title: BET inhibition restores NPM1c+-mediated deregulation of chromatin in AML

city: Huddinge

first: Andreas

last: Lennartsson

state: Stockholm

address: Halsovagan 7C

department: Biosciences and Nutrition

country: Sweden

institute: Karolinska Institutet

summary: Acute Myeloid Leukemia is a severe hematological malignancy with poor outcomes in adults and children. Among the most common mutations in AML is a heterozygous mutation in the genenucleophosmin(NPM1), which results in the cytoplasmic translocation of NPM1 protein (NPM1c+) along with several of its interacting partners. Here, we show that several members of the cohesin complex have increased cytoplasmic presence in AML cells that carry the NPM1 mutation. Treatment with BET inhibitors results in decreased levels of NPM1c+, causing activation of cohesin-regulated genes and super enhancers, demonstrating a differential response to BET inhibitors compared to NPM1 wild type cells. In addition, we demonstrate that BETi diminish the levels of ribosomal polysomes, with a putative impact on translation. Our results demonstrate novel promising avenues for the usage of BET inhibitors in therapies to treat AML.

overall_design: AML cell line treated with DMSO, JQ1, and OTX015.

first: Sophia

last: Miliara

first: Bogumil

last: Kaczkowski

first: Elisabetta

last: Cozzi

first: Kathleen

last: Watt

first: Ri-ichiroh

last: Manabe

first: Yasushi

last: Okazaki

first: Sören

last: Lehmann

first: Ola

last: Larsson

first: Erik

last: Arner


title: AVE0991 regulates HOTAIRM1/miR-223-3p/α-synuclein to improve behaviour and protect dopaminergic neurons in human α-syn (A53T) overexpressing mice

status: Public on Nov 06 2024

city: nanjing

first: Rui

last: Duan

address: Yanshan road 139

country: China

institute: Nanjing First hospital

type: Non-coding RNA profiling by high throughput sequencing

summary:
Objective: Parkinson's disease (PD) is part of a common type of neurodegenerative disease. AVE0991, a non-peptide analogue of Ang-(1-7), by which the progression of PD has been discovered to be ameliorated, but the specific mechanism whereby AVE0991 modulates the progression of PD remains unclear.
Materials and Methods: During the study, the mice overexpressing of human α-syn(A53T) were established to simulate PD pathology, and we also constructed an in vitro model of mouse dopaminergic neurons overexpressing hα-syn(A53T). The [18F] FDG-PET/CT method was also employed to assess FDG uptake in human α-syn(A53T) overexpressing mice. Level of Lnc HOTAIRM1, miR-223-3p were detected via RT-qPCR. Flow cytometry was deployed to assay cell apoptosis.
Results: AVE0991 improved behavior disorder and decreased α-syn expression in the substantia nigra in mice with Parkinson's disease. AVE0991 inhibited apoptosis of dopaminergic neurons overexpressing hα-syn(A53T) by LncRNA HOTAIRM1. MiR-223-3p binds to HOTAIRM1 as a ceRNA and directly targets α-syn.
Conclusion:  The angiotensin-(1–7) analogue AVE0991 targeted the HOTAIRM1/miR-223-3p axis to degrade α-synuclein in PD mice, and showed neuroprotection in vitro.

overall_design: The right SNpc tissues of lncRNA profiles in human α-syn (A53T) overexpressing mice  and human α-syn (A53T) overexpressing mice  were treated with AVE0991

first: Feng

last: Wang

first: Xue

last: Xue

first: Qing

last: Gao


title: Characterization of cuprizone mouse model at single-cell and spatial transcriptomics level[snRNA-seq]

city: Cambridge

first: Baohong

last: Zhang

state: MA

address: 225 Binney St

country: USA

institute: Biogen Inc.

type: Expression profiling by high throughput sequencing

summary: We generated a comprehensive dataset utilizing the cuprizone model. This dataset encompasses bulk RNA-seq, single-nucleus RNA-seq (snRNA-seq), and spatial transcriptomics, with the aim of investigating the molecular changes linked to the cuprizone-induced demyelination phenotype. Integration of these omics dataset allowed us to investigate the changes occurring at both the single-cell and spatial levels, thereby enabling a deeper understanding of the cellular dynamics and molecular interactions associated with the cuprizone-induced demyelination phenotype.

overall_design: In the cuprizone (CPZ) group, male mice aged 6-8 weeks were administered a 0.3% Cuprizone diet for 4 weeks to induce demyelination in the brain (n = 3). In the recovery group, mice were administered CPZ diet for 4-weeks and then switched to a control diet for an additional 2 weeks (n = 3). In the control group, mice received the control diet throughout the entire 6-week study period (n = 4). At 4 (CPZ) and 6 weeks (Control and Recovery), mice were euthanized by carbon dioxide (CO2) inhalation, and their brains were subsequently dissected. Each brain was cut sagittally to separate left and right hemispheres, one brain hemisphere was trimmed into three coronal segments and embedded in OCT for snRNA-seq or spatial transcriptomic study, the other hemisphere was snap frozen for bulk RNA-seq study (Figure 1). To enrich for sequencing of cells from the corpus collosum and cortex, only the top half of the coronal section was collected for snRNA-seq, which includes the dorsal cortex, CC, and hippocampus.

first: Hui-Hsin

last: Tsai

first: Sarbottam

last: Piya

first: Jing

last: Zhu


title: Identification of Rbm25-binding RNAs in bone-marrow-derived macrophages by RIP-seq

city: Shanghai

first: Xingguang

last: Liu

address: Xiangyin road 800

department: National Key Laboratory of Immunity & Inflammation

institute: Naval medical university

summary: To identify the potential mRNAs that bound by Rbm25, which might be the direct target of Rbm25 for alternative splicing in murine macrophages.

overall_design: RIP-seq assays were performed using antibody against Rbm25 in M-CSF-differentiated BMDMs, following the instructions of Magna RIP RNA-Binding Protein Immunoprecipitation Kit (Millipore).

first: Yunkai


title: Modeling high-risk blastemal and metastatic Wilms tumors by reprogramming WiT49 cells

city: Madison

first: Wei

last: Xu

state: WI

address: 7459 WIMR II

department: McArdle Laboratory for Cancer Research

institute: University of Wisconsin-Madison

summary: Wilms' tumor (WT) is the most common pediatric kidney cancer with more than a 90% overall survival rate in response to standard chemotherapy. However, less-differentiated blastemal type of WT often metastasize and relapse. To remodel the high-risk WT for therapeutic intervention, we partially reprogrammed WIT49, a mixed type of WT cell line, to iPSCs, which we termed as WiT49-PRCs (Partial reprogrammed iPSCs). WiT49-PRCs express stem cell markers. When implanted into the kidney capsule in mice, WiT49-PRCs formed kidney tumors and developed both liver and lung metastases, whereas WiT49 tumors do not metastasize. Histological characterization and gene expression signatures demonstrated that WiT49-PRC recapitulates blastema-dominant WTs. Moreover, screening FDA-approved drugs in isogeneic WiT49 and WiT49-PRC cells led to the identification of epithelial- or blastemal-dominant WT-sensitive drugs. A subset of drugs was discovered with selectivity towards blastemal WT patient derived xenografts (PDXs).  HDAC inhibitors (e.g. panobinostat and romedipsin) were found universally effective across different WT and more potent than doxorubicin in PDXs. Taken together, WiT49-PRC serves as a blastemal-dominant WT model for therapeutic intervention to improve the treatment of high-risk WT patients.

overall_design: Wilms tumor cell line, WiT49 was partially reprogrammed into iPSC by transfecting the cells with episomal vectors. Real-time quantitative PCR was used to test the expression level of stem cell markers of the partial reprogrammed WiT49 cells (PRCs) and Parental cells. Orthotopic xenograft was performed to detect tumor growth and metastasis to the liver and lung. HE staining and RNA-seq was applied to determine the histology and gene expression signatures of WiT49-Parental and WiT49-PRCs. The histology and gene signatures of WiT49-Parental and WiT49-PRCs were compared with Wilms tumor patient and PDX samples. Drug screening was performed by using WiT49-Parental and WiT49-PRC models. Selected drugs including HDAC inhibitors were tested in epithelial and blastemal Wilms tumor PDX models.

first: Gui

last: Ma

first: Peng


title: H3K9ac and H3K27ac Cut&Tag profiling of wild type and Rbm25-deficient Bone Marrow Derived macrophage

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Purpose: To transcriptome widely reveal histone acetylation modification H3K9ac and H3K27ac regulation by Rbm25, we performed Cleavage Under Targets and Tagmentation (CUT&Tag) analysis of wild-type (WT) and Rbm25-deficiency BMDMs. Methods: Mouse BMDMs were generated from bone marrow cells in RPMI-1640 medium with recombinant mouse M-CSF (20ng/ml). BMDMs were stained to confirm the surface expression of CD11b and F4/80. Cells with purity >97.5% were used for subsequent experiments. WT and Rbm25 deficient BMDMs were stimulated with LPS (100ng/ml) for 4 hours. Results: We carried out CUT&Tag assays using antibody against H3K9ac or H3K27ac, and found the global influence of Rbm25 in regulating H3K9ac and H3K27ac of transcription regulatory regions of key genes for inflammatory macrophage effector function.

overall_design: Cleavage Under Targets and Tagmentation (CUT&Tag) analysis for histone modifications H3K9ac and H3K27ac in WT and Rbm25-deficiency BMDMs stimulated with LPS.


title: Next Generation Sequencing Facilitates Quantitative Analysis of wild type and Rbm25-deficient Bone Marrow Derived macrophages

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

overall_design: Refer to individual Series


title: Biological effects of recombinant S100A8, recombinant S100A9, and recombinant S100A8/S100A9 on human renal tubular epithelial cells (HK-2)

city: Guiyang

state: Guizhou

address: Zhongshan Road 83

department: Department of Urology

institute: Guizhou Provincial People's Hospital

summary: In order to explore how S100A8 and S100A9 may participate in the kidney stone formation, we used recombinant S100A8, recombinant S100A9, or recombinant S100A8/S100A9 heterodimer to culture the HK-2 cells and then sequenced total cellular mRNAS.

overall_design: We cultured the HK-2 cells with 5mg/mL recombinant S100A8, recombinant S100A9, or recombinant S100A8/S100A9 protein for 48h and then sequenced the total cellular mRNAS. mRNAS from HK-2 cells cultured with DMEM medium containing corresponding amount of PBS was set as the control group.

first: Jianqing

first: Kehua

last: Jiang

first: Fa

last: Sun


title: Next Generation Sequencing Facilitates Quantitative Analysis of wild type and Rbm25-deficient Bone Marrow Derived macrophage Transcriptomes

summary: Purpose: The purpose of this study is to detect activated or silenced genes during wild type (WT) and Rbm25-deficient bone marrow derived macrophages (BMDMs). Gene expression differences between two samples could be found using transcriptome profiling (RNA-seq) analysis. Methods: Mouse BMDMs were generated from bone marrow cells in RPMI-1640 medium with recombinant mouse M-CSF (20ng/ml). BMDMs were stained to confirm the surface expression of CD11b and F4/80. Cells with purity >97.5% were used for subsequent experiments. WT and Rbm25 deficient BMDMs were stimulated with LPS (100ng/ml) for 0, 2 or 8 hours, of which RNA profiles were generated by deep sequencing, using Illumina. Results: We mapped about 10 million sequence reads per sample to the mouse genome, identified hundreds of genes with significant mRNA variation between WT and Rbm25 deficient BMDMs.

overall_design: mRNA profiles of WT and Rbm25 deficient BMDMs were generated by deep sequencing.


title: The expression profile of serum lncRNAs in pregnant women with high hepatitis B viral load during antiviral and non-antiviral treatment

city: Nanning

first: wang

last: Cuimin

address: No. 6, Taoyuan Road, Qingxiu District

institute: Guangxi Academy of Medical Sciences

summary: This research analyzes the potential of long non-coding RNAs (lncRNAs) as markers in determining the necessity of antiviral treatment in pregnant women by examining alterations in the expression profile of serum lncRNAs in pregnant women with elevated hepatitis B viral load (HBVL) under antiviral and non-antiviral treatment regimens between the second trimester and delivery.

overall_design: Serum was obtained from six second-trimester pregnant women with high high hepatitis B viral load (HBVL) and no intrauterine infection. Then, three of these women were randomly selected for antiviral treatment, while the remaining three women were not subjected to antiviral treatment. Serum samples were again collected from these six women prior to delivery

first: Wang


title: Transcriptomic analysis of high-fat diet-fed mice treated with CYP4A inhibitors

city: Cheongju

first: Gun-Hwa

last: Kim

address: 162 Yeongudanji-ro

country: South Korea

institute: Korea Basic Science Institute

summary: Cytochrome P4504A (CYP4A) is known to be related to the development of type 2 diabetes (T2DM) and non-alcoholic fatty liver disease (NAFLD). We discovered selective CYP4A inhibitors, C481 (C1) and C482 (C2), and confirmed the therapeutic effects of these inhibitors on T2DM and NAFLD. In order to confirm the mechanisms of C1 and C2, inhibitors were treated in high-fat diet (HFD)-fed mice and RNA sequencing was performed using the liver tissues.

overall_design: Comparative gene expression profiling of RNA-seq data from the liver of HFD-fed mice and HFD-fed mice treated with C1 or C2.

first: Minji

last: Lee

first: Gun

middle: H


title: Transcriptional response of Ustilago maydis to hemin treatment to identify key proteins involved in hemin uptake

city: Vancouver

first: James

last: Kronstad

state: BC

address: 2185 E Mall

department: Mircobiology and Immunology

country: Canada

institute: University of British Columbia

summary: Many phytopathogens such as Ustilago maydis rely on their hosts for nutrients during disease. In this study, we tried to identify key genes involved in heme uptake and gain a deeper understanding of the transcriptional response to hemin treatment. We observed upregulations in ergosterol biosynthesis pathway as well as identified an Abc1 protein with pleitropic contributions to cell surface functions.

overall_design: Pnar1::hem12 strains were treated for 1 hour in ON/NM or OFF/AM or OFF + 15µM hemin or OFF + 15µM FeCl3 prior to RNA isolation. 3 biological replicates were used for each treatment.

first: Djihane

last: Damoo

first: Christopher

middle: W


title: RNA helicase D1PAS1 resolves R-loops and forms a complex for mouse pachytene piRNA biogenesis required for male fertility

city: Bethesda

first: Heejin

last: Choi

state: Maryland

address: 50 South drive, Building 50, Room 3131

department: NIDDK

institute: NIH

summary: To investigate the function of RNA helicase D1PAS1 in mouse spermatogenesis, we established D1Pas1 knockout (KO) and D1Pas1-FLAG knockin (KI) lines in which the D1Pas1 gene has been knocked out by deleting the transcription start site and the 3XFLAG sequences added at the end of C-term by CRISPR/Cas9. We then performed gene expression profiling analysis using data obtained from RNA-seq of 3 different biological replicates at three different developmental stages. Investigated small RNA abundance from WT and KO testis via small RNA-seq. To profile the genome-wide D1PAS1 RNA helicase dependent R-loop loci, we performed BisMapR sequencing analysis with D1PAS1 KI and KO spermatocytes.

overall_design: Expression profiling of differentially expressed genes by RNA-seq at three different developmental stages, small RNA abundance by small RNA-seq, genome-wide RNA:DNA hybrids (R-loop) profiling by BisMapR, and D1PAS1-bound RNA by eCLIP-sequencing.

first: Lecong

last: Zhou

first: Yangu

last: Zhao

first: Jurrien

last: Dean


title: Novel Mouse Model for Tissue-specific Extracellular Vesicle Isolation and Characterization

city: Rochester

first: Gabriela

last: Mendez-Pacheco

state: MN

address: 200 1st St SW

department: Quantitative Health Sciences

institute: Mayo Clinic

summary: Extracellular vesicles (EVs) are key mediators of intercellular communication, with important roles in numerous physiological and pathological processes, including profound effects on bone metabolism. These small membrane-bound vesicles are produced and released in the extracellular environment by virtually all cell types, including cells in the osteogenic lineage such as bone marrow-derived mesenchymal stem cells (MSCs), osteoblasts, osteoclasts and osteocytes. EVs serve as potent carriers of bioactive molecules, such as nucleic acids, proteins, lipids and metabolites, where they can influence recipient cells through fusion with target cell membranes to deliver these functional biomolecules. However, once released, the source cell of the EV is difficult to ascertain with any certainty. To overcome this obstacle, we developed a conditional (e.g. Cre-mediated) mouse model that expresses an EV tag, containing a fusion of CD81 and multiple C-terminal tags, termed the “Snorkel-tag”. By crossing with a Cre of interest, representing a specific cell-type or tissue, the specific EV subpopulation that is released can be isolated using antibody affinity columns.  We crossed the CAGS-Snorkel mouse with Prx1-Cre and Ocn-Cre, representing cell-types in the early vs late stages of osteoblast differentiation. Isolation of Prx1-EVs and Ocn-EVs was performed from the mouse bone marrow plasma. We performed miRNA-sequencing to determine the specific miRNA cargo in these different EV subpopulations and found miRNAs involved in bone metabolism and function to be expressed, some of which are enriched in the Ocn-EVs. In summary, the CAGS-Snorkel mouse model will be useful in the characterization of EVs from diverse cell- and tissue-types in the mouse.

overall_design: We crossed the CAGS-Snorkel mouse with either the Prx1-Cre (n=10, 5 male/5 female) or Ocn-Cre (n=6, 3 male/3 female), all mice were 6 months old at sacrifice. All mice were in the C57BL/6N background. EVs were isolated from the bone marrow plasma from these mice using an HA-antibody magnetic-bead affinity column. RNA was isolated from the EVs using the Rneasy Plus Kit (Qiagen) and miRNA-sequencing was performed.

first: David

middle: G

last: Monroe

first: Chantal

middle: E

last: McCabe

first: Bryan

middle: T

last: Piatkowski

first: Sundeep

last: Khosla


title: Exonuclease-assisted identification of pseudouridine sites in single-stranded RNA

city: Wuhan

first: Ziang

last: Lu

address: Wuhan University, No.299, Bayi Road, Wuchang District

institute: Wuhan University

summary: Pseudouridine is considered as the most abundant modified nucleotides in RNA, playing an indispensable role in various life processes. The identification of pseudouridine sites provides the basis for the study of their function. Here, we proposed a new method for the identification of pseudouridine sites with a higher signal-to-noise ratio, combining CMC-specific labeling of pseudouridine sites and exonuclease-assisted strategy. We called this method exonuclease-assisted identification of pseudouridine sites (EAIPS).

overall_design: By using exonuclease XRN1 to digest the RNA strands that were not labeled by CMC, we could greatly reduce the background signal of unlabeled strands, while the pseudouridine sites that were specifically labeled by CMC could terminate exonuclease digestion at one nucleotide 5’ to the pseudouridine sites due to the steric hindrance of CMC. Moreover, we used EAIPS to distinguish pseudouridine sites in single-stranded and double-stranded regions of RNA. Our results indicated that CMC could only specifically label pseudouridine sites in single-stranded regions, but not in double-stranded regions, and thus EAIPS enabled selectively identification of pseudouridine sites in the single-stranded RNA.

first: Xin

last: Fang

first: Xiaocheng

last: Weng

first: Xiang


title: Characterization of N6-Methyladenosine lncRNAs in sporadic congenital cataract and age-related cataract

first: zhennan

last: zhao

address: Fenyang Road 83

institute: Fudan university EENT

summary: To characterize the N6-methyladenosine (m6A) modification patterns in long non-coding RNAs (lncRNAs) in sporadic congenital cataract (CC) and age-related cataract(ARC).

overall_design: anterior capsule of the lens were collected from patients with CC and ARC. m6A-modified RNA immunoprecipitation sequencing and RNA sequencing were performed to identify M6A-tagged lncRNAs and lncRNAs expression. Gene Ontology annotation and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses were used to predict possible functions of the m6A-lncRNAs.

first: Hongfei

last: Ye

first: Zhennan

first: Peiquan


title: WT MSCs displayed a different transcriptional profile than KO MSCs.

city: Guangzhou

first: Jingrou

last: Chen

address: Zhongshan 2nd Road, Yuexiu District

institute: Sun Yat-Sen University

summary: To explore the molecular basis of the therapeutic function of MSCs, we performed RNA-sequencing of LPS-treated MSCs.Transcriptome analysis identified the upregulation of 673 genes and downregulation of 831 genes, and plot the top 100 differentially expressed genes into a heatmap.KEGG pathway enrichment analysis indicated that energy metabolism pathways were highly enriched in the cell cycle.

overall_design: WT and KO MSCs were stimulated with/without 3 μg/mL LPS for 24 h.Total RNA was extracted and purified using TRIzol reagent (Invitrogen, USA) according to the manufacturer’s protocol.The library was sequenced with Illumina Novaseq™ 6000 by 2×150bp paired-end sequencing (PE150) (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol. T

first: Chen

last: Jingrou

first: Peng

last: Yanwen

first: Qiu

last: Dongbo

first: Xie

last: Shujuan


title: Next Generation Sequencing Facilitates Quantitative Analysis of undamage chondrocyte and damage chondrocyte whole Transcriptomes

city: guangzhou

first: dianbo

last: long

state: guangdong

address: Zhongshan second road

institute: First Affiliated Hospital of Sun Yat-sen University

summary: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare undamage chondrocyte and damage chondrocyte whole transcriptomes

overall_design: Whole Transcriptomes profiles of undamage chondrocyte and damage chondrocyte were generated by deep sequencing

first: Dianbo

first: Guping

last: Mao

first: Guangxin

last: Huang

first: Zengfa

last: Deng

first: Yan

last: Kang

first: Aishan

last: He

first: Ziji

last: Zhang


title: Epigenetic-driven Synergistic and Antagonistic regulation on Transposable Elements Carried Out by HDA6 and LDL1/2 [ncRNA-Seq]

city: Taipei

first: Pao-Yang

address: 128 Sec. 2, Academia Rd, Nankang,

department: Institute of Plant and Microbial Biology

country: Taiwan

institute: Academia Sinica

summary: Histone deacetylases (HDAs) are evolutionally conserved enzymes and often form a multiprotein complex with histone Lysine-Specific Demethylase 1 (LSD1) to play central roles in epigenetic silencing in yeast and animals. In Arabidopsis, either HDA6 or LSD1-LIKE 1 and 2 (LDL1/2) are known to silence transposable element (TE), but their joint effect remains unexplored. Here, we revealed the individual and joint effects of HDA6 and LDL1/2 carefully by examining the transcriptomes, the genome wide distribution of H3Ac, H3K4me2, and DNA methylation in wildtype and mutants (hda6, ldl1/2 and hda6/ldl1/2). We found that HDA6 silenced 517 TEs by itself, LDL1/2 silenced 2 TEs alone and HDA6 silenced 15 TEs in cooperation with LDL1/2; suggesting that HDA6 has a stronger impact on TE silencing than LDL1/2; the effect of HDA6 is mostly independent of LDL1/2 whereas most LDL1/2 effect requires HDA6. Also, we observed that the expression of TE showed clear synergistic (enhanced de-repression in hda6/ldl1/2) and antagonistic (lower de-repression in hda6/ldl1/2) effects at different sets of TEs. Further analysis showed that the TEs targeted by either of the two effects exhibited totally different epigenome patterns.

overall_design: To investigate the role of HDA6 and LDL1/2 on transposon regulation, we conducted whole genome bisulfite sequencing (WGBS), ATAC-seq and smRNA-seq from WT, hda6, ldl1/2 and hda6/ldl/1/2 plants

first: Jo-Wei

middle: A

last: Hsieh

first: Ming-Ren

last: Yen


title: Epigenetic-driven Synergistic and Antagonistic regulation on Transposable Elements Carried Out by HDA6 and LDL1/2

type: Methylation profiling by high throughput sequencing


title: Epigenetic-driven Synergistic and Antagonistic regulation on Transposable Elements Carried Out by HDA6 and LDL1/2 [WGBS]


title: The PAF1 Complex Regulates Transcriptional Termination and Reinitiation [TT-seq]

first: Aiwei

last: Wu

state: Shanghai

address: 800 Dongchuan Road

department: School of Life Sciences and Biotechnology

institute: Shanghai Jiao Tong University

summary: Chromatin places fundamental physical constraints on transcription (Gamarra and Narlikar, 2021). The PAF1 complex (PAF1C), a hexamer of PAF1, LEO1, CTR9, SKI8, CDC73 and RTF1, plays a critical role in transcription with incompletely understood mechanisms. During transcriptional elongation, PAF1C is one of the positive elongation factors in complex with RNA polymerase II (Pol II) to facilitate elongation through chromatin (Vos et al., 2018), but it is unclear yet if negative elongation factors are needed concurrently to restrain elongation. Here we show that besides decreasing elongation rate, LEO1 knockout in human K562 cells increases transcriptional readthrough and cellular level of C-terminal domain (CTD) phosphorylated Pol II while increases and decreases transcriptional output of several hundred genes, respectively. Mechanistic analyses taking proteomic, functional genomic and biochemical approaches discovered that PAF1C regulates transcriptional termination in part through recruiting PNUTS-PP1γ complex and facilitates Pol II transcriptional re-initiation through recruiting TOX4-PP1α complex. Moreover, Paf1 conditional knockout in mice severely blocks T cell development, increases cellular level of CTD phosphorylated Pol II, mainly decreases Pol II occupancy and transcriptional output in double positive T cells, and importantly, the regulation of re-initiation by PAF1C through TOX4-PP1α complex is conserved between mouse and human. Our results also suggest that PNUTS-PP1γ and TOX4-PP1α bind PAF1C to restrain Pol II elongation through chromatin. These findings not only establish PAF1C as a critical regulator of transcriptional termination and re-initiation besides elongation but also advanced current understanding of elongation.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: TT-seq of proteins envolved in transcription regulation in control , LEO1 KO and PNUTS KO human K562 cells and in WT and Paf1 cKO DP thymocytes

first: Ming

last: Yu

first: Ziling

last: Liu

first: Talang

last: Wang


title: Epigenetic-driven Synergistic and Antagonistic regulation on Transposable Elements Carried Out by HDA6 and LDL1/2 [ATAC-Seq]

last: Chen


title: The PAF1 Complex Regulates Transcriptional Termination and Reinitiation [ChIP-seq]

overall_design: ChIP-seq of total Pol II in control and PAF1 knockdown HEL cells


title: The PAF1 Complex Regulates Transcriptional Termination and Reinitiation [RNA-seq]

overall_design: RNA-seq in control , LEO1 KO and PNUTS KO human K562 cells, in WT and Paf1 cKO DP thymocytes, and in control and PAF1 knockdown HEL or CCRF-CEM cells.


title: Low input RNA Sequencing of effector and naive WT and NCOR1-cKO CD4+ Treg cells

city: Vienna

first: Wilfried

last: Ellmeier

address: Lazarettgase 19

department: Institute of Immunology

country: Austria

institute: Medical University of Vienna

summary: Analysis of Treg cells isolated from WT and NCOR1-cKO mice indicated an important function of NCOR1 in regulating the transition from naïve to effector Treg cells. The aim of this NGS experiment was to determine the transcriptome profile of ex vivo isolated naïve and effector WT and NCOR1-cKO Treg cells under steady state condition.

overall_design: mRNA expression profiles of naïve (CD44loCD62L+) and effector (CD44hiCD62L-) WT and NCOR1-cKO Treg cells were generated by low input RNA Sequencing. Therefore, Treg cells were isolated from the spleen and lymph nodes of either WT mice or mice with a conditional deletion of NCOR1 (using Ncor1fl/fl Cd4-Cre mice). The mice additionally harbored a DEREG Foxp3-eGFP reporter, in which GFP expression is driven by Fopx3 regulatory elements (Lahl et a. 2007). Cells were FACS sorted using a SH800 Sorter (SONY).

first: Valentina

last: Stolz


title: Tumor cell-specific Gpx4 deficiency reshaps tumor microenvironment and promotes NSCLC progression.

status: Public on Nov 05 2024

first: 鹏

last: 王

email: wangp00678@163.com, wangp94@whu.edu.cn

state: 湖北省

address: 169 Donghu nan road,Wucang District

institute: 武汉大学

summary: Knockout or inhibition of glutathione peroxidase 4 (GPX4) induces ferroptosis which has been proposed as a potential therapeutic strategy for cancer. Here we unexpectedly found that inducible knockout of GPX4 in tumor cells significantly promotes non-small cell lung cancer (NSCLC) progression in the autochthonous KrasLSL-G12D/+Lkb1fl/fl (KL) and KrasLSL-G12D/+Tp53fl/fl (KP) mouse models, whereas inducible overexpression of GPX4 in tumor cells had an opposite effect. Mechanistically, knockout of GPX4 in tumor cells results in the accumulation of triacylglycerol (TAG) that was stored in lipid droplets in tumor cells and the efflux of TAG that induces ferroptosis of macrophages in the tumor microenvironment (TME), thereby igniting an immunoinhibitory TME characterized by the dysfunction of anti-tumor T cells and the decrease of antigen-presenting macrophages. Consistently, treatment with liprostatin-1 or inducible overexpression of GPX4 in tumor cells significantly rescues the ferroptosis of macrophages and ignites the activation of T cells in the TME, thereby inhibiting NSCLC progression. These findings highlight a previously uncharacterized role of tumor cell-specific GPX4 in NSCLC progression by modulating TAG metabolism in the TME  and provide potential therapeutic strategies for NSCLC.

overall_design: Comparative gene expression profiling analysis of single cell RNA-seq data in immune cells sorted from tumor-burdened lungs of KrasLSL-G12D/+Tp53fl/flIL8 mice.

first: Wang

last: Peng

first: Dandan

last: Lin

first: Bo

last: Zhong


title: The PAF1 Complex Regulates Transcriptional Termination and Reinitiation [4sUDRB-seq]

overall_design: 4sUDRB-seq in control, LEO1 KO and PNUTS KO human K562 cells


title: Gene expression at single cell level of cells from genetically modified mouse colon tumors

city: Glasgow

first: Kathryn

last: Gilroy

address: Switchback Road

country: United Kingdom

institute: Cancer Research UK Scotland Institute

summary: In the colonic epithelium, fetal programming is induced by Yes-associated protein (YAP) signaling, which is associated with tumorigenesis and progression in colorectal cancer (CRC). While CRC was long considered a Wnt driven disease, we showed fetal programmed cells with activated YAP signaling can arise independently of Wnt activation. Fetal programmed cells, in the presence of hyper- or hypo-activated Wnt, have different characteristics and are associated with poor relapse. Furthermore, using various mouse models, we demonstrated the conserved characteristics of two different fetal programmed cell states with different Wnt activation, which can be switched from hyperactivated to hypoactivated Wnt state based on genetic alteration, particularly Kras mutation. Altogether, these data redefine the key determinants of epithelial cell states in colorectal cancer and integrate emerging preclinical biology into a robust landscape of states observed in human and mouse.

overall_design: Colonic tumour cells with combinations of Apc, Braf, Kras, P53, Notch and Tgfbr1 mutations were isolated by fluorescence activated cell sorting (FACS) and analysed using scRNAseq.

first: Tamsin

last: Lannagan

first: Megan

last: Mills

first: Yourae

last: Hong

first: Owen

last: Sansom


title: Defects in CYB5A and CYB5B Impact Sterol C4 Demethylation in Cholesterol Biosynthesis and Demonstrate Regulatory Roles of Dimethyl Sterols

city: wuhan

first: meiyan

last: ma

institute: wuhan university

summary: All RNA-sequencing data included in this study were included in this data set.

overall_design: There were four groups: WT-NC Fasted, WT-NC refed, Liver-Cyb5b_shCyb5a Fasted, and Liver-Cyb5b_shCyb5a Refed

first: Meiyan

last: Ma


title: The PAF1 Complex Regulates Transcriptional Termination and Reinitiation

first: Aiwei

last: Wu

overall_design: Refer to individual Series


title: Transcriptomic and metabolomic changes might predict frailty in SAMP8 mice

city: Milan

first: Letizia

last: Messa

address: Piazza Leonardo Da Vinci 32

department: Electronics, Informatics and Bioengineering

country: Italy

institute: Politecnico di Milano

summary: Frailty is a geriatric multi-dimensional syndrome which reflects multisystem physiological change and is a transversal measure of reduced resilience to negative events. It is characterized by weakness, frequent falls, cognitive decline, increased hospitalization and dead, and represents a risk factor for the development of Alzheimer’s disease (AD). The fact that frailty is recognized as a reversible condition, encourages the identification of earlier biomarkers to timely predict and prevent its occurrence. SAMP8 (Senescence-Accelerated Mouse Prone-8) mice represent the most appropriate preclinical model to this aim and were used in this study to carry transcriptional and metabolic analyses in the brain and plasma respectively, upon a characterization at cognitive, motor, structural and neuropathological level at 2.5, 6 and 9 months of age. At 2.5 months SAMP8 mice started displaying memory deficits, muscle weakness and motor impairment. Functional alterations were associated with a neurodevelopment deficiency associated with reduced neuronal density and glial cell loss. Through transcriptomics we identified specific genetic signatures well distinguishing SAMP8 mice at 6 months and correlating with motor and cognitive dysfunction, whereas plasma metabolomics allowed to segregate SAMP8 mice from SAMR1 already at 2.5 months of age by detecting constitutively lower levels of acylcarnitines and lipids in SAMP8 at all ages investigated. Our findings suggest that specific genetic alterations at central level, as well as metabolomic changes in plasma, might allow to early assess a frail condition leading to dementia development, which paves the foundation for future investigation in a clinical setting.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for SAMP8 with respect to SAMR1 mice in frailty

last: Dacomo

first: Pietro

last: La Vitola

first: Laura

last: Brunelli

first: Edoardo

last: Micotti

first: Luisa

last: Artioli

first: Elena

last: Sinopoli

first: Greta

last: Cecutti

first: Susanna

last: Leva

first: Stella

last: Gagliardi

first: Orietta

last: Pansarasa

first: Stephana

last: Carelli

first: Antonio

last: Guaita

first: Roberta

last: Pastorelli

first: Gianluigi

last: Forloni

first: Cristina

last: Cereda

first: Claudia

last: Balducci


title: Phytic acid improves the skin barrier function in murine models of atopic dermatitis through skin microbiota‑derived indole-3-propionic acid

first: wang

last: piao

address: jingxi street

department: nanfang hospital

institute: southern medical university

summary: To explore the specific mechanism of phytic acid improving atopic dermatitis，we then and RNA-seq analysis to investigate whether phytic acid improves AD by affecting tryptophan metabolism

overall_design: Comparative gene expression profiling analysis of RNA-seq data for MC903-treatment and MC903 plus PA treatment

first: Piao

last: Wang

first: Gaofeng


title: Blood gene expression profiles of children with wheezing

city: Memphis

first: Zhaohui

last: Xu

state: TN

address: 262 Danny Thomas Place

department: Infectious Diseases

institute: St. Jude Children's Research Hospital

summary: Analyze the gene expression changes in children with or without wheezing during the first 3 years of life

overall_design:
Total RNA obtained from whole blood of children in the first 15 days of life (Y0) and sequentially evaluated at 1 year of age (Y1), 2 (Y2) and 3 years (Y3)
*** Submitter declares that IDAT files are not available anymore. ***

first: Rosa

last: Rodriguez

first: Octavio

last: Ramilo

first: Asuncion

last: Mejias


title: Decreases in adiponectin mediate inhibition of regenerative lung growth in obese mice

city: Milwaukee

first: Akiko

last: Mammoto

address: 8701 Watertown Plank rd

institute: Medical College of Wisconsin

summary: Obesity is associated with impairments of wound healing and tissue regeneration. Angiogenesis, the formation of new blood capillaries, plays a key role in organ regeneration and repair. Inhibition of lung angiogenesis impairs regenerative lung growth after unilateral pneumonectomy (PNX). However, the effects of obesity on post-PNX lung vascular and alveolar morphogenesis remain unclear. In this report, we have demonstrated that regenerative lung growth and angiogenic factor VEGFA expression induced by PNX are inhibited in Lepob/ob obese mice compared to Lepob/- mice. The levels of adiponectin, one of the adipokines that exhibits pro-angiogenic and vascular protective properties, increase in endothelial cells (ECs) isolated from remaining mouse lungs after unilateral PNX, while these effects are attenuated in Lepob/ob obese mice. Post-PNX lung growth, vascular and alveolar morphogenesis, and VEGFA levels in the lungs are inhibited in adiponectin knockout mice. Adiponectin agonist, AdipoRon stimulates post-PNX lung growth and vascular and alveolar morphogenesis in Lepob/ob obese mice. These findings suggest that obesity impairs lung vascular and alveolar regeneration and adiponectin may be one of the key molecules to improve lung regeneration in obese people.

overall_design: Mouse lung endothelial cells were isolated from C57Bl6J mouse lungs (8 week old male mice) 7 days after PNX and sham-operated mouse lungs (n=3 per group, each n was pooled from 2 male mice) using anti-CD31 conjugated magnetic beads for transcriptome analysis.

first: Tadanori

first: Kathryn

last: Hendee


title: The PAF1 Complex Regulates Transcriptional Termination and Reinitiation [CUT&Tag]

city: Shanghai

first: Aiwei

last: Wu

overall_design: CUT&Tag of proteins envolved in transcription regulation in control , LEO1 KO and PNUTS KO human K562 cells and in WT and Paf1 cKO DP thymocytes

first: Ming

last: Yu

first: Ziling

last: Liu

first: Talang


title: Conserved role for spliceosomal component PRPF40A in microexon splicing

city: Riverside

first: Adam

middle: David

last: Norris

state: CA

address: 3401 Watkins Drive

institute: University of California, Riverside

summary: Microexons (exons ≤30 nts) are important features of neuronal transcriptomes, but pose mechanistic challenges to the splicing machinery. We previously showed that PRP-40, a component of the U1 spliceosome, is globally required for microexon splicing in C. elegans. Here we show that the homologous PRPF40A is also globally required for microexon splicing in mouse neuroblastoma cells. We find that PRPF40A co-regulates microexons along with SRRM4, a neuron-specific regulator of microexon splicing. The relationship between exon size and dependence on PRPF40A/SRRM4 is distinct, with SRRM4-dependence exhibiting a size threshold (~30 nts) and PRPF40A-dependence exhibiting a graded decrease as exon size increases. Finally, we show that PRPF40A knockdown causes an increase in productive splicing of its spliceosomal binding partner Luc7l by skipping of a small “poison exon.” Similar homeostatic cross-regulation is often observed across paralogous RNA binding proteins. Here we find this concept likewise applies across evolutionarily unrelated but functionally and physically coupled spliceosomal components.

overall_design: Mouse neuroblastoma N2a cells treated with siRNAs against PRPF40a, or PRPF40b, or SRRM4. Each condition performed in biological triplicate


title: The spatially resolved transcriptional profile of acute T cell-mediated rejection in a kidney allograft

city: New York

first: Miguel

last: Fribourg

state: NY

address: 1 Gustave Levy Pl

department: Medicine

institute: Icahn School of Medicine at Mount Sinai

summary: Herein, we used the whole exome GeoMX Digital Space Profiling platform to study five tubular and three glomerular regions of interest in the kidney graft biopsy from a patient with a chronic-active TCMR episode and in analogous areas from two different normal kidney control biopsies. All kidney sections were from paraffin blocks. Overall, inflammatory genes were significantly upregulated in the tubular areas of the TCMR biopsy and showed an enrichment for gene-ontology terms associated with T-cell activation, differentiation, and proliferation. Enrichment analysis of the 100 genes with the highest coefficient of variation across the TCMR tubular regions of interest revealed that these highly variable genes are involved in kidney development and injury and interestingly do not associate with the 2019 Banff classification pathology scores within the individual regions of interest. Spatial transcriptomics allowed us to unravel a previously unappreciated variability across different areas of the TCMR biopsy related to the graft response to the alloimmune attack, rather than to the immune cells

overall_design: Serially sectioned formalin fixed and paraffin embedded kidney biopsies from healthy control pateints (n=2) and a kidney receipient with acute cellular rejection (n=1),  were processed for digital spatial profiling to explore compartment-specific transcriptional programs of the selected 6 glomeruar and 13 tubular regions.

first: Paolo

last: Cravedi


title: Fibroblast-derived extracellular vesicles contain SFRP1 and mediate pulmonary fibrosis

city: Dijon

first: Olivier

last: Burgy

state: Côte-d'Or

address: 7 boulevard Jeanne d'Arc

department: U1231 Center For Translational and Molecular Medicine

country: France

institute: Université de Bourgogne

summary: Idiopathic pulmonary fibrosis (IPF) is a lethal chronic lung disease characterized by aberrant intercellular communication, extracellular matrix deposition and destruction of functional lung tissue. While extracellular vesicles (EVs) accumulate in the IPF lung, their cargo and biological effects remain unclear. We interrogated the proteome of EV and non-EV fractions during pulmonary fibrosis and characterize their contribution to fibrosis. EVs accumulated 14 days post-bleomycin challenge, correlating with decreased lung function and initiated fibrogenesis in healthy precision-cut lung slices. Label-free proteomics of broncho-alveolar lavage fluid (BALF)-EVs collected from mice challenged with bleomycin or control identified 107 proteins enriched in fibrotic vesicles. Multiomic analysis revealed fibroblasts as a major cellular source of BALF-EV cargo, which was enriched in Secreted Frizzled Related Protein 1 (SFRP1). Sfrp1 deficiency inhibited the activity of fibroblast-derived EVs to potentiate lung fibrosis in vivo. SFRP1 led to increased transitional cell markers, such as Krt8, and WNT/β-catenin signaling in primary alveolar type 2 cells. SFRP1 is expressed within the IPF lung and localized at the surface of EVs from patient-derived fibroblasts and BALF. Our work reveals altered EV protein cargo in fibrotic EVs promoting fibrogenesis and identifies fibroblast derived vesicular SFRP1 as fibrotic mediator and potential therapeutic target for IPF.

overall_design: EVs were concentrated from the conditioned media of Sfrp1-/- and Sfrp1+/+ primary mouse lung fibroblasts and instilled intratracheally into mice previously challenged with bleomycin at D0. EVs were administered repeatedly starting day 8 post-bleomycin (n=4 mice BLM + Sfrp1+/+pmLF-EVs, n=4 mice BLM + Sfrp1-/-pmLF-EVs). At D21, lung tissue samples were collected and flash frozen in liquid nitrogen before analysis. mRNA sequencing on whole lung extract was carried out to shed light in the mechanisms involved in vesicular SFRP1 effects during fibrosis. Total RNA was extracted using a Trizol standard protocol. Messenger RNAs were purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using dTTP. It was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries were pooled and sequenced on Illumina platform (NovaSeq PE150), according to effective library concentration and data amount (30M reads/sample).

first: Melanie

last: Königshoff

first: Gerald

last: Burgstaller

first: Qianjiang

last: Hu


title: SOX4/11 Enhances NGN2 Reprogramming Glioblastoma Cells into Neuron Cells by Modulating RhoA and CDC42/RAC1 Pathway Activity

city: DALLAS

first: jianjing

last: Yang

state: TX

address: 6000 Harry Hines Blvd

department: Molecular Biology

institute: UT Southwestern Medical Center

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


title: Single cell RNA sequencing of CD45+ immune cells from tumor and tumor-adjacent mammary adipose tissue in a postmenopausal breast cancer model of lean, obese, and weight loss Trem2+/+ and Trem2-/- mice

city: Nashville

first: Matthew

last: Cottam

address: 2301 Vanderbilt Place

department: Surgical Sciences

institute: Vanderbilt University Medical Center

summary: Triggering receptor expressed on myeloid cells 2 (Trem2) has been shown to be immunosuppressive in cancer and increased in obese adipose tissue. We utilized high fat and low fat diet to generate lean, obese, and weight loss mice in Trem2 wild-type (Trem2+/+) and Trem2 deficient (Trem2-/-) conditions. Once obesity and weight loss were established, mice were injected with E0771 breast cancer cells and tumors were allowed to grow for 4 weeks. We wanted to better understand the immune landscape of both the tumor and the surrounding adjacent mammary adipose tissue (mAT). Therefore, the CD45+ immune cells from both the tumor and tumor-adjacent mAT were isolated and sequenced using single-cell RNA sequencing and V(D)J sequencing.

overall_design: Samples include live CD45+ cells from the tumor and tumor-adjacent mammary adipose tissue of lean, obese, and weight loss Trem2+/+ and Trem2-/- C57BL/6J mice. A sample size of 3-4 is included for each group.

first: Elysa

last: Pierro

first: Alyssa

last: Hasty

first: Barbara

last: Fingleton

first: Jeffrey

middle: C

last: Rathmell

last: Wellen

first: Liza

last: Makowski


title: CRISPR-StAR, a paradigm leveraging internal controls, empowers genetic screening in vivo

first: Esther

last: Uijttewaal

address: Dr Bohrgasse 3

institute: IMBA


title: CRISPR-StAR, a paradigm leveraging internal controls, empowers genetic screening in vivo (batch 2)

summary: Pooled genetic screening with CRISPR/Cas9 has enabled genome-wide high-resolution assignment of genes to phenotypes. To assess the effect of a given genetic perturbation, each sgRNA must be evaluated in hundreds of cells to overcome stochastic genetic drift and obtain robust results. In complex models that display particularly high heterogeneity, such as organoids or tumors transplanted into mice however, sufficient representation typically requires unreasonable scaling, thus preventing genome-wide screens at high resolution. Here we present CRISPR-StAR, a screening paradigm that overcomes intrinsic and extrinsic heterogeneity as well as genetic drift in bottlenecks by leveraging internal controls generated through activating sgRNAs only in half of the progenies of each cell. We use CRISPR-StAR to reveal in vivo-specific genetic dependencies in a genome-wide screen in mouse melanoma. Benchmarking to a conventional screening setup highlights the improved data quality this technology delivers. We anticipate CRISPR-StAR to set a new standard for genetic screening in complex models, foremost in vivo.

overall_design: To investigate the in vivo-specific dependencies in melanoma, we performed a genome-wide CRISPR/Cas9 screen, as well as smaller validation screens. The samples obtained from the screened in vivo tumors and in vitro cells were processed with NGS. And subsequently analysed using Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout (MAGeCK). However, we performed analysis according the CRISPR-StAR analysis method.  Genome-wide screen was performed in 2 batches.

first: Ulrich

last: Elling


title: Monocyte-derived IL-6 Programs Microglia to Rebuild Damaged Brain Vasculature

city: Bethesda

first: Kory

middle: R

last: Johnson

state: MD

address: 10/3B01, 9000 Rockville Pike

department: DIR IT & Bioinformatics

institute: NINDS/NIH

summary: Cerebrovascular injury (CVI) is a common pathology caused by infections, injury, stroke, neurodegeneration, and autoimmune disease. Rapid resolution of a CVI requires a coordinated innate immune response. In this study, we sought mechanistic insights into how CNS infiltrating monocytes program resident microglia to mediate angiogenesis and cerebrovascular repair following intracerebral hemorrhage. In the penumbrae of human stroke brain lesions, we identified a subpopulation of microglia that express VEGFA. These cells, termed repair associated microglia (RAM), were also observed in a rodent model of CVI and co-expressed IL-6Ra. Cerebrovascular repair did not occur in IL-6 knockouts or in mice lacking microglial IL-6Ra expression, and single cell transcriptomic analyses revealed faulty RAM programming in the absence of IL-6 signaling. Infiltrating CCR2+ monocytes were the primary source of IL-6 following CVI and were required to endow microglia with proliferative and pro-angiogenic properties. Faulty RAM programming in the absence of IL-6 or inflammatory monocytes resulted in poor cerebrovascular repair, neuronal destruction, and sustained neurological deficits that were all restored via exogenous IL-6 administration. These data provide a molecular and cellular basis for how monocytes instruct microglia to repair damaged brain vasculature and promote functional recovery after injury.

overall_design: Brain samples from 4 different mice representing Sham injury (Ctrl) under IL-6 WT (+/+) condition (S1), Cerebrovascular injury (CVI) under IL-6 WT (+/+) condition (S2), Sham injury (Ctrl) under IL-6 KO (-/-) condition (S3), and Cerebrovascular injury (CVI) under IL-6 KO (-/-) condition (S4) were analyzed by scRNAseq.

first: Bo-Ran

last: Choi

first: Dragan

last: Maric

first: Dorian

middle: B

last: McGavern


title: CRISPR-StAR, a paradigm leveraging internal controls, empowers genetic screening in vivo (batch 1)


title: Credentialling a c-MYC–driven genetic neuroblastoma model for pre-clinical studies

first: Xiang

last: Chen

department: Computational Biology

institute: St.Jude Children's Research Hospital

summary: single cell nuclear RNAseq of transgenic murine neuroblastoma model driven by conditional c-MYC induction in dopamine β-hydroxylase-expressing cells,

overall_design: Th-Cre/CAG-MYC mice were scanned using ultrasound to detect tumors.Single cell Nuclei was isolated from Frozen tissue following protocol ST based method Slyper et al 2020,Nat.Medicine. The isolated nuclei was processed on 10X Genomics Chromium platform following the ScRNASeq v3 protocol.

first: Tingting

last: Wang

first: Lingling

last: Liu

first: Fang

last: Jie

first: Hongjian

last: Jin

first: Jun


title: Credentialling a c-MYC-driven genetic neuroblastoma model [RNAseq-NB]

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hospital

summary: This project is to compare the transcriptomics of neuroblastomas and pancreatic neuroendocrine tumors derived from transgenic Myc mouse models.

overall_design: To investigate the gene expression profiles in different mouse tumor models, tumor total RNA were isolated and perform RNA-seq.

first: Jie

last: Fang

first: Ruoning

last: Yang


title: Transcriptional remodeling of human hematopoeitic stem cells in vitro by Interleukin-1β

city: Parkville

first: Boris

last: Novakovic

state: Victoria

address: Murdoch Children's Research Institute, Royal Children's Hospital, Flemington Road

country: Australia

institute: Murdoch Children's Research Institute

summary: Trained immunity is a phenomenon where innate immune cells develop and long-lasting pro-inflammatory reprogramming mediated by epigenetic and metabolic reprogramming. Trained immunity can be peropheral (circulating monocytes) or central (bone marrow) and it can be caused by exposure to β-glucan, BCG and Western Type Diet vial IL-1β signaling.

overall_design: HPCs were isolated from bone marrow mononuclear cells by CD34+ mangenitc separation. CD34+ cells were then exposed for 4 hours to 10 ng/ml IL1b. After incubation, cells were washed and seeded in 24-well plates at a density of 50,000 cells per well for expansion (10 days) and differentiation into monocytes for 7 days (see details in Growth protocol). At day 7 of differentiation, pan monocytes were magenetically separated. 500.000 cells per condition were then incubated for 4 hours with medium only or LPS 10 ng/ml; after the incubation time, the cells were washed and stored in RNAlater until further RNA extraction. RNA isolation was done using the QIAGEN AllPrep DNA/RNA micro-kit according to manufacturer’s instructions.

first: Daniela

last: Flores-Gomez

first: Elise

middle: L

last: Kessler

first: Niels

last: Riksen

first: Siroon

last: Bekkering


title: Credentialling a c-MYC-driven genetic neuroblastoma model

overall_design: To investigate the gene expression profile difference between pancreas tumor and normal pancreas, normal pancreas and tumor RNA were isolated and RNA-seq was performed.


title: Distinct pathways for removal of defective RNA polymerase II transcription complexes at a promoter-proximal pause checkpoint

city: Aurora

first: Ryan

last: Sheridan

state: CO

address: 12801 East 17th Avenue

institute: University of Colorado Anschutz Medical Campus

summary: The Integrator complex interacts with RNA polymerase II (RNAPII) at promoter-proximal pause sites but its function there remains uncertain. Here, we show that when Integrator function is compromised by loss of INTS6, RNAPII interacts increasingly with proteins that mediate its dissociation from DNA, including CUL3-ARMC5, which ubiquitylates Ser5-phosphorylated Rpb1 and targets it for degradation. ARMC5-dependent RNAPII ubiquitylation is activated by defects in factors required for correctly regulated promoter-proximal pausing, including Integrator, DSIF and mRNA capping enzyme. This ARMC5 checkpoint curtails an appreciable fraction of RNAPII transcription, with ARMC5 knockout cells producing uncapped, nascent RNA transcripts that fail to mature into stable mRNA. Concomitant loss of INTS6 and ARMC5 greatly stabilizes RNAPII at the pause and has severe consequences for cell growth and viability. Our data support a model in which CRL3ARMC5 functions alongside Integrator in a checkpoint mechanism that removes faulty RNAPII complexes at promoter-proximal pause sites to safeguard transcription integrity.

overall_design: To investigate the role of INTS6 in pol II pausing, eNET-seq was performed for INTS6 knockout cells

first: Daniel

last: Blears

first: Jesper

last: Svejstrup

first: Nova

last: Fong

first: David

last: Bentley


title: The PAF complex regulates alternative splicing.

city: Warszawa

first: Krzysztof

last: Goryca

address: Banacha 2c

department: CeNT

country: Poland

institute: Uniwersytet Warszawski

summary: The conserved Eukaryotic PAF complex binds to transcribing RNA polymerase II to control deposition of histone marks during transcription. Recently its role in alternative polyadenylation (selection of mRNA 3’end cleavage sites by CPSF) was described. In this work we show that the PAF complex also regulates alternative splicing.

overall_design: Effect of depletion of PAF complex subunit [CTR9 (main scaffold) or WDR61] on differential gene expression in HEK293Flip-In T-Rex cell lines.

first: Małgorzata

last: Drabko

first: Rafał

last: Tomecki

first: Aneta

last: Jurkiewicz

first: Kamil

last: Kobyłecki

first: Miłosz

last: Ludwinek

first: Dominik

last: Cysewski

first: Łukasz

last: Borowski

last: Płoski

first: Agnieszka

last: Tudek


title: Single-cell RNA sequencing analysis of irradiated mouse medulloblastoma tumors

city: Philadelphia

first: Yi

last: Fan

state: PA

address: 3400 Civic Center Blvd, SCTR 8-168

department: Radiation Oncology

institute: University of Pennsylvania

summary: To investigate the effects of radiation on transcriotome change in medulloblastoma on a single cell level, we performed RNA sequcening analysis with single cells derived from mouse medulloblastoma tissue, after mice received FLASH and standard proton irradiation.

overall_design: Mice bearing medulloblastoma was treated by 10-Gy FLASH and standard radiotherapy. Tumor-derived single cells were analyzed by single-cell RNAseq analysis.

first: Ni

last: Haiwei

first: Paul

last: Ritama

first: Zhang

last: Duo

first: Fan

last: Yi


title: Effect of the sGC activator BAY 60-2770 on human proximal tubular (HK-2) cells under hypoxia and after TGF-β1 treatment

city: Berlin

first: Pratik

middle: Hemant

last: Khedkar

address: Charitéplatz 1

department: Institute of Translational Physiology

country: Germany

institute: Charité - Universitätsmedizin Berlin

summary: Increasing cGMP levels by modulating soluble guanylyl cyclase (sGC) can be renoprotective. While sGC stimulators can modulate cGMP levels, their application is limited as they require native sGC to function. sGC activators on the other hand can function with heme-free sGC. Therefore, we tested the renoprotective effects of the sGC activator BAY 60-2770 that also functions with oxidized sGC in an acute kidney injury (AKI) model with transition to chronic kidney disease (CKD). In order to study the effects of BAY 60-2770 on gene expression in tubular cells, we used the proximal tubular cell line HK-2 as a model. To mimic the ischemia and fibrosis observed in vivo, we subjected HK-2 cells to hypoxia and TGF-β1 treatment, respectively. RNASeq analysis showed that BAY 60-2770 had a significant influence on the expression of genes involved in fibrosis, inflammation and tissue damage after both hypoxia and TGF-β1 treatments.

overall_design: HK-2 cells were treated with BAY 60-2770 or solvent control and incubated for 24h either under hypoxia (0.3% oxygen) or normoxia. In another set of experiments, HK-2 cells were treated with TGF-β1 alone or in combination with BAY 60-2770 and incubated for 24h under normoxia. Analysis of RNA-seq data was performed using DESeq2 with a multifactor design within two experiments, comparing both treatment effects and sGC activator status to the respective controls.

first: Falk-Bach

last: Lichtenberger

first: Tobias

last: Sieckmann

first: Andreas

last: Patzak


title: Loss of atrial natriuretic peptide signaling causes mitochondrial dysfunction, insulin resistance and low endurance capacity

city: Copenhagen

first: Lars

middle: Roed

last: Ingerslev

address: Blegdamsvej 3B

department: NNF Center for Basic Metabolic Research

country: Denmark

institute: Copenhagen University

summary: Type 2 diabetes (T2D) and obesity are strongly associated with low natriuretic peptide (NP) plasma levels and impaired NP signaling with a down-regulation of NP guanylyl cyclase receptor-A (GCA) in skeletal muscle and adipose tissue. However, no study has so far provided evidence for a causal link between ANP/GCA deficiency and T2D development. Here, we show that both ANP and GCA deficiency in mice promotes metabolic disturbances and prediabetes. In GCA haploinsufficient mice, skeletal muscle insulin resistance is associated with altered mitochondrial function and impaired endurance running capacity. Muscle RNA-seq analyses reveal down-regulation of various gene sets related to mitochondrial protein complexes and translation. Despite normal mitochondrial content, GCA haploinsufficient mice exhibit increased proton leak and reduced content of mitochondrial oxidative phosphorylation (OXPHOS) proteins. Using various clinical studies and cohorts, we further show that GCA is related to various metabolic traits in T2D and positively correlates with markers of oxidative capacity in human skeletal muscle. Altogether, these results indicate that ANP/GCA signaling controls muscle mitochondrial integrity and oxidative capacity in vivo and plays a causal role in the development of T2D.

overall_design: Twelve weeks old Nppa-/- and Npr1+/- male mice (B6.129P2-Nppatm1Unc/J and B6.129-Npr1tm1Gar/J mice were backcrossed to C57BL/6J mice for at least ten generations), and their littermate controls Nppa+/+ and Npr1+/+ respectively were used. Mice were fed with a high fat diet (HFD) (60% kcal lipids) for 12 weeks and were housed in a pathogen-free barrier facility (12h light/dark cycle) with ad libitum access to water and food in standard animal care facility rooms at 21°C. Mice were weighted weekly and body composition was assessed by the use of an EchoMRI. At the end of the protocol, mice were killed and muscle tissues were rapidly excised and snap frozen in liquid nitrogen before being stored at -80°C. RNA seq libraries were constructed from these samples.

first: Deborah

last: Carper

first: Marlène

last: Lac

first: André

last: Märtens

first: Marine

last: Coue

first: Mie

last: Mechta

first: Justine

middle: V

last: Petit

first: Claire

last: Maslo

first: Laurent

last: Monbrun

first: Peggy

last: Del Carmine

first: Yannis

last: Sainte-Marie

first: Virginie

last: Bourlier

last: Laurens

first: Gilles

last: Mithieux

first: Denis

last: Joanisse

first: Charles

last: Coudray

first: Christine

last: Feillet-Coudray

first: Emilie

last: Montastier

first: Nathalie

last: Viguerie

first: Geneviève

last: Tavernier

first: Remy

last: Mounier

first: Karsten

last: Hiller

first: Jens

last: Jordan

first: Romain

last: Barrès

last: Pesta

first: Cedric

last: Moro


title: TNFSF13 insuffiency causes epithelial and immune disruption in the human colon II

first: Noor

last: Dawany

state: Pennsylvania

address: 421 Curie Blvd

institute: CHOP

summary: Objective: Cytokines produced by epithelial and immune cells can act upon one another to promote mucosal healing- a process that goes awry with chronic inflammation as in inflammatory bowel disease. TNFSF13 is a cytokine important for B cell function, but its role in epithelial cell behavior and contribution to inflammatory bowel disease is poorly understood.  Design: We performed histological and functional assays, single cell transcriptomics, and imaging mass cytometry on tissue-derived colonoids or biopsies from a patient with very early onset inflammatory bowel disease (VEO-IBD) harboring a novel TNFSF13 variant. To confirm causal, variant-driven phenotypes, parallel experiments were performed in induced pluripotent stem cell (iPSC)- derived colon organoids engineered with the same TNFSF13 variant.  Results: TNFSF13 variant colonoids exhibited reduced TNFSF13 expression associated with increased proliferation and reduced apoptosis, which was confirmed in iPSC-derived colon organoids. Single cell RNA-sequencing and flow cytometry defined FAS as the predominant colonic epithelial receptor for TNFSF13. TNFSF13 variant colon biopsies demonstrated a shift in tissue B cell populations consistent with altered differentiation of memory B cells. Finally, imaging mass cytometry revealed an increase in epithelial-associated B cells in TNFSF13 variant colon tissue sections compared to healthy and non-monogenic VEO-IBD controls.  Conclusions: The current study defines a previously unknown role for the cytokine TNFSF13 as a regulator of colonic epithelial proliferation and apoptosis. Furthermore, this study suggests that variant TNFSF13 can contribute to aberrant epithelial- B cell crosstalk in the human colon.

overall_design: scRNA-seq analysis of epithelial and stromal cells from colon biopsies of a patient with VEO-IBD and a healthy control

first: Kathryn

last: Hamilton

first: Judith

last: Kelsen


title: Transcrioptome analysis of irradiated mouse macrophages

first: Yi

last: Fan

summary: The global RNA expression was assayed in irradiated and un-irradiated mouse macrophages using RNAseq.

overall_design: Bone marrow-derived cells were isolated from mice. Cells were irradiated by FLASH or standard proton beam, or un-irradiated as controls. Cells were then incubated with CSF-1 to induce macrophage differentiation, followed by treatment with LPS (for M1 polarization), IL-4 (for M2 polarization), or control medium (for M0 condition). RNA was isolated and analyzed by RNAseq.

first: Ni

last: Haiwei

first: Zhang

last: Duo

first: Fan

last: Yi


title: TNFSF13 insuffiency causes epithelial and immune disruption in the human colon

overall_design: Refer to individual Series


title: TTC33-associated network (TAN) is a novel vertebrate-specific complex formed by TTC33, WDR61 and PHF5A

first: Krzysztof

last: Goryca

summary: TTC33 is an uncharacterized vertebrate-specific structural protein composed of tetratricopeptide repeat motifs. TTC3 forms a trimeric complex with WDR61 and chromatin binding PHF5A, coined TAN for TTC33-associated network. The TAN complex is associated with structural protein CCDC97, SF3A/B U2 splicing factor sub-complex, PP2A phosphatase and UNG DNA glycosylase.

overall_design: Effect of depletion of TTC33 or CCDC97 on differential gene expression in HEK293Flip-In T-Rex cell lines.

first: Małgorzata

last: Drabko

first: Rafał

last: Tomecki

first: Aneta

last: Jurkiewicz

first: Kamil

last: Kobyłecki

first: Miłosz

last: Ludwinek

first: Dominik

last: Cysewski

first: Łukasz

last: Borowski

last: Płoski

first: Agnieszka

last: Tudek


title: TNFSF13 insuffiency causes epithelial and immune disruption in the human colon I

last: Dawany

overall_design:
scRNA-seq analysis of colonoids from 2 controls, 2 patients with VEO-IBD and 1 patient with VEO-IBD and variant in TNFSF13 (APRIL).  Samples included untreated colonoids as well as colonoisd treated with TNFa, IFNg or TRAIL. Cell hashing was used to allow for multiplexing of untreated and treated colonoids from the same sample ID.
HTO barcode sequence hastagged sample
TotalSeq-B0251 anti-human Hashtag 1 GTCAACTCTTTAGCG Untreated
TotalSeq-B0252 anti-human Hashtag 2 TGATGGCCTATTGGG TNFa-treated
TotalSeq-B0253 anti-human Hashtag 3 TTCCGCCTCTCTTTG IFNg-treated
TotalSeq-B0254 anti-human Hashtag 4 AGTAAGTTCAGCGTA TRAIL-treated


title: ARMC5-mediated degradation of RNA polymerase II as a last resort in the promoter-proximal pausing checkpoint [TTchem-Seq]

city: Copenhagen N

first: Jesper

last: Svejstrup

state: Denmark

address: Blegdamsvej 3, 18.6

department: Department of Cellular and Molecular Medicine

institute: University of Copenhagen

summary: RNA polymerase II (RNAPII) promoter-proximal pausing is an early step in the transcription cycle, which occurs alongside important events such as mRNA capping. Here, we identify a ubiquitin ligase complex, CUL3-ARMC5 (CRL3ARMC5) which is required for targeting promotor-proximally paused RNAPII for degradation. While a basal level of ARMC5-dependent RNAPII ubiquitylation/degradation occurs even in unperturbed cells, depletion of proteins regulating promoter-proximal pausing results in markedly increased ubiquitylation. We suggest that such RNAPII ubiquitylation/degradation serves as a “last resort” pathway for removing inept polymerases at a promoter-proximal pause checkpoint to avoid their release for unproductive transcript elongation. In agreement with this idea, ARMC5 knockout cells display increased levels of nascent transcription but with pre-mRNAs exhibiting capping defects. Together, our findings support a model in which promoter-proximal pausing functions as a transcription cycle checkpoint and indicate broad role for the CRL3ARMC5 ligase in RNAPII poly-ubiquitylation and degradation.

overall_design: We performed TTchem-Seq in WT and ARMC5 KO cells to study how ARMC5 deletion affects genome-wide nascent transcription.

first: Jiangman

last: Lou

first: Daniel

last: Blears

first: Richard

last: Mitter

first: Miriam

last: Llorian Sopena

middle: Q


title: An Intrinsically Disordered Region Controlling Condensation of a Circadian Clock Component and Rhythmic Transcription in the Liver

first: KUN

last: ZHU

address: 3400 Civic Center Blvd, SCTR-12-196


title: Single-cell transcriptome profiles of tumor tissues from lung cancer patients receiving immune checkpoint inhibitors.

city: Seoul

first: Hae-Ock

last: Lee

address: 222 Banpo-daero, Seocho-gu

department: Department of Microbiology

institute: College of Medicine, The Catholic University of Korea

summary: We performed single-cell RNA sequencing of lung cancer patients receiving immune checkpoint inhibitors. Tumor signatures and immune cell profiles associated with ICI response were identified in lung cancer.

overall_design:
A total of 33 samples covering metastatic lymph nodes, metastatic liver tissues, and lung/bronchus tumor tissues from 26 patients with lung cancer were collected and analyzed using single-cell RNA sequencing.
---------------------------------------------
Authors state "EGA accession number is EGAD00001008703".

first: Myung-Ju

last: Ahn


title: IL1beta and soluble crosstalk modulate NF-κB activity in living Multiple Myeloma and stromal cells

city: Milan

first: Anna Sofia

last: Tascini

address: Via Olgettina, 60

department: Center for Omics Science

institute: IRCCS, Ospedale San Raffaele

summary: Multiple myeloma (MM) progression is linked to chronic NF-κB activation in myeloma cells. However, the identity and source of autocrine/paracrine signals driving NF-κB activation and the role of the 3D microenvironment have been scarcely investigated both in vivo and in vitro. To investigate them, we knocked-in the Venus (YFP) ORF in the NF-κB p65 gene in both MM and stromal cells. Surprisingly, a large fraction of p65-YFP MM cells engrafted in mouse bone marrow showed overall low levels of NF-κB activation whereas a small fraction was highly activated.  To understand these in vivo data, we investigated NF-κB dynamics in MM and stromal cells, both alone and in co-culture. In vitro experiments exploiting microfluidics, bioreactor and microchip cell cultures highlighted crosstalk between the myeloma and stromal components that leads to mild basal activation. In contrast, we found that high-density cultures within 3D scaffolds dampen NF-κB activation in MM and stromal cells, both in basal and inflammatory conditions.  It has been recently hypothesized that IL1β, and the inflammatory ME, shape the overall activity of ME components and promote the transition of Mesenchimal Stromal Cells (MSCs) toward an inflammatory NF-κB driven transcriptional phenotype (iMSCs). We tested this hypothesis in our system and found that IL1β strongly activates NF-κB in stromal but not in myeloma cells. In addition, secreted molecules from IL1β-stimulated MSCs strongly activate NF-κB only in a small fraction of MM cells. We propose that the balance between activating stimuli from iMSCs and dampening feedbacks from the 3D ME, maintains a mild NF-κB activation in myeloma cells in the patients’ BM to avoid exceedingly harmful responses.

overall_design: Droplet-based scRNAseq on MM.1S and HS-5 cells from independent cultures and MM.1S-HS-5 co-culture

first: Federica

last: Colombo

first: Jose

middle: M

last: Garcia-Manteiga

first: Anna

middle: S

first: Cise

last: Kizilirmak

first: Elena

last: Carelli

first: Margherita

last: Silani

first: Daniela

last: Cesana

first: Pierangela

last: Gallina

first: Maurilio

last: Ponzoni

first: Marina

last: Ferrarini

first: Elisabetta

last: Ferrero

first: Marco

last: Rasponi

last: Bianchi

first: Samuel

last: Zambrano

first: Alessandra

last: Agresti


title: ARMC5-mediated degradation of RNA polymerase II as a last resort in the promoter-proximal pausing checkpoint [RNA-Seq]

first: Jesper

last: Svejstrup

overall_design: We performed total RNA-Seq in WT and ARMC5 KO cells to study how ARMC5 deletion affects transcription, including mRNA and nascent RNA.

first: Jiangman

last: Lou

first: Daniel

last: Blears

first: Richard

last: Mitter

first: Miriam

last: Llorian Sopena


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


title: PfMORC modulates gene expression through interactions with heterochromatin in Plasmodium falciparum

city: State College

first: Manuel

last: Llinás

address: W122 Millennium Science Complex, Pollock Road

department: Biochemistry and Molecular Biology

institute: Pennsylvania State University

summary: Dynamic control of gene expression is critical for blood stage development of malaria parasites. Here, we used multi-omic analyses to investigate transcriptional regulation by the chromatin-associated microrchidia protein, PfMORC, during asexual blood stage development of the human malaria parasite Plasmodium falciparum. PfMORC (PF3D7_1468100) interacts with a suite of nuclear proteins, including APETALA2 (AP2) transcription factors (PfAP2-G5, PfAP2-O5, PfAP2-I, PfAP2-MRP and PF3D7_0420300, PF3D7_0613800, and PF3D7_1239200), a DNA helicase DS60 (PF3D7_1227100), and other chromatin remodelers (PfCHD1, PfEELM2, and PfISWI). Transcriptomic analysis of PfMORCHA-glmS knockdown parasites revealed 163 differentially expressed genes belonging to hypervariable multigene families, along with upregulation of genes mostly involved in host cell invasion. In vivo genome-wide chromatin occupancy analysis during both trophozoite and schizont stages of development demonstrates that PfMORC is recruited to repressed, multigene families, including the var genes in subtelomeric chromosomal regions. Collectively, we find that PfMORC is found in chromatin complexes that play a role in the epigenetic control of asexual blood stage transcriptional regulation.

overall_design: Two biological replicates of chromatin immunoprecipitation followed by sequencing (ChIP-seq) was used to identify the genome-wide binding sites of chromatin-assocaited factor, PfMORC (gene ID: PF3D7_1468100), Plasmodium falciparum parasite line with a C-terminal 3xHA tag.

first: Maneesh

middle: K

last: Singh

first: Victoria

last: Bonnell

first: Israel

last: Da Silva

first: Verônica

last: Feijoli Santiago

last: Moraes

first: Christian

last: Doerig

first: Giuseppe

last: Palmisano

first: Celia

last: Garcia


title: SOXC factors as suppressors modulate Rho activity to promote neuronal reprogramming of human glioblastoma cells

first: jianjing

last: Yang

institute: UT Southwestern Medical Center

summary: Transcriptome changing during neuron reprogramming by NEUROG2 and SOX11 in U251

overall_design: RNA-seq of Total RNA (18 datasets) of U-251 glioblastoma cells over-expressing NEUROG2, SOX11 or both NEUROG2 and SOX11. Included in RNA-seq of U251 cells with no overexpression.

first: Derek

last: Smith

first: Jianjing

first: Chun-Li

last: Zhang


title: The involvement of long non-coding RNAs in the formation of high temperature-induced grain chalkiness in rice

city: nanjing

first: rongjian

last: luo

state: jiangsu

address: weigang road No.1

institute: Nanjing Agricutural University

summary: A period of exposure to high ambient temperatures can damage the process of grain filling in rice, potentially inducing the endosperm to become chalky. Given the established involvement of long non-coding RNAs (lncRNAs) in regulating plant development and its stress response, the purpose here was to reveal the extent to which lncRNA activity contributes to the endosperm chalkiness syndrome. Among 578 lncRNAs identified in spikelets harvested ten days post anthesis from plants exposed to high temperature stress, 14 were found to be more abundant than in control plants, while 45 were less abundant. Of these 59 differentially abundant sequences, 32 were identified as interacting with five mRNAs involved in starch metabolism and catabolism, indicating an involvement of these lncRNAs in starch formation in the endosperm, and hence in causing the chalkiness syndrome.

overall_design: lncRNA and mRNA profiles of rice 10DAP under normal temperature and high temperature conditions were generated by ssRNA sequencing, in triplicate, using Hiseq 4000.

first: Rongjian

last: Luo


title: ARMC5-mediated degradation of RNA polymerase II as a last resort in the promoter-proximal pausing checkpoint [PRO-seq]

first: Jesper

last: Svejstrup

overall_design: We performed PRO-Seq in WT and ARMC5 KO cells to study how ARMC5 deletion affects nascent transcription with in vitro nuclear run-on and genome-wide RNAP II distribution especially RNAP II at promoter proximal region of genes.

first: Jiangman

last: Lou

first: Daniel

last: Blears


title: Trained immunity suppression determines kidney allograft survival [ChIP]

status: Public on Nov 04 2024

city: Nijmegen

first: Joost

last: Martens

state: Nederland

address: Geert Grooteplein 28

department: RIMLS

country: Netherlands

institute: Radboud University

summary: The innate immune system plays an essential role in regulating the immune responses to kidney transplantation, but the mechanisms through which innate immune cells influence long-term graft survival are unclear. The current study highlights the vital role of trained immunity in kidney allograft survival. Trained immunity describes the epigenetic and metabolic changes that innate immune cells undergo following an initial stimulus, allowing them have a stronger inflammatory response to subsequent stimuli. We stimulated healthy peripheral blood mononuclear cells with pretransplant and posttransplant serum of kidney transplant patients and immunosuppressive drugs in an in vitro trained immunity assay and measured tumor necrosis factor and interleukin 6 cytokine levels in the supernatant as a readout for trained immunity. We show that the serum of kidney transplant recipients collected 1 week after transplantation can suppress trained immunity. Importantly, we found that kidney transplant recipients whose serum most strongly suppressed trained immunity rarely experienced graft loss. This suppressive effect of posttransplant serum is likely mediated by previously unreported effects of immunosuppressive drugs. Our findings provide mechanistic insights into the role of innate immunity in kidney allograft survival, uncovering trained immunity as a potential therapeutic target for improving graft survival.

overall_design: Investigate the differences in the transcriptome of kidney transplant patients' monocytes. Therefore we isolated PBMCs from kidney transplant patients for ChIP-sequencing

first: Inge

last: Jonkman

first: Maaike

last: Jacobs

first: Yutaka

last: Negishi

first: Cansu

last: Yanginlar

first: Marijke

last: Baltissen

first: Michiel

last: Vermeulen

first: Martijn

last: Hoogen

first: Marije

last: Baas

first: Johan

last: Vlag

first: Zahi

last: Fayad

first: Abraham

last: Teunissen

first: Joren

last: Madsen

first: Jordi

last: Ochando

first: Leo

last: Joosten

first: Mihai

last: Netea

first: Willem

last: Mulder

first: Musa

last: Mhlanga

first: Luuk

last: Hilbrands

first: Nils

last: Rother

first: Raphael

last: Duivenvoorden


title: Atorvastatin improved ulcerative colitis in association with gut microbiota-derived tryptophan metabolism

city: Tianjin

first: Shijiao

last: Cai

address: 154 Anshan Road,Heping District

department: Department of Pharmacy

institute: Tianjin Medical University General Hospital

summary: Aims: Atorvastatin is a commonly used cholesterol-lowering drug that possesses non-canonical anti-inflammatory properties. However, the precise mechanism underlying its anti-inflammatory effects remains unclear. Materials and methods: The acute phase of ulcerative colitis (UC) was induced using a 5 % dextran sulfate sodium (DSS) solution for 7 consecutive days and administrated with atorvastatin (10 mg/kg) from day 3 to day 7. mRNA-seq, histological pathology, and inflammatory response were determined. Intestinal microbiota alteration, tryptophan, and its metabolites were analyzed through 16S rRNA sequencing and untargeted metabolomics. Key findings: Atorvastatin relieved the DSS-induced UC in mice, as evidenced by colon length, body weight, disease activity index score and pathological staining. Atorvastatin treatment reduced the level of pro_x0002_inflammatory cytokines interleukin-6 (IL-6) and tumor necrosis factor alpha (TNF-α). Atorvastatin also relieved the intestinal microbiota disorder caused by UC and decreased the proliferation of pernicious microbiota such as Akkermansia and Bacteroides. Atorvastatin dramatically altered tryptophan metabolism and increased the fecal contents of tryptophan, indolelactic acid (ILA), and indole-3-acetic acid (IAA). Furthermore, atorvastatin enhanced the expression level of aryl hydrocarbon receptor (AhR) and interleukin-22 (IL-22) and further promoted the expression level of intestinal tight junction proteins, such as ZO-1 and occludin, in colitis mice. Significance: These findings indicated that atorvastatin could alleviate UC by regulating intestinal flora disorders, promoting microbial tryptophan metabolism, and repairing the intestinal barrier.

overall_design: To investigate the function of atorvastatin on ulcerative colitis, female C57BL/6 J mice were used as experimental animals. The normal group was treated by gavage with the vehicle alone (0.5% CMC-Na).The model group was treated by gavage with 5 % DSS solution for consecutive 7 days. The atorvastatin group was treated by gavage with 10 mg/ kg atorvastatin. Atorvastatin was administered strictly once daily for 5 days in a volume of 0.2 mL from day 3 to day 7. We then performed gene expression profiling analysis using data obtained from RNA-seq.

first: Yidan

last: Gou

first: Weilong

last: Zhong

first: Hengjie

last: Yuan


title: Trained immunity suppression determines kidney allograft survival

first: Joost

last: Martens

overall_design: Investigate the differences in the transcriptome of kidney transplant patients' monocytes. Therefore we isolated PBMCs from 12 kidney transplant patients for RNA-sequencing

first: Inge

last: Jonkman

first: Maaike

last: Jacobs

first: Yutaka

last: Negishi

first: Cansu

last: Yanginlar

first: Marijke

last: Baltissen

first: Michiel

last: Vermeulen

first: Martijn

last: Hoogen

first: Marije

last: Baas


title: 3D chromatin hubs as regulatory units of identity and survival in acute T-cell leukemia [HiChIP]

city: New York

first: Javier

last: Rodriguez Hernaez

state: New York

address: East 30th Street. 8th Floor

institute: NYU Langone Health

summary: Cancer progression is associated with genetic and epigenetic aberrations that affect chromatin 3D organization in the nucleus. Changes in loop extrusion or phase separation alter the relationships between enhancer and promoter elements, defining novel gene expression programs that are selected to promote growth and survival. Here, we provide an integrative approach based on chromatin conformation, accessibility and transcription, further validated by CRISPR interference screenings in order to identify chromatin topologies relevant to different subtypes of T-cell leukemia, namely T-ALL and ETP-ALL. By focusing on highly interconnected elements, we characterized 3D hubs as headquarters of leukemia progression and identity, demonstrating that oncogenes and disease markers are regulated by multiple cis-regulatory regions.

overall_design: Primary samples and prototypical cell lines of T cell acute lymphoblastic leukemia (T-ALL) and early T cell precursor leukemia (ETP-ALL) were collected and analyzed for H3K27ac HiChIP. To enrich for blast representation, samples were sorted based on clinical immune-phenotype, for CD2 and/or CD7 surface expression

first: Boccalatte

last: Francesco

first: Rodriguez-Hernaez

last: Javier

first: Gambi

last: Giovanni

first: Nadorp

last: Bettina

first: Aifantis

last: Ioannis

first: Tsirigos

last: Aristotelis


title: Characterization of innate immune responses to AS03 adjuvanted H5N1 vaccine compared to non-adjuvanted H5N1 vaccine.

first: Foo

last: Cheung

address: Bethesda

institute: NIH

summary:
The primary objective is to compare multiplex immune response signatures following two (primary and a boost) vaccinations with the GSK AS03 adjuvanted H5N1 influenza vaccine or the non-adjuvanted form of the H5N1 influenza vaccine
at the 3.75 mcg dose and given 21 days apart and identify differences in very early innate immune responses. These immune signatures will also be correlated with the clinical observations especially safety related local and systemic events.

overall_design: Immune response signatures following two (primary and a boost) vaccinations with the GSK AS03 adjuvanted H5N1 influenza vaccine or the non-adjuvanted form of the H5N1 influenza vaccine


title: 3D chromatin hubs as regulatory units of identity and survival in acute T-cell leukemia [scATAC-Seq]

overall_design: Primary samples of T cell acute lymphoblastic leukemia (T-ALL) and early T cell precursor leukemia (ETP-ALL) were collected and analyzed by single-cell ATAC sequencing

first: Lin

last: Ziyan


title: 3D chromatin hubs as regulatory units of identity and survival in acute T-cell leukemia [etp82a_RNA-seq]

overall_design: Primary samples and prototypical cell lines of T cell acute lymphoblastic leukemia (T-ALL) and early T cell precursor leukemia (ETP-ALL) were collected and analyzed. To enrich for blast representation, samples were sorted based on clinical immune-phenotype, for CD2 and/or CD7 surface expression


title: An Intrinsically Disordered Region Controlling Condensation of a Circadian Clock Component and Rhythmic Transcription in the Liver [ChIP-seq]

first: KUN

last: ZHU

summary: Circadian gene transcription is fundamental to metabolic physiology. Here we report that the nuclear receptor REV-ERBalpha, a repressive component of the molecular clock, forms circadian condensates in the nuclei of mouse Liver. These condensates are dictated by an intrinsically disordered region (IDR) located in the protein’s hinge region which specifically concentrates nuclear receptor corepressor 1 (NCOR1) at the genome. IDR deletion diminishes the recruitment of NCOR1 and disrupts rhythmic gene transcription in vivo. REV-ERBalpha condensates are located at high-order transcriptional repressive hubs in the Liver genome that are highly correlated with circadian gene repression. Deletion of the IDR disrupts transcriptional repressive hubs and diminishes silencing of target genes by REV-ERBalpha. This work demonstrates physiological circadian protein condensates containing REV-ERBalpha  whose IDR is required for hub formation and the control of rhythmic gene expression.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for REV-ERBalpha, anti-H3K4me3, anti-H3K27ac, anti-NCOR1 at different circadian time points (ZT22/ZT10) or different AAV virus combinational injection (Ctrl, DKO+YFP, DKO+WT, DKO+ΔhIDR)

first: Kun

last: Zhu

first: Mitchell

last: Lazar


title: Cross-species Single-cell Transcriptomics Reveals Neuronal Similarities and Heterogeneity in Amniote Pallium

city: shenzhen

first: CNSA

last: CNGB

address: BGI

institute: BGI

summary: The amniote pallium, a vital component of the forebrain, has undergone considerable evolutionary divergence across species and is critical for a variety of functions including sensation, memory and learning. The relationship between pallial subregions in different species remain elusive, particularly regarding the identification of homologous neurons and their similar or distinct signatures. Here, we utilized single-nucleus RNA sequencing to examine over 130,000 nuclei from macaque (Macaca fascicularis) neocortex, alongside datasets from human (Homo sapiens), mouse (Mus musculus), zebra finch(Taeniopygia guttata), turtle (Chrysemys picta bellii), and lizard (Pogona vitticeps), for a cross-species comparison.

overall_design: To compare gene expression difference among among amniote pallium cell, we performed snRNA-seq using two adult macaque.

first: Fubaoqian

last: Huang

first: Kuo

last: Liao

first: Youning

last: Lin

first: Zhenkun

last: Zhuang


title: An Intrinsic Disorder Region Controlling Condensation of a Circadian Clock Component and Rhythmic Transcription in the Liver [ChIA-PET]

summary: Circadian gene transcription is fundamental to metabolic physiology. Here we report that the nuclear receptor REV-ERBalpha, a repressive component of the molecular clock, forms circadian condensates in the nuclei of mouse liver. These condensates are dictated by an intrinsically disordered region (IDR) located in the protein’s hinge region which specifically concentrates nuclear receptor corepressor 1 (NCOR1) at the genome. IDR deletion diminishes the recruitment of NCOR1 and disrupts rhythmic gene transcription in vivo. REV-ERBalpha condensates are located at high-order transcriptional repressive hubs in the liver genome that are highly correlated with circadian gene repression. Deletion of the IDR disrupts transcriptional repressive hubs and diminishes silencing of target genes by REV-ERBalpha. This work demonstrates physiological circadian protein condensates containing REV-ERBalpha  whose IDR is required for hub formation and the control of rhythmic gene expression.

overall_design: In-situ Chromatin Interaction Analysis with Paired-End Tag (In-situ ChIA-PET) for REV-ERBalpha  at different circadian time points (ZT22/ZT10) or different AAV virus combinational injection (DKO+WT, DKO+ΔhIDR)


title: Virus modified paraspeckles are essential hubs for gene expression and their formation drives genomic instability

city: Leeds

first: Timothy

middle: James

last: Mottram

address: Faculty of Biological Sciences

institute: University of Leeds

summary: The nucleus is a highly organised yet dynamic environment containing distinct membrane nuclear bodies. This spatial separation enables a subset of components to be concentrated within bimolecular condensates, allowing efficient and discrete processes to occur which regulate cellular function. One such nuclear body, paraspeckles, are comprised of multiple paraspeckle proteins (PSPs) built around the architectural RNA, NEAT1_2. Paraspeckle function is yet to be fully elucidated but has been implicated in a variety of developmental and disease scenarios.  We demonstrate that Kaposi’s sarcoma-associated herpesvirus (KSHV) drives formation of structurally distinct paraspeckles with a dramatically increased size and altered protein composition that are essential for productive lytic replication. We highlight these virus-modified paraspeckles form adjacent to virus replication centres, functioning as RNA processing hubs for both viral and cellular transcripts during infection. Notably, we reveal that PSP sequestration into virus-modified paraspeckles results in increased genome instability during both KSHV and Epstein Barr virus (EBV) infection, implicating their formation in virus-mediated tumorigenesis.

overall_design: To determine the RNA population of nuclear condensates formed during KSHV lytic replication, we used hybridsation based proximity labelling coupled with NGS in TREx-BCBL1 Rta cells undergoing lytic KSHV replication.

first: Katherine

last: Harper

first: Elena

last: Harrington

first: Connor

last: Hayward

first: Chinedu

last: Anen

first: Wiyada

last: Wongwiwat

first: Robert

last: White

first: Adrian

last: Whitehouse


title: Cell-autonomous IL6ST activation suppresses prostate cancer development via STAT3/ARF/p53-driven senescence and confers an immune-active tumor microenvironment

city: Brno

first: Core Facility

last: Bioinformatics

address: Kamenice 5

country: Czech Republic

institute: CEITEC - Masaryk University

summary: Prostate cancer ranks as the second most frequently diagnosed cancer in men worldwide. Recent research highlights the crucial roles IL6ST-mediated signaling pathways play in the development and progression of various cancers, particularly through hyperactivated STAT3 signaling. Here, we find that genetic cell-autonomous activation of the IL6ST receptor in prostate epithelial cells triggers active STAT3 signaling and significantly reduces tumor growth in vivo. Mechanistically, genetic activation of IL6ST signaling mediates senescence via the STAT3/ARF/p53 axis and anti-tumor immunity via recruitment of cytotoxic T-cells, ultimately impeding tumor progression. Our findings reveal a context-dependent role of IL6ST/STAT3 in carcinogenesis and a tumor-suppressive function in prostate cancer development. We challenge the prevailing concept of blocking IL6ST/STAT3 signaling as functional prostate cancer treatment and instead propose cell-autonomous IL6ST activation as a novel therapeutic strategy.

overall_design: mRNA expression profiles of prostate epithelial cells derived from 19-week-old mice. Single cell suspension of mouse prostate tissue of wild type (B),  mice with probasin promoter-controlled Cre-mediated homozygous deletion of Pten and/or insertion of L-gp130 construct resulting in L-gp130peKI/KI (C), PtenpeΔ/Δ (E) and PtenpeΔ/Δ;L-gp130peKI/KI (F) mice was done  and magnetic cell separation was performed for EpCAM positive fraction. EpCAM  expressing cells were enriched by MACS sorting.

first: Christina

last: Sternberg

first: Karolína

last: Trachtová

first: Lukas

last: Kenner

first: Stefan

last: Rose-John


title: Polyamine uptake transporter 2 is essential for systemic acquired resistance establishment in Arabidopsis.

city: SAN LUIS POTOSI

first: Cesaré

last: Ovando-Vázquez

state: SAN LUIS POTOSI

address: Camino a la Presa de San José 2055. Lomas 4 sección

department: CNS

country: Mexico

institute: CONACyT IPICyT

summary: Plants have evolved a tightly regulated and inducible immune system to resist pathogen attack. After the initial contact with the pathogen, plants are significantly more resistant to future challenges, even from unrelated pathogens, an event known as systemic acquired resistance (SAR). In plants polyamines are involved in the regulation and establishment of the defense response by modulating their metabolism, specifically their biosynthesis, conjugation and catabolism. However, it is not known whether polyamine transport is involved in the plant defense response. Herein, we demonstrate that the PUT2/LAT4 transporter is required to establish local immunity and systemic defense responses in the A. thaliana-Pseudomonas syringae pv. tomato DC3000 (Pst) pathosystem. Our data revealed a dual phenotype in the put2-1 mutant after Pst inoculation, on one side, SAR was abolished in the systemic leaves while on the other, basal resistance to Pst was enhanced. Remarkably, this phenotype persisted even upon inoculation with unrelated pathogens such as Botrytis cinerea, highlighting a broad-spectrum SAR deficiency. To gain deeper insights into the involvement of PA transport in SAR, transcriptomic and metabolomic data of the put2-1 mutant were obtained.

overall_design:
To investigate the participation of the polyamine uptake transporter 2 (PUT2) gene in SAR, we used six-week-old plants and selected the lower leaves [8, 9 and 10; for mock or local priming with Pseudomonas syringae pv. tomato DC30000 (Pst)] and collected the upper leaves of Arabidopsis thaliana rosette (13, 14, and 15; non-inoculated or systemically challenged with Pst). Therefore  four conditions were established: native plant status (a), local priming (b), systemic challenge (c), and both local priming and systemic challenge (d). Three biological replicates were submitted for standard mRNA sequencing.
We then performed gene expression profiling analysis of RNAseq data from the WT and the put2-1 mutant line under native or SAR conditions. Samples of the native plant status (a) and local priming (b) were obtained from the upper leaves, 24 h after mock or Pst inoculation of the lower leaves. Sampleas of the systemic challenge (c), and both local priming and systemic challenge (d), were obtained from the upper leaves 24 h after inoculation of the upper leaves with Pst. This second inoculation was performed 48 h after the first inoculation in local leaves.
Comparative gene expression analysis of SAR vs. native conditions between WT and the put2-1 mutant were performed.

first: Emmanuel

last: Flores-Hernández

first: Paulina

last: Alvarado-Guitron

first: María

last: Gonzalez

first: Juan

middle: F

last: Jiménez-Bremont

first: Sanja

last: Ä†avar-ZeljkoviÄ‡

first: Nuria

last: De Diego

first: Margarita

last: Rodríguez-Kessler


title: Whole transcriptome analysis of human primary activated pan CD4/CD8 T cells treated with mRNA, double-stranded DNA or circular single stranded DNA.

city: Cambridge

first: Keqiang

last: Xie

state: MA

address: 625 Mount Auburn Street, Suite 105

institute: Full Circles Therapeutics, Inc.

summary: We compared dsDNA- and cssDNA-mediated whole transcriptome response in cultured primary T cells. T cells were electroporated with the same amount (1 µg) of dsDNA or cssDNA, GFP mRNA or vehicle (H2O).  24 hours post treatment, cell pellets were collected for transcriptome analysis by RNA sequencing.

overall_design: RNA were extracted from treated T cells RNAeasy kit (Qiange). The mRNA was then purified using NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, E7490), processed with the NEBNext Ultra II RNA Library Prep Kit for Illumina (New England Biolabs, E7770), followed by deep sequencing analysis using Illumina sequencing (2 × 150-base pair paired end; ~30G for each sample). To exclude nonspecific effect caused by electroporation, we included the mock group in which we only electroporated cells.