title: Preconception Paternal Alcohol Exposure Decreases IVF Embryo Survival and Pregnancy Success Rates in a Mouse Model

city: College Station

first: Michael

last: Golding

state: Texas

address: Veterinary Research Building, Bldg 1197, Rm 334, 588 Raymond Stotzer Pkwy

department: Veterinary Physiology & Pharmacology

institute: Texas A&M University

summary: In this study, we describe the use of high-throughput sequencing to investigate the developmental basis of preimplantation embryos sired by alcohol-exposed males through in vitro fertilization (IVF). We exposed C57BL/6J male mice to one of three treatment groups. Sexually mature males were randomly selected to voluntarily consume 0% ethanol (control), 6% ethanol, or 10% ethanol for ten weeks. After treatment, the males were sacrificed for sperm collection and cryopreservation for IVF procedures. C57BL/6J donor females remained naïve to alcohol and were synchronized and superovulated before being sacrificed for oocyte collection. Oocytes underwent IVF with the cryopreserved semen and incubated until they reached the morula stage. The morulae sired by ethanol-exposed sperm exhibited altered transcriptional signatures compared to the control-sired morulae. Quick Biology Inc. sequencing core isolated total RNA from three pools (10-15 cells) of unsexed morulae from each control and ethanol preconception treatment. After obtaining the sequencing data, we conducted deep-sequencing analyses of the morulae transcriptomes. This experiment revealed sire alcohol consumption modifies preimplantation embryo genetic pathways controlling mitochondrial dysfunction and oxidative phosphorylation. This experiment furthers our understanding of growth and development changes induced by preconception paternal exposures.

overall_design: Examination of paternal preconception alcohol consumption influence on gene expression in IVF morula stage embryos.

first: Alexis

middle: N

last: Roach

first: Katherine

last: Zimmel

first: Kara

last: Thomas

first: Ali

last: Basel

first: Sanat

middle: S

last: Bhadsavle


title: Establishment of 3D chromatin structure after fertilization and the metabolic switch at the morula-to-blastocyst transition require CTCF [Hi-C]

status: Public on Oct 07 2022

city: Madrid

first: Miguel

last: Manzanares

address: Melchor Fernandez Almagro, 3

department: Cell and Developmental Biology

country: Spain

institute: National Center of Cardiovascular Diseases

summary: The eukaryotic genome is tightly packed inside the nucleus, where it is organized in 3D at different scales. This structure is driven and maintained by different chromatin states and by architectural factors that bind DNA, such as the multi-zinc finger protein CTCF. Zygotic genome structure is established de novo after fertilization, but the impact of such structure on genome function during the first stages of mammalian development is still unclear. Here, we show that deletion of the Ctcf gene in mouse embryos impairs the correct establishment of chromatin structure, but initial lineage decisions take place and embryos are viable until the late blastocyst stage. Furthermore, we observe that maternal CTCF is not necessary for development. Transcriptomic analyses of mutant embryos show that the changes in metabolic and protein homeostasis programs that occur during the progression from the morula to the blastocyst depend on CTCF. Yet, these changes in gene expression do not correlate with disruption of chromatin structure, but mainly with proximal binding of CTCF to the promoter region of genes downregulated in mutants. Our results show that CTCF regulates both 3D genome organization and transcription during mouse preimplantation development, but mostly as independent processes.

overall_design: Hi-C experiments on biological replicates of single embryos at the blastocyst stage.

first: Maria

middle: J

last: Andreu

first: Alba

last: Alvarez-Franco

first: Marta

last: Portela

first: Daniel

last: Gimenez-Llorente

first: Ana

last: Cuadrado

first: Claudio

last: Badia-Careaga

last: Tiana

last: Losada


title: Single-cell profiling of complex plant responses to Pseudomonas syringae infection [scRNA-seq]

city: Berkeley

first: Benjamin

middle: Jeremy

last: Cole

state: CA

address: 1, Cyclotron Road

country: USA

institute: DOE-Joint Genome Institute

type: Expression profiling by high throughput sequencing

summary: Plant response to pathogen infection varies within a leaf, yet this heterogeneity is not well resolved. We exposed Arabidopsis to Pseudomonas syringae or mock treatment and profiled the transcriptomes of 11,000 individual cells using single-cell RNA sequencing. Integrative analysis of cell populations from Pseudomonas and mock inoculated leaves identified five distinct pathogen responsive cell clusters exhibiting transcriptional responses ranging from immunity to susceptibility. Pseudotime analyses through pathogen infection revealed a continuum of disease progression from an immune to susceptible state. Confocal imaging of promoter reporter lines for pathogen responsive cell clusters visualized immune activated cell clusters surrounding substomatal cavities colonized by bacteria, suggesting immune clusters are sites of early pathogen invasion. Susceptibility cell clusters exhibited more general localization and were highly induced at later stages of infection. Overall, our work uncovers cellular heterogeneity within an infected leaf and provides unique insight into plant differential response to infection at a single-cell level.

overall_design: 4-week old Arabidopsis thaliana leaves syringe-infiltrated with Pseudomonas syringae pv. tomato DC3000 or a mock treatment for 24 hours. After treatment, cells were isolated from leaf tissue using a tape-sandwich method to enrich for the mesophyll layer, and cells were subjected to single-cell transcriptomics profiling using the Chromium technology (10x Genomics, version 3), targeting 10,000 cells per library.

first: Jie

last: Zhu

first: Signe

last: Lolle

first: Brian

last: Kvitko

first: Gitta

last: Coaker


title: MLL3 loss drives metastasis and therapeutic resistance by promoting a hybrid EMT state [RNA-seq]

city: Bronx

first: Jihong

last: Cui

state: NY

address: 1301 Morris Park Avenue, Room 108/114

institute: Albert einstein college of medicine

summary:
Loss of MLL3 facilitates mesenchymal cells to acquire a mesenchymal/epithelial hybrid state during metastatic colonization.
The MET occurring in distant metastases is likely driven by stromal signals in the metastatic niche. One signaling pathway that promotes the MET is the activation of protein kinase A (PKA). The MET hybrid cells can be identified as CD44+CD104+/high.
Forskolin treatment generated significantly more CD44+CD104high hybrid cells in MLL3-mutant cells than the WT MDA-MB-231 cells. While both WT and MLL3-mutant CD44+CD104high hybrid EMT cells showed significantly increased lung metastatic ability than the counterpart CD44+CD104low mesenchymal cells, the MLL3-mutant hybrid cells showed a much greater metastasis-initiating ability than the WT hybrid cells.
Here we reported the gene expression profiles of CD44+CD104high E/M hybird and CD44+CD104-/low mesenchymal cell populations sorted from Foskolin-treated, MLL3-null MDA-MB-231 cells.

overall_design: We treated the WT and MLL3-mutant MDA-MB-231 cells with the PKA activator forskolin for 14 days and used flow cytometry to isolate CD44+CD104high hybrid EMT and CD44+CD104low mesenchymal tumor cells. RNA was isolated from these populations and RNA-seq was preformed for comparison the gene expression.

first: Wenjun

last: Guo


title: Postnatal expansion of the lymph node stromal cell pool towards reticular and CD34+ stromal cell subsets [RNA-seq]

city: Lausanne

first: Joern

last: Pezoldt

address: Station 19, SV 3818.A

department: SV

country: Switzerland

institute: EPFL

summary: Gut-draining mesenteric lymph nodes (mLNs) provide the framework to shape intestinal adaptive immune responses. We previously delineated transcriptional signatures in LN stromal cells (SC), pointing to tissue-specific variability in SC composition and immunomodulatory function. Here, using scRNA-seq we dissected the developmental trajectory of SCs within mLNs derived from postnatal to aged mice, and identified two putative progenitors, namely CD34+ SC and fibroblastic reticular stromal cell (FRC) progenitors, which both feed the rapid LN expansion postnatally. We further unraveled the tissue-specific chromatin accessibility and DNA methylation landscape of non-endothelial SCs, and identified a microbiota-independent core epigenomic signature, showcasing differences between SCs from mLN and skin-draining peripheral LN. Irf3 was inferred from the epigenomic landscape of SCs, being dynamically expressed along the differentiation trajectories of FRCs. Lentiviral overexpression of Irf3 in a mesenchymal stem cell line established a Cxcl9+ FRC molecular phenotype. The relevance of Irf3 for SC biology was further underscored by the diminished proportion of Ccl19+ and Cxcl9+ FRCs in LNs from Irf3-/- mice. Together, our data constitute a comprehensive transcriptional and epigenomic map of LNSC development in early life and dissect location-specific, microbiota-independent properties of non-endothelial SCs.

overall_design: RNA-seq on FACS-isolated CD45-CD24-CD31-Pdpn+ cells from skin- or gut-draining lymph nodes of SPF or GF housed mice

first: Carolin

last: Wiechers

first: Michael

last: Beckstette

first: Jochen

last: Huehn


title: MLL3 Loss Drives Metastasis by Promoting a Hybrid Epithelial-Mesenchymal Transition State [RNA-seq MDA231 KO vs WT]

summary:
Loss of MLL3 facilitates mesenchymal cells to acquire a mesenchymal/epithelial hybrid state during metastatic colonization.
MLL3 loss led to IFNg signaling upregulation, which contributes to the induction of hybrid EMT cells and the enhanced metastatic capacity.
Here we reported the gene expression profiles of WT and MLL3-KO MDA-MB-231 cells.

overall_design: RNA-seq was preformed for comparison the gene expression of WT and MLL3-KO MDA-MB-231 cells.


title: The Long Noncoding RNA FEDORA is a Cell-Type and Sex-Specific Regulator of Mood

city: New York

first: Aarthi

last: Ramakrishnan

state: New York

address: 1425 Madison Avenue

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

summary: Major depressive disorder (MDD) strikes women twice as often as men, yet the molecular mechanisms contributing to this sex difference are poorly understood. Here, we explored the regulation of long noncoding RNAs (lncRNAs) in human postpartum brain tissue and found a robust baseline sex difference in lncRNA expression levels that is profoundly lost in MDD. We highlight one such lncRNA, that is upregulated in females with MDD, therefore we named FEDORA. FEDORA arose in humans and is expressed primarily in oligodendrocytes as well as in neurons. We tested FEDORA’s causal role in MDD, by utilizing a cell-type-specific approach to express it in the prefrontal cortex (PFC) of mice of both sexes. We found that expressing FEDORA in either neurons or oligodendrocytes promoted depression-like behaviors in females only, which mirrored the human sex-specific phenotype. These behavioral changes were associated with cell-type-specific changes in electrophysiological properties, myelin thickness, and gene expression. Finally, we found that blood FEDORA levels have diagnostic and prognostic features only for women with MDD. Together, these findings suggest that lncRNAs play key roles in shaping the sex-specific landscape of the brain and contribute to sex differences in MDD.

overall_design: Over expression of FEDORA or GFP in Neurons and Oligodendrocytes of PFC in mice

first: Orna

last: Issler

first: Yentl

middle: Y

last: van der Zee

first: Li

last: Shen

first: Eric

last: Nestler


title: Postnatal expansion of the lymph node stromal cell pool towards reticular and CD34+ stromal cell subsets [scRNA-seq II]

summary: Gut-draining mesenteric lymph nodes (mLN) provide the framework and microenvironment to shape intestinal adaptive immune responses. We previously delineated transcriptional signatures in LN stromal cells (SC), pointing to tissue-specific variability in composition and immuno-modulatory function of SCs.  Here, we dissect the tissue-specific epigenomic DNA accessibility and CpG methylation landscape of LN non-endothelial SCs and identify a microbiota-independent core epigenomic signature of LN SCs. By combined analysis of transcription factor (TF) binding sites together with the gene expression profiles of non-endothelial SCs, we delineated TFs poising skin-draining peripheral LN (pLN) SCs for pro-inflammatory responses. Furthermore, using scRNA-seq, we dissected the developmental trajectory of mLN SCs derived from postnatal to aged mice, identifying two distinct putative progenitors, namely CD34+ SC and fibroblastic reticular stromal cell (FRC) progenitors, which both feed the rapid postnatal LN expansion. Finally, we identified Irf3 as a key differentiation TF inferred from the epigenomic signature of mLN SCs that is dynamically expressed along the differentiation trajectories of FRCs, and validated Irf3 as a regulator of Cxcl9+ FRC differentiation.  Together, our data constitute a comprehensive transcriptional and epigenomic map of mLN development and dissect location-specific, microbiota-independent properties of mLN non-endothelial SCs. As such, our findings represent a valuable resource to identify core transcriptional regulators that impinge on the developing mLN early in life, thereby shaping long-lasting intestinal adaptive immune responses.

overall_design: Single cell RNA-seq on FACS-isolated CD45-CD24- mesenteric and skin draining lymph node stromal cells of germ-free mice

first: Maria

last: Litovchenko

first: Mangge

last: Zou

first: Ehsan

last: Vafardanejad

first: Antoine-Emmanuel

last: Saliba


title: Calsyntenin-3b constrains lipid droplet expansion to promote a multilocular adipocyte phenotype and thermogenesis

city: Los Angeles

first: Peter

last: Tontonoz

address: 675 Charles E. Young Drive South, MRL 6619

department: Pathology and Laboratory Medicine

institute: UCLA

summary: Multilocular adipocytes are a hallmark of thermogenic adipose tissue, but the factors that enforce this cellular phenotype are unknown.  Here, we show that an adipocyte-specific product of the Clstn3 locus (CLSTN3b) present only in placental mammals facilitates the rapid utilization of stored triglyceride by limiting lipid droplet (LD) size.  CLSTN3b is an integral ER protein that localizes to ER-LD contact sites via a conserved hairpin domain.  Mice lacking CLSTN3b have altered LD morphology and increased lipid accumulation in BAT, as well as heightened sensitivity to cold challenge, despite having no defect in adrenergic signaling.  Conversely, forced expression of CLSTN3b promotes a multilocular LD phenotype in cultured cells and BAT and facilitates triglyceride utilization.  Mechanistically, CLSTN3b associates with CIDE proteins and impairs their ability to transfer lipid between droplets, thereby limiting LD expansion.  These findings define a molecular mechanism that maximizes LD surface area to facilitate lipid utilization in thermogenic adipocytes.

overall_design: RNA-seq was performed on brown adipose tissue (BAT) from 10 week old male WT and adipocyte-specific CLSTN3B knockout (AdC3KO) mice acclimated to thermoneutrality (30 C) for 2 weeks (n = 3, 3) and subsequently exposed to cold (4 C) for 6 hours (n = 4, 4). Total RNA was extracted using TRIzol and the RNeasy Mini Kit with on-column DNase I digestion (Qiagen). Library preparation and sequencing was done at GENEWIZ. Adapter and quality trimming of raw FASTQ files was performed using Trimmomatic. FastQC was used to analyze FASTQ files before and after trimming. Trimmed FASTQ files were aligned to GRCm38/mm10 using STAR. HTSeq-count was used to extract gene counts and differential gene expression analysis was performed using DESeq2.

first: Kevin

last: Qian


title: Establishment of 3D chromatin structure after fertilization and the metabolic switch at the morula-to-blastocyst transition require CTCF [RNA-seq]

first: Miguel

last: Manzanares

overall_design: RNAseq experiments on biological replicates of single embryos at the morula and blastocyst stages.

last: Andreu

first: Alba

last: Alvarez-Franco

first: Marta

last: Portela

first: Daniel

last: Gimenez-Llorente

first: Ana

last: Cuadrado

first: Claudio

last: Badia-Careaga

last: Tiana

last: Losada


title: Establishment of 3D chromatin structure after fertilization and the metabolic switch at the morula-to-blastocyst transition require CTCF.

status: Public on Oct 06 2022

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

overall_design: Refer to individual Series


title: DNA methylation dynamics underlie metamorphic gene regulation programs in Xenopus tadpole brain [ChIP-seq]

status: Public on Oct 05 2022

city: Ann Arbor

first: Robert

last: Denver

state: Michigan

address: 1105 North University Ave

department: MCDB

institute: University of Michigan

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Association of thyroid hormone receptors (TRs) in chromatin across the genome of neural cells in the preoptic area/hypothalamus/thalamus of metamorphic climax stage Xenopus tropicalis tadpoles, analyzed by chromatin-immunoprecipitation sequencing (ChIP-seq).

overall_design: The middle brain region containing the preoptic area/hypothalamus/thalamus was microdissected from Xenopus tropicalis tadpoles at metamorphic climax, Nieuwkoop-Faber (NF) stage 62. We isolated chromatin from tadpole brain and conducted chromatin-immunoprecipitation (ChIP) sequencing.

first: Samhitha

last: Raj

first: Christopher

last: Sifuentes


title: RfaH counter-silences inhibition of transcript elongation by H-NS–StpA H-NS nucleoprotein filaments in pathogenic E. coli

city: Madison

last: Landick

state: WI

address: 5445 Microbial Science Building 1550 Linden Dr.

department: Biochemistry

institute: University of Wisconsin-Madison

summary: Expression of virulence genes in pathogenic E. coli is controlled in part by the transcription silencer H-NS and its paralogs (e.g., StpA), which sequester DNA in multi-kb nucleoprotein filaments to inhibit transcription initiation, elongation, or both. Some activators counter-silence initiation by displacing H-NS from promoters. How H-NS inhibition of elongation is overcome is not understood. In uropathogenic E. coli (UPEC), elongation regulator RfaH aids expression of some H-NS-silenced pathogenicity operons (e.g., hlyCABD encoding hemolysin). RfaH associates with elongation complexes (ECs) via direct contacts to a transiently exposed, nontemplate DNA-strand sequence called ops (operon polarity suppressor). RfaH–ops interactions establish long-lived RfaH–EC contacts that allow RfaH to recruit ribosomes to the nascent mRNA and to suppress transcriptional pausing and termination. Using ChIP-seq, we mapped the genome-scale distributions of RfaH, H-NS, StpA, RNA polymerase (RNAP), and σ70 in the UPEC strain CFT073. We identify 8 RfaH-activated operons, all of which were bound by H-NS and StpA. Four are new additions to the RfaH regulon. Deletion of RfaH caused premature termination whereas deletion of H-NS and StpA allowed elongation without RfaH. Thus, RfaH is an elongation counter-silencer of H-NS. Consistent with elongation counter-silencing, deletion of StpA alone decreased the effect of RfaH. StpA increases DNA bridging, which inhibits transcript elongation via topological constraints on RNAP. Residual RfaH effect when both H-NS and StpA were deleted was attributable to targeting of RfaH-regulated operons by a minor H-NS paralog, Hfp. These operons have evolved higher levels of H-NS–binding features, explaining minor-paralog targeting.

sample_organism:
Escherichia coli
Escherichia coli CFT073

overall_design: ChIP-seq of RfaH, H-NS, StpA, RNAP, and σ70 in Escherichia coli CFT073 and H-NS in E. coli RL3000.

first: Christine

middle: M

last: Hustmyer

first: Michael

middle: B

last: Wolfe

first: Rodney

middle: A

last: Welch


title: Postnatal expansion of the lymph node stromal cell pool towards reticular and CD34+ stromal cell subsets [BRB-seq]

first: Joern

last: Pezoldt

overall_design: 3'RNA-seq (methods used BRB-seq) on C3H10T1/2 lentivirally transduced with indicated transcription factor.

first: Marjan

last: Biocanin

first: Wanze

last: Chen

first: Bart

last: Deplancke


title: Postnatal expansion of the lymph node stromal cell pool towards reticular and CD34+ stromal cell subsets

type: Methylation profiling by high throughput sequencing


title: Postnatal expansion of the lymph node stromal cell pool towards reticular and CD34+ stromal cell subsets [scRNA-seq]

overall_design: Single cell RNA-seq on FACS-isolated CD45-CD24-gut-draining lymph nodes of SPF housed mice

first: Carolin

last: Wiechers

first: Maria

last: Litovchenko

first: Mangge

last: Zou

first: Ehsan

last: Vafardanejad

first: Emmanuel

last: Saliba

first: Jochen

last: Huehn


title: MLL3 loss drives metastasis and therapeutic resistance by promoting a hybrid EMT state

first: Jihong

last: Cui


title: TNF-α-induced endothelial differentiation of human mesenchymal stem cells

city: Seoul

first: Soon Young

last: Shin

address: 120, Neungdong-ro, Gwangjin-gu

department: Department of Biological Sciences

country: South Korea

institute: Konkuk University

summary: Mesenchymal stem cells (MSCs) can differentiate into endothelial cells; however, the mechanisms underlying this process in the tumor microenvironment (TME) remain elusive. This study shows that tumor necrosis factor alpha (TNF-α), a key cytokine present in the TME, promotes the endothelial differentiation of MSCs by inducing vascular endothelial growth factor receptor 2 (VEGFR2) gene expression. EGR1 is a member of the zinc-finger transcription factor family induced by TNF-α. Our findings indicate that EGR1 directly binds to the VEGFR2 promoter and transactivates VEGFR2 expression. We also demonstrate that EGR1 forms a complex with c-JUN activated by c-JUN N-terminal kinase (JNK) to promote VEGFR2 transcription and endothelial differentiation in MSCs in response to TNF-α stimulation. The shRNA-mediated silencing of EGR1 or c-JUN abrogates TNF-α-induced VEGFR2 transcription and the endothelial differentiation of MSCs. Collectively, these findings demonstrate that the JNK-EGR1 signaling axis plays a crucial role in the TNF-α-induced endothelial differentiation of MSCs in the TME, which could be a potential therapeutic target for solid tumors vasculatures.

overall_design: To identify the genes that regulate the TNF-α-induced endothelial differentiation of MSCs, we examined the gene expression profile of nontreated or TNF-α-treated (18 h) BM-MSCs using an Agilent human whole genome microarray.

first: Euitaek

last: Jung

first: Young

middle: H

last: Lee

first: Soon


title: Enhancer decommissioning by MLL4 ablation elicits dsRNA-interferon signaling and GSDMD-mediated pyroptosis to potentiate anti-tumor immunity

city: Tianjin

first: Shan

last: Huang

address: Qi Xiangtai Road

country: China

institute: Tianjin Medical University

summary: Transcriptional enhancers instruct spatiotemporal gene expression and their dysfunction has long been known as one of the primary mechanisms that drive tumorigenesis and confer malignant tumor cell behaviors. However, it is largely unknown about whether tumor cell enhancer regulation plays a role in tumor immune evasion and anti-tumor immune response. Here, we demonstrate that tumor cell deletion of Mll3 and Mll4, two members of COMPASS family for enhancer H3K4 mono-methylation, increases tumor cell immunogenicity and promotes anti-tumor immune response. Loss of Mll4 potentiates therapeutic response to anti-Pd1 blockade in the murine melanoma model. Mechanistically, Mll4 loss leads to the widespread decrease of epigenetic signatures at both typical and super-enhancers, including the super-enhancer for Ago2 subunit of RNA-induced silencing complex (RISC) and the enhancers for DNA methyltransferases Dnmt3a and Dnmt1. Downregulation of Ago2 expression leads to double-stranded RNA (dsRNAs) stress to elicit interferon response while decreased expression of Dnmt3a and Dnmt1 derepresses Gsdmd and inflammatory caspases to trigger Gsdmd-mediated pyroptosis in Mll4-deficient tumor cells. Notably, transcriptional induction of interferon signaling and Gsdmd-mediated tumor cell pyroptotic death is crucial for the increased anti-tumor immunity and the improved immunotherapeutic efficacy in Mll4-deficient tumors. These findings reveal an important immune regulatory role of tumor cell enhancer regulation and provide molecular insights into the immunotherapeutic vulnerabilities of tumors bearing MLL3/MLL4 deficiency or loss of function mutations.

overall_design: RNA-seq of wild-type, Mll4-knockout or Mll3-knockout B16-F10 cells. ChIP-seq of H3K27 acetylation or H3K4 monomethylation for wild-type or Mll4-knockout B16-F10 cells.

first: Renyong

last: Zhi

first: Jinhua

last: Liu


title: Postnatal expansion of the lymph node stromal cell pool towards reticular and CD34+ stromal cell subsets [WGBS]

first: Joern

last: Pezoldt

overall_design: Whole Genome Bisulfite Sequencing on FACS-isolated CD45-Ter119-CD31-Pdpn+ cells from skin- or gut-draining lymph nodes of SPF or GF housed mice

first: Stefan

last: Floess

first: Michael

last: Beckstette


title: Postnatal expansion of the lymph node stromal cell pool towards reticular and CD34+ stromal cell subsets [scRNA-seq III]

first: Carolin

first: Antoine-Emmanuel


title: Blockade of the Protease ADAM17 Ameliorates Experimental Pancreatitis

city: Melbourne

first: Jamie

last: Gearing

address: 27-31 Wright St

country: Australia

institute: Hudson Institute of Medical Research

summary: Acute and chronic pancreatitis, the latter associated with fibrosis, are multifactorial inflammatory disorders and leading causes of gastrointestinal disease-related hospitalisation, including death. Despite the global health burden of pancreatitis, currently there are no effective therapeutic agents. In this regard, the protease A Disintegrin And Metalloproteinase 17 (ADAM17) mediates inflammatory responses through shedding of bioactive inflammatory cytokines and mediators, including tumour necrosis factor α (TNFα) and the soluble interleukin (IL)-6 receptor (sIL-6R), the latter of which drives proinflammatory IL-6 trans-signalling. However, the role of ADAM17 in pancreatitis is unclear. To address this, Adam17ex/ex mice – which are homozygous for the hypomorphic Adam17ex allele resulting in marked reduction in ADAM17 expression – and their wild-type (WT) littermates were exposed to the cerulein-induced acute pancreatitis model, and acute (1-week) and chronic (20-weeks) pancreatitis models induced by the cigarette smoke carcinogen nicotine-derived nitrosamine ketone (NNK). Our data reveal that ADAM17 expression was upregulated in pancreatic tissues of animal models of pancreatitis. Moreover, the genetic (Adam17ex/ex mice) and therapeutic (ADAM17 prodomain inhibitor; A17pro) targeting of ADAM17 ameliorated experimental pancreatitis, which was associated with a reduction in the IL-6 trans-signalling/STAT3 axis. This led to reduced inflammatory cell infiltration, including T cells and neutrophils, as well as necrosis and fibrosis in the pancreas. Furthermore, upregulation of the ADAM17/IL-6 trans-signalling/STAT3 axis was a feature of pancreatitis patients. Collectively, our findings indicate that the ADAM17 protease plays a pivotal role in the pathogenesis of pancreatitis, which could pave the way for devising novel therapeutic options to be deployed against this disease.

overall_design: RNA transcriptome sequencing to profile the differential regulation of gene networks in pancreatic tissues of WT and Adam17ex/ex mice subjected to cerulein-induced acute pancreatitis (AP) and compared to PBS controls.

first: Mohamed

middle: I

last: Saad

first: Linden

first: Brendan

last: Jenkins


title: Accumulation of auranofin in white adipose tissues lowers leptin levels and exerts anti-diabetic effects

city: Houston

first: Aaron

middle: R

last: Cox

state: TX

address: 1825 Pressler St

department: Institute of Molecular Medicine

institute: University of Texas Health Science Center at Houston

summary: Low-grade, sustained inflammation in white adipose tissue (WAT) characterizes obesity and frequently coincides with insulin resistance and type 2 diabetes (T2D). However, pharmacological targeting of WAT inflammation lacks durable therapeutic effects. Through a computational screen, we identified the FDA-approved rheumatoid arthritis drug auranofin is a putative small molecule for obesity treatment. We discovered that allometrically scaled safe auranofin doses homed to WAT and improved insulin sensitivity in obese wild-type mice. To assess the transcriptional changes underlying the beneficial effects of auranofin, we performed RNA-seq analysis on adipose and liver tissue after 4 weeks of treatment with vehicle or auranofin.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for liver, epididymal and inguinal white adipose tissue, and intrascapular brown adipose tissue from C57Bl/6 mice. Mice were ffed 60% HFD diet for 12 weeks before receiving vehicle or auranofin (1 mg/kg BW) 3 times per week for 4 weeks.

first: Peter

last: Masschelin

first: Pradip

middle: K

last: Saha

first: Jessica

last: Felix

first: Robert

last: Sharp

first: Zeqin

last: Lian

first: Yan

last: Xia

first: Natasha

last: Chernis

first: David

last: Bader

first: Kang

last: Kim

first: Xin

last: Li

first: Jun

last: Yoshino

first: Gang

first: Zheng

last: Sun

first: Huaizhu

last: Wu

first: Christian

last: Coarfa

middle: D

last: Moore

first: Samuel

last: Klein

first: Kai

first: Sean

last: Hartig


title: MLL3 Loss Drives Metastasis by Promoting a Hybrid Epithelial-Mesenchymal Transition State [ChIP-seq UTX and MLL4]

first: Jihong

last: Cui

summary:
Phenotypic plasticity associated with the hybrid epithelial-mesenchymal transition (EMT) state is crucial to metastatic seeding and outgrowth. However, the mechanisms controlling the induction of hybrid EMT remain poorly defined.
We showed that deletion of the epigenetic regulator MLL3, a tumor suppressor frequently altered in human cancer, promoted the acquisition of the hybrid EMT state in both epithelial and mesenchymal breast cancer cells by facilitating EMT and MET, distinct from other known EMT regulators mediating unidirectional changes. Consequently, MLL3 deletion greatly increased metastasis by enhancing metastatic outgrowth during colonization. Mechanistically, MLL3 loss led to IFNγ signaling upregulation, which contributes to the induction of hybrid EMT cells and the enhanced metastatic capacity.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for UTX and MLL4 in MLL3-WT and Mut MCF7 and MDA-MB-231 cells.

first: Chi

last: Zhang

first: Wenjun

last: Guo


title: RNA Sequencing of SKMEL2 NT and GRAMD1B KO cells

first: Shruthy

last: Suresh

address: 417 E 68th St

institute: Memorial Sloan Kettering Cancer Center

summary: We performed RNA Sequencing of SKMEL2 human melanoma cells expressing a NT sgRNA or sgRNA against GRAMD1B to identify differentially expressed genes in the GRAMD1B KO cells.

overall_design: Human SKMEL2 cell RNA Samples were prepared in biological triplicates, n=3 for NT group and n=3 for KO group.

first: Richard

last: White


title: Ornithine decarboxylase supports ILC3 responses in infectious and autoimmune colitis through positive regulation of IL-22 transcription

city: St. Louis

first: Vincent

last: Peng

state: MO

address: 660 S. Euclid Ave.

institute: Washington University School of Medicine in St. Louis

summary: Group 3 innate lymphoid cells (ILC3s) are RORγT+ lymphocytes that are predominately enriched in mucosal tissues and produce IL-22 and IL-17A. They are the innate counterparts of Th17. While Th17 lymphocytes utilize unique metabolic pathways in their differentiation program, it is unknown whether ILC3s make similar metabolic adaptations. We employed single-cell RNA sequencing and metabolomic profiling of intestinal ILC subsets to identify an enrichment of polyamine biosynthesis in ILC3s, converging on the rate-limiting enzyme ornithine decarboxylase (ODC1). In vitro and in vivo studies demonstrated that exogenous supplementation with the polyamine putrescine or its biosynthetic substrate, ornithine, enhanced ILC3 production of IL-22. Conditional deletion of ODC1 in ILC3s impaired mouse antibacterial defense against C. rodentium infection, which was associated with a decrease in anti-microbial peptide production by the intestinal epithelium. Furthermore, in a model of anti-CD40 colitis, deficiency of ODC1 in ILC3s markedly reduced the production of IL-22 and severity of inflammatory colitis. We conclude that cell-intrinsic polyamine biosynthesis facilitates efficient defense against enteric pathogens as well as augments autoimmune colitis, thus representing an attractive target to modulate ILC3 function in intestinal disease.

overall_design: Untreated (n=2), IL23-stimulated (n=2), putrescine-treated (n=2), and IL-23-stimulated and putrescine-treated (n=2) MNK-3. WT CCR6+ ILC3 (n=2) and ODC1 KO CCR6+ ILC3 (n=2).

first: Marco

last: Colonna


title: Cognate Microglia - T cell interactions shape the functional regulatory T cell pool in EAE pathology

city: REHOVOT

first: Steffen

last: Jung

address: Herzl

department: Immunology and Regenerative Biology

country: Israel

institute: The Weizmann Institute of Science

summary: Microglia, the parenchymal brain macrophages of the central nervous system (CNS), have emerged as critical players in brain development and homeostasis. Immune functions of these cells, however, remain less well defined. We investigated contributions of microglia in a relapsing remitting (RR) multiple sclerosis paradigm, experimental autoimmune encephalitis (RR-EAE) in C57BL/6 / SJL F1 mice. Fate mapping-assisted translatome profiling during the RR disease course revealed the potential of microglia to interact with T cells through antigen presentation, co-stimulation, and co-inhibition. Abundant microglia - T cell aggregates, as observed by histology and flow cytometry, supported the notion of functional interactions of microglia and T cells during remission, with a bias towards T regulatory cells. Finally, microglia_x0002_restricted Ifng receptor and MHC mutagenesis significantly affected the functionality of the regulatory T cell compartment in the diseased CNS and remission. Collectively, our data establish critical non-redundant cognate and cytokine-mediated interactions of microglia with CD4+ T cells during autoimmune neuro-inflammation.

overall_design: RNAseq of Cx3cr1-CreER:RPL22-HA using IP poling down of the HA tag in different stages of relapsing-remitting multiple sclerosis paradigm, experimental autoimmune encephalitis. Creating mice lacking their INFg - Cx3cr1-CreER:RPL22-HA:Ifngr ko/fl  and sequencing their microglia using their HA tag and sorting their T cells.

first: Zhana

last: Haimon

first: Gal

last: Frumer

first: Jung-Seok

first: Sébastien

last: Trzebanski

first: Rebecca

first: Shifra

last: Ben-Dor

first: Ziv

last: Porat

first: Andreas

last: Muschaweckh

first: Louise

last: Chappell-Maor

first: Sigalit

last: Boura-Halfon

first: Thomas

last: Korn


title: Hypoxia and ERα Transcriptional Crosstalk Is Associated with Endocrine Resistance in Breast Cancer

city: Fougeres

first: Denis

last: Habauzit

address: 10 B rue Claude Bourgelat

department: TC unit

country: France

institute: ANSES

summary: Estrogen receptor-alpha (ERα) is the driving transcription factor in 70% of breast cancers and its activity is associated with hormone dependent tumor cell proliferation and survival. Given the recurrence of hormone resistant relapses, understanding the etiological factors fueling resistance is of major clinical interest. Hypoxia, a frequent feature of the solid tumor microenvironment, has been described to promote endocrine resistance by triggering ERα down-regulation in both in vitro and in vivo models. Yet, the consequences of hypoxia on ERα genomic activity remain largely elusive. In the present study, transcriptomic analysis shows that hypoxia regulates a fraction of ERα target genes, underlying an important regulatory overlap between hypoxic and estrogenic signaling. This gene expression reprogramming is associated with a massive reor-ganization of ERα cistrome, highlighted by a massive loss of ERα binding sites. Profiling of en-hancer acetylation revealed a hormone independent enhancer activation at the vicinity of genes harboring hypoxia inducible factor (HIFα) binding sites, the major transcription factors governing hypoxic adaptation. This activation counterbalances the loss of ERα and sustains hor-mone-independent gene expression. We describe hypoxia in luminal ERα (+) breast cancer as a key factor interfering with endocrine therapies, associated with poor clinical prognosis in breast cancer patients.

overall_design:
4 replicates: Control MCF7 + EtOH
4 replicates: Control MCF7 + E2
4 replicates: Hypoxic MCF7 + EtOH
4 replicates: Hypoxic MCF7 + E2
4 replicates: Rescue MCF7  + EtOH
4 replicates: Rescue MCF7  + E2

first: Charly

last: Jehanno

first: Pascale

last: Le Goff

first: Yann

last: Le Page

first: Sylvain

last: Lecomte

first: Estelle

last: Lecluse

first: Frédéric

last: Percevault

first: Stéphane

last: Avner

first: Raphael

last: Métivier

last: Michel

first: Gilles

last: Flouriot


title: Effect of amino acid restriction diet (SARD) combined with anti-PD-L1 on gene expression of cecum orthotopic CT26 tumors.

city: Beijing

first: Taohua

last: Yue

address: 8 Xi Shiku Street, Beijing

institute: Peking university first hospital

summary:
Since both endogenous synthesis in tumor cells and bacterial sulfur reduction activities are sources of H2S in colon cancer microenvironment, in addition to using CBS -/+ mice, we also investigated the roles of reducing H2S through adopting a sulfur amino acid restriction diet (SARD) (0.15% methionine and 0% cystine) on immunotherapy (anti-PD-L1) of colon cancer.
Tumor bulk sequencing was performed in cecum orthotopic CT26 tumors collected from IgG and anti-PD-L1 treated mice both receiving normal diet and SARD.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for 4 groups of cecum orthotopic CT26 tumors (ND + IgG, SARD + IgG, ND + anti-PD-L1, SARD + anti-PD-L1).

first: Jichang

last: Li

first: Jing

last: Zhu

first: Xin

last: Wang

first: Yucun

last: Liu

first: Pengyuan

first: Shanwen

last: Chen


title: Standard ATAC-seq from sorted Olig2-expressing cells for CaTS-ATAC QC

city: London

first: M Joaquina

last: Delas

address: 1 Midland Road

department: Briscoe Lab

country: United Kingdom

institute: The Francis Crick Institute

summary: In many developing tissues the spatial and temporal pattern of gene expression is organised by secreted signals functioning in a graded manner over multiple cell diameters. Cis Regulatory Elements (CREs) interpret these graded inputs to control gene expression. How this is accomplished remains poorly understood. The morphogen Sonic hedgehog (Shh) acts in a graded manner to direct neural progenitor specification in the neural tube. Here, we uncover two distinct ways in which CREs translate graded Shh signaling into differential gene expression. A common set of CREs are used to control gene activity in the majority of ventral neural progenitors. These CREs integrate cell type specific inputs to control gene expression. By contrast, the most ventral progenitors use a unique set of CREs. These are established by the pioneer factor FOXA2, paralleling the role of FOXA2 in endoderm. Moreover, FOXA2 binds a subset of the same sites in neural and endoderm cells. Together the data identify distinct cis regulatory strategies for the interpretation of morphogen signaling and raise the possibility of an evolutionarily conserved role for Foxa2-mediated cell specification across tissues.

overall_design: ATAC-seq was performed from sorted mKate2-positive cells (from an Olig2-2A-mKate2 cell line) to compare live ATAC-seq and CaTS-ATAC. Samples were harvested from day 5 of differentiation at 100 nM SAG.

first: M

first: James

last: Briscoe


city: Isehara-shi

first: Atsushi

last: Fukuda

country: Japan

institute: Tokai University

summary: Bulk RNA sequencing to characterize female hES cells with null DNMT3A/3B deletion and WT cells.

overall_design: Transcriptome sequencing of 16 total RNA samples from human stem cells.


title: Molecular mechanism of Arabidopsis thaliana seedlings in response to phytotoxicity of yttrium oxide nanoparticles

city: Linfen

first: lin

middle: jin

last: feng

state: Shanxi

address: gongyuan 1 street

department: College of Life Sciences

institute: Shanxi Normal University

summary: Due to the wide application of rare earth oxides nanoparticles in different fields, they will inevitably be released into the environment, and their potential toxicity and ecological risks in the environment have become a concern of people. Yttrium oxide nanoparticles are important members of rare earth oxides nanoparticles. The molecular mechanism of its influence on plant growth and development and plant response to them is unclear. In this study, we found that yttrium oxide nanoparticles above 2 mM significantly inhibited the growth of Arabidopsis seedlings. Using the Arabidopsis marker lines reflecting auxin signal, it was found that the treatment of yttrium oxide nanoparticles led to the disorder of auxin signal in root cells: the auxin signal in quiescent center cells and columella stem cells decreased; while the auxin signal in the stele cells was enhanced. In addition, trypan blue staining showed that yttrium oxide nanoparticles caused the death of root cells. Transcriptome sequencing analysis showed that yttrium oxide nanoparticles specifically inhibited the expression of lignin synthesis related genes, activated mitogen-activated protein kinase (MAPK) signaling pathway, and enhanced ethylene and ABA signaling pathways in plants. This study revealed the phytotoxicity of yttrium oxide nanoparticles at the molecular level, and provided a new perspective at the molecular level for plants to respond to rare earth oxide stress.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Arabidopsis seedlings treated with yttrium oxide nanoparticles and the control group.

first: Jin

first: Shifeng

last: Zhao

first: Zhuoxuan

first: Jianxiang

last: Chai

first: Jinlin

last: Feng

first: Rong

last: Han


title: Transcriptional constraint of EWS/FLI by an ETS transcription factor promotes Ewing sarcoma growth.

city: Boston

first: Kenneth

last: Ross

state: MA

address: 450 Brookline Ave., Room LC6115

department: Pediatric Oncology

institute: Dana-Farber Cancer Institute

overall_design: Refer to individual Series


title: Biphasic Cell Cycle Defect Causes Impaired Neurogenesis in Down Syndrome [PAX6 ChIP-Seq]

city: Pune

first: Nishant

last: Singhal

state: Maharashtra

address: Ganeskhind Road

country: India

institute: National Centre for Cell Science

summary: Using integrative approach involving human and mouse iPSCs, we have unravelded the cellular and molecular mechanisms of reduced neurogenesis in Down syndome

overall_design: Isogenic normal and Down syndrome iPSCs were differentiated into cortical progenitor cells (CPCs) for 24 day in vitro (DIV24). Isogenic normal CPCs and down syndrome CPCs were crosslinked and sheared chramatin was prepared. ChIP was carried out using PAX6 antibody. Purified ChIPed DNA was used for high throughput seqencing. A total of samples were that one replicate of isogenic normal and one replicates of Down syndrome were used for ChIPseq library preperation. ChIPseq libraries were used for single end high throughput sequencing.

first: Long

last: Do

first: Aniruddha

last: Deshpande

first: Vishi

last: Sharma

first: Sunita

last: Nehra

first: Anwesha

last: Ghosh


title: Biphasic Cell Cycle Defect Causes Impaired Neurogenesis in Down Syndrome [Pluripotency, RNA-Seq]

overall_design: 2N and Ts65Dn mouse embryonic fibroblasts (MEFs) were used to generate 2N and Ts65Dn induced pluripotent stem cells (iPSCs) respectively. In addition to these cells, mouse embryonic stem  cells ESD3 were used for total RNA preparation. A toal of 15 samples having 3 replicates of each that is 2N MEFs, Ts65DN MEFs, 2N iPSCs, Ts65Dn iPSCs and ESD3 were used for mRNA seq library preperation. libraries were subjected to paired end high thoughput sequencing.


title: RNA sequencing of SiHa cells treated with oleic acid and radiation

status: Public on Oct 04 2022

last: Zhang

address: 4511 Forest Park Parkway

department: Radiation Oncology

institute: Washington University School of Medicine

summary: The impact of obesity on radiation therapy outcome is unclear. Previously, we reported that obese patients with cervical cancer have superior outcomes following chemoradiation. We hypothesized that excess mono- and di- unsaturated fatty acids (uFFAs) enhance response to radiation. Here, using preclinical models, we show that uFFAs radiosensitize cervical cancer through a novel p53-dependent mechanism. UFFAs signaled through PPARgand p53 to promote lipid uptake, storage and metabolism after radiation. Stable isotope labeling confirmed that cervical cancer cells increase both catabolic and anabolic oleate metabolism in response to radiation, with associated increases in dependence on mitochondrial fatty acid oxidation for survival. In vivo, supplementation with exogenous oleate improved tumor growth delay in xenografts after radiation, an effect which could be partially mimicked in tumors from high fat diet induced obese mice. These results suggest that supplementation with uFFAs may improve tumor responses to radiation therapy, particularly in TP53 wild type tumors.

overall_design:
p53 and PPARγ related gene expression in SiHa Cells
SiHa cells 48 hrs after no treatment (Ctrl), 48 hrs after treatment with a single fraction dose of 6 Gy (IR), 48 hrs after treatment with oleic acid (OA) and 48 hrs after treatment oleic acid and radiation (OA + IR)

first: Naoshad

last: Muhammad

first: Fiona

last: Ruiz

first: Jennifer

last: Stanley

first: Ramachandran

last: Rashmi

first: Kevin

last: Cho

first: Kay

last: Jayachandran

first: Michael

last: Zahner

first: Yi

last: Huang

first: Stephanie

last: Markovina

first: Gary

last: Patti

first: Julie

last: Schwarz


title: Biphasic Cell Cycle Defect Causes Impaired Neurogenesis in Down Syndrome

first: Nishant

last: Singhal

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: scRNA-seq analysis in human pluripotent stem cells

first: Atsushi

last: Fukuda


title: PTEN directs developmental and metabolic signaling for innate-like T cells fate and tissue homeostasis [scRNA-seq and scTCR-seq Exp2]

city: Memphis

first: Hongbo

last: Chi

state: TN

address: 262 Danny Thomas Place

department: Immunology

institute: St Jude Children's Research Hospital

summary: Developmental and metabolic signaling networks underpinning type-17 cell fate decisions in dictating tissue homeostasis versus tissue homeostasis

overall_design: We used scRNA-seq and scTCR-seq to profile pre-selection DP, post-selection DP, and CCR6+CD127+TCRb+ thymocytes of WT and Cd4CrePtenfl/fl mice

first: Isabel

last: Risch

first: Yu

last: Sun

first: Hao

last: Shi


title: PTEN directs developmental and metabolic signaling for innate-like T cells fate and tissue homeostasis [Stat3KO rescue]

summary: Developmental and metabolic signaling networks underpinning type-17 cell fate decisions and functional effects at coordination of PTEN-dependent tissue homeostasis

overall_design: We used microarray analysis to compare the global transcription profiles of post-selection DP cells in WT, Cd4CrePtenfl/fl, and Cd4CrePtenfl/flStat3fl/fl mice

first: Jana

last: Raynor


title: Biphasic Cell Cycle Defect Causes Impaired Neurogenesis in Down Syndrome [CPC RNA-Seq]

overall_design: Isogenic normal and Down syndrome iPSCs were differentiated in to cortical progenitor cells (CPCs) for 24 day in vitro(DIV24). CPCs were used for total RNA isolation. A total of 6 samples that is 3 replicates of isogenic normal CPCs and 3 replicates of Down syndrome CPCs were used for mRNA-seq library preperation. Libraries wer subjected to single end high throughout sequencing.

first: Long

last: Do

first: Aniruddha

last: Deshpande

first: Vishi

last: Sharma

first: Sunita

last: Nehra

first: Anwesha

last: Ghosh


title: Single nuclei transcriptomic of Populus tremula x alba apex

city: Gainesville

first: Daniel

last: Conde

state: FL

address: 2033 Mowry road

institute: University of Florida

summary: Here we applied a novel approach to isolate nuclei from complex plant tissues (https://doi.org/10.1371/journal.pone.0251149), to dissect the transcriptome profiling of the hybrid poplar (Populus tremula × alba) vegetative shoot apex at single-cell resolution.

overall_design: We harvested 20 shoot apices from 3-weeks-old in vitro grown plants and performed high-throughput, microfluidic-based single-nuclei RNA sequencing (snRNA-seq) using the 10× Genomics Chromium technology. For all quality control and analytical steps, we used Asc-Seurat, a comprehensive web application that encapsulates a series of tolls for scRNA-seq data analysis. To annotate each cluster, we assessed the abundance of transcripts of poplar homologous to Arabidopsis well-known cell type marker genes for the different domains of the vegetative or reproductive shoot apex.

first: Paolo

last: Triozzi

first: Wendell

last: Pereira

first: Kelly

last: Balmant

first: Henry

middle: W

last: Schmidt

first: Christopher

last: Dervinis

first: Matias

last: Kirst


title: Histone methyltransferase DOT1L regulates macrophage lipid biosynthesis and inflammatory responses and affects atherosclerotic plaque stability [ChIP-seq]

city: Amsterdam

first: Lisa

last: Willemsen

address: Meibergdreef 9

country: Netherlands

institute: Amsterdam UMC - locatie AMC

summary: Macrophages are critical immune cells in inflammatory diseases and their differentiation and function are tightly regulated by epigenetic alterations. H3K79 methylation is an epigenetic modification associated with active gene expression and DOT1L is the only histone methyltransferase for H3K79. Here we determine the role of DOT1L in macrophages by applying a selective DOT1L inhibitor in mouse and human macrophages and using myeloid-specific Dot1l deficient mice. We found that DOT1L directly regulates macrophage function by controlling lipid biosynthesis gene programs including central lipid regulators like sterol regulatory element-binding proteins SREBP1 and SREBP2. DOT1L inhibition also leads to macrophage hyperactivation which is associated with disrupted SREBP pathways. In vivo, myeloid Dot1l deficiency reduces atherosclerotic plaque stability and increases the activation of inflammatory plaque macrophages. Our data show that DOT1L is a crucial regulator of macrophage inflammatory responses and lipid regulatory pathways and suggests a high relevance of H3K79 methylation in inflammatory disease.

overall_design: In total, 7 samples were analyzed (3 biological replicates of SGC0946 treated BMDMs, 3 biological replicates of DMSO (control) treated BMDMs, and 1 BMDM input sample)

first: Koen

last: Prange

first: Annette

middle: E

last: Neele

first: Cindy

middle: P

last: van Roomen

first: Marion

last: Gijbels

first: Guillermo

last: Griffith

first: Myrthe

last: den Toom

first: Linda

last: Beckers

first: Hung-Jen

last: Chen

first: Laura

last: Bosmans

first: Heinz

last: Jacobs

first: Fred

last: vanLeeuwen

first: Menno

last: deWinther


title: Effect of sex on human ES cell and iPS cell [scRNA-Seq]

first: Atsushi

last: Fukuda

summary: We report that the effect of sex differences on the gene expression pattern in female and male human ES cell and iPS cell by single cell  RNA-sequencing.

overall_design: Examination of gene expression levels in female and male human ES cell and iPS cell.


title: Histone methyltransferase DOT1L regulates macrophage lipid biosynthesis and inflammatory responses and affects atherosclerotic plaque stability [RNA-seq II]

overall_design: In total, 12 samples were analyzed (3 biological replicates of DOT1L WT BMDMs (WT_ZLPS), 3 biological replicates of DOT1L KO BMDMs (KO_ZLPS), 3 biological replicates of 3h LPS treated DOT1L WT BMDMs (WT_MLPS), 3 biological replicates of 3h LPS treated DOT1L KO BMDMs (KO_MLPS)).

last: vanRoomen

first: Nathanael

last: Spann


title: Histone methyltransferase DOT1L regulates macrophage lipid biosynthesis and inflammatory responses and affects atherosclerotic plaque stability


title: ChIP-seq and RNA-seq for TCSs in Pseudomonas syringae

city: Hong Kong

first: Xin

last: DENG

address: 1/F, Block 1, To Yuen Building, City University of Hong Kong, 31 To Yuen Street, Kowloon Tong

department: Department of Biomedical Sciences

country: Hong Kong

institute: City University of Hong Kong

summary: Bacteria relies on two-component systems (TCSs) to respond to a wide range of stimuli or environmental cues for their survival and virulence. However, the functions and synergistic actions of TCSs in genomic level remains unclear. Here, in model phytopathogen Pseudomonas syringae, by integrating multiomics data, we developed a network-based PSTCSome (Pseudomonas syringae two-component systems regulome) to identify functions and crosstalk among global TCSs under either virulence suppressing (King’s B medium, KB) or activating conditions (minimal medium, MM). Transcriptome profiling identifies 2,099 differentially expressed genes (DEGs) in KB and 1,250 DEGs in MM, while ChIP-seq identifies 1,628 target genes across the whole genome. The multiomics results are applied to perform not only gene ontology (GO) analysis to detect the biological processes that TCSs involved in, but also subnetworks and co-expression analysis of 8 virulence-related pathways to decipher the TCSs regulated pathogenic behaviors. The following phenotypic experiments newly confirmed 8 TCSs that regulates type III secretion system (T3SS) (PSPPH_0253, PSPPH_2606, PSPPH_4416, and PSPPH_4451) and surface attachment (PSPPH_0253, PSPPH_3041, PSPPH_3473, PSPPH_3736, PSPPH_4001). We then compute 259 functional genes in KB and 161 in MM for those cluster TCSs. Analysis of cluster TCSs regulons led to the identification of either novel functions or 2 master regulatory TCSs (RhpS/RhpR and PSPPH_4827/4828) toward virulence. Our results show that TCSs in P. syringae dynamically adjust their regulatory networks by sensing the external environment, and then switch bacteria between pathogenic and non-pathogenic states in a sophisticated way. Furthermore, we present an online platform of PSTCSome to facilitate updating, network visualization and user-customized analyses.

sample_organism: Pseudomonas savastanoi pv. phaseolicola 1448A

overall_design:
RNA-seq for Pseudomonas syringae histidine kinases in KB and MM medium; ChIP-seq for Pseudomonas syringae response regulators in KB medium (monoclonal Anti-FLAG-Agarose antibody produced in mouse (SigmaAldrich, A2220, SLBX3759))

Each processed data for RNA-seq samples was generated from both replicates and is linked to the corresponding rep1 (*-1) sample records.

last: Deng


title: Transcriptome profile of melanoma cell lines A375 and M14 w/o treatment or with QNC and/or MBZ

status: Public on Oct 03 2022

city: Pozzuoli

first: Rossella

last: De Cegli

address: Via Campi Flegrei 34

country: Italy

institute: Tigem

summary: To analyse gene expression differences between QNC- and MBZ-treated and untreated A375 and M14.

overall_design: Total RNA was extracted from n=3 A375 and M14 treated with QNC and/or MBZ (2uM) for 48h and vehicle control (DMSO, 0.01%).

first: R

first: P

last: Carotenuto


title: Metabolic reprogramming of innate-like T cell fate and tissue homeostasis by PTEN  [scRNA- and scTCR-seq]

first: Hongbo

last: Chi

summary: Developmental and metabolic signaling networks underpinning type-17 cell fate decisions in dictating tissue homeostasis versus fatal autoimmunity

overall_design: We used scRNA-seq and scTCR-seq to profile CCR6+CD127+TCRb+ thymocytes of wild-type mice and mice with PTEN T cell-specific knockout and heterozygous.

first: Hao

last: Shi

first: Nicole

last: Chapman


title: Influence of Staphylococcus aureus strain background on Sa3 phage life cycle switches

city: Tübingen

first: Christiane

last: Wolz

address: Elfriede-Aulhorn-Strasse 6

country: Germany

institute: University Tübingen

summary: Staphylococcus aureus (S. aureus) is a known pathogen able to infect humans and animals. Human S. aureus isolates are often associated with carriage of Sa3int prophages combined with loss of beta-hemolysin production due to gene disruption, whereas animal isolates are positive for beta-hemolysin associated with absence of Sa3int prophages. Sa3int prophages are known to contribute to staphylococcal fitness and virulence in human host by providing human-specific virulence factors encoded on the prophage genome. Strain-specific differences in regard to phage transfer, lysogenization and induction are attributable to yet unknown staphylococcal factors specifically influencing prophage gene expression. In this work we used tagRNA-sequencing approach to specifically search for these unknown host factors and differences in prophage gene expression. For this purpose, we established a workflow revealing the first direct comparison for differential gene expression analysis on two distinct single-lysogenic S. aureus isolates. Further, global gene expression patterns were investigated in two S. aureus isolates upon mitomycin C treatment and compared to uninduced conditions. This provides new insights into the tightly linked host-phage interaction network.

overall_design: Samples of 8325-4phi13kana and MW2cphi13kana were grown to OD600 = 0.7 (late exponential growth phase) followed by induction with mitomycin C or without treatment as a control. Each strain and condition was performed in biological triplicates

first: Carina

last: Rohmer

first: Ronja

last: Dobritz


title: RNAseq on 1mm and 5 mm germinating seeds with/without PEG treatment from dissected radicles and cotyledons

city: Angers

first: Jerome

last: Verdier

address: Rue Georges Morel

institute: INRAE / IRHS

summary: RNAseq from Medicago truncatula early post germination (1 and 5mm radicle seeds) from dissected radicles and cotyledons with and without PEG treatment to identify genes induced during the reinduction of the desiccation tolerance at early germination. Dessication tolerant tissues were radicles from 1mm radicle seeds treated with PEG: R1P, and cotyledons from 1- and 5-mm radicle seeds treated or not with PEG: C1, C5, C1P, C5P and desiccation sensitive tissues were radicles from 1mm radicle seeds (R1) and 5mm radicle seeds (R5).

overall_design: Two biological replicates of radicles/cotyledons isolated from 50 germinating seeds for each sample.

first: David

last: Windels

first: Jaiana

last: Malabarba


title: Histone methyltransferase DOT1L regulates macrophage lipid biosynthesis and inflammatory responses and affects atherosclerotic plaque stability [RNA-seq III]

first: Lisa

last: Willemsen

overall_design: In total, 20 samples were analyzed (4 biological replicates of SGC0946 treated BMDMs, 4 biological replicates of DMSO (control) treated BMDMs, 3 biological replicates of SGC0946 + LPS (3h) treated BMDMs, 3 biological replicates of DMSO + LPS (3h) treated BMDMs, 3 biological replicates of SGC0946 + GW3965 (17h) treated BMDMs, and 3 biological replicates of DMSO + GW3965 (17h) treated BMDMs.

first: Koen

last: Prange

first: Annette

last: Neele

first: Cindy

first: Marion

last: Gijbels

first: Guillermo

last: Griffith

first: Myrthe

last: den Toom

first: Linda

last: Beckers

first: Hung-Jen

last: Chen

first: Laura

last: Bosmans

first: Heinz

last: Jacobs

first: Fred

last: vanLeeuwen

last: deWinther


title: Thymic development of type-17 innate-like T cells depends on PTEN

first: Hongbo

last: Chi

overall_design: Refer to individual Series


title: DNA sequencing of Medicago truncatula from ATAC-seq experiment - roots of germinated seeds at 1mm, 1mm+PEG, 5mm

summary: We analysed chromatin changes in Medicago (A17) between radicles from germinated tolreant to desiccation (R1P) or icompared to intolerant to desiccation (R1 and R5). Roots at 1mm were dried for 72hours and are desiccation sensitive, roots at 1mm plus incubation in PEG 8000 at -1.7Mpa for 72h at 10°C then dried for 72hours are desiccation tolerant and roots at 5mm dried for 72h are desiccation sensitive

overall_design: Each replicate consists of at least 30 radicles at each stages

first: Naoto

last: Sano


title: Multi-omic profiling reveals the ataxia protein sacsin is required for integrin trafficking and synaptic organization

first: Paul

last: Chapple

address: Charterhouse Square

department: Faculty of Medicine & Dentistry

institute: Queen Mary University of London

summary:
Autosomal recessive spastic ataxia of Charlevoix-Saguenay (ARSACS) is a childhood-onset cerebellar ataxia caused by mutations in SACS, which encodes the protein sacsin. Cellular ARSACS phenotypes include mitochondrial dysfunction, intermediate filament disorganization, and the progressive death of cerebellar Purkinje neurons.
It is unclear how the loss of sacsin function causes these deficits, or why they manifest as cerebellar ataxia. To investigate this, we performed multi-omic profiling of sacsin knockout cells and compared them to wild-type controls

overall_design: We generated an SH-SY5Y cell line by CRISPR/Cas9 genome editing that do not express sacsin. The transcriptomes of these sacsin KO cells was then compared with WT controls by RNASeq. Both KO and WT cells underwent neuronal differentiation before RNA extraction and we used three replicates per group.

middle: L

last: Romano

first: Tatiana

middle: V

last: Novoselova

first: Charlotte

last: Hall

first: Suran

last: Nethisinghe

first: J

first: Justin

last: Wolter


title: Integrated transcriptome-proteome analyses of human stem cells reveal source-dependent differences in their regenerative signature

city: Palo Alto

first: Avnesh

last: Thakor

state: California

address: 3155 Porter Dr

department: Radiology

institute: Stanford Medicine

summary:
Purpose: Most studies conducted towards understanding the differences among the adult sources of MSCs (BM-MSC and AD-MSC) and UC-MSCs have focused on their phenotypic properties which cannot provide an idea of the functional characteristics changing at the molecular level. Even NGS studies done before, each each study focuses on a different profiling methodology, which makes it difficult to establish a molecular equivalency among the various datasets. We undertake an integrative omics comparison between UC-MSC and two other popular sources of adult MSC (BM-MSC and AD-MSC), with the reasoning that a joint modeling of the changes occurring at the various functional levels will provide greater in-depth insight into the molecular heterogeneity related to different sources of MSCs.
Methods: human Mesenchymal Stem Cell  (MSC) mRNA cultured under basal conditions in Xeno-free media were  subjected to deep sequencing. Three  different MSC sourcers : adipose (AD-MSC), bone-marrow (BM-MSC) and Wharton-jelly umbilical cord (UC-MSC) were used and three donors from each tissues source along with three biological replicates for each donor were sequenced using the Illumina PE 150 platform.  The sequence reads that passed quality filters Q30≥ 80% were analyzed using DESeq2.
Results: Using an optimized data analysis workflow, we  identified 24,804 transcripts among the three different sources of MSCs. Among these 2127 transcripts (~10%) were found to be differentially expressed among the three sources of MSC, with a\Log2FC| ≥2 and FDR <0.05.  Hierarchical clustering of differentially expressed genes uncovered significant differences among the neonatal source (UC-MSC) and adult-MSCs (AD-MSC and BM-MSC). Altered gene expression profiles among the sources was also confirmed using a proteomics study of the same three sources of MSC with the same donors. Further, secretory immune-regulatory molecules which were confirmed to be differentially expressed among the MSC sources using the integrated transcriptomics-proteomics approach was validated using  a Luminex cytokine profiling study.
Conclusions: Our study represents the first detailed integrated analysis of differential gene expression profiling among source-specific human Mesenchymal Stem Cells using a multi-omics approach to validate the observed transcriptomic changes at both the translational as well as secretory levels. Our results offer a comhrehensive evaluation of the differences in immune signaling that exists among the different sourcrs of MSC based on their tissue of origina nd which subsequently plays a decisive role in determining the "regenrative siganture" of these MSCs based on the match between "immune-signature" and "disease type".

overall_design: Integrated Transcriptomics-Proteomics and Secretome Profiling of human Mesenchymal Stem Cells from three different sources - adult sourcces (AD-MSC and BM-MSC) and noenatal source (UC-MSC)

first: Abantika

last: Ganguly

first: Ganesh

last: Swaminathan

first: Fernando

middle: J

last: Marques

first: Sobha

last: Regmi

first: Reza

last: Yarani

first: Rosita

last: Primevera

first: Shashank

last: Chetty

first: Abel

last: Bermudez

first: Ken

last: Lau

first: Sharon

last: Pitteri

middle: S


title: Histone methyltransferase DOT1L regulates macrophage lipid biosynthesis and inflammatory responses and affects atherosclerotic plaque stability [ChIP-seq II]

first: Lisa

last: Willemsen

overall_design: SREBP1/2 ChIP-seq was performed as described previously (Oishi et al, 2017).

first: Koen

last: Prange

first: Annette

last: Neele

first: Cindy

last: vanRoomen

first: Marion

last: Gijbels

first: Guillermo

last: Griffith

first: Myrthe

last: den Toom

first: Linda

last: Beckers

first: Hung-Jen

last: Chen

first: Laura

last: Bosmans

first: Heinz

last: Jacobs

first: Fred

last: vanLeeuwen

first: Menno

last: deWinther


title: PTEN directs developmental and metabolic signaling for innate-like T cells fate and tissue homeostasis [Raptor_or_Rictor_KO_rescue]

first: Hongbo

last: Chi

overall_design: We used microarrays to compare the global transcription profiles of pre and post-selected DP cells WT, Cd4CrePtenfl/fl Cd4CrePtenfl/flRaptorfl/fl, Cd4CrePtenfl/flRictorfl/fl chimeras

first: Wei

last: Li

first: Yu

last: Sun

first: Hao

last: Shi


title: Sequencing analysis of immunopanned embryonic and early postnatal mouse RGCs

city: Los Angeles

first: Riki

last: Kawaguchi

address: 760 Westwood Plaza, Room 37-420

department: Department of Neurology and Department of Psychiatry

institute: University of California Los Angeles

summary: We report the genome-wide RNA sequencing changes to isolated retinal ganglion cells (RGCs) from immunopanned embryonic day 18 (E18) and early postnatal (P5) wildtype mouse retinas.  We report the transcriptomic change associated with RGCs in a survival and regenerative state, and use gene-set enrichment analysis (GSEA) to predict the upstream transcription factors likely regulating these observed changes.

overall_design: Time-course analysis of RGC transcriptomes in embryonic versus postnatal states.

first: Sahil

last: Shah

first: Ephraim

last: Trakhtenberg

first: Yuqin

last: Yin

first: Giovanni

last: Coppola

first: Daniel

last: Geschwind

first: Larry

last: Benowitz

first: Jeffrey

last: Goldberg


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.

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: Differential expression of miRNAs in plasma exosomes between ESCC patients with lymph node metastasis(LNM+) and those without lymph node metastasis(LNM-)

status: Public on Oct 02 2022

city: Jinan

first: Zhaohua

last: Xiao

state: Shandong

address: The second Hosiptal of Shandong University, 247Beiyuan Avenue, Jinan, Shandong 250033,P.R. China

institute: Shandong University

type: Non-coding RNA profiling by high throughput sequencing

summary: To identify the candidate exosomal miRNAs involved in ESCC metastasis, we conducted  small RNA sequencing to determine the miRNA expression profiles of plasma exosomes from 5 LNM+ and 5 LNM- ESCC patients

overall_design: Comparative the exosomal miRNA profiles of plasma from 10 ESCC patients with or without LNM

first: Xiaogang

last: Zhao

first: Zhongxian

last: Tian

first: Xumei

last: Feng


title: Distinct Gene Profiles of Bone Marrow-Derived Macrophages and Microglia During Neurotropic Coronavirus-Induced Demyelination

city: Cleveland

first: Jihye

last: Kim

state: Ohio

address: 9500 Euclid Ave.

institute: Cleveland Clinic

summary: Multiple Sclerosis (MS) is a chronic inflammatory disease of the central nervous system (CNS) characterized by demyelination and axonal loss. Demyelinating lesions are associated with infiltrating T lymphocytes, bone marrow-derived macrophages (BMDM), and activated resident microglia. Tissue damage is thought to be mediated by T cell produced cytokines and chemokines, which activate microglia and/or BMDM to both strip myelin and produce toxic factors, ultimately damaging axons and promoting disability. However, the relative contributions of BMDM and microglia to demyelinating pathology are unclear, as their identification in MS tissue is difficult due to similar morphology and indistinguishable surface markers when activated. The CD4 T cell-induced autoimmune murine model of MS, experimental autoimmune encephalitis (EAE), in which BMDM are essential for demyelination, has revealed pathogenic and repair-promoting phenotypes associated with BMDM and microglia, respectively. Using a murine model of demyelination induced by a gliatropic coronavirus, in which BMDM are redundant for demyelination, we herein characterize gene expression profiles of BMDM versus microglia associated with demyelination. While gene expression in CNS infiltrating BMDM was upregulated early following infection and subsequently sustained, microglia expressed a more dynamic gene profile with extensive mRNA upregulation coinciding with peak demyelination after viral control. This delayed microglia response comprised a highly pro-inflammatory and phagocytic profile. Furthermore, while BMDM exhibited a mixed phenotype of M1 and M2 markers, microglia repressed the vast majority of M2-markers. Overall, these data support a pro-inflammatory and pathogenic role of microglia temporally remote from viral control, whereas BMDM retained their gene expression profile independent of the changing environment. As demyelination is caused by multifactorial insults, our results highlight the plasticity of microglia in responding to distinct inflammatory settings, which may be relevant for MS pathogenesis.

overall_design: SC-derived microglia and SC-derived bone marrow derived monocytes (BMDM) during MHV-JHM CNS infection were analysed using Nanostring nCounter 'mouse nCounter Myeloid Innate Immune Panel

first: Savarin

last: Carine

first: Dutta

last: Ranjan

first: Bergmann

last: Cornelia C


title: Thymic development of type-17 innate-like T cells depends on a PTEN-coordinated two-step process linking TCR and IL-23–IL-23R–Stat3 axis

first: Hongbo

last: Chi

summary:
PTEN orchestrates a two-step process downstream of TCR and IL-23–Stat3 signaling to control type-17 innate-like T cell generation. Complete or partial deletion of PTEN led to the massive and selective accumulation of IL-17-producing thymocytes
We used microarrays to compare the global transcription profiles of WT, Cd4CrePtenfl/fl, and Cd4CrePten+/fl thymocyte population

overall_design: In total 18 samples were analyzed:pre-selection DP WT (n=3); pre-selection DP Pten-Het (n=3); pre-selection DP Pten-KO (n=3);post-selection DP WT (n=3); post-selection DP Pten-Het (n=3); post-selection DP Pten-KO (n=3)

last: Blanco

first: Hao

last: Shi

first: Yogesh

last: Dhungana


title: GPR174 Knockdown Enhances Blood Flow Recovery in Hindlimb Ischemia Mice Model by Upregulating AREG Expression

city: Shanghai

first: Jin

last: Liu

address: 180 Fenglin Road

institute: Zhongshan Hospital, Fudan University

summary: Regulatory T cells (Tregs) are critically involved in neovascularization, an important compensatory mechanism in peripheral artery disease (PAD). The contribution of G protein coupled receptor 174 (GPR174), which is a regulator of Treg function and development, in neovascularization remains elusive. Here, we reveal that genetic deletion of GPR174 in Tregs potentiated blood flow recovery in mice after hindlimb ischemia (HLI). GPR174 deficiency upregulates amphiregulin (AREG) expression in Tregs, thereby enhancing endothelial cell functions and reducing pro-inflammatory macrophage polarization and endothelial cell apoptosis. Mechanically, GPR174 regulates AREG expression by inhibiting the nuclear accumulation of early growth response protein 1 (EGR1) via Gαs/cAMP/PKA signal pathway activation. Collectively, these findings demonstrate that GPR174 negatively regulates angiogenesis and vascular remodeling in response to ischemic injury and that GPR174 may be a potential molecular target for therapeutic interventions of ischemic vascular diseases.

overall_design: mRNA profiles of ischemic muscle from WT and GPR174-KO mice 7 days after HLI

first: Lihong

last: Pan

first: Wenxuan

last: Hong

first: Aijun

last: Sun


title: A single administration of hIL-7-hyFc induces long-lasting T-cell expansion with maintained effector functions and TCR repertoire diversity

city: Seoul

first: Sojeong

address: 50-1 Yonsei-ro, Seodaemun-gu

department: Blood Cancer Research Institute

institute: Yonsei University College of Medicine

summary: Interleukin-7 (IL-7) is an essential cytokine for T-cell homeostatic proliferation and maintenance. Clinical studies have shown the potential benefits of IL-7 therapy in various diseases associated with lymphopenia. However, the kinetics of the T-cell response to a single administration of IL-7 in humans have not been fully elucidated. Here, we investigated the effects of Fc-fused long-acting recombinant human IL-7 (hIL-7-hyFc, efineptakin alfa) on lymphocytes in healthy adults after a single subcutaneous or intramuscular administration.  Administration of hIL-7-hyFc increased the CD8+ and CD4+ T-cell numbers up to 2.5-fold, with corresponding upregulation of Ki-67 and Bcl-2 expression, peaking at day 3 or 7. Regulatory T cells did not expand. Among CD8+ and CD4+ T cells, all T-cell subsets (TN, TEM, TCM, TEMRA, and TSCM) increased for 56 days. The TCR repertoire diversity of naïve CD8+ and CD4+ T cells was increased by hIL-7-hyFc, while the memory T-cell subsets did not differ between D56 and D0. Transcriptomic analysis revealed that hIL-7-hyFc induced robust T-cell expansion without changes in gene expression profiles associated with T-cell functions or genes related to T-cell exhaustion, senescence, and anergy. The effector functions of antigen-specific CD8+ T cells were preserved after hIL-7-hyFc administration. Our results suggest that hIL-7-hyFc administration induced a sustained increase in the numbers of CD8+ and CD4+ T cells, but not regulatory T cells, without qualitative changes. These results support the potential of hIL-7-hyFc as a treatment for patients with compromised T-cell immunity or as a vaccine adjuvant.

overall_design: RNA-seq using RNA of isolated naïve and memory CD4 and CD8 T cells from PBMCs of healthy donors before (D0) and after a single-dose administration of hIL-7-hyFc (D7 and Post (D21-56)), and IR-seq  using RNA of isolated naïve and memory CD4 and CD8 T cells from PBMCs of healthy donors before (D0) and after a single-dose administration of hIL-7-hyFc (Post)

first: Sang

last: Lee

first: June-Young

last: Koh

first: Donghoon

last: Choi

first: Minkyu

last: Heo

first: Jae-Yong

last: Chung

first: Byung

first: Se

last: Yang

first: Young

middle: C

last: Sung

first: Howard

first: Eui-Cheol

last: Shin

first: Su-Hyung

last: Park


title: Condensation of SEUSS promotes hyperosmotic stress tolerance in Arabidopsis

status: Public on Oct 01 2022

city: Beijing

first: Xiaofeng

last: Fang

address: Hai dian

institute: Tsinghua University

summary: Osmotic stress imposed by drought and high salinity inhibits plant growth and crop yield. However, our current knowledge on the mechanism by which plants sense osmotic stress is still limited. Here, we identify the transcriptional regulator, SEUSS (SEU) as a key player during hyperosmotic stress in Arabidopsis. SEU rapidly coalesces into liquid-like nuclear condensates when extracellular osmolarity increases. The intrinsically disordered region 1 (IDR1) of SEU directly senses cell volume decrease resulted from osmotic stress. IDR1 undergoes conformational changes to adopt more compact states upon the increase of macromolecular crowding both in vitro and in cells, and two predicted α-helical peptides are required. SEU condensation is indispensable for osmotic stress tolerance and loss of SEU dramatically compromises the expression of stress-tolerance genes. Our work uncovers a critical role of biomolecular condensates in cellular stress perception and response, and expands our understanding of the osmotic stress pathway.

overall_design: Transcriptome profiles of Col-0 and seu-6 mutant plants with or without NaCl treatment and Sorbitol treatment using RNA-seq (two biological replicates)

first: Boyu

last: Wang

first: Honghong

last: Zhang

first: Junling

last: Huai

first: Fangyu

last: Peng

first: Jie

last: Wu

first: Rongcheng

last: Lin


title: Transcriptome of Pseudomonas putida KT2440 in response to selenite

city: London

first: Jose

last: Jimenez

address: South Kensington Campus

institute: Imperial College London

summary: The bacterium Pseudomonas putida KT2440 has the ability to reduce selenite forming nanoparticles of elemental selenium. This is the transcriptome of the organism when cultured in the presence of selenite.

overall_design: P. putida KT2440 was cultured in LB medium in the absence or presence of 1 mM selenite for 1 hour prior to RNA extraction.

first: Said

last: Muñoz-Montero

first: Juhyun

last: Kim

first: Manuel

last: Salvador

first: José

last: Jiménez


title: Sex-biased effects on hippocampal circuit development by perinatal SERT expression in CA3 pyramidal neurons

city: Bronx

first: Ji

middle: Ying

last: Sze

address: 1300 Morris Park Ave

department: Molecular Pharamcology

institute: Albert Einstein College of Medicine

summary: We demonstrate in mice that perinatal SERT expression in glutamatergic pyramidal neurons in the hippocampus and mPFC modulates sexually dimorphic gene expression during hippocampal circuit assembly and is a source for sex-biased susceptibilities to cognitive and behavioral impairments.

overall_design: Comparative gene expression profiling analysis of RNA-seq data from dorsal hippocampal tissues dissected from P7 SERTPyramid and SERTfl/fl control pups in three replicates; each replicate consisted of dorsal hippocampus tissue pooled from four mice.

first: Roberto

last: De Gregorio

first: Galadu

last: Subah

first: Jennifer

last: Chan

first: Luisa

last: Speranza

first: Xiaolei

first: Aarthi

last: Ramakrishnan

first: Li

last: Shen

first: Ian

last: Maze

first: Patric

last: Stanton

middle: Y


title: DNA sequencing of Medicago truncatula from ChIP-seq experiment - roots of germinated seeds at 1mm, 1mm+PEG, 5mm (after immunoprecipitation of H2AK119Ub)

first: Jerome

last: Verdier

summary: We performed Chromatine ImmunoPrecipitation of the Histone H2AK119Ub mark in 1- and 5mm Medicago (A17) radicles which were desiccation sensitive (R1 and R5) and desiccation tolerant (R1P). Roots at 1mm were dried for 72hs and are desiccation sensitive, roots at 1mm plus incubation in PEG 8000 at -1.7Mpa for 72h at 10°C then dried for 72hs are desiccation tolerant and roots at 5mm dried for 72h are desication sensitive

overall_design: Two replicates of at least 700 radicles at each stages

first: Jaiana

last: Malabarba

first: David

last: Windels


title: Motor neurons use push-pull signals to direct vascular remodeling critical for their connectivity

city: Milano

first: Stefano

last: de Pretis

address: Via Olgettina, 58

department: Center for Omics Sciences

institute: IRCCS San Raffaele Institute

summary: The nervous system requires metabolites and oxygen supplied by the neurovascular network, but this necessitates close apposition of neurons and endothelial cells. We find motor neurons attract vessels with long-range VEGF signaling, but endothelial cells in the axonal pathway are an obstacle for establishing connections with muscles. It is unclear how this paradoxical interference from heterotypic neurovascular contacts is averted. Through a mouse mutagenesis screen, we show that Plexin-D1 receptor is required in endothelial cells for development of neuromuscular connectivity. Motor neurons release Sema3C to elicit short-range repulsion via Plexin-D1, thus displacing endothelial cells that obstruct axon growth. When this signaling pathway is disrupted, epaxial motor neurons are blocked from reaching their muscle targets and concomitantly vascular patterning in the spinal cord is altered. Thus, an integrative system of opposing push-pull cues ensures detrimental axon-endothelial encounters are avoided while enabling vascularization within the nervous system and along peripheral nerves.

overall_design: Comparative gene expression analysis of RNA-seq data of E12.5 mouse embryo Motor Neurons (MN) or Endothelial cells (EC) purified from the spinal cord parenchyma or the surrounding meninges. MNs were FACS-isolated based on expression of ISL1::GFP reporter. ECs were FACS-isolated based on expression of Kdr::Cherry reporter.

first: Dario

last: Bonanomi


title: DNA sequencing of Medicago truncatula from ChIP-seq experiment - roots of germinated seeds at 1mm, 1mm+PEG, 5mm (after immunoprecipitation of H3k27me3)

summary: We performed Chromatine ImmunoPrecipitation of the Histone H3K27me3 mark in 1- and 5mm Medicago (A17) radicles which were desiccation sensitive (R1 and R5) and desiccation tolerant (R1P). Roots at 1mm were dried for 72hs and are desiccation sensitive, roots at 1mm plus incubation in PEG 8000 at -1.7Mpa for 72h at 10°C then dried for 72hs are desiccation tolerant and roots at 5mm dried for 72h are desication sensitive


title: Interactions in CSF1-driven Tenosynovial Giant Cell Tumors

city: Stanford

first: Matt

last: van de Rijn

address: 300 Pasteur Drive

institute: Stanford University

summary: A major component of cells in Tenosynovial Giant Cell Tumor (TGCT) consists of bystander macrophages responding to CSF1 that is overproduced by a small number of neoplastic cells with a chromosomal translocation involving the CSF1 gene. An autocrine loop was postulated where the neoplastic cells are stimulated through CSF1R expressed on their surface. Here we use single cell RNA sequencing to investigate cellular interactions in TGCT.

overall_design: A total of 18,788 single cells from three TGCT and two Giant Cell Tumor of Bone (GCTB) samples underwent singe cell RNAseq. PacBio IsoSeq was performed on the three TGCT cases.

last: van Ijzendoorn


title: Structure-Based Discovery of Potent WD Repeat Domain 5 Inhibitors that Demonstrate Efficacy and Safety in Preclinical Animal Models

city: Nashville

first: Jing

last: Wang

address: 2220 Pierce Avenue

institute: Vanderbilt University Medical Center

summary: WD repeat domain 5 (WDR5) is a core scaffolding component of many multi-protein complexes that perform a variety of critical chromatin-centric processes in the nucleus. WDR5 is component of the mixed lineage leukemia MLL/SET complex and localizes MYC to chromatin tumor-critical target genes. Overexpression of WDR5 promotes oncogenesis in a variety of human cancers that are often associated with poor prognoses. Thus, WDR5 has been recognized as an attractive therapeutic target for treating both solid and hematological tumors. Previously, small-molecule WDR5 WIN-site inhibitors and WDR5 degraders have demonstrated robust in vitro cellular efficacy in cancer cell lines and established the therapeutic potential of WDR5. However, these agents have not demonstrated significant in vivo efficacy at pharmacologically relevant doses by oral administration in animal disease models. We have discovered WDR5 WIN-site inhibitors that feature bicyclic heteroaryl P7 units through structure-based design and address the limitations of our previous series of small-molecule inhibitors. Importantly, our new lead compounds exhibit enhanced on-target potency, excellent oral pharmacokinetic (PK) profiles, and potent dose-dependent in vivo efficacy in a mouse MV4:11 subcutaneous xenograft model by oral dosing. Furthermore, these in vivo probes show excellent tolerability under a repeated high dose regimen in rodents to demonstrate the safety of the WDR5 WIN site inhibition mechanism. Collectively, our results provide strong support for WDR5 WIN-site inhibitors to be utilized as potential anticancer therapeutics.

overall_design: MV4:11 cells were treated with DMSO or WIN site inhibitors C16 and C10. RNA-Seq was used to monitor long-term transcriptional changes.

first: William

last: Tansey

first: Soumita

last: Goswami

first: Gregory

last: Howard

first: Qi

last: Liu


title: Neurotensin expressed in the granulosa cells regulates selective genes that are potentially involved in the ovulatory process

city: Lexington

first: Thomas

middle: E.

last: Curry Jr.

state: KY

address: 800 Rose St, Room MS331

department: OB/GYN

institute: University of Kentucky

summary: Neurotensin (NTS) is a small 13 amino acid neuropeptide. In the mouse ovary, the expression of Nts ovary increases 250-fold 4h after hCG. Similarly, in granulosa cells, the mRNA levels of Nts increased rapidly at 4h after hCG stimulation. Interestingly, the Nts mRNA levels in granulosa cells were approximately 8-fold higher at 4 h after hCG than in whole ovaries. However, the potential mechanisms of NTS action in the ovulatory process are unknown. The present study determined the regulatory mechanisms driving the expression of Nts and functions of the NTS using primary mouse granulosa cells. hCG activated PKA and p38MAPK signaling pathways, and inhibitors for these pathways abolished hCG-induced increases in the levels of Nts. To identify the genes regulated by NTS, high throughput RNA sequencing was performed using Nts silenced mouse granulosa cells treated with or without hCG. Sequencing data analysis revealed that Nts knockdown affects the expression of several genes that were not previously identified in the ovary. qPCR analysis verified hCG-induced, Nts-regulated expression of a selection of these genes. This study revealed novel genes regulated by NTS, thereby providing a function for NTS in the ovulatory process.

overall_design: Cultured mouse granulosa cells transfected either with siRNA negative control (si-NC) or siRNA specific to mouse Nts (si-Nts) and treated with or without hCG were used to perform RNA-seq analysis.

first: Ketan

last: Shrestha

first: Misung

last: Jo

last: Curry Jr


title: Involvement of the SAGA and TFIID coactivator complexes in transcriptional dysregulation caused by separation of core and tail Mediator modules

city: Bloomington

first: Moustafa

last: Saleh

state: IN

address: 915 E 3rd St

department: Biology

institute: Indiana University

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

overall_design: Refer to individual Series


title: Expression profiling in brain microvascular endothelial cells and astrocytes in mouse models of Cranial Cavernous Malformation disease

city: La Jolla

first: Miguel

middle: Alejandro

last: Lopez-Ramirez

state: Ca

address: 9500 Gilman Dr

department: Medicine

institute: University of California, San Diego

summary: Cerebral Cavernous Malformations (CCMs) are neurovascular lesions caused by loss-of-function mutations in one of three genes, including KRIT1 (CCM1), CCM2, and PDCD10 (CCM3). Following onset, disease severity ranges from minimal vascular defects to numerous vascular dilations (lesions) distributed throughout the brain. Although the precise pathogenic mechanisms resulting in such a broad range of disease severity are unknown, inter-cellular communication between heterogeneous brain cell types including microvascular endothelial cells, astrocytes, and neurons are likely important in disease progression. To further understand these cell type relationships in the context of CCM, Riboseq was performed in astroctytes and mRNA expression profiling was performed from whole brain extracts as well as isolated brain microvascular endothelial cells.

overall_design: Pdcd10BECKO (Slco1c1-iCreERT2;Pdcd10fl/fl) and Pdcd10fl/fl control mice were crossed with a ribosome tagged mouse line (Aldh1l1-EGFP/Rpl10a). Following CCM induction with tamoxifen administration, brain tissue was harvested. Ribosome-bound RNA was purified from astrocytes and mRNA was purified from whole brain tissue or from purified brain microvascular endothelial cells. Sequencing was then performed on resultant RNA samples.

first: Catherine

last: Lai

first: Bliss

last: Nelsen

first: Eduardo

last: Frias-Anaya

first: Helios

last: Gallego-Gutierrez

first: Marco

last: Orecchioni

first: Hao

last: Sun

first: Omar

middle: A

last: Mesarwi

first: Klaus

last: Ley

first: Brendan

last: Gongol


title: Loss of colonic primary cilia promotes inflammation and carcinogenesis.

city: Marseille

first: Quentin

last: Da Costa

address: 232 boulevard de Sainte Marguerite

institute: Institut Paoli-Calmettes

summary: Primary cilia (PC) are important signaling hubs and their deregulation is associated with various diseases.  The 2P-CF cultures plus starvation mimic the in vivo proportion of PC on colonic fibroblasts (CF) in an intact colon and thus allow to explore the biology of PC. We generated conditioned starvation medium from colons of DSS treated (termed inflammatory conditioned medium, i.e. inf-CM) and untreated control animals (termed co-CM) and cultured 2P-CF in those media for 24 hours. 30-40% of 2P-CF starved in control medium displayed PC, whereas PC number on 2P-CF starved in inf-CM was consistently lower. We performed RNAseq analysis of 2P-CF starved in inf-CM or in co-CM to gain insight in the molecular traits of those cell cultures.

overall_design: CFs were isolated from the distal colons of 6-week-old mice, cultured for two passages and treated for 24h in presence of control and inflammatory conditioned medium. RNA sequencing was performed on an Illumina NextSeq 500.

first: Michael

last: Hahne

first: Emilie

last: Mamessier


title: The pausing zone and control of RNA polymerase II elongation by Spt5: implications for the pause-release model

city: Aurora

first: Ryan

last: Sheridan

state: CO

address: 12801 East 17th Avenue

institute: University of Colorado Anschutz Medical Campus

summary: The pause-release model of transcription proposes that pol II pauses 40-100 bases from the start site resulting in a pile-up that is relieved by subsequent release into productive elongation.  Pause release is facilitated by PTEFb phosphorylation of the pol II elongation factor, Spt5.  We mapped paused polymerases by eNETseq and found frequent pausing in zones that extend ~0.3-3kb into genes, even when PTEFb is inhibited. The fraction of paused polymerases or “pausiness” declines gradually over several kb, and not abruptly as predicted for a discrete pause release event. Spt5 depletion extends pausing zones suggesting that it promotes maturation of elongation complexes to a low-pausing state.  Expression of mutants after Spt5 depletion showed that phosphomimetic substitutions in the Spt5 CTR1 domain diminished pausing throughout genes. In contrast mutants that prevent phosphorylation of the Spt5 RNA-binding domain strengthened pausing. Thus distinct Spt5 phospho-isoforms set the balance between pausing and elongation.

overall_design: anti-pol II mNET-seq & ChIP-seq

first: David

last: Bentley


title: Involvement of the SAGA and TFIID coactivator complexes in transcriptional dysregulation caused by separation of core and tail Mediator modules (nsRNA-Seq)

summary: Regulation of RNA polymerase II (RNAPII) transcription requires the concerted efforts of several multisubunit coactivator complexes, which interact with the RNAPII preinitiation complex (PIC) to stimulate transcription. We previously showed that separation of the Mediator core (cMed) from Mediator’s tail module results in modest overactivation of genes annotated as highly dependent on TFIID for expression. However, it is unclear if other coactivators are involved in this phenomenon. Here, we show that the overactivation of certain genes by cMed/tail separation is blunted by disruption of the SAGA complex through removal of its structural Spt20 subunit, though this downregulation does not appear to depend on reduced SAGA association with the genome. Consistent with the enrichment of TFIID-dependent genes among genes overactivated by cMed/tail separation, depletion of the essential TFIID subunit Taf13 suppressed overactivation of these genes when Med16 was simultaneously removed. As with SAGA, this effect did not appear to be dependent on reduced genomic association of TFIID.

overall_design: nsRNA-seq of auxin-inducible degron strains treated with DMSO or 3-IAA

middle: M

first: Gabriel

last: Zentner


title: RNA-seq analysis of human esophageal mucosal tissue from achalasia and healthy control subjects

city: Chicago

first: Marie-Pier

last: Tetreault

state: IL

address: 300 East Superior Street

department: Medicine/GI&Hep division

institute: Northwestern University

summary: Despite recent advances in achalasia diagnosis, our understanding of the pathogenesis of achalasia at the molecular level is still very limited and gene expression profiling has yet to be performed. We performed bulk RNA-sequencing on esophageal mucosa from 14 achalasia and 8 healthy subjects.

overall_design: Total RNA was isolated from human esophageal mucosal biopsies from type I and type II achalasia and healthy control subjects

first: Caroline

middle: K

last: Patel

first: Nathan

middle: B

last: Hodge


title: Involvement of the SAGA and TFIID coactivator complexes in transcriptional dysregulation caused by separation of core and tail Mediator modules (ChEC-Seq)

first: Moustafa

last: Saleh

summary: Regulation of RNA polymerase II (RNAPII) transcription requires the concerted efforts of several multisubunit coactivator complexes, which interact with the RNAPII preinitiation complex (PIC) to stimulate transcription. We previously showed that separation of the Mediator core (cMed) from Mediator’s tail module results in modest overactivation of genes annotated as highly dependent on TFIID for expression. However, it is unclear if other coactivators are involved in this phenomenon. Here, we show that the overactivation of certain genes by cMed/tail separation is blunted by disruption of the SAGA complex through removal of its structural Spt20 subunit, though this downregulation does not appear to depend on reduced SAGA association with the genome. Consistent with the enrichment of TFIID-dependent genes among genes overactivated by cMed/tail separation, depletion of the essential TFIID subunit Taf13 suppressed overactivation of these genes when Med16 was simultaneously removed. As with SAGA, this effect did not appear to be dependent on reduced genomic association of TFIID.   Given that the observed changes in gene expression could not be clearly linked to alterations in SAGA or TFIID occupancy, our data may suggest that the cMed/tail connection is important for modulation of SAGA and/or TFIID conformation and/or function at target genes.

overall_design: ChEC-seq of SAGA and TFIID subunits in Med16 deletion or depletion strains.


title: Hippocampal RNA-seq in mice selectively bred for high and low open-field activity (OFA)

city: BOULDER

first: Winona

last: Booher

address: 5441 White place

department: Institute for Behavioral Genetics

institute: University of Colorado Boulder

summary:
Purpose: To investigate the effect that selective breeding for high and low OFA has on gene expression
Methods: Male and female High and Low Activity mice (n=4 per strain/sex) were euthanized at postnatal day 70 and hippocampi were immediately collected. Paired-end RNA-seq methods were employed to assess hippocampal mRNA expression.
Results: The expression of thousands of transcripts were altered by selective breeding for high and low OFA.

overall_design: Poly-A RNA from the hippocampi was profiled using Illumina NovaSEQ 6000 (2x150). Tissue was generated from 16 High and Low Activity mouse strains (n=4 per strain/sex). Mice were euthanized at postnatal day 70 for immediaite hippocampi collection.

first: Lauren

last: Vanderlinden

first: Lucy

last: Hall

first: Aimee

last: Thomas

first: Laura

last: Saba

first: Marissa

last: Ehringer