title: Direct lysine dimethylation of IRF3 by the methyltransferase SMYD3 attenuates antiviral innate immunity

status: Public on Jan 01 2025

city: 武汉

first: zixuan

last: wang

state: 湖北省

address: 湖北省武汉市东湖南路7号

institute: 中国科学院水生生物研究所

summary: Interferon regulatory factor 3 (IRF3) is the key transcription factor in the type I IFN signaling pathway, whose activation is regulated by multiple posttranslational modifica_x0002_tions. Here, we identify SMYD3, a lysine methyltransferase, as a negative regulator of IRF3. SMYD3 interacts with IRF3 and catalyzes the dimethylation of IRF3 at lysine 39. This modification reduces IRF3 phosphorylation, dimerization, and subsequent nuclear translocation, leading to the inhibition of downstream type I interferon production. In addition, Smyd3-deficient mice are more resistant to RNA and DNA viral infections. Zebrafish lacking smyd3 or treated with the inhibitor BCI121 are also more resistant to viral infection. Our findings reveal a role for SMYD3 in the regulation of antiviral innate immunity and provide insight into a unique modulation of IRF3 that affects its activation.

overall_design: Whole RNA from MEF cells infected with VSV was purified using the RNeasy Mini Kit (QIAGEN, #74104). To ensure the quality of the information analysis, fastp software was used to remove the splice sequences, filter the low quality, N bases (indicating that the base information could not be determined), and obtain high quality clean data. The clean data and the number of bases and sequences of the clean data were counted. At the same time, the GC, Q20, Q30 contents of the clean data were calculated (Benagen Technology, Wuhan, China). Volcano Plot were generated using the ggplot2 software. Heatmaps were generated using the Multi Experiment Viewer (MeV) software. Gene Ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses for the differentially expressed genes (DEGs) was performed using Cluster Profiler version 3.8.

first: Zixuan

last: Wang

first: Xiaoyun

last: Chen

first: Xing

first: Wuhan

last: Xiao


title: Effect of depletion of Bckdha or Acad8 on gene expression in differentiated, cultured 3T3-L1 adipocytes

status: Public on Jan 02 2025

city: La Jolla

first: Christian

middle: M

last: Metallo

state: CA

address: 10010 N Torrey Pines Rd

department: Molecular and Cell Biology Laboratory

country: USA

institute: Salk Institute for Biological Studies

type: Expression profiling by high throughput sequencing

summary:
To investigate the function of the BCAA catabolic pathway via Bckdha or Acad8 deficiency in adipocytes, we established 3T3-L1 cell lines in which each target gene or a Control non-targeting sequence has been knocked down by CRISPR/Cas9.
We then performed gene expression profiling analysis using data obtained from RNA-seq of 3 different single guides of Bckdha and Acad8 or 1 Control guide (7 cell lines total)

overall_design: Comparative gene expression profiling analysis of RNA-seq data for 3T3-L1 adipocytes and its KD derivatives (sgBckdha, sgAcad8, sgControl).

first: Courtney

middle: R

last: Green

first: Martina

last: Wallace

first: Rory

last: Turner


title: Bacillus strains act independently of immune system activation and compensate for its absence

city: Jerusalem

first: Moshe

last: Alon

state: Israel

address: Gelber

country: Israel

institute: Hebrew University of Jerusalem

summary: The microbiota plays a crucial role in protecting plants from pests and pathogens. The protection provided by the microbiota constitutes not just the plant’s first line of defense, but possibly its most potent one, as experimental disruptions to the microbiota cause plants to succumb to otherwise asymptomatic infections. To understand how microbial plant defense is deployed, we applied a complex and tractable plant-soil-microbiome microcosm. This system, consisting of Arabidopsis plants and a 150-member bacterial synthetic community, provides a platform for the discovery of novel bacterial plant-beneficial traits, under a realistically complex microbial community context. To identify which components of the plant microbiota are critical for plant defense, we deconstructed this microcosm top-down, removing different microbial groups from the community to examine their protective effect on the plant when challenged with the leaf pathogen Pseudomonas syringae. This process of community deconstruction revealed a critical role for the genus Bacillus in protecting the plant from infection. Using plant RNA-seq and bacterial co-culturing experiments, we demonstrated that Bacillus-provided plant protection is independent of plant immune system activation. We also show that the level of plant protection is strongly dependent on the diversity of the protective inoculum. We show that deconstructing the microbiome top-down is a powerful tool for identifying and prioritizing microbial taxa with specific functions within it.

overall_design: To validate our hypothesis that Bacillus protects the plant via direct inhibition of pathogen growth and not via activation of plant immunity, we investigated how the presence of Bacillus in the soil affects the expression of immune system genes in plants. We performed RNA-seq on the leaves of plants treated with different SynCom configurations, specifically comparing the full SynCom, Bacillota dropout, and Bacillus dropout groups in both uninfected and Pto-infected plants.

first: Amal

last: Ghosheh


title: The transcription factor OsWRKY36 regulates lamina joint development and the leaf angle in rice by modulating brassinosteroid signalling

city: Kunming

first: Lirong

last: Zhao

state: Yunnan

address: No.88 Xuefu Road

department: Xishuangbanna Tropical Botanical Garden

country: China

institute: Chinese Academy of Sciences

summary: We identified a key regulator of the rice leaf angle and plant architecture, OsWRKY36, from a rice oswrky mutant library. OsWRKY36 is highly expressed in the leaf lamina joint and promotes cell growth and expansion in adaxial parenchyma cells, leading to a greater leaf angle.

overall_design: Total RNA was extracted from the lamina joint tissues and total plants of 10-day-old Nip, oswrky36 mutants, and OsWRKY36-overexpresing seedlings. Sequencing was performed  using Illumina Hiseq technology.


title: NKCLR3 impairs natural killer cell cytotoxicity by epigenetically targeting the Natural Cytotoxicity Triggering Receptor 1 (NCR1) [lncRNA-seq]

city: Changchun

first: Xiumin

last: Shi

state: Jilin

address: No.1 Xinmin Street

department: Department of Hematology

institute: The First Hospital of Jilin University

type: Non-coding RNA profiling by high throughput sequencing

summary: Natural killer cells (NK cells) play a critical role in the surveillance of tumor immunity. However, NK cell-based immunotherapy, including autologous and allogeneic NK cell reinfusion, has not brought significant clinical benefits to patients. To identify factors that control the intrinsic cytotoxicity of NK cells, we utilized the histone deacetylase inhibitor valproic acid (VPA) to develop a NK cell cytotoxicity suppression model. With RNA-seq and functional assays, we identified a previously uncharacterized lncRNA, NKCLR3 (NK cytotoxicity-associated long noncoding RNA 3), as a negative regulatory factor of NK cell-mediated cytotoxicity. NKCLR3 was significantly upregulated in VPA-treated NK cells and was negatively associated with the cytotoxicity of NK cells. Knockdown of NKCLR3 enhanced antitumor activity in NK-92MI cells. Using reverse transcription-associated capture sequencing (RAT-seq), we found that NKCLR3 functioned by targeting the Natural cytotoxicity triggering receptor 1 (NCR1) gene, which encodes the activating receptor NKp46 involved in the natural cytotoxicity. Mechanistic studies revealed that NKCLR3 interacted with the regulatory elements of NCR1 and blocked the formation of an intrachromosomal interaction that is required for optimal expression of NCR1. In addition, NKCLR3 inhibited the synthesis of NCR1 enhancer RNA. Through these dual mechanisms, NKCLR3 induced a suppressive epigenotype in the NCR1 promoter and suppressed the expression of the NCR1 gene. Thus, the NKCLR3-NCR1 axis identified in this study may serve as a novel target to improve therapeutic intervention of NK cells in tumor immunotherapy.

first: Jifan

last: Hu


title: Single-Cell RNA Sequencing of Trav4 Gene-Edited Mouse Lung Tissue

city: Guilin

first: Honghao

last: Yu

state: Guangxi

address: Guilin Medical College, Lingui District, Guilin City, Guangxi

institute: Guilin Medical University

summary: This dataset contains single-cell RNA sequencing data from lung tissues of Trav4 gene-edited mice .  The samples were collected for the investigation of molecular changes induced by Trav4 gene mutations, specifically focusing on lung injury.  The dataset includes gene expression profiles of individual cells and enables the study of cell-type-specific responses, immune cell changes, and alterations in key cellular pathways.  This dataset is useful for further understanding the pathophysiology of lung injury associated with Trav4 gene mutations.

overall_design: Lung tissues from Trav4 gene-edited mice were collected, and single cells were isolated for RNA sequencing. The single-cell suspension was processed using the SeekOne® Digital Droplet Single Cell Library Kit, followed by sequencing on the Illumina NovaSeq 6000 platform.

first: Pengpeng

last: Yue

first: Haobo

first: Zhihao

last: Li

first: Yong

first: Lantao

last: Gu

first: Can

last: Fu


title: The subunit 3 of the SUPERKILLER 3 (SKI3) complex mediates miR172-directed cleavage of Nodule Number Control 1 (NNC1) to modulate nodulation in Medicago truncatula

city: La Plata

first: Soledad

last: Traubenik

state: Buenos Aires

department: Ciencias Biologicas

country: Argentina

institute: Universidad Nacional de La Plata

summary: Legumes and rhizobia establish a nitrogen-fixing symbiosis that involves the formation of a lateral root organ, the nodule, and the infection process that allows intracellular accommodation of rhizobia within nodule cells. This process involves significant gene expression changes regulated at the transcriptional and post-transcriptional levels. We have previously shown that a transcript encoding the subunit 3 of the Superkiller Complex (SKI), which guides mRNAs to the exosome for 3´-to-5´ degradation, is required for nodule formation and bacterial persistence within the nodule, as well as the induction of early nodulation genes (e.g., MtENOD40) during the Medicago truncatula-Sinorhizobium meliloti symbiosis. Here, we reveal through transcript degradome and small RNA sequencing analysis that knockdown of MtSKI3 impairs the miR172-directed endonucleolytic cleavage of the mRNA encoding Nodule Number Control 1 (MtNNC1), an APETALA2 transcription factor that negatively modulates nodulation. Knockdown of MtNNC1 enhances nodule number, bacterial infection, and the induction of MtENOD40 upon inoculation with S. meliloti whereas overexpression of a miR172-resistant form of MtNNC1 significantly reduces nodule formation. This work identifies miR172 cleavage of MtNNC1 and its control by MtSKI3, a component of the 3´-to- 5´mRNA degradation pathway, as a new regulatory hub controlling indeterminate nodulation.

overall_design: Small RNA Seq in GUS RNAi mock and SKI3 RNAi mock Medicago truncatula roots

first: Mauricio Alberto

last: Reynoso

first: Francisco

last: Sánchez-Rodríguez

first: Milagros

last: Yacullo

first: Aurelie

last: Christ

first: Maureen

last: Hummel

first: Thomas

last: Blein

first: Martin

last: Crespi

first: Julia

last: Bailey-Serres

first: Flavio Antonio

last: Blanco

first: María Eugenia

last: Zanetti


title: TPPU alleviate cartilage degradation in temporomandibular joint osteoarthritis by inhibiting M1 macrophage polarization through the EETs/IL-17/NF-KB signaling pathway

city: DaLian

first: YiDing

last: Liu

address: wwde

institute: Dalian Medical University

summary: In the treatment of inflammatory diseases, TPPU has shown potential therapeutic effects on a variety of inflammatory conditions, including reshaping the body's pro-inflammatory/anti-inflammatory balance by stabilizing endogenous anti-inflammatory substances EETs. In cardiovascular diseases, TPPU can regulate the NF-κB signaling pathway to modulate macrophage polarization and reduce inflammation. To explore the mechanism of TPPU in regulating M1 macrophages in TMJOA, we treated M1 macrophages with TPPU. In short, we attempted to verify the key signaling molecules and pathways regulated by TPPU in M1 macrophages.

overall_design: We performed RNA-sequencing on a total of six LPS-induced RAW264.7 macrophage samples, with three samples treated with TPPU and the other three serving as untreated controls.

first: Lu

last: Gao

first: Bing

last: Yan

first: Yiding


title: RNA-seq and sRNA-seq analysis of rice lines of wild type (Zhenong 34) and its sgs3 mutant

city: Hangzhou

first: Xiaoli

last: Jin

state: Zhejiang

address: Yuhangtang road 866

institute: Zhejiang University

summary: The study was conducted to characterize the  mutant; identify the candidate gene for the mutant trait with the map-based cloning approach; investigate the segregation of target gene with the mutant characteristics, and examine the metabolic pathways of differentially expressed genes between WT and its mutant with comparative transcriptome analysis.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for the WT (Zhenong 34) and sgs3 mutant.


title: NKCLR3 impairs natural killer cell cytotoxicity by epigenetically targeting the Natural Cytotoxicity Triggering Receptor 1 (NCR1)

first: Xiumin

last: Shi

type: Genome binding/occupancy profiling by high throughput sequencing

summary: RNA-Seq reveals that NKCLR3 (NK cytotoxicity-associated long noncoding RNA 3, NONHSAT026854) is differentially expressed in VPA-treated human NK cells. To determine whether it is functionally important in NK cell cytotoxicity, we used a RNA reverse transcription-associated trap sequencing (RAT-Seq) approach to profile the genome-wide binding targets for NKCLR3. This dataset will help study the mechanisms underlying the role of NKCLR3 in NK cell cytotoxicity.

overall_design: RAT-Seq was used to map the genome wide targets of lncRNAs. For RAT-Seq, NK-92MI cells were first cross-linked to fix the lncRNA-chromatin structure. The regulatory element-interacting RNAs were reverse transcribed in situ in the nucleus using lncRNA-specific complementary primers in a reaction mixture containing biotin-dCTP. The RNA-biotin cDNA chromatin complex was pulled down with streptavidin beads and the target gene DNAs were purified for library sequencing. Using RAT-Seq, we mapped the genome wide target for NKCLR3 (NK cytotoxicity-associated long noncoding RNA 3, NONHSAT026854). As the RAT control, RAT control dataset was generated by random oligo primers. NKCLR3 was negatively associated with the antitumor activity of NK cells. It was more highly expressed in VPA-treated NK cells.

first: Jifan

last: Hu


title: The conserved disulfide isomerase PDIA3/ERp60 regulates intestinal epithelial homeostasis in response to shifts in ether phospholipid metabolism.

city: Halifax

first: Francesca

last: Di Cara

state: Nova Scotia

address: 5850/5980 University Avenue

country: Canada

institute: Dalhousie University

summary: Intestinal epithelium regeneration and homeostasis must be tightly regulated. Alteration of epithelial homeostasis is a major contributing factor to diseases such as colorectal cancer and inflammatory bowel diseases. Many pathways involved in epithelial regeneration have been identified, but more regulators remain undiscovered. Metabolism has emerged as an overlooked regulator of intestinal epithelium homeostasis. Using the model organism Drosophila melanogaster, we found that ether lipid metabolism is required to maintain intestinal epithelial homeostasis. Its dysregulation in intestinal progenitors causes the activation of the unfolded protein response of the endoplasmic reticulum (UPR) that activates Xbp1 and upregulates the disulfide isomerase PDIA3/ERp60. Activation of the Xbp1-ERp60 signaling causes Jak/Stat-mediated increase in progenitor cells, compromising epithelial barrier function and survival in males but not females. This study identified ether lipids-PDIA3/ERp60 as a key regulator of intestinal progenitor homeostasis in health that, if altered, causes pathological conditions in the intestinal epithelium.

overall_design: FACS-isolated Drosophila wildtype and Pex5-depleted intestinal progenitor cells.

first: Stephanie

last: Makdissi

first: Rihab

last: Loudhaief

first: Smitha

last: George

first: Tabatha

last: Weller

first: Minna

last: Salim

first: Ahsan

last: Malik

first: Yizhu

last: Mu

first: Brendon

middle: D

last: Parsons


title: Non-small cell lung cancer-associated Keap1 mutations lead to epigenetic reprogramming and tumorigenesis through CHD6 stabilization

city: Shanghai

first: Yingji

last: Chen

address: 2005 Songhu Road, Yangpu District

department: School of Life Sciences

institute: Fudan University

summary: The E3 ubiquitin ligase substrate recognition subunit Keap1 mediates the ubiquitination and degradation of the oxidative stress transcription factor NRF2. Approximately 30% of non-small cell lung cancers (NSCLCs) harbor inactivating mutations in Keap1 or activating mutations in NRF2, both of which lead to the stabilization of NRF2 and activation of the downstream antioxidant pathway. Recent studies have found that the oncogenic effects of Keap1 and NRF2 mutations are not entirely equivalent, suggesting that Keap1 may have other regulatory substrates. In previous work, we used affinity immunopurification and mass spectrometry to identify the epigenetic regulator CHD6 as a Keap1-interacting protein, with Keap1 mediating the ubiquitination and degradation of CHD6. NSCLC-derived Keap1 mutants lost the ability to bind and ubiquitinate CHD6. Additionally, CHD6 interacts with NRF2 and promotes the enrichment of NRF2 at the promoters of its target genes, enhancing their transcription.This project aims to elucidate the mechanism by which the abnormal accumulation of CHD6 protein, due to disruption of its Keap1-mediated degradation, drives epigenetic reprogramming in the context of Keap1-mutant NSCLC development and progression. The findings will provide a theoretical basis for the development of NRF2 pathway inhibitors targeting CHD6 as a drug target.

overall_design: RNA seq of  Human non-small cell lung cancer cells in control and knock out CHD6 group


title: KLF2-dependent transcriptional regulation safeguards the heart against pathological hypertrophy

city: ShenZhen

first: Juan

last: Huang

address: Langshan Road

department: Shenzhen Key Laboratory of Cardiovascular Disease

institute: Fuwai Hospital Chinese Academy of Medical Sciences

summary: Our previous single-cell RNA sequencing study in the adult human heart revealed that cardiomyocytes from both the atrium and ventricle display high activities of Krüppel-like factor 2 (KLF2) regulons. However, the role of the transcription factor KLF2 in cardiomyocyte biology remains largely unexplored. We employed transverse aortic constriction surgery in male C57BL/6J mice to develop an in vivo model of cardiac hypertrophy, and generated different in vitro cardiac hypertrophy models in neonatal rat ventricular myocytes and human embryonic stem cell-derived cardiomyocytes. Our results demonstrated a significant reduction in KLF2 expression during the progression of cardiac hypertrophy. In vitro, KLF2 deficiency exacerbates cardiac hypertrophy and enhances hypertrophic reprogramming, while KLF2 overexpression attenuates cardiac hypertrophy and reverses hypertrophic transcriptome reprogramming. Mechanistically, combined RNA-seq and cleavage under targets & tagmentation (CUT&Tag)  analysis revealed that KLF2 exerts its protective effects by directly regulating a set of genes associated with cardiac hypertrophy. In vivo, KLF2 overexpression specifically in cardiomyocytes effectively prevents TAC-induced cardiac hypertrophy in mice. Additionally, we found that simvastatin elevates KLF2 expression in cardiomyocytes, which subsequently alleviates cardiomyocyte hypertrophy. This study provides the first evidence that transcription factor KLF2 serves as a negative regulator of cardiac hypertrophy. Our findings highlight the therapeutic potential of enhancing KLF2 expression, particularly through simvastatin administration, as a promising strategy in the treatment of cardiac hypertrophy.

overall_design: RNA-seq profiling of NRVMs with KLF2 knockdown or overexpression under control or PE treatment conditions.CUT-Tag assay in neonatal rat ventricular myocytes with KLF2 overexpression.

first: Li

last: Wang

first: Wanqing

last: Zhao

first: Yujuan

last: Song

first: Yongqi

last: Wu


title: Effects of Triad1-knockdown on ribosome/polysome profiles are reversed by Gcn1-knockdown

city: Chicago

first: Marcelo

middle: G.

last: Bonini

state: IL

address: 303 E. Superior St. Suite 7-123

department: Feinberg School of Medicine

institute: Northwestern University

summary: Previously, we identified ARIH2, the gene encoding Triad1, as a HoxA10 target gene. We found that HoxA10-induced expression of Triad1 was necessary for termination of emergency granulopoiesis, and antagonized leukemogenesis in a murine model of KMT2A-rearranged AML. In this study, we found that knockdown Triad1 increased polysome-specific mRNAs regulating the cellular response to stress, the DNA-damage response, ribosomal biogenesis, or protein catabolism, but decreased mRNAs regulating mitosis, DNA-repair, DNA and RNA metabolism, or Tp53 activity in U937 cells.  Polysome-specific mRNAs for Solute Carrier Proteins (SLCs) were also increased by Triad1-knockdown, consistent with correction of metabolic defects during the ISR. This included SLCs involved in import of amino acids, long chain fatty acids and glucose, and lactate export.  In comparison of polysome-specific mRNA profiles with Triad1-knockdown versus knockdown of Triad1 plus Gcn1, we identified the same gene and pathway differences as in comparison of Triad1-knockdown to control cells. There were only minor differences in polysome specific mRNAs in cells with Triad1- plus Gcn1-knockdown versus control cells, encompassing fewer differences than with Triad1-knockdown alone. This suggested that Triad1-knockdown on ribosome/polysome profiles are reversed by Gcn1-knockdown in U937 cells.

overall_design: We first analyzed the effect of Triad1-knockdown on ribosome/polysome profiles in U937 stable transfectant pools. Then to determine if effects of Triad1-knockdown were due to Gcn1-stabilization, we generated additional stable transfectant pools with shRNA knockdown of both Gcn1 and Triad1. To determine Gcn1-dependent influences of Triad1 on the translatome, we sequenced polysome associated mRNA from these stable transfectant pools. These results were compared to sequencing total mRNA from the same cells to identify polysome-specific differences in mRNA abundance. We compared cells with Triad1-knockdown, Triad1- plus Gcn1-knockdown, or scrambled shRNA controls.  Statistically significant translatome differences were determined, and gene ontology analysis applied to implicate pathway activity.

first: Elizabeth

middle: A

last: Eklund

first: Hao

first: Brian

last: Wray


title: mRNA-sequencing uncovered the underlying mechanisms of xylazine related liver injury

city: Guang zhou

first: Shuquan

state: Guangdong

address: zhongshan second road 74

institute: Sun Yat-sen University

summary: Objective: The present study is aimed to study the liver injury in xylazine poisoning and uncover the underlying mechanism.  Method: Forty male SD rats were randomly dived into four groups, control (saline), low dose (10mg/kg xylazine), median dose (20mg/kg xylazine) and high dose (40mg/kg xylazine). And the rats were injected the drug intraperitoneal continuous 28 days, and then collected serum and liver tissues, Elisa, RNA sequencing, histopathology examination, RT-qPCR were performed. Results: Compared to the control group, the body weight of 40mg/kg group was decreased, the level of ALT and AST in serum of 40mg/kg group was increased. Histopathological examination showed fatty degeneration, necrosis and fibrosis of the liver. 192 up-regulated and 277 down-regulated genes were identified through RNA sequencing in the 40mg/kg group and the PPAR signaling pathway ranked first in the KEGG pathway analysis, The common DEG in the 10mg/kg and 40mg/kg (Lox), four common DEGs in the 20mg/kg and 40mg/kg (Srebf1, Nr1dl, Fasn, SCD1), and four genes PCK1, FABP5, ACOX2, CPT2 in the PPAR signaling pathway in the 40mg/kg group were validated through Real-Time PCR Analysis. Conclusion：Long term xylazine injection can cause liver injury and the PAPR signaling pathway play a core role in the process of xylazine related liver injury.

overall_design: Forty male SD rats were randomly dived into four groups, control (normal saline), low dose (10mg/kg xylazine), median dose (20mg/kg xylazine) and high dose (40mg/kg xylazine) and injected 28 days to investigate the liver injury of xylazine.

first: Shanyong

last: Yi

first: Tingting

last: Mai

first: Ying

last: Fang

first: Qishuo

last: Tian


title: JAKaL: Phase Ib study of itacitinib, a selective JAK1 inhibitor, for the management of advanced stage hepatocellular cancer after failure of first line therapy.

city: London

first: Rohini

last: Sharma

state: London

address: Du Cane Road

department: Surgery and Cancer

country: United Kingdom

institute: Imperial College London

summary: Background: Hepatocellular carcinoma (HCC) develops on background chronic liver disease where exposure to uncontrolled inflammation drives hepatocarcinogenesis. Current first-line therapies have limited response, and most patients will eventually progress. There are no agents that specifically target the underlying liver inflammation.  We investigated the safety and efficacy of itacitinib, a highly selective JAK1 inhibitor, as a potential second- or third-line therapy in patients with advanced HCC. Biomarkers of response were investigated.  Methods: Participants with advanced stage HCC, Child Pugh <B7 who had progressed through at least one previous line of therapy received 400mg of itacitinib QID every 28 days. Treatment-related adverse events (trAEs) were assessed weekly during cycle 1 then every 28 days (CTC-AE version 4.03). Response was assessed 8-weekly using RECIST 1.1. Progression-free (PFS) and overall survival (OS) were reported as secondary endpoints.  Tumour samples were analysed for targeted transcriptomics. Sequential serum samples were assessed for metabonomic determinants of toxicity and response.    Results: Nineteen patients were enrolled. The most common trAEs were thrombocytopenia (31%), fatigue (26%) and palmar-plantar erythrodysesthesia syndrome (26%); four episodes of dose-limiting thrombocytopaenia were observed. Over a median follow-up of 3.5 months, the best overall response was stable disease (47%).  Median PFS and OS were 3.5 (95% CI: 2.6 - 4.5 months) and 7.4 months (95% CI: 4.3-10.5 months), respectively. Subgroup analysis illustrated a significantly increased risk of progression for patients that had received combination immunotherapy prior to itacitinib (HR 4.7, 95%CI 1.3-16.6, p=0.016).  Untargeted tumour and serum transcriptomics identified a signature predictive of response.  Discussion:  Itacitinib either as second- or third-line therapy showed promising activity.  We identified a transcriptomic signature predictive of response.

first: Sultan

last: Alharbi


title: Disruption of macrophage polarization promote adipocyte disfunction via APOE-APP Intercellular communication

city: Beijing

first: Hui

last: Yang

address: 7 Panjiayuan Nanli, Room314

department: Department of Toxicology

institute: China National Center for Food Safety Risk Assessment (CFSA)

summary: Human exposure to endocrine disrupting chemicals (EDCs) such as plasticizers contributes to part of metabolic disorders especially in children and adolescents. Immune cells especially macrophages were essential targets of plasticizers, however their roles on plasticizers induced metabolic disorders and the underlying mechanism were poorly elucidated. Here we reported that dicyclohexyl phthalate (DCHP), one substitute for di-2-ethylhexyl phthalate (DEHP), prepubertal exposure decreased adipose tissue mass and increased plasma triglycerides in mice. Mechanistically, adipose tissue macrophages, particularly lipid associated macrophages (LAM), played key role in this systemic metabolic disorder. Phthalates facilitated the formation of LAMs. And LAMs communicated with adipocyte precursors, especially adipose progenitor cells, via APOE-APP interaction, leading to abnormal adipogenesis. Blocking LAMs formation via macrophage-specific PPARγ knockout enabled adaptive adipogenesis, ameliorating DCHP-induced metabolic disorder. Our data highlights the essential role of LAMs in inhibiting adaptive adipogenesis, supplying a scientific basis for EDCs associated metabolic disorder, especially environmental related lipodystrophy.

overall_design: Human APP conditional knockout preadipocytes and adipogenesis assays were conducted using hTERT A41hWAT-SVF cells. An APP knockout cell line was established employing the CRISPR-Cas9 system to investigate the role of APP in regulating adipogenesis. Total RNA was extracted using TRIzol for transcriptome sequencing, with three biological replicates set for both hTERT A41hWAT-SVF and APP knockout cell lines.

first: Miao

last: Xu

first: Yaru

first: Lijuan

last: You

first: Yongning

last: Li

first: Lei

last: Shi

first: Xudong

last: Jia

first: Yi

last: Wan


title: The transcriptional landscape of the developing chick trigeminal ganglion

city: Washington

first: Chunling

state: DC

address: 3700 O St NW

department: Oncology

institute: Georgetown University

summary: The trigeminal ganglion is a critical structure in the peripheral nervous system, responsible for transmitting sensations of touch, pain, and temperature from craniofacial regions to the brain. Trigeminal ganglion development depends upon intrinsic cellular programming as well as extrinsic signals exchanged by diverse cell populations. With its complex anatomy and dual cellular origin from cranial placodes and neural crest cells, the trigeminal ganglion offers a rich context for examining diverse biological processes, including cell migration, fate determination, adhesion, and axon guidance. Avian models have, so far, enabled key insights into craniofacial and peripheral nervous system development. Yet, the molecular mechanisms driving trigeminal ganglion formation and subsequent nerve growth remain elusive. In this study, we performed RNA-sequencing at multiple stages of chick trigeminal ganglion development and generated a novel transcriptomic dataset that has been curated to illustrate temporally dynamic gene expression patterns. This publicly available resource identifies major pathways involved in trigeminal gangliogenesis, particularly with respect to the condensation and maturation of placode-derived neurons, thus inviting new lines of research into the essential processes governing trigeminal ganglion development.

overall_design: RNA-seq profiling of pooled trigeminal ganglia from chicken embryos at multiple developmental stages (HH13/14, HH15/16, and HH17/18) with 3 biological replicates per stage.

first: Carrie

middle: E

last: Leonard

first: Alec

last: McIntosh

first: Johena

last: Sanyal

first: Lisa

last: Taneyhill


title: scRNAseq profile of hepatocellular carcinoma (HCC) tumors and adjacent tissues with or without hepatitis-B virus (HBV) infection

city: Shenzhen

first: Zhao

last: Shizheng

address: Shenzhen

department: LIFS

institute: Undefined

summary: In this study, we collected both the tumors and tumor-adjacent tissues from HBV-positive and HBV-negative HCC patients, conducted scRNA-seq, and compared the immune microenvironment of HBV-positive and HBV-negative tumors.

overall_design: To generate a single-cell atlas of the HCC, we recruited 6 HCC patients with primary tumors. All the tumors of the patients, aged from 49 to 75, including both males and females, do not display the vascular invasion and metastatic features. Overall, we obtained the transcriptomic data of 121848 single cells, with an average of 1892 detected genes per cell.

first: SHAO

last: ximing


title: Delayed crosstalk between astrocytes and neurons leads to depressive-like behaviors

first: Guoping

last: Liu

address: 138 Yi Xue Yuan Road

summary: The proper function establishment of nervous system is characterized by closely crosstalk among multiple cell types during the critical periods. Impeding or delaying the crosstalk results in abnormal neural functions and neurodevelopmental disorders. However, the lack of robust mouse models to study the crosstalk between astrocytes and neurons thus renders unclear the implications of impeding such interactions. Here we found that Egfr knockout led to the absence of astrocytes during the critical period of neuronal maturation, with recovery observed in adult mice, providing an exceptional opportunity to investigate the consequences of delaying crosstalk between astrocytes and neurons. We show that glial progenitor cells exhibit a rounded and smooth morphology, displaying few or no protrusions, in the absence of Egfr, which stands in stark contrast to the multi-protrusion morphology observed in the control cells. This phenomenon arises as a direct consequence of the impaired Egfr-pERK-Epb41l2 signaling axis, leading to delayed crosstalk between astrocytes and neurons. This delay results in reduced neuronal dendritic complexity and decreased neuronal excitability (due to damage to the Sema6a-Plxna2/4 receptor pair between astrocytes and neurons during the critical period), ultimately leading to the manifestation of depressive-like behaviors in adult mice.

overall_design: scRNA-Seq: FlashTag (CellTrace Yellow, Life Technologies, #C34567, 0.5 μl of 10 mM) was injected into the cortical lateral ventricle of control mice, hGFAP-Cre; Egfr-cko and hGFAP-Cre; MAP2k1/2-dcko mice at E18 and E16, respectively. P2 and E17 brains were harvested respectively and submerged in fresh ice-cold Hanks’ balanced salt solution (Gibco 14175-095). The dorsal cortices were cut into small pieces and dissociated into a single-cell suspension using a Papain Cell Dissociation Kit by following the manufacturer’s instruction. The tdTomato+ (tdT+) cells were captured and harvested through fluorescence-activated cell sorting (FACS). The Chromium droplet-based sequencing platform (10X Genomics) was used to generate scRNA-Seq libraries, following the manufacturer’s instructions (manual document part number: CG00052 Rev C). The cDNA libraries were purified, quantified using an Agilent 2100 Bioanalyzer, and sequenced on an Illumina Novaseq 6000.RNA-Seq: The P50 PFC tissue was collected from hGFAP-Cre; Egfr-cko and same-litter homozygotes . Direct-zol RNA Miniprep kit (Zymo, catalog #R2050) was used to isolate total RNA following the manufacturer’s instructions. The quality of RNA was assessed by measuring RNA concentration and purity, as well as evaluating RNA integrity (RIN > 7). After removing rRNA from the sample, purified mRNA was obtained. Following cDNA synthesis, a sample library is constructed and subjected to sequencing analysis. Gene expression levels were reported as fragments per kilobase of exon model per million mapped reads (FPKM). P value <0.05 grip was defined as differentially expressed genes.

first: Xin

last: Jiang

first: Zhengang


title: Expression of tsRNAs in early stage hepatocellular carcinoma

city: Nantong

first: Jie

last: Yuan

address: 20# Xisi Road

institute: Affiliated Hospital of Nantong University

summary: This work utilized Arraystar Human tRF&tiRNA sequencing technology to conduct a thorough investigation of tsRNA expression profiles. The objective was to identify and assess the potential of tsRNAs as early diagnostic indicators for HCC. Effectively identifying a specific set of tsRNAs that displayed distinct expression patterns in Barcelona Clinic Liver Cancer (BCLC) 0/A stage HCC tissues in comparison to normal liver tissues.

overall_design: RNA-seq profiling of Barcelona Clinic Liver Cancer (BCLC) 0/A stage HCC tissues and paraneoplastic tissue.

first: Shaoqing

last: Ju

first: Tianxin

first: Xian


title: IL-21 Shapes the B Cell Response in a Context-Dependent Manner [RNA-seq

city: New York

first: Jayanta

last: Chaudhuri

state: NY

address: 417 E 68th St

institute: Memorial Sloan Kettering Cancer Center

summary: The cytokine interleukin-21 (IL-21) is a pivotal T cell-derived signal crucial for germinal center (GC) responses, but the precise mechanisms by which IL-21 influences B cell function remain elusive. Here, we investigated the B cell-intrinsic role of IL-21 signaling by employing a novel IL-21 receptor (Il21r) conditional knock-out mouse model and ex vivo culture systems and uncovered a surprising duality of IL-21 signaling in B cells. While IL-21 stimulation of naïve B cells led to Bim-dependent apoptosis, it promoted robust proliferation of pre-activated B cells, particularly class-switched IgG1+ B cells ex vivo. Consistent with this, B cell-specific deletion of Il21r led to a severe defect in IgG1 responses in vivo following immunization. Intriguingly, Il21r-deleted B cells are significantly impaired in their ability to transition from a pre-GC to a GC state following immunization. Although Il21r-deficiency did not affect the proportion of IgG1+ B cells among GC B cells, it greatly diminished the proportion of IgG1+ B cells among the plasmablast/plasma cell population. Collectively, our data suggest that IL-21 serves as a critical regulator of B cell fates, influencing B cell apoptosis and proliferation in a context-dependent manner.

overall_design: To examine the B cell-intrinsic role of IL-21 signaling, we performed RNA-sequencing (RNA-seq) on naïve B cells stimulated ex vivo with combinations of αCD40, IL-4, and IL-21 for 6 or 24 hours

first: Youngjun

last: Kim


title: IL-21 Shapes the B Cell Response in a Context-Dependent Manner [CUT&RUN]

overall_design: To identify STAT3 binding sites in IgM+ and IgG1+ B cells upon IL-21 stimulation, we sorted these cell populations after 96 hours of ex vivo aCD40 + IL-4 stimulation. Subsequently, cells were restimulated with either aCD40 + IL-4 or aCD40 + IL-21 for one hour and subjected to CUT&RUN using an anti-STAT3 antibody.


title: Nrf1 deficiency promotes tubular ferroptosis by regulating ACSL4 in cisplatin-induced acute kidney injury

city: jilin

first: hu

last: jianqiang

address: changchun

institute: jilin University

summary: Nrf1 is a transcription factor that is highly conserved and reacts to oxidative, proteotoxic and endoplasmic reticulum stress in cells; nonetheless, its function in the context of acute kidney injury (AKI) remains unclear. Using a model of cisplatin-induced nephrotoxicity in vitro and in vivo, we found that the expression of Nrf1, which is expressed at high levels in renal tubular cells, was significantly downregulated after cisplatin treatment. Proximal tubule-specific Nrf1 knockout worsened and Nrf1 overexpression attenuated cisplatin-induced (CI)-AKI. RNA sequencing analysis revealed that Nrf1 overexpression decreased the number of transcripts involved in cell death, specifically those associated with ferroptosis, after cisplatin treatment. Furthermore, ferroptosis responses, characterized by increased lipid peroxidation and iron content and decreased FPN, XCT and glutathione peroxidase 4 levels, were attenuated in Nrf1-overexpressing HK-2 cells but worsened in Nrf1-knockout mice and Nrf1-knockdown HK-2 cells. Moreover, lipidomic and RNA sequencing results indicated that Nrf1 regulated the levels of polyunsaturated fatty acids (PUFAs) and inhibited the expression of ACSL4. Additionally, ChIP experiments revealed that Nrf1 bound to the promoter region of ACSL4, thereby inhibiting its transcription. Furthermore, inhibitors of ACSL4 significantly reduced the sensitivity of HK-2 cells to ferroptosis induced by Nrf1 knockdown. Collectively, these findings suggest that Nrf1 is a novel target for inhibiting ferroptosis in renal tubule cells by suppressing the transcription and expression of ACSL4, thereby reducing PUFA levels. Consequently, activators developed for Nrf1 may hold therapeutic potential in the treatment of patients with CI-AKI.

overall_design: RNA sequencing analysis revealed that Nrf1 overexpression decreased the number of transcripts involved in cell death, specifically those associated with ferroptosis, and inhibited the expression of ACSL4 after cisplatin treatment .

first: Jianqiang

last: Hu

first: Yan

last: Zhang

first: Yanmin

first: Xinxin

last: Ci


title: DNA virus infections shape transposable element activity in vitro and in vivo (HCMV,KSHV,DUX4)

city: Freiburg

first: Florian

last: Full

address: Hermann-Herder-Str. 11

country: Germany

institute: institute of Virology, University Medical Center Freiburg

summary: We show strong activation of TEs in the context of DNA virus infection and investigate the molecular mechanisms of how TEs are induced. We demonstrate that herpesvirus infection leads to a robust expression of the MLT and THE1-class of LTR containing retrotransposons as well as a subset of long-interspersed nuclear elements-1 (LINEs), Alu-elements and some HERVs. Mechanistically we demonstrate that this TEs upregulation is induced by two pathways that act synergistically: de-repression of KAP1/TRIM28 mediated by phosphorylation and expression of the pioneer factor double-homeobox 4 (DUX4).

overall_design: RNA-sequencing was performed from HCMV,KSHV infection and DUX OE; CUT&RUN was performed from HSV-1 infection.

first: Jiang

last: Tan

first: Vedran

last: Franke

first: Eva

last: Neugebauer

first: Justine

last: Lagisquet

first: Anna

last: Katharina Kuderna

first: Stephanie

last: Walter

first: Armin

last: Ensser

first: Markus

last: Landthaler

first: Thomas

last: Stamminger

last: Gramberg

first: Altuna

last: Akalin

first: Emanuel

last: Wyler


title: Single-Cell RNA Sequencing of Galt Gene-Edited Mouse Lung Tissue

city: Guilin

first: Honghao

last: Yu

address: Guilin Medical College, Lingui District, Guilin City, Guangxi

institute: Guilin Medical University

summary: This dataset contains single-cell RNA sequencing data from lung tissues of Galt gene-edited (GAL) mice and wild-type (WT) mice.  The samples were collected for the investigation of molecular changes induced by Galt gene mutations, specifically focusing on lung injury.  The dataset includes gene expression profiles of individual cells and enables the study of cell-type-specific responses, immune cell changes, and alterations in key cellular pathways.  This dataset is useful for further understanding the pathophysiology of lung injury associated with Galt gene mutations and provides a resource for research into the molecular mechanisms of galactosemia.

overall_design: Lung tissues from Galt gene-edited (GAL) and wild-type (WT) mice were collected, and single cells were isolated for RNA sequencing. The single-cell suspension was processed using the SeekOne® Digital Droplet Single Cell Library Kit, followed by sequencing on the Illumina NovaSeq 6000 platform.

first: Pengpeng

last: Yue

first: Zhihao

last: Li

first: Haobo

last: Wang

first: Yong

first: Lantao

last: Gu

first: Can

last: Fu


title: Disruption of the Wnt-antagonist APC in the pituitary stem cells drives adamantinomatous craniopharyngioma

first: Carles

last: Gaston-Massuet

address: Charterhouse Sq

department: Endocrinology

institute: Queen Mary University  of London

summary: Adamantinomatous craniopharyngioma (aPCs) are complex intracranial neoplasms that arise in the sellar or parasellar region affecting the endocrine system and leading to severe comorbidities. Activating mutations resulting in degradation resistant from of  b-Catenin (CTNNB1 gene) have been shown to be the main driver for a large proportion of these neoplasms. However, the underlying genetic driver for a proportion of these tumours is still unknown. Using murine transgenic models, we show that genetic deletion of the Wnt-antagonist and tumour suppressor, Adenomatous Polyposis Coli (Apc) within the pituitary progenitors/stem cells leads to pituitary tumours that closely resemble human aCPs. These tumours present classical histopathological hallmarks of aCPs such as clusters of accumulating nuclear b-catenin that are slow dividing and undergo secretory phenotype. These tumours present wet keratin, stellar-reticular-like structures and cystic components. We show that a hypomorphic allele of Apc is sufficient for tumour development indicating that disruption of Apc function can lead to aCP formation independent of b-Catenin mutations. Moreover, we identify that bi-allelic loss of Apc in the Sox2+ve pituitary stem cells is sufficient to initiate tumour formation, indicating that Sox2+ve stem cells are the cell origin of these Apc-driven tumours. Transcriptomic analyses of early tumour-initiating cells reveal that clusters of accumulating b-Catenin, undergo p21-mediated cellular senescence and that the secretory phenotype is composed of inflammasome, angiosome and developmental growth factors which are different from the   b-Catenin-driven aCP tumours. Our data, unequivocally shows, that disruption of the tumour suppressor Apc in the pituitary progenitors/stem cells is a main driver of aCPs independent of mutations in b-Catenin. We provide two novel murine models that represents a genetic subtype of aCPs which helps to further understand aCP pathogenesis.

overall_design: Transcriptomic analyses comparing FAC-sorted purified APC-mutant cells compared to wildtype pituitary stem cells to identify the gene regulatory network downstream of oncogenic APC in pituitary tumours


title: Nuclei isolation from frozen heart tissues through an easy-to-operating, prompt, and inexpensive method for single-nucleus Multiome-seq

city: Duarte

first: Zhao

address: 1500 E Duarte Rd

department: Diabetes and Cancer Metabolism

institute: City of Hope

summary: Existing protocols are difficult to obtain high-quality sequencing data for isolating nuclei from long-term cryopreserved frozen tissues, especially such as hearts that contain rich fibrous connective tissue for single-nucleus multiome sequencing (snMultiome-seq, including snRNA-seq and snATAC-seq for the same nucleus). Here, we optimize some current methods for isolating nuclei from frozen tissues and describe an easy-to-operating, prompt, and inexpensive method for obtaining high-quality single-nucleus sequencing data, which is named as Douncer-Filter-Gradient-Centrifugation (DFGC). This protocol takes about 1.5h to complete, including mincing (1min), douncing (3min), filtering (20min) and density gradient centrifugating (40min), depending on how many samples are done at the same time, and does not require special reagents and instruments, so it is versatile and economical for most laboratories. We selected two commonly used isolating nuclei methods, microBeads- and FACS-, as controls and all analysis processes are carried out in accordance with unified standardization, including nucleus morphology, library construction, library quality inspection, data parameters, clustering, cell-type identification, and gene expression distribution. This protocol provides a step-by-step guide to nuclei isolating from frozen heart tissues to generate high-quality single nucleus gene expression and chromatin transposase accessibility sequencing data for the same nucleus.

overall_design: We isolated nuclei from the frozen heart tissues of C57BL/6J mice with three different protocols to examine the quality differences.

first: Yin

first: Di

last: Ren

first: June-Wha

last: Rhee

middle: V


title: Viruses hijack FPN1 to disrupt iron withholding and suppress host defense

city: 济南

first: 辉

middle: 家

last: 僮

address: 济南趵突泉街道文化西路44号

institute: 山东大学

summary: Iron withholding controls infections by limiting the pathogens’ access to iron from the host. Viruses directly utilize intracellular materials, including iron, to complete their life cycles. Emerging evidence suggests the importance of withholding iron in limiting viral infections. However, the mechanisms through which viruses disrupt host iron homeostasis and the impact of intracellular iron on the host’s antiviral defense remain unknown. Here we show that viral infections facilitate the polyubiquitination and degradation of ferroportin (FPN1, the only cellular iron exporter) by upregulating the host E3 ubiquitin ligase DTX3L, leading to an elevation in cellular iron levels. Excessive ferrous suppresses type I IFN responses and autophagy by promoting TBK1 hydroxylation and STING carbonylation in macrophages. FPN1 deficiency suppresses host antiviral defense and facilitates viral replication in vitro and in vivo, while DTX3L deficiency has the opposite effect. These results reveal that viruses hijack host FPN1 to disrupt iron withholding and achieve immune escape, and suggest that iron homeostasis maintained by FPN1 is required for the optimal activation of TBK1- and STING-dependent antiviral responses.

overall_design: To investigate the mechanism of iron restriction in the host, we performed gene expression profiling ananlysis using data obtained from RNA-seq of macrophages at 3 viral infections situation.

first: Li

last: Tong

first: Chunyuan

last: Zhao

first: Wei

first: Chengjiang

last: Gao


title: PCYT2 inhibits epithelial-to-mesenchymal transition in colorectal cancer by elevating YAP1 phosphorylation

city: 四川省

first: SU

last: ZHANG

address: 四川省成都市武侯区人民南路三段17号

institute: 四川大学

summary: Metabolic reprogramming is a common feature in tumor progression and metastasis. Like proteins, lipids can transduce signals through lipid-protein interactions. During tumor initiation and metastasis, dysregulation of the Hippo pathway plays a critical role. Specifically, the inhibition of YAP1 phosphorylation leads to the relocation of YAP1 to the nucleus to activate transcription of genes involved in metastasis. Although recent studies reveal the involvement of phosphatidylethanolamine (PE) synthesis enzyme phosphoethanolamine cytidylyltransferase 2 (PCYT2) in tumor chemoresistance, the impact of PCYT2 on tumor metastasis remains elusive. Here, we showed that PCYT2 was significantly downregulated in metastatic colorectal cancer (CRC) and acted as a tumor metastasis suppressor. Mechanistically, PCYT2 increased the interaction between PEBP1 and YAP1-phosphatase PPP2R1A, thus disrupting PPP2R1A-YAP1 association. As a result, phosphorylated-YAP1 levels were increased, leading to YAP1 degradation through the ubiquitin protease pathway. YAP1 reduction in the nucleus repressed the transcription of ZEB1 and Snail2, eventually resulting in metastasis suppression. Our work provides insight into the role of PE synthesis in regulating metastasis and presents PCYT2 as a potential therapeutic target for CRC.

overall_design: In order to find downstream genes related to PCYT2 in colorectal cancer, we knocked down PCYT2 in SW480 and performed RNA-seq. The experiment was designed into 3 groups, namely shNT, shPcyt2-1, shPcyt2-2, with 2 replicates in each group.

first: Lian

last: Zhou

first: Su

last: Zhang

first: Lingli

first: Xueqing

last: Liu

first: Xuyang

last: Yang

first: Lei

last: Qiu

first: Ying

first: Qing

last: Huang

first: Yang

last: Meng

first: Xue

last: Lei

first: Linda

last: Wen

first: Junhong

last: Han


title: Effect of LGP2 in the development of glioma [ChIP-seq]

city: 上海

first: 晋

last: 李

address: 上海市徐汇区东安路130号复旦大学上海医学院

institute: 复旦大学基础医学院药理学系

summary: To investigate the function LGP2 in the regulation of tumor progression and development, we established 2 T98G  cell lines in which LGP2 gene has been overexpressed.

overall_design: Comparative gene expression profiling analysis of CHIP-seq data for T98G cells and its OE derivatives (OE-LGP2)

first: Minfeng

last: Shu

first: Bowen

last: Yin


title: Effect of LGP2 in the development of glioma [RNA-seq]

address: 上海市徐汇区东安路130号复旦大学上海医学院

institute: 复旦大学基础医学院药理学系

overall_design: Comparative gene expression profiling analysis of RNA-seq data for T98G cells and its OE derivatives (OE-LGP2)


title: Embryo-derived macrophages are more proliferative and resistant to cell death than monocyte-derived macrophages even after ex vivo expansion [ATAC-seq]

city: Kumamoto

first: Naofumi

last: Takahashi

address: 2-2-1 Honjo, Chuo-ku

country: Japan

institute: Kumamoto University

summary: Tissue macrophages have been thought to be maintained by the differentiation of bone marrow-derived monocytes. However, recent studies have revealed that embryo-derived macrophages persist in many adult tissues, presumably due to their high self-renewing capacity. Here, we show that yolk sac-derived macrophages are more proliferative and resistant to cell death than monocyte-derived macrophages even after ex vivo expansion. The self-renewing macrophages were expanded from mouse bone marrow (BM), fetal liver (FL), or yolk sac (YS), by the long-term culture. Their phenotypes were overlapped but not identical. All of them stably proliferated in unlimited numbers, in the presence of the cytokine M-CSF. However, the proliferation speed of YS lines was the fastest and that of BM lines was the slowest. Moreover, YS and FL lines were more resistant to cell death caused by M-CSF-depletion or two apoptosis-inducers than BM lines. In line with these phenotypic similarity and difference, YS and FL lines were relatively similar in gene expression and chromatin accessibility whereas YS and BM lines showed the most distinct profiles. Furthermore, after transfer into mice, the YS line restores the high expression level of the core cell surface markers of embryonic macrophages that was lost during the long-term culture. These results suggest that ex vivo-expanded self-renewing macrophages are convenient and useful models, and provide a new opportunity for mechanistic analysis of macrophage self-renewal.

overall_design: genomic DNA was extracted from self-renewing macrophage for ATAC-seq

first: Sara

last: Habash

first: Randa

last: Abdelnaser

first: Youssef

last: Eltalkhawy

first: Hiromi

last: Aoki-Ogata

first: Seiji

last: Okada

first: Hiroshi

last: Takizawa

first: Shingo

last: Usuki

first: Kan

last: Etoh

first: Shinjiro

last: Hino

first: Saori

last: Morino-Koga

first: Minetaro

last: Ogawa

first: Shinya

last: Suzu


title: PTBP1 Regulates DNMT3B Alternative Splicing by Interacting with RALY to Enhance the Radioresistance of Prostate Cancer

city: Guangzhou

first: Qianghua

last: Zhou

address: Urology

institute: Sun yat-sen memorial hospital

summary: Radiotherapy is a curative arsenal for prostate cancer (PCa), but radioresistance seriously compromises its effectiveness. Dysregulated RNA splicing factors are extensively involved in tumor progression. Nonetheless, the role of splicing factors in radioresistance remains largely unexplored in PCa. Here, we identified 23 splicing factors that are differentially expressed between PCa and adjacent normal tissues across multiple public PCa databases. Among those genes, polypyrimidine tract binding protein 1 (PTBP1) was significantly upregulated in PCa and was positively associated with advanced clinicopathological features and poor prognosis. Gain- and loss-of-function experiments demonstrated that PTBP1 markedly reinforced genomic DNA stability to desensitize PCa cells to irradiation in vitro and in vivo. Mechanistically, PTBP1 interacted with the HnRNP associated with lethal yellow protein homolog (RALY) and regulated exon 5 splicing of methyltransferase 3b (DNMT3B) from DNMT3B-S to DNMT3B-L. Furthermore, upregulation of DNMT3B-L induced promoter methylation of dual-specificity phosphatase-2 (DUSP2) and subsequently inhibited DUSP2 expression, thereby increasing radioresistance in PCa. Our findings highlight the role of splicing factors in inducing aberrant splicing events in response to radiotherapy and the potential role of PTBP1 and DNMT3B-L in reversing radioresistance in PCa.

overall_design: Prostate cancer cell line DU145 was transfected with the contol siRNA, PTBP1 siRNA  or DNMT3B-L siRNA for 48h, respectively. The RNA of the treated cells was extracted and sequenced on Illumina HiSeq 2500 platform and 100-bp paired-end reads were generated.

first: Haixia

last: He

first: Tianxin

last: Lin

first: Xu

last: Chen


title: RNA-seq analysis using A549 cells with TRIM22 knockdown and control A549 cells with or without ionizing radiation treatment.

first: Li

last: Xinyan

address: No.17, Panjiayuan Nanli, Chaoyang District, Beijing

institute: Cancer Hospital Chinese Academy of Medical Sciences

summary: In this study, we explored the role of TRIM22 in the response to ionizing radiation (IR) in A549 human lung cancer cells. TRIM22 was stably knocked down in A549 cells using shRNA, and four experimental groups were established: control A549 cells (non-irradiated), control A549 cells (irradiated), TRIM22 knockdown A549 cells (non-irradiated), and TRIM22 knockdown A549 cells (irradiated). RNA sequencing (RNA-seq) was performed to identify gene expression changes associated with TRIM22 knockdown and irradiation. This dataset provides insights into the molecular mechanisms by which TRIM22 influences the cellular response to radiation and its potential impact on cancer therapy.

overall_design: The experiment was designed to investigate the impact of TRIM22 knockdown on the gene expression profile of A549 cells following ionizing radiation. A549 cells were stably transfected with shRNA targeting TRIM22 or a control shRNA. The experiment included four groups: (1) control A549 cells without irradiation, (2) control A549 cells exposed to irradiation, (3) TRIM22 knockdown A549 cells without irradiation, and (4) TRIM22 knockdown A549 cells exposed to irradiation.Each group included three biological replicates, totaling 12 samples. RNA was extracted from all 12 samples and subjected to RNA sequencing to compare the transcriptomic changes induced by TRIM22 knockdown and ionizing radiation. This design allows for the analysis of the specific role of TRIM22 in the cellular response to radiation.

first: Xinyan

last: Li

first: Min

last: Deng


title: Embryo-derived macrophages are more proliferative and resistant to cell death than monocyte-derived macrophages even after ex vivo expansion [RNA-seq]

first: Naofumi

last: Takahashi

overall_design: Total RNA was extracted from self-renewing macrophages and sent for RNA-seq

first: Sara

last: Habash

first: Randa

last: Abdelnaser

first: Youssef

last: Eltalkhawy


title: Impact of Exposure to an Environmentally Relevant Mixture of Organophosphate Esters on the Adrenal Glands of Sprague Dawley Rats

city: Montreal

first: Zixuan

state: Quebec

address: 3655 Promenade Sir-William-Osler

institute: McGill University

summary: To investigate the gene expression changes observed with exposure to organophosphate esters in the adrenal glands of Sprague Dawley rats.

overall_design: We did RNA-sequencing analysis on the adrenal glands of both male and female rats at 4 different conditions (control, 30x OPE, 1000x OPE, 30000x OPE).

last: Zixuan

first: Hales

last: Barbara F

first: Robaire

last: Bernard


title: ChREBP-mediated choline deprivation and chemokine secretion shape TAMs to promote immune evasion

city: Wuhan

first: jianhong

last: zhao

state: Hubei

address: Donghu Road, No. 115

institute: Wuhan University

summary: Tumor metabolic reprogramming has been recognized as a critical determinant in tumor development and cancer immunotherapy. Aberrant choline metabolism is emerging as a defining hallmark of cancer. However, its impact on antitumor immunity remains largely unclear. Carbohydrate responsive element binding protein (ChREBP)-mediated choline deprivation impels tumor-associated macrophages (TAMs) reprogramming and maintains an immunosuppressive tumor microenvironment (TME). Mechanistically, ChREBP interacts with SP1 to increase the expression of immunosuppressive chemokines CCL2 and CXCL1, as well as choline transporter SLC44A1. As such, high expression of CCL2 and CXCL1 expression promotes recruitment of TAMs and MDSCs in the TME. Tumor cells with high SLC44A1 expression compete consuming choline with M1-like TAMs, inhibiting cGAS-STING signaling and promoting the polarization of M1 to M2 macrophages. Clinically, ChREBP-SP1-choline metabolism axis expression is associated with poor clinical outcome in CRC. Inhibiting ChREBP reduces M2-like TAMs and MDSCs to enhance anti-tumor immunity, suggesting ChREBP as a potential immunotherapy target in cancer.

overall_design:
To elucidate the mechanisms underlying ChREBP-mediated antitumor immunity, we subjected shNC and Chrebp-deficient MC38 tumors (in C57BL/6 mice) to RNA sequencing (RNA-Seq).
BMDMs were incubated with LPS and IFN-γ for 4 h, followed by treatment with fresh RPMI-1640 containing 200 μM choline for 24 h.
Comparative gene expression profiling analysis of RNA-seg data for tumor tissues (from shNC/shChrebp MC38-bearing C57BL/6 mice).

first: Jianhong

last: Zhao

first: Baoxiang

first: Yanrong

first: Lifang

last: Fan

first: Siyuan

last: Yin

first: Haisheng

last: Yu

first: Yongchang

last: Wei

first: Jing

last: Dai

first: Qun

last: Qian

first: Quanjiao

first: Xianghai

last: Ren

first: Xiaoyu

last: Xie

first: Wenyi

first: Jinfang

last: Zhang

first: Congqing

last: Jiang


title: Conjugation of dn-OPDA with amino acids inhibits its hormonal bioactivity in Marchantia polymorpha

city: Madrid

first: Salvador

last: Torres Montilla

address: Calle Darwin, 3

country: Spain

institute: Centro Nacional de Biotecnologia

summary: Jasmonates are important phytohormones activating plant tolerance to biotic and abiotic stress, as well as different development processes. These responses are mediated by a conserved signalling pathway activated by different hormones in different plants: dinor-12-oxo-phytodienoic acid (dn-OPDA) isomers in bryophytes and lycophytes, and JA-Ile in most vascular plants. The final responses depend, in many cases, on the accumulation of secondary metabolites. To identify novel compounds regulated by the dn-OPDA pathway in Marchantia, untargeted metabolomic analyses were carried out in response to dn-OPDA-regulated stress. A novel group of molecules were identified as dn-OPDA-amino acid conjugates (dn-OPDA-aas), and its accumulation after wounding and herbivory confirmed by targeted metabolic profiling in Marchantia and all species in which we previously found dn-iso-OPDA. Mutants in GRETCHEN-HAGEN 3A (MpGH3A) failed to accumulate dn-OPDA-aa conjugates, and showed a constitutive activation of the OPDA pathway and increased resistance to herbivory. Our results show that dn-iso-OPDA bioactivity is reduced by conjugation with amino acids. Therefore, an apparent dichotomous role of jasmonate conjugation in land plants is highlighted: jasmonic acid (JA) conjugation with isoleucine (Ile) produce the bioactive JA-Ile in tracheophytes, whereas conjugation of dn-iso-OPDA with different amino acids disactivate the hormone in bryophytes and lycophytes.

overall_design: To study the effect of MpGH3a gene in Marchantia polymorpha, we generated CRISPR-Cas9 nickase-mediated mutagenesis on this gene as target.

first: Wenting

last: Liang

first: Angel

last: Zamarreño

last: Torres-Montilla

first: Antonio

last: de la Torre

first: Jean

middle: C

last: Totozafy

first: Takuya

last: Kaji

first: Minoru

last: Ueda

first: Massimiliano

last: Corso

first: JM

last: García-Mina

first: Roberto

last: Solano

first: Andrea

last: Chini


title: Excessive Antioxidant Activity Impedes Neonatal Cardiomyocyte Regeneration

city: Charleston

first: Allison

last: Trouten

state: SC

address: 173 Ashley Ave Room BSB 642

department: Regenerative Medicine and Cell Biology

institute: Medical University of South Carolina

summary: Significance Heart disease accounts for 1 in 4 deaths in the United States annually, making it one of the leading causes of death and related morbidity resents a significant economic burden. Mammalian cardiomyocytes are terminally differentiated with low turnover rate, insufficient to repopulate myocardium after heart attack caused by myocardial infarction (MI). As such, there is an urgent need for the development of non-invasive, effective, and efficient therapeutic approaches for treating MI. One strategy is to promote proliferation in mature cardiomyocytes, inspired by the observation of a transient regenerative window in neonatal mouse cardiomyocytes. During postnatal development, it is believed that cardiomyocytes exit cell cycle in response to high oxygen environment and a metabolic shift to oxidative phosphorylation. Strategies to lower oxidative stress in neonatal mouse hearts to prolong regenerative time window have been reported. While many studies have focused on mitigating injury-related ROS, it is not clear whether the developmental ROS increase in neonatal cardiomyocytes plays a role during postnatal myocardial maturation and establishment of injury response. The following study details the crucial role of neonatal ROS as signaling molecules in cardiomyocyte injury response after MI.

overall_design: Mouse pups were treated with N-acetylcysteine (NAC) or saline P0-P1 before MI or sham surgery at P2. At P3, cardiomyocytes were isolated by enzymatic digestion of pooled whole ventricular tissue followed by selection via a neonatal cardiomyocyte isolation kit.  Three replicates were included per group to understand the transcriptomic differences of NAC treat in an uninjured and injured state.

first: Min

first: Ge

last: Tao


title: Potential developmental neurotoxicity of short-chain di-n-alkyl phthalates and their mixtures to neurospheres derived from human neural progenitor cell lines

city: Daejeon

first: Soontag

last: Jung

address: 141 Gajeong-ro, Yuseong-gu

department: Developmental and reproductive toxicology

country: South Korea

institute: Korea Institute of Toxicology

summary: Short-chain phthalates (SCPs), are commonly found in personal care products (PCPs) as solvents, leading to complex human exposures. PCPs are primarily utilized by women, with heightened usage during pregnancy. While SCPs absorbed through the skin can traverse the placenta, their potential for developmental neurotoxicity (DNT) remains inadequately investigated. This study evaluated the impacts of single and combined SCP exposures to assess proliferation, migration, differentiation, and neurite outgrowth in human neural progenitor cell lines. Three individual SCPs—diethyl phthalate (DEP, 46.9% ± 7.55%), dipropyl phthalate (DPrP, 64.2% ± 7.16%), and dipentyl phthalate (DPP, 31.9% ± 9.10%)—significantly reduced only neurite outgrowth at 100uM100 μM compared to the vehicle control. The equimolar-mixture of these SCPs (Mix) also showed a similar reduction (57.5% ± 2.46%). In RNA-seq analysis, DEP, DPrP, DPP, and Mix treatments identified neurite outgrowth inhibition related 720 common DEGs showing the functional annotations most strongly enrichimentenrichment associated with oxidative phosphorylation. Additionally, individual SCPs and Mix significantly reduced mitochondrial ATP production and were able to bind to mitochondrial respiratory complexes I, III, IV, and V, as confirmed by docking analysis. Treatment with exogenous ATP and vitamin B complex could restore the inhibition of neurite outgrowth caused by SCP exposure. In conclusion, this study identified the possibility that SCPs induce DNT by interfering with mitochondrial energy metabolism, with similar effects observed even in mixtures with low individual concentrations. Future research is needed to evaluate the cumulative effects of SCPs.

overall_design: This study aimed to investigate the potential developmental neurotoxicity (DNT) of SCPs exposure in vitro. Among the various SCPs, we focused on DEP, which is commonly used in PCPs, and di-n-alkyl phthalate, a linear phthalate similar to DEP but differing only in the number of carbon atoms. In this study, we investigated the DNT of chemicals using a neurosphere Assay. This assay relies on human neural stem cells (hNPCs) and is an important part of an in vitro test battery recommended by the OECD to assess DNT hazards. The neurosphere assay helps assess potential hazards of chemicals to developing brains by evaluating key events (KE) in neural development, such as NPC proliferation (NPC1), NPC migration (NPC2), neuronal differentiation (NPC3), neurite outgrowth (NPC4), and oligodendrocyte differentiation (NPC5). Here, we replaced the original use of primary hNPCs with an ReNcell VM, an NPC line. This change was made to improve the ease of obtaining cells, ensure consistent results between experiments, and make the testing process more manageable. Given that humans are exposed to multiple phthalates simultaneously, individual SCPs and composite SCPs were assessed to understand the mechanisms involved in SCP-induced DNT.

first: Yixian

last: Quah

first: Onju

last: Ham

first: Seung-Jin

last: Lee

first: Wook-Joon

last: Yu


title: Two distinct chromatin modules regulate proinflammatory gene expression [ChIP-seq]

city: Heidelberg

first: Isabelle

last: Seufert

address: Im Neuenheimer Feld 280

institute: DKFZ

summary: Various mechanisms have been proposed to explain gene activation and co-regulation, including enhancer-promoter interactions via chromatin looping and the enrichment of transcription factors into hubs or condensates. However, these conclusions often stem from analyses of individual loci, and genome-wide studies exploring mechanistic differences in coupled gene expression are lacking. In this study, we dissected the proinflammatory gene expression program induced by TNFα in primary human endothelial cells using NGS- and imaging-based techniques. Our findings, enabled by our novel RWireX approach for single-cell ATAC-seq analysis, revealed two distinct regulatory chromatin modules: autonomous links of co-accessibility (ACs) between separated sites, and domains of contiguous co-accessibility (DCs) with increased local transcription factor binding. ACs and DCs associate with different transcriptional bursting kinetics, highlighting the existence of two structurally and functionally distinct regulatory chromatin modules in proinflammatory response. This identification provides a novel mechanistic framework for understanding how cells achieve both rapid and precise control of gene expression.

first: Panagiotis

last: Liakopoulos

first: Petros

last: Kolovos

first: Argyris

last: Papantonis

first: Karsten

last: Rippe


title: Platelets Transfer Aldolase via Extracellular Vesicles to Facilitate the Metabolic Reprogramming of Kupffer Cells in Acute Liver Injury

city: Kunming

first: Xue

middle: Ruo

last: Yang

address: Wujiaying Street, Chenggong District, Kunming, Yunnan

institute: Yunnan university

summary: The interaction between Kupffer cells and platelets has been observed in various liver diseases, yet the specific effects of platelets on Kupffer cells remain poorly understood. This study aims to investigate the impact of platelets on Kupffer cells and their implications in acute liver injury.

overall_design: Kupffer cells were isolated after acetaminophen treated for different time points

first: Ruoxue


title: Two distinct chromatin modules regulate proinflammatory gene expression [snATAC]

first: Irene

last: Gerosa


title: Two distinct chromatin modules regulate proinflammatory gene expression [snRNA]


title: Intricate regulation of breast cancer stemness, self-renewal and differentiation via ERK/CDK4/6 activation by Wnt signaling

city: Bronx

first: Rachel

last: Hazan

state: Bronx

address: 1300 Morris Park Ave

department: Pathology

institute: Albert Einstein College of Medicine

summary: The partial EMT program drives breast cancer stemness and metastasis. This process is governed by transcriptional regulators that maintain the epithelial/mesenchymal (E/M) bipotent stem cell state and by differential growth factor signaling driving self-renewal vs differentiation. Here we show that TCF1/Wnt signaling stimulates transient ERK/CDK4/6 activation which upregulates FOXC2,  and in turn TAp63 and ΔNp63 isoforms, thereby maintaining the partial EMT state.  In parallel, ERK/CDK4/6 promotes FOXC2 expression and S-phase transition while activating FOXM1 to drive E/M cell self-renewal. Interestingly, transient ERK activation by Wnt3a inactivates EGFR, thus preventing EGF from causing a robust and sustained ERK phosphorylation that causes E/M to M differentiation, resulting in CSC exhaustion. Consistent with these data, ERK/CDK4/6 inhibition suppressed CSC organoid forming ability. Collectively, these findings illustrate an intricate mechanism integrating cancer stemness with self-renewal and differentiation via Wnt-stimulated ERK/CDK4/6 activation, underscoring the implication of these findings for cancer stem cell therapy.

overall_design: To elucidate novel transcriptional regulators of the intermediate EMT state, we performed RNA sequencing comparing MDA-MB-468 bulk to E/M and M subpopulations sorted by CD104/CD44 expression.

first: Huizhi

last: Liang

first: Outhiriaradjou

last: Benard

first: Viney

last: Kumar

first: Zuen

last: Ren

first: Kimita

last: Suyama

first: Anthony

last: Griffen

first: Jingli

last: Wang

first: Xusheng

last: Zhang

first: Jinghang

first: Lindsay

last: LaFave

first: Larry

last: Norton

middle: B


title: Two distinct chromatin modules regulate proinflammatory gene expression [scRNA]

first: Isabelle

last: Seufert


title: Two distinct chromatin modules regulate proinflammatory gene expression [snMultiome]

first: Karsten


title: Identification of miRNAs and Their Target Genes Associated with Sunitinib Response in Clear Cell Renal Cell Carcinoma Patients

city: Donostia-San Sebastián

first: María

last: Armesto

state: NorthEurope

address: Paseo Dr. Begiristain s/n

department: Molecular Oncology

institute: IIS Biogipuzkoa

type:
Expression profiling by array
Non-coding RNA profiling by array

summary:
clariom D and miRNA v4.0 microarray analyses of FFPE-RNA   from ccRCC cases: sunitinib responders and non responders
we used intergrated pathway network analysis to identify miRNA-target gene pairs involved in the response to sunitinib treatment

platform_organism:
Homo sapiens
synthetic construct

overall_design: The gene and miRNA expression was studied in sunitinib responders and non-responders to provide a better understanding of the mechanisms behind sunitinib resistance and to identify potential candidates as biomarkers of treatment response

first: Charles

last: Lawrie


title: DNA damage drives DNA methylation generation and evolution in plant [BiSulfite-seq]

city: Shanghai

first: wenjie

last: liang

address: Guoquan North Road

institute: Fudan university

type: Methylation profiling by high throughput sequencing

summary: In mammals, it has long been hypothesized that DNA damage could induce DNA hypermethylation and contribute to carcinogenesis. However, the evidence that DNA damage is a cause of genome hypermethylation is still insufficient. Here, we demonstrated that, in plant, DNA damage can induce DNA hypermethylation in the context of symmetric CG, CHG as well as asymmetric CHH. Mechanically, DNA damage regulates the DREAM complex, to induce CG and CHG methylation. Moreover, DNA damage also utilizes the RdDM pathway to induce CHH hypermethylation. The hypermethylation sites of CG and CHG resulting from DNA damage tend to localize to gene body, and a large proportion of them are de nove generated. In contrast, the hypermethylation sites of CHH induced by DNA damage were mainly concentrated in the centromere and pre-centromere regions, and most of them are amplification of existing CHH methylation. Importantly, withdrawing the DNA damage or blocking the DNA damage response signal could fully abolish the CHH hypermethylation, partially rescue the CHG hypermethylation, but rarely recover the CG hypermethylation, indicating that DNA damage leaves symmetric DNA methylation as genetic imprinting. Collectively, our results suggest that DNA damage drives DNA methylation generation and evolution in plants.

overall_design: whole genome bisulfite sequencing of seedlings total DNA from different arabidopsis thaliana samples cultured for 14 days

first: Jinchao

last: Li

first: Wenjie

first: Weiqiang

last: Qian


title: Two distinct chromatin modules regulate proinflammatory gene expression

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

overall_design: Refer to individual Series


title: Prediabetes is associated with musculoskeletal dysfunction independent of total body adiposity

city: Columbia

first: Bettina

last: Mittendorfer

state: MO

address: 1030 Hitt St, 3rd floor

department: Nutrition and Exercise Physiology

institute: University of Missouri - Columbia

summary: It has been proposed that there is a direct pathophysiological link between metabolic dysfunction and musculoskeletal degeneration in people with obesity but direct evidence for this proposition is lacking. We performed a comprehensive assessment of musculoskeletal status in people with obesity and prediabetes and a control group of sex-, age- and adiposity-matched participants with normoglycemia. We find muscle mass and bone mineral density scores, muscle growth markers, myofiber size, myofiber capillarization, and muscle type 2 macrophage content are lower, and intramyocellular lipid, but not inter- or intra-muscular adipose tissue, content are higher in people with prediabetes compared with the control group. Moreover, muscle strength during repeated maximum voluntary contractions declines faster in people with prediabetes. These findings demonstrate a close interrelationship between metabolic and musculoskeletal dysfunction in people with obesity and have direct clinical implications, because greater muscle fatigability in people with prediabetes may present a barrier to physical activity.

overall_design:
We enrolled 30 human subjects (normoglycemic and prediabetic obese) to evaluate putative muscle factors that can affect muscle mass and strength (Cross-sectional study). All participants had muscle biopsies performed and also had functional tests performed to evaluate muscle strength and fatigability.
Muscle biopsy samples were then submitted for RNAseq, proteomics, and histology procedures in order to have a comprehensive view of global alterations of muscle proteostasis.

first: Alan

last: Fappi

first: Clifton

middle: J

last: Holmes

first: Chao

last: Cao

first: Vasavi

last: Shabrish

first: Aman

middle: P

last: Aher

first: Karen

last: Shen

first: Gretchen

last: Meyer

first: Paul

middle: K

last: Commean

first: Dwight

last: Towler

first: Dominic

middle: N

last: Reeds


title: DNA damage drives DNA methylation generation and evolution in plant [RNA-seq]

overall_design: RNA_seq of seedlings polyA RNA from different arabidopsis thaliana samples cultured for 14 days

last: Liang


title: Efficient and economical iron metabolism of Aspergillus fumigatus protects its mitochondria in the absence of Mn-superoxide dismutase

city: Debrecen

first: Tamas

last: Emri

address: Egyetem ter 1

country: Hungary

institute: University of Debrecen

summary: The importance of manganese superoxide dismutase (Mn-SOD), an evolutionarily ancient metalloenzyme maintaining the integrity and functions of mitochondria, was studied in oxidative stress treated Aspergillus fumigatus cultures. Deletion of the Mn-SOD gene (sodB) increased both the menadione sodium bisulfite (MSB) elicited oxidative stress, and the deferiprone (DFP) induced iron limitation stress sensitivity of the strain. Moreover, DFP treatment enhanced the MSB sensitivity of both the gene deletion mutant and the reference strain. Concurring with these results, RNS sequencing data also demonstrated that deletion of sodB largely altered the MSB induced oxidative stress response. The difference between the oxidative stress responses of the two strains manifested mainly in the intensity of the response. Importantly, upregulation of “Ribosome protein”, “Iron uptake”, and Fe-S cluster assembly” genes, alterations in the transcription of “Fe-S cluster protein” genes, downregulation of “Heme binding protein” genes under MSB stress were characteristic for only the DsodB gene deletion mutant. We assume that the elevated superoxide level generated by MSB treatment may have destroyed Fe-S cluster proteins of mitochondria in the absence of SodB mediated protection. Re-synthesis of Fe-S cluster proteins enhanced translation and increased iron demand changing iron metabolism and increasing DFP sensitivity considerably.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for mycelia of Aspergillus fumigatus reference strain, and DsodB mutant under menadione sodium bisulfite (MSB) treated and untreated conditions with three biological replicates.

first: Klaudia

last: Pákozdi

first: Tamás

first: Károly

last: Antal

first: István

last: Pócsi


title: Myelin regulatory factor (Myrf) is a critical early regulator of retinal pigment epithelial development [P0 scRNA-seq]

city: Ann Arbor

first: Lev

last: Prasov

state: MI

address: 1241 Catherine Street, 5704 Med Sci II

department: Department of Human Genetics

institute: University of Michigan

summary: Myelin regulatory factor (Myrf) is a critical transcription factor in early retinal and retinal pigment epithelial development, and human variants in MYRF are a cause for nanophthalmos. Single cell RNA sequencing (scRNAseq) was performed on Myrf conditional knockout mice (Rx>Cre Myrffl/fl) at 3 developmental timepoints. Myrf was expressed specifically in the RPE, and expression was abrogated in Rx>Cre Myrffl/fl eyes. scRNAseq analysis revealed a loss of RPE cells at all timepoints resulting from cell death.  GO-term analysis in the RPE revealed downregulation of melanogenesis and anatomic structure morphogenesis pathways, which were supported by electron microscopy and histologic analysis. Novel structural target genes including Ermn and Upk3b, along with macular degeneration and inherited retinal disease genes were identified as downregulated, and a strong upregulation of TGFß/BMP signaling and effectors was observed.  Regulon analysis placed Myrf downstream of Pax6 and Mitf and upstream of Sox10 in RPE differentiation. Together, these results suggest a strong role for Myrf in the RPE maturation by regulating melanogenesis, cell survival, and cell structure, in part acting through suppression of TGFß signaling and activation of Sox10.

overall_design: Eyes were collected from e13.5, e15.5, and P0 litters, the cornea, lens, and optic nerve were removed.  Three Myrffl/fl and three Rx>cre Myrffl/fl samples were pooled for each time point, dissociated, and scRNAseq was performed.

first: Michelle

middle: L

last: Brinkmeier

first: SuQing

last: Wang

first: Hannah

last: Pittman

first: Leonard

middle: Y

last: Cheung


title: Comparative analysis of chromatin accessibility during chondrogenesis and in osteoarthritis

city: Newcastle upon Tyne

first: Matt

last: Barter

address: International Centre For Life

institute: Newcastle University

summary: To reveal the organisation of the cartilage cell chondrocyte genome and identify changes that occur within this organisation during development and due to osteoarthritis (OA).  Methods  Assay for Transposase -Accessible Chromatin using Sequencing (ATAC-seq) was performed on chondrocytes isolated from 16 patients undergoing total hip replacement because of OA (n=7) or due to a neck of femur fracture (NOF, n=9). ATAC-seq was similarly performed on bone-marrow mesenchymal stem cells (BM-MSC) and differentiated chondrocytes of two donors. DNA sequence reads (av. 50 million/sample) were aligned to human genome Hg38. Peaks were called using MACS2 and differential accessibility identified by DiffBind. Interexperiment comparisons and intersection with published gene expression changes, chondrogenesis ChIP-seq, knee ATAC-seq and human tissue scATAC-seq were performed in Galaxy and R. OA GWAS signal regions were overlapped with our defined chondrocyte ATAC-seq peaks.   Results  In BM-MSC and derived chondrocytes we mapped 138005 open chromatin regions, of which 20979 and 50699 significantly increased and decreased respectively during cell differentiation. In hip chondrocytes we identified 115295 open chromatin regions, 1383 and 573 were more or less differentially accessible respectively when comparing OA with NOF samples. In both data sets ‘newly accessible regions were enriched at enhancer regions (defined by ChIP-seq). Comparing the data with the ATAC-seq from the single cell ATLAS we identified 11866 open regions exclusive to chondrocytes. Genes associated with these regions were significantly enriched for cartilage-related gene ontology terms. Taking the 420 OA GWAS signals present in the GWAS catalogue, 313 of the OA regions (defined as lead SNP + proxy SNPs with r2 ≥ 0.8) overlapped with a chondrocyte ATAC-seq region.   Conclusions  Here we have mapped chromatin accessible region changes during chondrogenesis, showing that newly accessible regions are enriched at enhancer regions and positively correlate with gene expression. Open chromatin region changes between OA and NOF cartilage were fewer, and peak differences were subtle. Overall, we have associated OA GWAS loci with accessible regions and defined regions of the genome specific to cartilage and chondrogenesis.

overall_design: To reveal the organisation of the cartilage cell chondrocyte genome and identify changes that occur within this organisation during development and due to osteoarthritis (OA). Assay for Transposase -Accessible Chromatin using Sequencing (ATAC-seq) was performed on chondrocytes isolated from 16 patients undergoing total hip replacement because of OA (n=7) or due to a neck of femur fracture (NOF, n=9). ATAC-seq was similarly performed on bone-marrow mesenchymal stem cells (BM-MSC) and differentiated chondrocytes of two donors

first: David

last: Young


title: Myelin regulatory factor (Myrf) is a critical early regulator of retinal pigment epithelial development [e15 scRNA-seq]


title: Myelin regulatory factor (Myrf) is a critical early regulator of retinal pigment epithelial development [e13 scRNA-seq]


title: Gliomagenesis mimics an injury response orchestrated by neural crest-like cells

city: Toronto

first: Akram

last: Hamed

department: Molecular Genetics

institute: University of Toronto

summary: The data related to this study are deposited in GSE278511 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE278511


title: SCGB2A1 deficiency impairs endometrial stromal cell decidualization by decreasing CDK3-mediated proliferation in patients with recurrent implantation failure

first: Yan

last: Zhou

address: 197 Ruijin 2nd Road

department: Department of Reproductive Medical Center

institute: Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University

summary: Recurrent implantation failure (RIF) presents a significant challenge in the field of assisted reproductive technology, primarily stemming from compromised decidualization that impacts endometrial receptivity. Despite ongoing research efforts, the comprehensive molecular regulatory mechanisms involved in RIF remain incompletely understood. This study revealed significantly reduced levels of secretoglobin, family 2A, member 1 (SCGB2A1) in both the mid-secretory endometrium and uterine fluid of RIF patients compared to control subjects. Besides, combined with RNA sequencing results, we demonstrated that the suppression of SCGB2A1 results in reduced cell proliferation and impaired decidualization by modulating CDK3 signaling during cell cycle transition in immortalized human endometrial stromal cells (T-HESCs) and primary HESCs. Furthermore, our findings indicated that inhibition of endometrial SCGB2A1 in a rat model hinders embryo implantation and disrupts decidualization. In conclusion, this study provides evidence that SCGB2A1 serves as a novel biomarker for endometrial receptivity and plays a crucial role in the regulation of human endometrial decidualization. The findings offer valuable insights into the pathogenesis of decidualization-related RIF and have the potential to enhance strategies for improving pregnancy outcomes.

overall_design: To determine the potential molecular mechanism associated with the involvement of SCGB2A1, high-throughput RNA-seq was conducted on T-HESCs transfected with siCtrl and siSCGB2A1.


title: Transcriptome analyses of Leishmania donovani promastigotes depleted of SET7 and SET29 proteins, under normal and oxidative growth environment [exp1]

city: New Delhi

first: Swati

last: Saha

state: Delhi

address: Benito Juarez Road

department: Department of Microbiology

country: India

institute: University of Delhi South Campus

summary: This study was performed with the goal of understanding the roles of Leishmania donovani SET7 and SET29 proteins in gene regulation. Using homologous recombination to knock out set7 and set29 genes, set7 and set29 mutant parasites were created. This was folllowed by transcriptome analyses of wild type parasites, set7 mutant parasites and set29 mutant parasites, that were carried out using RNA-seq.  In the first experimental set, transcriptomes of wild type parasites cultured under normal conditions as well as under hydrogen peroxide (H2O2) -induced oxidizing conditions were analysed, along with transcriptomes of set7 mutant parasites that were similarly grown under normal growth conditions as well as under H2O2-induced oxidizing conditions. Using the data obtained, the transcriptome of wild type parasites exposed to H2O2 has been compared with the transcriptome of wild type parasites grown under normal conditions. The transcriptome of set7 mutant parasites grown under H2O2-induced oxidizing conditions versus normal conditions have been similarly compared. In addition, the transcriptome of set7 mutant parasites grown under normal conditions has been compared to that of similarly grown wild type parasites. In the second experimental set, transcriptomes of wild type parasites cultured under normal growth conditions, set29 mutant parasites grown under normal conditions, as well as set29 mutant parasites grown under H2O2-induced oxidizing conditions, were analysed. Using the data obtained, the transcriptome of set29 mutant parasites grown under normal conditions has been compared to that of similarly grown wild type parasites. The transcriptome of set29 mutant parasites grown under H2O2-induced oxidizing conditions versus normal conditions have been similarly compared. Our data reveals, that knock out of set7 modulates transcription of specific clusters of genes on particular chromosomes, with almost 10 % of the total genes being regulated. On the other hand, depletion of SET29 modulates transcription of a very small set of genes distributed primarily in two clusters. This datasheet is for first experimental set.

overall_design: Two experimental sets were performed, each with two biological replicates of all samples. For transcriptome analysis, we first depleted the cells of LdSET7 and LdSET29 expression by sequentially knocking out two alleles of both the genes, which led to creation of set7-/- and set29-/-/+ cell lines. In the first experimental set, RNA was isolated  from logarithmically growing wild type and set7-/- promastigotes (two biologicals). RNA was also isolated  from logarithmically growing wild type and set7-/- promastigotes (two biologicals) that had been exposed to H2O2 (100 µM) for 5h followed by transfer of cells into fresh medium for 3 hours. In the second set of experiments, RNA was isolated  from logarithmically growing wild type and set29-/-/+ promastigotes (two biologicals). RNA was also isolated  from logarithmically growing set29-/-/+ promastigotes (two biologicals) that had been exposed to H2O2 (100 µM) for 5h followed by transfer of cells into fresh medium for 3 hours.This was followed by RNA sequencing. We then performed comparative gene expression profile analysis, among different samples. This datasheet is for first experimental set

first: Varshni

last: Sharma

first: Jyoti

last: Pal

first: Somdeb

last: Chattopadhyay

first: G.

last: Arimbasseri


title: Expression profile of p16High primary peritonal macrophages

city: Nice

first: Francisco

last: Triana-Martinez

address: 30 avenue Voie Romaine - Batiment K

country: France

institute: Institute for Research on Cancer and Aging, Nice

summary: In our laboratory, we developed a new knock-in murine model to trace p16 cells ex vivo using EGFP as a reporter gene under the control of the endogenous promoter (exon 3) of the p16 locus from the CDKN2A gene (p16-Cre/Rosa26-mtmg). We showed previously that cells positive for p16-EGFP accumulated during natural aging. We previously reported (Grosse et al, 2020) that among this cells, liver endothelial cells and macrophages from liver and other tissues are the main population going into p16 activation. We are now analyzing the characteristics of p16High tissue resident peritoneal macrophages to understant the roll they have during adulhood and aging.

overall_design:
F4/80+ macrophages from peritoneal cavity of a 1 year old mice were isolated by magnetic separation (MACS-magnetic beads). Then, the population was separated in EGFP (p16High cells) or tdTomato (p16Low cells) by fluorescence-activated cell sorting, FACS).RNA was isolated and sequencing. Comparative analysis was done comparing both population (p16high vs p16Low).
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Raw data files could not be provided for these records.
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last: Triana Martinez

first: Laurent

last: Grosse

first: Dmitry

last: Bulavin


title: Comprehensive assessment of activity, specificity, and safety of hypercompact TnpB systems for gene editing

city: Beijing

first: Changchang

last: Xin

state: Beijing

address: No.5 Yiheyuan Road Haidian District,Beijing,P.R.China

institute: Peking University

summary: As the ancestor of CRISPR-Cas12 nucleases, TnpB represents the most compact gene editing tool currently available. Recent studies have identified multiple TnpB systems with gene editing activity in mammalian cells, and the potential of TnpB in treating diseases has been demonstrated in animal models. However, the editing characteristics of various TnpB systems, comparable to CRISPR tools, require more extensive investigation. Using a standardized evaluation framework, we conducted a thorough analysis of the editing properties of four TnpB variants alongside representative Cas12 and Cas9 tools. Overall, TnpBs exhibit intermediate editing activity and safety profiles among all tested systems, with ISYmu1 TnpB demonstrating a good performance in both editing activity and specificity. Considering its compact size, potent editing efficiency and high specificity, ISYmu1 TnpB represents a promising candidate for in vivo gene therapy applications.

overall_design: We employed primer-extension-mediated sequencing (PEM-seq) to study the gene-editing outcomes for various TnpB systems and CRISPR-Cas nuclease, including: SpCas9, Nme2-C.NR, AsCas12a, CasMINI, ISDra2, ISDge10, ISAam1, ISYmu1. Twelve different editing sites were targeted for each nuclease.

first: Guanghai

last: Xiang

first: Shiwei

last: Cui

first: Yuhong

first: Jiazhi

last: Hu

first: Haoyi


title: Targeting LRRC25 enhances antitumor immunity of tumor-associated macrophages through CD8+ T cells [scRNA-seq]

city: Tianjin

first: Guorong

last: Zhang

address: qixiangtai street 22

institute: Tianjin Medical University

summary: Leucine-rich repeat containing 25 (LRRC25), a type I membrane protein, is specifically expressed in myeloid cells. The anti-inflammatory function of LRRC25 has been established in multiple sterile and pathogenic models, however, its role in cancer remains largely unexplored. In this study, we demonstrated that LRRC25 is highly expressed in tumor-associated macrophages (TAMs) across human and mouse tumors. Lrrc25 deficiency in mice suppressed various tumor types by reprogramming TAMs toward an antitumoral phenotype and enhancing CD8+ T cell activation. Lrrc25 deficiency facilitated the reprogramming of TAMs through activation of the Nox2-ROS-Nlrp3-Il1β signaling pathway. Additionally, our findings confirmed the host safety of Lrrc25 deficiency. Overall, our results elucidate the role of LRRC25 in orchestrating TAMs and suggest that LRRC25 could serve as an effective and safe immunotherapy target for cancer treatment.

overall_design: At day 14 after B16F10 cells inoculation, or day 26 after MC38 cells inoculation, the tumors from 3 WT and 3 Lrrc25-/- mice were harvested, and 100 mm3 of each tumor was collected. Tumor tissues from 3 mice of the same group were randomly pooled into one mixed sample, and dissociated. Cell counts and viability were determined after removal of erythrocytes , and then debris and dead cells were removed using commercial kit. Fresh cells were washed twice in RPMI1640 and then resuspended at 1×106 cells per ml in 1×PBS containing 0.04% bovine serum albumin (BSA). Finally, CD45+ immune cells were isolated using magnetic beads and mixed with the original cell suspension at a ratio of 5:1.

first: Jingjing

last: Liu

first: Ge

last: Dong

first: Zhigang

last: Cai