title: Transcriptomic and Metabolomic Analyses Reveal Distinctive Metabolic Characteristics of Superficial and Deep Subcutaneous Adipose Tissues

first: Taehee

last: Jo

address: 1035 Dalgubeol daero

department: Department of Plastic and Reconstructive Surgery

institute: Keimyung University Dongsan Hospital

summary:
Background: The purpose of the study was to find out the molecular and metabolic characteristics of human superficial (SSAT) and deep subcutaneous adipose tissue (DSAT) by performing transcriptomics and metabolomics analysis
Methods: We conducted RNA-sequencing and metabolome analysis of SSAT and DSAT in a 48-year-old female patient with a BMI of 27.6 kg/m2. Six samples for each group were collected during a deep inferior epigastric perforator flap breast reconstruction. The calculated transcripts per million values were processed for unsupervised hierarchically clustered heat map generation, and Gene set enrichment analysis. For metabolomics analysis, the samples were analyzed in two modes for cationic and anionic metabolites by Capillary Electrophoresis Time-of-Flight Mass Spectrometry (CE-TOFMS). The metabolome was processed for principal component analysis (PCA) and heat map generation. For indirect metabolic flux analyses, primary adipocytes obtained from SSAT and DSAT were analyzed with Seahorse® extracellular flux analyzer.
Results: PCA and heat map data revealed global differences in the transcriptome and metabolome of SSAT and DSAT. The top up-regulated gene sets in the SSAT were related to adipogenesis (FDR q < 0.0001), oxidative phosphorylation (FDR q < 0.0001), fatty acid metabolism (FDR q < 0.0001) and glycolysis (FDR q = 0.001), while inflammatory response (FDR q < 0.05) was the top up-regulated gene set in DSAT. Consequently, the metabolites related to glycolysis were abundant in SSAT, while the metabolites related to fatty acid metabolism and oxidative phosphorylation were abundant in DSAT. In cellular flux analysis, SSAT showed higher level of glycolysis and spare oxidative phosphorylation capacities.
Conclusion: The global transcriptome and metabolome difference suggest that human superficial and deep subcutaneous adipose tissue are metabolically distinguishable subcompartments.

overall_design: Adipose mRNA profiles of human abdominal superficial and deep subcutnaeous adipose tissue


title: Guanylate binding protein 5 accelerates gastric cancer progression via a JAK1-STAT1/GBP5/CXCL8 positive feedback loop

status: Public on Oct 29 2024

city: Wu Han

first: Gongcai

last: Tao

state: Hu Bei Province

address: No. 9, Zhangzhidong Road, Wuchang District

department: Department of Gastrointestinal Surgery

country: China

institute: Renmin Hospital of Wuhan University

type: Expression profiling by high throughput sequencing

summary:
To verify the role of GBP5 in GC progression, we established GBP5 -overexpressed MKN45 cells and control cells.
We then performed gene expression profiling analysis using data obtained from RNA-seq of 2 different cells with 3 duplicates each.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for GBP5 -overexpressed MKN45 cells and control cells.

first: Fengyu

last: Cao

first: Dan

last: Song


title: The role of CMTM4 in hepatocellular carcinoma

status: Public on Oct 28 2024

city: Nanning

first: Xuefeng

last: Guo

state: Guangxi Zhuang Autonomous Region

address: 22 Shuangyong Road

department: 1.	Department of Epidemiology and Health Statistics

institute: Xuefeng Guo

summary: Dysregulation of CMTM4 has been observed in serveral cancers. Recent studies have showed that CMTM4 plays a key role in immune checkpoint therapy in tumors. To obtain a detailed view of genes and related pathways regulated by CMTM4 in the liver cancer, we used RNA-seq in liver Hep 3B cells with CMTM4 knockdown.

overall_design: The expression of CMTM4 was knocked down by lentiviral-mediated short-hairpin RNAs (shRNAs). The array analysis was performed in Hep 3B cells with CMTM4 knockdown (n=3) and Hep 3B cells transfected with the control virus (n=3).

first: Shengkui

last: Tan

first: Xiaonian

last: Zhu


title: Effect of MSMP inhibition on the gene expression profiles of rheumatoid fibroblast-like synoviocytes

city: guangzhou

first: cuicui

last: wang

state: guangdong

address: 1 Pan Fu Road

department: rheumatology

institute: Guangzhou First People’s Hospital, The Second Affiliated Hospital of South China University of Technology

summary: To explore the downstream target of MSMP, RNA-sequencing (RNA-seq) was used to display gene expression profiles in fibroblast-like synoviocytes (FLSs) from 3 patients with rheumatoid arthritis (RA) between control siRNA (siC) group and siMSMP-2 group (with the highest interference efficiency for MSMP). The heatmap and volcano diagram showed a total of 216 differentially expressed genes with 77 upregulated genes and 139 downregulated genes (Fold change≥1.5，p<0.05)

overall_design: We demonstrated gene expression profiles between control siRNA (siC) group and MSMP knock down group (siMSMP-2) in FLSs from 3 patients with rheumatoid arthritis (RA) using RNA sequencing (RNA-seq)

first: Cuicui

last: Wang


title: SLC25A33-mediated mitochondrial DNA synthesis plays a critical role in the inflammatory response of M1 macrophages by contributing to mitochondrial ROS and VDAC oligomerization

city: DAEGU

first: Daehoon

last: Kim

address: Buk-Gu

country: South Korea

institute: Kyungpook National Univ

summary: M1 macrophage polarization is modulated by the release of mitochondrial DNA (mtDNA) and subsequent its inflammatory response is augmented by production of mitochondrial reactive oxygen species (mtROS). The pyrimidine-transporting carrier SLC25A33 is located in the mitochondrial inner membrane and has been linked to mtDNA synthesis, but the role of SLC25A33 in inflammatory response of M1 macrophage remains unclear. Here, we elucidate the regulatory mechanisms responsible for up-regulation of SLC25A33 during M1 macrophage polarization and SLC25A33-mediated mtROS production and inflammatory response. Our findings reveal that expression of SLC25A33 was significantly elevated in CD14+ monocytes derived from a patient with sepsis and LPS/IFN-γ-stimulated PMs. We demonstrate that SLC25A33 is upregulated by ATF4 through the MyD88-PI3K-mTORC1 pathway in LPS/IFN-γ-stimulated PMs. Furthermore, SLC25A33 enhanced mtDNA synthesis and its release into the cytosol, facilitated by mtROS-mediated VDAC oligomer formation, thereby contributing to activation of the cGAS-STING inflammatory pathway. Conversely, SLC25A33 knockdown and pyridoxal 5'-phosphate treatment mitigate mtDNA release and reduce M1 polarization and associated inflammatory responses. These findings were consistent across in vitro and in vivo sepsis models, as well as in septic patients with liver abscess. Our findings underscore the significant role of SLC25A33 in inflammation, suggesting that targeting of SLC25A33 could represent a promising therapeutic strategy for managing M1 macrophage-mediated inflammatory diseases, including sepsis.

overall_design: To investigate the involvement of mitochondrial carriers in M1 macrophage polarization, we firstly determined the gene expression levels of SLC25 family proteins in LPS/IFN-γ-treated PM by mRNA sequencing (mRNA-seq).

first: Jonghwa

last: Jin

first: Yu rim

last: Lee

first: Keun gyu

last: Park


title: The Integrated Stress Response Promotes Macrophage Inflammation

city: Chicago

first: Raghavendra

middle: G

last: Mirmira

state: IL

address: 900 E 57th street

department: Medicine

country: USA

institute: University of Chicago

summary: Macrophages infiltrate islets early in the pathogenesis of Type 1 Diabetes (T1D), instigating islet inflammation and subsequent recognition by the adaptive immune system. A reanalysis of a publicly available single-cell RNA sequencing dataset from a pre-diabetic female non-obese diabetic (NOD) mouse revealed that the Integrated Stress Response (ISR), an evolutionarily conserved cellular pathway, is upregulated in macrophages during T1D progression. Triggered by environmental and pathological stressors, the ISR coordinates adaptive changes in gene expression to maintain cell functionality and survival and is identified as a candidate for targeted intervention. Following this, in vitro experiments on macrophage polarization and migration were conducted to evaluate changes resulting from ISR modulation. Results showed that ISR inhibition reduced the propensity of macrophages to polarize to a pro-inflammatory state without affecting anti-inflammatory polarization and reduced the migratory capabilities of pro-inflammatory macrophages. Observations from pre-diabetic female NOD mice administered ISRIB, a pharmacological ISR inhibitor, indicated a reduction in macrophage numbers within the islets, with increased PD-L1 expression on the macrophages.

overall_design: Bone marrow-derived macrophages (BMDM) were isolated as described previously and cultured for 6 days in complete medium (RPMI containing 10% FBS, 10 mM HEPES, and 100 U/ml penicillin/ streptomycin) supplemented with 10 ng/ml M-CSF.  On day 6, BMDM were pre-treated with vehicle or 50nM ISRIB for 1 h and then stimulated with 10 ng/ml LPS and 25 ng/mL IFN-γ for M1-like polarization for 16 h in the presence of vehicle or ISRIB. RNA was isolated using RNAeasy Mini kit (Qiagen) and did RNA sequencing experiments.

first: Jiayi

middle: E

first: Charanya

last: Muralidharan

first: Titli

last: Nargis

first: Jacob

middle: R

last: Enriquez

first: Ryan

middle: M

last: Anderson

first: Sarah

middle: A

last: Tersey


title: The control of H. pylori-mediated gastric cancer development and progression through YAP/TAZ signal regulation

city: Seoul

first: BYEONGMIN

last: YU

address: Yonsei University college of medicine

institute: Department of Internal Medicine, Yonsei University College of Medicine

summary: Helicobacter pylori(H. pylori), a gastrointestinal pathogen, is known to increase the risk of gastric cancer by activating chronic pro-inflammatory signaling pathways in epithelial cells. Cytotoxin-related protein A (CagA) is known to play an important role in gastric cancer development. CagA has been reported to induce tumors by inducing overexpression of YAP/TAZ, a component of Hippo signaling, and dysregulation of the pathway, thereby promoting cell proliferation and resistance to apoptosis. However, the role of H.pylori-mediated YAP/TAZ has not yet been fully investigated. Our study aimed to investigate the role of YAP/TAZ in H.pylori-mediated Hippo pathway dysregulation in gastric carcinogenesis using H.pylori-infected gastric cancer cell lines, knockout mice, and patient-derived organoids. CagA-mediated YAP overexpression in gastric epithelial cells induced intestinal epithelial metaplasia and induced intracellular rearrangement of the binding protein ZO1, thereby conferring cell motility.

overall_design: Comparative gene expression profiling analysis of RNA-seq data from gastric cancer epithelial cell line AGS with/ without Helicobacter pylori (60190, ΔCagA) infection.

first: ByeongMin

last: Yu

first: YongChan


title: TBK1 and IKKε protect target cells from IFNgamma-mediated inflammatory apoptosis

city: Rochester

first: Adrian

middle: T.

last: Ting

state: MN

address: 200 First St SW

department: Immunology

institute: Mayo Clinic

summary: T cells produce interferon gamma (IFNγ), but it is unclear whether they can use IFNγ to directly kill target cells. Here, we report that tumor targets lacking TBK1 and IKKε are killed by IFNγ, which induces expression of TNFR1 and the Z-nucleic acid sensor, ZBP1 to trigger RIPK1-dependent apoptosis. Concurrent with apoptosis, IFNγ unexpectedly also induces hyperactivation of NFκB in TBK1 and IKKε double-deficient cells. The two kinases normally function to inhibit IKKa/b activity and in their absence, IFNγ induces elevated expression of inflammatory genes. Thus, IFNγ can induce an inflammatory form of apoptosis that is normally suppressed by TBK1 and IKKε. These kinases regulate three responses: (1) induction of type I IFN; (2) inhibition of RIPK1-dependent death; and (3) inhibition of NFκB-dependent inflammation. We propose that these kinases evolved these intertwined functions so that cells infected by pathogens encoding TBK1/IKKε antagonists to block type I IFN expression will be killed by IFNγ-secreting T cells to generate an alternate NFκB-dependent inflammatory response.

overall_design: To determine if target cells deficient in TBK1 and IKKε are sensitive to IFNγ-mediated cell death, we established  B16-F1 melanoma cells with both kinases knocked-out by Crispr-Cas (DKO). B16 cells were also transduced with a non-targeting sgRNA as a control (NTNT). NTNT and DKO B16-F1 cells were treated with either media or IFNγ for 16 and 24 hours. We performed gene expression profiling and gene set enrichment analysis with the data obtained from RNA-seq comparing the 4 sample groups.

first: Nicholas

middle: D

last: Sun

first: Allison

last: Carr

first: Adrian T


title: Electroacupuncture-Driven Angiogenesis After Cerebral Infarction: Modulating VEGFR via the rno_circ_011971/miR-196c-5p/ARL13B Pathway

status: Public on Oct 27 2024

city: Tianjin

first: Lanyu

last: Jia

address: No. 354, Beima Road, Hongqiao District, Tianjin

institute: Tianjin Academy of Traditional Chinese Medicine Affiliated Hospital, Tianjin, China

summary: Background and Objective: Cerebral infarction (CI) is a severe neurological disorder caused by localized disruption of blood supply to brain tissue, leading to high rates of disability and mortality. Circular RNAs (circRNAs), highly expressed in the brain, have been identified as potential therapeutic targets for CI. Although acupuncture has been shown to promote neurological recovery, the precise molecular mechanisms, particularly the role of circRNAs in regulating angiogenesis, remain insufficiently understood. This study is the first to demonstrate that electroacupuncture (EA) promotes angiogenesis by regulating the circRNA_011971/miR-196c-5p/ARL13B axis, enhancing the proliferation and migration of brain microvascular endothelial cells (BMECs), and accelerating angiogenesis. These findings provide new insights into the molecular mechanisms of acupuncture treatment for CI and identify potential therapeutic targets.  Methods: Male Wistar rats were used to establish a cerebral infarction model via middle cerebral artery occlusion (MCAO). The rats were divided into a model group, an EA treatment group, and a control group. Immediately after MCAO induction, the EA group received acupuncture at the GV26 acupoint. Neurological deficits were assessed using the modified Neurological Severity Score (mNSS), and infarct volumes were measured using TTC staining. Immunofluorescence double staining was performed to detect angiogenesis markers CD31 and Ki67 in the peri-infarct area. CircRNA expression profiles in brain tissue were obtained through circRNA microarray analysis, and key circRNAs were validated via qRT-PCR and fluorescence in situ hybridization (FISH). In BMECs, circRNA_011971 knockdown was achieved using shRNA, and its biological functions were assessed through CCK8, wound healing, and transwell assays. The expression levels of Arl13b, VEGFA, and VEGFR2 were measured using qRT-PCR and Western blot after circRNA_011971 knockdown or overexpression. Molecular interactions among circRNA_011971, miR-196c-5p, and ARL13B were explored using dual-luciferase reporter assays, RNA immunoprecipitation (RIP), and co-immunoprecipitation (Co-IP).  Results: Compared to the untreated group, the EA group exhibited significantly smaller infarct volumes, suggesting immediate EA treatment at GV26 following infarction can effectively limit infarct progression. Immunofluorescence analysis revealed a marked increase in the co-expression of CD31 and Ki67 in the peri-infarct region of the EA-treated rats, indicating enhanced angiogenesis. CircRNA microarray analysis showed that circRNA_011971 was significantly upregulated following ischemia and downregulated after EA treatment. In BMECs, circRNA_011971 knockdown inhibited cell proliferation, migration, and invasion, whereas its overexpression promoted these processes. Further mechanistic studies revealed that EA downregulated rno_circ_011971 expression, lifting its inhibition on miR-196c-5p and activating the ARL13B/VEGF signaling pathway, thereby significantly promoting angiogenesis. This study discover a molecular mechanism by which EA regulates post-CI angiogenesis through the circRNA/miRNA axis for the first time, offering new potential targets for acupuncture therapy.  Conclusion: EA improves neurological function, reduces infarct size, and promotes angiogenesis, potentially through regulating of VEGFR via the rno_circ_011971/miR-196c-5p/ARL13B axis.

overall_design: 9 samples ,Blank group, electroacupuncture group and model group, 3 mice in each group

first: Jiaxin

last: Zhang

first: Jiangpeng

last: Cao

first: Zemeng

last: Chen

first: Xiumei

last: Yin

first: Rui

last: Zhao

first: Xiaohui

last: Liu

first: Min

first: Shu


title: Multi-omic Analysis of an Mucolipidosis II Neuronal Cell Model Uncovers Involvement of Pathways Related to Neurodegeneration and Drug Metabolism

city: Greenwood

first: Heather

last: Flanagan-Steet

state: South Carolina

address: 113 Gregor Mendel Cir.

department: J.C. Self Research Institute

institute: Greenwood Genetic Center

summary: Defining the molecular consequences of lysosomal dysfunction in neuronal cell types remains an area of investigation that is needed to understand many underappreciated phenotypes associated with lysosomal disorders.  Here we characterize GNPTAB-knockout DAOY medulloblastoma cells using different genetic and proteomic approaches, with a focus on how altered gene expression and cell surface abundance of glycoproteins may explain emerging neurological issues in individual with mucolipidosis (ML). The two knockout clones that were characterized demonstrated all the biochemical hallmarks of this disease, including loss of intracellular glycosidase activity due to impaired mannose 6-phosphate-dependent lysosomal sorting, lysosomal cholesterol accumulation, and increased markers of autophagic dysfunction.  RNA sequencing identified altered transcript abundance of several neuronal markers and genes involved in drug metabolism and transport, and neurodegeneration-related pathways.  Using selective exo-enzymatic labeling (SEEL) coupled with proteomics to profile cell surface glycoproteins, we demonstrated altered abundance of several glycoproteins in the knockout cells.  Most striking was increased abundance of the amyloid precursor protein and apolipoprotein B, indicating that loss of GlcNAc-1-phosphotransferase function in these cells corresponds with elevation in proteins associated with neurodegeneration.  The implication of these findings on lysosomal disease pathogenesis and the emerging neurological manifestations of GNPTAB-related disorders is discussed

overall_design:
To investigate the effects of GNPTAB knockout on the phenotype of neuronal cells, we established two knockout clones derived from Daoy medulloblastoma cells.
We then performed gene expression profiling of the parental cells and both knockout clones from RNA-seq collected in quadruplicate from each cell line.
Differential gene expression analysis and pathway enrichment from RNA-seq data were performed comparing the clones to parental control.

first: Lorenzo

last: Badenetti

first: Maxwell

middle: B

last: Colonna

last: Flannagan-Steet

first: Richard

last: Steet


title: Developing novel flavonoid senolytics through phenotypic drug screening and drug design

city: Minneapolis

first: Lei

middle: Justan

address: 312 Church Street SE

department: Department of Biochemistry, Molecular Biology, and Biophysics

institute: University of Minnesota

summary: The discovery of effective senolytics offers a promising approach for treating many age-related diseases. In this study, we employed a phenotypic drug discovery approach, combining drug screening and drug design, to identify and develop novel senolytic agents based on the flavonoid fisetin. We successfully developed two novel flavonoid analogs, SR29384 and SR31133, which demonstrated significantly enhanced senolytic activities compared to fisetin. These analogs showed broad-spectrum efficacy in eliminating various senescent cell types, reducing tissue senescence, extending healthspan in mice, and prolonging lifespan in Drosophila. Through RNA sequencing, machine learning, and computational screening, our mechanistic studies suggest that these novel flavonoid senolytics may target PARP1, BCL2L1, and CDK2 to induce senescent cell death.

overall_design: Primary mouse embryonic fibroblasts (MEFs) cells were used. WT MEFs non-senescent (proliferative control) and WT MEFs induced to senescence by oxidative stress (H2O2) and genotoxic stress (etoposide). Cells were treated with two novel flavonoid analogs, SR29384 and SR31133  for 12 hours. 3 biological replicates per group.

first: Carolina

last: Soto-Palma

middle: J

first: Paul

last: Robbins


title: HIV-1 infection is associated with depletion of germinal center B cells and a decrease in IgA+ plasma cells in the GI tract

city: New York

first: Darwin

last: D'Souza

state: NY

address: 1470 Madison Avenue

department: ImmunoBio

institute: Human Immune Monitoring Center

summary: Gastrointestinal (GI) B cells and plasma cells (PCs), critical to mucosal homeostasis, play an important role in the host response to HIV-1 infection. Here, high resolution mapping of human B cells and PCs from colon and ileum during both viremic and suppressed HIV-1 infection identified a significant reduction in germinal center (GC) B cells and Follicular Dendritic Cells (FDCs) during HIV-1 viremia. Further, IgA+ PCs, the major cellular output of intestinal GCs were significantly reduced during viremic HIV-1 infection. PC-associated transcriptional perturbations, including type I interferon signaling persisted in antiretroviral therapy (ART) treated individuals, suggesting ongoing disruption of the intestinal immune milieu during ART. GI humoral immune perturbations associated with changes in intestinal microbiome composition and systemic inflammation. Herein, we highlight a key immune defect in the GI mucosa due to HIV-1 viremia, with major implications.

overall_design: We investigated the differences in immune cell types, focusing on B cell and plasma cell lineages, as well as  transcriptional profile of immune cells in the gut-associated tissue of people with HIV infection and uninfected controls

first: Francesca

last: Cossarini


title: Mouse Gata1 3’UTR modulates Gata1 levels to affect erythropoiesis

city: Yangzhou

first: Ling

last: Ling

address: 136 Jiangyang Road

department: Medical College

institute: Yangzhou university

summary: The 3' untranslated region (3'UTR) of mRNA plays several important roles in post-transcriptional gene regulation. Some of its functions include regulating mRNA stability by polyadenylation and microRNAs. However, the overall function of the Gata1 3’UTR in mammals has not been defined. In this study, we used CRISPR/CAS9 technology to knock out the sequence of the mouse Gata1 3’UTR. We found a defect in erythropoiesis in mutant mice, evidenced by macrocytic anemia at the baseline. Ablation of Gata1 3’UTR also resulted in a reduced number of erythroid precursors that might be associated with the cell cycle, especially G2/M disruption in fetal livers. Mechanistically, deletion of the Gata1 3’UTR destabilizes the Gata1 mRNA and ultimately reduces Gata1 protein levels. The low stability of the Gata1 mRNA is unlikely to be caused by the loss of binding of microRNAs or lack of polyadenylation; rather, in part, by the dissociation of AU-rich elements in the 3’UTR with a trans-activating factor Elavl1. Specifically, we transcribed Gata1 3’UTR in vitro and performed an RNA pulldown assay followed by mass spectrometry to profile the proteins that bind the 3’UTR. Gene Ontology analysis demonstrated that several proteins specifically targeting the 3’UTR were found to potentially bind Gata1 3’UTR, among which Elavl1 was in almost all categories related to mRNA stabilization. Western blotting and RNA immunoprecipitation confirmed the direct interaction of Gata1 3’UTR with Elavl1. Manipulation of Elavl1 activity and protein levels by the small molecule inhibitor Dihydro-tanshinone-I and Elavl1 overexpression in fetal liver erythroblasts confirmed Elavl1 as a stabilizing factor for Gata1 mRNA. Our findings shed light on the functional significance of the 3’UTR of Gata1 mRNA in the context of erythroid development. More importantly, our findings highlight the complexity and diversity of regulatory mechanisms that govern Gata1 mRNA stability and precise expression at the post-transcriptional levels. In addition, our findings prove that miRNAs are not always essential in vivo for controlling transcription factor levels to maintain body homeostasis.

overall_design: To identify genes and pathways that were differentially regulated during fetal erythropoiesis, we conducted RNA sequencing on fetal liver cells from E14.5 embryos.

first: Duonan

last: Yu


title: Mechanistic elucidation of human pancreatic acinar development using single cell transcriptome analysis on a human iPSC differentiation model

city: Kyoto

first: Kenji

last: Osafune

address: Shogoin-Kawahara-cho 53

department: Center for iPS Cell Research and Application (CiRA)

country: Japan

institute: Kyoto University

summary:
To elucidate the differentiation mechanisms of pancreatic acinar lineages, we performed single-cell RNA-seq analysis on the grafts obtained by implanting human iPSC-derived pancreatic endoderm cells into NOD-SCID mice.
We then performed single cell transcriptome analysis using data obtained from single-cell RNA-seq of the 3 samples.

overall_design: Single cell transcriptome analysis of single-cell RNA-seq data for 585A1 cell line-derived pancreatic endoderm cells and the grafts obtained by implanting human iPSC-derived pancreatic endoderm cells into NOD-SCID mice.

first: Atsushi

last: Mima

first: Azuma

last: Kimura

first: Ryo

last: Ito

first: Yu

last: Hatano

first: Hiraku

last: Tsujimoto

first: Shin-Ichi

last: Mae

first: Wataru

last: Fujibuchi

first: Norimitsu

last: Uza

first: Taro

last: Toyoda

first: Hiroshi

last: Seno


title: Effects of RG2833 (HDAC1/3 Inhibitor) on the gene expression of Female TgF344 Alzheimer’s disease Rat model.

first: Kelechi

last: Ndukwe

address: 695 Park Ave, New York, NY 10065

department: Biology

institute: Hunter College City University of New York Graduate Center

summary: We investigated the long-term therapeutic effects of oral administration of a brain-penetrant HDAC1/3 inhibitor RG2833 in a Fisher transgenic 344-AD (TgF344-AD) rats model of AD. We treated for 6 months, starting at 5 months of age administering the drug in rodent chow at ~30mg/kg of body weight. After treatment we performed experiements to show the effects of drug treatment on spatial memory deficits. We show significantly improved hippocampal-dependent spatial memory performance in TgF344-AD female.

overall_design:
To investigate the effect of RG2833 on hippocampal gene expression, we have 5 (chow treated rats) TgF344 and 5 (RG2833 chow treated) rats.
At 11 months of age, the rats were anaesthetized intraperitoneally with ketamine (100 mg/kg) and xylazine (10 mg/kg) and transcardially perfused with cold RNAse-free 1× PBS. Left hippocampi were removed and snap frozen for RNAseq analysis.
Left hemisphere of the hippocampus. F1 – F5 (untreated transgenic rats), FRG1 – FRG5 (transgenic AD rats treated with the drug RG2833).
Female Rats started RG2833 treatment at 5-months of age and were treated for 6 months untli they were 11 months old. ). For this experiment, the gene expression for the drug treated transgenic rats will be compared to that of the untreated transgenic group (FRG/F)

first: Osama

last: Chaudry

first: Lei

last: Xie

first: Patricia

last: Rockwell

first: Maria

last: Figueiredo-Pereira

first: Peter

last: Serrano


title: Effects of RG2833 (HDAC1/3 Inhibitor) on the gene expression of Male and Female TgF344 Alzheimer’s disease Rat model.

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

overall_design: Refer to individual Series


title: Effects of RG2833 (HDAC1/3 Inhibitor) on the gene expression of Male TgF344 Alzheimer’s disease Rat model.

summary: We investigated the long-term therapeutic effects of oral administration of a brain-penetrant HDAC1/3 inhibitor RG2833 in a Fisher transgenic 344-AD (TgF344-AD) rat model of AD. We treated for 6 months, starting at 5 months of age administering the drug in rodent chow at ~30mg/kg of body weight. After treatment we performed experiments to show the effects of drug treatment on spatial memory deficits and gene expression.

overall_design:
To show the effects of RG2833-treatment on gene expression levels, Hippocampi of 5 drug-treated and 5 untreated transgenic rats of male rats were analysed for gene expression by RNAseq
At 11 months of age, the rats were anaesthetized intraperitoneally with ketamine (100 mg/kg) and xylazine (10 mg/kg) and transcardially perfused with cold RNAse-free 1× PBS. Left hippocampi were removed and snap frozen for RNAseq analysis.
Left hemisphere of the hippocampus. M1 – M5 (untreated transgenic rats), MRG1 – MRG5 (transgenic AD rats treated with the drug RG2833).
Male Rats started ibudilast tretment at 5-months of age and were treated for 6 months untli they were 11 months old. ). For this experiment, the gene expression for the drug treated transgenic rats will be compared to that of the untreated transgenic group (MRG/M)


title: A Fast Chemical Reprogramming System to Generate Human Pluripotent Stem Cells

city: Beijing

first: Jingxiao

last: Cao

state: Beijing

address: No.5 Yiheyuan Road, Yanyuan Street, Haidian District, Beijing

department: Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.

institute: Peking University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Chemical reprogramming enables the generation of human pluripotent stem cells (hCiPSCs) from somatic cells using small molecules, providing a novel and promising strategy for regenerative medicine. However, the current method for generating hCiPSCs is time consuming, and some cell lines from different donors are resistant to chemical induction, significantly limiting the utility of these cells for personalized medicine. Here, we developed a fast-reprogramming system capable of generating hCiPSCs in as few as 10 days. This accelerated method enables efficient generation of hCiPSCs with a consistent 100% success rate across 15 different donors. In particular, the efficiency of reprogramming within 16 days for cells refractory to previously reported protocols increased more than 30-fold. Mechanistically, we identified KAT3A/B and KAT6A as key epigenetic obstacles, as suppression of these factors facilitated the transition of somatic cells to a poised state by triggering switches in the epigenome, a process essential for this fast-reprogramming system. These results highlight the superiority of this novel system for generating hCiPSCs, which represents a next-generation approach for manufacturing cells for clinical applications. This work also advances our understanding of human cell reprogramming and paves the way for broader applications of chemical reprogramming in regenerative medicine.

overall_design:
To characterize human chemically induced pluripotent stem cells (hCiPSCs), human somatic cells, cells induced from hADSC by CUT&TAG.
To characterize human chemically induced pluripotent stem cells (hCiPSCs by scATAC-seq.


title: Screening FUS-binding RNA with HEK293 cells overexpressing FUS

city: Guangzhou

first: Xueying

last: Chen

address: 58 Zhongshan Road II

department: Department of Endocrinology and Diabetes Center

institute: The First Aﬃliated Hospital of Sun Yat-sen University

type: Non-coding RNA profiling by high throughput sequencing

summary: The flag-tagged human FUS was overexpressed in HEK293 cells. Extract RNA from the cell lysate, some of which are enriched with flag antibody. The high-throughput sequencing method was used to detect the difference between the total RNA and flag-enriched RNA profiles.

overall_design: RNA profiles of human FUS-overexpressed HEK 293 cells lysate. HEK293 cells containing stable human FUS-overexpression were used for lncRNA-seq to detect the difference between the total RNA and flag-enriched RNA profiles.

first: Yanbing

last: Li

first: Xiaoying

last: He


title: Functional heterogeneity analysis of Vibrio algalinolyticus cells in biofilm based on M20 single-cell sequencing

city: Xiamen

first: qiu

last: li

address: No. 185, Yinjiang Road, Jimei District, Xiamen City, Fujian Province

institute: Jimei University

summary: The heterogeneity of bacterial cells in biofilms is an important property. We performed single-cell sequencing to profile heterogeneous cell populations within Vibrio alginolyticus biofilm. Our analysis has revealed the key functional compartments for  the composition and development of biofilms

overall_design: After 60 hours of incubation at 28°C on LB agar, Vibrio algalinolyticus developed mature biofilms, which were collected for single-cell sequencing to investigate the functional heterogeneity of bacterial cells within the biofilm.

first: Qiu

first: Lixing

last: Huang


title: Characterization of the AR cistrome in ER-negative breast cancer cell lines

city: ADELAIDE UNIVERSITY

first: Geraldine

last: Laven-Law

state: South Australia

address: Adelaide Health & Med Sci Bldg, Corner George St & North Terrace

country: Australia

institute: The University of Adelaide

summary: Although molecular apocrine and some triple negative breast cancer tumours express high levels of AR, how AR signalling impacts their proliferative rate remains an area of controversy. The precise molecular mechanisms by which the AR can induce divergent proliferative effects in estrogen receptor-negative breast cancers has not been described. The potent androgen, DHT, inhibits proliferation of the MFM-223 estrogen receptor-negative breast cancer cell line. In contrast, activation of the AR by DHT either stimulates, or has no effect, on MDA-MB-453 cell proliferation. The AR cistrome was examined in order to identify candidate factors which mediate oncogenic versus tumour suppressive AR activity in ER-negative breast cancer.

overall_design: Two cell line models of estrogen receptor-negative breast cancer; MDA-MB-453 and MFM-223; were cultured in steroid-deplete conditions and treated for 4 hours with either a vehicle (0.001% ethanol) or 10 nM DHT. Three replicate AR ChIP-seq experiments were performed, each corresponding to independent and consecutive passages of cells. One input file is provided for each cell line. Peak files are provided for each replicate, and one bigwig file is provided for each treatment, corresponding to a merge of the data from all 3 replicates.

first: E

last: Mustafa

first: G

first: Z

last: Kikhtyak

first: W

last: Tilley

first: T

last: Hickey


title: Next Generation Sequencing Facilitates Quantitative Analysis of shControl and shLINC00205 Gastric Cancer Cell Lines Transcriptomes

first: longtao

last: huangfu

address: No.52, Fucheng Road, Haidian District, Beijing, China

department: Cancer Hospital

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare the transcriptome differences between knockdown LINC00205 and negative control gastric cancer cells.
Methods: Total RNA from the BGC823 cells with LINC00205 knockdown and negative control were isolated using RNeasy mini kit (Qiagen, Germany). Paired-end libraries were synthesized by using the TruSeq RNA Sample Preparation Kit (Illumina, USA) following TruSeq RNA Sample Preparation Guide. Briefly, The poly-A containing mRNA molecules were purified using poly-T oligo-attached magnetic beads. Purified libraries were quantified by Qubit 2.0 Fluorometer (Life Technologies, USA) and validated by Agilent 2100 bioanalyzer (Agilent Technologies, USA) to confirm the insert size and calculate the mole concentration. Cluster was generated by cBot with the library diluted to 10 pM and then were sequenced on the Illumina HiSeq X-ten (Illumina, USA). The library construction and sequencing was performed at Shanghai Biotechnology Corporation. STAR (version:2.7.6a) was used to map the cleaned reads to the human GRCh38 reference genome with two mismatches 1. Then ,we ran Subread/featureCounts (version:2.0.2) with a reference annotation to generate gene expression counts and FPKM values for known gene model.
Results: We identified a set of differentially expressed genes after LINC00205 knockdown.  The result of GO and KEGG enrichment analysis showed high confidence of genes enriched in the function of cell proliferation, cell cycle, and cell adhesion, consistent with the canonical molecules of these pathways significantly modulated.
Conclusion:The results suggested that LINC00205 could affect the key regulated pathway that controls the progression and metastasis of GC.

overall_design: mRNA profiles of LINC00205 knockdown and negative control gastric cancer cells

first: Longtao

last: Huangfu

first: Gangjian

last: Wang


title: A cancer-associated mutation in H2A.Z decreases nucleosome stability and impairs mitotic progression

city: Sendai

first: Masahiko

last: Harata

address: 468-1 Aramaki Aza Aoba, Aoba-ku

department: Graduate School of Agricultural Science

institute: Tohoku University

summary: The histone variant H2A.Z is one of the most evolutionally conserved histone variants. Here, we identified a cancer-associated mutation in H2A.Z and evaluate the mutation. Structural and biochemical in vitro analyses showed that the H2A.Z mutation destabilizes nucleosome containing it. Then we applied the genetic complementation analysis to analyze cellular functions of the H2A.Z mutant. Although the H2A.Z mutant is deposited into nucleosome and rescues the lethality of H2A.Z DKO cells, the mutant does not complement mitotic defects of H2A.Z DKO cells, suggesting that stability of H2A.Z nucleosome is required for proper mitotic progression. Importantly, the H2A.Z mutant led to mitotic defects even in the presence of a larger pool of wild-type H2A.Z. Thus, it is implicated that the cancer-associated mutation appeared in an allele of the H2A.Z isoform genes would be involved in carcinogenesis through causing mitotic defects.

overall_design: DT40 H2A.Z DKO cells stably expressing exogenous H2A.Z.1 or its mutant (H2A.Z-R80C) were cultured in the DMEM medium without tetracycline. Total RNAs were extracted with the RNeasy mini kit (QIAGEN) according to the manufacturer's protocol. 100 ng of total RNAs was processed for microarray by using the Agilent expression array (Agilent).

first: Masayuki

last: Kusakabe

first: Naoki

last: Horikoshi

first: Hiroyuki

last: Oku

first: Hitoshi

last: Kurumizaka


title: Genetic Evidence for the Gatekeeping Role of Ybx1 in Controlling Follicle Activation and Early Folliculogenesis by Regulation of Cdkn1a in the Zebrafish

city: Boston

first: Bo

last: Zhu

state: MA

address: 1 Blackfan Circle

department: Biology of Vascular Program

institute: Boston Children's Hospital

summary: Y box-binding protein 1 (YB-1; Ybx1/ybx1) regulates transcription and translation of targeted genes by DNA/RNA-binding. Our previous proteomic study demonstrated a dramatic drop in Ybx1 protein during follicle activation in zebrafish ovary. In this study, we created an ybx1 mutant with CRISPR/Cas9, and showed that the folliculogenesis in the mutant ovary (ybx1-/-) was blocked at pre-vitellogenic (PV)-to-early vitellogenic (EV) transition, leading to small ovaries. The mutant females were therefore sub-fertile with reduced fecundity. RNA-seq and Western blot analyses identified a variety of genes that showed differential expression between mutant ovary (ybx1-/-) and the control (ybx1+/-) including cdkn1a (p21). Disruption of cdkn1a resulted in embryonic lethality. In p21 heterozygotes (cdkn1a+/-), however, follicle activation and maturation in the ovary were both enhanced in contrast to ybx1 mutant (ybx1-/-). Interestingly, partial loss of p21 in heterozygotes (cdkn1a+/-) could rescue the phenotype of ybx1 mutant (ybx1-/-). Folliculogenesis resumed in ybx1-/-;p21+/- females with normal follicle activation, in contrast to the PV-EV blockade in ybx1-/- mutant. Interestingly, the follicle cells from the ybx1-/- mutant follicles displayed a poor proliferative activity in vitro; however, the cells from the ybx1-/-p21+/- follicles resumed normal proliferation compared to that from the wildtype fish. In summary, we demonstrated in this study that Ybx1 played a gatekeeping role in controlling PV-to-EV transition and it might act by suppressing the expression of cdkn1a, a cell cycle inhibitor.

overall_design: Considering our histological PV-to-EV follicle blockade, we further isolated PV follicles from both WT (ybx1+/+) and  ybx1-/- zebrafish. After RNA isolation, we then estbalished bulk-RNAseq libraries according to NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. After libraries preparation, we performed sequencing using the Genomics, Bioinformatics and Single Cell Analysis Core at the Univerisity of Macau.

first: Lakhansing

last: Pardeshi

first: Yingying

last: Chen

first: Wei

last: Ge


title: 2cChIP-seq: an efficient and reliable method for epigenomic profiling of small cell numbers and single cells [RNA-seq]

city: Shanghai

first: Xiaodong

last: Zhao

address: 800 Dongchuan RD

institute: Shanghai Jiao Tong University

summary: We developed a new technique by supplementing carrier materials during ChIP procedures (thereafter referred to as 2cChIP-seq), dramatically improving immunoprecipitation efficiency and reducing sample loss. Using 2cChIP-seq, we generated high-quality epigenomic profiles of histone modifications and DNA methylation in 10-1,000 cells. Moreover, 2cChIP-seq reliably captures genomic regions with histone modification at single-cell level. We characterized the methylome of differenting female germline stem cells (FGSCs) with this this approach. Through comparing the methylome patterns of undifferentiated and differentiating FGSCs, we observed a particular DNA methylation signature potentially involved in differentiation of mouse germline stem cells. Hence, we provide a robust and universal approach for epigenomic profiling starting with extremely lower input.

overall_design: The mRNA profiles of differentiated female germline stem cells

first: Congxia

last: Hu

first: Jun

last: Wu

first: Pengxiao

last: Li


title: MobiChIP: a compatible library construction method of single-cell ChIP-seq based droplets

city: shanghai

first: Yu

last: Xianhong

institute: Mobidrop

summary: In order to illustrate the epigenetic heterogeneity, versatile tools of single-cell ChIP-seq(scChIP-seq) are necessary to meet the convenience and accuracy. Here, we develop MobiChIP, a compatible ChIP-seq library construction method based current sequencing platform with single cell level. As a novel capture strategy, MobiChIP is efficient to capture the fragments from tagmented nuclei of numerous species and execute the mixing of samples from different tissues or species. Especially, this strategy enables the flexible sequencing manipulation and sufficient nucleosome amplification without customized sequencing primers. MobiChIP reveals the landscape of chromatin regulation regions with active(H3K27ac) and repressive(H3K27me3) histone modification markers in peripheral blood mononuclear cells (PBMCs), and accurately unveiled the epigenetic repression of hox gene cluster in PBMCs than ATAC-seq. Meanwhile, we complete the bioinformatics pipeline to integrate the scChIP-seq and scRNA-seq data to illustrate the cellular epigenetic and genetic heterogeneity.

sample_organism:
Homo sapiens
Cricetulus griseus
Mus musculus

overall_design: Single cell Chromatin immunoprecipitation DNA-sequencing (ChlP-seq) for histone  modifications H3K27ac in cell line.


title: Maternal social environment shapes yolk testosterone allocation and embryonic neural gene expression in tree swallows

city: Norman

first: Alexandra

last: Bentz

state: OK

address: 730 Van Vleet Oval

institute: University of Oklahoma

summary: A female's behavioral and physiological response to her environment can have lasting effects on the development of her offspring. This type of non-genetic inheritance (or maternal effect) occurs across taxa but is particularly well-studied in birds due to the relative ease of measuring maternal hormones in externally developing eggs. For example, females breeding in areas of high social competition allocate more of the hormone testosterone (T) to their egg yolks. These high-T offspring exhibit numerous phenotypic changes, including faster juvenile growth and enhanced aggression well into adulthood, which are potentially beneficial traits in high-competition areas. Thus, females may be able to communicate the current social environment to their offspring and prepare them for adverse conditions. Yet, the proximate mechanisms underlying how maternal hormones affect offspring are largely ignored, impairing our understanding of an ecologically important source of phenotypic plasticity. Here, we explored the effects of the maternal social environment on yolk T allocation and genome-wide patterns of neural gene expression in male and female tree swallow (Tachycineta bicolor) embryos. We observed a population of free-living tree swallows breeding at sites with variable breeding densities. We performed behavioral observations to record the rate of physical aggression at these sites, which was significantly higher at high density sites. We collected eggs at two developmental timepoints: the day laid to measure maternally derived T concentrations and embryonic day 11 (ED11) to measure gene expression patterns in whole brains using RNA-seq. We took a genome-wide approach to help clarify the potentially diverse mechanisms regulated by early T exposure across variable social environments. We additionally molecularly sexed the embryos to explore sex-specific effects.

overall_design: Whole brains collected from embryos incubated to embryonic day 11 exposed to natural variation in maternal breeding density.

first: M

middle: L

last: Bailey

first: Cameron

last: Nixon

first: Douglas

last: Rusch

first: Aaron

last: Buechlein

first: Kimberly

last: Rosvall


title: Biomarker discovery in pre-menstrual endometrial biopsies

city: Coventry

first: Jan

last: Brosens

address: University Hospital Coventry and Warwickshire

department: Warwick Medical School

country: United Kingdom

institute: University of Warwick

summary: The endometrium undergoes profound progesterone-driven remodeling during the secretory phase of the menstrual cycle in a process called decidualization. In the absence of pregnancy, circulating progesterone levels fall and tissue-wide inflammation and influx of neutrophils precede tissue breakdown and menstrual shedding. These changes are accompanied by wide-scale transcriptomic changes that co-ordinate temporal changes throughout the secretory phase. Here, we sequenced whole endometrial biopsies to identify molecular biomarkers that mark specific stages of the secretory phase, including pre-menstrual tissues. 20 biopsies were timed to specific phases of the secretory cycle based on the donor’s reported LH, the physical morphology of tissues observed via IHC and serum progesterone levels.

overall_design: Endometrial mRNA profiles of biopsies obtained at different points of the menstrual cycle were generated by deep sequencing.

first: Paul

last: Brighton

first: Pavle

last: Vrljicak

first: Sascha

last: Ott


title: 2cChIP-seq: an efficient and reliable method for epigenomic profiling of small cell numbers and single cells

type: Methylation profiling by high throughput sequencing

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Spatial targeting of the prostaglandin receptor EP2 is essential in driving a sustained PGE2-mediated cAMP signaling in the human endometrium

summary: In a process known as decidualization, progesterone signaling in the human endometrium converges with local cAMP production to drive morphometric and transcriptomic changes that prepare the endometrium for pregnancy. The source of cAMP has been contentious but the prostaglandin PGE2 signaling through EP2, its G-protein coupled receptor, remains a strong candidate. Cells often employ additional receptor regulation to diversify and prolong the cAMP signal and its down-steam effects, most notably through internalization and trafficking of receptors through endosomes. Here, we decidualized cultured endometrial stromal cells for 4-days with PGE2 and MPA (a progestin) and compared transcriptomic profiles with those depleted of either GIPC or APPL1, adaptor proteins involved in trafficking and recycling of EP2 respectively.

overall_design: Cultured Endometrial Stromal Cell mRNA profiles of cells decidualized with PGE2 and MPA following spatial manipulation of EP2 receptors

first: Aylin

last: Hanyaloglu


title: CDKN1A Deficiency in Zebrafish Promote Follicle Maturation and Degeneration Mediated by CRISPR/Cas9 Targeted Disruption

first: Bo

last: Zhu

summary: CDKN1A plays multiple roles in distinctive biological processes, such as cellular proliferation, apoptosis, DNA repairing, and etc. In mouse, Cdkn1a deficiency led to cell arrest at G1 phase, and also reported that Cdkna1-deficient mice were susceptible to tumorigenesis. However, the functions of Cdkn1a in zebrafish were still elusive due to few studies. Our previous study indicated that Cdkn1a might be closely associated with folliculogenesis, and to further investigate its specific role during folliculogenesis, Cdkn1a was targeted disrupted by CRISPR/Cas9. Interestingly, Cdkn1a-deficient zebrafish were embryonic lethality, resulted in approximate 2% homozygous mutants in adult stage. Furthermore, homozygous mutants have accelerated follicle maturation that faster than WT, and were fertile at young age (2 month). However, the matured or large follicles in mutant soon become dysfunctional due to abnormal oocyte that led to infertile at 3 months. Gradually, the abnormal follicles were undertaken follicle degeneration, resulted in PG follicle enrichment in mutant ovary at 6 months. Similar follicle degeneration phenomenon was also observed in heterozygous mutant ovary at 8 months. The degenerating follicles in mutant were convinced by in situ apoptosis detection kit. To further explore molecular mechanism, RNA-seq and qPCR validation were adopted to identify underlying molecular pathway that involved in Cdkn1a deficient apoptosis. This study firstly reported the functions of Cdkn1a in zebrafish, particular in its critical role in maintenance of normal follicle development, and the special phenotypes in folliculogenesis perfectly interpretation of its dual roles on both proliferation and apoptosis at two different phases, which replenished its novel role in folliculogenesis that expanded our insights.

overall_design: Considering Cdkn1a homozygous mutants are embryonically lethal, we use heterozygous mutants for experiments. We isolated primary folliicles (PGs) from both early 50 days post-fertilization (dpf) and 8 months post-fertilization (mpf) for both the WT (Cdkn1+/+) and Cdkn1a (+/-) zebrafish. We then established bulk-RNAseq libraries according to NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. After libraries preparation, we performed sequencing using the Genomics, Bioinformatics and Single Cell Analysis Core at the Univerisity of Macau.

first: Lakhansing

last: Pardeshi

first: Yingying

last: Chen

first: Wei

last: Ge


title: A Fast Chemical Reprogramming System to Generate Human Pluripotent Stem Cells [RNA-seq]

first: Jingxiao

last: Cao

overall_design:
To characterize human chemically induced pluripotent stem cells (hCiPSCs), hCiPSCs, human somatic cells and human embryonic stem cells (hES) by RNA-seq.
To characterize human chemically induced pluripotent stem cells (hCiPSCs) by scRNA-seq.


title: Changes of transcriptome in Alfalfa (Medicago sativa L.) under selenium treatment

city: zhengzhou

first: jinke

last: hu

state: henan

address: Zhengzhou City, Henan Province

institute: zhengzhou

summary: We studied the application of transcriptome technology in alfalfa selenium treatment. After spraying sodium selenite on the leaves, the process of selenium absorption and assimilation of alfalfa is unknown. The time point of transcriptome determination was determined by measuring the change of selenium content. Our results showed that 12 h was the key point of the change of selenium content in alfalfa, that is, the selenium content increased continuously before 12 h, decreased gradually after 12 h, and remained stable after 48 h. Transcriptome sequencing showed that phosphorus transporter and endocytosis related genes may be involved in selenium absorption at 12 h compared with 0 H. 12-48 h, some thiometabolic pathways may be involved in selenium metabolism and ubiquitination pathway, which may be the detoxification pathway of selenoprotein.

overall_design: Three time points (0 h, 12 h, 48 h), with three repetitions at each time point of leaves rreated with Se.

first: Qingdong

last: Wang

first: Huafeng

last: Hu

first: Jinke


title: 2cChIP-seq: an efficient and reliable method for epigenomic profiling of small cell numbers and single cells [single-cell 2cChIP-seq]

first: Xiaodong

last: Zhao

summary: We developed a new technique by supplementing carrier materials of both chemically modified mimics with epigenetic marks and dUTP-containing DNA fragments during ChIP procedures (thereafter referred to as 2cChIP-seq), dramatically improving immunoprecipitation efficiency and reducing sample loss. Using this strategy, we generated high-quality epigenomic profiles of histone modifications or DNA methylation in 10–1,000 cells. Moreover, 2cChIP-seq reliably captured genomic regions with histone modification at single-cell level. Lastly, we characterized the methylome of differentiated female germline stem cells (FGSCs) with this approach. Through comparing the DNA methylation patterns of the undifferentiated and differentiated FGSCs, we observed a particular DNA methylation signature potentially involved in differentiation of mouse germline stem cells. Hence, we provided a reliable and robust epigenomic profiling approach for small cell numbers and single cells.

overall_design: Based on Tn5 transposition of chromatin, 2cChIP-seq was applied to profile H3K4me3 histone modifications in single-cell E14_ESC.

first: Congxia

first: Jun

last: Wu

first: Pengxiao

last: Li


title: 2cChIP-seq: an efficient and reliable method for epigenomic profiling of small cell numbers and single cells [2cChIP-seq and 2cMeDIP-seq]

overall_design: Extremely low-input ChIP-seq. Fragmentized chromatin DNA supplemented with carrier was enriched with antibody, and followed by library construction.

first: C

first: J

first: P

first: X


title: Gene expression response to L-aminooxyphenylpropionic acid (AOPP) in Arabidopsis

city: Yokohama

first: Yukihisa

last: Shimada

state: Kanagawa

address: Maiokacho, Totsuka

department: Kihara Institute for Biological Science

institute: Yokohama City University

summary: To identify genes responsive to AOPP, Gene expression profiles in response to AOPP were analyzed in Arabidpsis seedlings

overall_design: To identify AOPP-responsive genes, Arabidopsis seedlings were grown in miliQ water for 3 days. Then, the seedlings were treated with or without 50 µM AOPP for 3 h. Alternatively the seedlings were treated with 50 µM AOPP for 2 h, and then treated with 1 µM IAA or 100 µM IPyA for additional 1 h. Total RNAs were extracted by RNEasy Plant Mini Kit (Qiagen), and then analyzed by Affymetrix ATH1 genome array as described previously (Goda et. al., 2008). Three independent biological replicates were conducted.


title: X-ray-induced more serious damage to CD8+ T cells in patients with hypopharyngeal squamous cell carcinoma (HPSCC) than those in healthy individuals

status: Public on Oct 26 2024

first: Jingyu

last: Ma

state: --- Select One ---

address: 83 Fenyang Road, Shanghai, China

institute: Eye & ENT Hospital, Fudan University

summary: Radiotherapy (RT) is a commonly used clinical management for hypopharyngeal squamous cell carcinoma (HPSCC), which represents the most unfavorable prognosis among all subtypes of head and neck squamous cell carcinoma. However, radiation may cause lymphopenia, a significantly adverse event with detrimental prognostic implications for patients. While CD8+ T cells are vital in tumor immunity, the specific effects of RT on CD8+ T cells as well as the underlying mechanisms have not been clearly elucidated. Here we found that subpopulations of peripheral T lymphocytes exhibited differential profiles in patients with HPSCC compared to healthy individuals both pre- and post-irradiation. Importantly, CD8+ T cells from HPSCC patients showed greater reduction of cytokine production, more severe proliferation defect, and increased apoptosis compared to those of healthy individuals after in vitro irradiation. Mechanistically, ATM-Chk2 pathway mediated the attenuated radiation-induced apoptosis of CD8+ T lymphocytes from HPSCC patients. Our study demonstrated that CD8+ T cells in patients with HPSCC are more sensitive to the radiation-induced damage than those in healthy individuals. Therefore, our findings present a potential immunotherapeutic target for safeguarding CD8+ T cells against radiation-induced damage.

overall_design: Peripheral blood mononuclear cells (PBMCs) were extracted using Ficoll density gradient centrifugation. CD8+ T lymphocytes were isolated with EasySepTM human whole blood CD8 positive selection kit (STEMCELL) according to the manufacturer’s instructions. CD8+ T cells were untreated or irradiated at the dose of 2 Gy within an X-ray irradiator (RS2000, Rad Source, Georgia) in a dose equivalent time frame. Cells were harvested for RNA sequencing after 24 hours.

first: Hanqing

last: Lin

first: Lei

last: Tao

first: Liming

last: Lu


title: Integrated insight into the molecular mechanisms of selenium modulates MPP+ induced cytotoxicity in Parkinson’s disease model

city: Wuhan

first: Xiang

state: China

address: Donghu Road

department: Neurosurgery

institute: Wuhan University, China

summary: Parkinson’s disease (PD) is a common neurodegenerative disease, which associated with oxidative stress. Due to the antioxidant function of Selenium (Se), it may have a neuroprotective function in PD. Nevertheless, the Se involved and its role in the protective function is still unclear. 1-methyl-4-phenylpyridinium (MPP+), which inhibits mitochondrial respiration, is usually used to produce a reliable PD cellular model. In this study, we discovered that Se could modulate cytotoxicity in MPP+ induced PD model and used genome wide high throughput sequencing to capture the gene expression profiles of MPP+ treatment PC12 cells with or without Se. We identified 351 differentially expressed mRNAs (DEGs) and 14 differentially expressed long non-coding RNAs (DELs) in MPP+ group vs. normal control group, 244 DEGs and 27 DELs in Se + MPP+ group vs. MPP+ group. Functional annotation analysis of DEGs and DELs cis-target genes revealed that they were enriched in reactive oxygen species (ROS) metabolic process and mitochondrial control of apoptosis. Our data suggests that DEGs, Txnrd1, siglec1 and Klf2, and the DEL AABR07044454.1 cis-acting on target gene Cdkn1a, may act a protective function in PD model. For the first time, our study systematically demonstrated that mRNAs and lncRNAs induced by Se involved in neuroprotection in PD and provided new insight into how Se modulates cytotoxicity in MPP+ induced PD model.

overall_design: RNA profiles of a control PC12 cell line group, PC12 cell lines treated with MPP+ and PC12 cell lines exposed to Se followed with incubation in MPP+.

first: Jincao

first: Wen

last: Liu

first: Feiyang

last: Zhang

first: Kaixin

last: Huang


title: 2cChIP-seq: an efficient and reliable method for epigenomic profiling of small cell numbers and single cells [2cMeDIP-seq]

first: Xiaodong

overall_design: DNA methylation profiling analysis in GV oocytes with 2cMeDIP-seq

first: Congxia


title: Roles of super-enhancer-driven genes in T-ALL cells

city: Suzhou

first: Zimu

state: Jiangsu

address: Zhongnan Street

institute: Children’s Hospital of Soochow University

summary: Many key oncogenes have been reported to be driven by super-enhancers. To explore novel oncogenes, ChIP-seq for H3K27ac profiling and super-enhancer analysis was conducted in T-ALL cells.

overall_design: ChIP using antibody against H3K27ac in J.gamma1 cells and bone marrow cells from T-ALL patients.

first: Juanjuan

last: Yu

first: Shuiyan

first: Shaoyan

first: Jian

last: Pan


title: Overexpressed Malat1 drives metastasis through inflammatory reprogramming of lung adenocarcinoma microenvironment

city: West haven

first: Antariksh

last: Tyagi

state: CT

address: 830 West Campus Dr

institute: Yale University

summary: Although the expression of some long noncoding RNAs (lncRNAs), including MALAT1 (metastasis-associated lung adenocarcinoma transcript 1), is predictive of metastasis, their impact and mechanism of action remain elusive. Here we use CRISPR activation (CRISPRa) to model MALAT1/Malat1 overexpression in patient-derived lung adenocarcinoma (LUAD) cell lines and in the autochthonous K-ras/p53 LUAD mouse model. The results indicate that Malat1 overexpression alone is sufficient to enable the progression of LUAD to metastatic disease. We show that overexpressed MALAT1/Malat1 enhances cell mobility and promotes the recruitment of pro-tumor macrophages to the tumor microenvironment through paracrine secretion of the CCL2/Ccl2 cytokine. We determine that Ccl2 upregulation results from an increase in global chromatin accessibility upon Malat1 overexpression. Importantly, macrophage depletion and Ccl2 blockade counteracted the effects of Malat1 overexpression. These data demonstrate that a single lncRNA can drive LUAD metastasis through reprogramming of the tumor microenvironment.

overall_design: To test whether overexpressed Malat1 alters the tumor microenvironment in lung adenocarcinoma, we performed tumor-specific CRISPRa using Tomato (con) or Malat1 (mA1) targeting dRNAs in the KP LUAD model at the time of tumor initiation. At 16 weeks post-tumor initiation, we performed single cell RNA sequencing (scRNA-seq) of 4 Con and 4 mA1 tumors.

first: Elena

last: Martinez-Terroba

first: Leah

last: Plasek Hegde

first: Fernando

last: de Miguel

first: Vincent

first: Ioannis

last: Chiotakakos

first: Camila

last: Robles-Oteiza

first: Katerina

last: Politi

first: Jesse

last: Zamudio

first: Nadya

last: Dimitrova


title: Myofibre-specific knockout of TGF-β type I receptors triggers muscle hypertrophy and promotes contraction and oxidative metabolism

city: Amsterdam

first: Andi

last: Shi

address: De Boelelaan 1105

country: Netherlands

institute: vu

summary: Transforming growth factor-β (TGF-β) signaling is associated with progressive skeletal muscle wasting and fibrosis, while double knockout of TGF-β type I receptors Acvr1b and Tgfbr1 results in hypertrophy. Gaining insights in how myofibre-specific knockout of these receptors affects muscle transcriptome, strength and mitochondrial activity could aid in the development of therapeutic interventions to improve muscle function. Here, we show that 3 months of myofibre-specific knockout of both receptors (dKO) in mice induced a 1.6-fold increase in gastrocnemius medialis mass and a 1.3-fold increase in maximal force. Soleus muscle mass and maximal force both increased 1.2-fold in dKO mice. Muscle hypertrophy in dKO mice was accompanied by a proportional increase in succinate dehydrogenase enzyme activity. Single receptor knockout caused minor phenotypical alterations. Transcriptome analyses revealed that gastrocnemius medialis had 1811 and soleus had 295 differentially expressed genes, mainly related to muscle contraction, hypertrophy, filament organization and oxidative metabolism. Hgf and Sln genes were strongly upregulated in both muscles of dKO mice, while Sntb1 was downregulated. This in combination of transcriptional changes are associated with muscle hypertrophy and increased mitochondrial biosynthesis. Our study highlights that myofibre-specific interference with both TGF-β type I receptors concurrently stimulates myofibre hypertrophy and mitochondrial activity.

overall_design: To investigate the phenotypic effect of Acvr1b and/or Tgfbr1, myofibre-specific knockout of Acvr1b and/or Tgfbr1 was established in 6-week-old mice. Euthanasia was performed and muscle samples were collected 3 months after knockout. Both fast-type muscles, gastrocnemius medialis, and slow-type muscles, soleus, were dissected for analysis from the left legs of 4 mice. Four types of transgenic animals were used.

first: Michèle

last: Hillege

first: Wendy

last: Noort

first: Carla

last: Offringa

first: Gang

last: Wu

first: Tim

last: Forouzanfar

first: Willem

last: Hoogaars

first: Rob

last: Wüst

first: Richard

last: Jaspers


title: A Comparison of Hepatic Gene Expression Between Wild Type and Cgref1-depleted Mice

city: Hong Kong

first: Pearl

last: Chan

address: 21 Sassoon Road, Lab Block, Pokfulam

department: School of Biomedical Sciences

country: Hong Kong

institute: The University of Hong Kong

summary: Previous reports on the functions and physiological effects of secretory protein Cell Growth Regulator with EF-Hand Domain 1 (Cgref1) are limited. Primarily, our group aims to find out if Cgref1 has any major impact on different tissues. Thus, an extensive study has been carried out. Among the range of experiments and observations recorded, we compared the gene expression in the liver tissues between wild type and Cgref1-knockout mice of C57BL/6 strain using high-throughput RNA sequencing (n=3 per group). Particularly, the results revealed that Cgref1-knockout (KO) mice has significantly downregulated expression of several fatty acid biosynthesis genes – acetyl-coA carboxylases 1 (Acaca) and 2 (Acacb), and stearoyl-coA desaturase 1 (Scd1). Such finding provides supportive evidence that Cgref1 may promote de novo lipogenesis in the liver.

overall_design: To investigate hepatic gene expression, total RNA was extracted from mouse liver tissues of both wild type and Cgref1-KO groups for RNA sequencing.

last: CHAN

first: Chi-Ping

first: Dong-Yan

last: JIN


title: Hepatic Gene Expression

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

overall_design: Refer to individual Series


title: IRF2BP2 affects T-ALL cell proliferation by cooperating with master transcription factors [Cut&Tag]

first: Zimu

last: Zhang

summary: Knocking down IRF2BP2 led to decreased T-cell acute lymphoblastic leukemia (T-ALL) cell survival and growth both in vitro and in vivo. To explore IRF2BP2-dependent gene regulation, RNA-seq analysis was conducted and the differently expressed genes were revealed in the IRF2BP2-knockdown J.gamma1 cells in comparison to control group. Cleavage Under Targets and Tagmentation (CUT&Tag) showed the co-localization of IRF2BP2 with several master transcription factors on chromatin in J.gamma1 cells.

overall_design: CUT&Tag using antibody against IRF2BP2, RUNX1, ERG, ELF1 and ETS1 in J.gamma1 cells.

first: Juanjuan

last: Yu

first: Shaoyan

last: Hu

first: Jian

last: Pan


title: IRF2BP2 affects T-ALL cell proliferation by cooperating with master transcription factors


title: IRF2BP2 affects T-ALL cell proliferation by cooperating with master transcription factors [RNA-Seq]

summary: Knocking down IRF2BP2 led to decreased T-cell acute lymphoblastic leukemia (T-ALL) cell survival and growth both in vitro and in vivo. To explore IRF2BP2-dependent gene regulation, RNA-seq analysis was conducted and the differently expressed genes were revealed in the IRF2BP2-knockdown J.gamma1 cells in comparison to control group.

overall_design: mRNA profiles of J.gamma1 cells transfected with control shRNA-Control (shNC) or shRNA-IRF2BP2 (shIRF2BP2) were generated by RNA sequencing, in double, using Illumina NovaSeq6000. mRNA profiles of CD3+ T cells isolated from the spleens of Irf2bp2 fl-fl-/Vav-iCre+/- mice were generated by RNA sequencing.


title: Predicting modulaters of TE-driven chromatin 3D structure (HiC)

city: Shenzhen

first: Andrew

middle: P

last: Hutchins

address: 1088 Xueyuan Rd

department: Bioinformatics

institute: Southern University of Science and Technology

summary: DNA is tightly packaged in the human nucleus and is wrapped in complex three-dimensional (3D) structures that have been implicated in regulatory processes However, no comprehensive model describes the formation of the 3D genome. At least 40% of the human genome consists of fossilized inactive transposable element (TE) sequences. A role for TEs in 3D genome structure has been suggested by several studies that illustrate how TEs are involved in 3D genome formation. However mechanisms that mediate the formation of TE-mediated 3D contacts is lacking. As TEs are rich in TF binding sites it seems likely that TFs bound to TEs are responsible for forming the 3D genome structure. We used the comprehensive TF binding data available in human and mouse pluripotent stem cells (PSCs), coupled with HiC data to explore the role of TFs bound to TEs in 3D genome organization. Based on these computational predictions we divide TFs into three main classes, those that utilize TEs to drive 3D genome formation, those that are neutral, and a third class that breaks 3D contacts at specific TEs. We then experimentally validate four proteins, and show that SMARCA5 and MAFK are involved in promoting chromatin contacts at TEs, whilst E2F6 and KDM1A are disruptive.

overall_design: Human pluripotent stem cells were transfected with shRNAs targetting SMARCA4, MAFK, E2F6 or KDM1A, and LUC (as a control) and subjected to RNA-seq to measure gene expression changes and HiC to determine chromsome contacts. All experiments were performed in biological duplicate

first: Hutchins

last: Andrew

first: Zhen

last: Xiao

first: Liyang


title: Predicting modulaters of TE-driven chromatin 3D structure


title: Predicting modulaters of TE-driven chromatin 3D structure (RNA-seq)

last: Shi


title: Kupffer cell diversity maintaines liver function in alcohol associated liver disease [scRNA-seq]

status: Public on Oct 25 2024

city: Kansas City

first: Sumedha

middle: S

last: Gunewardena

state: Kansas

address: 2146 West 39th Avenue

department: Dept. of Molecular and Integrative Physiology

institute: University of kansas medical center

summary: Background & Aims: Liver macrophages are heterogeneous and play an important role in alcohol_x0002_associated liver disease (ALD) but there is limited understanding of the functions of specific macrophage subsets in the disease. We used a Western Diet Alcohol (WDA) mouse model of ALD to examine the hepatic myeloid cell compartment by scRNA seq and targeted Kupffer cell (KC) ablation to understand the diversity and function of liver macrophages in ALD. Approach and Results: In the WDA liver, KCs and infiltrating monocytes/macrophages (IMs) each represented about 50% of the myeloid pool. Five major KC clusters all expressed genes associated with receptor mediated endocytosis and lipid metabolism, but most were predicted to be non_x0002_inflammatory and antifibrotic with one minor KC cluster having a pro-inflammatory and extracellular matrix degradation gene signature. IM clusters, in contrast, were predicted to be pro_x0002_inflammatory and pro-fibrotic. In vivo diphtheria toxin based selective KC ablation during alcohol exposure resulted in a liver failure phenotype with increases in PT/INR and bilirubin, loss of differentiated hepatocyte gene expression, and an increase in expression of hepatocyte progenitor markers such as EpCAM, CK-7 and Igf2bp3. Gene set enrichment analysis of whole liver RNAseq from the KC ablated WDA mice showed a similar pattern as seen in human alcoholic hepatitis. Conclusions: In this ALD model, KCs are anti-inflammatory and are critical for maintenance of hepatocyte differentiation. IMs are largely pro-inflammatory and contribute more to liver fibrosis. Future targeting of specific macrophage subsets may provide new approaches to treatment of liver failure and fibrosis in ALD.

overall_design: We performed scRNAseq of total liver immune cells of chow fed (n=2), Western Diet only (WD) (n=4), and Western Diet Alcohol (WDA) (n=4) mice after 16 weeks of western diet and alcohol feeding. Total nonparenchymal cells (NPCs) were isolated by liver perfusion, and FACS sorted CD45+ cells were sequenced. Sequencing yield averaged 8,000-9,000 cells per sample and results from all 10 animals were combined for initial clustering.

first: Kyo

last: Sasaki

first: Sheetalnath

last: Rooge

first: Janice

last: Hintz

first: Priyanka

last: Ghosh

first: Isabel

last: Aranzazu Pulido Ruiz

first: Kyle

last: Yuquimpo

first: Michael

last: Schonfeld

first: Heer

last: Mehta

first: Heather

last: Stevenson

first: Omar

last: Saldarriaga

first: Esteban

last: Arroyave

first: Irina

last: Tikhanovich

first: Ann

last: Wozniak

first: Steven

last: Weinman


title: Analysis of aortic gene expression in mice with aortic dissection treated with colchicine

city: Hefei

first: Yaping

last: Zhao

address: No. 443 Huangshan Road

institute: University of Science and Technology of China

summary: Colchicine is an alkaloid found in the plant Colchicum, which is currently used for the treatment of acute gout and familial Mediterranean fever, and is being considered for the treatment of a variety of cardiovascular diseases such as pericarditis, atrial fibrillation, and coronary syndromes due to its significant anti-inflammatory effects. Aortic dissection is a cardiovascular disease characterised by a tear in the intima and congestion of the vessel wall leading to vessel wall delamination, with a rapid onset and high lethality. This study investigated the role of colchicine in BAPN-induced aortic dissection in mice. Gavage administration of colchicine along with BAPN modelling for three weeks showed a significant decrease in morbidity and mortality, indicating that colchicine can inhibit the occurrence of aortic dissection in mice.

overall_design: 3-week-old C57BL/6J male mice were fed with chow diet, and BAPNwas mixed into the drinking water and dissolved at a concentration of 1 g/kg/day for 3 weeks. Mice were simultaneously gavaged with colchicine (200 μg/kg/day) or equivalent doses of saline.

first: Suowen

last: Xu

first: Hui

last: Jiang


title: Hepatic Gene Expression Induced by CREB-H-ΔTC

first: Pearl

last: Chan

summary:
The cAMP-response element binding protein H (CREB-H) is a transcription factor expressed in liver and intestinal tissues. It is well known for regulating many lipid and glucose metabolism genes.
Our group aimed to screen for additional or potential genes that may be downstream of CREB-H transcription. To prevent inaccuracy arisen from endogenous CREB-H expression, we used CREB-H-knockout (CREB-H KO) mice for this study.

overall_design: We intraperitoneally injected liver-specific adeno-associated virus that was conjugated to the CREB-H-ΔTC transcript i.e., the active form of CREB-H (AAV-CREB-H- ΔTC) which regulates gene transcription into CREB-H KO mice. Whereas, for the control group, CREB-H KO mice received GFP expression (AAV-GFP). The sample size was n=3 per group. Mice were sacrificed two weeks after the injection. Liver tissues were extracted and processed for microarray analysis.

first: Dong-Yan

last: JIN

first: Chi-Ping

last: CHAN


title: Myocardin Attenuates Aortic Aneurysm and Dissection Through the Maintenance of VSMC Homeostasis

city: Zhongshan

first: Jie

last: Sun

state: Guangdong

address: Sun Wendong Road No. 2

department: Department of Cardiology

institute: Zhongshan City People Hospital

summary: Myocardin (Myocd) plays an important role in the maintenance and homeostasis of the vasculature. The loss of Myocd results in vascular smooth muscle cell (VSMC) phenotypic transition and thoracic aortic aneurysms and dissections (TAADs) by downregulating VSMC contractile genes. VSMC phenotypic transition plays a key role in the formation of abdominal aortic aneurysms and dissections (AAADs). However, little is known about the role of Myocd in AAAD. The effect of Myocd on AAA formation was proven in an angiotensin II (Ang II)-induced AAD model. Myocd overexpression or knockdown was achieved by the injection of the corresponding adeno-associated virus serotype 9 (AAV9) through the tail vein. The knockdown of Myocd in C57BL/6J mice treated with angiotensin II promoted the formation of AAAD, as demonstrated by increases in the maximal aortic diameter, vascular inflammation and elastin degradation relative to the control group, while Myocd-overexpressing ApoE-/- mice infused with Ang II were less likely to develop AAAD. Mechanistically, Myocd deficiency significantly repressed VSMC marker gene expression. In addition, qPCR results showed that Myocd knockdown promoted the expression of lncRNAs, which showed increased levels in human AAD tissues. Our results indicated the pivotal role of Myocd in protecting against AAAD formation.

overall_design: In this study, mouse aortic vascular smooth muscle cells (VSMCs) were isolated and transfected with adenoviruses for knockdown of Myocd. RNA-seq was performed on Myocd knockdown VSMCs and wildtype VSMCs.

first: Xin

last: Liu

first: Jianting

last: Dong

first: Yanchun

last: Zhang

first: Fei

last: Li

first: Bing

last: Hu

first: Cui

first: Li

last: Feng

first: Yong

last: Yuan


title: Discovery and analysis of NFE2L1's non-transcriptional activity by transcriptome sequencing in hepatocellular carcinoma HepG2 cells

city: Zhengzhou

first: Lu

last: Qiu

state: Henan

address: No.1 East Jianshe Road, Erqi District

institute: The First Affiliated Hospital of Zhengzhou University

summary: Antitumor transcription activator NFE2L1 regulates redox homeostasis, protein turnover, and material metabolism, playing a crucial role in embryonic development and the specialization of tissue and organ functions. Deficiency of the NFE2L1 gene in different regions yields distinct phenotypes, suggesting that NFE2L1 may possess functions independent of its transcription factor activity. In this study, we originally discovered the non-transcription factor activity of NFE2L1 by constructing a truncated protein, NFE2L1ΔC, which lacks the 152 amino acids at the C-terminus and loses its transcription factor activity. By studying the function of the truncated NFE2L1 protein, we revealed that the suppressor effect of NFE2L1 on tumor cells does not require its transcription factor activity and nuclear localization. Then, transcriptome sequencing was performed to decipher the function of NFE2L1, and the results revealed that NFE2L1 regulated redox homeostasis, proteasome function, and antiviral and proinflammatory responses primarily through its transcriptional activation function in the nucleus. In contrast, NFE2L1’s regulation of developmental related signals, ribosome function, and canceration were closely associated with its non-transcription factor activity in the cytoplasm. In this study, the non-transcription factor activity of NFE2L1 was discovered and described for the first time, laying a foundation for both basic and applied research on NFE2L1.

overall_design: We established NFE2L1 and NFE2L1DC overexpression HepG2 cell lines, and then performed gene expression profiling analysis using data obtained from RNA-seq of 3 cell lines.


title: RNA-seq_Medaka_THC_Exposure

city: Greensboro

first: Ramji

middle: Kumar

last: Bhandari

state: NC

address: 321 McIver St

institute: University of North Carolina Greensboro

summary: Medaka transcriptomes sequenced using RNA-seq

overall_design: Three biological replicates for each treatment

middle: K


title: Complexity of synovial fluid-derived monocyte–macrophage lineage cells in knee osteoarthritis

city: Olomouc

first: Eva

last: Kriegová

address: Hněvotínská 976/3

country: Czech Republic

institute: Univerzita Palackého v Olomouci

summary: Synovial fluid (SF)-derived monocyte–macrophage lineage (MON–Mϕ) cells in knee osteoarthritis (KOA) remain poorly understood. This lineage consists of four subpopulations with considerable interindividual variability that correlates with the distribution and activation of other immune cells. The most abundant subpopulation was that of CD11b+CD14−CD16− myeloid dendritic cells (mDCs; type cDC2), which were inactive and exhibited low cytokine production, low T-lymphocyte stimulation, high migratory ability comparing to other MON–Mϕ cells. Other major subpopulations included CD11b+CD14+CD16− monocyte-like cells and CD11b+CD14+CD16+ macrophages.  A subpopulation of CD11b−CD14−CD16− mDCs (type cDC1) was less common. To confirm the identity of MON–Mϕ subpopulations characterised through flow cytometry, we performed bulk RNA-seq analysis on sorted CD11b+CD14−CD16−, CD11b+CD14+CD16− and CD11b+CD14+CD16+ MON–Mϕ subpopulations from the SF of four patients with KOA with a predominance of MON–Mϕ lineage cells. The CD11b+CD14+CD16− and CD11b+CD14+CD16+ cells shared a similar transcriptomic profile. However, CD11b+CD14−CD16− cells were remarkably distinct from other CD11b+ populations. The dataset is part of a study published by Mikulkova et al. Cell Reports.

overall_design:
To investigate the identity of MON–Mϕ subpopulations characterised through flow cytometry, we performed bulk RNA-seq analysis on sorted CD11b+CD14−CD16−, CD11b+CD14+CD16− and CD11b+CD14+CD16+ MON–Mϕ subpopulations from the SF of patients with KOA with effusion.
We performed bulk RNA-seq analysis on sorted CD11b+CD14−CD16−, CD11b+CD14+CD16− and CD11b+CD14+CD16+ MON–Mϕ subpopulations from the SF of four patients with KOA with effusion with a predominance of MON–Mϕ  lineage cells.
Comparative gene expression profiling analysis of RNA-seq data for three subpopulations (CD11b+CD14−CD16−, CD11b+CD14+CD16− and CD11b+CD14+CD16+) of MON–Mϕ lineage cells from the SF of patients with KOA with effusion.

first: Zuzana

last: Mikulkova

first: Jiri

last: Gallo

first: Marketa

last: Trajerova

first: Jakub

last: Savara

last: Kriegova


title: Compound mutations in HRC and MYBPC3 synergistically increase cardiac pathogenicity

status: Public on Oct 24 2024

city: Tucson

first: Sakthivel

last: Sadayappan

state: AZ

address: 1656 E Mabel Street, Medical Research Building, Rm 315, Cellular and Molecular Medicine

department: Cellular and Molecular Medicine

institute: University of Arizona College of Medicine

summary: Hypertrophic cardiomyopathy (HCM) and arrhythmia are two leading causes of sudden cardiac death (SCD). A 25-base pair deletion in intron 32 of cardiac myosin binding protein C (MYBPC3Δ25bp) results in cardiomyopathies in 6% of South Asians. Within this population, another compounded genetic variant of a Serine to Alanine mutation in the 96th codon of HRC (HRCS96A) is present with frequencies of 48% (heterozygous) and ~16% (homozygous), resulting in a higher incidence of sudden death in dilated cardiomyopathy (DCM).  To elucidate the pathogenicity of impaired Ca2+-cycling and arrhythmias by the HRCS96A polymorphism in the setting of altered sarcomere function instrumented by the MYBPC3Δ25bp variant. Using transgenic mouse models, we studied the effects of the MYBPC3Δ25bp and the HRC mutation (murine S81A) alone and together (double variant, DV).  Electrocardiogram tracing of DV mice also indicated increased stress-induced arrhythmias, such as ventricular tachycardia, after caffeine and epinephrine administration. In vitro, IonOptix experiments using freshly isolated adult cardiomyocytes revealed DV mice significantly decreased fractional shortening, Ca2+ transient amplitude, and higher number of after-contraction. When challenged with transverse aortic constriction (TAC), the DV mice also displayed more severe systolic and diastolic dysfunction as measured by echocardiography. In subsequent RNA sequencing studies, compared to the non-transgenic controls, the DV mice had significantly more dysregulated genes than the single-variant mice. A perturbagen screen followed the RNA sequencing study to predict small molecules could revert these pathological gene signatures in the DV mice.  These studies highlight the increased pathogenicity of compound variants in calcium handling and sarcomeric genes, as evidenced by increased cardiac dysfunction at baseline and post-TAC and increased pathological gene dysregulation in the double variant mice.

overall_design: Transgenic mouse models carrying HRC mutation or 25bp deletion or both were generated and RNA Sequencing was performed using the heart samples collected from each of these mice and compared with the nontransgenic mice (n=3 /group)

first: Kalyani

last: Ananthamohan

first: Lisa

middle: C

last: Green

first: Mohit

last: Kumar

first: Sholeh

last: Bazrafshan

first: Perundurai

last: Dhandapany

first: Kobra

last: Haghighi

first: Rohit

last: Singh

first: Michelle

last: Nieman

first: Anil

last: Jegga

first: John

last: Lorenz

first: Evangelia

last: Kranias


title: The cytokine receptor Fn14 regulates neuronal transcription during development and brain function in the adult [RNA-seq]

city: Cold Spring Harbor

first: Lucas

last: Cheadle

address: 1 Bungtown Rd

department: Neuroscience

institute: Cold Spring Harbor Laboratory

summary: Signaling between the cytokine TWEAK and its receptor Fn14 is critical for neural circuit development in the postnatal brain. However, the downstream mechanisms through which TWEAK and Fn14 mediate synapse development have remained unclear. Here, we apply single-nucleus RNA-sequencing to Fn14 and TWEAK KO mice to characterize the genes that are regulated by this pathway in the developing dorsal lateral geniculate nucleus of the thalamus at single-cell resolution. We identify robust cohorts of genes that are misregulated in the absence of either Fn14 or TWEAK, providing insight into the transcriptional mechanisms through which cytokine signaling between microglia and neurons regulates a key phase of postnatal brain development that is driven by sensory experience.

overall_design: We performed single-nucleus RNA-sequencing using the inDrops approach on the dorsal lateral geniculate nuclei (dLGNs) of Fn14 and TWEAK knockout mice and their respective wild type littermates. Two biological replicates were included in the Fn14 dataset and four biological repliates were included in the TWEAK dataset.


title: The cytokine receptor Fn14 regulates neuronal transcription during development and brain function in the adult [ATAC-seq]

overall_design: ATACseq on Fn14 KO and WT mice or WT mice depleated of microglia and control mice.


title: LncRNA NONMMUT104330.1-miR-709-DDX58 axis mediates enoxaparin sodium bone cement to regulate M2 polarization of macrophages and play an anti-inflammatory immunomodulatory role

city: Shijiazhuang

first: Weiye

last: Fan

address: No. 139 Ziqiang Road, Qiaoxi District

institute: Department of Orthopaedic Surgery, Hebei Medical University Third Hospital

summary: PMMA bone cement is biologically inert and exhibits poor biological activity. Following implantation, it generates bone cement particles, which can easily induce tissue inflammation around the implant . Compared with PMMA bone cement, ES-PMMA bone cement had anti-inflammatory effect by inducing M2 polarization of macrophages. RNA sequencing was used to explore the underlying molecular mechanisms.

overall_design: To explore the molecular basis of the anti-inflammatory effect of ES-PMMA bone cement. We prepared PMMA bone cement and ES-PMMA bone cement sample extract medium. RAW264.7 cells were induced by LPS for 24 hours, and then the culture medium was changed to different bone cement extract medium for further culture. RAW264.7 cells treated with different bone cement extracts were collected for RNA sequencing to screen out differentially expressed genes.


title: Molecular fingerprints for bone marrow cells, myelodysplastic syndrome and aplastic anemia

city: Kuopio

first: Merja

last: Heinäniemi

address: Yliopistonranta 1E

department: School of Medicine, Institute of Biomedicine

country: Finland

institute: University of Eastern Finland

summary: The overall goal of this study was to characterize bone marrow cells based on their transcriptome, surface protein expression and BCR- and TCR VDJ-profile across disease diagnosis for accurate identification of clinically relevant cell states. This project has received funding from the European Union Horizon 2020 research and innovation programme under grant agreement No 824110 (EASI-Genomics).

overall_design:
CITE-seq (scRNA-seq, scADT-seq) and scVDJ-seq samples were generated from bone marrow mononuclear cells using the 10X Genomics Chromium platform and protocols. Bone marrow samples were retrieved from The Finnish Hematology Registry and Clinical Biobank (FHRB, adult donors). A mix of three leukemia cell lines (Nalm-6, HL-60, Jurkat) were used as control to assess reproducibility across sample preparation batches. Single cell suspensions representing sample pools (2-3 per pool) were loaded to Chromium Controller instrument and processed for sequencing. Sample annotation follows tissue term ontology from EFO https://www.ebi.ac.uk/efo/

***************************************************************
Raw fastq files are available from the FHRB Biobank.  Since the data corresponds to sequencing reads and includes sensitive patient information, it will only be shared through a controlled-access data repository, in accordance with ethical consents.
***************************************************************

first: Tiina

last: Tuononen

first: Mari

last: Lahnalampi

first: Konstantin

last: Ivanov


title: Kupffer cell diversity maintaines liver function in alcohol associated liver disease [bulk RNA-seq]

first: Sumedha

last: Gunewardena

overall_design: We performed whole liver RNAseq comparing chow fed mice livers to Clec4f-DTR western diet alcohol fed mice treated with either serial saline or serial DT injections

first: Kyo

last: Sasaki

first: Sheetalnath

last: Rooge

first: Janice

last: Hintz

first: Priyanka

last: Ghosh

first: Isabel

last: Pulido Ruiz

first: Kyle

last: Yuquimpo

first: Michael

last: Schonfeld

first: Heer

last: Mehta

first: Heather

last: Stevenson

first: Omar

last: Saldarriaga

first: Esteban

last: Arroyave

first: Irina

last: Tikhanovich

first: Ann

last: Wozniak

first: Steven

last: Weinman


title: Microglia Depletion Reduces Human Neuronal APOE4-Driven Pathologies in a Chimeric Alzheimer’s Disease Model

city: San Francisco

first: Nuo

last: Chen

state: California

address: 1650 Owens St

department: GIND

institute: Gladstone Institutes

summary: Despite strong evidence supporting the involvement of both apolipoprotein E4 (APOE4) and microglia in Alzheimer’s Disease (AD) pathogenesis, the effects of microglia on neuronal APOE4-driven AD pathogenesis remain elusive. Here, we examined such effects utilizing microglial depletion in a chimeric model with human neurons in mouse hippocampus. Specifically, we transplanted homozygous APOE4, isogenic APOE3, and APOE-knockout (APOE-KO) induced pluripotent stem cell (iPSC)-derived human neurons into the hippocampus of human APOE3 or APOE4 knock-in mice, and depleted microglia in half the chimeric mice. We found that both neuronal APOE and microglial presence were important for the formation of Aβ and tau pathologies in an APOE isoform-dependent manner (APOE4 > APOE3). Single-cell RNA-sequencing analysis identified two pro-inflammatory microglial subtypes with high MHC-II gene expression that are enriched in chimeric mice with human APOE4 neuron transplants. These findings highlight the concerted roles of neuronal APOE, especially APOE4, and microglia in AD pathogenesis.

overall_design: Single-cell RNA sequencing on isolated microglia from hippocampi of chimeric mice with human neurons transplanted into mouse hippocampus. Specifically, homozygous APOE4 (hE4), isogenic APOE3 (hE3), and APOE-knockout (hEKO) induced pluripotent stem cell (iPSC)-derived human neurons were transplanted into the hippocampus of human APOE3 or APOE4 knock-in (E3KI and E4KI) mice. The five groups of mice are: E4KI, hE4-E4KI, E3KI, hE3-E3KI, and hEKO-E4KI.

first: Rao

last: Antara

first: Chen

last: Nuo

first: Hao

last: Yanxia

first: Yadong

last: Huang


title: Gene sequencing of taste bud tissue in rat tongue epithelium

city: Lanzhou

first: Qiaozhen

last: Zhou

address: No.199 Donggang West Road

department: School/Hospital of Stomatology Lanzhou University

institute: Lanzhou University

summary:
Purposes: To investigate the effect of periodontitis on taste sensitivity through RNA sequencing
Methods: Three chronic periodontitis rats and non-periodontitis rats were selected for circumvallate papilla, and RNA sequencing was performed on Illumina NexSeq
Results: If P ≤ 0.05, fold change ≥ 1.5 as the cut off, 21 differential genes were up-regulated and 74 were down-regulated。 KEGG analyzed 4 up-regulated and 8 down-regulated expression pathways.
Conclusion: There were 21 up-regulated differential genes and 74 down-regulated differential genes in rat circumvallate papilla tissue samples.

overall_design: Gene sequencing of circumvallate papilla tissue in periodontitis rats and non-periodontitis rats

first: Shuting

last: Gao

first: Baoping

last: Zhang


title: Microglia and Fn14 regulate transcription and chromatin accessibility in developing neurons

first: Lucas

last: Cheadle

state: NY

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

overall_design: Refer to individual Series


title: Effects of moderate doses of ionizing radiation on experimental abdominal aortic aneurysm

city: Fontenay-aux-Roses

first: Guillaume

last: Vares

country: France

institute: IRSN

summary: Objectives: Exposure to ionizing radiation has been linked to cardiovascular diseases. However, the impact of moderate doses of radiation on abdominal aortic aneurysm (AAA) remains unknown. Approaches : Angiotensin II-infused Apoe-/- mice were irradiated (acute, 1 Gray) either 3 days before (Day-3) or 1 day after (Day+1) pomp implantation. Primary aortic smooth muscle cells (SMCs) isolated were irradiated (acutely 1 Gray) for mechanistic studies and functional tested in vitro. Results: Day-3 and Day+1 irradiation resulted in a significant reduction in aorta dilation (Control: 1.39+/-0.12; Day-3: 1.12+/-0.11; Day+1: 1.15+/-0.08 mm, P<0.001) and AAA incidence (Control: 81.0%; Day-3: 33.3%, Day+1: 53.3%) compared to the non_x0002_irradiated group. Day-3 and Day+1 irradiation led to an increase in collagen content in the adventitia (Thickness control: 23.64+/-2.9; Day-3: 54.39+/-15.5; Day+1 37.55+/- 10.8 mm, P=0.006). However, the underlying protective mechanisms were different between Day-3 and Day+1 groups. Irradiation before Angiotensin II (AngII) infusion mainly modulated vascular smooth muscle cells (VSMCs) phenotype with a decrease in contractile profile and enhanced proliferative and migratory activity. Irradiation after AngII infusion led to an increase in macrophage content with a local anti-inflammatory phenotype characterized by the upregulation of M2-like gene and IL-10 expression. Conclusion: Moderate doses of ionizing radiation mitigates AAA either through VSCM phenotype or inflammation modulation according to the time of irradiation.

overall_design: Aortas from Angiotensin II-infused Apoe-/- mice, irradiated 3 days before or 1 day after pomp implantation, were used for RNA-seq analysis.

first: Goran

last: Riazi

first: Chloe

last: Brizais

first: Imene

last: Garali

first: Rida

last: Al-Rifai

first: Helene

last: Quelquejay

first: Virginie

last: Monceau

first: Lea

last: Oul-Boukhitine

first: Damien

last: Aubeleau

first: Florian

last: Gilain

first: Celine

last: Gloaguen

first: Morgane

last: Dos-santos

first: Hafid

last: Ait-Oufella

first: Teni

last: Ebrahimian


title: MBNL splicing factors regulate the microtranscriptome of skeletal muscles [smallRNA-Seq]

city: Poznan

first: Michał

last: Szcześniak

address: Uniwersytetu Poznanskiego 6

department: Institute of Human Biology and Evolution

country: Poland

institute: Adam Mickiewicz University

summary: Muscleblind-like proteins (MBNLs) regulate various RNA-processing steps, including alternative splicing, polyadenylation, RNA stability, and mRNA intracellular localization. In myotonic dystrophy type 1 (DM1), the most common muscular dystrophy in adults, MBNLs are sequestered on toxic RNA containing expanded CUG repeats, which leads to disruption of MBNL-regulated processes and disease features of DM1. Herein, we showed the significance of MBNLs in the regulation of microtranscriptome dynamics during postnatal development of skeletal muscles and in microRNA (miRNA) misregulation observed in mouse models and patients with DM1. We identified multiple miRNAs sensitive to insufficiency of MBNL proteins and revealed that many of them were postnatally regulated, which was correlated with increases in the activity of these proteins during this process. In adult Mbnl1-knockout mice, miRNA expression exhibited an adult-to-newborn shift. We identified two mechanisms through which MBNLs influence miRNA levels. First, MBNL loss induces transcriptional changes in miRNA precursors. Second, MBNLs affect miRNA biogenesis by regulating the alternative splicing of miRNA primary transcripts.

overall_design: To assess the global impact of MBNLs on the skeletal muscle microtranscriptome, we sequenced a small RNA pool isolated from the quadriceps of 12-week-old HSALR mice (3xWT, 3xHSALR)


title: RNA-seq human bronchial epithelial cells THC Exposure

first: Ramji

last: Bhandari

department: Biology

summary: Human bronchial epithelial cells transcriptomes sequenced using RNA-seq

overall_design: Three biological replicates for each THC treatment