title: Supplementation with amino acid sources facilitates fermentative growth of Shewanella oneidensis MR-1 in defined media

city: Hachioji

first: Atsushi

last: Kouzuma

state: Tokyo

address: 1432-1 Horinouchi

institute: Tokyo University of Pharmacy and Life Sciences

summary: Shewanella oneidensis MR-1 is a facultative anaerobe that grows by respiration using a variety of electron acceptors. This organism serves as a model to study how bacteria thrive in redox-stratified environments. A glucose-utilizing engineered derivative of MR-1 has been reported to be unable to grow in glucose minimal medium (GMM) in the absence of electron acceptors, despite this strain having a complete set of genes for reconstructing glucose to lactate fermentative pathways. To gain insights into why MR-1 is incapable of fermentative growth, this study examined a hypothesis that this strain is programmed to repress the expression of some carbon metabolic genes in the absence of electron acceptors. Comparative transcriptomic analyses of the MR-1 derivative were conducted in the presence and absence of fumarate as an electron acceptor, and these found that the expression of many genes involved in carbon metabolism required for cell growth, including several tricarboxylic acid (TCA) cycle genes, was significantly downregulated in the absence of fumarate. This finding suggests a possibility that MR-1 is unable to grow fermentatively on glucose in minimal media owing to the shortage of nutrients essential for cell growth, such as amino acids. This idea was demonstrated in subsequent experiments that showed that the MR-1 derivative fermentatively grows in GMM containing tryptone or a defined mixture of amino acids. We suggest that gene regulatory circuits in MR-1 are tuned to minimize energy consumption under electron acceptor-depleted conditions, and that this results in defective fermentative growth in minimal media. IMPORTANCE It is an enigma why S. oneidensis MR-1 is incapable of fermentative growth despite having complete sets of genes for reconstructing fermentative pathways. Understanding the molecular mechanisms behind this defect will facilitate the development of novel fermentation technologies for the production of value-added chemicals from biomass feedstocks, such as electro-fermentation. The information provided in this study will also improve our understanding of the ecological strategies of bacteria living in redox-stratified environments.

overall_design: Total 8 samples, 4 biological replicates for each sample

first: Sota

last: Ikeda

first: Kazuya

last: Watanabe


title: Chromatin Accessibility of LPS stimulated Activated B cells

status: Public on Jun 20 2023

city: Atlanta

first: Chris

last: Scharer

state: GA

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

country: USA

institute: Emory University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Chromatin accessibility profiles of activated B cells that were derived from CD43 negative splenic B cells that were for 72 hours with LPS, IL-2 and IL-5.

overall_design: ATAC-seq of LPS activated B cells in triplicate

first: Christopher

middle: D


title: Effect of deletion of Sisfha on gene expression of Saccharolobus islandicus REY15A in the presence of 4-nitroquinoline 1-oxide (NQO)

city: Qingdao

first: Qihong

last: Huang

state: Shandong

address: 72 Binhaidadao, Aoshanwei, Jimo

country: China

institute: Shandong University

type: Expression profiling by high throughput sequencing

summary: To investigate the function of the FHA protein SisFha in the regulation of gene transcription during DNA damage response, we constructed Sisfha deletion mutant of S. islandicus and treated with NQO.

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of 2 different cells, the wild type strain E233S and Δsisfha, treated or mock-treated with NQO for 6 h.

first: Zhichao

last: Jiang

first: Zijia

last: Lin

first: Yulong

last: Shen


title: The HSV-1 ICP22 protein selectively impairs histone repositioning upon Pol II transcription downstream of genes (RNA-seq II)

city: München

first: Caroline

last: Friedel

address: Amalienstr. 17

department: Institut für Informatik

country: Germany

institute: Ludwig-Maximilians-Universität München

summary: Part 1: Human telomerase reverse transcriptase (hTERT)-Immortalized cell line (T-HF) inducibly expressing ICP22 or ICP27 (doxycycline-induced) were analyzed for gene expression and read-through transcription by RNA-seq (total RNA). This experiment was performed in parallel to the corresponding OMNI-ATACseq libraries in replicate wells. ICP22 or ICP27 expression was induced for 24 h prior to other treatments or harvest, respectively. ICP22 expressing cells were additionally treated with KCl (200 mM) or control for 2 h prior to harvest. Part 2: Human telomerase reverse transcriptase (hTERT)-Immortalized cell line (T-HF) doxycycline-inducibly expressing an artificial miRNA against SSRP1 (two separate cell lines expressing different amiRNAs) were mock, HSV-1 strain F wild type or US1 deletion mutant infected to analyze gene expression and read-through transcription. This experiment was performed in parallel to the corresponding OMNI-ATACseq libraries in replicate wells. Expression of amiRNAs was induced for 72 h prior to infection. Cells were inoculated for 1 h and then incubated for another 8 h. The experiment was conducted with PAA (350 ug/ml) treatment, which was added after the inoculum was removed, and doxycycline where indicated.

overall_design: Part 1: ICP22 or ICP27 expression in T-HFs was induced with 5 ug/ml doxycycline for 24 h prior to other treatments or harvest, respectively. ICP22 expressing cells were additionally treated with KCl (200 mM) or control for 2 h prior to harvest. OMNI-ATACseq libraries were prepared with 50000 cells/sample as described by Corces et al. (2017). Two biological replicates were prepared. Part 2: Human telomerase reverse transcriptase (hTERT)-Immortalized cell line (T-HF) doxycycline-inducibly expressing an artificial miRNA against SSRP1 (two separate cell lines expressing different amiRNAs) were mock, HSV-1 strain F wild type (MOI 10) or US1 deletion mutant (MOI 10) infected to analyze gene expression and read-through transcription. This experiment was performed as a control in parallel to the corresponding OMNI-ATACseq libraries in replicate wells. Expression of amiRNAs was induced with 5 ug/ml doxycycline for 72 h prior to infection. Cells were inoculated for 1 h with MOI 10 and then incubated for another 8 h (inoculum was replaced with fresh medium). The experiment was conducted with PAA (350 ug/ml) treatment, which was added after the inoculum was removed, and 5 ug/ml doxycycline where indicated. Each amiRNA represents a separate biological replicate. For both parts the samples were harvested in TRIZOL and processed by standard methods. RNA was depleted of rRNA and libraries were prepared using the Truseq stranded library prep kit.

first: Lara

last: Djakovic

first: Thomas

last: Hennig

first: Katharina

last: Reinisch

first: Andrea

last: Milic

first: Adam

middle: W

last: Whisnant

last: Wolf

first: Elena

last: Weiß

first: Tobias

last: Haas

first: Arnhild

last: Grothey

middle: S

last: Jürges

first: Michael

last: Kluge

first: Florian

last: Erhard

middle: C

first: Lars

last: Dölken


title: Jasmonate signaling controls negative and positive effectors of salt stress tolerance in rice

city: Strasbourg

first: Thierry

last: HEITZ

address: 12 rue du General Zimmer

department: IBMP

country: France

institute: CNRS

summary:
The JA deficient mutant (aoc) showed weaker symptoms than WT when both are exposed to salt. JAs signaling in WT, appeared then to impair salt tolerance and we were interested, through this transcriptomic approach, to highlight the JA-dependent component of the salt stress response that could explain the differential phenotype
We report, for root and 2nd leaf, the compared transcriptomes of WT and aoc, before and at 3 different times (1 h, 6 h and 72 h) after salt exposure. The study reveals some key JA-regulated negative and positive effectors of salt stress tolerance in rice

overall_design: WT and aoc seedlings were grown in hydroponic system for 11 days before being exposed to 100 mM NaCl solution. Samples were then harvested from root and 2nd leaf at two early (1 h and 6 h) and one late time point (72 h) to compare the transcriptionnal response of the two genotypes.

last: Heitz

last: Riemann

first: Simon

last: Ndecky

first: Valérie

last: Cognat


title: Hepatic responses of mice and rats to equivalent acetaminophen (APAP) insult [rat]

city: Liverpool

first: Ian

last: Copple

address: Ashton Street

department: Department of Pharmacology and Therapeutics

country: United Kingdom

institute: University of Liverpool

summary:
The well-known difference in sensitivity of mice and rats to acetaminophen (APAP) liver injury has been related to differences in the fraction that is bioactivated to the reactive metabolite N-acetyl-p-benzoquinoneimine (NAPQI).
Physiologically-based pharmacokinetic modelling was used to identify doses of APAP (300 and 1000 mg/kg in mice and rats, respectively) yielding similar hepatic burdens of NAPQI, to enable the comparison of temporal liver tissue responses under conditions of equivalent chemical insult.

overall_design: Male C57Bl/6J mice (8 weeks old; 15-22 g body weight) or Sprague-Dawley rats (5 weeks old; 119-144 g body weigh) were fasted for 16 h prior to dosing. Acetaminophen (APAP) was solubilised in 1% (w/v) hydroxyethylcellulose (both, Sigma-Aldrich). Mice (n=5 per time point) and rats (n=5 per time point) were administered 300 mg/kg and 1000 mg/kg APAP, respectively, or vehicle (1% hydroxyethylcellulose) by oral gavage. The animals were sacrificed by exsanguination under isoflurane anaesthesia at baseline (0 h) and at 3, 6, 9 and 24 h after administration of APAP or vehicle. Liver tissue was collected for RNA extraction and hybridization on Affymetrix microarrays.

first: Giusy

last: Russomanno

first: Rowena

last: Sison-Young

first: Lucia

middle: A

last: Livoti

first: Hannah

last: Coghlan

first: Rosalind

middle: E

last: Jenkins

first: Steven

middle: J

last: Kunnen

first: Ciarán

middle: P

last: Fisher

first: Dennis

last: Reddyhoff

first: Iain

last: Gardner

first: Adeeb

middle: H

last: Rehman

first: Stephen

last: Fenwick

first: Andrew

middle: R

last: Jones

first: Guy

last: Vermeil De Conchard

first: Gilles

last: Simonin

first: Helene

last: Bertheux

first: Richard

last: Weaver

first: Robert

middle: L

last: Johnson

last: Liguori

first: Diana

last: Clausznitzer

first: James

last: Stevens

first: Christopher

last: Goldring

middle: M


title: The HSV-1 ICP22 protein selectively impairs histone repositioning upon Pol II transcription downstream of genes (Omni-ATAC-seq I)

first: Caroline

last: Friedel

summary: T-HF cells were grown either in the presence or absence of DOX. Upon DOX exposure, cells expressed either HA-ICP22 or HA-ICP22 and V5-ICP27. T-HF HA-ICP22 cells were treated with salt stress for 2 hours before proceeding with Omni-ATAC-seq. OMNI-ATAC-seq was conducted for the KOS1.1 strain and compared to a full US1 deletion mutant.

overall_design: T-HF cells were grown either in the presence or absence of DOX (5 µg/ml) for 48 h. Upon DOX exposure, cells expressed either HA-ICP22 or HA-ICP22 and V5-ICP27. T-HF HA-ICP22 cells were treated with 80 mM KCl (salt stress) for 2 hours before proceeding with Omni-ATAC-seq. HFFF cells were infected for 8h under PAA treatment with MOI 10 of KOS1.1 and an isogenic US1 deletion mutant.

first: Lara

last: Djakovic

first: Thomas

last: Hennig

first: Katharina

last: Reinisch

first: Andrea

last: Milic

first: Adam

last: Whisnant

last: Wolf

first: Tobias

last: Haas

first: Arnhild

last: Grothey

last: Jürges

first: Michael

last: Kluge

first: Florian

last: Erhard

first: Lars

last: Dölken


title: Hepatic responses of mice and rats to equivalent acetaminophen (APAP) insult

first: Ian

last: Copple

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

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus

overall_design: Refer to individual Series


title: The HSV-1 ICP22 protein selectively impairs histone repositioning upon Pol II transcription downstream of genes (ATAC-seq II)

summary: Primary human fetal foreskin fibroblasts (HFFF) were infected with wild-type simplex virus 1 (HSV-1) strain F and null-ICP22 mutant at a multiplicity of infection (MOI) of 10. ATAC-seq libraries were prepared starting with 50,000 cells per condition following the protocol described by Buenrostro et al., Nature Methods 2013

overall_design: HFFFs were infected with HSV-1 strain F or ICP22-null mutant for 8 or 12 hours. PAA was used at 350 μg/mL during the course of infection. ATAC-seq samples were prepared at the indicated times of infection. Two independent biological replicates were analysed.

first: Elena

last: Weiß


title: Nova proteins direct synaptic integration of somatostatin interneurons through activity- dependent alternative splicing

city: New York City

first: Alireza

last: Khodadadi-Jamayran

state: NY

address: 550 1st Ave, MSB 304

department: Division of Advanced Research Technologies (DART)

institute: New York University, NYU Langone Medical Center

summary: Somatostatin interneurons are the earliest born population of inhibitory cells. They are crucial to support normal brain development and function; however, the mechanisms underlying their integration into nascent cortical circuitry are not well understood. In this study, we begin by demonstrating that the maturation of somatostatin interneurons is activity dependent. We then investigated the relationship between activity, alternative splicing and synapse formation within this population. Specifically, we discovered that the Nova family of RNA-binding proteins are activity-dependent and are essential for the maturation of somatostatin interneurons, as well as their afferent and efferent connectivity. Moreover, in somatostatin interneurons, Nova2 preferentially mediates the alternative splicing of genes required for axonal formation and synaptic function. Hence, our work demonstrates that the Nova family of proteins are centrally involved in coupling developmental neuronal activity to cortical circuit formation.

overall_design: Somatostatin SST interneurons were isolated by FACS from the S1 cortex and subjected to RNAseq library preparation following standard Illumnia guidelines.

first: Brie

last: Wamsley

first: Gord

last: Fishell


title: ELL3 promotes stem cell native to primed transition through LINE-based enhancers

city: Nanjing

first: Xiaoxu

last: Liu

state: Jiangsu

address: 2 Sipailou

department: Institute of Life Sciences

institute: Southeast University


title: The HSV-1 ICP22 protein selectively impairs histone repositioning upon Pol II transcription downstream of genes (Omni-ATAC-seq III)

first: Caroline

last: Friedel

summary: We report that HSV-1 gives rise to transposase accessible chromatin in gene downstream areas, in regions that show transcription termination defects. We show that the viral protein ICP22 is responsible for this open chromatin.

overall_design: We used BAC-derived strain 17 HSV-1 WT and US1 deletion mutant and examined the opening of chromatin downstream of transcription termination sites of affected genes. Two biological replicates of cells infected with MOI 10 of the indicated viruses.

last: Djakovic

last: Hennig

first: Christopher


title: The HSV-1 ICP22 protein selectively impairs histone repositioning upon Pol II transcription downstream of genes (ChIPmentation)

summary: To look at the deposition of the histone marks in the downstream regions of DoTT genes, HFFF cells were either mock, WT HSV-1 (strain F and 17) or ΔICP22 virus infected. Throught the course of infection (for the marked samples), cells were treated with 350 ug/ml PAA. Samples were processed according to the original ChIPmentation protocol (Schmidl C et al. ChIPmentation: fast, robust, low-input ChIP-seq for histones and transcription factors. Nat Methods. 2015) with few changes as explained in the Materials and Methods section.

overall_design: We profiled several canonical histones as well as marks of repressive and active chromatin on mock and WT HSV-1 infected cells with ChIPmentation. For the histone H1, cells were also infected with ΔICP22.

first: Lara

first: Thomas

last: Reinisch

last: Milic

last: Whisnant


title: Hepatic responses of mice and rats to equivalent acetaminophen (APAP) insult [mouse]

first: Giusy

last: Russomanno

first: Rowena

last: Sison-Young

first: Lucia

last: Livoti

first: Hannah

last: Coghlan

first: Rosalind

last: Jenkins

first: Steven

last: Kunnen

first: Ciarán

last: Fisher

first: Dennis

last: Reddyhoff

first: Iain

last: Gardner

first: Adeeb

last: Rehman

first: Stephen

last: Fenwick

first: Andrew

last: Jones

first: Guy

last: Vermeil De Conchard

first: Gilles

last: Simonin

first: Helene

last: Bertheux

first: Richard

last: Weaver

first: Robert

last: Johnson

last: Liguori

first: Diana

last: Clausznitzer

first: James

last: Stevens

last: Goldring


title: R-loop dependent promoter-proximal termination ensures genome stability [ChIP-seq]

city: Shanghai

first: Jiwei

last: Chen

address: 130 DongAn Road

institute: Fudan University

summary: Precise regulation of transcription is essential to maintain genome integrity, yet key mechanisms coordinating transcription, genome stability and downstream cellular functions remain incomplete. Here we report the identification of SOSS-INTAC, a stable association of the genome stability regulator Sensor of Single-stranded DNA (ssDNA) (SOSS) complex and transcription regulator Integrator-PP2A (INTAC). Via SSB1-mediated ssDNA recognition at its targets, SOSS-INTAC stimulates early termination of transcription and thus attenuates paused Pol II-induced formation of R-loops to prevent its aberrant accumulation that has the risk of increasing chromatin accessibility and compromising genome stability. SOSS-INTAC-mediated attenuation of R-loops is greatly enhanced by SSB1's unique property of forming liquid-like condensates. In contrast, preventing SSB1 condensation through deletion or cancer-associated mutation within its intrinsically disordered region (IDR) leads to pervasive accumulation of R-loops at a genome-wide level. Thus, our study highlights the genomic surveillance function of SOSS-INTAC that enables timely transcriptional termination to constrain aberrant R-loop accumulation and ensure genomic stability.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for SSB1, INTS3, INTS5, polII, as well as the histone modifications H3K27ac and H3K4me1 with 2 biological replicates in DLD-1 cells.

first: Congling

last: Xu

first: Chengyu

last: Li

first: Yan

last: Xiong

first: Huasong

last: Lu

first: Fei

middle: X


title: The HSV-1 ICP22 protein selectively impairs histone repositioning upon Pol II transcription downstream of genes (OMNI-ATAC-seq IV)

first: Caroline

last: Friedel

summary: Human telomerase reverse transcriptase (hTERT)-Immortalized cell line (T-HF) inducibly expressing ICP22 or ICP27 (doxycycline-induced) were analysed for downstream open chromation region (dOCR) formation. ICP22 or ICP27 expression was induced for 24 h prior to other treatments or harvest, respectively. ICP22 expressing cells were additionally treated with KCl (200 mM) for 2 h prior to harvest. OMNI-ATACseq libraries were prepared with 50000 cells/sample as described by Corces, M., Trevino, A., Hamilton, E. et al. An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. Nat Methods 14, 959–962 (2017). https://doi.org/10.1038/nmeth.4396

overall_design: ICP22 or ICP27 expression in T-HFs was induced with 5 ug/ml doxycycline for 24 h prior to other treatments or harvest, respectively. ICP22 expressing cells were additionally treated with KCl (200 mM) or control for 2 h prior to harvest. OMNI-ATACseq libraries were prepared with 50000 cells/sample as described by Corces et al. (2017). Two biological replicates were prepared. Libraries were quantified by Bioanalyzer (200-1000 bp window), pooled to equimolar concentration, subsequently size selected (200-1000 bp) and sequenced on a Nextseq500.

first: Lara

last: Djakovic

first: Thomas

last: Hennig

first: Katharina

last: Reinisch

first: Andrea

last: Milic

first: Adam

last: Whisnant

last: Wolf

first: Elena

last: Weiß

first: Tobias

last: Haas

first: Arnhild

last: Grothey

first: Christopher

last: Jürges

first: Michael

last: Kluge

first: Florian

last: Erhard

first: Lars

last: Dölken


title: ELL3 promotes stem cell native to primed transition through LINE-based enhancers [ChIP-Seq]

first: Xiaoxu

last: Liu

type: Methylation profiling by high throughput sequencing

summary: Long interspersed nuclear elements-1 (LINE-1) are the clade of retrotransposons still possessing autonomous mobility in mammals. LINE-1 transcription contributed to global chromatin opening in mouse early embryos.Whether LINE-1 element plays a direct role in the local regulation of its nearby genes remains largely obscure.ELL3 occupies and represses the youngest LINE-1 family members L1Md_T and L1Md_Gf in naïve mouse ES cells.We found that the enhancer function of the evolutionally young LINE-1s, and suggests that ELL3 act as a key drivers of the naïve-primed transition through regulating the young LINE-1 based enhancers.

overall_design: ChIpSeq

first: Chengqi

last: Lin


title: RNAseq of TLR agonist and SLE Immune complex stimulated SLE patient PBMCs with and without depletion of pDCs with CSL362

status: Public on Jun 19 2023

city: Melbourne

first: Katherine

last: Monaghan

state: Victoria

address: 30 Flemington Rd, Parkville

department: Research and Development

country: Australia

institute: CSL Limited

summary: Stimulation experiments were done with PBMC from SLE or healthy donors treated with CSL362 or isotype control before stimulation with various stimuli including the TLR9 agonist 0.25 μM CpGc; the TLR4 agonist 10 μg/ml LPS; and the TLR3 agonist 10 μg/ml POLY I:C. As well as the SLE specific stimuli SLE immunoglobulin (Ig) + necrotic cell lysates (NCL) to form immune complexes; control healthy donor Ig + NCL; and SLE sera + NCL; or healthy donor sera + NCL to understand the specific effects of pDC depletion on different inducible gene transcripts.

overall_design: PBMC from SLE or healthy donors were cultured with 1 microgram/ml CSL362 or isotype control for 20 hours. The supernatant was then removed and cells were resuspended in various stimuli (0.25 micromolar 0.25 μM CpGc, 10 microgram/ml 10 μg/ml LPS, 10 microgram/ml 10 μg/ml POLY I:C, 0.1 mg/ml healthy donor immunoglobulin (Ig) + 0.1 mg/ml necrotic cell lysates (NCL), 0.05-0.1 mg/ml SLE Ig + 0.1 mg/ml NCL, 20% SLE sera + 0.1 mg/ml NCL, 20% HD sera + 0.1 mg/ml NCL) for 24 hours at 37 degrees celcius. Cell pellets were then stored in RNAprotect before the RNA was later extracted using a qiagen RNAeasy miniplus kit. Samples underwent an illumina stranded RNA polyA library prep and HiSeq HT chemistry 100 bp single reads.

first: Alberta

last: Hoi

first: Cristina

last: Gamell

first: Tsin

middle: Y

last: Tai

first: Bryan

last: Linggi

first: Jarrat

last: Jordan

first: Matteo

last: Cesaroni

first: Takahiro

last: Sato

first: Milica

last: Ng

first: Shereen

last: Oon

first: Jacqueline

last: Benson

first: Ian

last: Wicks

first: Eric

last: Morand

first: Nicholas

last: Wilson


title: Proxalutamide reduces SARS-CoV-2 infection and associated inflammatory response

city: Ann Arbor

first: Arul

middle: M.

last: Chinnaiyan

state: MICHIGAN

address: 1500 E. Medical Center Dr

institute: University of Michigan

summary: Early in the COVID-19 pandemic, data suggested that males had a higher risk of developing severe disease and that androgen deprivation therapy might be associated with protection. Combined with the fact that TMPRSS2, a host entry factor for the SARS-CoV-2 virus, was a well-known androgen-regulated gene, this led to an upsurge of research investigating androgen receptor (AR)-targeting drugs. Proxalutamide, a newer AR antagonist, was shown in initial clinical studies to benefit COVID-19 patients; however, further validation is needed as one study was retracted. Due to continued interest in proxalutamide, which is in several phase 3 trials, we examined its ability to impact SARS-CoV-2 infection and associated downstream inflammatory responses. Proxalutamide exerted similar effects as enzalutamide, an AR antagonist commonly prescribed for advanced prostate cancer treatment, in decreasing AR signaling and expression of TMPRSS2 and ACE2, the SARS-CoV-2 receptor. However, proxalutamide led to degradation of AR protein, an effect that was not observed with enzalutamide. Proxalutamide inhibited SARS-CoV-2 infection with an IC50 value of 97 nM, compared to 281 nM for enzalutamide. Importantly, proxalutamide inhibited infection by multiple SARS-CoV-2 variants and synergized with remdesivir. Proxalutamide also protected against cell death in response to TNF and IFN, and overall survival of mice was increased with proxalutamide treatment prior to cytokine exposure. Mechanistically, we found that proxalutamide increased levels of NRF2, an essential transcription factor that mediates antioxidant responses, and could decrease lung inflammation. These data provide compelling evidence that proxalutamide can prevent SARS-CoV-2 infection and cytokine-induced lung damage, suggesting that promising clinical data may emerge from ongoing phase 3 trials.

overall_design: To compare the transcriptomic changes associated with proxalutamide and enzalutamide, RNA-sequencing (RNA-Seq) analysis was carried out in androgen receptor (AR)-positive prostate cancer LNCaP cells using either 20 µM proxalutamide or enzalutamide for eight hours of treatment.

first: Yuanyuan

last: Qiao

first: Jesse

last: Wotring

first: Yang

last: Zheng

first: Charles

last: Zhang

first: Yuping

first: Xia

last: Jiang

first: Carla

last: Pretto

first: Sanjana

last: Eyunni

first: Abhijit

last: Parolia

first: Tongchen

last: He

first: Caleb

last: Cheng

first: Xuhong

last: Cao

first: Rui

last: Wang

first: Fengyun

last: Su

first: Stephanie

last: Ellison

first: Yini

first: Jun

last: Qin

first: Honghua

last: Yan

first: Qianxiang

last: Zhou

first: Liandong

last: Ma

first: Jonathan

middle: Z

last: Sexton


title: Decreased IGF1R Attenuates Senescence and Improves Function in Pancreatic beta-Cells

city: Boston

first: Hui

last: Pan

address: 1 Joslin Place

department: Bioinformatics and Biostatistics Core

institute: Joslin Diabetes Center

summary: We previously reported that increased expression of IGF1R in mouse and human beta-cells is a marker of older beta-cells; however, its contribution to age-related dysfunction and cellular senescence remains to be determined. In this study, we explored the direct role of IGF1R in beta-cell function and senescence using inducible beta-cell specific IGF1R knockdown (betaIgf1rKD) mice. Adult betaIgf1rKD mice showed improved glucose clearance and glucose-induced insulin secretion, accompanied by decreased p21Cip1 protein expression in beta-cells. RNASeq of islets isolated from these betaIgf1rKD mice revealed restoration of 3 signaling pathways known to be downregulated by aging: sulfide oxidation, autophagy, and mTOR signaling. Additionally, deletion of IGF1R in mouse beta-cells increased transcription of genes important for maintaining beta-cell identity and function, such as Mafa, Nkx6.1, and Kcnj11, while decreasing senescence-related genes, such as Cdkn2a, Il1b, and Serpine 1. These results suggest that IGF1R signaling plays a causal role in aging-induced beta-cell dysfunction.

overall_design: Islets isolated from 4 betaIgf1rKD and 4 betaIgf1r mice were resuspended in RNA extraction buffer and the RNeasy Micro Kit (No. 74004) was used to purify RNA and submitted for sequencing.

first: Kanako

last: Iwasaki

first: Cristina

last: Aguayo-Mazzucato


title: The HSV-1 ICP22 protein selectively impairs histone repositioning upon Pol II transcription downstream of genes (Omni-ATAC-seq II)

first: Caroline

last: Friedel

summary: Human telomerase reverse transcriptase (hTERT)-Immortalized cell line (T-HF) with or without DOX-induced KD of SSPR1 and SPT6 were infected with wild-type simplex virus 1 (HSV-1) strain F or with ICP22-null mutant at a multiplicity of infection (MOI) of 10. Omni-ATAC-seq libraries were prepared starting with 50,000 cells per condition following the protocol described by Corces, M., Trevino, A., Hamilton, E. et al. An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. Nat Methods 14, 959–962 (2017). https://doi.org/10.1038/nmeth.4396

overall_design: T-HFs were treated with DOX for 72h prior to infection to induce knock down of either SPT6 or SSRP1. Cells were infected with HSV-1 strain F or ICP22-null mutant for 8 hours. PAA was used at 350 μg/mL during the course of infection. Omni-ATAC-seq samples were prepared at the indicated times of infection. Two independent biological replicates were analysed.

first: Florian

last: Erhard

first: Thomas

last: Hennig

first: Katharina

last: Reinisch

first: Andrea

last: Milic

first: Adam

last: Whisnant

last: Wolf

first: Elena

last: Weiß

first: Tobias

last: Haas

first: Arnhild

last: Grothey

first: Christopher

last: Jürges

first: Michael

last: Kluge

first: Lars

last: Dölken


title: Cancer cell non-autonomous tumor progression from chromosomal instability

city: NEW YORK

first: Ashley

last: Laughney

state: New York

address: 413 East 69th Street

department: Physiology, Biophysics, and Systems Biology

institute: Weill Cornell Medicine

summary: Chromosomal instability (CIN) is a driver of cancer metastasis and immune evasion. Yet, the extent to which this effect depends on the immune system remains unknown. Here we show that CIN-induced chronic activation of the cGAS-STING pathway in cancer cells induces signal re-wiring downstream of STING, promoting a pro-metastatic tumor microenvironment (TME). Using ContactTracing, a newly developed, validated, and benchmarked tool to infer conditionally-dependent cell-cell interactions from single cell transcriptomic data, we identify a cancer cell-derived STING-dependent ER stress response that remodels a TME replete with immune suppressive myeloid cells and dysfunctional T cells. Simultaneously, CIN-induced chronic STING activation leads to interferon-specific tach-yphylaxis reinforcing immune suppression. Reversal of CIN, depletion of cancer cell STING, or inhibition of ER stress signaling upends CIN-dependent effects on the TME and suppresses metastasis in immune competent, but not severely immune compromised settings. Treatment with STING inhibitors reduces CIN-driven metastasis in melanoma, breast, and colorectal cancer. Finally, we show that CIN and pervasive cGAS activation in micronuclei are associated with ER stress signaling, immune suppression, and metastasis in human triple-negative breast cancer; highlighting a viable strategy to identify and therapeutically intervene in tumors spurred by CIN-induced inflammation.

overall_design: Single-cell RNA sequencing was performed on 13 samples of syngeneic models of murine triple negative breast cancer using the Illumina NovaSeq platform.

first: Jun

last: Li

first: Melissa

last: Hubisz

first: Ethan

last: Earlie

first: Mercedes

last: Duran

first: Christy

last: Hong

first: Austin

last: Varela

first: Emanuele

last: Lettera

first: Matthew

last: Deyell

first: Bernardo

last: Tavora

last: Havel

first: Su

last: Phyu

first: Amit

last: Amin

first: Karolina

last: Budre

first: Erina

last: Kamiya

first: Julie-Ann

last: Cavallo

last: Garris

first: Simon

last: Powell

first: Jorge

last: Reis-Filho

first: Hannah

last: Wen

first: Sarah

last: Bettigole

first: Atif

last: Khan

first: Benjamin

last: Izar

first: Eileen

last: Parkes

first: Samuel

middle: F

last: Bakhoum


title: Age-related gene expression signature in limb skeletal muscles and the diaphragm in mice and rats [mouse]

city: Tarrytown

first: Kun

last: Xiong

address: 777 Old Saw Mill River Road

department: Molecular Profiling and Data Science

institute: Regeneron Pharmaceuticals

summary: As a result of aging, skeletal muscle undergoes atrophy and a decrease in function.  This age-related skeletal muscle weakness is known as “sarcopenia.”  To understand the changes in gene expression that occur as a result of age in skeletal muscles, we generated a multi-time point gene expression signature throughout the lifespan of mice and rats, as these are the most commonly used species in preclinical research and intervention testing

overall_design: Gastrocnemius, tibialis anterior, soleus, and diaphragm muscles from male and female C57Bl/6J mice and male Sprague Dawley rats were analyzed at ages 6, 12, 18, 21, 24 and 27 months, plus an additional 9 month group was used for rats

first: Tea

last: Shavlakadze

first: Shawn

last: Mishra

first: Corissa

last: McEwen

first: Abhilash

last: Gadi

last: Wakai

first: Hunter

last: Salmon

first: Michael

last: Stec

first: Nicole

last: Negron

first: Min

last: Ni

first: Yi

last: Wei

first: Gurinder

last: Atwal

first: Yu

last: Bai

first: David

last: Glass


title: Mislocalization of pathogenic RBM20 variants in dilated cardiomyopathy is caused by loss-of-interaction with Transportin-3

city: Heidelberg

first: Julia

last: Kornienko

state: Baden-Württemberg

address: Meyerhofstraße 1

institute: EMBL

summary: First, we compared gene expression and alternative splicing changes between differentially-localized P633L-RBM20, WT-RBM20, and R634Q-RBM20 in iPSC-CMs. Using ICS, we sorted iPSC-CMs with differentially-localized RBM20 based on correlation with nuclear staining. This was followed by RNA-sequencing of the sorted populations. Second, we analysed gene expression and splicing changes in iPSC-CMs overexpressing of WT-, R634Q-, or NLS-tagged R634Q-RBM20 in splice deficient cells carrying the homozygous frameshift mutation (S635FS). Third, we performed RNA sequencing of our HeLa Tet:Cas9 eGFP-RBM20-WT and -R634Q to compare their gene expression to iPSC-CMs. Lastly,  we performed two genome-wide CRISPR ICS screens in HeLa cells stably expressing eGFP-RBM20-WT and -R634Q, and TetO-Cas9, to identify genes essential for RBM20 nuclear import.

overall_design: Gene expression and PSI analyses from RNA-seq data in iPSC-CMs; gene expression analysis from RNA-seq data in HeLa, gene statistics from ICS screens in eGFP-RBM20 HeLa reporter lines.

first: Marta

last: Rodríguez-Martínez

first: Lars

last: Steinmetz


title: The Effects of Low Temperature on the Global Increase of N6-methyldeoxyadenosine in Arabidopsis thaliana and Rice

city: Fuzhou

first: mao

last: fei

state: Fujian

address: Shangxiadianlu NO.15

department: National Engineering Research Center of JUNCAO

institute: Fujian Agriculture and Forestry University

summary: N6-methyldeoxyadenosine (6mA) is a newly-discovered DNA modification that plays a role in regulating plant adaptation to abiotic stresses. However, the changes and molecular regulatory mechanisms of N6-methyldeoxyadenosine under cold stress in plants remain uncertain. Here, we found the global level of 6mA in both Arabidopsis and rice are raised after cold treatment. Genome-wide profiling of 6mA revealed that 6mA peaks are primarily distributed within gene body regions under both normal and low-temperature conditions. Additionally, genes that were up-methylated were enriched in various biological processes, while down-methylated genes did not exhibit any significant enrichment. Association analysis showed that 6mA was positively correlated with gene expression level and 6mA-containing genes displayed a significantly higher expression level than non-6mA-containing genes. Joint analysis of the 6mA methylome and transcriptome of Arabidopsis and rice revealed that the fluctuations in 6mA levels caused by exposure to cold did not correlate with the changes of transcript levels in response to low temperatures. Moreover, we found that 6mA modified orthologous genes exhibit high expression levels. However, upon cold treatment, only a small amount of differentially 6mA-methylated orthologous genes were shared between Arabidopsis and rice. In sum, this study profiled the changes of 6mA in response to cold temperature and has unlocked the potential of this DNA modification in regulating the expression of stress-related genes.

sample_organism:
Arabidopsis
Oryza sativa

platform_organism:
Arabidopsis
Oryza sativa

overall_design: Comparative gene expression profiling analysis of 6mA-IP-seq ang RNA-seq data for Low Temperature in Arabidopsis thaliana and Rice.

first: Fei

last: Mao

first: Hairong

last: Xie

first: Shuai

last: Wang

first: Yufeng

last: Wu


title: Prostate cancer cell lines modulated with OC2 Protein or 3' UTR

city: Los Angeles

first: Minhyung

last: Kim

state: CA

address: 8700 Beverly Blvd

department: Urology

institute: Cedars-Sinai Medical Center

summary:
The transcription factor ONECUT2 (OC2) is a master transcriptional regulator operating in metastatic castrate-resistant prostate cancer (mCRPC) that suppresses AR activity and promotes neural differentiation and tumor cell survival. OC2 mRNA possesses an unusually long (14,575 nt), evolutionarily conserved 3’-untranslated region (3’-UTR) with many microRNA binding sites, including up to 26 miR-9 sites. This is notable because miR-9 targets many of the same genes regulated by the OC2 protein. Paradoxically, OC2 expression is high in tissues with high miR-9 expression. The length and complex secondary structure of the OC2 mRNA suggests it is a potent master competing endogenous RNA (ceRNA) capable of sequestering miRNAs. Here we describe a novel role for the OC2 3’-UTR in lethal prostate cancer consistent with a function as a ceRNA.
A plausible ceRNA network in OC2-driven tumors was constructed computationally then confirmed in prostate cancer cell lines. Genes regulated by the OC2 3’-UTR exhibited high overlap (up to 45%) with genes driven by overexpression of the OC2 protein in the absence of the 3’-UTR, indicating a cooperative functional relationship between the OC2 protein and its 3’-UTR. These overlapping networks suggest an evolutionarily conserved mechanism to reinforce OC2 transcription by protection of OC2-regulated mRNAs from miRNA suppression. Both the protein and the 3’ UTR showed increased Polycomb Repressive Complex activity. Expression of OC2 3’-UTR mRNA alone (without protein) dramatically increased metastatic potential by in vitro assays. Additionally, OC2 3’-UTR increased expression of Aldo-Keto Reductase and UDP-glucuronyl transferase family genes responsible for altering the androgen synthesis pathway. ONECUT2 represents the first described dual-modality transcript that operates as both a key transcription factor driving castration resistant prostate cancer but also as a master ceRNA that promotes and protects the same transcriptional network

overall_design: All samples performed in replicates, replicates that failed QC were dropped

last: Freeman

first: Kenneth

last: Steadman

first: Dustin

middle: V

last: Srinivas

first: Lila

last: Mouakkad

first: Yiwu

last: Yan

first: Smrruthi

last: Venugopal

first: Hisashi

last: Tanaka

first: Sungyong

last: You


title: METTL14 Regulates Chromatin Bivalent Domains in Mouse Embryonic Stem Cells [ChIP-seq]

first: Hongjie

last: Shen

state: Shanghai

address: No.130, Dong'an Road, Xuhui District

department: Institutes of Biomedical Sciences

summary: METTL14 (methyltransferase-like 14) is an RNA binding protein that partners with METTL3 to mediate N6-methyladenosine (m6A) methylation of mRNA. Recent studies identified a function for METTL3 in heterochromatin and transcription, but the role of METTL14 in these contexts remains unclear. Here we show that METTL14 binds and regulates mouse embryonic stem cell bivalent domains, which are marked with tri-methylation at lysine 27 of histone H3 (H3K27me3) and tri-methylation at lysine 4 of histone H3 (H3K4me3). Knockout of Mettl14 results in decreased H3K27me3 but increased H3K4me3 levels at bivalent regions, resulting in the resolution of the bivalency and in increased transcription. We demonstrate that bivalent domain regulation by METTL14 is independent of METTL3 or m6A modification. Instead, METTL14 enhances H3K27me3 and reduces H3K4me3 by interacting with and probably recruiting the histone 3 lysine 27 (H3K27) methyltransferase complex PRC2 and the histone 3 lysine 4 (H3K4) demethylases KDM5B to chromatin. Our findings identify a METTL3-independent function of METTL14, important for maintaining the bivalent domains in mESCs, thus revealing a new mechanism of bivalent domain regulation in mammals.

overall_design: Examination of METTL3 binding, METTL14 binding, PRC2 binding and histone modifications in Parental, METTL14 KO and rescue mESCs.

first: Mandi

last: Mu

first: Wenqi

last: Xu

first: Yang

last: Shi


title: Malaria-specific Type 1 Regulatory T cells are more abundant in first pregnancies and associated with placental malaria

status: Public on Jun 18 2023

city: Stanford

first: Adam

last: Kirosingh

address: 1265 Welch Rd

department: Microbiology & Immunology

institute: Stanford University

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

overall_design: Refer to individual Series


title: Blood transcriptome following BCG vaccination administered via different routes in rhesus macaques

first: Yiran

last: Liu

address: 291 Campus Drive

summary: To determine the blood transcriptional response to BCG vaccination administered via different routes in rhesus macaques and identify correlates of vaccine-mediated protection against Mycobacterium tuberculosis (Mtb) challenge.

overall_design: Thirty-six macaques received BCG vaccination through different routes: aerosol (AE, n=7), intradermal (ID, n=7), high-dose intradermal (HD-ID, n=8), combined aerosol and intradermal (AE/ID, n=7), and intravenous (IV, n=7). IV-vaccinated macaques received 5x10^7 CFUs of BCG (high-dose). Macaques were challenged with Mtb six to ten months following BCG vaccination and euthanized 11-15 weeks following challenge or at humane endpoint. Bulk RNA sequencing was performed on whole blood samples collected at baseline and two days, two weeks, and twelve weeks following vaccination.

first: Patricia

last: Darrah

first: Joseph

last: Zeppa

first: Megha

last: Kamath

first: Farida

last: Laboune

first: Daniel

last: Douek

first: Pauline

last: Maiello

first: Mario

last: Roederer

first: JoAnne

last: Flynn

first: Robert

last: Seder

first: Purvesh

last: Khatri


title: BCG vaccination in rhesus macaques


title: Dynamic panoramic presentation of skin function after fractional CO2 laser treatment

status: Public on Jun 17 2023

city: Changsha

first: Haoran

last: Guo

address: No.138 Tongzipo Road, Yuelu District, Changsha, China

institute: The Third xiangya Hospital

summary: Fractional CO2 laser, as a typical ablative laser, has been used to assist in the treatment of many skin diseases, such as photoaging, atrophic scar, hypertrophic scar, superficial pigmentation, vitiligo, and so on. However, the dynamic changes in skin function after fractional CO2 laser treatment are still unclear. This study explored the changes in local skin function and possible regulatory mechanisms after fractional CO2 laser treatment for 1, 3, 5 and 7 days through transcriptome high-throughput sequencing. The results showed that fractional CO2 laser tended to transform the “lesions” into “normal skin”, regulate the skin barrier, coordinate the rearrangement of collagen, enhance the local microvascular circulation, activate the immune system to secrete a large number of cytokines, and act as an auxiliary tool to assist drug transport. According to the basic principle of destruction before reconstruction, fractional CO2 laser plays a key role of balancer in skin reconstruction. In conclusion, the gene expression profiles of fractional CO2 laser-treated skin undergo dynamic changes over time. Skin barrier, collagen arrangement, drug metabolism, immune system and skin defense system all present obvious characteristics of timing change after fractional CO2 laser treatment.

overall_design: A total of 12 guinea pigs were used in the experiment, and were divided into 4 time points for testing and sampling (3 guinea pigs treated each time). After adapting to the environment for four days, the back skin of guinea pigs was depilated one day before a single fractional CO2 laser treatment.The right side was irradiated with a single fractional CO2 laser (Kinglaser, KL type, JiLin, China). The energy of the laser is 140 mJ, the size of the spot is 2 x 2 cm2, and the spacing between the beams is 0.6 mm, while the left of back skin was not irradiated. On day 1, 3, 5 and 7 after treatment, Skin tissue was collected separately.

first: Xiangyu

last: Zhang

first: Hui

last: Li

first: Chuhan

last: Fu

first: Ling

last: Jiang

first: Yibo

last: Hu

first: Jinhua

last: Huang

first: Jing

last: Chen

first: Qinghai

last: Zeng


title: Identification of RBM39-dependent alternative splicing events in HeLa cells

city: London

first: Marc-David

last: Ruepp

address: 5 Cutcombe Road

department: Dementia Research Institute

institute: King's College

summary: We report a comprehensive analysis of alterations in gene expression and alternative splicing upon RBM39 depletion and rescue in HeLa cells.

overall_design: siRNA-mediated Ctrl or RBM39 knockdown in HeLa cells and rescue using RNAi-resistant FLAG-RBM39. Three biological replicates each.

last: Jutzi

first: Sebastien

last: Campagne

first: Martino

last: Colombo


title: Differential gene expression and splicing in apc mutant zebrafish

city: Philadelphia

first: Peter

last: Klein

state: PA

address: 3400 Civic Center Blvd

department: Medicine

institute: University of Pennsylvania School of Medicine

summary: APC is a classical tumor suppressor in humans, and truncating mutations are early somatic events in most cases of sporadic colon cancer. APC directly enhances the activity of glycogen synthase kinase 3 (GSK-3) and therefore loss of full length APC reduces GSK-3 activity, leading to stabilization of b-catenin protein and activation of downstream Wnt/b-catenin signaling. GSK-3 also phosphorylates multiple core mRNA splicing factors and loss of Gsk3a/b in mouse ES cells and human lymphocytes alters mRNA splicing at a genome wide level. We therefore predict that loss of APC should similarly alter splicing by reducing GSK-3 activity. Here we use RNA-seq to assess differential gene expression and altered splicing in apc-mcr mutant zebrafish embryos at 48hpf. We find robust activation of known Wnt/b-catenin target genes, as expected. Surprisingly, we also find markedly increased expression of multiple genes related to inflammation and cytokine signaling. We also identify 340 mRNA splicing variations in apc mutant zebrafish. Many of these local splice variants (LSVs) occur in mRNAs the regulate cell adhesion, migration, and morphogenesis.

overall_design: WT/het and apcmcr/mcr embryos (3 biological replicates; 20 embryos/replicate) were treated with vehicle (0.1% DMSO) or 100nM Rapamycin (beginning at 24hpf) and harvested at 48hpf with Triazol followed by DNaseI treatment and re-purification on RNeasy (RIN > 8). Total RNA was submitted to Genewiz for polyA-selection and generation of stranded Illumina RNA-Seq library. Sequencing was at a depth of ≥100 million reads per individual replicate. Alternative splicing and differential expression analyses were based on RNA-Seq reads that were mapped to the zebrafish reference genome (GRCz10) using STAR. Differential splicing analysis was performed comparing WT/het and apcmcr/mcr samples using MAJIQ (Modeling Alternative Junction Inclusion Quantification) deltapsi with intron retention quantification enabled. Results were filtered for high confidence changing local splice variants (LSVs) with a change in percent spliced in (dPSI) ≥20% (in which junctions had a ≥90% probability of expected dPSI).

first: Xiaolei

last: Liu

first: Mathieu

last: Quesnel-Vallières

first: William

last: Jones

first: John

last: Tobias


title: Young blood-derived platelet factors abate inflammation and rescue recognition in aging.

first: Julien

last: Couthouis

address: 279 Campus Dr

department: Genetics

summary: We show that platelet factors transfer rejuvenating effects of young plasma to the aging brain. Proteomic analysis of plasma from young and aged mice identified age-related changes in platelets. Systemic exposure of aged animals to the platelet fraction of young plasma decreased hippocampal neuroinflammation at a transcriptional and cellular level and ameliorated cognitive impairments. We identified the platelet-derived chemokine CXCL4/Platelet Factor-4 (PF4) as a pro-youthful circulating factor. Systemic PF4 administration decreased age-related neuroinflammation, restored the aging peripheral immune system to a more youthful state, and improved hippocampal-dependent learning and memory in aged mice.

overall_design: Examination of hippocampi from aged mice treated with young plasma, young plasma-derived platelets or saline control (samples 8-24). Examination of hippocampal microglia isolated from aged mice treated with platelet factor 4 (PF4) or saline vehicle control (samples 1-7).

first: Adam

middle: B

last: Schroer

first: Saul

last: Villeda


title: Dissecting the mechanisms underlying the Cytokine Release Syndrome (CRS) mediated by T Cell Bispecific Antibodies

city: Schlieren

first: Marina

last: Bacac

address: Wagistrasse 10

department: Oncology Discovery

country: Switzerland

institute: Roche Glycart AG


title: Discovery and targeting of a noncanonical mechanism of sarcoma resistance to ADI-PEG20 mediated by the microenvironment

city: St. Louis

first: Brian

last: Van Tine

state: Missouri

address: 4515 McKinley Ave

institute: Washington University in St. Louis

summary: To investigate the effects of ADI-PEG20 and chloroquine treatment alone and in combination on the growth of Ass1 KO murine sarcomas, the BVMA01R murine sarcoma cell line was grafted into syngeneic C57BL/6J mice, and tumors were treated as indicated. We then performed gene expression profiling analysis using data obtained from RNA-seq of 3 tumors from each of the 4 treatment groups.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for BVMA01R tumors with and without both ADI-PEG20 and chloroquine treatment. 3 replicates of each.

first: Leonard

last: Rogers


title: Blood transcriptome following intravenous BCG vaccination in rhesus macaques

first: Yiran

summary: To determine the blood transcriptional response to intravenous (IV) BCG vaccination in rhesus macaques and identify correlates of vaccine-mediated protection against Mycobacterium tuberculosis (Mtb) challenge.

overall_design: Thirty-four rhesus macaques of Indian origin were vaccinated with half-log increasing doses of IV BCG (between 3.9x10e4 and 2.5x10e7 CFU) and challenged with Mtb twenty-four weeks later. Bulk RNA sequencing was performed on whole blood samples collected at baseline (four weeks pre-vaccination) and at two days, two weeks, four weeks, and twelve weeks following IV BCG vaccination. All timepoints were prior to Mtb challenge.

first: Patricia

last: Darrah

first: Joseph

last: Zeppa

first: Megha

last: Kamath

first: Farida

last: Laboune

first: Daniel

last: Douek

first: Pauline

last: Maiello

first: Mario

last: Roederer

first: JoAnne

last: Flynn

first: Robert

last: Seder

first: Purvesh

last: Khatri


title: Age-related gene expression signature in limb skeletal muscles and the diaphragm in mice and rats [rat]

first: Kun

last: Xiong

first: Tea

last: Shavlakadze

first: Shawn

last: Mishra

first: Corissa

last: McEwen

first: Abhilash

last: Gadi

first: Matthew

last: Wakai

first: Hunter

last: Salmon

first: Michael

last: Stec

first: Nicole

last: Negron

first: Min

last: Ni

first: Yi

last: Wei

first: Gurinder

middle: S

last: Atwal

first: Yu

last: Bai

first: David

last: Glass


first: Marina

last: Bacac

summary: We performed bulk RNAseq of HUVECs exposed to cytokine-rich supernatant from T cell dependent cytotoxicity assay with CEA-TCB or DP47-TCB (untargeted-TCB; negative control) to study their activation and contribution to cytokine release.

overall_design: Supernatants from T cell dependent cytotoxicity assay with DP47-TCB (untargeted-TCB) or CEA-TCB were collected and transferred to HUVECs for 6 hrs. At assay endpoints (6hrs), HUVECs were collected, washed and lysed for bulk RNAseq.

first: Gabrielle

last: Leclercq-Cohen

first: Sabrina

last: Danilin

first: Roberta

last: Bianchi

first: Marlene

last: Biehl

first: Llucia

last: Alberti-Servera

first: Sina

last: Nassiri


title: Chromatin opening ability of pioneer factor Pax7 depends on unique isoform and C-terminal domain (ATAC-Seq)

city: Montreal

first: Arthur

middle: Jules

last: Gouhier

state: Quebec

address: 110 Avenue des Pins

country: Canada

institute: IRCM

summary: Pioneer factors are transcription factors (TFs) that have the unique ability to recognise their target DNA sequences within closed chromatin. Whereas their interactions with cognate DNA is similar to other TFs, their ability to interact with chromatin remains poorly understood. Having previously defined the modalities of DNA interactions for the pioneer factor Pax7, we have now used natural isoforms of this pioneer as well as deletion and replacement mutants to investigate the Pax7 structural requirements for chromatin interaction and opening. We show that the GL+ natural isoform of Pax7 that has two extra amino acids within the DNA binding paired domain is unable to activate the melanotrope transcriptome and to fully activate a large subset of melanotrope-specific enhancers targeted for Pax7 pioneer action. This enhancer subset remains in the primed state rather than being fully activated, despite the GL+ isoform having similar intrinsic transcriptional activity as the GL- isoform. C-terminal deletions of Pax7 lead to the same loss of pioneer ability, with similar reduced recruitments of the cooperating TF Tpit and of the co-regulators Ash2 and BRG1. This suggest complex interrelations between the DNA binding and C-terminal domains of Pax7 that are crucial for its chromatin opening pioneer ability.

overall_design: ATAC-seq in AtT-20 cell line

first: Virginie

last: Bascunana

first: Audrey

last: Pelletier

first: Amandine

last: Bemmo

first: Aurelio

last: Balsalobre

first: Jacques

last: Drouin


title: Chromatin opening ability of pioneer factor Pax7 depends on unique isoform and C-terminal domain (ChIP-Seq)

overall_design: ChIP-seq in AtT-20 cell line


title: Protein Arginine Methyltransferase 1 is therapeutic vulnerability in Multiple Myeloma

status: Public on Jun 16 2023

city: Cluj-Napoca

first: Oana

last: Tudoran

address: Str. Republicii 34-36

department: Department of Genetics

country: Romania

institute: The Oncology Institute “Prof. Dr. Ion Chiricuță” in Cluj-Napoca

summary: Multiple myeloma (MM) is a devastating plasma cell malignancy characterized by the expansion of aberrant monoclonal plasma cells in the bone marrow, leading to severe clinical manifestations and poor prognosis, particularly in relapsed/refractory cases. Identifying novel therapeutic targets is crucial to improve treatment outcomes in these patients. In this study, we investigated the role of protein arginine methyltransferase 1 (PRMT1) in MM pathogenesis and explored its potential as a therapeutic target. We observed that PRMT1, responsible for majority of asymmetric di-methylation in cells, exhibited the highest expression among PRMT family members in MM cell lines and primary MM cells. Importantly, PRMT1 expression was significantly elevated in relapsed/refractory patients compared to newly diagnosed patients. High expression of PRMT1 expression was strongly associated with poor prognosis. We found that genetic or enzymatic inhibition of PRMT1 impaired MM cell growth, induced cell cycle arrest, and triggered cell death. Treatment with MS023, a potent PRMT type I inhibitor, demonstrated a robust inhibitory effect on viability of primary cells isolated from both newly diagnosed and proteasome inhibitor-relapsed/refractory patients in a dose-dependent manner. In vivo studies using a xenograft model revealed that targeting PRMT1 by either CRISPR/Cas9-mediated knockout or MS023 treatment significantly attenuated MM tumor growth and prolonged the survival of tumor-bearing mice. Histological analysis further confirmed increased apoptotic cell death in MS023-treated tumors. Collectively, our findings establish PRMT1 as an indispensable and novel therapeutic vulnerability in MM. The elevated expression of PRMT1 in relapsed/refractory patients underscores its potential as a target for overcoming treatment resistance. Moreover, our results highlight the efficacy of MS023 as a promising therapeutic agent against MM, offering new avenues for therapeutic approaches in relapsed/refractory MM.

overall_design: Cells were treated with DMSO or MS023 (10uM) for 3 days; isgCtrl and iPRMT1_1 JJN3 cells were induced with Dox for 3 days, then purify RNA for seq

first: Ngoc

middle: T

last: Tran

first: Hong

last: Nguyen

first: Anh

middle: Q

last: Le

first: Brian

last: Walker

first: Enze

last: Liu


title: The Expression profile of splenic Ly6C low/Ly6C high macrophages in SLC29A3 deficient mice

city: Tokyo

first: Takuma

last: Shibata

state: Tokyo-to

address: 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, 4th Building, 2nd Floor

department: The Institute of Medical Science

country: Japan

institute: The University of TOKYO

summary: Loss-of-function mutations in the lysosomal nucleoside transporter SLC29A3 lead to the accumulation of nucleosides in lysosomes and result in histiocytosis, characterized by the excessive accumulation of phagocytes in multiple organs. However, the underlying mechanism by which lysosomal nucleoside storage drives histiocytosis remains poorly understood. Herein, we provide evidence that histiocytosis in Slc29a3–/– mice is dependent on Toll-like receptor 7 (TLR7), which senses a combination of guanosines and oligoribonucleotides. TLR7 increased phagocyte populations by driving the proliferation of immature Ly6C high splenic macrophages and their subsequent maturation into Ly6C low phagocytes in Slc29a3–/– mice. Interestingly, TLR7 activation in nucleoside-laden splenic macrophages failed to induce inflammatory responses. Our data demonstrate that TLR7 responses to lysosomal nucleoside stress drive unique immune responses distinct from inflammation in SLC29A3-related disorders.

overall_design: To examine the characteristics of splenic macrophages that accumulate in Slc29a3–/– mice, we isolated Ly6C low or Ly6C high splenic macrophages from wild-type/Slc29a3–/–/Slc29a3–/–TLR7–/– mice using FACS sorting. Subsequently, we performed gene expression profiling analysis by employing RNA-seq data obtained from 6 distinct macrophage samples.

first: Kensuke

last: Miyake

first: Kiyoshi

last: Yamaguchi


title: Plucked scalp hair follicle samples are useful RNA sources for mRNA analysis of genodermatosis-associated genes

city: Nagoya

first: So

last: TAKEUCHI

address: 65 Tsurumai-cho, Showa-ku

department: Dermatology

institute: Nagoya University Graduate School of Medicine

summary: Using RNA samples extracted from plucked hair follicles and skin samples, we conducted comprehensive RNA sequencing and evaluated expression levels of 347 genes causative of genodermatoses.

overall_design: We extracted total RNAs from six skin specimens (non-lesional skin samples excised at the time of skin tumor excision) and five pulled scalp hairs of healthy volunteers.

last: Takeuchi

first: Takuya

last: Takeichi

first: Yoshinao

last: Muro

first: Teppei

last: Shimamura

first: Masashi

last: Akiyama


title: Single-cell RNA sequencing analysis of humanized liver

city: New Haven

first: Rihao

last: Qu

state: CT

address: 300 George Street

institute: Yale University

summary: Single cell RNA sequencing of liver cells enriched for Non-Parenchymal cells (NPCs) to see the percentage of humanizaton, the gene signature and the heterogeneity of most types of human NPCs in a humanized liver.

overall_design: Single cell RNA sequencing of the liver cells enriched in Non-Parenchymal cells (NPCs). Liver cells were isolated from median and left lobe of the mouse after enzymatic treatment with Collagenase II and DNAase. The vast majority of hepatocytes were removed by centrifugation in low spped  (80g).  Single cell RNA sequencing was performed with .......

first: Richard

middle: A

last: Flavell

first: Eleanna

last: Kaffe


first: Marina

last: Bacac

summary: We performed bulk RNAsequencing of neutrophils isolated from whole blood treated with CD20-TCB to study the early kinetics of cytokine release in neutrophils.

overall_design: Whole blood from 4 donors was treated with 0.2 μg/mL CD20-TCB or DP47-TCB (untargeted-TCB). At assay endpoints (4 and 20 hrs), blood was collected for neutrophil isolation using the MACSxpress whole blood neutrophil isolation kit (Miltenyi).

first: Gabrielle

last: Leclercq-Cohen

first: Sabrina

last: Danilin

first: Llucia

last: Alberti-Servera

first: Stephan

last: Schmeing

first: Hélène

last: Haegel

first: Sina

last: Nassiri


title: DNA methylation dynamic in male rat germ cells during gametogenesis

city: Laval

first: Geraldine

last: Delbes

address: 531 Boul des Prairies

department: Biology

institute: INRS Centre Armand-Frappier Santé Biotechnologie

summary: To study the dynamic of DNA methylation during male gametogenesis 9 stages of germ cells were purified, then DNA samples (n=4/stage) were analyzed by Rat Methyl seq capture

overall_design: After running the classic pipeline of DNA methylation data processing, DNA methylation was extracted for each samples and each mapped locus, then this data were segmented into segments with at least 50bp and finally we performed DMR search and explored the segments.

first: Rhizlane

last: El omri-Charai

first: Isabelle

last: Gilbert

first: Rebecka

last: Desmarais

first: Mariana

last: Gabriela Ghinet

first: Julien

last: Prunier

first: Claude

last: Robert

first: Guylain

last: Boissonneault

first: Géraldin


title: Malaria-specific Type 1 Regulatory T cells are more abundant in first pregnancies and associated with placental malaria [PBMCs RNA-seq]

first: Adam

last: Kirosingh

summary: To investigate Tr1 cells and TNFa single expressing cells we stimulated PBMCs from primigravid women with VAR2CSA expressing P. falciparum and sorted CD4+ T cells expressing both IL10 and IFNg or only TNF

overall_design: Cytokine capture assay CD4+ T cells expressing either both IL10 and IFNg or only TNFa.

first: Prasanna

last: Jagannathan

first: Sanchita

last: Bhattacharya

first: Alea

last: Delmastro


title: Circular RNA cPLOD2 regulates pericyte function by targeting KLF4

city: Würzburg

first: Kathi

last: Zarnack

address: Biocenter, Am Hubland

department: Theodor Boveri Institute

institute: University Würzburg

summary:
Circular RNAs (circRNAs) are generated by back-splicing and control cellular signaling and phenotypes.
Pericytes stabilize the capillary structure and play an important role in the formation and maintenance of new blood vessels.
Here, we characterized hypoxia-regulated circRNAs in human pericytes and showed that circPLOD2 is induced by hypoxia and regulates pericyte functions.
Silencing of circPLOD2 increased pericyte proliferation, endothelial-pericyte interactions and tube formation.
Transcriptional profiling of circPLOD2-depleted cells and epigenomic analyses revealed widespread changes in gene expression and identified the regulation of the transcription factor KLF4 as a key effector of these changes. Importantly, overexpression of KLF4 was sufficient to reverse the effects on pericyte proliferation and endothelial-pericyte interactions observed after circPLOD2 depletion.
Together, these data reveal a novel function of circPLOD2 in the control of pericyte proliferation and capillary formation and show that circPLOD2-mediated regulation of KLF4 significantly contributes to the transcriptional response to hypoxia.

overall_design: Human brain vascular pericytes transfected with control siRNA or siRNA targeting cPLOD2 (3 replicates each).

first: Simone-Franziska

last: Glaser

first: Andre

last: Brezski

first: Marius

last: Klangwart

first: Nina

last: Baumgarten

first: Andreas

last: Heumüller

first: Ranjan

middle: K

last: Maji

first: Matthias

last: Leisegang

first: Stefan

last: Guenther

first: Christoph

last: Zehendner

first: David

last: John

first: Marcel

last: Schulz

first: Stefanie

last: Dimmeler


title: Humanized liver  Jun 16, 2023   approved  None

first: Rihao

last: Qu

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

overall_design: Refer to individual Series


title: Increased protein solubility contributes to heat priming of the plant pathogenic fungus Botrytis cinerea

city: Tel Aviv

first: Metsada

last: Pasmanik-Chor

address: Ramat Aviv

country: Israel

institute: Tel Aviv University

summary: Botrytis cinerea causes grey mold disease in leading crop plants. The disease develops only at cool temperatures, but the fungus remains viable in warm climates and can survive periods of extreme heat. We discovered a strong heat priming effect in which the exposure of B. cinerea to moderately high temperatures greatly improves its ability to cope with subsequent, potentially lethal temperature conditions. We showed that priming promotes protein solubility during heat stress and discovered a group of priming-induced serine-type peptidases. Several lines of evidence, including transcriptomics, proteomics, pharmacology and mutagenesis data, link these peptidases to the B. cinerea priming response, highlighting their important roles in regulating priming-mediated heat adaptation. By imposing a series of sub-lethal temperature pulses that subverted the priming effect, we managed to eliminate the fungus and prevent disease development, demonstrating the potential for developing temperature-based plant protection methods by targeting the fungal heat priming response.

overall_design: Here we show that MHT had a strong priming effect on B. cinerea, namely it greatly improved the ability of the fungus to cope with a subsequent potentially lethal heat stress. we were able to differentiate the priming from a general heat stress effect and showed that priming improves protein solubility during severe heat stress.

first: Mingzhe

last: Zhang

first: Naomi

last: Trushina

first: Tabea

last: Lang

middle: P

last: Chor

first: Amir

last: Sharon


title: A method for polyclonal antigen-specific T cell-targeted genome editing (TarGET) for adoptive cell transfer applications

city: Basel

first: Rocio

last: Castellanos Rueda

state: --None--

address: Mattenstrasse 26

department: D-BSSE

institute: ETH

summary: Adoptive cell therapy of donor-derived, antigen-specific T cells expressing native T cell receptors (TCRs) is a powerful strategy to fight viral infections in immunocompromised patients. Determining the fate of T cells following patient infusion hinges on the ability to track them in vivo. While this is possible by genetic labeling of parent cells, the applicability of this approach has been limited by the non-specificity of the edited T cells. Here, we devised a method for CRISPR-targeted genome integration of a barcoded gene into Epstein-Barr virus-antigen-stimulated T cells and demonstrated its use for exclusively identifying expanded virus-specific cell lineages. Our method facilitated the enrichment of antigen-specific T cells, which then mediated improved cytotoxicity against EBV-transformed target cells. Single-cell and deep sequencing for lineage tracing revealed the expansion profile of specific T cell clones and their corresponding gene expression signature. This approach has the potential to enhance the traceability and the monitoring capabilities during immunotherapeutic T cell regimens.

overall_design: PBMCs from two EBV reactive healthy donors were pulsed with Peptivator EBV Consensus peptide pool in presence of IL4 and IL7. After three days of culture, T cells were engineered using CRISPR/Cas9 genome editing to integrate a GFP barcoded reporter gene with a library diversity of 3x10e4 into the CCR5 locus. After 7 additional days of expansion, single cell RNA sequencing data of GFP+ and GFP- sorted samples was generated.

first: Darya

last: Palianina

first: Raphaël

last: Di Roberto

first: Rocío

last: Castellanos-Rueda

first: Sai

last: Reddy

last: Khanna


title: Malaria-specific Type 1 Regulatory T cells are more abundant in first pregnancies and associated with placental malaria [Whole Blood RNA-seq]

first: Adam

last: Kirosingh

address: 1265 Welch Rd

summary: To investigate gravidity dependent immunity to malaria we sequenced whole blood RNA from women with and without parasitemia and both pregnant and non-pregnant controls.

overall_design: Whole blood RNAsequencing data among pregnant and non-pregnant women in Eastern Uganda.

first: Prasanna

last: Jagannathan

first: Sanchita

last: Bhattacharya

first: Alea

last: Delmastro


title: Bulk RNA sequencing analysis of hepatocytes isolated from humanized liver

last: Qu

summary: The goal of this experiment was to identify differentially expressed human genes in the hepatocyte fraction between two groups. Group A includes mice having only human hepatocytes and group B includes mice having both human hepatocytes and human Non-Parenchymal Cells (NPCs).

overall_design: Two biological replicates per group.Hepatocytes were isolated after digestion of freshly isolated liver tissue (median and left lobe) with Collagenase type II and DNAase. After two-step low speed centrifugation the majority of NPCs are removed. Part of remaining hepatocyte fraction was snap frozen in trizol for RNA isolation.

first: Richard

last: Flavell

first: Eleanna

last: Kaffe


title: Chromatin opening ability of pioneer factor Pax7 depends on unique isoform and C-terminal domain

first: Arthur

last: Gouhier


title: RBFOX2 recognizes N6-methyladenosine to suppress transcription and block myeloid differentiation [RNA-CLIP]

city: Shanghai

first: Xiaoyang

last: Dou

address: 320 Yue Yang Road

institute: CAS Center for Excellence in Molecular Cell Science, CAS

summary: N6-methyladenosine (m6A)methylationcan be deposited on chromatin-associated RNAs (caRNAs) by the RNA methyltransferase complex (MTC) to regulate chromatin state and transcription. How the MTC is recruited to distinct genomic loci to accomplish selective transcriptional regulation remains elusive. Here we identify RBFOX2, a well-established RNA-binding protein (RBP), as a chromatin factor that recognizes m6A on caRNAs and recruits RBM15, an MTC component, to install methylation on promoter-associated RNAs (paRNAs). RBM15 also physically interacts with YTHDC1 to facilitate the recruitment of Polycomb repressive complex 2 (PRC2) to RBFOX2-bound loci for chromatin silencing and transcription suppression. Furthermore, we found that this m6A/RBM15/YTHDC1/PRC2 axis is essential to myeloid leukemia. Downregulation of RBFOX2 notably inhibits AML cell survival/proliferation and promotes myeloid differentiation of AML cells. RBFOX2 is also required for self-renewal of leukemia stem/initiation cells (LSCs/ LICs) and AML maintenance. Together, our study presents a clear pathway of m6A MTC recruitment and m6A deposition on caRNAs to achieve locus-specific chromatin regulation with potential therapeutic implications.

overall_design: CLIP-seq in K562 cells

first: Yu

last: Xiao

first: Chuan

last: He


title: Lysosomes mediate the mitochondrial UPR via mTORC1-dependent ATF4 phosphorylation

city: Lausanne

first: Terytty Yang

last: Li

address: EPFL SV IBI-SV LISP AI 1145

institute: EPFL

summary: Lysosomes are central platforms for not only the degradation of macromolecules but also the integration of multiple signaling pathways. However, whether and how lysosomes mediate the mitochondrial stress response (MSR) remain largely unknown. Here, we demonstrate that lysosomal acidification via the vacuolar H+-ATPase (v-ATPase) is essential for the transcriptional activation of the mitochondrial unfolded protein response (UPRmt). Mitochondrial stress stimulates v-ATPase-mediated lysosomal activation of the mechanistic target of rapamycin complex 1 (mTORC1), which then directly phosphorylates the MSR transcription factor, activating transcription factor 4 (ATF4). Disruption of mTORC1-dependent ATF4 phosphorylation blocks the UPRmt, but not other similar stress responses, such as the UPRER. Finally, ATF4 phosphorylation downstream of the v-ATPase/mTORC1 signaling is indispensable for sustaining mitochondrial redox homeostasis and protecting cells from reactive oxygen species (ROS)-associated cell death upon mitochondrial stress. Thus, v-ATPase/mTORC1-mediated ATF4 phosphorylation via lysosomes links mitochondrial stress to UPRmt activation and mitochondrial function resilience.

overall_design: Wild-type MEFs treated with DMSO control or Concanamycin A (ConA, 200 nM), in the absense or presence of mitochondrial stress inducers: Doxycycline (Dox, 30 μg/ml), antimycin A (AntiA, 2 μM) and FCCP (2 μM), for 24 h.

first: Terytty

first: Qi

last: Wang

first: Arwen

middle: W

last: Gao

first: Xiaoxu

last: Sun

first: Adrienne

last: Mottis

first: Minho

last: Shong

first: Johan

last: Auwerx


title: Engineered MED12 mutations drive uterine fibroid-like transcriptional and metabolic programs by altering the 3D genome compartmentalization [MED12_G44N_spheroid_RNA_seq]

city: CHICAGO

first: MAZHAR

last: ADLI

state: IL

address: 303 E SUPERIOR STREET

department: OBGYN

institute: NORTHWESTERN UNIVERSITY

summary:
We employed CRISPR knock-in with a sensitive PCR-based screening strategy to precisely engineer cells with mutant MED12 Gly44.
Critically, the engineered myometrial SMC cells recapitulate several UF-like cellular, transcriptional and metabolic alterations, including enhanced proliferation rates in 3D spheres and altered Tryptophan/kynurenine. metabolism

overall_design: We  performed gene expression profiling analysis using data obtained from RNA-seq of MED12-WT spheroid cells and MED12-G44 mutant spheorid cells

first: Kadir

last: Buyukcelebi

first: Xintong

last: Chen

first: Fatih

last: Abdula

first: Alexander

last: Duval

first: Harun

last: Ozturk

first: Fidan

last: Seker-Polat

first: Qiushi

last: Jin

first: Ping

last: Yin

first: Yue

last: Feng

first: Jian

middle: J

last: Wei

first: Serdar

middle: E

last: Bulun

first: Feng

last: Yue

first: Mazhar

last: Adli


title: A cellular and molecular spatial atlas of dystrophic muscle

city: Tarrytown

first: Michael

last: Stec

address: 777 Old Saw Mill River Rd

institute: Regeneron Pharmaceuticals

summary: Asynchronous skeletal muscle degeneration/regeneration is a hallmark feature of Duchenne muscular dystrophy (DMD); however, traditional -omics technologies that lack spatial context make it difficult to study the biological mechanisms of how asynchronous regeneration contributes to disease progression. Here, using the severely dystrophic D2-mdx mouse model, we generated a high-resolution cellular and molecular spatial atlas of dystrophic muscle by integrating spatial transcriptomics and single-cell RNAseq datasets.

overall_design: Gene expression profiling analysis of spatial transcriptome data taken from wildtype (DBA2/J) and dystrophic (D2-mdx) mouse gastrocnemius/plantaris muscle

first: Qi

last: Su

first: Christina

last: Adler

first: Lance

last: Zhang

first: Min

last: Ni

first: Yi

first: Gurinder

last: Atwal

first: Gabor

last: Halasz


title: Engineered MED12 mutations drive uterine fibroid-like transcriptional and metabolic programs by altering the 3D genome compartmentalization [CUT&Tag]

first: MAZHAR

last: ADLI

overall_design: CUT&Tag sequencing for histone variants H3K27Ac in MED12-WT and MED12-G44 mutant hTERT uterine smooth muscle cell

first: Kadir

last: Buyukcelebi

first: Xintong

last: Chen

first: Fatih

last: Abdula

first: Alexander

last: Duval

first: Harun


title: Engineered MED12 mutations drive uterine fibroid-like transcriptional and metabolic programs by altering the 3D genome compartmentalization [MED12_G44N_2D_RNA_seq]

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of MED12-WT,MED12-G44 mutant and MED12-KO hTERT cells.

last: Ozturk

first: Fidan

last: Seker-Polat

first: Qiushi

last: Jin

first: Ping

last: Yin

first: Yue

last: Feng

first: Jian

first: Serdar


title: Uric acid-inducible genes in bacteria from the human gut microbiome

city: Stanford

first: Dylan

last: Dodd

address: 269 Campus Drive

department: Pathology

institute: Stanford University

summary: Approximately 15% of US adults have circulating levels of uric acid above its solubility limit, which is causally linked to the inflammatory disease gout. In most mammals, uric acid elimination is facilitated by the enzyme uricase. However, human uricase is a pseudogene, having been inactivated early in hominid evolution. Though it has long been known that a substantial amount of uric acid is eliminated in the gut, the role of the gut microbiota in hyperuricemia has not been studied. Here we identify a gene cluster, widely distributed in the gut microbiome, that encodes a pathway for uric acid degradation. Stable isotope tracing demonstrates that gut bacteria metabolize uric acid to xanthine or short chain fatty acids such as acetate, lactate and butyrate. Ablation of the microbiota in uricase-deficient mice causes profound hyperuricemia, and anaerobe-targeted antibiotics increase the risk of gout in humans. These data reveal a role for the gut microbiota in uric acid excretion and highlight the potential for microbiome-targeted therapeutics in hyperuricemia.

sample_organism:
Collinsella aerofaciens ATCC 25986
Clostridium sporogenes ATCC 15579
[Clostridium] saccharolyticum WM1

overall_design:
To investigate which genes are induced by uric acid for anaerobically grown gut bacteria in pure culture.
Clostridium sporogenes ATCC 14479, Collinsella aerofaciens ATCC 25986, and Lacrimispora saccharolyticum WM1 treated with uric acid or untreated.
Clostridium sporogenes ATCC 14479, Collinsella aerofaciens ATCC 25986, and Lacrimispora saccharolyticum WM1 were streaked from frozen stocks onto blood agar plates. Three individual colonies were selected for each bacterium and were inoculated into separate overnight cultures in Mega medium. The following day, each culture was precultured in Mega medium, and after three hours diluted to an OD of 0.1 into two experimental cultures, one containing standard Mega medium and one with Mega medium containing 5 mM uric acid. Bacteria were allowed to grow until reaching an OD that was commensurate with approximately 50% uric acid degradation as determined by previous experiments. Cell cultures were then combined with two volumes of RNAprotect (Qiagen) in an anaerobic chamber, mixed thoroughly and then allowed to sit for five minutes. Cells were then centrifuged (5,000 x g, 4 °C, 10 min) and the supernatant was decanted. Cells were then subjected to lysozyme digestion, Proteinase K digestion and mechanical disruption with a mixer mill (RETSCH MM400) at 4 °C, 25/s, for 30 min. RNA was then purified using RNeasy kit (Qiagen), followed by DNase digestion and second RNA purification step using the RNeasy kit (Qiagen). RNA integrity was determined using a bioanalyzer (Agilent) and RNA-seq was performed by the Roy J. Carver Biotechnology Center at the University of Illinois.

first: J

last: Jarman

first: Yuanyuan

last: Liu


title: RBFOX2 recognizes N6-methyladenosine to suppress transcription and block myeloid differentiation [MeRIP-seq]

first: Xiaoyang

last: Dou

summary: N6-methyladenosine (m6A) methylation can be deposited on chromatin-associated RNAs (caRNAs) by the RNA methyltransferase complex (MTC) to regulate chromatin state and transcription. How the MTC is recruited to distinct genomic loci to accomplish selective transcriptional regulation remains elusive. Here we identify RBFOX2, a well-established RNA-binding protein (RBP), as a chromatin factor that recognizes m6A on caRNAs and recruits RBM15, an MTC component, to install methylation on promoter-associated RNAs (paRNAs). RBM15 also physically interacts with YTHDC1 to facilitate the recruitment of Polycomb repressive complex 2 (PRC2) to RBFOX2-bound loci for chromatin silencing and transcription suppression. Furthermore, we found that this m6A/RBM15/YTHDC1/PRC2 axis is essential to myeloid leukemia. Downregulation of RBFOX2 notably inhibits AML cell survival/proliferation and promotes myeloid differentiation of AML cells. RBFOX2 is also required for self-renewal of leukemia stem/initiation cells (LSCs/ LICs) and AML maintenance. Together, our study presents a clear pathway of m6A MTC recruitment and m6A deposition on caRNAs to achieve locus-specific chromatin regulation with potential therapeutic implications.

overall_design: m6A MeRIP-seq in K562 cells

first: Yu

last: Xiao

first: Chuan

last: He


title: RBFOX2 recognizes N6-methyladenosine to suppress transcription and block myeloid differentiation [SAC-seq]

overall_design: m6A-selective allyl chemical labeling and sequencing (m6A-SAC-seq) in K562 cells


title: Insights into the Synergistic Antibacterial Activity of Silver Nitrate with Potassium Tellurite Against Pseudomonas aeruginosa

status: Public on Jun 15 2023

city: Calgary

first: Raymond

last: Turner

address: 447-Biological Sciences Building, 2500 University Dr. NW

institute: University of Calgary

summary:
To investigate the individual and synergistic antibacterial mechanisms of silver nitrate and potassium tellurite, Pseudomonas aeruginosa cultures were exposed to a shock treatment of these metal salts (individually and in combination) at inhibitory concentrations.
Differential gene expression was identified by contrasting each metal salt challenge against a PBS-treated control.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for silver nitrate and potassium tellurite (individual and synergistic) antibacterial challenges in Pseudomonas aeruginosa.

first: Ali

last: Pormohammad

first: Andrea

last: Firrincieli

first: Daniel

last: Salazar-Alemán

first: Mehdi

last: Mohammadi

first: Dave

last: Hansen

first: Martina

last: Cappelletti

first: Davide

last: Zannoni

first: Mohammad

last: Zarei


title: ChIP-seq for histone H1.2 in iWAT of C57BL/6 mice under normal conditions or upon cold exposure

city: Wuhan

first: yangmian

last: yuan

state: --- Select a state ---

address: wuhan

institute: Wuhan University

summary: Our study represents the detailed analysis of whole-genome DNA-binding sites of linker histone variant H1.2 in iWAT  of male C57BL/6 mice under normal conditions or upon cold exposures, with biologic replicates, generated by ChIP-seq technology

overall_design: DNA samples for histone H1.2 ChIP were  extracted from inguinal adipose tissue of 10-week-old male mice.  For normal conditions, mice were housed at 22℃; for cold conditions, mice were housed at 6℃ for 3 days. Two biological replicates of immunoprecipitated DNA samples were sent for sequencing.

first: Yangmian

last: Yuan

last: Fan

first: Yihao

last: Zhou

first: Rong

last: Qiu

first: Wei

last: Kang

first: Yuchen

last: Chen

first: Chenyu

last: Wang

first: Jiajian

last: Shi

first: Chengyu

first: Yangkai

last: Li

first: Min

last: Wu

first: Kun

last: Huang

first: Yong

first: Ling

last: Zheng


title: RBFOX2 recognizes N6-methyladenosine to suppress transcription and block myeloid differentiation [ChIP-Seq]

first: Xiaoyang

last: Dou

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for H3K4me3, H3K27me3, SUZ12, EZH2 and RBM15 and YTHDC1 in K562 cells.

first: Yu

last: Xiao

first: Chuan

last: He


title: Identification of cell-types in Arabidopsis callus

city: Wako

first: Itoshi

last: NIKAIDO

state: Saitama

address: 2-1 Hirosawa

department: TRIP Headquarters Advanced General Intelligence for Science Program

institute: RIKEN

summary: We determined the cell types present in Arabidopsis callus by single-cell RNA-seq with Quartz-Seq2.

overall_design: We dissociated Arabidopsis callus generated from hypocotyl explants to single-cell by enzymatic treatment. Single cell was sorted into lysis buffer in each well of a 384-well PCR plate using BD FACS Aria II SORP cell sorter or CellenOne. Sequence library DNA was prepared according to Quartz-Seq2 method. We analyzed the sequence library DNA using NextSeq500. Digital expression matrix was calculated with fastq files.

first: Momoko

last: Ikeuchi

first: Tasuku

last: Ito

first: Toshiaki

last: Tameshige

first: Keiko

last: Sugimoto

first: Yoshimi

last: Iwayama

first: Kenji

last: Ohtawa

first: Kensuke

last: Fukumoto

first: Nobuko

last: Mataga

first: Takumi

last: Ichikawa

first: Yohei

last: Sasagawa

last: Nikaido


title: Single-cell ATAC sequencing of murine dermal cells at E14.5 and E18.5

city: Pullman

first: Ryan

middle: Roy

last: Driskell

state: Washington

address: 100 Dairy Rd. BLS 202A

department: Molecular Biosciences

institute: Washington State University

summary: Single Cell open chromatin fragments genome-wide using Chromium Single Cell ATAC kit from murine dermal cells at E14.5 and E18.5

overall_design: scATAC-seq data of whole skin unsorted Wild Type mice at E14.5 and E18.5 using 10X Genomics Chromium Next GEM v1.1

first: Quan

last: Phan


title: Single-cell sequencing of gene expression profiles comparing murine skin at E14.5, E17.5, P5 WT.

summary: Gene expression at single-cell level 10X Genomics of whole skin collected from WT E14.5, E17.5, and P5 mice.

overall_design: scRNA-seq data of WT whole skin across 3 timepoints using 10X Genomics 3' Gene Expression (v2)


title: Epigenetic regulation of embryonic skin development

summary:
We performed ChIP-seq for H3K27me3 using dermal fibroblasts of E18.5 WT and Kdm6bKO mice.
Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for H3K27me3 Fibroblasts at various time points and one Kdm6bKO condition.

overall_design: Phan, Quan

first: Driskell

last: Ryan


title: Single-cell sequencing of gene expression profiles comparing murine skin at E18.5 of wild type and Kdm6b/Jmjd3-cKO.

summary: Gene expression at single-cell level 10X Genomics of whole skin collected from E18.5 WT and Kdm6bKO mice.

overall_design: scRNA-seq data of WT and Kdm6bKO whole skin using 10X Genomics 3' Gene Expression (v3)


title: Brain rhythms control microglial response and cytokine expression via NFkB signaling

city: Atlanta

first: Levi

middle: B.

last: Wood

state: GA

address: 315 Ferst Dr NW Rm 3303

institute: Georgia Institute of Technology

summary: Microglia, the brain’s primary immune cells, transform in response to changes in sensory or neural activity, like sensory deprivation. However, little is known about how specific frequencies of neural activity, impact microglia, immune signaling, or other pathways within the brain. Here , we exposed mice to 1h of audio/visual noninvasive flickering sensory stimulation (flicker) to induce electrical neural activity at different frequencies: 40Hz within the gamma band and 20Hz within the beta band. We then isolated RNA from the visual cortices and used bulk RNAseq to quantify pathway changes.

overall_design: Wild-type male mice, right visual cortices. Three experimental groups: ambient light control, 20Hz audiovisual flicker, and 40Hz audiovisual flicker (1hr, n=4)

first: Alyssa

last: Pybus

first: Sara

last: Bitarafan

first: Annabelle

middle: C

last: Singer


overall_design: Wild-type (resulting from the breeding of 5xFAD mice on a B6SJL background) mouse visual Cortices. Two experimental groups: 20Hz and 40Hz (1hr, N=7)


title: Engineered MED12 mutations drive uterine fibroid-like transcriptional and metabolic programs by altering the 3D genome compartmentalization

first: MAZHAR

last: ADLI

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

overall_design: Refer to individual Series


title: Bulk RNA sequencing analysis of the humanized liver

first: Rihao

last: Qu

summary: The goal of this experiment was to see the percentage of human reads over total (mouse and human reads) for unique hepatocyte genes that are zonated as well as for other unique genes for endothelial cells, stellate cells and cholangiocytes.

overall_design: Part of right liver lobe was snap frozen and used for RNA isolation. The RNA was sent for bulkRNAsequencing. From the same liver,the median and left lobe were used for liver cell isolation for single cell-RNAsequencing.

first: Richard

last: Flavell

first: Eleanna

last: Kaffe


title: Epigenetic regulation of embryonic skin development (H3K27me3 ChIP-Seq)

summary: We performed ChIP-seq for H3K27me3 using dermal fibroblasts of WT skin at E14.5 and E18.5

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for H3K27me3 Fibroblasts at various time points.

first: Lucia

last: Salz


title: RBFOX2 recognizes N6-methyladenosine to suppress transcription and block myeloid differentiation [KAS-Seq]

first: Xiaoyang

last: Dou

overall_design: Kethoxal-assisted single-stranded DNA sequencing (KAS-seq) in K562 cells

first: Yu

last: Xiao

first: Chuan

last: He


title: Inhibition of NETosis via PAD4 could alleviate the inflammation of giant cell myocarditis

city: Tianjin

first: Xiuxue

last: Mo

address: Weijin Road 94, Nankai District

institute: Nankai University

summary: Giant cell myocarditis (GCM) is a rare, often rapidly progressive and potentially  fatal, disease caused by T-cell-mediated cardiac inflammation that typically affects  young and middle-aged adults. The detailed inflammatory response remained  unknown, especially the formation of multinucleate giant cells.Methods and Results:  Rats were treated with myosin heavy-chain-α peptides to generate a GCM model. We  performed single-cell RNA sequencing analysis of 15,714 Cd45 + cells extracted from  hearts from GCM rat model and normal rats. We identified 24 subclusters including  macrophages, neutrophils, T cells and so on. The GCM was characteristic with  macrophage cluster 1, neutrophil cluster 3, macrophage cluster 2, neutrophil cluster 1  and Th17 cells. Two specific macrophage clusters involved in the GCM have roles in  phagocytosis, and NETosis was found to contribute into the process of GCM. Its  receptor, Ccdc25 , expressed in the macrophage cluster 1 and Th17, suggesting that  neutrophils could regulate other immune cells in GCM. Importantly, inhibitor of  NETosis, GSK484, could alleviate the inflammation of GCM in vivo. Finally, MPO (a  marker of neutrophils) and H3cit (a marker of NETosis) were expressed at higher  levels in GCM patients than in DCM patients and healthy controls and neutrophils were  part of multinucleated giant cells. IMC analysis revealed that the formation of  multinucleate giant cells of GCM.Conclusions: We herein present a comprehensive  single-cell landscape of the cardiac immune cells in GCM. In addition, we elucidated  the contribution of NETosis to the pathogenesis of GCM, which may serve as a  potential therapeutic target in the clinic.

overall_design: Rats were treated with myosin heavy-chain-α peptides to generate a GCM model compare a normal rat model

first: Zhan

last: Hu

first: Xiumeng

last: Hua

first: Yuan

last: Chang

first: Xiao

last: Chen

first: Zhenyu

last: Xu

first: Mengtao

last: Tao

first: Gang

first: Jiangping

last: Song


title: Engineered MED12 mutations drive uterine fibroid-like transcriptional and metabolic programs by altering the 3D genome compartmentalization [Hi-C]

first: MAZHAR

overall_design: We performed High-throughput chromosome conformation capture (Hi-C)  in MED12-WT and MED12-G44 mutant hTERT uterine smooth muscle cell to understand the 3D genome compartmentalization

first: Kadir

last: Buyukcelebi

first: Xintong

first: Fatih

last: Abdula

first: Alexander

last: Duval

first: Harun

last: Ozturk

first: Fidan

last: Seker-Polat

first: Qiushi

last: Jin

first: Ping

last: Yin

first: Yue

last: Feng

first: Jian

last: Wei

first: Serdar

last: Bulun

first: Feng

last: Yue

first: Mazhar

last: Adli


title: RBFOX2 recognizes N6-methyladenosine to suppress transcription and block myeloid differentiation [RNA-seq]

first: Xiaoyang

last: Dou

summary: N6-methyladenosine (m6A)methylationcan be deposited on chromatin-associated RNAs (caRNAs) by the RNA methyltransferase complex (MTC) to regulate chromatin state and transcription. How the MTC is recruited to distinct genomic loci to accomplish selective transcriptional regulation remains elusive. Here we identify RBFOX2, a well-established RNA-binding protein (RBP), as a chromatin factor that recognizes m6A on caRNAs and recruits RBM15, an MTC component, to install methylation on promoter-associated RNAs (paRNAs). RBM15 also physically interacts with YTHDC1 to facilitate the recruitment of Polycomb repressive complex 2 (PRC2) to RBFOX2-bound loci for chromatin silencing and transcription suppression. Furthermore, we found that this m6A/RBM15/YTHDC1/PRC2 axis is essential to myeloid leukemia. Downregulation of RBFOX2 notably inhibits AML cell survival/proliferation and promotes myeloid differentiation of AML cells. RBFOX2 is also required for self-renewal of leukemia stem/initiation cells (LSCs/ LICs) and AML maintenance. Together, our study presents a clear pathway of m6A MTC recruitment and m6A deposition on caRNAs to achieve locus-specific chromatin regulation with potential therapeutic implications.

overall_design: RNA-seq in K562 and NB4 cells

first: Yu

last: Xiao

first: Chuan

last: He


title: Transcriptomic profiling of tissue environments critical for post-embryonic patterning and morphogenesis of zebrafish skin

city: Seattle

first: Lauren

last: Saunders

state: WA

address: 3720 15th Ave NE

department: Genome Sciences

institute: University of Washington

summary: Pigment patterns and skin appendages are prominent features of vertebrate skin. In zebrafish, regularly patterned pigment stripes and an array of calcified scales form simultaneously in the skin during post-embryonic development. Understanding mechanisms that regulate stripe patterning and scale morphogenesis may lead to discovery of fundamental mechanisms that govern development of animal form. To learn about cell types and potential signaling interactions that govern skin patterning and morphogenesis we generated and analyzed single cell transcriptomes of skin with genetic or induced defects in pigmentation and squamation. These data reveal a previously undescribed population of epidermal cells that express transcripts encoding enamel matrix proteins, suggest hormonal control of epithelial-mesenchymal signaling, clarify the signaling network that governs scale papillae development, and identify a critical role for the hypodermis in supporting pigment cell development. Additionally, this comprehensive single-cell transcriptome data from biomedically relevant skin conditions provide a useful resource to accelerate discovery of mechanisms governing skin development.

overall_design: Dissected skin tissue from post-embryonic zebrafish (9.6 SSL) from four genetic backgrounds (wild-type, eda mutant, bnc2 mutant, and hypothyroid) were profiled with with sci-RNA-seq2.

first: David

last: Parichy

first: Andrew

last: Aman

first: Cole

last: Trapnell


title: RNA-seq results in the adipose tissue of male adipocyte-specific histone H1.2 knockout mice

city: WuHan

first: Dong

last: Yang

address: No.5  HangKong Road

institute: Huazhong University of Science and Technology

summary: Our study represents the first detailed analysis of transcriptomes in iWAT and BAT of male adipocyte-specific H1.2 knockout mice to understand key pathways and regulatory genes, with biologic replicates, generated by RNA-seq technology

overall_design: Each sample consists of a pool of RNAs extracted from inguinal adipose tissue or brown adipose tissue of 3 different 10-week-old male mice. For each experimental group, two biological replicates of RNA samples were sent for RNA-seq.

first: Yangmian

last: Yuan

first: Ling

last: Zheng

first: Kun

last: Huang


title: Separation of transcriptional repressor and activator functions in HDAC3

city: Stockholm

first: Mattias

last: Mannervik

address: Svante Arrhenius väg 20C

country: Sweden

institute: Stockholm University