title: Genome-wide distribution of H3K4me3 in Medicago truncatula wild type R108 and Mting2-1 mutant.

city: Auckland

first: Joanna

last: Putterill

state: Auckland

address: 3A Symonds Street

department: School of Biological Sciences

country: New Zealand

institute: The University of Auckland

summary: Medicago truncatula (Medicago) flowering is promoted by winter cold (vernalization) followed by long day photoperiods (VLD). By analysing a Tnt1 insertion mutant and 17 CRISPR-Cas9 gene-edited lines with delayed flowering, we identified INHIBITOR OF GROWTH (ING) 2 (MtING2) encoding a plant homeodomain (PHD) zinc finger and predicted H3K4me2/3 epigenome reader in Medicago. There are two ING genes in most plants, but their physiological role has not been described. Mting2 mutants had many developmental abnormalities including delayed flowering particularly in VLD, compact architecture, abnormal leaves with extra leaflets but no trichomes and smaller seeds and seed barrels. RNA-Seq experiments indicated that >7000 genes are mis-expressed in the Mting2 mutant consistent with its strong mutant phenotypes. Mting2 did not show reduced accumulation of the strong floral promoter FLOWERING LOCUS T-LIKE gene, MtFTa1, but did have increased expression of MtTFL1c, consistent with the delayed flowering of the mutant. ChIP-Seq analysis identified >5000 novel H3K4me3 locations in the genome of Mting2-1 mutant compared to wild type, which overlapped with some differentially expressed genes. Overall, our study has uncovered an important physiological role of a plant ING gene in development, flowering and gene expression, which likely involves an epigenetic mechanism.

overall_design: Germinated seeds from wild type R108 and Mting2-1 mutant plants were grown under vernalised long day conditions in sterile culture. Whole aerial tissues were harvested from 14–17-day-old plants at 4 h after dawn (ZT4). Three biological replicates for each genotype were harvested. Chromatin Immunoprecipitated DNA were extracted and a total of 6 ChIP-seq libraries were constructed using NEBNext ChIP-Seq Library Prep Kit for Illumina (NEB, USA) and sequenced.

first: Mauren

last: Jaudal

first: Axel

last: Poulet

first: Yongyan

last: Peng


title: Effect of ∆Np63 deletion on epigenomic rewiring via differential H3K27ac and H3K27me3 enrichment

status: Public on Nov 11 2022

city: Philadelphia

first: Andrew

middle: E

last: Vaughan

state: PA

address: 3800 Spruce Street, Old Vet 370 E

country: USA

institute: University of Pennsylvania

type: Genome binding/occupancy profiling by high throughput sequencing

summary:
Basal cells were isolated from an influenza-infected non-tamoxifen treated Krt5CreERT2; RFP; ∆Np63flox/flox mouse and cultured, allowing for inducible ∆Np63 deletion in vitro.
These basal cells were plated as monolayers and treated with 1uM 4OHT for +4OHT (∆Np63 KO)  or equivalent volume DMSO for -4OHT (solvent only, ∆Np63 WT) for 48 hours. Technical triplicates of ∆Np63 WT and ∆Np63 KO treated in parallel were harvested for each IP for p63 and each histone modification for ChIP-seq.

overall_design: Comparative ChIP-seq of ±∆Np63 post-injury basal cell monolayers for H3K27ac, H3K27me3, and p63

first: Aaron

last: Weiner


title: A novel ERK substrate regulates wide varieries of IEGs

city: Shirokanedai

first: Mutsuhiro

last: Takekawa

state: Minato-ku, Tokyo

department: Institute of Medical Science

country: Japan

institute: The University of Tokyo

type: Expression profiling by high throughput sequencing

summary: The ERK pathway induces cell proliferation in response to growth factor stimulation. Although ERK controls various transcription factors in the nucleus, gene regulation mechanisms underlying the rapid IEG inductions were not fully elucidated. Here we report that ERK phosphorylates an unique novel substrate. We found that ERK facilitates rapid transcription of IEGs through the phosphorylation of the substrate.

overall_design: mRNA expressions of EGF-treated or non-treated HEK293-WT and -4A cells

first: Seina

last: Ohe

first: Yuji

last: Kubota

first: Kiyoshi

last: Yamaguchi

first: Yoichi

last: Furukawa

first: Yuko

last: Hata

first: Masaaki

last: Oyama


title: Global differential gene expression between Medicago truncatula wild type R108 and Mting2-1 mutant.

status: Public on Nov 10 2022

summary: Medicago truncatula (Medicago) flowering is promoted by winter cold (vernalization) followed by long day photoperiods (VLD). By analysing a Tnt1 insertion mutant and 17 CRISPR-Cas9 gene-edited lines with delayed flowering, we identified INHIBITOR OF GROWTH (ING) 2 (MtING2) encoding a plant homeodomain (PHD) zinc finger and predicted H3K4me2/3 epigenome reader in Medicago. There are two ING genes in most plants, but their physiological role has not been described. Mting2 mutants had many developmental abnormalities including delayed flowering particularly in VLD, compact architecture, abnormal leaves with extra leaflets but no trichomes and smaller seeds and seed barrels.   RNA-Seq experiments indicated that >7000 genes are mis-expressed in the Mting2 mutant consistent with its strong mutant phenotypes. Mting2 did not show reduced accumulation of the strong floral promoter FLOWERING LOCUS T-LIKE gene, MtFTa1, but did have increased expression of MtTFL1c, consistent with the delayed flowering of the mutant. ChIP-Seq analysis identified >5000 novel H3K4me3 locations in the genome of Mting2-1 mutant compared to wild type, which overlapped with some differentially expressed genes. Overall, our study has uncovered an important physiological role of a plant ING gene in development, flowering and gene expression, which likely involves an epigenetic mechanism.

overall_design: Germinated seeds from wild type R108 and Mting2-1 mutant plants were grown under vernalised long day conditions in sterile culture. Trifoliate leaves or shoot apices were harvested from 13–15-day-old plants at 4 h after dawn (ZT4). Three biological replicates per tissue type for each genotype were harvested. Total RNA was extracted and sent for RNA-sequencing. Three biological replicates of leaves and shoots from wild type R108 and Mting2-1 mutant made up a total of 12 RNA-Seq libraries.

first: Annabel

last: Whibley


title: The nuclear granule Paraspeckles interacts with the chromatin remodeling SWI/SNF complex to regulate alternative splicing

city: Kansas City

first: Madelaine

last: Gogol

state: MO

address: 1000 E. 50th Street

department: Computational Biology Core

institute: Stowers Institute

summary: There are three major goals of the study 1) Understand if the differential effect of depletion of ARID1 paralogs on the trancriptome of HEK293FRT cells 2) Understand if NEAT1 depletion effects any alternative splicing pathways in HEK293FRT cells 3) Is the regulation of alternative splicing pathways by NEAT1 ARID1B dependent?

overall_design: siRNA specific to either ARID1A, ARID1B or NEAT1 was used for experimental data sets. For both the controls, Wildtype or Parental a scrambled siRNA was used. In brief, 2 rounds of transfection with siRNA was employed with 24 hour interval in between each transfection. All the cells were harvested post 72 hours of first siRNA transfection and processed for RNA extraction.

first: Divya

last: Reddy

first: Jerry

last: Workman


title: Targeting cardiomyocyte ADAM10 ectodomain shedding promotes survival early after myocardial infarction

city: Dresden

first: Erik

last: Klapproth

address: Fiedlerstraße 42

department: Institute of Pharmacology and Toxicology

country: Germany

institute: Technische Universität Dresden

summary: Myocardial infarction (MI) contributes to cardiac mortality and morbidity. After myocardial infarction the innate immune response is pivotal in clearing of tissue debris as well as scar formation, but exaggerated cytokine and chemokine secretion with subsequent leukocyte infiltration also leads to further tissue damage. Post-translational regulation of cytokine / chemokine signaling occurs via ectodomain shedding through a disintegrin and metalloproteases (ADAMs). Here, we address the value of targeting a previously unknown ADAM10 / CX3CL1 axis in the regulation of neutrophil recruitment early after MI. We show that myocardial ADAM10 is distinctly upregulated in biopsies from patients with ischemia-driven cardiomyopathy and correlates with heart failure progression. Intriguingly, upon MI in mice, pharmacological treatment with the ADAM10 inhibitionor GI254023X  as well as genetic cardiomycyte-specific ADAM10 deletion improves survival with markedly enhanced heart function and reduced scar size. Mechanistically, this is driven by abolished ADAM10-mediated CX3CL1 ectodomain shedding followed by diminished IL-1β-dependent inflammation, reduced neutrophil bone marrow egress as well as myocardial tissue infiltration. Genetic cardiomycyte-specific ADAM10 deletion confirmes the small-molecule data and leads to improved cardiac function and reduction in inflammatory markers after ischemic myocardial injury. Thus, our data shows a conceptual insight into how acute MI induces chemotactic signaling via ectodomain shedding in cardiomyocytes.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for mouse hearts of ADAM10 inhibitor (A10i = GI254023X)-treated (samples A116, A117, A119, A120) and DMSO-treated control mice (samples A105, A127, A128, A129) 3d after infarction via LAD ligation.

first: Ali

last: El-Armouche


title: PR-DUB preserves Polycomb repression by preventing excessive accumulation of H2Aub1, an antagonist of nucleosome stacking (ATAC-Seq)

status: Public on Nov 09 2022

city: Martinsried

first: Jürg

last: Müller

state: Bavaria

address: Am Klopferspitz

institute: Max Planck Institute of Biochemistry

summary: The Polycomb repression machinery in Drosophila comprises PRC1 that monoubiquitinates histone H2A at lysine 118 (H2Aub1) and PR-DUB, a major H2Aub1 deubiquitinase, but how H2Aub1 levels must be balanced for Polycomb repression remains enigmatic.  We show that H2Aub1 is enriched at Polycomb target genes in early embryos but depleted from these genes during developmental stages when PRC1 represses their transcription.  Accordingly, Polycomb targets remain repressed in H2Aub1-deficient animals.  In PR-DUB catalytic mutants, high-level H2Aub1 accumulation at Polycomb targets increases chromatin accessibility, consistent with disruption of chromatin fiber folding by H2Aub1 in vitro.  Consequently, PR-DUB mutants show defective Polycomb repression, while general transcription is largely unperturbed by the genome-wide, low-level H2Aub1 increase.  Changes in H2Aub1 levels alter H3K27 methylation-kinetics but PRC2 nevertheless generates canonical H3K27me3 domains in PRC1 or PR-DUB catalytic mutants.  PR-DUB therefore acts as a rheostat that removes excessive H2Aub1 that, though deposited by PRC1, antagonizes PRC1-mediated chromatin compaction.

overall_design: Analysis of ATAC-seq profiles generated from wild-type and mutant Drosophila embryos.

first: Jacques

last: Bonnet


title: RNA sequencing of human regulatory T cell clones, both Faecalibacterium prausnitzii-reactive DP8a (CD4,CD8alphalow) Tregs and (CD4,CD25high,CD127low) Foxp3 Tregs obtained  from the colon lamina propria and from the blood.

city: Nantes

first: Raluca

last: TEUSAN

address: IRS-UN - 8 quai Moncousu - BP 70721

country: France

institute: Inserm

summary: We generated  human DP8a Treg (CD4, CD8alow, CCR6+, CXCR6+, F. praunsitzii-reactive) and FoxP3 Treg (CD4, CD25high, CD127low) clones from  healthy colon  lamina propria-derived  lymphocytes (LPL) (from colorectal cancer patients) and  from  blood lymphocytes from healthy volunteers).  Through DEseq2 analysis) we identified activation-induced genes in  these clones and  compared gene expression between resting and activated  DP8a and  Foxp3 clones.

overall_design: This experiment compare the gene expression of 8  groups of  human regulatory T cell clones:  resting and activated colon-derived DP8a clones, resting and activated colon-derived FoxP3 Treg clones, resting and activated blood-derived DP8a clones and resting and activated  blood-derived FoxP3 clones

first: Emmanuelle

last: Godefroy

first: Francine

last: Jotereau

first: Joudy

last: Alameddine

last: Teusan


title: PR-DUB preserves Polycomb repression by preventing excessive accumulation of H2Aub1, an antagonist of nucleosome stacking (RNA-Seq)

overall_design: Analyses of RNA-seq datasets generated from wild-type and mutant stage 16 single embryos.


title: Targeted erythrophagocyte reprogramming of Kupffer cells halts cancer immunotherapy associated liver toxicity [Multiplexed_CD40]

city: Schlieren

first: Marc

last: Pfefferle

state: Schweiz

address: Wagistrasse 12

country: Switzerland

institute: University hospital Zürich (USZ)

summary: Agonistic CD40 monoclonal antibodies have emerged as promising immunotherapeutic compounds with impressive anti-tumoral effects. However, one of the main limitations of their use in patients is the severe liver necro-hepatitis they can induce. Up to this point,  no effective treatment for anti-CD40 liver toxicity that does not hinder anti-tumor efficacy has been found. In the present study , we show that anti-CD40 liver toxicity is dependent on liver macrophages and recruitment of monocytes and neutrophils. We specifically reprogrammed the phenotype of liver macrophages to anti-inflammatory erythrophagocytes by using repeated injection of anti-erythrocyte murine Ter119 (mTer119) antibody. mTer119 administration induced phagocytosis of erythrocytes by liver macrophages and their transformation to Hmoxhigh/Marcohigh/MHC-IIlow erythrophagocytes. mTer119 treatment prevented anti-CD40 induced liver toxic side-effect, with significantly reduced elevation of plasma transaminases level and area of liver necrosis on histology,  while preserving the anti-tumoral efficiency of anti-CD40. Our study offers a novel targeted therapeutic approach to treat immune-related liver adverse side effects of immunotherapies.

overall_design: C57BL/6J mice were injected with 20 mg/kg anti-CD40 antibody (InVivoPlus BP0016-2) intraveinously or saline (Control mouse). At 7, 14 or 22 hours post injection, mice were euthanized and their liver digested into a non-parenchymal single-cell suspension. Cells were enriched for leucocytes using CD45+ coated magnetic beads (MagniSort™ Mouse CD45 Positive Selection Kit, 8802-6865-74), stained with Totalseq B hashtag antibodies (Biolegend) and pooled together at equal cell count before processing for single-cell RNA sequencing (Chromium Single Cell 3' Reagent Kits User Guide (v3.1 Chemistry Dual Index) with Feature Barcoding technology for Cell Surface Protein).

first: Florence

last: Vallelian

last: Pfefferlé

first: Irina

last: Dubach

first: Dominik

middle: J

last: Schaer


title: Integrin α5-SRC signaling induces TET1 mediated hydroxymethylation of genes critical for maintenance of hepatic polarity

city: beijing

first: Yuejiao

last: Ma

address: No. 10.wai xi tou tiao, you an men street.

country: China

type: Methylation profiling by high throughput sequencing

summary: Conclusions: 1. ITGα5-SRC signalling regulates the CLDN1 expression and hepatic polarity. 2. ITGα5-SRC signalling regulates the TET catelyzed DNA 5hmc/5mc level. 3. Itgα5 regulates hydroxymethylation level of genes critical for polarity in vivo. 4. Excessive deposition of ECM blocks the regulatory effect of ITGα5 on CLDN1 in vitro and in vivo.

overall_design: Examination of liver tissues from 3 control KD mice and 3 integrin α5 KD mice.

first: Haiyan

last: Zhang


title: Multi cytokine producing liver CD4+ T cells characterize the liver of NASH patients

status: Public on Nov 08 2022

city: Hamburg

first: Tianran

address: Falkenried 94

institute: University Medical Center Hamburg-Eppendorf

summary: Single cell RNA-seq of liver CD4+ T cells from NAFLD and NASH patients.

overall_design: Single cell RNA-seq of FACS sorted liver memory CD45RA− CD4+ T cells from 3 NAFLD and 3 NASH patients.

first: Anna

last: Woestemeier

first: Pasquale

last: Scognamiglio

first: Yu

last: Zhao

first: Christian

last: Casar

first: Nicola

last: Gagliani


title: Targeted erythrophagocyte reprogramming of Kupffer cells halts cancer immunotherapy associated liver toxicity [Ter119 experiment]

summary: Agonistic CD40 monoclonal antibodies have emerged as promising immunotherapeutic compounds with impressive anti-tumoral effects. However, one of the main limitations of their use in patients is the severe liver necro-hepatitis they can induce. Up to this point, no effective treatment for anti-CD40 liver toxicity that does not hinder anti-tumor efficacy has been found. In the present study , we show that anti-CD40 liver toxicity is dependent on liver macrophages and recruitment of monocytes and neutrophils. We specifically reprogrammed the phenotype of liver macrophages to anti-inflammatory erythrophagocytes by using repeated injection of anti-erythrocyte murine Ter119 (mTer119) antibody. mTer119 administration induced phagocytosis of erythrocytes by liver macrophages and their transformation to Hmoxhigh/Marcohigh/MHC-IIlow erythrophagocytes. mTer119 treatment prevented anti-CD40 induced liver toxic side-effect, with significantly reduced elevation of plasma transaminases level and area of liver necrosis on histology,  while preserving the anti-tumoral efficiency of anti-CD40. Our study offers a novel targeted therapeutic approach to treat immune-related liver adverse side effects of immunotherapies.

overall_design: A C57BL/6J mouse was injected with a single injection of murine Ter119 antibody subcutaneously (35 ug) followed by 10 daily injections at lower dose (10 ug). Another C57BL/6J mouse was injected with similar volume of saline solution.  At 24 after the last injection, mice were euthanized and their liver digested into a non-parenchymal single-cell suspension. Cells were enriched for macofphages using a mixture of anti-F4/80 and anti-CD11b coated magnetic beads (Anti-Rat IgG Dynabeads), stained with Totalseq B hashtag antibodies (Biolegend) and pooled together at equal cell count before processing for single-cell RNA sequencing (Chromium Single Cell 3' Reagent Kits User Guide (v3.1)).


title: Targeted erythrophagocyte reprogramming of Kupffer cells halts cancer immunotherapy associated liver toxicity

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

overall_design: Refer to individual Series


title: RNA A>I editing of tau circular RNAs

city: Paris

first: Noémie

last: Robil

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

institute: GenoSplice technology

type: Non-coding RNA profiling by high throughput sequencing

summary: tau circular RNAs undergo Adenosine to inosine editing, which promotes their translation. To map editing sites,we cotransfected expression constructs for tau 7->12 and 10->12 circRNAs with expression constructs for GFP, ADAR1, ADAR2 and ADAR3 in HEK293 cells. RNA from these transfected cells was isolated and A>I editing was identified by A>G changes in the cDNA.

overall_design: 1 µg for the 7->12 circ Tau RNA construct flanked by endogenous introns was 1 µg of expression constructs for either GFP, ADAR1, ADAR2 or ADAR3. Similarly, expression constructs for the 12->10 circRNAs, either flanked by endogenous tau introns or ZKSCAN1 heterologous introns were cotransfected with expression constructs for either GFP, ADAR1, ADAR2 or ADAR3. Total RNA was isolated after 72 hrs using Rnaesy kit (Qiagen) and sequenced using Illumina.Backsplice junctions were searched within raw sequences using zgrep with ATTAATTATCTGCACCTTTTTATTTCCTCC for R1 files or GGAGGAAATAAAAAGGTGCAGATAATTAAT for R2 files. Subsequent read IDs (both read of each positive pair) were used to define new fastq files using the subseq function from seqtk (v1.0-r32). Reads were then aligned to the reference tau circRNA fasta file (including Tag) using Bowtie2 (v2.2.3) and the “--very-sensitive-local” parameter. Samtools (v1.11) mpileup and pileup2base script were used to study sequence composition at each position. Only positions with A>G and at least 1% of “G” in one sample were considered.

first: Stefan

last: Stamm

first: Pierre

last: de la Grange


title: Transcriptomic and chromatin accessibility analyses of porcine alveolar macrophages exposed to Fumonisin B1

city: 扬州

first: 靳

last: 健

state: 江苏

address: 扬州大学荷花池校区

institute: 扬州大学

summary: Fumonisin B1 (FB1) is a mycotoxin that poses a great threat to agricultural production and human and animal health. However, the molecular mechanism underlying the cytotoxic effect of FB1 to mammals has not been systematically elucidated. Here, we utilized the porcine alveolar macrophage cell line 3D4/21 as model, and applied RNA sequencing (RNA-seq) to analyze the genome-wide transcriptional alterations of mRNA, lncRNA, circRNA and miRNA before and after exposure to FB1 in six samples. To further reveal the underlying regulatory mechanism, we applied Assay for Transposase-Accessible Chromatin with high-throughput sequencing (ATAC-seq) to determine the genome-wide chromatin accessibility alterations in response to FB1-induced cytotoxicity. We anticipate that this dataset will serve as valuable resource for clarifying the transcriptional and regulatory mechanism underlying the cytotoxic effect of FB1, and facilitate the identification of the key genes and signaling pathways contributing to cellular response to FB1 exposure.

overall_design: We analyzed the transcriptional alterations of mRNA, lncRNA, circRNA and miRNA in porcine alveolar macrophages before and after exposure to FB1 using RNA-Seq. Using ATAC-seq technology, we determined changes in genome-wide chromatin accessibility in porcine alveolar macrophages in response to FB1-induced cytotoxicity.

first: Jian

last: Jin

first: Jiayao

last: Jiang

first: Zhengchang

last: Wu

first: Ruihua

last: Huang

first: Mingan

last: Sun

first: Wenbin

last: Bao


title: PRC2 molecule EZH1 is a target of epigenetic therapy of neuroblastoma

city: Kitaadachi-gun

first: Hisanori

last: Takenobu

state: Saitama

address: 818, Komuro, Ina-machi

department: Research Institute for Clinical Oncology

institute: Saitama Cancer Center

summary: In the present study, we found that EZH1 depletion in MYCN-amplified neuroblastoma cells resulted in significant cell death as well as xenograft inhibition. EZH1 depletion decreased the level of H3K27me1; the interaction and protein stabilization of MYCN and EZH1 appear to play roles in epigenetic transcriptional regulation. Transcriptome analysis of EZH1-depleted cells resulted in down-regulation of the cell cycle progression-related pathway. In particular, GSEA revealed down-regulation of reactome E2F-mediated regulation of DNA replication along with key genes of this process, TYMS, POLA2, and CCNA1. TYMS and POLA2 were transcriptionally activated by MYCN and EZH1-related epigenetic modification. Treatment with the EZH1/2 inhibitor UNC1999 also induced cell death, decreased H3K27 methylation, and reduced the levels of TYMS in NB cells. Previous reports indicated neuroblastoma cells are resistant to 5-fluorouracil (5-FU) and TYMS (encoding thymidylate synthetase) has been considered the primary site of action for folate analogues. Intriguingly, UNC1999 treatment significantly sensitized MYCN-amplified neuroblastoma cells to 5-FU treatment, suggesting that EZH inhibition may be an effective strategy for development of a new epigenetic treatment for neuroblastoma.

overall_design: RNA was extracted at 2 days after shEZH1-expressing lentiviral infection, and a microarray analysis was performed using the Agilent platform of 8x60 K design ID G4851B (Agilent Single Color. 39494, Agilent Technologies). Two hundred nanograms of total RNA was labeled with Cyanine3 using a Low Input Quick-Amp Labeling Kit (one color, Agilent Technologies) according to the manufacturer’s instructions. Purified labeled total RNA was hybridized to the expression microarray. Hybridization, the scanning of microarrays, and data extraction from scanned images were conducted according to Agilent protocol version 6.9.

first: Yoshitaka

last: Shinno

first: Ryuichi

middle: P

last: Sugino

first: Miki

last: Ohira

first: Takehiko

last: Kamijo


title: Transgenerational inheritance of obesity correlates with transmission of epigenetic alterations in the Fto gene [Hi-C]

city: Atlanta

first: Yoonhee

last: Jung

state: Georgia

address: 615 Michael Street

department: Human Genetics

institute: Emory university

summary: Evidence suggestive of inter- and transgenerational inheritance of epiphenotypes in mammals has been reported extensively. Numerous studies suggest a link between parental environments and a variety of effects in the offspring. For example, exposure of laboratory animals or humans to endocrine disrupting compounds leads to increased reproductive dysfunction, cancer, obesity, diabetes, and behavioral disorders. However, the mechanisms by which these epiphenotypes are transmitted between the exposed and subsequent generations through the paternal germline remain poorly understood. Here we show that exposure of pregnant mouse females during E7.5-E13.5 to bisphenol A (BPA) results in obesity in the F2 progeny. This epiphenotypes can be transmitted through the male and female germlines up to the F6 generation and disappears in F7. Analysis of chromatin changes in the sperm of the F1 generation reveals a widespread increase in chromatin accessibility at binding sites for CTCF, FoxA1, ESR1, ESR2, AR, and Pparg. Changes in CTCF/cohesin are accompanied by alterations in 3D organization that affect enhancer-promoter interactions. Comparison of the transmission of obesity with alterations in the binding of these transcription factors points to the activation of an enhancer in an intron of the Fto gene as the cause of transgenerational transmission of obesity. The results suggest that both genetic and epigenetic alterations of the same gene can lead to adverse effects on human health.

overall_design: Analysis of transcription factors in sperm.

first: Yoon

middle: H

first: Hsiao

middle: L

last: Wang

first: Hannah

last: Linsenbaum

first: Brianna

last: Bixler

first: Andrew

middle: M

last: Shafik

first: Daniel

last: Ruiz

first: Peng

first: Victor

last: Corces


title: Transgenerational inheritance of obesity correlates with transmission of epigenetic alterations in the Fto gene [m6A-seq]

last: Jin


title: Transgenerational inheritance of obesity correlates with transmission of epigenetic alterations in the Fto gene [RNA-seq]

overall_design: Analysis of gene expression


title: Cross-regulome profiling of RNA polymerases highlights the regulatory role of polymerase III on mRNA transcription by maintaining local chromatin architecture [RNA-seq]

status: Public on Nov 07 2022

city: Beijing

first: Xiong

last: Ji

address: Haidian District, Beijing Summer Palace Road No. 5

department: School of Life Sciences

institute: Peking University

summary: Mammalian nuclei contain Pol I, Pol II, and Pol III. However, to what extent and how they are cross-regulated remains elusive. Here, we performed orthogonal multi-omics profiling after acute degradation of the largest subunits of Pol I, Pol II, and Pol III, and showed that they mainly affect specific genes. In contrast, the loss of Pol I or Pol II causes few changes for other RNA polymerases and confirms those known. The changes of Pol II transcription after Pol III depletion are the largest among all the cross-regulatory types. Meta-analyses reveal that Pol III depletion increases nucleosome positioning, reduces the FACT complex occupancy, and perturbs Pol II elongation for nearby mRNA genes. Furthermore, the nucleosome positioning changes also underpinning the Pol II effects on Pol III-mediated tRNA transcription. Our results suggest that Pol III works together with Pol II to coordinate their transcription activities by maintaining local chromatin architecture.

overall_design: We performed EU-seq, RNA-seq, PRO-seq, ChAR-seq, ATAC-seq, and ChIP-seq to investigate the roles of various specialized subunits in transcription and post-transcriptional regulation. The V6.5 mouse ES (mES) cell line was used for all the high-throughput analyses. Degron mES cells were treated with 1 μg/ml Doxycycline for different hours refer to individual Series.

first: Yongpeng

last: Jiang

first: Jie

first: Kai

last: Tian

first: Haonan

last: Zheng


title: Transgenerational inheritance of obesity correlates with transmission of epigenetic alterations in the Fto gene [ChIP-seq]

overall_design:
Analysis of transcription factors in sperm.

ChIP-seq with androgen receptor


title: Cross-regulome profiling of RNA polymerases highlights the regulatory role of polymerase III on mRNA transcription by maintaining local chromatin architecture [EU-Seq]

last: Huang


title: Transgenerational inheritance of obesity correlates with transmission of epigenetic alterations in the Fto gene [BS-seq]


title: Transgenerational inheritance of obesity correlates with transmission of epigenetic alterations in the Fto gene


title: Transgenerational inheritance of obesity correlates with transmission of epigenetic alterations in the Fto gene [ATAC-seq]

overall_design:
Analysis of transcription factors in sperm

Analysis of transcription factor binding by ATAC-seq


title: Transcriptional Response of Mycobacterium tuberculosis H37Rv to Ca2+

city: Seattle

first: Christoph

last: Grundner

state: WA

address: 1900 9th Ave

department: Center for Global Infectious Disease Research

institute: Seattle Children's Research Institute

summary: To understand the response of M. tuberculosis (MTB) to Ca2+, we performed transcriptomics on MTB bacilli grown in chelex treated Sauton's medium with or without 1mM Ca2+ .

overall_design: Bacteria were harvested at different timepoints (1hr, 6hr, day 1, day 3).  RNA was isolated and gene expresion quantified by sequencing.

first: Vishant

last: Boradia

last: Frando


title: Cross-regulome profiling of RNA polymerases highlights the regulatory role of polymerase III on mRNA transcription by maintaining local chromatin architecture [ATAC-seq]

summary:
Genome binding/occupancy profiling by high throughput sequencing ｜ Expression profiling by high throughput sequencing | Other
Mammalian nuclei contain Pol I, Pol II, and Pol III. However, to what extent and how they are cross-regulated remains elusive. Here, we performed orthogonal multi-omics profiling after acute degradation of the largest subunits of Pol I, Pol II, and Pol III, and showed that they mainly affect specific genes. In contrast, the loss of Pol I or Pol II causes few changes for other RNA polymerases and confirms those known. The changes of Pol II transcription after Pol III depletion are the largest among all the cross-regulatory types. Meta-analyses reveal that Pol III depletion increases nucleosome positioning, reduces the FACT complex occupancy, and perturbs Pol II elongation for nearby mRNA genes. Furthermore, the nucleosome positioning changes also underpinning the Pol II effects on Pol III-mediated tRNA transcription. Our results suggest that Pol III works together with Pol II to coordinate their transcription activities by maintaining local chromatin architecture.

overall_design: We performed PRO-seq, ChAR-seq, ATAC-seq, and ChIP-seq to investigate the roles of various specialized subunits in transcription and post-transcriptional regulation. The V6.5 mouse ES (mES) cell line was used for all the high-throughput analyses. Degron mES cells were treated with 1 μg/ml Doxycycline for different hours refer to individual Series.


title: Cross-regulome profiling of RNA polymerases highlights the regulatory role of polymerase III on mRNA transcription by maintaining local chromatin architecture [ChAR-seq]


title: Epididymal epithelial degeneration and lipid metabolism impairment account for male infertility in occludin knockout mice

city: Shanghai

first: Winnie

last: Shum

address: 393 Hua Xia Middle Rd. Pudong District

institute: ShanghaiTech University

summary: Occludin (OCLN) is a tight junction protein and Ocln deletion mutation causes male infertility in mice. However, the role of OCLN in male reproductive system remains unknown. In this study, we found defective proximal epididymis in Ocln-null mice with impaired sperm motility and fertilization, but no defects in testicular spermatogenesis. Integrative omics analysis revealed the downregulation of gene clusters enriched in acid secretion and fatty acid metabolism in the Ocln-null epididymis, especially the enzymes related to the unsaturated arachidonic acid pathway. The number of proton-pump V-ATPase-expression clear cells, a key player of luminal acidification in the epididymis, declined drastically from prepubertal age before sperm arrival but not in the early postnatal-age. This was accompanied by clear cell apoptosis and increase in pH in the epididymal fluid of OCLN-deficient mice. The lipidomics results showed significantly increased levels of specific DAGs conjugated to unsaturated fatty acids in the Ocln-mutant. Immunofluorescent labeling showed that the arachidonic acid converting enzyme PTGDS and phospholipase PLA2g12a were prominently altered in the principal cells and luminal contents of the Ocln-mutant epididymis. Whereas the carboxylate ester lipase CES1, originally enriched in the WT basal cells, was found upregulated in the Ocln-mutant principal cells. Overall, this study demonstrates that OCLN is essential for maintaining the survival of acid-secreting clear cells and unsaturated fatty acid catabolism in the mouse epididymis, as well as ensuring sperm maturation and male fertility.

overall_design: mRNA profiles of whole epididymis of adult wild type (WT) and Ocln-/- mice were generated by deep sequencing, in triplicate, using Illumina HiSeq X Ten.

first: Baoli

last: Zhang

first: Baoying

last: Liu

first: Dayuan

last: Gao


title: Creb5 coordinates synovial joint formation with the genesis of articular cartilage

city: Boston

first: Zhu

last: Zhuo

state: MA

address: 401 Park Dr

department: Department of Biostatistics

institute: Harvard TH Chan School of Public Health

summary: While prior work has established that articular cartilage arises from Prg4-expressing perichondrial cells, it is not clear how this process is specifically restricted to the perichondrium of synovial joints.  We document that the transcription factor Creb5 is necessary to initiate the expression of signaling molecules that both direct the formation of synovial joints and guide perichondrial tissue to form articular cartilage instead of bone. Creb5 promotes the generation of articular chondrocytes from perichondrial precursors in part by inducing expression of Wif1, which blocks a Wnt5a autoregulatory loop in the perichondrium.  Postnatal deletion of Creb5 in the articular cartilage leads to loss of both flat superficial zone articular chondrocytes coupled with a loss of both Prg4 and Wif1 expression; and a non-cell autonomous up-regulation of Ctgf.   Our findings indicate that Creb5 promotes both joint formation and the subsequent development of articular chondrocytes by disrupting a Wnt5a positive-feedback loop in the perichondrium.

overall_design: We have identified genes expressed in bovine superficial zone articular chondrocytes whose expression was altered following shRNA-mediated knockdown of the transcription factor, Creb5. We performed RNA-Seq analysis of bovine superficial zone articular chondrocytes that had been infected with lentivirus programmed to express either a control shScramble or shCreb5.   We cultured the infected superficial zone articular chondrocytes for forty-eight hours in the presence of either the EGFR ligand, TGFalpha (condition A), or in the presence of both TGFalpha and TGFbeta-2 (condition AB).

first: Cheng-Hai

first: Yao

first: Han-Hwa

last: Hung

first: Alan

last: Grodzinsky

middle: B

last: Lassar


title: Cross-regulome profiling of RNA polymerases highlights the regulatory role of polymerase III on mRNA transcription by maintaining local chromatin architecture


title: Meteorin-like enhances aged muscle regeneration

status: Public on Nov 06 2022

city: Durham

first: James

last: White

state: nc

address: 300 N Duke Street

institute: Duke University SOM

summary: Pathologies associated with sarcopenia include decline in muscular strength, lean mass and regenerative capacity. Despite the substantial impact on quality of life, no pharmacological therapeutics are available to counteract the decline of functional capacity, loss of independence and resilience. Evidence suggests immune-secreted cytokines can improve muscle regeneration; a strategy which we leverage in this study by rescuing the age-related deficiency in Meteorin-like (Metrnl) through several in vivo add-back models. Notably, a direct, intramuscular peptide injection of recombinant METRNL was sufficient to improve muscle regeneration in aging. This RNAseq dataset substantiates that rMETRNL treatment via intramuscular injections is sufficient to rejuvenate the aged muscle regenerating transcriptome to that of young controls.

overall_design: RNA-seq comparing muscle cell suspension gene expressions between young control, old control and old Meteorin-like treated mouse muscle 4 days following injury.

first: David

last: Lee

first: Lauren

middle: K

last: McKay


title: Cross-regulome profiling of RNA polymerases highlights the regulatory role of polymerase III on mRNA transcription by maintaining local chromatin architecture [ChIP-seq]

first: Xiong

last: Ji

first: Yongpeng

last: Jiang

first: Jie

last: Tian


title: Cross-regulome profiling of RNA polymerases highlights the regulatory role of polymerase III on mRNA transcription by maintaining local chromatin architecture [PRO-seq]

last: Huang

first: Kai

first: Haonan

last: Zheng


title: Depressive patient-derived GABA interneurons reveal abnormal neural activity associated with HTR2C

city: Nanjing

first: Yan

state: Jiangsu

address: 101Longmian Avenue, Jiangning District

department: School of Pharmacy

institute: Nanjing Medical University

summary: Major depressive disorder with suicide behavior (sMDD) is a severe mood disorder, bringing tremendous burden to family and society. Although reduced gamma aminobutyric acid (GABA) level has been observed in postmortem tissues of sMDD patients, the molecular mechanism by which GABA levels are altered remains elusive. In this study, we generated induced pluripotent stem cells (iPSC) from five sMDD patients and differentiated the iPSCs to GABAergic interneurons and ventral forebrain organoids. sMDD GINs exhibited altered neuronal morphology and increased neural firing, as well as weakened calcium signaling propagation, compared to controls. Transcriptomic sequencing revealed a decreased expression of serotoninergic receptor 2C (5-HT2C) may cause the defected neuronal acitivity in sMDD. Furthermore, targeting 5-HT2C receptor, using a small molecule agonist or genetic approach, restored neuronal activity deficits in sMDD GINs. Our findings provide a human cellular model for studying the molecular mechanisms and drug discoveries for sMDD.

overall_design: For bulk RNA-seq, 3 patient cell lines vs. 3 control cell lines. For scRNA-seq, 1 patient cell line, 1 control cell line and 1 patient cell line with Trazodone hydrochloride.

first: Hong

last: Yuan


title: RNA Seq of passages of a small colony variant P. aeruginosa clinical isolate

status: Public on Nov 05 2022

city: Hanover

first: Susanne

last: Häußler

address: Feodor-Lynen-Str. 7

department: Molecular Bacteriology

institute: Twincore

summary:
Purpose : The goal of this study was to use RNA Seq to explore the correlation of gene expression of a collection of clinical P. aeruginosa isolates to various phenotypes, such as colony morphology, c-di-GMP production and biofilm formation
Methods : mRNA profiles were generated for Pseudomonas aerugionsa clinical samples by deep sequencing.Ribosomal RNA was removed by using the RiboZero Bacteria kit (Illumina). cDNA libraries were synthesized using the SMARTScribe Reverse Transcriptase (Takara) followed by a PCR enrichment using the AccuPrime HiFi Taq polymerase (Invitrogen). Enzymatic reactions were carried out in the presence of SUPERase·In™ RNase Inhibitor (Invitrogen); RNACleanXP beads (Agencourt) were used for all RNA purification steps. Quality checks were performed before, during and after cDNA library preparation with the RNA Nano Kit and an Agilent Bioanalyzer 2100 (Agilent Technologies). Libraries were sequenced on an Illumina NovaSeq 6000 (paired-end mode; 2 x 50 bp) and mRNA reads were trimmed using the tool ‘cutadapt’ (version 3.5) with customized settings and mapped to the NC_008463.1 (PA14) reference genome from NCBI using ‘bowtie2’ (version 2.3.5.1) with the settings “--very-sensitive-local; --no-mixed; --fr; --no-unal”.

overall_design:
mRNA profiles from Pseudomonas aeruginosa derived from liquid LB cultures grown to an OD600 = 2  and deep sequenced using Illumina HiSeq 2500
mRNA profiles from Pseudomonas aeruginosa derived from liquid LB cultures grown to an OD600 = 2  and deep sequenced using Illumina NovaSeq6000

first: Michal

last: Koska

first: Sven

last: Willger

first: Adrian

last: Kordes


title: DAP5 enables main ORF translation on mRNAs with structured and uORF-containing 5’ leaders

first: Ramona

last: Weber

department: Institute for Regenerative Medicine

institute: University of Zurich

summary: Half of mammalian transcripts contain short upstream open reading frames (uORFs) that potentially regulate translation of the downstream coding sequence (CDS). The molecular mechanisms governing these events remain poorly understood. Here, we find that the non-canonical initiation factor Death-associated protein 5 (DAP5 or eIF4G2) is required for translation initiation on select transcripts. Using ribosome profiling and luciferase-based reporters coupled with mutational analysis we show that DAP5-dependent translation occurs on messenger RNAs (mRNAs) with long, structure-prone 5′ leader sequences and persistent uORF translation. These mRNAs preferentially code for signalling factors such as kinases and phosphatases. We also report that cap/eIF4F- and eIF4A-dependent recruitment of DAP5 to the mRNA facilitates main CDS, but not uORF, translation suggesting a role for DAP5 in translation re-initiation. Our study reveals important mechanistic insights into how a non-canonical translation initiation factor involved in stem cell fate shapes the synthesis of specific signalling factors.

overall_design: Two cell types with two biological replicates analysed using RNA-Seq and Ribo-Seq

first: Cátia

last: Igreja


title: DNA methylation profiling of CNS tumors of the novel CNS embryonal tumor type ET, PLAGL

status: Public on Nov 04 2022

city: Heidelberg

first: Martin

last: Sill

address: Im Neuenheimer Feld 280

department: Division of Pediatric Neurooncology

institute: DKFZ

type: Methylation profiling by genome tiling array

summary: We have generated DNA methylation profiles for 31 human CNS tumors that represent our cohort of ET, PLAGL tumors

overall_design: 31 ET, PLAGL tumors were profiled on IlluminaHumanMethylation 450k and 850k arrays: 17 tumors with PLAGL2 amplification, 11 tumors with PLAGL1 amplification, 3 tumors without PLAGL1/2 amplification

first: Michaela

last: Keck

last: Solomon

last: Jones


title: NEDDylated-Cullin 3 mediates the adaptive response to topoisomerase 1 inhibitors (RNA-Seq)

city: Solna

first: Jan

middle: Eric

last: Grosser

address: Solnavägen 9

country: Sweden

institute: Karolinska institutet

summary: DNA topoisomerase 1 (Top1) inhibitors are mainstays of anticancer therapy. These drugs trap Top1 on DNA, stabilizing the Top1-cleavage complex (Top1-cc). The accumulation of Top1-ccs perturbs DNA replication fork progression, leading to DNA breaks and cell death. By analyzing the genomic occupancy and activity of Top1, we show that cells adapt to treatment with multiple doses of Top1 inhibitor by promoting the degradation of Top1-ccs, allowing cells to better tolerate subsequent doses of Top1 inhibitor. The E3-RING Cullin 3 Ligase in complex with the BTBD1 and BTBD2 adaptor proteins promote Top1-cc ubiquitination and subsequent proteasomal degradation. NEDDylation of Cullin 3 activates this pathway and inhibition of protein NEDDylation or depletion of Cullin 3 sensitizes cancer cells to Top1 inhibitors. Collectively, our data identify a novel NEDD8-Cullin 3 pathway involved in the adaptive response to Top1 inhibitors, which can be targeted to improve the efficacy of Top1 drugs in cancer therapy.

overall_design: Differential gene expression analysis of RNA-seq in hTERT RPE-1 cells untreated or treated with camptothecin pre-dose.

first: Alice

last: Meroni

first: Sumedha

last: Agashe

first: Natasha

last: Ramakrishnan

first: Jessica

last: Jackson

first: Priyanka

last: Verma

first: Laura

last: Baranello

first: Alessandro

last: Vindigni


title: NEDDylated-Cullin 3 mediates the adaptive response to topoisomerase 1 inhibitors

overall_design: Refer to individual Series


title: TATTOO-seq delineates spatial and cell type-specific regulatory programs in the developing limb

city: Chicago

first: François

last: Spitz

state: IL

address: 920 E 58th St

department: Department of Human Genetics

institute: University of Chicago

summary: The coordinated differentiation of progenitor cells into specialized cell types and their spatial organization into distinct domains is central to embryogenesis. Here, we applied a new unbiased spatially resolved single-cell transcriptomics method to identify the genetic programs underlying the emergence of specialized cell types during limb development and their spatial integration. We identify multiple transcription factors whose expression patterns are predominantly associated with cell type specification or spatial position, suggesting two parallel yet highly interconnected regulatory systems. We demonstrate that the embryonic limb undergoes a complex multi-scale re-organization upon perturbation of one of its spatial organizing centers, including the loss of specific cell populations, specific alterations of pre-existing cell states’ molecular identities and changes in their relative spatial distribution. Our study shows how multi-dimensional single-cell, spatially resolved molecular atlases can allow the deconvolution of spatial identity and cell fate and reveal the interconnected genetic networks that regulate organogenesis and its reorganization upon genetic alterations.

overall_design: Forelimb cells of the KikGR1 and KikGR1;DEL(PolL-SHFM) mice were sorted into 384-well plates by Fluorescence-activated cell sorting (FACS) and analyzed using scRNA-seq (MARS-Seq).

first: Sébastien

last: Bastide

first: Elad

last: Chomsky

first: Baptiste

last: Saudemont

first: Yann

last: Loe-Mie

first: Sandrine

last: Schmutz

first: Sophie

last: Novault

first: Heather

last: Marlow

first: Amos

last: Tanay


title: Surviving the host: microbial metabolic genes required for growth of Pseudomonas aeruginosa in physiologically-relevant conditions

city: Vancouver

first: Robert

middle: E. W.

last: Hancock

state: British Columbia

address: 2259 - Lower Mall Research Station

department: Department of Microbiology & Immunology

country: Canada

institute: University of British Columbia

summary: Here, we used a saturated transposon insertion mutant pool of P. aeruginosa strain PAO1 and transposon insertion sequencing (Tn-Seq), to identify genes conditionally important for survival under conditions mimicking the environment of a nosocomial infection. Conditions tested included tissue culture medium with and without human serum, a murine abscess model, and a human skin organoid model.

overall_design: Pseudomonas aeruginosa PAO1 TnSeq mutant pools were grown under physiologically-relevant conditions to identify genes conditionally essential to growth. Tested growth conditions included LB (planktonic), Mueller-Hinton Broth (MHB), RPMI supplemented with MHB (RPMI), RPMI supplemented with MHB and human serum (Serum), in-vivo murine skin abscess model that was left untreated (Abs_unt), and air-liquid interface human N/TERT skin organoid model (skin).

first: Corrie

last: Belanger

first: Melanie

last: Dostert

first: Travis

last: Blimkie

first: Amy

last: Lee

first: Bhavjinder

last: Dhillon

first: Bing

middle: C

last: Wu

first: Noushin

last: Akhoundsadegh

first: Negin

last: Rahanjam

first: Javier

last: Castillo-Arnemann

first: Reza

last: Falsafi

first: Daniel

last: Pletzer

first: Cara

last: Haney


title: NEDDylated-Cullin 3 mediates the adaptive response to topoisomerase 1 inhibitors (ChIP-Seq)

first: Jan

last: Grosser

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for Topoisomerase 1 (Top1) in hTERT RPE-1 cells.

first: Alice

last: Meroni

first: Sumedha

last: Agashe

first: Natasha

last: Ramakrishnan

first: Jessica

last: Jackson

first: Priyanka

last: Verma

first: Laura

last: Baranello

first: Alessandro

last: Vindigni


title: Single cell ATAC-seq of mouse hair follicle morphogenesis

city: Yangling

first: fang

last: li

state: Shaanxi

address: 22# Xinong Road

institute: Northwest A&F University

summary: Mouse, also known as a good model animals, is widely uaed in the research of hair follicle development. Unraveling the dynamic accessibility of regulatory chromatin at single-cell resolution is key to understanding stem/progenitor cell fate choices. and it's therefore of significance to investigate the chromatin accessibility and transcriptional  regulation mechanism during mouse hair follicle development.  To provides comprehensively understanding on the transcriptional  regulation mechanism and cell lineage cell fate decisions, we performed single-cell ATAC sequencing on  23,716 single cells from induction (embryonic day 13.5), organogenesis (embryonic day 16.5) and cytodifferentiation (postnatal day 0) stage fetus mouse dorsal skin. Based on unsupervised clustering analysis, cell lineage inference and etc, the single cell map of chromatin open area was drawn from each cell type and the mechanism of cell transcription regulation was explored. Collectively, our data here provide a reference for deeply exploring the epigenetic regulation mechanism of mouse hair follicles development.

overall_design: We performed single-cell ATAC sequencing on 23,716 single nuclear samples from induction (embryonic day 13.5), organogenesis (embryonic day 16.5) and cytodifferentiation (postnatal day 0) stage fetus C57BL/6 mouse dorsal skin.


title: Transcripts identified by microarray analysis that were deregulated in E14.5 Sox2(creERT2);Tbx2(fl/fl) (Sox2-Tbx2LOF) cochlear duct.

city: Hannover

first: Mark-Oliver

last: Trowe

address: Carl-Neuberg-Str. 1

department: Molekularbiologie

institute: Medizinische Hochschule Hannover

summary: Evaluation of transcriptional changes in the E14.5 cochlear duct epithelium upon tamoxifen-induced loss of Tbx2 in prosensory cells.

overall_design: Total RNA was extracted from E14.5 cochlear ducts of Sox2-Tbx2LOF and control embryos, after a single pulse of tamoxifen at E12.5, and analyzed by microarray analysis.

first: Andreas

last: Kispert

first: Marina

last: Kaiser


title: Macrophage extracellular traps originated from the vascular smooth muscle cells play key roles in atherosclerosis progression [RNA-seq]

first: Ming

last: Zhai

state: Massachusetts

address: Avenue Louis Pasteur

department: Cardiovascular Division, Department of Medicine

institute: Brigham and Women's Hospital

summary: Smooth muscle cells (SMC) play significant roles in atherosclerosis via phenotypic switching, a pathological process in which SMC transdifferentiation into macrophage-like SMCs. Furthermore, during transdifferentiation, the SMCs' expression of PADI4 upregulating and SMC generated extracellular trap, a web-like structure, which plays key role in the development of atherosclerosis plaque. To reveal the potential mechanism of the SMC derived macrophages generated ETs surducing surrounding SMCs within the media of artery during the process of atherosclerosis plaque development, we utilized the dsDNA and H3CIT protein to stimuli the SMCs, the SMC stimulated with 0.2%BSA as coontrol group, we collect the cells and did RNA-sequencing between two groups to find the potential signaling pathway participating in the process

overall_design: RNA-seq: mRNA profiles of RASMC stimulated with H3CIT+dsDNA or BSA as control


title: Macrophage extracellular traps originated from the vascular smooth muscle cells play key roles in atherosclerosis progression.

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

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus


title: Macrophage extracellular traps originated from the vascular smooth muscle cells play key roles in atherosclerosis progression [scRNA-seq]

summary: Smooth muscle cells (SMC) play significant roles in atherosclerosis via phenotypic switching, a pathological process in which SMC transdifferentiation into macrophage-like SMCs. Furthermore, during transdifferentiation, the SMCs' expression of PADI4 upregulating and SMC generated extracellular trap, a web-like structure, which plays key role in the development of atherosclerosis plaque. To reveal the function of SMC's generating ETs during atherosclerosis and to identify molecular targets for disease therapy, we combined SMC fate mapping and single-cell RNA sequencing of  mouse  atherosclerotic plaques.

overall_design: SMC-lineage tracing mice, B6-G/R; Myh11-CreERT2;Padi4(flox/flox) mice, were crossed onto B6-G/R Myh11cre group as control group and B6-G/R Myh11cre Padi4flox/flox group as case group to specific knock out the Padi4 within SMC. Mouse single cells digested from arterial tissues (including ascending aorta, brachiocephalic artery and thoracic aorta) for scRNA-seq were prepared from six mice of each group  at the same timepoint of Western diet (WD) feeding (26 weeks). Alive tdTomato+ cells (SMC-lineage cells) and ZsGreen cells (none-SMC linage cells) were sorted separately and were immediately subjected to scRNA-seq using Chromium Single Cell Gene Expression system (10x Genomics) in parallel.


title: LN-stem, tumor stem, tumor terminally differentiated CD8 T cells from human kidney cancer

status: Public on Nov 03 2022

first: Haydn

last: Kissick

address: 1462 Clifton Rd

institute: Emory University

summary: This work aimed to understand the source of TCF1+ CD8 T cells in tumors. By studying human tumor draining lymph-nodes (TDLNs), we find that CD8 T cells activate in TDLN but fail to acquire the normal effector program. Instead, these CD8 T cells share functional, transcriptional, and epigenetic traits with TCF1+ stem-like cells in the tumor. This suggests that these activated cells are a precursor to the stem-like CD8 T cells in tumors. By using mouse models, we show that tumor-specific CD8 T cells are activated in TDLN, but do not acquire an effector phenotype. These cells then migrate into the tumor where they require additional co-stimulation from antigen presenting cells to acquire the effector program. This is strikingly different from canonical CD8 T cell activation to acute viruses, where the effector program is acquired immediately. This model of T cell differentiation has important implications to improve immunotherapy.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
CD8 T cell populations were sorted from human PBMCs, lymph nodes, and tumor. RNA was extracted using qiagen micro all-prep columns. RNA was sequenced on an Illumina Hiseq 3000

Cell sorting was performed byFACS Aria II (BD Biosciences). For scRNA-seq (10x) of mouse samples live, CD3-CD19-Ly6G+ I-A/I-E+ cells were sorted from naïve LN, tumor-draining LN, and TRAMPC1-GP tumors. For human scRNA-seq (10x) fresh kidney tumors were used, antigen-presenting cells were sorted as live, CD45+, CD3-, HLADR+

first: Nataliya

last: Prokhnevska


title: Transcripts identified by microarray analysis that were deregulated in E18.5 Sox2(creERT2);Tbx2(fl/fl) (Sox2-Tbx2LOF) organ of Corti.

summary: Evaluation of transcriptional changes in the E18.5 organ of Corti upon tamoxifen-induced loss of Tbx2.

overall_design: Total RNA was extracted from E18.5 organs of Corti of Sox2-Tbx2LOF and control embryos, after a single pulse of tamoxifen at E16.5, and analyzed by microarray analysis.


title: Effect of the depletion of RBP33 (Tb927.8.990) on chromatin accesibility in bloodstream Trypanosoma brucei [ATAC-seq]

city: Armilla

first: Antonio

last: Estevez

state: Granada

address: Avda. del Conocimiento 17

department: Lopez-Neyra

country: Spain

institute: CSIC

summary: Depletion of RBP33 by RNAi does not seem to have profound effects on chromatin accesibility

overall_design: ATAC-seq was performed in the parental cell line (control samples) and in RBP33-depleted bloodstream trypanosomes after 48h of RNAi induction (RNAi samples). A genomic DNA control sample was treated in the same manner. There are three biological replicates for control and three biological replicates for RNAi, plus one sample for genomic DNA control.

last: Estévez


title: Gene expression profile at single cell level of hematopoietic stem and progenitor cells (HSPCs) from mouse bone marrow cultured in M3434 StemCell methylcellulose media

status: Public on Nov 02 2022

city: Nashville

first: Dalton

middle: Lee

last: Greenwood

state: TN

address: 2201 West End Ave

department: PMI

institute: Vanderbilt University

summary: Hematopoiesis generates a variety of cell types after M3434 culture. We treated HSPCs with small-molecule inhibitors of Acly (SB204990), Gls (CB-839), or Vehicle (DMSO) and compared them to freshly isolated HSPCs by single-cell RNA-seq and single-cell ATAC-seq to examine the diverse cell types emerging from these conditions.

overall_design: HSPCs were isolated by Lineage-depletion and c-Kit enrichment by MACS cell sorting and either cultured for 2 weeks in M3434 or isolated fresh from BL/6 mice and analyzed using scRNAseq or scATAC-seq.

first: Jeffrey

last: Rathmell


title: An avb3 integrin checkpoint is critical for efficient TH2 cytokine polarisation and potentiating antigen-specific immunity [RNA-seq]

city: Cambridge

first: Alastair

last: Crisp

address: Francis Crick Avenue

country: United Kingdom

institute: MRC Laboratory of Molecular Biology

summary:
To investigate the role of avb3 integrin in TH2 immunity.
We performed gene expression profiling analysis using control vs av-KO TH cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for control vs av-KO TH1 and TH2 cells.

first: Aydan

last: Szeto

first: Ana

last: Ferreira

first: Jonathan

last: Mannion

first: Paula

middle: A

last: Clark

first: Meera

last: Sivasubramaniam

first: Morgan

middle: W

last: Heycock

first: Helen

last: Jolin

first: Patrycja

last: Kozik

first: Martin

middle: D

last: Knolle

first: Andrew

middle: N

last: McKenzie


title: An avb3 integrin checkpoint is critical for efficient TH2 cytokine polarisation and potentiating antigen-specific immunity [ChIP-seq]

overall_design: ChIP-seq using anti-Gata3 antibody.


title: Co-depletion of NIPBL and WAPL balance cohesin activity to correct gene misexpression

city: Philadelphia

first: Jennifer

middle: Mary

last: Luppino

state: Pennsylvania

address: 415 Curie Blvd., Room: 570

department: Genetics

institute: University of Pennsylvania

summary: The relationship between cohesin-mediated chromatin looping and gene expression remains unclear. NIPBL and WAPL are two opposing regulators of cohesin activity; depletion of either is associated with changes in both chromatin folding and transcription across a wide range of cell types. However, a direct comparison of their individual and combined effects on gene expression in the same cell type is lacking. We find that NIPBL or WAPL depletion in human HCT116 cells each alter the expression of ~2,000 genes, with only ~30% of the genes shared between the conditions. We find that clusters of differentially expressed genes within the same topologically associated domain (TAD) show coordinated misexpression, suggesting some genomic domains are especially sensitive to either more or less cohesin. Finally, co-depletion of NIPBL and WAPL restores the majority of gene misexpression as compared to either knockdown alone. A similar set of NIPBL-sensitive genes are rescued following CTCF co-depletion. Together, this indicates that altered transcription due to reduced cohesin activity can be functionally offset by removal of either its negative regulator (WAPL) or the physical barriers (CTCF) that restrict loop-extrusion events.

overall_design:
PRO-seq was performed for two biological replicates each of a control sample, NIPBL knockdown, WAPL knockdown, CTCF knockdown, NIPBL and WAPL double knockdown, and CTCF and NIPBL double knockdown in the human colorectal cancer cell line, HCT-116

In situ Hi-C was performed for one biological replicate each of control siRNA treated HCT-116 cells.

RAD21 and CTCF ChIP-seq were performed in two biological replicates each of HCT-116 cells treated with control siRNA. In situ Hi-C was performed for one biological replicate each of control siRNA treated HCT-116 cells.

last: Field

first: Son

last: Nguyen

first: Daniel

middle: S

last: Park

first: Parisha

last: Shah

first: Richard

last: Abdill

first: Yemin

last: Lan

first: Rebecca

last: Yunker

first: Rajan

last: Jain

first: Karen

last: Adelman

first: Eric

middle: F

last: Joyce


title: Effect of Trpc1 or Trpc6 knockout on gene expressions in the hearts of endotoxemic mice

first: Wei

last: Cao

address: No.3 Taicheng Road

department: Department of Pharmacy

institute: School of Chemistry & Pharmacy, Northwest A&F University,

summary: To investigate the mechanism of TRPC1 or TRPC6 on the regulation of endotoxemic cardiac dysfunction, we established Trpc1-/- and Trpc6-/- mice. LPS-challenged endotoxemic mouse model was built, and the gene expression profile was analyzed using data obtained from RNA-seq of WT, LPS-challenged WT, LPS-challenged Trpc1-/-, and LPS-challenged Trpc6-/- mice hearts.

overall_design: Comparative gene expression profiling analysis about RNA-seq data for three mice hearts of control and endotoxemic mouse model. The groups are as follows, WT+vehicle, WT+LPS, Trpc1-/-+LPS, and Trpc6-/-+LPS.

last: Tang

first: Wen

last: Tian

first: Xiao-Qiang

last: Li


title: The RNA-binding protein RBP33 dampens non-productive transcription in trypanosomes

first: Antonio

last: Estevez


title: Breast cancer prevention by short-term inhibition of TGFβ signaling

first: Kornelia

last: Polyak

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary: Cancer prevention has a profound impact on cancer-associated mortality and morbidity. We previously identified TGFβ signaling as a candidate regulator of mammary epithelial cells associated with breast cancer risk. Here, we show that short-term TGFBR inhibitor (TGFBRi) treatment of peripubertal ACI inbred and Sprague Dawley outbred rats induces lasting changes and prevents estrogen- and carcinogen-induced mammary tumors, respectively. We identify TGFBRi-responsive cell populations by single cell RNA-sequencing, including a unique epithelial subpopulation designated secretory basal cells (SBCs) with progenitor features. We detect SBCs in normal human breast tissues and find them to be associated with breast cancer risk. Interactome analysis identifies SBCs as the most interactive cell population and the main source of insulin-IGF signaling. Accordingly, inhibition of TGFBR and IGF1R decrease proliferation of organoid cultures. Our results reveal a critical role for TGFβ in regulating mammary epithelial cells relevant to breast cancer and serve as a proof-of-principle cancer prevention strategy.

overall_design: Examination of changes in the mammary gland (normal and tumor) epithelium and immune cells, after treatment with a TGFBR inhibitor/vehicle on peripubertal ACI and SD rats  in the context of tumor prevention.

first: Simona

last: Cristea

first: Franziska

last: Michor

first: Masa

last: Aleckovic

first: Carlos

last: Gil Del Alcazar


title: Effect of the depletion of RBP33 (Tb927.8.990) on the transcriptome of bloodstream and procyclic Trypanosome brucei [RNA-seq]

summary: RBP33 depletion results in the overexpression of 40% (bloodstream) or 20% (procyclic) of all transcripts annotated in the 427 2018 genome

overall_design: Total RNA was obtained from control or RBP33-depleted trypanosomes after 48h of RNAi induction. Three biological replicates for control and three biological replicates for RNAi = 6 samples from bloodstream forms and another 6 samples from procyclic forms.

last: Estévez


title: Dual RNA-seq of chlamydial and host cell transcriptomes during nutritional stress

city: New Haven

first: Eduardo

last: Groisman

state: Connecticut

address: Boyer Center for Molecular Medicine, 295 Congress Ave

department: Department of Microbial Pathogenesis

institute: Yale School of Medicine

summary: We utilized host-pathogen dual RNA-sequencing to elucidate the transcriptomes of both Chlamydia trachomatis and the infected HeLa cell during nutritional conditions that induce persistence.

sample_organism:
Homo sapiens
Chlamydia trachomatis L2/434/Bu

overall_design: We examined two different conditions, iron (by chelation with 2,2-bipyridyl) and media-defined tryptophan starvation, under two treatment regimes: one which started at the time of infection, and one which began at 8 hpi to allow for the establishment of a productive infection.

first: Nick

last: Pokorzynski

first: Rey

last: Carabeo


title: Genome-wide CRISPR screen reveals a key role for integrin avb3 in TH2 cell polarisation.

first: Alastair

last: Crisp

overall_design: Refer to individual Series


title: Stellate cell expression of SPARC-related modular calcium-binding protein 2 is associated with human non-alcoholic fatty liver disease severity

city: Odense M

first: Kim

last: Ravnskjaer

address: Campusvej 55

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

summary: Non-alcoholic fatty liver disease (NAFLD) and its progressive form, non-alcoholic steatohepatitis (NASH), are the hepatic manifestations of metabolic syndrome. Histological assessment of liver biopsies is the gold standard for diagnosis of NASH. A Liver biopsy is resource heavy and can lead to complications such as bleeding and, moreover, does not fully capture the tissue heterogeneity of the fibrotic liver. Therefore, non-invasive biomarkers that can reflect an integrated state of the liver is highly needed to improve diagnosis and sampling bias. Hepatic stellate cells (HSCs) are central in development of hepatic fibrosis, a hallmark of NASH. Secreted HSC-specific proteins may, therefore, reflect disease state in the NASH liver and thereby serve as non-invasive diagnostic biomarkers. We performed RNA-sequencing on liver biopsies from a discovery cohort (n = 30) of histological characterised obese patients (body mass index > 35 kg/m2) to identify and evaluate HSC-specific genes encoding secreted proteins. Bioinformatical analysis was used to identify potential biomarkers and their expression at single-cell resolution. We validated our findings by single-molecule fluorescence in situ hybridization (smFISH) and ELISA to detect mRNA in liver tissue and protein levels in plasma, respectively. Hepatic expression of SPARC-related modular calcium-binding protein 2 (SMOC2) was increased in NASH (steatosis ≥ 1, lobular inflammation ≥ 1, and hepatocyte ballooning ≥ 1) compared no-NAFLD (p.adj < 0.001). Single-cell RNA-sequencing data indicated SMOC2 expression by HSCs, which was validated using smFISH. Moreover, plasma SMOC2 was elevated in NASH compared to no-NAFLD (p < 0.001) with a predictive accuracy of AUROC 0.88. In conclusion, we propose increased SMOC2 in plasma reflects HSC activation, a key cellular event associated with NASH progression, and may serve as a non-invasive biomarker of NASH.

overall_design: 30 RNAlater and snap-frozen samples were processed for RNA sequencing on the Illumina NovaSeq6000 platform

first: K

first: L

last: Groentved

first: F

middle: T

last: Larsen


title: RNA-Seq of delta-cyaA E.coli mutant at 10 different cAMP concentration

city: Bangalore

first: Shweta

last: Chakraborty

state: Karnataka

address: Rajiv Gandhi Nagar, Kodigehalli

country: India

institute: National Centre for Biological Sciences

summary: Most research involved in studying the response of gene expression to cAMP have done so under binary states, that is, presence and absence of cAMP in the cell. However, cAMP concentrations in the cell have been reported to vary in a continuous fashion. Systematic studies of global transcription response to continuous changes in intracellular cAMP are largely missing. Here, we study the gene expression kinetics of the E.coli transcriptome in response to an increasing exposure to cAMP.

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

overall_design: We treated delta-cyaA E.coli cells, that cannot make intracellular cAMP, with 10 different concentrations of extracellular cAMP ranging from 0 to 4mM cAMP and performed RNA-seq at each cAMP concentration. We determined the effect of increasing cAMP on the expression of a gene by calculating its foldchange at that cAMP concentration compared to the 0mM delta-cyaA mutant state.

first: Aalap

last: Mogre

first: Aswin

last: Narain Seshasayee


title: RNA-seq analysis of uterine flushing fluids of three donor and recipient Xianan cows 7 days after fertilization

status: Public on Nov 01 2022

city: Zhengzhou

first: Shijie

last: Lyu

address: Huayuan Road 116

institute: Henan Academy of Agricultural Sciences

summary: To explore the role of miRNAs in intrauterine exosomes in cattle pregnancy, we analyzed the expression levels of the exosomal miRNAs in Xianan cows, a beef cattle breed in China.

overall_design: Comparative miRNAs expression profiling analysis of RNA-seq data for three donor and recipient cows

first: Eryao

last: Wang

first: Yaying

last: Zhai


title: Ecto-5’-Nucleotidase (Nt5e/CD73)-Mediated Adenosine Signaling Attenuates TGFβ-2 Induced Elastin and Cellular Contraction

city: Pittsburgh

first: Rolando

middle: Andres

last: Cuevas

state: PA

address: W1744 1 BST MEDICINE

department: Medicine

institute: University of Pittsburgh

summary: To investigate the broad transcriptional consequences of Nt5e knock-out on mice vascular smooth cells in culture at baseline.

overall_design: Differenctial gene expression profiling analysis was genetaed using the RNA-seq output of 6 diffrernt cell samples by RNA-seq at baseline after 48h of growing at 0.5% FBS (starvation media)

first: Rolandfo

first: Cynthia

last: St. Hilaire


title: Prostate cancer androgen receptor activity dictates efficacy of bipolar androgen therapy through MYC [RNA-seq]

city: Baltimore

first: Immunometabolism

last: Department

state: Maryland

address: 1650 Orleans Street

department: Immunometabolism

institute: Johns Hopkins University

summary: Testosterone is the canonical growth factor of prostate cancer but can paradoxically suppress its growth when present at supraphysiological levels. We have previously demonstrated that the cyclical administration of supraphysiological androgen (SPA), entitled Bipolar Androgen Therapy (BAT), can result in tumor regression and clinical benefit for patients with castration-resistant prostate cancer. However, predictors and mechanisms of response and resistance have been ill-defined. Here we show that growth inhibition of prostate cancer models by SPA requires high androgen receptor (AR) activity and is driven in part by downregulation of MYC. Using matched sequential patient biopsies, we show that high pre-treatment AR activity predicts downregulation of MYC, clinical response, and prolonged progression-free and overall survival for patients on BAT. BAT induced strong downregulation of AR in all patients, which is shown to be a primary mechanism of acquired resistance to SPA. Acquired resistance can be overcome by alternating SPA with the AR inhibitor enzalutamide, which induces adaptive upregulation of AR and re-sensitizes prostate cancer to SPA. This work identifies high AR activity score as a predictive biomarker of response to BAT and supports a new treatment paradigm for prostate cancer involving alternating between AR inhibition and activation

overall_design: LNCaP were culture in the absence of presence of supraphysiological androgen using 10nM R1881 for 5 and 26 days. 2 biological replicates were isolated, processed and analyzed.

first: Laura

last: Sena

first: David

middle: E

last: Sanin


title: Genome-wide CRISPR screen reveals a key role for integrin avb3 in TH2 cell polarisation [CRISPRscr]

first: Alastair

summary: T helper 2 (TH2) cells play critical roles in protective immunity against parasitic helminth infections and in tissue repair. However, misdirected TH2 cell responses promote allergy and asthma. Using whole-genome CRISPR-Cas9 screens in developing TH2 cells we defined a functional TH2ome for TH2 differentiation and validated a diverse array of molecules not previously linked to TH2 cell development and function. Strikingly, we discovered that integrin avb3 plays a key and previously unappreciated role in the differential polarisation of TH2 cells and their type 2 cytokine expression.  Conversely, we did not identify the LFA-1 integrin which mediates inside-out signalling following TCR ligation as part of the T cell synapse and preferentially promotes TH1 differentiation. We find that TH2 cell expression of integrin avb3 is required for the formation of TH2 cell clusters that exhibit enhanced T cell activation, promoting proliferation and TH2 cell differentiation, and thereby potentiating antigen-driven TH2 cell responses.

overall_design: Transcriptomic analyses of sorted T helper cell populations with CRISPR- or flox mediated knockout.

first: Aydan

last: Szeto

first: Ana

last: Ferreira

first: Jonathan

last: Mannion

first: Paula

last: Clark

first: Meera

last: Sivasubramaniam

first: Morgan

last: Heycock

first: Helen

last: Jolin

first: Patrycja

last: Kozik

first: Andrew

last: McKenzie


title: Identification of underexplored mesenchymal and vascular-related cell populations in human skeletal muscle

city: Halifax

first: Adam

last: Johnston

state: NS

address: 1344 Summer Street

department: Medical Neuroscience

institute: Dalhousie University

summary: Skeletal muscle repair and maintenance are directly and indirectly supported by stromal populations such as vascular cells and fibro-adiopgenic progenitors (FAPs), a subset of which express Twist2 and possess direct myogenic potential in rodents. However, less is understood of the complexity and heterogeneity of human skeletal muscle stromal cells. To this end, we performed single-cell RNA-sequencing on ~2000 cells isolated from the human semitendinosus muscle of young individuals. This demonstrated the presence of two poorly described cell populations. First, we detected a vascular-related cell type that expressed pericyte and pan-endothelial genes that we localized to large blood vessels within skeletal muscle cross-sections and termed endothelial-like pericytes (ELPCs). RNA velocity analysis demonstrated that ELPCs may represent a "transition state" between endothelial cells and pericytes. Analysis of published single-cell RNA-seq datasets revealed evidence for ELPCs in trunk and heart musculature, which showed transcriptional similarity. Additionally, we identified a subset of FAPs expressing TWIST2 mRNA and protein. Human TWIST2-expressing cells were anatomically and transcriptionally comparable to mouse Twist2 cells as they were restricted to the myofiber interstitium, expressed fibrogenic genes but lacked satellite cell markers and colocalized with the FAPs marker PDGFRα in human muscle cross-sections. Taken together, these results highlight the complexity of stromal cells residing in human skeletal muscle and support the utility of single-cell RNA-sequencing for discovery and characterization of poorly described cell populations.

overall_design: Semitendinosus muscle was collected from consenting young adults (n = 5; 2 males, 3 females, mean age = 23.4 years) undergoing routine orthopedic surgery for anterior cruciate ligament repair and sequenced following dissociation into single cells using 10x Genomics' Chromium single-cell platform (v3).

first: Griffen

middle: M

last: Wakelin

first: Alasdair

last: Cameron

middle: P


title: Prostate cancer androgen receptor activity dictates efficacy of bipolar androgen therapy through MYC [ATAC-seq]


title: Modeling ischemic cholangiopathy in human cholangiocyte organoid for screening of novel cholangio-protective agents

city: Rotterdam

first: Henk

middle: P.

last: Roest

state: Choose State

address: Doctor Molewaterplein 40

department: Surgery

country: Netherlands

institute: Erasmus MC

summary: Ischemic cholangiopathy refers to biliary damage caused by disruption of blood supply in the peribiliary plexus. Detailed knowledge of ischemic cholangiopathy pathogenesis remains scarce due to the lack of appropriate in vitro models. We aimed to recapitulate ischemia-evoked biliary damage using human intrahepatic cholangiocyte organoids (ICOs) in vitro for the study of ischemic cholangiopathy and preclinical drug discovery. In our study, we found that ICOs can recapitulate ischemic cholangiopathy in vitro, featured by extensive apoptosis and reduced cell proliferation, which could be partially restored by reoxygenation. AAT is identified as a novel cholangiocellular protective agent by restoring proliferation and preventing apoptosis.

overall_design: Examine the transcriptional profiles of human cholangiocyte organoids cultured under different oxygen concentrations, including normoxia (21%), hypoxia (1%) and hypoxia followed by reoxygenation (1% to 21%).

first: Shaojun

last: Shi

first: Monique

last: Verstegen

first: Luc

middle: J

last: van der Laan


title: Transcriptome analysis of in vitro hematopoietic stem cells (HSC) and stage 3 (ST3) NK cell progenitors cells expressing a IRF2-specific shRNA.

city: Ghent

first: Georges

last: Leclercq

address: C. Heymanslaan

country: Belgium

institute: Ghent University

summary: To investigate the function of IRF2 in the regulation of natural killer (NK) cell differentiation, we established in vitro NK cell differentation cultures starting with cordblood derived HSC in which IRF2 has been knocked down with shRNA by lentiviral transduction. We then performed transcriptome analysis of the HSC population at day 3 and ST3 population at day 7.

overall_design: mRNA profile of HSC (d3) and ST3 (d7) transduced with shIRF2 in comparison to control transduced cells

first: Eva

last: Persyn

first: Wouter

last: Van Loocke


title: microRNA expression in serum exosomes from Caucasian and African American breast cancer patients

city: Winston Salem

first: Dan

last: Zhao

state: NC

address: 1 Medical Center Blvd

department: Cancer Biology

institute: Wake Forest University School of Medicine

summary: There is drastic racial disparities between Caucasian (CA) and African American (AA) for breast cancer. Circulating microRNAs exhibit stability and may serve as biomarkers in clinical settings. To discover potential microRNAs that mediate intercellular crosstalk and as biomarkers underlying the breast cancer racial disparity, serum exosomes from CA and AA were extracted and analyzed for its microRNA contents using small RNA sequencing.

overall_design: Exosomes from 6 pooled serum samples each from CA and AA cancer patients were isolated by Exoquick. RNA were isolated using the RNeasy Micro Kit (Qiagen) and subjected to library construction and Illumina sequencing.

first: Kerui

last: Wu

first: Shih

middle: Y

first: Tyagi

last: Abhishek

first: Pramond

last: Deshpande

first: Kounosuke

last: Watabe


title: Concurrent inhibition of CDK2 adds to the anti-tumor activity of CDK4/6 inhibition in GIST

city: Boston

first: Inga-Marie

last: Schaefer

state: MA

address: 75 Francis Street

department: Department of Pathology

institute: Brigham and Women's Hospital

summary: Background: Advanced gastrointestinal stromal tumor (GIST) is characterized by genomic perturbations of key cell cycle regulators. Oncogenic activation of CDK4/6 results in RB1 inactivation and cell cycle progression. Given that single-agent CDK4/6 inhibitor therapy failed to show clinical activity in advanced GIST, we evaluated strategies for maximizing response to therapeutic CDK4/6 inhibition.  Methods: Targeted next-generation sequencing and multiplexed protein imaging were used to detect cell cycle regulator aberrations in GIST clinical samples. The impact of inhibitors of CDK2, CDK4, and CDK2/4/6 was determined through cell proliferation and protein detection assays. CDK-inhibitor resistance mechanisms were characterized in GIST cell lines after long-term exposure.  Results: We identify recurrent genomic aberrations in cell cycle regulators causing co-activation of the CDK2 and CDK4/6 pathways in clinical GIST samples. Therapeutic co-targeting of CDK2 and CDK4/6 is synergistic in GIST cell lines with intact RB1, through inhibition of RB1 hyperphosphorylation and cell proliferation. Moreover, RB1 inactivation and a novel oncogenic cyclin D1 resulting from an intragenic rearrangement (CCND1::chr11.g:70025223) are mechanisms of acquired CDK inhibitor resistance in GIST.  Conclusions: These studies establish the biologic rationale for CDK2 and CDK4/6 co-inhibition as therapeutic strategy in patients with advanced GIST, including metastatic GIST progressing on tyrosine kinase inhibitors.

overall_design: We performed RNA sequencing analysis to determine the effects of CDK4/6 inhibition on the transcriptomic landscape in GIST430/654 parental cells, and the palbociclib-resistant GIST430/654/RB1- and GIST430/654/CCND1 fusion sub-lines treated with palbociclib versus DMSO control (24h).

first: Matthew

middle: L

last: Hemming


title: RNAseq analysis of CD4+EGFP+ and CD8+EGFP+ regulatory T cells

city: Nantes

first: Victor

last: GOURAIN

address: 30 Bd Jean Monnet

institute: Centre de recherche en transplantation et immunologie

summary: Gene-edited rats were generated in which EGFP was placed under the transcriptional control of the Foxp3 promoter. EGFP expression by CD4+ and CD8+ T cells allowed to define regulatory T cells (Treg) in both T cell compartments. This Foxp3-EGFP rats constitute a useful model to identify CD4+ and CD8+ natural and induced Treg. Transcriptomic analyses showed similarities but also differences among CD4+ and CD8+ EGFP+ cells, this being the first description of the transcriptomic profile in natural FOXP3+ CD8+ Treg.

overall_design: CD4+ and CD8+ Treg were defined by their cell surface markers (CD25high and CD127low) and (CD45RClow/-), respectively and EGFP was then used as a marker of Treg to define populations of EGFP+ and EGFP- cells within each of the Treg subsets. RNAseq analysis of this 4 populations of cells was performed.

first: Ignacio

last: Anegon

first: Séverine

last: Ménoret

last: Gourain


title: Diverse but unique astrocytic phenotypes during embryonic stem cell differentiation, culturing and aging

city: Berlin

first: Andranik

last: Ivanov

address: Chariteplatz 1

department: Core Unit Bioinformatics

institute: Berlin Institute of Health

summary: We report a side-by-side-comparison of embryonic stem cell (ESC)-derived astrocytes as well as primary neonatal and adult astrocytes, revealing major differences on a functional and transcriptomic level

overall_design: Examination of transcriptomic profile changes of murine astrocytes upon culturing, aging and embryonic stem cell origin

first: Kiara

last: Freitag

first: Pascale

last: Eede

first: Tatiana

last: Borodina

first: Sascha

last: Sauer

first: Dieter

last: Beule

first: Frank

last: Heppner


title: Chromatin-associated Microprocessor assembly is regulated by PRP40 – U1 snRNP auxiliary protein

city: Poznan

first: Jakub

middle: Jacek

last: Dolata

address: Uniwersytetu Poznanskiego 6

department: Department of Gene Expression

country: Poland

institute: Adam Mickiewicz University

summary: In order to assess the possible effects of prp40ab double mutant on co-transcriptional miRNA biogenesis, small RNA sequencing was performed as well as RNA PolII and DCL1 distribution were tested on MIR genes (ChIPseq).

overall_design: Examination of miRNA biogenesis and RNA PolII, DCL1 distribution in prp40ab mutant

first: Agata

last: Stepien

first: Dawid

last: Bielewicz

first: Artrur

last: Jarmolowski


title: RNA Sequencing of HEK293T cells expressing a Dual-specificity Aptamer that specifically increases O-GlcNAcylation on beta-catenin

first: Yi

last: Zhu

address: 511 WBSB, 725 N. Wolfe St.

department: Biological Chemistry

institute: Johns Hopkins University, School of Medicine

summary: O-GlcNAc is a dynamic post-translational modification on thousands of intracellular proteins, it regulates protein functions and is involved in many metabolic diseases. Using a dual-specificity aptamer, we targeted the O-GlcNAc transferase (OGT) to endogenous β-catenin and specifically increased O-GlcNAcylation of β-catenin. To study how O-GlcNAcylation of β-catenin regulates the transcriptome, we performed RNA sequencing on HEK293T cells expressing individual (Ctrl.) or dual-specificity aptamers. We found that O-GlcNAcylation of β-catenin shifts the transcriptome in a Wnt-dependent manner: it repressed the expression of about 100 genes in the absence of Wnt, while it activated the expression of these genes when Wnt signaling was turned on.

overall_design: 12 samples from 4 groups of HEK293T cells were analyzed: cells were expressing Ctrl (T1 ∙ bc339) or Dual-specificity (3JB8F+12) aptamers and exposed to Wnt- or Wnt+ medium. Each group contains 3 replicates.

first: Gerald

last: Hart


title: The bone marrow niche regulates redox and energy balance in leukemia stem cells

city: Pamplona

first: Itziar

last: Cenzano

state: Navarra

address: Avenida de Pio XII, 55

institute: CIMA Universidad de Navarra

summary: The Cxcr4-Cxcl12 axis has been postulated as a critical pathway dictating leukemia stem cell (LSCs) chemoresistance in AML due to its role in controlling cellular egress from the marrow. Nevertheless, the cellular source of Cxcl12 in the AML microenvironment and the mechanism by which Cxcl12 exert its protective role in AML in vivo remain unresolved. We have evaluated the functional role of Cxcl12 secreted by early mesenchymal stromal cells (MSCs) and osteolineage committed cells in acute myeloid leukemia (AML) maintenance in vivo. Our results demonstrate that early MSCs, in contrast to committed osteoblasts, are integral part of the MLL::AF9 derived AML niche and control LSCs maintenance through Cxcl12 secretion. Cxcl12 from MSCs regulates the oxidative state of LSCs and promotes energy metabolism. Furthermore, the protective role of the niche through the activation of the CXCL12-CXCR4 axis, may also represent a biological hallmark in human pediatric and adult AML, hence, reinforcing the notion that targeting the MSCs-derived CXCL12 may help eradicate leukemia.

overall_design: LSCs mRNA profiles from Prx1-Cxcl12-Ctrl and Prx1-Cxcl12-Mut mice (n=2 technical replicates of 9 mice and 7000 cells/mouse) 30 days post leukemia induction.

first: Borja

last: Saez

first: Felipe

last: Prosper


title: Genome-wide CRISPR screen reveals a key role for integrin avb3 in TH2 cell polarisation [RNA-seq I]

city: Cambridge

first: Alastair

last: Crisp

address: Francis Crick Avenue

institute: MRC Laboratory of Molecular Biology

first: Aydan

middle: C

last: Szeto

first: Ana

last: Ferreira

first: Jonathan

last: Mannion

first: Paula

middle: A

last: Clark

first: Meera

last: Sivasubramaniam

first: Morgan

last: Heycock

first: Helen

last: Jolin

first: Patrycja

last: Kozik

first: Andrew

last: McKenzie


title: γδ T cells are effectors of immunotherapy in cancers with HLA class I defects

city: Leiden

first: Natasja

middle: de

last: Vries

address: Albinusdreef 2

institute: Leiden University Medical Center

summary: DNA mismatch repair deficient (MMR-d) cancers present an abundance of neoantigens that likely underlies their exceptional responsiveness to immune checkpoint blockade (ICB). However, MMR-d colon cancers that evade CD8+ T cells through loss of Human Leukocyte Antigen (HLA) class I-mediated antigen presentation frequently remain responsive to ICB, suggesting the involvement of other immune effector cells.

overall_design: We performed single-cell RNA-sequencing on γδ T cells isolated from five treatment-naive MMR-deficient colon cancers, to invesigate which γδ T cell subsets are present and what their functional characteristics are.

last: de Vries

first: Dina

last: Ruano

first: Noel

last: de Miranda


title: miRNAs expression of  prostate cancer with neoadjuvant hormonal therapy

city: Jinan

first: Jing

last: Hu

address: Wenhua xi road

institute: Shandong University

summary: The aim of this research was to identify  miRNAs that are  associated with neoadjuvant hormonal therapy resisitance in prostate cancer.

overall_design: miRNA expression profiling  was performed on prostate cancer with  neoadjuvant hormonal therapy resistant  (n=5) and -sensitive tissues (n=5).

first: Xueli

last: Wang

first: Bo

last: Han


title: RNA Sequencing of HEK293T cells expressing a Dual-specificity Aptamer that specifically increases O-GlcNAcylation on beta-catenin when O-GlcNAc transferase was inhibited

first: Yi

last: Zhu

summary: O-GlcNAc is a dynamic post-translational modification on thousands of intracellular proteins, it regulates protein functions and is involved in many metabolic diseases. Using a dual-specificity aptamer, we targeted the O-GlcNAc transferase (OGT) to endogenous β-catenin and specifically increased O-GlcNAcylation of β-catenin. To study how O-GlcNAcylation of β-catenin regulates the transcriptome, we performed RNA sequencing on HEK293T cells expressing individual (Ctrl.) or dual-specificity aptamers. We found that O-GlcNAcylation of β-catenin shifts the transcriptome in a Wnt-dependent manner: it repressed the expression of about 100 genes in the absence of Wnt, while it activated the expression of these genes when Wnt signaling was turned on. This dataset is from the control experiment in which all samples were treated with the OGT inhibitor Ac5S.

overall_design: 12 samples from 4 groups of HEK293T cells were analyzed: cells expressing Ctrl (T1 ∙ bc339) or Dual-specificity (3JB8F+12) aptamers were exposed to Wnt- or Wnt+ medium. Each group contains 3 replicates. Cells in all replicates were treated with an OGT inhibitor (Ac5S).

first: Gerald

middle: W

last: Hart


title: Global landscape of replicative DNA polymerase usage in the human genome

city: Tokyo

first: Yasukazu

last: Daigaku

address: 3-8-31 Ariake Koto-ku

department: Cancer institute

institute: Japanese Foundation for Cancer Research

summary: The division of labour between DNA polymerase underlies the accuracy and efficiency of replication. However, the roles of replicative polymerases have not been directly established in human cells. We developed polymerase usage sequence (Pu-seq) in HCT116 cells and mapped Polε and Polα usage genome wide. The polymerase usage profiles show Polε synthesises the leading strand and Polα contributes mainly to lagging strand synthesis. Combining the Polε and Polα profiles, we accurately predict the genome-wide pattern of fork directionality, plus zones of replication initiation and termination. We confirm that transcriptional activity contributes toshapes  the patterns of initiation and termination and, by separately analysing the effect of transcription ofon both both  co-directional and converging forks, demonstrate that coupled DNA synthesis of leading and lagging strands in both co-directional and convergent forks is compromised by transcription. Polymerase uncoupling is particularly evident in the vicinity of large genes, including the two most unstable common fragile sites, FRA3B and FRA3D, thus linking transcription-induced polymerase uncoupling to chromosomal instability.

overall_design: We mapped ribonucleotide-incorporation by the mutated DNA polymerase α and ε (POLE1-M630F and POLA1-Y865F) at single-nucleotide resolution in HCT116 cells and subsequent informatics analysis was performed to generate datasets listed here.

first: Eri

last: Koyanagi

first: Yoko

last: Kakimoto

first: Tamiko

last: Minamisawa


title: The dynamic effec of genetic variation on the in vivo ER stress transcriptional response in different tissues

city: Salt Lake City

first: Clement

last: Chow

state: UT

address: EIHG 5200 15 North 2030 East

institute: University of Utah

summary: The genetic regulation of gene expression varies greatly across tissue-type and individuals and can be strongly influenced by the environment. Many variants, under healthy control conditions, may be silent or even have the opposite effect under diseased stress conditions. This study uses an in vivo mouse model to investigate how the effect of genetic variation changes with cellular stress across different tissues. Endoplasmic reticulum (ER) stress occurs when misfolded proteins accumulate in the ER. This triggers the unfolded protein response (UPR), a large transcriptional response which attempts to restore homeostasis. This transcriptional response, despite being a conserved, basic cellular process, is highly variable across different genetic backgrounds, making it an ideal system to study the dynamic effects of genetic variation. In this study, we sought to better understand how genetic variation alters expression across tissues, in the presence and absence of ER stress. The use of different mouse strains and their F1s allow us to also identify context specific cis- and trans- regulatory variation underlying variable transcriptional responses. We found hundreds of genes that respond to ER stress in a tissue- and/or genotype-dependent manner. The majority of the regulatory effects we identified were acting in cis-, which in turn, contribute to the variable ER stress- and tissue-specific transcriptional response. This study demonstrates the need for incorporating environmental stressors across multiple different tissues in future studies to better elucidate the effect of any particular genetic factor in basic biological pathways, like the ER stress response.

overall_design: Examination of both control and TM treated livers and kidneys of B6, CAST, and F1 hybrid mice.

first: Nikki

middle: D

last: Russell


title: Age-dependent Lamin remodeling induces cardiac dysfunction via dysregulation of cardiac transcriptional programs [ATAC-Seq]

city: La Jolla

first: Adam

middle: Jeffrey

last: Engler

state: CA

address: 9500 Gilman Drive, MC 0412

department: Bioengineering

institute: UC San Diego

summary: As we age, structural changes contribute to progressive decline in organ function, which in the heart acts through poorly characterized mechanisms. Utilizing the rapidly aging fruit fly model with its significant homology to the human cardiac proteome, we found that cardiomyocytes exhibit progressive loss of Lamin C (mammalian Lamin A/C homologue) with age. Unlike other tissues and laminopathies, we observe decreasing nuclear size, while nuclear stiffness increases. Premature genetic reduction of Lamin C phenocopies aging’s effects on the nucleus, and subsequently decreases heart contractility and sarcomere organization. Surprisingly, Lamin C reduction downregulates myogenic transcription factors and cytoskeletal regulators, possibly via reduced chromatin accessibility. Subsequently, we find an adult-specific role for cardiac transcription factors and show that maintenance of Lamin C sustains their expression and prevents age-dependent cardiac decline. Our findings are conserved in aged non-human primates and mice, demonstrating age-dependent nuclear remodeling is a major mechanism contributing to cardiac dysfunction.

overall_design: Bulk ATAC-Sequencing of Drosophila melanogaster isolated hearts, conducted for control flies, w1118, at 1 week of age (n = 3) and 5 weeks of age (n = 3); Hand-Gal4 x attp2 control flies (n = 4) and Hand-Gal4 x LamC RNAi flies (n = 3) at 1 week of age; and Hand-Gal4 x attp40 control flies (n = 3) and Hand-Gal4 x LamB RNAi flies (n = 4) at 1 week of age. The purpose of sequencing was to identify differentially accessible regions that are common between aging and Lamin C RNAi expressing flies, and aging and Lamin B RNAi expressing flies.

first: Natalie

last: Kirkland