title: PCID2 dysregulates transcription and viral RNA processing to promote HIV-1 latency

city: Rotterdam

first: Tokameh

last: Mahmoudi

address: Dr Molewaterplein 40

country: Netherlands

institute: Erasmus Medical Center

summary: HIV-1 latency results from tightly regulated molecular processes that act at distinct steps of HIV-1 gene expression. To elucidate the molecular players that govern latency, we previously performed a dCas9-chromatin immunoprecipitation coupled with mass spectrometry (Catchet-MS) and identified the interactome of the latent HIV-1 LTR. Here we characterize the Catchet-MS-identified PCI domain-containing 2 (PCID2) protein, a component of the TREX2 complex, to play a dual role in promoting HIV-1 latency by enforcing both transcriptional repression and post-transcriptional blocks to HIV-1 gene expression. PCID2 bound the latent HIV-1 LTR and repressed transcription initiation during latency. Depletion of PCID2 remodelled the chromatin landscape at the HIV-1 promoter and resulted in transcriptional activation and reversal of latency. Immunoprecipitation coupled to Mass Spectrometry identified PCID2-interacting proteins to include members of the spliceosome, including negative viral RNA (vRNA) alternative splicing regulators, and PCID2 depletion resulted in over-splicing of intron-containing vRNA and misregulated expression of vRNA splice variants in cell lines and primary cells obtained from people living with HIV-1. We demonstrate that MCM3AP and DSS1, two other RNA-binding TREX2 complex subunits that comprise the dock of the complex also inhibit transcription initiation and viral RNA alternative splicing during latency and similarly to PCID2 function as prominent latency associated repressors of HIV-1 gene expression. Thus, PCID2 is a novel HIV-1 latency-promoting factor, which in context of the TREX2 sub-complex PCID2-DSS1-MCM3AP blocks transcription and dysregulates vRNA processing.

overall_design: 2 million shControl and shPCID2 J-Lat 11.1 cells were collected for RNA sequencing analysis in duplicate. Total RNA was isolated as described above and cDNA libraries were generated using the 3’ mRNA-seq Library Prep Kit Protocol for Ion Torrent (QuantSeq-LEXOGEN) following manufacturer’s instructions. Library quality was assessed on a Bionalayzer using the DNA High Sensitivity Kit reagent and protocol (Agilent Technologies). Libraries were pooled and template and enriched using an Ion Proton One Touch system with Ion PI Hi-Q OT2 200 Kit (Thermo Fisher Scientific). Sequencing was performed using the Ion PI Hi-Q Sequencing 200 Kit on Ion Proton PI V2 chips (Thermo Fisher Scientific) according to manufacturer’s protocols. Reads were mapped on the UCSC hg19 reference genome and processed for normalization as described before (elife paper). Differentially expressed gene analysis of obtained reads was performed using edgeR package under Galaxy (https://usegalaxy.eu/). Cut-off for false discovery rate was 0.01 and a 1.5 fold change for differentially expressed. Volcano plots were generated using Galaxy (https://usegalaxy.eu/).

first: Raquel

last: Crespo

first: Enrico

last: Ne

first: Julian

last: Reinders

first: Jenny

middle: I

last: Meier

first: Chengcheng

first: Sanne

last: Jansen

first: Alicja

last: Gorska

first: Selin

last: Kocer

first: Tsung

middle: W

last: Kan

first: Wouter

last: Doff

first: Dick

last: Dekkers

first: Jeroen

last: Demmers

first: Robert-Jan

last: Palstra

first: Shringar

last: Rao


title: Comparative transcriptional analysis of Candida auris biofilms following farnesol and tyrosol treatment

status: Public on Dec 11 2023

city: Debrecen

first: Agnes

last: Jakab

address: Nagyerdei krt 98.

country: Hungary

institute: University of Debrecen

type: Expression profiling by high throughput sequencing

summary: Candida auris is frequently associated with biofilm-related invasive infections. The resistant profile of these biofilms necessitates innovative therapeutic options, where quorum sensing may be a potential target. Farnesol and tyrosol are two fungal quorum-sensing molecules with antifungal effects at supraphysiological concentrations. Here, we performed genome-wide transcript profiling with C. auris biofilms following farnesol or tyrosol exposure using transcriptome sequencing (RNA-Seq). Since transition metals play a central role in fungal virulence and biofilm formation, levels of intracellular calcium, magnesium, and iron were determined following farnesol or tyrosol treatment using inductively coupled plasma optical emission spectrometry. Farnesol caused an 89.9% and 73.8% significant reduction in the calcium and magnesium content, respectively, whereas tyrosol resulted in 82.6%, 76.6%, and 81.2% decrease in the calcium, magnesium, and iron content, respectively, compared to the control. Genes involved in biofilm events, glycolysis, ergosterol biosynthesis, fatty acid oxidation, iron metabolism, and autophagy were primarily affected in treated cells. To prove ergosterol quorum-sensing molecule interactions, microdilution-based susceptibility testing was performed, where the complexation of farnesol, but not tyrosol, with ergosterol was impeded in the presence of exogenous ergosterol, resulting in a minimum inhibitory concentration increase in the quorum-sensing molecules. This study revealed several farnesol- and tyrosol-specific responses, which will contribute to the development of alternative therapies against C. auris biofilms.

overall_design: Comparative gene expression profiling analysis of RNA-seq data of tyrosol and farnesol treated and untreated Candida auris biofilms.

first: Ágnes

first: Fruzsina

last: Kovács

first: Noémi

last: Balla

first: Csaba

last: Nagy-Köteles

first: Ágota

last: Ragyák

last: Nagy

first: Andrew

middle: M

last: Borman

first: László

last: Majoros

first: Renátó


title: Neoadjuvant CD40 agonism remodels the tumor immune microenvironment in locally advanced esophageal/gastroesophageal junction cancer

status: Public on Dec 10 2023

city: San Francisco

first: Bridget

middle: P

last: Keenan

state: CA

address: 505 PARNASSUS AVE, ROOM 1296

department: Medicine

country: USA

institute: University of California San Francisco

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

overall_design: Refer to individual Series


title: Effect of depletion of BBX14 or GLK on gene expression in seedlings

status: Public on Dec 09 2023

city: Planegg

first: Tatjana

last: Kleine

address: Großhaderner Straße 2

department: Biologie I, Botanik

country: Germany

institute: Ludwig-Maximilians-Universität München

type: Non-coding RNA profiling by high throughput sequencing


title: Neoadjuvant CD40 agonism remodels the tumor immune microenvironment in locally advanced esophageal/gastroesophageal junction cancer [scRNA-seq]

summary: Sotigalimab (sotiga) is an agonistic anti-CD40 monoclonal antibody that can modulate anti-tumor immune responses. In a clinical trial of sotiga combined with neoadjuvant chemoradiation (CRT) in locally advanced esophageal/gastroesophageal junction cancer, treatment induced pathologic complete responses in 38% of patients. Using high-dimensional single cell techniques, we found that sotiga dramatically re-modeled both peripheral immune responses and the tumor microenvironment (TME), increasing components of antigen processing and presentation and altering metabolic pathways in myeloid cells. Concomitant with myeloid cell alterations, sotiga primed new T cell clonotypes, increased T cells with enhanced cytotoxic activity, and decreased the frequency of Tregs in the TME. Clinical responses were associated with both baseline and treatment-induced T cell states. These findings indicate that sotiga induces antigen presentation leading to enhanced T cell activation and clinical response, and that the immune composition of the TME at baseline is important in conferring sensitivity to this treatment approach.

overall_design: Tumor samples were obtained from patients pre- and on-treatment as part of a phase II clinical trial clinical trial (NCT03165994). Treatment regimen was carboplatin (AUC 2)/paclitaxel (50 mg/m2) weekly for 5 weeks and concurrent radiation 5040 cGy in 28 fractions, and up to 4 doses of sotigalimab 0.3mg/kg IV between weeks 1-10, followed by Ivor-Lewis esophagectomy. Tumor biopsies were performed prior to the initiation of treatment (pre-treatment) and 1-2 weeks after the first dose of sotiga prior to chemoradiation (post-treatment); when available, surgical resections were also collected for correlative analysis.

first: Maira

last: Soto

first: Erin

middle: L

last: Filbert

first: Hai

last: Yang

first: Stephanie

last: Starzinski

first: Alec

first: Marissa

last: Gin

first: Brandon

last: Chen

first: Phi

last: Le

first: Tony

last: Li

last: Bol

first: Alexander

last: Cheung

first: Li

last: Zhang

first: Frank

middle: J

last: Hsu

last: Ko

first: Lawrence

last: Fong


title: cDCBLD2 mediates sorafenib resistance in hepatocellular carcinoma by sponging miR-345-5p binding to the TOP2A coding sequence

city: Hangzhou

first: Yunkun

last: Lu

state: Zhejiang

address: No. 3, Qingchun East Rd

department: Sir Run Run Shaw Hospital

country: China

institute: Zhejiang University

summary: Sorafenib is a first-line chemotherapy drug for treating advanced hepatocellular carcinoma (HCC). However, its therapeutic effect has been seriously affected by the emergence of sorafenib resistance in HCC patients. The underlying mechanism of sorafenib resistance is unclear. Here, we report a circular RNA, cDCBLD2, which plays an important role in sorafenib resistance in HCC. We found that cDCBLD2 was upregulated in sorafenib-resistant (SR) HCC cells, and knocking down cDCBLD2 expression could significantly increase sorafenib-related cytotoxicity. Further evidence showed that cDCBLD2 can bind to microRNA (miR)-345-5p through a competing endogenous RNA mechanism, increase type IIA topoisomerase (TOP2A) mRNA stability through a miRNA sponge mechanism, and reduce the effects of sorafenib treatment on HCC by inhibiting apoptosis. Our findings also suggest that miR-345-5p can negatively regulate TOP2A levels by binding to the coding sequence region of its mRNA. Additionally, targeting cDCBLD2 by injecting a specific small interfering RNA (siRNA) could significantly overcome sorafenib resistance in a patient-derived xenograft (PDX) mouse model of HCC. Taken together, our study provides a proof-of-concept for a potential strategy to overcome sorafenib resistance in HCC patients by targeting cDCBLD2 or TOP2A.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for HCCLM3-SR cells and its KD derivatives (si_cDCBLD2, si_CTRL).

first: Yeling

last: Ruan

first: Tianyi


title: Distinct prefrontal projections oppositely orchestrate social competition and hierarchy

city: Seoul

first: Murim

last: Choi

address: 103 Daehakro, Jongrogu

country: South Korea

institute: Seoul National University

summary: The medial prefrontal cortex (mPFC) is known as a hub of social hierarchy determination in the brain, Using high throughput single cell transcriptomic analysis and projection-specific genetic manipulation, we discovered that the expression level of Pou3f1 in mPFC-VTA neurons controls social hierarchy.

overall_design: mPFC from social dominants (R1, n=5) and subordinates (R4, n=5) tissue punches were collected and dissected, and the resulting cells were subjected to a 10X Genomics scRNA-seq pipeline

first: Tae-Yong

first: Hyoungseok

last: Jeon

first: Sejin

last: Jeong

first: Eum

last: Kim

first: Jeongseop

first: Yun

middle: H

first: Byungsoo

last: Kang

first: Ja

last: Koo


title: A Molecular Switch for Neuroprotective Astrocyte Reactivity

city: Palo Alto

first: Evan

middle: G

last: Cameron

state: Ca

address: 1651 Page Mill Road

department: Department of Ophthalmology

institute: Stanford University

summary: Astrocytes differentiate into a spectrum of neurotoxic and neuroprotective reactive subpopulations after CNS injury and in disease.  In astrocyte conditional ADCY10 (sAC) knockout mice, reactive astrocytes exhibit a shift towards neurotoxic phenotypes implicating sAC as a critical regulator of neuroprotective astrocyte differentiation.

overall_design:
To induce reactive astrocyte differentiation wildtype (BL6) and conditional astrocyte sAC KO mice were subjected to bilateral optic nerve crush.
Optic nerves were collected and dissociated for single cell RNAseq analysis 3 and 7 days' post crush injury.
Comparative gene expression analysis was performed on WT naïve (no crush), WT crushed, and sAC KO crushed samples.

first: Anna

last: Toth

first: Michael

last: Nahmou

first: Lyong

last: Heo

first: Jeffrey

last: Goldberg


title: Gene expression changes in B-ALL and DLBCL cells induced by EdC, a replication stress-inducing nucleoside analog prodrug.

status: Public on Dec 08 2023

city: Philadelphia

first: Ramkrishna

last: Mitra

state: Pennsylvania

address: 233 S 10th street

institute: Thomas Jefferson University

summary: RNA-sequencing analysis of B-ALL and DLBCL cell lines validate the replication stress-inducing mechanism of action (MOA) of EdC. Downregulation of genes involved in cell cycle progression and DNA biosynthesis support initial findings that EdC induces G1/S phase arrest, and upregulation of genes involved in DNA damage response (DDR) and the interferon alpha and gamma response support initial findings that EdC induces DNA damage and apoptosis.

overall_design: Gene expression profiles after 16hr treatment with 1uM EdC were established using RNA-sequencing in B-ALL and DLBCL cell lines to further investigate the replication stress-inducing MOA of EdC.

first: Richard

last: Pomerantz

first: Marissa

last: Calbert


title: Genetic determinants of TCF7L2 binding and chromatin availability in mouse liver

city: Kuopio

first: Juho

middle: Mikael

last: Mononen

address: Yliopistonranta 1E

department: Faculty of Health Sciences

country: Finland

institute: University of Eastern Finland

type: Genome binding/occupancy profiling by high throughput sequencing


title: Skeletal muscle specific AMPKalpha1/2 deletion during hindlimb unloading

city: Salt Lake City

first: Micah

last: Drummond

state: UT

institute: University of Utah

summary: The primary goal of this study was to determine the role of AMPKalpha during disuse atrophy. Skeletal muscle-specific tamoxifen-inducible AMPKlpha1/alpha2 double knockout (KO) mice were generated and KO was induced for 4 weeks. After 2 weeks of KO, mice were hindlimb unloaded (HU) for 2 weeks to induce atrophy or maintained ambulatory (AMB). We observed that AMPKalpha double KO impaired skeletal muscle transcriptional profiles that may have carried over with HU.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for AMPKalpha double knock out soleus muscle samples with 7-8 replicates per group

first: Jonathan

last: Petrocelli

first: Chris

last: Stubben


title: Milk fat globule membrane modulates inflammatory pathways in human monocytes: A crossover human intervention study

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

institute: Wageningen University

summary: Intake of high-fat foods raises postprandial plasma triglycerides and inflammatory markers, which may depend on the type of fat ingested. Dairy products are commonly consumed, but not much is known about the impact of milk fat and the milk fat globule membrane on postprandial inflammation. Here, we aimed to study the effect of milk fat with and without milk fat globule membrane and vegetable blend fat on post-prandial inflammation, with a focus on blood monocyte gene expression. We performed a randomized, double-blind cross-over trial in middle-aged healthy male and female volunteers (BMI 22–27 kg/m2). The participants consumed a meal shake containing 95.5 g of fat consisting of either a vegetable fat blend (VEGE), anhydrous milk fat (AMF, without milk fat globule membrane), or cream (CREAM, containing milk fat globule membrane). Blood monocytes were collected at 0 and 6 hours postprandially and used for bulk RNA sequencing and ex vivo stimulation with LPS. Consumption of all three shakes significantly decreased the percentage of classical monocytes and increased the percentages of intermediate monocytes and non-classical monocytes. No differences in these measures were observed between shakes. Using a threshold of p < 0.01, 787 genes were differentially regulated postprandially between the three shakes. 89 genes were differentially regulated postprandially between AMF and VEGE, 373 genes between AMF and CREAM, and 667 genes between VEGE and CREAM, indicating that the effect of CREAM on monocyte gene expression was distinct from AMF and VEGE. Pathway analyses showed that VEGE significantly increased the expression of genes involved in inflammatory pathways, whereas this was less pronounced after AMF and not observed after CREAM. In addition, CREAM significantly down-regulated the expression of genes involved in energy metabolism-related pathways, such as glycolysis, TCA cycle, and oxidative phosphorylation, as well as HIF1 signaling. Compared to the consumption of an anhydrous milk fat without milk fat globule membrane and a vegetable fat blend, the consumption of cream with milk fat globule membrane downregulated inflammatory pathways in blood monocytes, thus suggesting a potential inflammation inhibitory effect of milk fat globule membrane.

overall_design: Blood mononuclear cells were isolated from participants before (t=0), and 6 hrs after consumption of a shake consisting either of milk fat with, or without milk fat globule membrane, or a vegetable blend, and subjected to gene expression profiling by RNA-sequencing.

first: Lei

last: Deng

first: Anouk

last: Feitsma

first: Sander

last: Kersten

first: Lydia

middle: A

last: Afman


title: Spatial transcriptomics data of HS lesional skin and healthy skin

first: Margaret

last: Lowe

address: 513 Parnassus Avenue, HSW1201B

institute: UCSF

summary: Hidradenitis suppurativa (HS) skin lesions are infiltrated by numerous inflammatory cell types, which may be subject to and can act upon surrounding tissue stroma and epithelium. Understanding how these networks are locally organized can help identify key nodes sustaining inflammatory and fibrotic processes.

overall_design: Spatial Transcriptomics data of two samples of HS lesional skin and one normal control

middle: D

last: Rosenblum


title: Estrobolome dysregulation is associated with altered immunometabolism in a mouse model of endometriosis

city: Columbia

first: Mitzi

last: Nagarkatti

state: SC

address: 6439 Garners Ferry Rd

department: PMI

institute: University of South Carolina School of Medicine

summary: Microbiome dysregulation affects the estrogen metabolism (estrobolome) profile which in turns affects the immunological response. Estrogen hormone is an essential hormone that regulates the sexual activity in females as well as immune response in both sexes. Endometriosis  is one of complicated disorder influnce the fertility of females due to escape of endometrial tissue into peritoneal cavity where the immunotoxicity will be undertaken. This study designed to investigate if there is any correlation between the microbiome dyregulation with the severity of endometriosis outcomes.

overall_design: Balb\c mice were used as an experimental model to mimic human enodmetriosis. Colonic contents were collected to estimate the short chain fatty acids and investigate the bacterial community alterations via 16s rRNA metagenomic analysis. Then to connect between these changes with the metabolism of immunocytes, namely T cells.

first: Hasan

last: Alghetaa

first: Amira

last: Mohammed

first: Prakash


title: Sperm chromatin accessibility’s involvement in the intergenerational effects of stress hormone receptor activation

city: Zurich

first: Vincent

middle: Valentin Tobias

last: Fischer

address: Wintherthurerstrasse 190

department: INS

country: Switzerland

institute: ETH Zurich

summary: Dexamethasone is a stress hormone receptor agonist used widely in clinics. We and others previously showed that paternal administration of dexamethasone in mice affects the phenotype of their offspring. The substrate of intergenerational transmission of environmentally induced effects often involves changes in sperm RNA, yet other epigenetic modifications in the germline can be affected and are also plausible candidates. First, we tested the involvement of altered sperm RNAs in the transmission of dexamethasone induced phenotypes across generations. We did this by injecting sperm RNA into naïve fertilized oocytes, before performing metabolic and behavioral phenotyping of the offspring. We observed phenotypic changes in discordance with those found in offspring generated by in vitro fertilization using sperm from dexamethasone exposed males. Second, we investigated the effect of dexamethasone on chromatin accessibility using ATAC sequencing and found significant changes at specific genomic features and gene regulatory loci. Employing q-RT-PCR, we show altered expression of a gene in the tissue of offspring affected by accessibility changes in sperm. Third, we establish a correlation between specific DNA modifications and stress hormone receptor activity as a likely contributing factor influencing sperm accessibility. Finally, we independently investigated this dependency by genetically reducing thymine-DNA glycosylase levels and observing concomitant changes at the level of chromatin accessibility and stress hormone receptor activity.

overall_design: Tn5 fragmented mouse sperm chromatin of 3 Tdg+/- and 2 Ctrls as well as 3 Dexamethasone injected mice and 2 Vehicles were analyzed in regard to their chromatin accessibility

first: Katharina

last: Gapp

first: Pierre-Luc

last: Germain

first: Miriam

last: Kretschmer

first: Faiza

last: Noreen

first: David

last: Schürmann

first: Primo

last: Schär


title: Lead exposure induced transgenerational developmental neurotoxicity by altering genome methylation in Drosophila

city: Nanjing

first: Mingkuan

last: Sun

state: jiangsu

address: 101 Longmian Ave

institute: Nanjing Medical University

type: Methylation profiling by high throughput sequencing

summary: Heavy metal toxicity is a worldwide health problem. Lead exposure is of particular concern due to the adverse effects of low concentrations on cognitive development in children. Although the mechanism of lead neurotoxicity has been well studied, the analysis and molecular mechanism of the transgenerational effects of lead exposure-induced neurotoxicity are lacking. To address this, Drosophila, a powerful developmental animal model, was exposed to lead acetate. We found that Pb exposure during the developmental stage affected the neurodevelopment of F0 fruit flies, resulting in a loss of the correlation between the motor terminal area and muscle fiber area and the increased frequency of β-lobe midline crossing phenotype in Mushroom bodies. We also found that Pb exposure led to an increase in BRP expression, suggesting an increase in synaptic vesicle release sites and a decrease in synaptic vesicle protein SYN expression in F0 generation. This explained the results of our electrophysiological data that Pb exposure led to an increase in the amplitude of evoked excitatory junctional potential (EJP) and an increase in the frequency of spontaneous excitatory junctional potential (mEJP). Our results further confirmed that the developmental neurotoxicity of parental Pb exposure has a transgenerational effect. Neurodevelopmental defects, abnormalities in synaptic function, and repetitive behavior also were observed in the F3 offspring of F0 exposed to lead. Our Medip-seq analysis showed that Pb exposure altered the DNA methylation levels of many neurodevelopmentally associated genes (eg, hppy, nrg, baz, and spn) in the F3 offspring of the F0 generation with Pb exposure. Our findings suggest that epigenetic mechanisms may underlie the transgenerational inheritance of acquired phenotypic traits resulting from exposure to environmental factors.

overall_design: To investigate the effect of lead exposure on the genome methylation ,we use MeDIPSeq to explore differentially enriched region between lead exposure group and control group.


title: Diverse injury responses of human oligodendrocyte to mediators implicated in multiple sclerosis

city: Montreal

first: Jack

last: Antel

state: Quebec

address: 3801 Rue University

country: Canada

institute: McGill University

summary: Early multiple sclerosis lesions feature relative preservation of oligodendrocyte cell bodies with dying back retraction of their myelinating processes. Cell loss occurs with disease progression. Putative injury mediators include metabolic stress (low glucose/nutrient), pro-inflammatory mediators (interferon γ and tumor necrosis factor a), and excitotoxins (glutamate). Our objective was to compare the impact of these disease relevant mediators on the injury responses of human mature oligodendrocytes. In the current study, we determined the effects of these mediators on process extension and survival of human brain derived mature oligodendrocytes in vitro and used bulk RNA sequencing to identify distinct effector mechanisms that underlie the responses. All mediators induced significant process retraction of the oligodendrocytes in dissociated cell culture. Only metabolic stress (low glucose/nutrient) conditions resulted in delayed (4-6 days) non-apoptotic cell death. Metabolic effects were associated with induction of the integrated stress response, which can be protective or contribute to cell injury dependent on its level and duration of activation. Addition of Sephin1, an agonist of the integrated stress response induced process retraction under control conditions and further enhanced retraction under metabolic stress conditions. The antagonist ISRIB restored process outgrowth under stress conditions, and if added to already stressed cells, reduced delayed cell death and prolonged the period in which recovery could occur.  Inflammatory cytokine functional effects were associated with activation of multiple signaling pathways (including Jak/Stat-1) that regulate process outgrowth, without integrated stress response induction. Glutamate application produced limited transcriptional changes suggesting a contribution of effects directly on cell processes.

overall_design: Investigation of the stress response mechanims of injured oligodendrocytes in situ and in vitro. We used fresh frozen brain tissue sections from MS patients and identified the implication of the integrated stress response in MS lesions in oligodendrocyte cells. We further investigated the function of this pathway in vitro in human primary oligodendrocyte cells under stress related conditions: metabolic, pro-inflammatory and excitotoxic insults. We finally modulated the integrated stress response using agonist and antagonist drugs and assessed the functional outcome in oligodendrocyte stress response.

first: Florian

last: Pernin

first: Julia

middle: X

last: Luo

first: Qiao-Ling

last: Cui

first: Manon

last: Blain

first: Milton

last: Fernandes

first: Moein

last: Yaqubi

first: Myriam

last: Srour

first: Jeff

last: Hall

first: Roy

last: Dudley

first: Hélène

last: Jamann

first: Catherine

last: Larochelle

first: Stephanie

middle: E

last: Zandee

first: Alexandre

last: Prat

first: Jo

last: Stratton

first: Timothy

last: Kennedy


title: In planta bacterial RNA-Seq of Xanthomonas L148

city: Cologne

first: Frederickson

last: Entila

state: Nordrhein-Westfalen

address: Carl-von-Linne-Weg 10

department: Plant-Microbe Interactions

institute: MPIPZ

summary: To gain insight on the role of ROS pathway on the modulation of the cooperative behavior of a potentiall pathogenic leaf commensal Xanthomonas L148, in planta bacterial transcriptome landscape was profiled.

overall_design: performed in planta bacterial RNA-Seq upon inoculation of Xanthomonas L148 on Col-0 or rbohD plants 2dpi

first: Kenichi

last: Tsuda

first: Paul

last: Schulze-Lefert


title: Gene expression by high-throughput sequencing of T47D-MTVL human breast cancer cells upon H1.2 knock-down

city: Barcelona

first: Albert

last: Jordan

address: Baldiri Reixac 4

department: Molecular Genomics

country: Spain

institute: IBMB-CSIC

summary: Gene expression of T47D-MTVL human breast cancer cells expressing Dox-inducible shRNAs against histone H1.2 (H1.2sh).

overall_design: Stable breast cancer-derived cell lines expressing an shRNA against H1.2 in response to doxycycline (Dox) were grown for six days in the presence or absence of doxycycline, RNA extracted, and high-throughput sequenced. Cell lines used: inducible shRNA against H1.2 histone H1 variant.

first: A

first: N

last: Serna

first: M

last: Salinas


title: A fluorescent assay for cryptic transcription in Saccharomyces cerevisiae

city: Vancouver

first: LeAnn

last: Howe

state: BC

address: 2350 Health Sciences Mall

department: Biochemistry and Molecular Biology

institute: University Of British Columbia

sample_organism:
Saccharomyces cerevisiae
Saccharomyces cerevisiae S288C


title: Overall gene expression was evaluated in lnc CHASERR  transfected  human glioma T98G cells. The transcriptome of T98G cells transfected with sh-NC and sh-lnc CHASERR were compared.

status: Public on Dec 07 2023

city: wuhu

first: Hui

last: Yang

state: Anhui

address: No.22 Wenchang West Road,Wuhu,Anhui 241002,P.R.China

institute: wannan medical college

summary: We used high-throughput sequencing to analyse differentially expressed genes among human glioma cells T98G transfected with sh-lnc CHASERR.

overall_design: In order to investigate the biological regulation of glioma by lnc CHASERR, we established T98G glioma cells that were knocked down by sh-lnc CHASERR. T98G cells transfected with sh-NC and sh-lnc CHASERR were selected. RNA was extracted and hybridised to Illumina NovaSeq 6000 microarrays. We attempted to obtain differentially expressed genes.

first: Xingwei

last: Wu


title: HDAC inhibitors directly modulate T cell gene expression and signaling and promote development of effector-exhausted T cells in murine tumors [Array]

city: Tampa

first: Amer

last: Beg

state: FL

address: 12902 Magnolia Drive

institute: Moffitt Cancer Center

summary: Epigenetic regulation plays a crucial role in the development and progression of cancer, including the regulation of antitumor immunity. The reversible nature of epigenetic modifications offers potential therapeutic avenues for cancer treatment. In particular, Histone deacetylase (HDAC) inhibitors (HDACi) have been shown to promote antitumor T cell immunity by regulating myeloid cell types, enhancing tumor antigen presentation, and increasing expression of chemokines. HDACi are currently being evaluated to determine whether they can increase the response rate of immune checkpoint inhibitors (ICIs) in cancer patients. While the potential direct effect of HDACi on T cells likely impacts antitumor immunity, little is known about how HDAC inhibition alters the transcriptomic profile of T cells. Here, we show that two clinical-stage HDACi profoundly impact gene expression and signaling networks in CD8+ and CD4+ T cells. Specifically, HDACi promoted T cell effector function by enhancing expression of TNFa and IFNg and increasing CD8+ T cell cytotoxicity. Consistently, in a murine tumor model, HDACi led to enrichment of CD8+ T cell subsets with high expression of effector molecules (Prf1, Ifng, Gzmk, Grmb) but also molecules associated with T cell exhaustion (Tox, Pdcd1, Lag3, Havcr2). HDACi further generated a TME dominated by myeloid cells with immune suppressive signatures. These results indicate that HDACi directly and favorably augment T cell effector function but also increase their exhaustion signal in the TME, which may add a layer of complexity for achieving clinical benefit in combination with ICIs.

overall_design: The  gene expression profile of CD4 and CD8 cells under treatment using Vorinostat and Romidepsin

first: Hong

last: Zheng

first: Zhihua

last: Chen

first: Xiaoqing

last: Yu


title: Generation of antigen-specific mature T cells from RAG1−/−RAG2−/−B2M−/− stem cells by engineering their microenvironment

city: Los Angeles

first: Gay

last: Crooks

address: 610 CHARLES E. YOUNG DRIVE EAST

department: Department of Pathology & Lab Medicine

institute: University of California, Los Angeles (UCLA)

summary: Pluripotent stem cells (PSCs) present promising engineering opportunities as sources of allogeneic T cells for off-the-shelf immunotherapies. However, the complex in vitro process of differentiation required to generate mature T cells from genetically engineered PSCs introduces unique challenges, as positive selection is dependent on the same molecular machinery that must be removed to prevent alloreactivity. We report an organoid-based method in which engineering of the stromal microenvironment induced generation of antigen-restricted, mature, conventional T cells from PSCs which lacked all endogenous TCR and Class I MHC expression. Transgenic signals required to rescue positive selection were supplied by separate cellular sources; T cell precursors from edited PSC expressed a single TCR, and a murine stromal line provided cognate human MHC and other critical T cell development signals. Edited T cells exhibited superior tumour control in vivo likely due to the absence of TCR mispairing. This in vitro method overcomes key biological impediments inherent to developing T cell immunotherapies from allogeneic PSCs.

overall_design: scRNA-sequencing of T cells, derived in vitro from human PSCs and sorted from PBMC

first: Patrick

middle: C

last: Chang

first: Xuegang

last: Yuan

first: Alexandre

last: Zampieri

first: Chloe

last: Towns

first: Sang

last: Yoo

first: Claire

last: Engstrom

first: Steven

last: Tsai

first: Christopher

middle: R

last: Robles

first: Yuhua

last: Zhu

first: Shawn

last: Lopez

first: Amelie

last: Montel-Hagen

middle: S

last: Seet


title: MCPIP1 controls effects of myeloid cells on skin carcinogenesis and hair growth

city: Warsaw

first: Michal

last: Mikula

address: Roentgena 5

department: Experimental Oncology

country: Poland

institute: Maria Skłodowska-Curie National Research Institute of Oncology

summary: Depletion of Mcpip1 in the cells of myeloid origin modifies the sensitivity to the cutaneous chemical carcinogenesis. It attenuates epidermal proliferation and increases the susceptibility to the formation of melanocytic nevi. Thus, myeloid Mcpip1 is an important modulator in the course of skin carcinogenesis.

overall_design: RNA-seq was performed to analyse transcriptome of chemically induced skin lesions and adjacent skin from four control and four Mcpip1(MKO) (myeloid-specific knockout) mice.

first: Weronika

last: Szukala

first: Krzysztof

last: Goryca

first: Izabela

last: Rumienczyk

first: Leopold

last: Eckhart

first: Joanna

last: Koziel

first: Jolanta

last: Jura

first: Agata

last: Lichawska-Cieslar


title: An IL-2 mutein increases IL-10 and CTLA-4-dependent suppression of dendritic cells by regulatory T cells

city: Seattle,

first: Stephanie

last: Osmond

state: WA

address: 1201 9th Ave

institute: Benaroya Research Institute

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

overall_design: Refer to individual Series


title: Smad4 restricts injury-provoked biliary proliferation and carcinogenesis (AKPS_EV_vs_Smad4_MethylSeq)

city: Rochester

first: Aram

middle: F.

last: Hezel

state: New York

address: 601 Elmwood Ave, Box 704

institute: Wilmot Cancer Institute

summary: Reduced representation bisulfite sequencing (RRBS) on the same TGFβ-treated AKPS lines (with EV or Smad4) revealed that Smad4 impacts DNA methylation (DNAme), with decreases in intergenic DNAme as the most impacted in our CCA models.

overall_design: Comparative methylation profiling analysis of bisulfite-seq data for TGFβ treated empty vector (EV) or Smad4-expressing AKPS lines

first: William

middle: B

last: Alexander


title: DARTseq identifies m6A targets in mouse primary cells

city: New York

first: Michael

middle: G.

last: Kharas

state: NY

address: 417 East 68th Street

department: Molecular Pharmacology Program

institute: Memorial Sloan Kettering Cancer Center

summary:
The goal of this study is to identify m6A targets in mouse HSC and MPP1-4 cells
Stem cells regulate their self-renewal and differentiation fate outcomes through both symmetric and asymmetric divisions. When exposed to stress such as inflammation, stem cells can rapidly undergo symmetric commitment divisions to generate differentiated progenitors for tissue regeneration and immune maintenance. m6A RNA methylation controls symmetric commitment and inflammation of hematopoietic stem cells (HSCs) through unknown mechanisms. Here, we demonstrate that the nuclear speckle protein SON is an essential m6A target required for murine HSC self-renewal, symmetric commitment, and inflammation control. Global profiling of m6A identified that m6A mRNA methylation of Son increases during HSC commitment. Upon m6A depletion, Son mRNA increases, but its protein is depleted. Reintroduction of SON rescues defects in HSC symmetric commitment divisions and engraftment. Conversely, Son deletion results in a loss of HSC fitness, while overexpression of SON improves mouse and human HSC engraftment potential by increasing quiescence. Additionally, SON nuclear speckles asymmetrically and symmetrically segregate during HSC division, correlating with hematopoietic differentiation. Mechanistically, we found that SON rescues MYC and suppresses the METTL3-HSC inflammatory gene expression program by indirectly reducing double-stranded RNAs and directly suppressing nascent transcription of proinflammatory chemokine CCL5. Depletion of CCL5 partially rescues the functional defect of m6A-deficient HSCs. Thus, our findings define a m6A-SON-CCL5 axis that controls inflammation and HSC fate.

overall_design: Hanzhi,Luo

first: Mariela

last: Cortés-López


title: Smad4 restricts injury-provoked biliary proliferation and carcinogenesis (Smad4_floxed_vs_WT_RNAseq)

summary: To understand the processes regulated by Smad4 in reactive cholangiocytes, Ctl and Smad4del mice were provided DDC diet for 2 weeks after which reactive cholangiocytes were isolated from digested injured mouse liver via FACS followed by RNA amplification and sequencing analysis. Gene set enrichment analysis of Smad4-perturbed reactive cholangiocytes implicates Smad4 in proliferative, metabolic, and inflammatory pathways.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for reactive cholangiocytes with and without Smad4


title: Smad4 restricts injury-provoked biliary proliferation and carcinogenesis


title: RNAseq identifies differentially expressed genes upon SON overexpression in WT and Mettl3 cKO LSK cells

address: 417 68th street

institute: Mamorial Sloan Kettering Cancer Center

summary: The goal of this study is to identify gene expression changes upon SON overexpression in WT and Mettl3 cKO LSK (Lin-cKit+Sca1+) cells

overall_design: Purified mouse Lin-cKit+Sca1+ cells from WT and Mettl3 cKO mice were transduced with SON overexpressing or empty vector control (lentiGFP). 48hr post infection, GFP+ cells were sorted. 3 replicates were performed.

first: Hanzhi

last: Luo

first: Cyrus

last: Tam


title: Targeting Arginine Methylation Suppresses Cancer Stem Cell Maintenance and Elicits cGAS-mediated anti-Cancer Immunity II

city: Monrovia

first: Ling

last: Li

address: 1218 S 5TH AVE

department: Hem Malignancies Trans Sci

institute: City of Hope National Medical Center

summary: Current anti-cancer therapies cannot eliminate all the cancer cells, which hijack normal arginine methylation as a means to promote their own maintenance via unknown mechanisms. Herein, we show that targeting protein arginine methyltransferase 9 (PRMT9), whose activities are elevated in leukemia stem cells (LSCs) from patients with acute myeloid leukemia (AML), eliminates disease via cancer-intrinsic mechanisms and cancer-extrinsic Type-I Interferon (IFN-I)-associated immunity. PRMT9 ablation in AML cells decreased arginine methylation of regulators of RNA translation and the DNA damage response, suppressing cell survival. Notably, PRMT9 inhibition promoted DNA damage and activated cGAS, which underlies the IFN-I response. Genetically activating cGAS in AML cells blocked leukemogenesis. We also report synergy of a PRMT9 inhibitor with anti-PD1 in eradicating PRMT9-proficient cancers, including AML and lymphoma. We conclude that PRMT9 governs LSCs survival and immune evasion, and that combining a PRMT9 inhibitor with an immune checkpoint inhibitor represents a novel anti-cancer strategy.

overall_design: BM cells in MA9 transplanted mice were collected for analysis.

first: Haojie

last: Dong

first: Xin

last: He

first: Lei

last: Zhang

first: Wei

last: Chen

first: Yi-Chun

last: Lin

first: Song-Bai

last: Liu

first: Huafeng

last: Wang

first: Victor

last: Huang

first: Min

first: Yinghui

last: Zhu

first: Dandan

last: Zhao

first: Lucy

last: Ghoda

first: Rui

last: Su

first: Jianjun

first: Ritin

last: Sharma

first: Patrick

last: Pirrotte

first: Xiwei

last: Wu

first: Weidong

last: Hu

last: Han

first: Binghui

last: Shen

first: Ya-Huei

last: Kuo

first: Jie

last: Jin

first: Amandeep

last: Salhotra

first: Jeffrey

first: Guido

last: Marcucci

first: Yun

last: Lyna


title: single cell RNAseq identifies differential expressed genes upon SON overexpression in WT and Mettl3 cKO LSK cells

first: Michael

last: Kharas

summary: The goal of this study is to identify gene expression changes upon SON overexpression in WT and Mettl3 cKO LSK (Lin-cKit+Sca1+) cells at single cell level

overall_design: Purified mouse Lin-cKit+Sca1+ cells from WT and Mettl3 cKO mice were transduced with SON overexpressing or empty vector control (lentiGFP). 48hr post infection,  GFP+ cells were sorted.

first: Hanzhi

last: Luo

first: Mariela

last: Cortés-López

first: Cyrus

last: Tam


title: The expression data from mandibular arch and tongue primordia in mouse embryos.

status: Public on Dec 06 2023

city: Fujimi, Chiyoda-ku

first: Taisuke

last: Hani

state: Tokyo

department: Pathology

country: Japan

institute: Nippon Dental University, School of Life Dentistry at Tokyo

summary:
The mouse hypoglossal nerve originates from the occipital motor nuclei and projects a long distance, reaching the vicinity of the tongue primordia, the lateral lingual swelling, at E11.5. However, the details of how the hypoglossal nerve correctly projects to the primordia are not well understood.
To investigate the molecular basis of hypoglossal nerve elongation, we employed cDNA microarray technology and screened for candidate genes involved in the axon guidance event.

overall_design: Tissues were dissected and pooled together in a single tube for microarray analysis. The following were collected into single tubes: E9.5 median mandibular arches (E9.5-MMA; 12 embryos/tube), E11.5 lateral lingual swellings (E11.5-LLS; 4 embryos/tube), E11.5 lateral mandibular arches (E11.5-LMA; 4 embryos/tube) and E14.5 median tongue (E14.5-T; 4 embryos/tube). Each of these regions were regarded as an independent tissue unit. We applied the ROKU method, an algorithm that can detect tissue-specific genes by comparing expression patters across different time periods and tissue regions.

last: HANI

first: Kazuya

last: FUJITA

first: Tomoo

last: KUDO

first: Yuji

last: TAYA

first: Kaori

last: SATO

first: Yuuichi

last: SOENO


title: Smad4 restricts injury-provoked biliary proliferation and carcinogenesis (AKPS_EV_vs_Smad4_RNAseq)

first: Aram

last: Hezel

summary: RNA-sequencing of TGFβ treated empty vector (EV) or Smad4-expressing AKPS lines followed by GSEA revealed a number of gene sets overlapping with those obtained from analyses in reactive cholangiocytes. Hallmark gene sets MYC, E2F, G2M checkpoint, and oxidative phosphorylation were enriched with loss of Smad4, while TGFβ signaling, EMT, and TNFα were enriched with intact Smad4 signaling, suggesting conserved growth suppressive functions of Smad4 in primary cholangiocytes and advanced cancer.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for TGFβ treated empty vector (EV) or Smad4-expressing AKPS lines

first: William

last: Alexander


title: scRNASeq Data of CD45- cells in HS lesional skin and healthy skin

city: San Francisco

first: Margaret

last: Lowe

address: 513 Parnassus Avenue, HSW1201B

institute: UCSF

summary: Hidradenitis suppurativa (HS) is an inflammatory skin disease with limited therapeutic options. Identifying transcriptional alterations within non-immune populations of HS lesions versus healthy controls could identify novel targets for therapy. We profiled subsets sorted as live, CD45 negative cells from biopsies of inflammatory lesions of three patients with HS and six specimens from healthy controls to determine what cell types and pathways were altered in HS inflammatory lesions.

overall_design: scRNASeq of live CD45 negative cells sort-purified from enzymatically digested skin of biopsied hidradenitis suppurativa inflammatory lesions or of healthy control skin

middle: M

last: Rosenblum


title: A fluorescent assay for cryptic transcription in Saccharomyces cerevisiae [RNA-seq]

first: LeAnn

last: Howe

summary: The disruption of chromatin structure can result in transcription initiation from cryptic promoters within gene bodies. While the passage of RNA polymerase II is a well-characterized chromatin-disrupting force, numerous factors, including histone chaperones, normally stabilize chromatin on transcribed genes, thereby repressing cryptic transcription. DNA replication, which requires a partially overlapping set of histone chaperones, is also inherently disruptive to chromatin, but a role for DNA replication in cryptic transcription has never been examined. In this study, we tested the hypothesis that, in the absence of chromatin-stabilizing factors, DNA replication can promote cryptic transcription in S. cerevisiae. Using a novel fluorescent reporter assay, we show that multiple factors, including Asf1, CAF-1, Rtt106, Spt6, and FACT, block transcription from a cryptic promoter, but are entirely or partially dispensable in G1-arrested cells, suggesting a requirement for DNA replication in chromatin disruption. Collectively, these results demonstrate that transcription fidelity is dependent on numerous factors that function to assemble chromatin on nascent DNA.

overall_design: We generated a fluorescent reporter for transcription from a cryptic promoter within the S. cerevisiae FLO8 gene. Cells with a temperature sensitive mutation in SPT16 show increased fluorescence when grown at the non-permissive temperature. To confirm that increased fluorescence is due to transcription initiating at the FLO8 cryptic promoter, we performed strand-specific RNA-seq.


title: HDAC inhibitors directly modulate T cell gene expression and signaling and promote development of effector-exhausted T cells in murine tumors [scRNA-seq]

first: Amer

last: Beg

overall_design: The goal of this study is to assess effect of HDACi and ICI alone and in combination on tumor microenvironment in KP mouse model using single-cell RNAseq

first: Hong

last: Zheng

first: Mohammed

middle: L

last: Ibrahim

first: Xiaoqing

last: Yu


title: HDAC inhibitors directly modulate T cell gene expression and signaling and promote development of effector-exhausted T cells in murine tumors


title: Modifiers of genetic dominance at the Arabidopsis self-incompatibility locus retain proto-miRNA features and act through non-canonical gene silencing pathways - AGO-IP data

city: Villeneuve d'Ascq

first: Vincent

last: Castric

address: Batiment SN2, bureau 207

country: France

institute: CNRS / Universite de Lille - Sciences et Technologies

summary: Self-incompatibility (SI) in flowering plants is a common mechanism that prevents self-fertilization and promotes outcrossing. In Brassicaceae, the locus controlling SI is highly diverse and dozens of distinct alleles are organized in a complex dominance hierarchy: the gene controlling SI specificity in pollen always shows monoallelic expression in heterozygote individuals, and this is achieved through the action of sRNA precursors that resemble miRNAs, although the mechanism behind this remains elusive. Here, we engineered Arabidopsis thaliana lines expressing components of the Arabidopsis halleri SI system and used a reverse genetics approach to pinpoint the pathways underlying the function of these sRNA precursors. We showed that they trigger a robust decrease in transcript abundance of the recessive pollen SI genes, but not through the canonical transcriptional or post transcriptional gene silencing pathways. Furthermore, we observed that single sRNA precursors are typically processed into hundreds of sRNA molecules, with distinct sizes, abundance levels and ARGONAUTE loading preferences. This heterogeneity closely resembles that of proto-miRNAs, the evolutionary ancestors of miRNAs. Our results suggest that these apparent arbitrary features, which are often associated with lack of effects in gene expression, are crucial in the context of the SI dominance hierarchy since they allow one sRNA precursor of a given allele to repress multiple other (more recessive) alleles. This study not only provides an in-depth characterization of the molecular features underlying complex dominance interactions, but also constitutes a unique example of how specific evolutionary constraints shape the progression of sRNA precursors within the proto-miRNA – miRNA evolutionary continuum.

overall_design: small RNA sequencing after ARGONAUTE Immunoprecipitation. AGO1- and AGO4-IPs were performed on immature floral buds of transgenic A. thaliana plants expressing the S locus sRNA precursors Ah04mir1887, Ah20mirS3 or Ah20mirS2 from A. halleri.

first: Rita

last: A Batista

first: Jacinthe

last: Azevedo-Favory

first: Thierry

last: Lagrange


title: RNA-seq profiling of mammary epithelial cell populations from Brca2 knockout and wildtype mice

city: Parkville

first: Gordon

middle: K

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

summary: Brca2(fl/fl)Trp53(fl/fl) mice were crossed with MMTV-cre mice to create mice with both alleles of Brca2 and one allele of Trp53 deleted (refered to as Brca2KO). Mature luminal, luminal progenitor and basal mammary epithelial cell populations were sorted from Brca2KO and wildtype mice. Transcriptional profiling revealed marked perturbation within the luminal Brca2KO compartment

overall_design: Bulk RNA-sequencing was performed on FACS-isolated mature luminal, luminal progenitor and basal mammary epithelial cell populations from 14 week old MMTV-cre(T/+)Brca2(delta/delta)Trp53(delta/+) mice (n=3 individual mice) and wildtype controls (n=3 individual mice). All mice were female.

first: Mengbo

last: Li

first: Rachel

last: Joyce

first: Rosa

last: Pascual

first: Geoff

middle: J

last: Lindeman

first: Jane

last: Visvader


title: Modifiers of genetic dominance at the Arabidopsis self-incompatibility locus retain proto-miRNA features and act through non-canonical gene silencing pathways


title: The in situ transcriptomic landscape of breast tumour-associated and normal adjacent endothelial cells

city: Brisbane

first: Akhilandeshwari

last: Ravichandran

state: Queensland

address: 60 Musk Avenue

institute: Queensland University of Technology

summary: With poor prognosis and low-survival rates, Triple Negative Breast Cancer (TNBC) has been associated with increased angiogenesis, which is known to aid tumour growth and metastasis. Anti-angiogenic therapies that were developed to address this have mostly generated disappointing clinical results. Further research into targeted approaches is limited by the lack of understanding of molecular profile of cancer-associated vasculature. Here, we have applied unbiased whole transcriptome spatial profiling of in situ gene expressions of endothelial cells localized in full-face patient TNBC tissues and adjacent normal breast tissues. Our comparative analysis showed that 2412 genes  were differentially expressed (padj<0.05) between the tumour endothelial cells and normal adjacent endothelial cells. Pathway enrichment showed the enrichment of gene sets related to cell-cell, cell-ECM adhesion, chromatin organization and remodeling, and protein-DNA complex subunit organization. Overall, the results have revealed unique molecular profiles and signalling pathways of tumour vasculature which can potentially enable the detection of potential targets for TNBC prognosis and anti-angiogenic treatments and provide a greater understanding of metastasis . The results of this pilot study need validation in larger independent cohorts.

overall_design: Differential gene expression of endothelial cells from tumor regions and normal-adjacent regions of full-face TNBC patient breast tissues (n=4).

first: Laura

last: Bray

first: Arutha

last: Kulasinghe


title: The UBP5 histone H2A deubiquitinase counteracts PRCs-mediated repression to regulate Arabidopsis development

city: Galway

first: Sara

last: Farrona

address: University Road

country: Ireland

institute: National University of Ireland Galway


title: DARTseq identifies m6A targets in human CD34+ HSPCs

first: Michael

last: Kharas

summary:
The goal of this study is to identify m6A targets in human CD34+ HSPCs with or without STM2457 treatment using DARTseq.
Purified human CD34+ HSPC cells were transduced with APOBEC-YTH or empty vector control (MIG). 24hr post infection, CD34+ cells were treated with STM2457 at a concentration of 20µM for 2 days. GFP+ cells were sorted the next day. 3 replicates were performed.

first: Mariela

last: Cortés-López

middle: G


title: The XX sex chromosome complement provides enhanced responses to heat-killed Streptococcus pneumoniae immunization in a gut microbiome-dependent manner.

city: Morgantown

first: Gangqing

last: Hu

state: West Virginia

address: 64 Medical Center Drive

department: MicroBiology, Immunology, and Cell Biology

institute: West Virginia University

summary: Differences in male vs. female immune responses are well-documented and have significant clinical implications. While the immunomodulatory effects of sex hormones are well established, the contributions of sex chromosome complement (XX vs. XY) and gut microbiome diversity on immune sexual dimorphisms have only recently become appreciated. Here we investigate the individual and collaborative influences of sex chromosome complements and gut microbiome bacteria on humoral immune activation. Sham-operated and gonadectomized male and female Four Core Genotype (FCG) mice were immunized with heat-killed Streptococcus pneumoniae (HKSP). Humoral immune responses were assessed and X-linked immune-related gene expression was evaluated to explain the identified XX-dependent phenotypes. Ex vivo studies investigated the functional role of Kdm6a, an X-linked epigenetic regulatory gene of interest, in mitogenic B cell activation. We further evaluated whether gut microbiome communities, or their metabolites, differentially influence immune cell activation in a sex chromosome-dependent manner. Endogenous gut microbiomes were antibiotically depleted and reconstituted with select short-chain fatty acid (SCFA)-producing bacteria prior to HKSP immunization and immune responses assessed. XX mice exhibited higher HKSP-specific IgM-secreting B cells and plasma cell frequencies than XY mice, regardless of gonadal sex. Although Kdm6a was identified as an X-linked gene overexpressed in XX B cells, inhibition of its enzymatic activity did not affect mitogen-induced plasma cell differentiation or antibody production in a sex chromosome-dependent manner ex vivo. Enhanced humoral responses in XX vs. XY immunized FCG mice were eliminated after microbiome depletion, indicating that the microbiome contributes to the identified XX-dependent immune enhancement. Reconstituting microbiota-depleted mice with select SCFA-producing bacteria increased humoral responses in XX, but not XY, FCG mice. This XX-dependent enhancement appears to be independent of SCFA production in males, while female XX-dependent responses relied on SCFAs. FCG mice have been used to assess sex hormones and sex chromosome complements influences on various sexually dimorphic traits. The current study indicates that the gut microbiome impacts humoral responses in an XX-dependent manner, suggesting that the collaborative influence of gut bacteria and other sex-specific factors should be considered when interpreting data aimed at delineating the mechanisms that promote sexual dimorphisms.

overall_design: Four Core Genotype mice were immunized with heat-killed Streptococcus pneumoniae and euthanized one week later to evaluate gene expression through RNA-Seq.

first: Carly

last: Menker

first: Jennifer

last: Franko

first: Quinn

last: Hopen

first: Rosana

last: Schafer

first: Jasleen

last: Gandhi

first: Lei

last: Wang


title: Co-culture of murine small intestinal organoids with type-3 innate lymphoid cells (ILC3)

city: London

first: Joana

middle: F

last: Neves

state: County

address: Guy’s Hospital, St Thomas Street

department: Host Microbiome Interactions

country: United Kingdom

institute: King's College London

summary: Type-3 innate lymphoid cells (ILC3) regulate homeostasis and orchestrate immunity in the intestine, mediated in part by their bi-directional communication with the intestinal epithelium. In order to define specific interactions between these two compartments, we used a reductionist co-culture system of murine epithelial small intestinal organoids (SIO) with ILC3. The transcriptomic profile of epithelial cells from these co-cultures was analysed by bulk RNAseq.

overall_design: Murine SIO cultures were established from small intestine of female 6-10 week old CD45.1 mice and maintained in Matrigel. These were then co-cultured with type-3 innate lymphoid cells isolated from the small intestine. After 4 days of co-culture, the SIO were sorted via FACS into into RLT (QIAGEN) lysis buffer for RNA isolation using the RNeasy MicroRNA isolation kit (QIAGEN).

first: Geraldine

last: Jowett

first: Emily

last: Read


title: A fluorescent assay for cryptic transcription in Saccharomyces cerevisiae [MNase-seq]

city: Vancouver

first: LeAnn

last: Howe

address: 2350 Health Sciences Mall

institute: University Of British Columbia

overall_design: We generated a fluorescent reporter for transcription from a cryptic promoter within the S. cerevisiae FLO8 gene. Cells with a temperature sensitive mutation in SPT16 show increased fluorescence when grown at the non-permissive temperature. To confirm that increased fluorescence is due tochromatin disruption st the FLO8 cryptic promoter, we performed MNase-seq.


title: Genomic analysis of mice with endothelium-specific TERT knockout (scRNA-Seq)

status: Public on Dec 05 2023

city: Houston

first: Yulin

last: Dai

state: TX

address: 7000 fannin, suite 600

department: School of Biomedical Informatics

institute: University of Texas health science center at Houston

summary: Health of endothelial cells (EC) is fundamental for function of vital organs. However, it has not been established whether EC senescence underlies the pathophysiology of aging. Here, we report a mouse model of EC senescence. Inactivation of telomerase (TERT) expression sets the stage for aging and predisposes cells to replicative senescence. TERT maintains telomere length and has telomere-independent effects on cell transcriptome and physiology. We generated mice with TERT gene knock-out (KO) specifically in EC. We analyzed EC from adipose tissues (AT) and skeletal muscle cells from Tert-EC-KO and control mice raised on either chow or high-calorie diet (HCD) and subjected them to RNA sequencing (RNAseq). Single cell RNAseq data were also obtained for subcutaneous and visceral AT. Preliminary analysis of data deposited online indicates that TERT KO induces premature cell senescence and dysfunction. Moreover, HCD feeding exacerbates the effect of TERT loss. We conclude that the Tert-EC-KO mice are a useful model to study EC senescence and its effects on aging-associated organ dysfunction.

overall_design: Tie2e-cre; TERT+/+; mTmG (WT) and Tie2e-cre; TERTfl/fl; mTmG (TERT-EC-KO) 7 month-old male mice were fed HFD for 5 months prior to cells isolation from subcutaneous AT (SC) and visceral intraperitoneal AT (IP).

first: Mikhail

last: Kolonin

first: Zhanguo

last: Gao


title: Evaluation of Immunomodulatory Effects ofFusariumMycotoxins Using Bacterial Endotoxin-Stimulated Bovine Epithelial Cells and Macrophages in Co-Culture

city: Guelph

first: Umesh

middle: K.

last: Shandilya

state: Ontario

address: 50 Stone Rd E

department: Animal Biosciences

institute: University of Guelph

summary: Mycotoxins are secondary metabolites produced by a variety of fungi that contaminate animal food and feeds and are capable of inducing a wide range of toxicities. Predictive in vitro models represent valuable substitutes for animal experiments to assess the toxicity of mycotoxins. The complexities of the interactions between epithelial and innate immune cells, vital for upholding barrier integrity and averting infections, remain inadequately understood. In the current study, a co-culture model of bovine epithelial cells (MAC-T) and macrophages (BoMac) was used to investigate the impact of exposure toFusariummycotoxins, namely deoxynivalenol (DON), zearalenone (ZEN), enniatin B (ENB), and beauvericin (BEA), on the inflammatory response elicited by the bacterial lipopolysaccharide (LPS) endotoxin. The MAC-T cells and BoMac were seeded on the apical side of a Transwell membrane and in the lower chamber, respectively, and mycotoxin exposure on the apical side of the membrane was carried out with the different mycotoxins (LC20; concentrations that elicited 20% cytotoxicity) for 48 h followed by an LPS immunity challenge for 24 h. The culture supernatants were collected from the basolateral compartment and these samples were submitted for cytokine/chemokine multiplex analysis. RNA-Seq analysis was performed using total RNA extracted from the MAC-T cells to acquire a more detailed insight into their cellular functions. The multiplex analysis indicated that IFN-γ, IL-1α, IL-8, and MCP-1 were significantly induced post-DON treatment when compared to control cells, and levels of IL-1α and IL-8 were enhanced significantly in all mycotoxin-treated groups post-LPS challenge. Analysis of the sequencing results showed that there were 341, 357, and 318 differentially expressed MAC-T cell genes that were up-regulated in the DON, ENB, and BEA groups, respectively. Gene ontology and pathway analysis revealed that these DEGs were significantly enriched in various biological processes and pathways related to inflammation, apoptosis signaling, and Wnt signaling. These results provide a comprehensive analysis of the co-culture cytokine/chemokine production and MAC-T cells’ gene expression profiles elicited byFusariummycotoxins, which further contributes to the understanding of early endotoxemia post-mycotoxin exposure.

overall_design: A co-culture model of bovine epithelial cells (MAC-T) and macrophages (BoMac) was established to investigate the impact of exposure toFusariummycotoxins, namely deoxynivalenol (DON), zearalenone (ZEN), enniatin B (ENB), and beauvericin (BEA), on the inflammatory response elicited by the bacterial lipopolysaccharide (LPS) endotoxin. The mycotoxin exposure on the apical side (MAC-T) of the co-culture was carried out with the different mycotoxins (LC20; concentrations that elicited 20% cytotoxicity) for 48 h followed by an LPS immunity challenge for 24 h. The culture supernatants were collected from the basolateral compartment and these samples were submitted for cytokine/chemokine multiplex analysis. RNA-Seq analysis was performed using total RNA extracted from the MAC-T cells to acquire a more detailed insight into their cellular functions. To assess the DEGs between different treatments, the comparison was made between DON vs. LPS-Control, ENB vs. LPS-Control, and BEA vs. LPS-Control. Each group had 3 replicates.

first: Ankita

last: Sharma

first: Ran

last: Xu

first: Maria

last: Muniz

first: Niel

middle: A

last: Karrow


title: Genomic analysis of mice with endothelium-specific TERT knockout (RNA-Seq)

summary: Health of endothelial cells (EC) is fundamental for function of vital organs. There is evidence accumulating that senescence of EC is associated with aging-related diseases. However, it has not been established whether EC senescence underlies the pathophysiology of aging. Here, we report a mouse model of EC senescence. Inactivation of telomerase (TERT) expression sets the stage for aging and predisposes cells to replicative senescence. TERT maintains telomere length and has telomere-independent effects on cell transcriptome and physiology. We generated mice with TERT gene knock-out (KO) specifically in EC. We analyzed EC from adipose tissues (AT) and skeletal muscle cells from Tert-EC-KO and control mice raised on either chow or high-calorie diet (HCD) and subjected them to RNA sequencing (RNAseq). Single cell RNAseq data were also obtained for subcutaneous and visceral AT. Preliminary analysis of data deposited online indicates that TERT KO induces premature cell senescence and dysfunction. Moreover, HCD feeding exacerbates the effect of TERT loss. We conclude that the Tert-EC-KO mice are a useful model to study EC senescence and its effects on aging-associated organ dysfunction.

overall_design: Tie2e-cre; TERT+/+; mTmG (WT) and Tie2e-cre; TERTfl/fl; mTmG (TERT-EC-KO) 8 month-old female mice were fed chow (C) or HFD (H). Cells isolated from subcutaneous AT (SAT), intraperitoneal visceral AT (VAT), and gastrocnemius skeletal muscle (M) were subjected to FACS sorting to isolate mG+ (GFP+) cells for mRNA extraction.


title: Stress-induced translation of KCNB1 contributes to the enhanced synaptic transmission of the lateral habenula

city: seoul

first: Hakyun

last: Ryu

address: 120, Neungdong-ro, Gwangjin-gu

institute: Konkuk univ.

summary: The lateral habenula (LHb) is a well-established brain region involved in depressive disorders. Synaptic transmission of the LHb neurons is known to be enhanced by stress exposure; however, little is known about genetic modulators within the LHb that respond to stress. Using recently developed molecular profiling methods by phosphorylated ribosome capture, we obtained transcriptome profiles of stress responsive LHb neurons during acute physical stress. Among such genes, we found that KCNB1 (Kv2.1 channel), a delayed rectifier and voltage-gated potassium channel, exhibited increased expression following acute stress exposure. To determine the roles of KCNB1 on LHb neurons during stress, we injected short hairpin RNA (shRNA) against the kcnb1 gene to block its expression prior to stress exposure. We observed that the knockdown of KCNB1 altered the basal firing pattern of LHb neurons. Although KCNB1 blockade did not rescue despair-like behaviors in acute learned helplessness (aLH) animals, we found that KCNB1 knockdown prevented the enhancement of synaptic strength in LHb neuron after stress exposure. This study suggests that KCNB1 may contribute to shape stress responses by regulating basal firing patterns and neurotransmission intensity of LHb neurons.

overall_design:
Taking advantage of the newly developed selective capturing technique of phosphorylated ribosomes, we aimed to obtain an unbiased molecular profile of the activated LHb during acute physical foot shock stress.
The total sample contained all mRNAs in LHb neurons and the IP sample contained mRNAs which are combined with phosphorylated ribosome to transcript

first: Han

last: Choi

first: Minseok

last: Kim

first: ChiHye

last: Chung


title: Massively parallel in vivo Perturb-seq reveals cell type-specific transcriptional networks in cortical development

city: San Diego

first: Xinhe

last: Zheng

state: California

address: 3528 General Atomics Court

department: Neuroscience

institute: The Scripps Research Institute

summary: Leveraging AAV's versatile tropism and labeling capacity, we expanded the scale of in vivo CRISPR screen with single-cell transcriptomic phenotyping across embryonic to adult brains and peripheral nervous systems. Through extensive tests of 86 AAV serotypes, combined with transposon systems, we substantially amplified labeling and accelerated in vivo gene delivery from weeks to days. Our proof-of-principle in utero screen identified the pleiotropic effects of Foxg1, highlighting its tight regulation of distinct networks essential for cell fate specification of Layer 6 corticothalamic neurons. Notably, our platform can label >6% of cerebral cells, surpassing the current state-of-the-art efficacy at <0.1% by lentivirus, to achieve analysis of over 30,000 cells in one experiment and enable massively parallel in vivo Perturb-seq. Compatible with various phenotypic measurements (single-cell or spatial multi-omics), it presents a flexible approach to interrogate gene function across cell types in vivo, translating gene variants to their causal function.

overall_design:
AAV transduced cells were dissociated and Fluorescent-activated sorted (FACS) to analyze the AAV transduction efficiency, gRNA capturing efficiency or perturbation effects with scRNA-seq
Please note that the Perturb_* samples are the standard scRNA-seq sample, while the Perturb_*_Foxgdialout samples are enriched library on Foxg1 only with a separate library prep and sequencing.

first: Sean

last: Simmons

first: Kwanho

first: Joshua

last: Park

middle: Z

last: Levin

first: Xin

last: Jin


title: HSL119 results in gene expression changes equivalent to HUNK shRNA

city: Indianapolis

first: Elizabeth

last: Yeh

state: Indiana

address: 635 Barnhill Drive, Medical Science Building A418

department: Pharmacology and Toxicology

institute: Indiana University School of Medicine

summary:
The goal of this study was to determine the gene similarities and overlap between human HER2+ breast cancer cells treated with a HUNK inhibitor (HSL119) and samples engineered with HUNK shRNA (KD1 and KD2).
A main objective was to determine if genes related to the AKT pathway were changed in HUNK treated or HUNK knockdown groups compared to control.

overall_design: Total of 15 samples: HSL (n=3), CTL (n=4), HUNK KD1 (n=4), HUNK KD2 (n=4). CTL is the control/reference sample.

first: Adrian

last: Oblak

first: Tinslee

last: Dilday


title: EGR1-mediated ibrutinib resistance

city: Madison

first: Lixin

last: Rui

state: WI - Wisconsin

address: 1111 Highland Ave R.4060

department: Medicine

institute: University of Wisconsin-Madison

summary: We established two representative ABC DLBCL cell lines (TMD8 and OCI-Ly10) with ibrutinib resistance by gradually increasing the concentration of ibrutinib during passage in culture. RNA-seq analysis demonstrated that the BCR pathway gene signature is enriched in resistant cell lines when compared to parental cells. The most upregulated gene is EGR1, a transcription factor that activates multiple oncogenic pathways including MYC and E2F. Elevated EGR1 expression is also observed in ibrutinib-resistant primary mantle cell lymphoma cells when treated with ibrutinib. Using multiple metabolic and genetic approaches, we discovered that overexpression of EGR1 causes metabolic reprogramming to oxidative phosphorylation (OXPHOS) and ibrutinib resistance. Mechanistically, EGR1 mediates metabolic reprogramming through transcriptional activation of PDP1, a phosphatase that dephosphorylates and activates the E1 component of the large pyruvate dehydrogenase complex. Therefore, EGR1-mediated PDP1 activation accelerates intracellular ATP production via the mitochondrial tricarboxylic acid (TCA) cycle, leading to sufficient energy to enhance the proliferation and survival of ibrutinib-resistant lymphoma cells. Finally, we demonstrate that targeting OXPHOS with IM156, a newly developed OXPHOS inhibitor, inhibits the growth of ibrutinib-resistant lymphoma cells both in vitro and in patient-derived xenograft mouse models.

overall_design: To study ibrutinib resistance, we developed ibrutinib-resistant ABC DLBCL cell lines by starting with a very low dose of 0.1 nM ibrutinib and increased the drug concentration stepwise up to 1000 nM for a period of 40 weeks. Resistant clones were generated by serial dilution at 1:3 ratio. Resistant phenotype were confirmed by treat cells with ibrutinib compared to parental cell lines

first: Li

last: Lu

first: Yunxia

last: Liu

first: Shuichi

last: Kimpara

first: Nguyet

last: Hoang


title: Transcription Factor Co-Expression Mediates Lineage Priming for Embryonic and Extra-Embryonic Differentiation [scRNA-Seq]

city: Copenhagen

first: Josh

last: Brickman

address: 3B Blegdamsvej

department: reNEW

country: Denmark

institute: Copenhagen University

summary: In this study, we characterised transcriptomes of mESC in different conditions EPSCM and KOSR subsetting them for their single expression of SOX2 or the double expression of SOX2 and GATA6 in these conditions. 2iLIF (sorted only by DAPI negative cells) were used as control.

overall_design: This study contains 3 conditions (2iLIF, EPSCM and KOSR) and 5 samples (2iLIF Dapi negative cells, EPSCM SOX2+, EPSCM DP, KOSR SOX2+ and KOSR DP) of mouse ESCs that have been in each condition for 4 to 5 passages. The single cells were specifically sorted for Dapi negative and SOX2:GFP+ only or SOX2:GFP and GATA6:mCherry double positive.

first: Alba

last: Riveiro

first: Jasmina

last: al-Mousawi

first: Madeleine

last: Linneberg-Agerholm

first: Martin

last: Proks

first: Marta

last: Perera Perez


title: Single-cell analysis reveals Cxcl14+ progenitor fibroblast accumulation in regenerating diabetic wound after carbon monoxide-releasing hydrogel therapy

city: Stockholm

first: Cheng

last: Zhao

state: Stockholm

address: H9 Klinisk vetenskap,171 77 Stockholm

department: Clinical Science

country: Sweden

institute: Karolinska institute

summary: Chronic and non-healing skin wound is one of grievous complications of diabetes. In this study, we demonstrated a gas (carbon monoxide)-releasing hyaluronic acid hydrogel (i.e. COHAG) in promoting diabetic wound healing. Our results show that  the COHAG significantly accelerated the healing process in diabtic rat full-thickness skin defect model, as compared with hydrogel without gas-releasing molecule and untreated group. Single-cell analysis of regenerating skin samples revealed that Cxcl14-overexpressing (Cxcl14+) fibroblast with progenitor properties are abundantly accumulated at the wound site after COHAG therapy.

overall_design: Rat skin tissue from diabetic SD rats at 8-10 weeks. Rat skin specimens（7 days of hydrogel treated wound）were cleaned with PBS and digested using the Epidermis Dissociation Kit (Miltenyi biotec, 130-095-928) for ~1 hours at 37℃ to obtain cell suspension. Single-cell RNA-seq libraries were made with the single cell 3 'Library and Gel Bead Kit V3.1(10x Genomics, 1000121)  and sequenced using an Illumina NovaSeq6000 (150bp x2, 25～40k reads/cell). It is estimated that approximately 8000 cells will be recovered per sample.

first: Ya

last: Li

first: Lu

last: Sun

first: Ranxi

last: Chen

first: Yuyun

last: Liang

first: Hexu

last: Zhang

first: Chaoyong

last: He

first: Bi

last: Shi

first: Sophie

last: Petropoulos

first: Liyang


title: Transcription Factor Co-Expression Mediates Lineage Priming for Embryonic and Extra-Embryonic Differentiation [CUT&RUN]

summary: In early mammalian development, cleavage stage blastomeres and cells of the inner cell mass (ICM) of the blastocyst co-express embryonic and extra-embryonic transcriptional determinants. Using a double protein-based reporter we identify embryonic stem cells (ESC) that co-express the extra-embryonic factor GATA6 alongside the embryonic factor SOX2 in specific conditions. Based on single cell transcriptomics we find these population resemble unsegregated ICM, exhibiting enhanced differentiation potential for endoderm while maintaining epiblast competence and suggesting they represent an ideal model to determine how GATA6 and SOX2 influence each other's DNA binding. To relate this binding to future fate, we describe a complete enhancer set in both ESCs and naïve extraembryonic endoderm stem cells and ask whether SOX2 and GATA6 recognize these elements in ICM-like ESC sub-population. Both factors support cooperative recognition in these lineages, with GATA6 bound alongside SOX2 on a fraction of pluripotency enhancers and SOX2 alongside GATA6 more extensively on endoderm enhancers. Our findings suggest that cooperative binding between these antagonistic factors both supports self-renewal and prepares progenitor cells for later differentiation

overall_design: 2 biological replicates for all conditions (B9 and B12) of the double reporter SGGC. Conditions tested: 2iLIF, NACL, KOSR SOX2 single positive, KOSR DP, nEnd. Antibodies used: H3K4me1, H3K27ac, SOX2, GATA6

last: Redó Riveiro

last: Al-Mousawi

first: Joshua


title: LUTI-dependent Downregulation of a Cell Cycle Transcription Factor is Key for Timely Meiotic Entry

city: Berkeley

first: Elcin

last: Unal

address: 1 Barker Hall

department: MCB

institute: UC Berkeley

summary: We used RNA-seq to monitor expression of early meiotic genes and expression of mitotic transcription factor SBF targets. Increased SBF activity was achieved through either overexpression of SBF unique subunit Swi4 ,  removal of LUTI-mediated regulation of Swi4 levels, or nuclear depeletion of negative regulator of SBF Whi5.

overall_design: Cells were grown as described in Su et al., 2023. Samples collected at 2 hours in SPO media. 2-3 biological replicates included for each genotype.

first: Amanda

last: Su

first: Siri

last: Yendluri


title: The hypermorphic PLCγ2 S707Y variant dysregulates microglial cell function – Insight into PLCγ2 activation in brain health and disease, and opportunities for therapeutic modulation

first: Daniel

last: Bull

address: Gower Street

institute: ARUK UCL Drug Discovery Institute

summary: Phospholipase C-gamma 2 (PLCγ2) is highly expressed in hematopoietic and immune cells, where it is a key signalling node enabling diverse cellular functions. Within the periphery, gain-of-function (GOF) PLCγ2 variants, such as the strongly hypermorphic S707Y, cause severe immune dysregulation. The milder hypermorphic mutation PLCγ2 P522R increases longevity and confers protection in central nervous system (CNS) neurodegenerative disorders, implicating PLCγ2 as a novel therapeutic target for treating these CNS indications. Currently, nothing is known about what consequences strong PLCγ2 GOF has on CNS functionality, and more precisely on the specific biological functions of microglia. Using the PLCγ2 S707Y variant as a model of chronic activation we investigated the functional consequences of strong PLCγ2 GOF on human microglia. PLCγ2 S707Y expressing human inducible pluripotent stem cells (hiPSC)-derived microglia exhibited hypermorphic enzymatic activity under both basal and stimulated conditions, compared to PLCγ2 wild type. Despite the increase in PLCγ2 enzymatic activity, the PLCγ2 S707Y hiPSC-derived microglia display diminished functionality for key microglial processes including phagocytosis and cytokine secretion upon inflammatory challenge. RNA sequencing revealed a downregulation of genes related to innate immunity and response, providing molecular support for the phenotype observed. Our data suggests that chronic activation of PLCγ2 elicits a detrimental phenotype that is contributing to unfavourable CNS functions, and informs on the therapeutic window for targeting PLCγ2 in the CNS. Drug candidates targeting PLCγ2 will need to precisely mimic the effects of the PLCγ2 P522R variant on microglial function, but not those of the PLCγ2 S707Y variant.

overall_design: RNA was extracted from PLCγ2 WT and S707Y hiPSC-derived microglia from three separately generated hematopoietic inductions, at different myeloid precursor differentiation ages (early, middle and late). Libraries were prepared using the KAPA RNA HyperPrep Kit and sequenced on an Illumina HiSeq 4000 sequencer at a minimum of 25 million paired-end reads (75 bp) per sample performed by UCL Genomics (London, England).

first: Julie

last: Matte

first: Carmen

last: Navarron

first: Rebecca

last: McIntyre

first: Paul

last: Whiting

first: Matilda

last: Katan

first: Fiona

last: Ducotterd

first: Lorenza

last: Magno


title: Transcription Factor Co-Expression Mediates Lineage Priming for Embryonic and Extra-Embryonic Differentiation

first: Josh

last: Brickman

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

overall_design: Refer to individual Series


title: Suppression of apoptosis impairs phalangeal joint formation in the pathogenesis of brachydactyly type A1

city: Pok Fu Lam

first: Peikai

last: Chen

address: Sassoon Road 5

department: Faculty of Medicine

country: Hong Kong

institute: The University of Hong Kong

summary: Brachydactyly type A1 (BDA1), due to mutations in IHH, is characterized with shortened and/or missing middle phalangeal bones. These mutations alter the capacity and range of IHH signaling, reducing mesenchymal cells recruiting into the cartilage anlagen of a growing digit, result in a shorter middle phalange. However, reason for a missing middle phalange is unclear. Here, in IhhE95K BDA1 mouse, we showed a link to impaired apoptosis normally needed for interzone cavitation, thus a joint is not formed and the middle phalange is deemed absence. Hedgehog interacting partners (PTCH, CDON, GAS1and HHIP) are expressed in the interzone. Our data support a model for interzone cavitation, where CDON/GAS1 function as dependency receptors. Normally, IHH level is low at the center of the interzone, and the “ligand-free” CDON/GAS1 activate cell death for cavitation. In BDA1 joint, this is suppressed due to excess IHH. Our findings provided new insights into the role of IHH and CDON in joint formation, with relevance to hedgehog signaling in developmental biology.

overall_design: Digit III M/P1 interzones (GFP-labelled) at E14.5 were dissected with minimum surrounding tissues (GFP negative) were harvested with the aid of Lgr5-GFP in WT (Ihh+/+; Lgr5GFP/+) and Lgr5-DTR-GFP in BDA1 (IhhE95K/E95K/Lgr5DTR-GFP/+). Two litters of the same father were used for each genotype and 14 joints were harvested per genotype. Dissected tissues were dissociated with 0.02% collagenase P (Roche 11213865001) for 45mins at 37oC, followed by 40M cell strainer. Single cells were encapsulated using 10X Genomics Chromium Single Cell Chip (10x genomics) for encapsulations with Chromium Single Cell 3’ Reagent Kits v2 according to manufacturer’s instructions, performed by Centre of PanorOmic Sciences, HKU. Libraries were sequenced by HiSeq1500 (Illumina) and NovaSeq6000 (Illumina).

first: Adrian

middle: O

last: Leung

first: Andrew

last: Poon

first: Wilson

last: Chan

first: Danny


title: Effect of TET3 expression on muscle insulin sensitivity

city: New Haven

first: Haining

last: Lyu

state: Connecticut

address: 1145 chapel street, 401

country: USA

institute: Yale

summary: To gain a mechanistic insight into TET3-mediated regulation of muscle insulin sensitivity, we performed genome-wide expression profiling (RNA-seq) on RNA isolated from GAS muscles of muscle TET3 specific knockdown mice and WT littermates.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for GAS muscle tissue of muscle TET3 specific knockdown mice and WT littermates.

first: Yingqun

last: Huang


title: The UBP5 histone H2A deubiquitinase counteracts PRCs-mediated repression to regulate Arabidopsis development

first: Sara

last: Farrona

summary: Polycomb Repressive Complexes (PRCs) control gene expression through the incorporation of H2Aub and H3K27me3. In recent years, there is increasing evidence of the complexity of PRCs’ interaction networks and the interplay of these interactors with PRCs in epigenome reshaping, which is fundamental to understand gene regulatory mechanisms. Here, we identified UBIQUITIN SPECIFIC PROTEASE 5 (UBP5) as a chromatin player able to counteract the deposition of the two PRCs’ epigenetic hallmarks  in Arabidopsis thaliana. We demonstrated that UBP5 is a plant developmental regulator based on functional analyses of ubp5-CRISPR Cas9 mutant plants. UBP5 promotes H2A monoubiquitination erasure, leading to transcriptional de-repression. Furthermore, preferential association of UBP5 at PRC2 recruiting motifs and local H3K27me3 gaining in ubp5 mutant plants suggest the existence of functional interplays between UBP5 and PRC2 in regulating epigenome dynamics. In summary, acting as an antagonist of the pivotal epigenetic repressive marks H2Aub and H3K27me3, UBP5 provides novel insights to disentangle the complex regulation of PRCs’ activities.

overall_design: Genome-wide profiling of the histone marks H2Aub and H3K27me3 in Col-0 and ubp5 using Chromatin immunoprecipitation DNA-sequencing (ChIP-seq)

first: James

last: Godwin

first: Mohan

last: Govindasamy

first: Kiruba

last: Nedounsejian

first: Clara

last: Bourbousse

first: Léa

last: Wolff

first: Antoine

last: Fort

first: Fredy

last: Barneche


title: Newly repopulated spinal cord microglia exhibit a unique transcriptome and contribute to pain resolution

status: Public on Dec 04 2023

city: Stanford

first: Vivianne

last: Tawfik

address: 1291 Welch Road, Grant Building S007

department: Anesthesiology, Perioperative and Pain Medicine

institute: Stanford University

summary: Microglia contribute to the initiation of pain, however, a translationally viable approach addressing how or when to modulate these cells remains elusive. We used a targeted, inducible, genetic microglial depletion strategy at both acute and acute-to-chronic transition phases in the clinically-relevant tibial fracture/casting pain model to determine the contribution of microglia to the initiation and maintenance of pain. We observed complete resolution of pain which coincided with the timeframe of full repopulation of microglia after transient microglial depletion at the acute-to-chronic phase. These repopulated microglia were morphologically distinct from control microglia, signifying they may exhibit a unique transcriptome. RNA sequencing of repopulated spinal cord microglia identified genes of interest using weighted gene coexpression network analysis (WGCNA). We intersected these genes with a newly generated single nuclei microglial dataset from human spinal cord dorsal horn and identified human-relevant genes that may ultimately promote pain resolution after injury. This work presents a novel approach to gene discovery in pain and provides comprehensive datasets for the development of future microglial-targeted therapeutics.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Establishment of a mandible defect model in rabbits infected with multiple bacteria and bioinformatics analysis

city: Kunming

first: Yuan

last: Zhao

state: Yunnan

address: No. 212, Daguan Road, Xishan District, Kunming City, Yunnan Province, China

institute: 920th Hospital of Joint Logistics Support Force of People's Liberation Army of China

summary: Objective: A model of infectious mandibular defect (IMD) caused by infection with Staphylococcus aureus and Pseudomonas aeruginosa was established to explore the occurrence and development of IMD and identify key genes by transcriptome sequencing and bioinformatics analysis. Methods: S. aureus and P. aeruginosa were diluted to 3×108 CFU/ml, and 6×3×3 mm defects lateral to the Mandibular Symphysis were induced in 28 New Zealand rabbits. Sodium Morrhuate (0.5%) and 50 μL bacterial solution were injected in turn; the effects were evaluated through postoperative observations, imaging and histological analyses. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, and protein‒protein interaction (PPI) network analyses were performed to investigate the function of the differentially expressed genes (DEGs). Results: Bioinformatics analysis showed a total of 1,804 DEGs, of which 743 were upregulated and 1061 were downregulated. GO and KEGG analyses showed that the DEGs were enriched in immunity and osteogenesis inhibition, and the core genes identified by the PPI network were enriched in the Hedgehog pathway, which plays a role in inflammation and tissue repair; the MEF2 transcription factor family was predicted by IRegulonConclusion: By direct injection of bacterial solution into the rabbit mandible defect area, the rabbit IMD model was successfully established. Bioinformatics analysis results showed that the Hedgehog pathway is potential therapeutic targets for IMD.

overall_design: Three bone tissue samples from the infectious bone defect group, and four bone tissue samples were collected from the healthy control group

first: Jun

last: Su

first: Chong-Yan

last: XU

first: Wen-Yun

last: Zhang


title: Newly repopulated spinal cord microglia exhibit a unique transcriptome and contribute to pain resolution (human)

overall_design: Human lumbar spinal cords were collected from donors and used to generate a novel single-nuclei dataset to compare with our mouse transcriptomic data. The dataset allows us to confirm whether the gene candidates identified in our mouse work are expressed in human microglia, strenghtening the case for each gene to be considered a therapeutic target in our research moving forward.

first: Lauren

last: Donovan

first: Caldwell

last: Bridges

first: Amy

last: Nippert

first: Meng

last: Wang

first: Shaogen

last: Wu

first: Thomas

last: Forman

first: Elena

last: Haight

first: Sabrina

last: Bond

first: Nolan

last: Huck

first: Claire

last: Jordan

first: Aysha

last: Gardner

first: Ramesh

last: Nair


title: Elucidating granulocytic myeloid-derived suppressor cell (G-MDSC) fate during S. aureus biofilm infection

city: White/Caucasian

first: Tammy

last: Kielian

state: NE

address: 985900 Nebraska Medical Center

institute: UNMC

summary: Myeloid-derived suppressor cells (MDSCs) are pathologically activated immature myeloid cells with immunosuppressive activity that expand during chronic inflammation, such as cancer and prosthetic joint infection (PJI). MDSCs can be broadly separated into two populations based on surface marker expression and function, namely monocytic MDSCs (M-MDSCs) and granulocytic MDSCs (G-MDSCs). In cancer models, M-MDSCs have been reported to transition into tumor-associated macrophages and/or dendritic cells, whereas G-MDSCs are considered terminally differentiated with short half-lives. G-MDSCs are the most abundant leukocyte infiltrate during PJI; however, how this population is maintained in vivo and cellular heterogeneity is currently unknown. In this study, we identified a population of Ly6G+Ly6C+F4/80+MHCII+ MDSCs during PJI that displayed immunosuppressive properties ex vivo. We leveraged F4/80 and MHCII expression by these cells for further characterization using cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq), which revealed a distinct transcriptomic signature of this population. F4/80+MHCII+ MDSCs displayed gene signatures resembling G-MDSCs, neutrophils, and monocytes, but had increased expression of genes involved in cytokine response/production, inflammatory cell death, and mononuclear cell differentiation. To determine whether F4/80+MHCII+ MDSCs represented an alternative differentiation state of G-MDSCs, Ly6G+Ly6C+F4/80-MHCII- G-MDSCs from CD45.1 mice were adoptively transferred into CD45.2 recipients using a mouse model of PJI. A small percentage of transferred G-MDSCs acquired F4/80 and MHCII expression in vivo, suggesting some degree of plasticity in this population. Collectively, these results demonstrate a previously unappreciated phenotype of G-MDSCs during PJI, which suggests a novel granulocytic-to-monocytic transition of MDSC infiltrates.

overall_design:
A mouse model of S. aureus prosthetic joint infection was used for this study. Implant-associated tissue was collected from WT mice at day 14 following S. aureus PJI, homogenized, and after red blood cells lysis, Fc receptors were blocked. Samples were stained with CD45-APC, Ly6G-PE, Ly6C-PerCP-Cy5.5, and Live/Dead fixable blue stain, whereupon live Ly6G+Ly6C+ and Ly6C+Ly6G- cells were collected using a BD Biosciences FACSAria. Next, these populations were labeled using TotalSeq-B0114 F4/80 (RRID: AB_2819847) and TotalSeq-B0117 I-A/I-E (MHCII; RRID: AB_2832367) barcoded antibodies (BioLegend) following the manufacturer’s protocol. The post-sort viability of Ly6C+Ly6G- and Ly6G+Ly6C+ populations was 79.6 and 89.4%, respectively, with minimal debris as determined using a Luna automated fluorescent cell counter (Logos Biosystems). Ly6G+Ly6C+ and Ly6C+G- cells (13,627 and 1,624, respectively) were processed using a 10X Genomics platform by the UNMC Genomics Core. Briefly, single cells were lysed, RNA was reverse-transcribed and barcoded using a Chromium Single-Cell 3’ Reagent Kit v3 (10X Genomics) according to the manufacturer’s protocol. Illumina compatible cDNA libraries were created and quantified by quantitative PCR using the KAPA Library Quant Kit (Illumina) and were loaded at a concentration of 1.3 pM on an Illumina NovaSeq instrument. Samples were sequenced following the parameters suggested by 10X Genomics to an average read depth of 100,000 reads/cell. Alignment was completed using 10X Genomics Cell Ranger with the Mus musculus mm10 genome as a reference.
ADT; Barcode sequence
TotalSeq-B0114 F4/80; TTAACTTCAGCCCGT
TotalSeq-B0117 I-A/I-E; GGTCACCAGTATGAT

first: Bertrand

last: Blake

first: Heim

last: Cortney

first: Koepsell

last: Scott

first: Kielian

last: Tammy


title: Endothelial Jagged1 levels and distribution are post-transcriptionally controlled by ZFP36 decay proteins

city: Los Angeles

first: Karolina Elzbieta

middle: Kaczor

last: Urbanowcz

state: CA

address: 10833 Le Conte Avenue

institute: UCLA

summary: Vascular morphogenesis requires a delicate gradient of Notch signaling that is controlled, at least in part, by the distribution of ligands (Dll4 and Jagged1). How jagged1 (JAG1) expression is compartmentalized in the vascular plexus remains unclear. Here we showed that Jag1 mRNA is a direct target of zinc finger protein 36 (ZFP36), an RNA-binding protein involved in mRNA decay that we found robustly induced by VEGF. Endothelial cells lacking ZFP36 displayed high levels of JAG1 and increased angiogenic sprouting in vitro. Similarly, mice lackingZfp36in endothelial cells display mispatterned and increased levels of JAG1 in the developing retinal vascular plexus. Abnormal levels of JAG1 at the sprouting front altered NOTCH1 signaling, increasing the number of tip cells; a phenotype that was rescued by imposing haploinsufficiency ofJag1. Our findings reveal an important feedforward loop, whereby VEGF stimulates ZFP36, consequently suppressing Jag1 to enable adequate levels of Notch signaling during sprouting angiogenesis.

overall_design: Comparative gene expression profiling analysis from RNA seq of HUVECs (3 biological replicates with 2 technical replicates each) pretreated with DMSO or ZM323 before stimulation with or without VEGF for 1h

first: Sunshine

last: Hannah L.

first: Kaczor-Urbanowicz

last: Karolina Elzbieta

first: Iruela-Arispe

last: M Luisa


city: Galway

first: Sara

last: Farrona

address: University Road

institute: National University of Ireland Galway

overall_design: Analysing the genome-wide occupancy of UBP5 using the ChIP-seq data from UBP5::UBP5-GFP;ubp5 lines.

first: James

last: Godwin

first: Mohan

last: Govindasamy

first: Kiruba

last: Nedounsejian

first: Clara

last: Bourbousse

first: Léa

last: Wolff

first: Antoine

last: Fort

first: Fredy

last: Barneche


title: Chronic stress and its effects on behavior, RNA expression of the bed nucleus of the stria terminalis, and the M-current of NPY neurons

city: New Brunswick

first: Thomas

last: Degroat

state: NJ

address: 10 Suydam Street, Apt 12

department: Animal Sciences

institute: Rutgers University

summary: Mood disorders, like major depressive disorder, can be precipitated by chronic stress and are more likely to be diagnosed in cisgender women than in cisgender men. This suggests that stress signaling in the brain is sexually dimorphic. We used a chronic variable mild stress paradigm to stress female and male mice for 6 weeks, followed by an assessment of avoidance behavior: the open field test, the elevated plus maze, the light/dark box emergence test, and the novelty suppressed feeding test. Additional cohorts were used for bulk RNA-Sequencing of the anterodorsal bed nucleus of the stria terminalis (adBNST) and whole-cell patch clamp electrophysiology in NPY-expressing neurons of the adBNST to record stress-sensitive M-currents. Our results indicate that females are more affected by chronic stress as indicated by an increase in avoidance behaviors, but that this is also dependent on the estrous stage of the animals such that diestrus females show more avoidant behaviors regardless of stress treatment.  Results also indicate that NPY-expressing neurons of the adBNST are not major mediators of chronic stress as the M-current was not affected by treatment. RNA-Sequencing data suggests sex differences in estrogen signaling, serotonin signaling, and orexin signaling in the adBNST. Our results indicate that chronic stress influences behavior in a sex- and estrous stage-dependent manner but NPY-expressing neurons in the BNST are not the mediators of these effects.

overall_design: To study differential expression of genes in the anterodorsal bed nucleus of the strai terminalis in mice after exposure to chronic variable mild stress or control conditions. Differential expression was analyzed with the following parameters: sex + condition + sex:condition.

first: Kimberly

last: Wiersielis

first: Katherine

last: Denney

first: Sowmya

last: Kodali

first: Sierra

last: Daisey

first: Jessica

last: Tollkuhn

first: Benjamin

last: Samuel

first: Troy

last: Roepke