomic remodeling associated with differentiation to DCs in the presence of GCs. Our analysis demonstrates a major role of MAFB in this process, in synergy with GR. Both GR and MAFB interact with methylcytosine dioxygenase TET2 and bind to genomic loci that undergo specific demethylation in tolDCs. We also show that the role of MAFB is more extensive, binding to thousands of genomic loci in tolDCs. Finally, MAFB knockdown erases the tolerogenic properties of tolDCs and reverts the specific DNA demethylation and gene upregulation. The preeminent role of MAFB is also demonstrated in vivo for myeloid cells from synovium in rheumatoid arthritis following GC treatment. These results support that, once directly activated by GR, MAFB takes over the main roles to orchestrate the epigenomic and transcriptomic remodelling that define the tolerogenic phenotype.

overall_design: GR and MAFB ChIP-seq in DCs and tolDCs differentiated from monocytes. Two biological replicates are included.

first: Octavio

last: Morante-Palacios

first: Laura

last: Ciudad

first: Raphael

last: Micheroli

first: Carlos

last: de la Calle-Fabregat

first: Gisela

last: Barbisan

first: Miranda

last: Houtman

first: Sam

last: Edalat

first: Mojca

last: Frank-Bertoncelj

first: Caroline

last: Ospelt


title: scRNAseq of isolated fetal liver erythroid progenitor cell subpopulations, and CITE-seq of mouse fetal liver erythroid progenitors

city: Cambridge

first: Hojun

last: Li

address: 500 Main St building 76

institute: Koch Institute

summary: We used scRNAseq to profile CD71/CD24low fetal liver erythroid progenitor cells isolated by 2 distinct methods: FACS and immunomagnetic isolation. Cells from both isolation methods were hashtagged using Biolegend mouse hashtag antibodies and library prepped together on the 10X chromium platform with the 3'RNA v3 kit. We also performed CITE-seq to profile proteogenomic expression of CD117 and CD71 on lineage-depleted mouse fetal liver erythroid progenitor cells. CITE-seq was performed through a separate library prep on the 10X chromium platform with the 3'RNAv3 kit.

overall_design: Cell hashing of scRNAseq profiling of 2 distinct methods of mouse fetal liver erythroid progenitor isolation, and CITE-seq for CD117 and CD71 protein expression on lineage-depleted mouse fetal liver erythroid progenitor cells.

first: Tatum

last: Braun

first: Michael

last: Kuoch

first: Eugene

last: Khandros


title: MAFB surrogates the glucocorticoid receptor ability to induce tolerogenesis in dendritic cells

type: Methylation profiling by genome tiling array


title: MAFB surrogates the glucocorticoid receptor ability to induce tolerogenesis in dendritic cells [Methylation_2 array]

overall_design: 4 donors, two different conditions: tolDCs with siCTL and tolDCs with siMAFB


title: Single-cell transcriptional profiling of splenic fibroblasts reveals subset-specific innate immune signatures in homeostasis and during viral infection

city: Lausanne

first: Joern

last: Pezoldt

address: Station 19, SV 3818.A

department: SV

country: Switzerland

institute: EPFL

summary: Our understanding of the composition and functions of splenic stromal cells remains incomplete. Here, based on analysis of over 20,000 single cell transcriptomes of splenic fibroblasts, we characterized the phenotypic and functional heterogeneity of these cells in a healthy state and during virus infection. We describe eleven transcriptionally distinct fibroblastic cell clusters, reassuring known subsets and revealing yet unascertained heterogeneity amongst fibroblasts occupying diverse splenic niches. We further identify striking differences in innate immune signatures of distinct stromal compartments in vivo. Compared to other fibroblasts and to endothelial cells, Ly6C+ fibroblasts of the red pulp showed enhanced interferon-stimulated gene expression in homeostasis, upon systemic interferon stimulation and during virus infection in vivo. Collectively, we provide an updated map of fibroblastic cell diversity in the spleen that suggests a specialized innate immune function for splenic red pulp fibroblasts.

overall_design: Bulk RNA-seq of splenic stromal cells from uninfected and 24h post-infected mice. Single cell RNA-seq of splenic stromal cells from uninfected and 24h post-infected mice

first: Carolin

last: Wiechers

first: Florian

last: Erhard

first: Ulfert

last: Rand

first: Tanja

last: Bulat

last: Beckstette

first: Andrea

last: Brendolan

first: Jochen

last: Huehn

first: Ulrich

last: Kalinke

first: Mathias

last: Mueller

first: Birgit

last: Strobl

first: Bart

last: Deplancke

first: Luka

last: Cicin-Sain

first: Katarzyna

middle: M

last: Sitnik


title: MAFB surrogates the glucocorticoid receptor ability to induce tolerogenesis in dendritic cells [RNA_SEQ]

first: Esteban

last: Ballestar

overall_design: RNA-seq in DCs and tolDCs differentiated from monocytes. Four biological replicates are included and three different conditions: DCs with siCTL, tolDCs with siCTL and tolDCs with siMAFB

first: Octavio

last: Morante-Palacios

first: Laura

last: Ciudad

first: Raphael

last: Micheroli

first: Carlos

last: de la Calle-Fabregat

first: Gisela

last: Barbisan

first: Miranda

last: Houtman

first: Sam

last: Edalat

first: Mojca

last: Frank-Bertoncelj

first: Caroline

last: Ospelt


title: MAFB surrogates the glucocorticoid receptor ability to induce tolerogenesis in dendritic cells [expression array]

overall_design: Monocytes from 3 donors were differentiated to DCs and tolDCs for 6 days. Three conditions: Monocytes, DC and tolDCs.


title: TASOR epigenetic repressor cooperates with a CNOT1 RNA degradation pathway to repress HIV

city: Paris

first: Roy

last: MATKOVIC

state: Select One

address: 22, Rue Mechain

department: Infection Immunity and Inflammation

country: France

institute: Institut Cochin

summary: The Human Silencing Hub (HUSH) complex constituted of TASOR, MPP8 and Periphilin is involved in the spreading of H3K9me3 repressive marks across genes and transgenes such as ZNF encoding genes, ribosomal DNAs, retroelements, including LINE-1 elements, or the integrated HIV provirus. The deposit of these repressive marks leads to heterochromatin formation and inhibits gene expression. The precise mechanisms of HUSH-mediated silencing are still poorly understood, but HUSH presents structural homology with the RNA-induced transcriptional silencing (RITS) complex found in fission yeast. During transcription elongation by RNA polymerase II, RITS recruits a TRAMP-like RNA degradation complex composed of CNOT1 partners, MTR4 and the exosome, to ultimately repress gene expression via H3K9me3 deposit. Here, we show that TASOR depletion or HIV-2 Vpx expression, which induces TASOR degradation, increases the accumulation of transcripts derived from the HIV-1 LTR promoter at a post-transcriptional level. Furthermore, using a yeast 2-hybrid screen, we identified new TASOR partners involved in RNA metabolism including the RNA deadenylase CCR4-NOT complex scaffold CNOT1. TASOR and CNOT1 interact in vivo and synergistically repress HIV expression from its LTR. Similar to the RITS complex, we show that TASOR interacts and cooperates with MTR4 and the exosome. We also highlight an interaction between TASOR and RNA Polymerase II, predominantly under its elongating state, and between TASOR and some HUSH-targeted nascent transcripts. Finally, we show that TASOR overexpression facilitates the association of the aforementioned RNA degradation proteins with RNA polymerase II and is detected at transcriptional centers. Altogether, we propose that HUSH operates at the transcriptional and post-transcriptional levels to repress HIV proviral gene expression.

overall_design: Identification of TASOR and CNOT1 target genes in HeLa cells.

last: Matkovic

first: Sophie

last: Lanciano

first: Gael

last: Cristofari

first: Fabienne

last: Bejjani

first: Florence

last: Margottin-Goguet


title: CLINICOPATHOLOGIC AND MOLECULAR ANALYSIS OF A BCOR-CCNB3+ UNDIFFERENTIATED SARCOMA OF THE KIDNEY REVEALS SIGNIFICANT EPI-GENETIC ALTERATION [methylation]

first: Eduardo

last: Cortes

state: NY

first: Tamara

last: Hagoel

first: Ajay

last: Gupta

first: Clare

last: Twist

first: Rafal

last: Kozielski

first: Jeffrey

last: Martin

first: Lingui

last: Gao

first: Joseph

last: Kuechle

first: Prashant

last: Singh

last: Lynch

first: Lei

last: Wei

first: Song

last: Liu

first: Jianmin

last: Wang

first: Joyce

last: Ohm


city: Schlieren

first: Caroline

last: Ospelt

address: Wagistrasse 14

department: Department of Rheumatology

institute: University Hospital Zurich

summary: Glucocorticoids (GCs) exert potent anti-inflammatory effects in innate immune cells through the glucocorticoid receptor (GR). Dendritic cells (DCs), central actors for coordinating immune responses, acquire tolerogenic properties in response to GCs. Tolerogenic DCs (tolDCs) have emerged as a potential treatment for different inflammatory diseases. To date, the underlying cell type-specific regulatory mechanisms orchestrating GC-mediated acquisition of immunosuppressive properties remain poorly understood.  In this study, we investigated the transcriptomic and epigenomic remodeling associated with differentiation to DCs in the presence of GCs. Our analysis demonstrates a major role of MAFB in this process, in synergy with GR. Both GR and MAFB interact with methylcytosine dioxygenase TET2 and bind to genomic loci that undergo specific demethylation in tolDCs. We also show that the role of MAFB is more extensive, binding to thousands of genomic loci in tolDCs. Finally, MAFB knockdown erases the tolerogenic properties of tolDCs and reverts the specific DNA demethylation and gene upregulation. The preeminent role of MAFB is also demonstrated in vivo for myeloid cells from synovium in rheumatoid arthritis following GC treatment.  These results support that, once directly activated by GR, MAFB takes over the main roles to orchestrate the epigenomic and transcriptomic remodelling that define the tolerogenic phenotype.

overall_design: Single cell RNAseq profiling of rheumatoid arthritis synovial tissues.

first: Raphael

last: Micheroli

first: Miranda

last: Houtman

first: Sam

last: Edalat

first: Mojca

last: Frank-Bertoncelj


title: Single-cell profiling of cranial neural crest diversification across a vertebrate lifetime

city: Los Angeles

first: Gage

last: Crump

address: 1425 San Pablo St.

department: Stem Cell

institute: USC

summary: The cranial neural crest (CNC) is a vertebrate-specific population that generates a huge diversity of derivatives, including the bulk of the connective and skeletal tissues of the head. How neural crest cells generate the appropriate cell types for distinct head regions over time remains unresolved. Here we profile RNA expression (scRNAseq) and chromatin accessibility (snATACseq) of the zebrafish cranial neural crest lineage at single-cell resolution from embryos to adults.

overall_design: To recover the cell heterogeneity and lineage information in the span of a life time of a fish, we collected the converted cells from embryonic stages (1.5, 2 dpf), larval stage (3, 5, and 14 dpf), juvinile stage (60 dpf), to adult stage (150 or 210 dpf). We used a cranial neural crest converted zebrafish line, -28.5Sox10:Cre;bactin:BFP-to-DsRed, to permanantly convert and label the CNCC-derived cells. The converted cells were collected and subjected to single cell sequencing for both their transcriptome and open chromatin region using Chromium platform of 10X Genomic. For biological and technical control, we include replicates for both scRNAseq and snATACseq at various stages. We include an additional line, fli1a:eGFP/sox10:dsRed, for a biological and positive control of CNCC of 1.5 dpf  sample.

first: Peter

last: Fabian

first: Kuo-Chang

last: Tseng

first: Hung-Jhen

last: Chen


title: scRNA-Seq of MC38 CD45+ Cells treated with EZH2 inhibitor PF-06821497

status: Public on Nov 10 2021

city: San Diego

first: Wenjing

last: Yanf

address: 10770 Science Center Drive

department: Oncology

institute: Pfizer

summary: The purpose of this study was to determine the effect of EZH2 inhibitor (EZH2i) PF-06821497 on CD45+ cells isolated from MC38 tumors at day 17 post implantation. Mice were either treated for 7 days prior to endpoint or 16 days prior to endpoint with the EZH2i or with vehicle control. CD45+ cells were isolated and scRNA-Seq was performed on cells

overall_design: Mice were implanted with MC38 tumor cells on day 0 and began treatment with either vehicle control or EZH2i PF-0682497 at 100 mg/kg on day 01 for 16 day treatment group or on day 10 for 7 day treatment group. All mice were euthanized, tumors removed, digested, and CD45+ cells were enriched. Libraries were generated using Single Cell 3' GEM, Library and Gel Bead Kit v3 (10X Genomics, PN-1000075), Chromium Single Cell B Chip (PN-100073), and Chromium i7 Multiplex Kit (PN-120262). Sequencing was performed by Novogene.

first: Yang

last: Wenjing

first: Xie

last: Tao

first: Zhang

last: Haikuo

first: Stairiker

last: Christopher


title: Organoid sensitivity correlates with therapeutic resonsein patients with pancreatic cancer

city: Boston

first: Lakshmi

last: Muthuswamy

address: 3 Blackfan circle

department: Department of Medicine

institute: Beth Israel Deaconess Medical Center

summary: We report a high degree of correlation between PDAC patient derived orgnanoid (PDO) drug sensitivity and clinical responses. This finding supports the utility of PDOs to tailor therapy for individual patients to improve clinical outcomes.

overall_design: PDOs were established from a heterogeneous population of patients with PDAC including both basal and classical PDAC subtypes.

first: Joe

last: Grossmann

first: Ling

last: Huang


title: Lipid droplet availability affects neural stem/progenitor cell metabolism and proliferation

first: Ludovic

last: Telley

address: Department of Biomedical Sciences University of Lausanne Rue du Bugnon 9

institute: UNIL

summary: Neural stem/progenitor cells (NSPCs) generate new neurons throughout adulthood. However, the underlying regulatory processes are still not fully understood. Lipid metabolism plays an important role in regulating NSPC activity: build-up of lipids is crucial for NSPC proliferation, whereas break-down of lipids has been shown to regulate NSPC quiescence. Despite their central role for cellular lipid metabolism, the role of lipid droplets (LDs), the lipid storing organelles, in NSPCs remains underexplored. Here we show that LDs are highly abundant in adult mouse NSPCs, and that LD accumulation is significantly altered upon fate changes such as quiescence and differentiation. NSPC proliferation is influenced by the number of LDs, inhibition of LD build-up, breakdown or usage, and the asymmetric inheritance of LDs during mitosis. Furthermore, high LD-containing NSPCs have increased metabolic activity and capacity, but do not suffer from increased oxidative damage. Together, these data indicate an instructive role for LDs in driving NSPC behaviour.

overall_design: Single cell RNA sequencing (scRNA-seq) on sorted Plin2-GFP NSPCs from two categories, namely the 25% highest versus the 25% lowest PLIN2-GFP NSPCs.

first: Mergim

last: Ramosaj

first: Sofia

last: Madsen

first: Vanille

last: Maillard

first: Valentina

last: Scandella

first: Daniel

last: Sudria-Lopez

first: Naoya

last: Yuizumi

first: Marlen

last: Knobloch


title: A Novel Non-Classical Monocyte-derived Macrophage Subset That Provides A Splenic Replication Niche For Intracellular Salmonella [scRNA-Seq]

city: Rehoboth

first: Dotan

last: Hoffman

address: Herzel St 234, Biological regulation

institute: Weizmann institute of science

summary: Interactions between intracellular bacteria and mononuclear phagocytes give rise to diverse cellular phenotypes that may determine the outcome of infection. Recent advances in single-cell RNA-seq (scRNA-seq) have identified multiple subsets within the mononuclear population, but implications to their function during infection remain unknown. Here, we applied microscopy, flow cytometry and scRNA-seq to survey the mononuclear niche of intracellular Salmonella Typhimurium (S.Tm) during early systemic infection in mice. We describe eclipse-like growth kinetics in the spleen, with a first phase of bacterial control mediated by tissue-resident red-pulp macrophages. A second phase involved extensive bacterial replication within a newly identified macrophage population characterized by CD9 expression. Using Nr4a1e2-/- mice we established that CD9+ macrophages originated from non-classical monocytes (NCM), and NCM-depleted mice were more resistant to S.Tm infection. Our study defines a novel host-pathogen interface, with macrophage subset-specific interactions that determines early infection dynamics and the infection outcome of the entire organism.

overall_design: Splenocytes were isolated from 6 mice 24 hours post infection with Salmonella enterica serovar Typhimurium. RNA was extracted from CD9 Mf and iNOS Mf

first: Yaara

last: Tevet

first: Sebastien

last: Trzebanski

first: Gili

last: Rosenberg

first: Leia

last: Vainman

first: Aryeh

last: Solomon

first: Noa

middle: B

last: Ben-Moshe

first: Shelly

last: Hen-Avivi

first: Roi

last: Avraham


title: Timecourse of epileptogenesis in an TSC1 inducible mouse model

city: Rotterdam

first: Ype

last: Elgersma

address: Doctor Molewaterplein 40

department: Neuroscience

institute: Erasmus MC

summary: To determine how the loss of TSC induces epileptogenesis, we made use of an inducible Tsc1 knock-out mouse model. Tsc1 was homozygously deleted in all CAMK2A positive neurons. Hippocampal tissue was collected at different time points after gene deletion and during epileptogenesis, of mice of both sexes. Also, mice treated with 10mg/kg rapamycin were included in the experiment. Using RNA-seq analysis, we identified differentially expressed genes encoding either ion channel and/or genes belonging to the GO-term ‘action potential’. Of these genes, 50% were already significantly dysregulated before or just around seizure onset, suggesting that these genes could be driver genes of epileptogenesis. Of the genes encoding ion channels or belonging to the Gene Ontology term action potential, 27 were differentially expressed just before seizure onset, suggesting a potential driving role in epileptogenesis. Our data highlight the complex changes driving epileptogenesis in TSC, including the changed expression of multiple ion channels. Our study emphasizes inhibition of the TSC/mTOR signaling pathway as a promising therapeutic approach to target epilepsy in patients with TSC.

overall_design: We extracted hippocampal tissue of 4 mice per time point (day 4, day 6, day 8 and day 13) and after rapamycin treatment.

first: Linda

last: Koene

first: Eva

last: Niggl

first: Ilse

last: Wallaard

first: Martina

last: Proietti-Onori

first: Diana

middle: C

last: Rotaru


title: Identification of a modular super-enhancer in murine retinal development

city: Memphis

first: Victoria

last: Honnell

state: Tennessee

address: 262 Danny Thomas

institute: St. Jude Children's Research Hospital

summary: Single cell RNA-sequencing shows cell type specific expression of genes in the retina. Single cell ATAC-sequencing of the wild type retina at multiple stages revealed that chromatin in the Vsx2 CRC SE, a stage- and cell type-specific core regulatory circuit super-enhancer (CRC-SE) upstream of the Vsx2 gene, was only open in bipolar cells in Region3 in adult retina. Chromatin in Region0 was open in retinal progenitor cells in E14.5 retina.

overall_design: Single cell RNA sequencing, single cell ATAC sequencing, bulk RNA sequencing,  and ChIP sequening from WT and VSX2SE Region deletion mice retina at E14.5 and adult stages

first: Jackie

last: Norrie

first: Anand

last: Patel

first: Michael

last: Dyer


title: ATAC-Seq based chromatin accessibilty profile of MPPs from mice treated with MV130 or its excipient

city: Madrid

first: Manuel

last: Gomez

state: Madrid

address: Melchor Fernández Almagro, 3

institute: CNIC

summary: MV130 is an inactivated polybacterial mucosal vaccine that confers protection to patients against recurrent respiratory infections, including those of viral etiology. We showed that  MV130 induces long term heterologous protection against viral respiratory infections in mice. Moreover, intranasal administration of MV130 provided protection against systemic candidiasis in wild-type and Rag1-deficient mice lacking functional lymphocytes, indicative of innate immune-mediated protection. As trained immunity acts via modulation of hematopoietic stem and progenitor cells  (Kaufmann et al., 2018; Mitroulis et al., 2018) we hypothesized that MV130 could confer systemic long-term protection through reprogramming of hematopoietic precursors. For that we measured the chromatin accessibility landscape in multipotent progenitors (MPPs) coming from mice treated with MV130 or its excipient using ATAC-seq.

overall_design: Two replicate samples (obtained pooling 2 biological replicates) of multipotent progenitors from mice exposed to MV130 or its excipient were used to identify changes in the chromatin accesibility profile using ATAC-seq.

first: Paola

last: Brandi

first: David

last: Sancho


title: ATAC-Seq based chromatin accessibilty profile of human monocytes treated with MV130 or its excipient

summary: MV130 is an inactivated polybacterial mucosal vaccine that confers protection to patients against recurrent respiratory infections, including those of viral etiology. We showed that  MV130 induces  long term heterologous protection against viral respiratory infections in mice  by a mechanism associated with the induction of trained immunity.  Moreover, we found that MV130 induces reprogramming of in vitro human monocytes promoting metabolic changes and enhanced cytokine production. To assess the role of epigenetic changes in MV130-mediated trained immunity induction in human monocytes  we measured the chromatin accessibility landscape using ATAC-seq.

overall_design: Three replicate samples of human monocytes were exposed to MV130 or its excipient to identify changes in the chromatin accesibility profile using ATAC-seq.


title: Dynamic transcriptome and chromatin architecture in granulosa cells during chicken folliculogenesis

city: chengdu

first: hua

last: kui

address: No 211 Huimin Road

institute: Sichuan Agricultural University

summary: Ovarian follicle development is a complex and well orchestrated biological process. Chromatin spatial organization has emerged as an important regulator of gene expression, but how these changes during follicle development are still unknown. Here, we integrated RNA-seq and Hi-C analyses of chicken follicular granulosa cells of 10 developmental stages. Our data revealed that SWF, F1, and POF had the greatest transcriptome differences from other stages. Our results provide a genome-wide atlas of chromatin interactions during chicken ovarian follicle development.

overall_design: Hi-C (3 stages with 2 biological replicates in each stage) analyses of chicken follicular granulosa cells

first: Chunyou

last: Ning

first: Jiaman

last: Zhang

first: Diyan

last: Li

first: Mingzhou


summary: Ovarian follicle development is a complex and well-orchestrated biological process. Granulosa cells (GCs) are the most important somatic cells in the ovary, which play important roles in the growth of follicles. Three-dimensional (3D) chromatin architecture has emerged as an important regulator of transcription in eukaryote, but how these changes in granulosa cells during folliculogenesis of chicken are largely unexplored. Here, we performed an integrative analysis of transcriptomic and chromatin structural characterization for chicken follicular granulosa cells of 10 and 3 growth stages respectively.

overall_design: In this study, focusing on the special folliculogenesis process in chicken, we conducted bulk RNA-seq of GCs at ten follicle growth stages (SWF, LWF, SYF, LYF, F5, F4, F3, F2, F1, and POF) and single cell RNA-seq (scRNA-seq) of GCs at three representative stages (SWF, F1, and POF) to depict the transcriptome landscapes during the stepwise folliculogenesis. We also performed in situ high-throughput chromatin conformation capture (Hi-C) sequencing, ATAC-seq, and ChIP-seq analyses for GCs at the three representative stages to further investigate the chromatin architecture dynamics and their close associations with the temporal gene expression profiling during the development.


title: Trained immunity induction by the inactivated mucosal vaccine MV130 protects against experimental viral respiratory infections

summary:
MV130 is an inactivated polybacterial mucosal vaccine that confers protection to patients against recurrent respiratory infections, including those of viral etiology. However, its mechanism of action remains poorly understood. Herein, we observe that intranasal prophylaxis with MV130 modulates the lung immune landscape and provides long term heterologous protection against viral respiratory infections in mice. Intranasal administration of MV130 provided protection against systemic candidiasis in wild-type and Rag1-deficient mice lacking functional lymphocytes, indicative of innate immune-mediated protection. Moreover, pharmacological inhibition of trained immunity with metformin abrogated the protection conferred by MV130 against Influenza A virus respiratory infection.  MV130 induced reprogramming of mouse bone marrow progenitor cells and human monocytes, promoting an enhanced cytokine production that relied on metabolic and epigenetic shifts. Our results unveil that the mucosal a  dministration of a fully inactivated bacterial vaccine provides protection against viral infections by a mechanism associated with the induction of trained immunity.
This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: MAFB surrogates the glucocorticoid receptor ability to induce tolerogenesis in dendritic cells [Methylation_1 array]

first: Esteban

last: Ballestar

summary: Glucocorticoids (GCs) exert potent anti-inflammatory effects in immune cells through the glucocorticoid receptor (GR). Dendritic cells (DCs), central actors for coordinating immune responses, acquire tolerogenic properties in response to GCs. Tolerogenic DCs (tolDCs) have emerged as a potential treatment for different inflammatory diseases. To date, the underlying cell type-specific regulatory mechanisms orchestrating GC-mediated acquisition of immunosuppressive properties remain poorly understood. In this study, we investigated the transcriptomic and epigenomic remodeling associated with differentiation to DCs in the presence of GCs. Our analysis demonstrates a major role of MAFB in this process, in synergy with GR. Both GR and MAFB interact with methylcytosine dioxygenase TET2 and bind to genomic loci that undergo specific demethylation in tolDCs. We also show that the role of MAFB is more extensive, binding to thousands of genomic loci in tolDCs. Finally, MAFB knockdown erases the tolerogenic properties of tolDCs and reverts the specific DNA demethylation and gene upregulation. The preeminent role of MAFB is also demonstrated in vivo for myeloid cells from synovium in rheumatoid arthritis following GC treatment. These results support that, once directly activated by GR, MAFB takes over the main roles to orchestrate the epigenomic and transcriptomic remodelling that define the tolerogenic phenotype.

overall_design: Monocytes from 4 donors were differentiated to DCs and tolDCs for 6 days. Three condiitons: Monocytes, Dcs and tolDCs.

first: Octavio

last: Morante-Palacios

first: Laura

last: Ciudad

first: Raphael

last: Micheroli

first: Carlos

last: de la Calle-Fabregat

first: Gisela

last: Barbisan

first: Miranda

last: Houtman

first: Sam

last: Edalat

first: Mojca

last: Frank-Bertoncelj

first: Caroline

last: Ospelt


title: Long non-coding RNAs Gabarapl2 and Chrnb2 positively regulate inflammatory signaling in a mouse model of dry eye

status: Public on Nov 09 2021

city: shanghai

first: xujiao

last: zhou

address: fenyang road 83

institute: Eye & ENT Hospital, Fudan University

summary:
Purpose: To elucidate the expression profile and the potential role of long non-coding ribonucleic acids (RNAs; lncRNAs) in a dry eye disease (DED) model.
Methods: A DED model was established in C57BL/6J mice with 0.2% benzalkonium chloride (BAC) twice a day for 14 days. The differentially expressed lncRNAs were detected by RNA-seq technology and the aberrantly expressed lncRNAs were further verified by RT-qPCR. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were conducted to predicate the related candidate genes and potential pathological pathways. Cells from a human corneal epithelial cell line (HCECs) were cultured under hyperosmolarity. The regulation of inflammatory factors by silencing potential targeted lncRNAs was verified in vitro in HCECs.
Results: In our study, a significant increase in corneal fluorescence staining and a reduction in tear production were observed in DED mice at all follow-ups compared with the controls, and the differences were increasing over time. In total, 2649 upregulated and 704 downregulated lncRNAs were identified in DED mice. We selected six aberrantly expressed and most abundant lncRNAs and performed RT-qPCR using the samples for RNA-seq. Chrnb2, Gabarapl2, and Usp31 were thereby confirmed as the most significantly altered lncRNAs. Pathway analysis revealed that the neuroactive ligand–receptor interaction signaling pathway was the most enriched, followed by the calcium signaling pathway and cytokine–cytokine receptor interaction. Following treatment of Gabarapl2 siRNA and Chrnb2 siRNA, tumor necrosis factor-α (TNF-α), interleukin (IL)-1β, and interleukin (IL)-6 were significantly downregulated in the HCECs.
Conclusion: Our study suggests that Chrnb2 and Gabarapl2 may be involved in the inflammation response by regulating TNF-α, IL-1β, and IL-6 in DED. These candidate lncRNAs may be both potential biomarkers and therapeutic targets for DED.

overall_design: CK and TREAT are the names of samples, where CK stands for blank control group and TREAT stands for dry eye mice model group. RNA-seq was performed to identify lncRNAs involved in the cornea with the dry eye model.

first: Yuhan

last: Yang

first: Minjie

last: Chen

first: Xujiao

last: Zhou

first: Jiaxu

last: Hong


title: Oxicam-type nonsteroidal anti-inflammatory drugs inhibit NPR1-mediated salicylic acid pathway

city: Yokohama

first: Shuta

last: Asai

address: 1-7-22, Suehiro-cho, Tsurumi-ku

institute: RIKEN

summary: Nonsteroidal anti-inflammatory drugs (NSAIDs), including salicylic acid (SA), target mammalian cyclooxygenases. In plants, SA is a defense hormone that regulates NON-EXPRESSOR OF PATHOGENESIS RELATED GENES 1 (NPR1), the master transcriptional regulator of immunity-related genes. We identify that the oxicam-type NSAIDs tenoxicam (TNX), meloxicam, and piroxicam, but not other types of NSAIDs, exhibit an inhibitory effect on immunity to bacteria and SA-dependent plant immune response. TNX treatment decreases NPR1 levels, independently from the proposed SA receptors NPR3 and NPR4. Instead, TNX induces oxidation of cytosolic redox status, which is also affected by SA and regulates NPR1 homeostasis. A cysteine labeling assay reveals that cysteine residues in NPR1 can be oxidized in vitro, leading to disulfide-bridged oligomerization of NPR1, but not in vivo regardless of SA or TNX treatment. Therefore, this study indicates that oxicam inhibits NPR1-mediated SA signaling without affecting the redox status of NPR1.

overall_design: Fourteen-day-old seedlings grown on 1/2 MS medium with 0.8% (w/v) agar and 1% (w/v) sucrose were transferred to 1/2 MS liquid medium with 1% (w/v) sucrose and further incubated for 1 day. SA and/or TNX were added to the liquid medium at 100 µM final concentrations and the seedlings were incubated for 1 day. RNA sequencing was performed by deep sequencing on Illumina Hiseq 2500 using EXPRSS tag-seq protocol (BMC Genomics 2014, 15:341). Each biological replicate set of samples were sequenced as one batch (biorep1, biorep2 and biorep3 in filenames).

first: Nobuaki

last: Ishihama

first: Seung-won

last: Choi

first: Ken

last: Shirasu


title: Intraperitoneal microbial contamination drives post-surgical peritoneal adhesions by mesothelial EGFR-signaling.

status: Public on Nov 08 2021

city: Bern

first: Daniel

last: Sanchez-Taltavull

address: Murtenstrasse 35

department: Department of BioMedical Research

institute: University of Bern

summary: Abdominal surgeries are lifesaving procedures but can be complicated by the formation of peritoneal adhesions, intra-abdominal scars that cause intestinal obstruction, pain, infertility, and significant health costs. Despite this burden, the mechanisms underlying adhesion formation remain unclear and no cure exists. Here, we show that contamination of gut microbes increases post-surgical adhesion formation. Using genetic lineage tracing we show that adhesion myofibroblasts arose from the mesothelium. This transformation was driven by epidermal growth factor receptor (EGFR) signaling. The EGFR ligands Amphiregulin and Heparin-binding Epidermal Growth Factor, were sufficient to induce these changes. Correspondingly, EGFR inhibition led to a significant reduction of adhesion formation in mice. Adhesions isolated from human patients were enriched in EGFR positive cells of mesothelial origin and human mesothelium showed an increase of mesothelial EGFR expression during bacterial peritonitis. In conclusion, bacterial contamination drives adhesion formation through mesothelial EGFR signaling. This mechanism may represent a therapeutic target for the prevention of adhesions after intra-abdominal surgery.

overall_design: C57/Bl6 mice underwent laparatomy with peritoneal button injury with or without cecal ligation and puncture. Mice were euthanized 24h after surgery and peritoneal buttons were processed for scRNA Sequencing.

first: Zindel

last: Joel

first: Sánchez

last: Daniel

first: Keogh-Stroka

last: Deborah

first: Candinas


title: Identifying non-genetic determinants of malignant clonal fitness at single cell resolution [tertiary leukemia LC-WGS]

city: Melbourne

first: Mark

last: Dawson

state: VIC

address: 305 Grattan Street

institute: Peter MacCallum Cancer Centre

type: Methylation profiling by high throughput sequencing

summary: All cancers emerge following a period of clonal selection and subsequent clonal expansion. Whilst the evolutionary principles imparted by genetic intra-tumour heterogeneity (ITH) are becoming increasingly clear, little is known about the non-genetic mechanisms that contribute to ITH and malignant clonal fitness. Using SPLINTR, a synthetic expressed barcoding strategy, in three clinically relevant mouse models of acute myeloid leukemia (AML) we find that malignant clonal dominance is a stable and heritable property that is facilitated by the repression of antigen presentation and the increased expression of Slpi, a leukocyte protease inhibitor that has not previously been characterised in AML. Increased transcriptional heterogeneity is a consistent feature enabling clonal fitness in diverse tissue / immune microenvironments and in the context of clonal competition between genetically distinct clones within a uniform microenvironment. Compared to extramedullary sites, leukemia initiating capacity is most enriched in malignant cells resident within the bone marrow microenvironment and leukemia stem cells (LSC), like normal haematopoietic stem cells, display heritable clone-intrinsic properties of high, and low clonal output that contribute to the overall tumour mass. Finally, we demonstrate that clonal output does not dictate sensitivity to chemotherapy and both high and low output LSC clones retain marked cellular plasticity enabling them to survive potent therapeutic challenge and persist as minimal residual disease. Together these data provide fundamental insights into the non-genetic transcriptional processes that underpin malignant clonal fitness which may inform future therapeutic strategies.

overall_design: low coverage whole genome sequencing of MLL-AF9 leukemia cells

first: Katie

last: Fennell

first: Dane

last: Vassiliadis


title: Identifying non-genetic determinants of malignant clonal fitness at single cell resolution [chemo scRNAseq]

overall_design: Single-cell RNA-seq of MLL-AF9 leukemia cells with SPLINTR barcodes transplanted into Ptprca mice


title: Identifying non-genetic determinants of malignant clonal fitness at single cell resolution [chemo barcode-seq]

overall_design: DNA barcode-seq of MLL-AF9 + KRASG12D leukemia cells following chemotherapy treatment


title: Ageing-dependent ribosome pausing and nascent polypeptide aggregation

city: Stanford

first: Kevin

middle: C.

last: Stein

state: California

address: Clark Center E200, 318 Campus Drive

department: Biology

institute: Stanford University

summary: Increased protein misfolding and aggregation are key hallmarks of ageing and many age-related diseases. As generating and maintaining a functional proteome (proteostasis) is crucial to every cellular process, this age-related decline in proteostasis is suggested to play a primary role in the breakdown of diverse cellular subsystems during ageing. Indeed, augmented proteostasis pathways are associated with extended lifespan across different species. With the ribosome as the earliest proteostasis checkpoint, decreased protein synthesis is also a conserved mechanism that extends lifespan. Yet, it remains unclear whether ageing impacts translation after initiation. Here, we use worms and yeast to investigate how ageing influences translation elongation. We show an age-dependent increase in ribosome pausing at diverse positions in coding sequences. This pausing is conserved in both worms and yeast, particularly at Arg and polybasic regions. We further show that such pausing is associated with the age-dependent aggregation of truncated nascent proteins involved in proteostasis pathways, notably aminoacyl tRNA synthetases. Moreover, we find that impairment in clearing truncated nascent proteins is associated with decreased lifespan. These data establish elongation kinetics and co-translational quality control as critical contributors of the age-related proteostasis collapse, which may precipitate the systemic decline observed during ageing.

sample_organism:
Saccharomyces cerevisiae
Caenorhabditis elegans

overall_design: Replicate ribosome profiling libraries were prepared during ageing of worms and yeast, including the long-lived sch9Δ yeast strain.

first: Judith

last: Frydman


title: Identifying non-genetic determinants of malignant clonal fitness at single cell resolution [cell of origin barcode-seq]

overall_design: DNA barcode-seq of In vivo cell of origin competition experiment using barcoded leukemias derived from GMP or LSK populations


title: Specialized injury-induced serotonergic neurons promote circuit reorganization and function restoration after spinal cord injury in zebrafish

city: Shanghai

first: Chun-Xiao

last: Huang

address: 65 Chifeng Road, Yangpu District

department: School of Medcine, Tongji University

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


title: Next Generation Sequencing of zebrafish intraspinal serotonergic neurons in the injury segment and distal segments after spinal cord injury

summary: The goals of this study is to compare transcriptome profiles (RNA-seq) of zebrafish intraspinal serotonergic neurons in the injury segment and distal segments after spinal cord injury. Bulk RNA-Seq samples of ISNs from the injury area and residual segments respectively were FAC-sorted from Tg(tph2:GFP) line. Total RNA was isolated using SMART-SeqTM v4 UltraTM Low Input RNA Kit for Sequencing (Clontech). Sequencing libraries (N=5-6) were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina following the manufacturer’s instructions (NEB). We mapped about 50-60 million sequence reads per sample to the zebrafish genome and identified 39,714 transcripts in the zebrafish intraspinal serotonergic neurons. Our study represents the detailed analysis of transcriptomes of zebrafish intraspinal serotonergic neurons in the injury segment and distal segments after spinal cord injury.

overall_design: Bulk RNA-Seq samples of intraspinal serotonergic neurons from the injury area and residual segments respectively were FAC-sorted from Tg(tph2:GFP) line. Total RNA was extracted and cDNA libraries (N=5-6) were subjected to Illumina sequencing according to the manufacturer’s protocol.

first: Jianren

last: Song

last: Guan


title: Identifying non-genetic determinants of malignant clonal fitness at single cell resolution [retransplant scRNAseq]


title: Next Generation Sequencing of zebrafish spinal cord transcriptomes before and after injury

summary: The goals of this study is to compare transcriptome profiles (RNA-seq) of zebrafish spinal cord before and after injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one, two, four, and six weeks post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries (N=4-5) were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate.We mapped about 40-80 million sequence reads per sample to the zebrafish genome and identified 37,603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before and after injury.

overall_design: For RNA sequencing of zebrafish spinal cord tissue, the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one, two, four, and six weeks post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent (Invitrogen), and cDNA libraries (N=4-5) were subjected to Illumina sequencing according to the manufacturer’s protocol.


title: Identifying non-genetic determinants of malignant clonal fitness at single cell resolution (clonal competition scRNAseq)

summary: All cancers emerge following a period of clonal selection and subsequent clonal expansion. Whilst the evolutionary principles imparted by genetic intra-tumour heterogeneity (ITH) are becoming increasingly clear, little is known about the non-genetic mechanisms that contribute to ITH and malignant clonal fitness. Using SPLINTR, a synthetic expressed barcoding strategy, in three clinically relevant mouse models of acute myeloid leukaemia (AML) we find that malignant clonal dominance is a stable and heritable property that is facilitated by the repression of antigen presentation and the increased expression of Slpi, a leukocyte protease inhibitor that has not previously been characterised in AML. Increased transcriptional heterogeneity is a consistent feature enabling clonal fitness in diverse tissue / immune microenvironments and in the context of clonal competition between genetically distinct clones within a uniform microenvironment. Compared to extramedullary sites, leukaemia initiating capacity is most enriched in malignant cells resident within the bone marrow microenvironment and leukaemia stem cells (LSC), like normal haematopoietic stem cells, display heritable clone-intrinsic properties of high, and low clonal output that contribute to the overall tumour mass. Finally, we demonstrate that clonal output does not dictate sensitivity to chemotherapy and both high and low output LSC clones retain marked cellular plasticity enabling them to survive potent therapeutic challenge and persist as minimal residual disease. Together these data provide fundamental insights into the non-genetic transcriptional processes that underpin malignant clonal fitness which may inform future therapeutic strategies.

overall_design: Single-cell RNA-seq of In vivo clonal competition experiment


title: Chemical Inhibition of H3K27me3 demethylases during B cell differentiation

city: Atlanta

first: Chris

last: Scharer

state: GA

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

institute: Emory University

summary: To understand the role of the H3K27me3 demethylases, UTX and JMJD3, in B cell differentiation. Naïve B cells were cultures ex vivo with LPS, IL-2,IL-5 in the presence of DMSO or GSK-J4, UTX/JMJD3 inhibitor. Plasmablasts and activated B cells were magnetically enriched after 3 days of culture.

overall_design: RNAseq on B cells treated with GSK-J4 or DMSO

first: CD

first: JM

last: Boss


title: Identifying non-genetic determinants of malignant clonal fitness at single cell resolution (clonal competition barcode-seq)

overall_design: DNA barcode-seq of In vivo clonal competition experiment


title: Identifying non-genetic determinants of malignant clonal fitness at single cell resolution (NSG vs. BL6 scRNAseq)

overall_design: Single-cell RNA-seq of MLL-AF9 leukaemia cells with SPLINTR barcodes transplanted into Ptprca or NSG mice


title: VID22 counteracts G-quadruplex-induced genome instability

city: Milan

first: Matteo

last: Chiara

address: via celoria 26

department: Biosciences

country: Italy

institute: University of Milan

summary: Genome instability is a condition characterized by the accumulation of various genetic alterations and is a hallmark of cancer cells. To uncover new genes and cellular pathways controlling the levels of endogenous DNA damage and affecting genome integrity, we exploited a Synthetic Genetic Array (SGA)-based screen in yeast. Among the positive genes, we identified VID22, a gene previously reported to be involved in DNA double-strand break repair. We found that vid22Δ cells exhibit chronic DNA damage response activation, show increased levels of increased endogenous DNA damage and accumulate DNA aberrations in sequences displaying high probabilities of forming G-quadruplexes (G4-DNA). If not resolved, these non-canonical DNA secondary structures can block the progression of both DNA and RNA polymerases and correlate with chromosome fragile sites. We show that Vid22 in vitro and in vivo binds directly to and protects DNA at G4-containing regions both in vitro and in vivo. In particular, loss of VID22 causes an increase in gross chromosomal rearrangement (GCR) events dependent on G-quadruplex forming sequences. We also demonstrate that the absence of Vid22 causes defects in the correct maintenance of G4-DNA rich elements, such as telomeres and mtDNA, and hypersensitivity to the G4-stabilizing ligand TMPyP4. We thus propose that Vid22 is directly involved in genome integrity maintenance as a novel regulator of G4 metabolism.

overall_design: 2 samples

first: Elena

last: Galati

first: Maria

last: Bosio

first: Federico

last: Lazzaro


title: Identifying non-genetic determinants of malignant clonal fitness at single cell resolution (retransplant barcode-seq)

overall_design: DNA barcode-seq of MLL-AF9 leukaemia cells transplanted into Ptprca or NSG mice


title: Identifying non-genetic determinants of malignant clonal fitness at single cell resolution (secondary leukaemia exome)

type: Genome variation profiling by high throughput sequencing

overall_design: Exome sequencing of MLL-AF9 leukaemias from mice


title: Next generation sequencing of changes in mesothelial transcriptome post-surgery

first: Daniel

last: Sanchez-Taltavull

summary: Purpose: The goal of this study was to investigate post-surgical transcriptomic changes in mesothelial cells  Methods: Mesothelial cells were immonopurified using anti-glycoprotein M6A antibody.

overall_design: Mesothelial mRNA profiles of 8-10 week old wild type C57BL/6 mice with different hygiene status (SPF, germ free) after different time points post surgery

first: Joel

last: Zindel

last: Candinas