title: Effects of TCDCA-FXR on obesity-induced endothelial dysfunction and hypertension

status: Public on Oct 31 2025

city: Jinan

first: Hanlin

last: Lu

address: Wenhuaxi Road

country: China

institute: Qilu Hospital of Shandong University

type: Expression profiling by high throughput sequencing

summary: Regarding the role of TCDCA in alleviating obesity-induced ED, we sought to identify the key targets that could directly clarify the biological effects of TCDCA. We carried out RNA-seq of human umbilical vein endothelial cells (HUVECs) treated with vehicle or TCDCA.To further explore the role of TCDCA and identify its endothelial receptor, we performed RNA-seq on HUVECs treated with vehicle or GW4064

overall_design: To investigate the role of TCDCA-FXR in endothelial cells, we performed RNA-seq in TCDCA- and GW4064-treated HUVECs.

first: Wencheng

last: Zhang


title: Effects of TCDCA-FXR on obesity-induced endothelial dysfunction and hypertension III

type: Genome binding/occupancy profiling by high throughput sequencing

summary: To investigate the role of TCDCA-FXR in endothelial cells, we performed  CUT&TAG in HUVECs.

overall_design: The transcription factor ATF4 has been reported to regulate the expression of the key enzymes involved in serine metabolism (PHGDH, PSAT1, and SHMT2) and one-carbon metabolism (MTHFD2, ALDH1L2). Knockdown of ATF4 in HUVECs treated with TCDCA led to a significant downregulation in the mRNA levels of PHGDH, PSAT1, and SHMT2. As a nuclear receptor and transcription factor, FXR can regulate gene expression upon TCDCA activation. To determine if FXR directly regulates ATF4 transcription, we performed cleavage under targets and tagmentation (CUT&TAG) assay using Flag antibody in HUVECs overexpressing Flag-tagged FXR. TCDCA treatment resulted in reduced nuclear enrichment of PHB1, while TUDCA maintained strong nuclear colocalization of FXR and PHB1. To further evaluated the role of PHB1, we performed CUT&TAG assay to evaluate the DNA-binding profiles of PHB1 in ECs


title: Nature-inspired IL-1 targeted therapy to treat chronic inflammatory diseases

city: Worcester

first: Yen

last: Yang

state: MA

address: 366 Plantation st, NERB / N9-3004D

department: Genetic and Cellular Medicine

country: USA

institute: Umass Chan Medical school

summary: The interleukin-1 (IL-1) pathway drives inflammation in rheumatoid arthritis (RA) and other autoinflammatory diseases. We developed a recombinant adeno-associated virus (rAAV) gene therapy that delivers a secreted human IL-1 receptor antagonist (sIL-1Ra) under an inflammation-inducible promoter. This vector responds to pro-inflammatory cytokines and BMPs enriched in inflamed joints, enabling on-demand sIL-1Ra production. In mouse models of RA and IL-1Ra deficiency, inflammation-inducible sIL-1Ra reduced IL-1 signaling, immune cell activation, inflammatory gene expression, joint swelling, and bone destruction. A single systemic dose provided long-lasting therapeutic benefit, supporting this approach as a targeted treatment for chronic inflammatory diseases.

overall_design: Synovial tissue was collected from SKG mice (N=3 per group) treated systemically with either an inflammation-inducible rAAV expressing secreted human IL-1 receptor antagonist (sIL-1Ra) or a matched control vector. Total RNA was extracted, bulk RNA-seq libraries were prepared, and sequencing was performed to compare transcriptomes between sIL-1Ra and control groups.

first: Yeon-Suk

first: Mi-Jeong

last: Kim

first: Sachin

last: Chaugule

first: Emma

last: Mayer

first: Ngoc

last: DeSouza

first: Hong

last: MA

first: June

last: Xie


title: G9a Epigenetically Suppresses CXCL10 Expression and Inhibits Anti-tumor Immunity in Hepatocellular Carcinoma

city: Hangzhou

first: xinxin

last: chai

state: State...

address: Zhejiang，Hangzhou

institute: Zhejiang University

summary: The immunosuppressive tumor microenvironment, characterized by limited immune cell infiltration, represents a major challenge for effective immunotherapy in hepatocellular carcinoma (HCC). Epigenetic dysregulation has emerged as a critical mechanism underlying tumorigenesis and progression; however, the specific epigenetic mechanisms governing immune infiltration remain poorly understood. Here, we investigated the role of G9a, a histone methyltransferase catalyzing H3K9 methylation, in modulating anti-tumor immunity in HCC. Bioinformatic analysis of human HCC datasets revealed a significant inverse correlation between G9a expression and T cell infiltration. Genetic ablation of G9a in hepatoma cells markedly enhanced CD8+ T cell recruitment and activation in immunocompetent mouse models. Through RNA sequencing and functional validation, we identified CXCL10 as a key chemokine directly repressed by G9a. Mechanistically, G9a mediates H3K9 dimethylation at the CXCL10 promoter, and G9a deletion or inhibition significantly reduced this repressive mark, resulting in increased CXCL10 expression and secretion. Importantly, neutralization of CXCL10 abolished G9a inhibition-induced enhancement of CD8+ T cell migration. In preclinical models, pharmacological inhibition of G9a with UNC0642 not only suppressed tumor growth by promoting T cell infiltration but also synergized with anti-PD1 therapy to achieve superior therapeutic efficacy. These findings establish G9a as an epigenetic regulator of anti-tumor immunity in HCC and provide evidence for combining G9a inhibitors with immune checkpoint blockade to improve outcomes for HCC patients who receiving immunotherapy.

overall_design: RNA-seq profiling of wildtype cell Hepa 1-6 cells and their knockout derivatives (G9a_KO)

first: Xinxin

last: Chai

first: Jingzhou

last: Chen

first: Yuanyuan

last: Zhao


title: A widely-occurring family of pore-forming effectors broadens the impact of the Serratia Type VI secretion system

city: Dundee

first: Megan

last: Bergkessel

state: Dundee

address: Dow Street

department: School of Life Sciences

country: United Kingdom

institute: University of Dundee

summary: The ability to compete with diverse competitors is essential for bacteria to succeed in microbial communities. A widespread strategy for inter-bacterial competition is the delivery of antibacterial toxins, or effector proteins, directly into rival cells using the Type VI secretion system (T6SS). Whilst a large number of broad-spectrum enzymatic T6SS effectors have been described, relatively few which form pores in target cell membranes have been reported. Here, we describe a widely-occurring new family of T6SS-dependent pore-forming effectors, exemplified by Ssp4 of Serratia marcescens Db10. We show that Ssp4 forms cation-selective pores in vitro and use molecular dynamics simulations to support a high resolution structural model of a tetrameric membrane pore formed by Ssp4. Notably, the ion selectivity of Ssp4, its distribution and its impact on intoxicated cells is distinct from that of Ssp6, the other cation-selective pore-forming toxin delivered by the same T6SS. We further discovered that Ssp4 is active against a wider range of target species than Ssp6, highlighting that T6SS effectors are not always broad-spectrum. Finally, use of Tn-seq to identify Ssp4-resistant mutants revealed that a mucA mutant of Pseudomonas fluorescens, which overproduces extracellular polysaccharide, provides resistance to T6SS attacks. We conclude that possession of two distinct T6SS-dependent pore-forming toxins may be a common strategy to ensure effective de-energisation of closely- and distantly-related competitors.

overall_design: In this Tn-Seq experiment, Pseudomonas fluorescens was mutagenised with a randomly inserting Tn5 transposon. Approximately 200,000 unique mutants were pooled and the pool was subjected to attack by Serratia marcescens Db10 D9 (a strain lacking all type VI secretion system effectors),  D9 + ssp4, or D9 + ssp6 (each of which could express only the indicated effector). Genomic DNA was extracted from the recovered bacteria and transposon insertion sites in the P. fluorescens genome were enriched and counted. P. fluorescens genes affecting fitness under type VI secretion system delivered Ssp4 and Ssp6 attack were identified based on mutation frequencies that were significantly different in populations recovered after attack by the D9 + ssp4 or D9 + ssp6 strains compared to the D9 strain.

first: Mark

last: Reglinski

first: Quenton

middle: W

last: Hurst

first: David

middle: J

last: Williams

first: Marek

last: Gierlinski

first: Alp

middle: T

last: Şahin

first: Katharine

last: Mathers

first: Adam

last: Ostrowski

first: Ulrich

last: Zachariae

first: Samantha

last: Pitt

first: Sarah

last: Coulthurst


title: RBMXL3 binds a wide range of RNA molecules in human TCam-2 cells (eCLIP data)

city: Poznan

first: IHG PAS

last: Bioinfo Team

state: Greater Poland

address: Strzeszynska 32

department: Bioinformatics Team

country: Poland

institute: Institute of Human Genetics, Polish Academy of Sciences

summary: RBMXL3 is a primate-specific gene localized on the X chromosome, which expression is detectable mainly in the male gonad. So far, very little is known about RBMXL3 protein function and its molecular network but recent reports mention the RBMXL3 gene in the context of human spermatogenesis, cancer, and also a breathing disorder that affects newborns. In this study, we investigate the RBMXL3’s molecular network on a genome-wide scale using the human seminoma cell line (TCam-2) as a male germline in vitro model. Our transcriptomic (RNAseq, eCLIP) and proteomic (Co-IP coupled with MS) data show that RBMXL3 is an important player involved in RNA metabolism in human cells. Moreover, we report for the first time that primate-specific RBMXL3 protein restricts human LINE-1 (L1) retrotransposition. Our data indicate that RBMXL3 could play a decent function in controlling transcriptome fate in germ cells and beyond.

overall_design: Two biological replicates of each sample, TCam-2 cells transfected with RBMXL3_FLAG and GFP_FLAG (as control), were used in eCLIP-seq performed by Eclipse BioInnovations (USA). Cells were crosslinked, then lysed, RNase I treated, and protein-RNA complexes were immunoprecipitated with anti-FLAG antibody coupled to magnetic beads. The eCLIP experiment was performed by Eclipse BioInnovations’ standard RBP-eCLIP pipeline. For the purpose of comprehensive analysis, we focused on binding sites that intersected between the two RBMXL3 replicates and were not detected in any of the GFP replicates.

first: Natalia

last: Rozwadowska

first: Agata

last: Barszcz

first: Erik

last: Dassi


title: High-grade serous ovarian cancer induced in different sites of origin in mice exemplifies diverse features of the human disease

city: Frederick

first: Ludmila

last: Szabova

state: MD

address: 1050 Boyles Street

department: CAPR

institute: Frederick National Laboratory for Cancer Research

summary: We have developed novel genetically engineered mouse models for high-grade serous carcinoma of the ovary. We compare expression profiles of 4 different models for HGSC, one developing carcinoma from the ovarian surface epithelium (OSE) and 3 others that develop carcinoma from Fallopian tube epithelium (FTE).  FTE-originating cancer models utilize either Pax8- or Ovgp1-promotor driven expression of inducible Cre recombinase (CreERT2) and the last model utilizes direct injection of adeno-virus expressing Cre recombinase into oviducts to induce the desired genetic aberrations: loss of Brca1, loss or mutation (R172H) of Trp53 and inhibition of proteins of the Rb family (via expression of K18GT121 transgene). We compare tumors from genetically engineered mouse models (GEMMs) and from GEM-derived allografts and compare them to corresponding normal tissue: ovary or oviduct (mouse equivalent of Fallopian tube). Expression profiling allowed us to investigate molecular subtypes of HGSC in these models and comparison to human HGSC.These well-defined, tractable models represent a valuable resource for assessing novel drugs and immunotherapies for patients with HGSC.

overall_design: OSE-BPR=model developing carcinoma from the ovarian surface epitheium. Genetic aberrations (loss of Brca1, loss of Trp53 and Rb inhibition) were induced by injection of adeno-Cre under ovarian bursa of the genetically engineered mice with a complex genotype Brca1 fl/fl, Trp53 fl/fl, K18GT121 Tg/+. Ad-BPR=model developing carcinoma from the oviductal epithelium. Genetic aberrations (loss of Brca1, loss of Trp53 and Rb inhibition) were induced by injection of adeno-Cre into the oviducts of the genetically engineered mice with a complex genotype Brca1 fl/fl, Trp53 fl/fl, K18GT121 Tg/+.  Pax8-BPR=model developing carcinoma from the oviductal epithelium utilizing  Pax8-CreERT2 transgene to direct the expression of Cre in the secretory cells of the oviductal epithelium. Genetic aberrations (loss of Brca1, loss of Trp53 and Rb inhibition) were induced by tamoxifen treatment of the genetically engineered mice with a complex genotype Brca1 fl/fl, Trp53 fl/fl, K18GT121 Tg/+, Pax8-CreERT2 Tg/+. Ovgp1-BPR= model developing carcinoma from the oviductal epithelium utilizing  Ovgp1-iCreERT2 transgene to direct the expression of Cre in the secretory cells of the oviductal epithelium. Genetic aberrations (loss of Brca1, Trp53 mutaion R172H and Rb inhibition) were induced by tamoxifen treatment of the genetically engineered mice with a complex genotypeBrca1 fl/fl, Trp53 fl/fl, K18GT121 Tg/+, Ovgp1-iCreERT2 Tg/+.All tumors were harvested at endpoint (multiple month post induction)

first: Lucy

last: Lu

first: Melanie

middle: B

last: Gordon

first: Kristine

last: Johnson

first: Theresa

middle: M

last: Guerin

first: Laura

last: Bassel

first: Deborah

last: Householder

first: Margalie

last: Edouard

first: Amy

last: Ries

first: Serguei

last: Kozlov

first: Keith

last: Collins

first: Wendi

last: Custer

first: Kathleen

last: Cho

first: Goli

last: Samimi

first: Robert

last: Shoemaker

first: Zoe

last: Weaver Ohler


title: IsomiR Utility in ALS Prognostication (ALS)

city: ראשון לציון

first: Iddo

last: Magen

state: Not in US

address: בן אליעזר 32, 17

country: Israel

institute: Weizmann Institute

type: Non-coding RNA profiling by high throughput sequencing

summary: Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease characterized by progressive motor neuron loss. IsomiRs are microRNA (miRNA) isoforms that arise from alternative processing or editing events during miRNA biogenesis. While isomiRs may carry distinct biological and clinical relevance, their potential as cell-free biomarkers in neurodegeneration remains largely unexplored. Here we investigated the prognostic utility of plasma isomiRs in ALS, using next-generation sequencing. We profiled cell-free isomiRs in 154 ALS patients from a British cohort and identified higher levels of one isomiR, let-7g-5p.t, to be associated with longer survival. This finding was independently validated in an international ALS cohort of 200 patients and was in two orthogonal approaches. let-7g-5p.t prognostic utility was comparable to that of neurofilament light chain (NfL) or miR-181. These results establish isomiRs as a novel class of blood-based biomarkers in ALS with potential to refine prognostication in clinical trials for neurodegenerative diseases.

overall_design: The molecular experimenters were blinded to the identity of the samples. Total RNA was extracted from 500μl plasma using miRNeasy Micro Kit following the manufacturer's protocol except adding 2.5ml of Qiazol to each plasma sample (Qiagen, #217084). RNA was quantified with a Qubit fluorometer using the RNA Broad Range Assay Kit (Thermo Fisher Scientific, #Q10211). Small RNA next-generation sequencing libraries were prepared using the QIAseq miRNA Library Kit (Qiagen, #331502) from 7.5 ng of total RNA. If RNA concentration was below the limit of detection, 5μl of undiluted RNA were used. Precise linear quantification of miRNAs was achieved by 12-nucleotide long unique molecular identifiers (UMIs). Samples were randomly assigned to the preparation of libraries indexed with QIAseq miRNA NGS 48 Index IL (Qiagen, #331595) and sequenced in batches of 48 or fewer samples. Library concentration was determined with a Qubit fluorometer (dsDNA High Sensitivity Assay Kit, Thermo Fisher Scientific, #Q32854) and library size with TapeStation D1000 (Agilent). Libraries with different indices were multiplexed and sequenced on a NextSeq 500/550 v2 (Illumina, #20024906) or a NovaSeq 6000 flow cell (Illumina, #20028401), with a 75-bp single read or paired-end reads with 6-bp index. FASTQ files were de-multiplexed using the user-friendly transcriptome analysis pipeline. Human miRNAs and isomiRs, as defined by miRBase - V22, were mapped using CLC genomic workbench 22.0 (Qiagen) only to the positive strand. Reads were trimmed in two consecutive fashions; Phred score, Q based error was calculated for every nucleotide, high values reflect poor read quality. A trimming score defined by the subtraction of the error from a threshold of 0.05 was set for each nucleotide. Then, a running sum of the nucleotide errors was calculated per read. The region between the first positive value of the running sum and the highest value of the running sum was kept with non-positive score reads being removed completely. Consecutively, reads’ ends were trimmed to keep the maximum length region containing 2 or fewer ambiguous nucleotides. This was followed by the library’s 3’-adaptors (TGGAATTCTCGGGTGCCAAGG) trimming, with reads that did not contain any adaptors being excluded from downstream analyses. Reads were filtered based on lengths of 15-55 bps. IsomiRs were considered as 2bps changes (insertion, deletion, shift, and mismatch) up/downstream from miRBase reference sequence with a maximum of 2 mismatches allowed in alignment. The algorithm prioritizes perfect matches to reference miRNAs, followed by sequences of increasing mismatch nucleotides. When a sequence aligns equally well to multiple isomiRs, counts are assigned uniformly across all matching forms.

first: Yahel

last: Cohen

first: Ilan

last: Sinai

first: Yehuda

last: Danino

first: Joanne

last: Wuu

first: Andrea

last: Malaspina

first: Michael

last: Benatar

first: Eran

last: Hornstein


title: Effects of TCDCA-FXR on obesity-induced endothelial dysfunction and hypertension II

first: Hanlin

last: Lu

first: Wencheng

last: Zhang


title: Bulk RNA sequencing for gene expression profiling of iPSC-derived liver sinusoidal endothelial cells and arterial endothelial cells

city: Kamakura

first: Shuntaro

last: Kawamura

state: Kanagawa

address: Tamanawa 1-6-42, Oak Tree Kamakura 103

country: Japan

institute: Institute of Science Tokyo

summary: Liver sinusoidal endothelial cells (LSECs) line liver sinusoids and regulate exchanges between blood and liver tissue, while maintaining hepatic vascular homeostasis through coagulation control, immune cell recruitment, and barrier function. To compare endotheial lineage markers, we performed bulk RNA-seq analysis of iPSC-derived LSECs (iLSECs) and arterial endotheial cells (iAECs). We here show that venous/LSEC programs in iLSECs (NR2F2, APLNR, CD36; STAB1, LYVE1, FCGR2B), whereas iAECs expressed higher pan-endothelial and arterial markers (PECAM1, CDH5; DLL4, HEY2, NRP1).

overall_design: RNA-seq profiling of iLSECs and iAECs differentiated from iPSCs for 21 days.

first: Norikazu

last: Saiki

first: Takanori

last: Takebe


title: PFOA impairs host immune response in viral infection

city: Galveston

first: hui

last: wang

state: Texas

address: 301 university blvd

department: Pathology

country: Armenia

institute: UTMB

summary: We performed scRNAseq on spleen cells pooled from 4 mice per group using the 10x Genomics scRNA-seq Flex assay, following the protocol outlined by the Chromium Fixed RNA Profiling Reagent Kit. Single cell sequencing of splenic lymphocyte revealed that PFOA. Furthermore, we leverage the lymphocytic choriomeningitis virus (LCMV) mouse model to quantify virus-specific immunity after PFAS exposure. PFOA exposure impaired the viral clearance and viral specific T cell response. Single cell RNA-seq analysis revealed downregulation of TNF-a signaling via NF-kB and interferon gamma response in effector CD8 and CCL5hi CD8 T cells.  exposure modulates the immune signatures in B and T cells, with decreased anti-viral genes and increased autoimmune related genes.

overall_design: Splenic immune cells in mice were isolated and scRNA sequencing was  performed using 10X genomics kits.

first: Wang

last: Hui

first: Liang

last: Yuejin

first: Firose

last: Khan


title: Transient inhibition of MEK/ERK and WNT pathways enhances direct differentiation of primed hPSCs into functional trophoblast stem cells

city: Guangzhou

first: Qifan

last: Jiang

state: Guangdong

address: No.1023,South Shatai Road, Baiyun District

institute: Southern Medical University

summary: The placenta plays a pivotal role in human pregnancy, yet research into placental development has been hindered by limited access to early-stage embryos and ethical constraints. Here, we developed a simplified and efficient strategy that enables direct, efficient conversion of primed hPSCs into stable, self-renewing hTSCs.

overall_design: Transcriptional profiles in primed PSCs (H1-ES), primed PSCs-derived cells induced by different strategies at two timepoints, YP medium-derived hTSCs (TS-YP).


title: Laser fixed-point timing and quantitatively induce venous thrombosis in zebrafish as a general model system to address the essential initial inflammation cytokines

city: Guiyang

first: Zhao

last: Yanchi

state: Guizhou

address: No. 9 Beijing Road

institute: Guizhou Medical University

summary: In recent years, a critical clinical problem that cannot be ignored is the incidence of venous thrombosis gradually increasing. Although many animal models of thrombosis have been established, the complex mechanism of thrombosis has not been elucidated. We successfully established a new animal model of venous thrombosis by infrared-pulse laser selectively targeting damage to the venous endothelium of zebrafish tail, resulting in the aggregation of red blood cells and platelets at the site of injury, forming a thrombus, like the formation of thrombi caused by damaged human venous endothelium. o-Dianisidine staining showed increased hemoglobin density at the injury site and decreased hemoglobin density at the heart site. Utilizing laser microdissection technology, we targeted the acquisition of localized thrombus cell clusters for high-throughput transcriptome sequencing. The data were further analyzed through gene set variation analysis (GSVA) and gene set enrichment analysis (GSEA), with the transcriptome data being examined against backgrounds of GO, KEGG, Reactome, and WP databases. Combining these analyses with molecular biology techniques such as RT-qPCR, WISH, and Western Blot, we observed that, compared to the normal group, macrophages were activated, and erythrocyte differentiation was more vigorous post-thrombus formation. Signaling pathways related to cell adhesion and leukocyte migration were activated, and the expression of inflammatory cytokines increased. Notably, IL-6 and TNF-α significantly increased at the thrombus site, while other cytokines such as IL-1β, IL-10, P-selectin, STAT3, phosphorylated STAT3, p65, and phosphorylated p65 were major players in the inflammatory response during venous thrombosis. The venous thrombosis model established in this study allows a high degree of visualization of thrombosis and provides a feasible and powerful protocol for studying the mechanism of thrombosis. This study may serve as a new venous thrombosis model for exploring the detailed kinetics and underlying mechanisms of thrombosis formation.

overall_design: Endothelial cells were laser-damaged at the posterior two somites of the zebrafish anal pore to establish a thrombus model, with the experimental procedure identical to the previous method. Sampling was conducted at the initial stage, peak formation, stabilization, and regression of thrombus at 1h, 3h, 6h, and 12h post-laser injury. The zebrafish larvae subjected to laser damage were sectioned using a sharp blade at five somites below the anal pore, removing the head and tail. The thrombus-forming tissue was sliced into 20 sections with a thickness of 20um each, and these frozen sections were adhered to slides coated with polyethylene naphthalate film (Figure 3A-C). Subsequently, thrombus tissue cells were captured via laser-capture microdissection on frozen sections, and the obtained thrombus tissue cells underwent microRNA extraction. Total RNA was extracted using Invitrogen TRizol reagent (California, USA). Generation of the Illumina RNA sequence library, along with paired end sequencing (300±50 bp) was conducted on an Illumina Hiseq 4000 (LC science, USA) using aliquots (5 mg) of qualified total RNA. Hisat software was used to align compare the sequencing data with the zebrafish reference genome (http://ftp.ensembl.org/pub/release-106/fasta/danio_rerio/dna/Danio_rerio.GRCz11.dna.toplevel.fa.gz). To assess the expression level of all mRNAs, sample reads were initially processed through StringTie, and then the FPKM (fragments per kilobase of transcript per million mapped reads) was calculated using stringtie and edgeR software. Subsequently, differentially expressed genes (DEGs) were identified using the R software package, based on the following criteria: log2 (fold-change) > 1 or <−1 and at p < 0.05. These DEGs were further analyzed for their functions and signaling pathways using Gene Ontology (GO; http://geneontology.org/) and Kyoto Encyclopedia of Genes and Genomes (KEGG; https://www.genome.jp/kegg/).

first: Yanchi

last: Zhao

first: Hua

last: Li

first: Liping

last: Shu


title: Transcriptomic profiling of DHA-treated human chondrocytes

city: 成都市

first: Mingyang

state: Anhui province

address: 四川省成都市高新区高朋大道17号吉泰安中心10楼1002

institute: West China Hospital, Sichuan University

summary: This study aimed to investigate the regulatory effects of docosahexaenoic acid (DHA) on lipid metabolism in human osteoarthritic chondrocytes. All cells were pretreated with 10 ng/mL interleukin-1β (IL-1β) for 24 hours to simulate the inflammatory environment of osteoarthritis. Subsequently, cells were divided into two groups: one treated with 25 μM DHA for 48 hours and the other with PBS as control. Total RNA was extracted and subjected to strand-specific paired-end RNA sequencing to examine transcriptomic changes related to lipid metabolic pathways.

overall_design: Human primary chondrocytes were pretreated with 10 ng/mL IL-1β for 24 hours. Cells were then treated with 25 μM DHA or PBS (control) for an additional 48 hours. Three biological replicates were included per group. Total RNA was extracted for strand-specific paired-end RNA-seq.

first: Li

last: Mingyang

first: Wu

last: Limin


title: IsomiR Utility in ALS Prognostication [control]

first: Iddo

last: Magen

address: בן אליעזר 32, 17

overall_design: Small RNA next-generation sequencing  The molecular experimenters were blinded to the identity of the samples. Total RNA was extracted from 500μl plasma using miRNeasy Micro Kit following the manufacturer's protocol except adding 2.5ml of Qiazol to each plasma sample (Qiagen, #217084). RNA was quantified with a Qubit fluorometer using the RNA Broad Range Assay Kit (Thermo Fisher Scientific, #Q10211). Small RNA next-generation sequencing libraries were prepared using the QIAseq miRNA Library Kit (Qiagen, #331502) from 7.5 ng of total RNA. If RNA concentration was below the limit of detection, 5μl of undiluted RNA were used. Precise linear quantification of miRNAs was achieved by 12-nucleotide long unique molecular identifiers (UMIs). Samples were randomly assigned to the preparation of libraries indexed with QIAseq miRNA NGS 48 Index IL (Qiagen, #331595) and sequenced in batches of 48 or fewer samples. Library concentration was determined with a Qubit fluorometer (dsDNA High Sensitivity Assay Kit, Thermo Fisher Scientific, #Q32854) and library size with TapeStation D1000 (Agilent). Libraries with different indices were multiplexed and sequenced on a NextSeq 500/550 v2 (Illumina, #20024906) or a NovaSeq 6000 flow cell (Illumina, #20028401), with a 75-bp single read or paired-end reads with 6-bp index. FASTQ files were de-multiplexed using the user-friendly transcriptome analysis pipeline. Human miRNAs and isomiRs, as defined by miRBase - V22, were mapped using CLC genomic workbench 22.0 (Qiagen) only to the positive strand. Reads were trimmed in two consecutive fashions; Phred score, Q based error was calculated for every nucleotide, high values reflect poor read quality. A trimming score defined by the subtraction of the error from a threshold of 0.05 was set for each nucleotide. Then, a running sum of the nucleotide errors was calculated per read. The region between the first positive value of the running sum and the highest value of the running sum was kept with non-positive score reads being removed completely. Consecutively, reads’ ends were trimmed to keep the maximum length region containing 2 or fewer ambiguous nucleotides. This was followed by the library’s 3’-adaptors (TGGAATTCTCGGGTGCCAAGG) trimming, with reads that did not contain any adaptors being excluded from downstream analyses. Reads were filtered based on lengths of 15-55 bps. IsomiRs were considered as 2bps changes (insertion, deletion, shift, and mismatch) up/downstream from miRBase reference sequence with a maximum of 2 mismatches allowed in alignment. The algorithm prioritizes perfect matches to reference miRNAs, followed by sequences of increasing mismatch nucleotides. When a sequence aligns equally well to multiple isomiRs, counts are assigned uniformly across all matching forms.

first: Yahel

last: Cohen

first: Ilan

last: Sinai

first: Yehuda

last: Danino

first: Joanne

last: Wuu

first: Andrea

last: Malaspina

first: Michael

last: Benatar

first: Eran

last: Hornstein


title: Transcriptomic responses in zebrafish ovary to PNX and receptor agonists

city: Gainesville

first: Christopher

last: Martyniuk

state: FL

address: 8891 SW 79th Avenue

institute: University of Florida

summary: Zebrafish ovary in vitro assays were completed using methods modified from Rajeswari et al., 2020. Briefly, female D. rerio (n = 14) were euthanized in 300 mg/L buffered MS-222 (Syncaine®, tricaine methanesulfonate, Syndel, Ferndale, WA, USA), weighed, and measured (total length (mm), TL). Zebrafish ovaries from each fish were partitioned into 5 sections of approximately equal size. Each of four of these sections were immersed into an assigned well within a 24-well plate containing 990 μl of culture media (90% Leibovitz’s L-15 medium [Sigma Cat# L1518], 1% Penicillin-Streptomycin [Gibco™ Cat# 15070-063], 0.5% bovine serum albumin [Sigma Cat# 81053N]), with either a DMSO control or one of 3 potential agonist treatments, 8535 (5 μM), PT-91 (5 μM), or PNX-20 (100 nM). Agonists were dissolved in DMSO and added to their respective wells in 10μl aliquots to achieve desired final concentrations in a final volume of 1ml in each well. The fifth section of ovary was photographed on a Sedgewick rafter cell with a Jenoptik ProgRes® C5 microscope camera to characterize egg stages for each fish. Four plates containing n=3-4 replicates per treatment were incubated for 6 hours at 28 ℃, each plate completed on different days to replicate the assay temporally. After incubation, ovarian tissues were snap frozen in RNAlater™ (Invitrogen Cat# AM7020) for transcriptome analysis and culture media were stored in glass tubes at -80°C for further steroid quantification analysis via liquid chromatography tandem mass spectrometry (LC-MS/MS).

overall_design: 16 RNA-seq libraries, n=4 fish/treatment (control, A8535, PNX, PT91)

first: Tim

last: Breton

first: Chris

first: Mattthew

last: DiMaggio

first: Casey

last: Murray

first: Charles

last: Heyder


title: Photobiomodulation mitigates LPS-induced astrocyte neuroinflammation via the STAT5A/SOCS3 axis

city: Haikou

first: Feifan

last: Zhou

address: 58 Renmin Avenue

institute: Hainan University

summary: Neuroinflammation plays an important role in the occurrence and development of neurological diseases. In addition to microglia, the role of astrocytes in neuroinflammation has gradually attracted attention. Photobiomodulation (PBM), as a non-invasive, safe and effective treatment, has been shown to alleviate neuroinflammation and show potential in improving astrocyte activation. In this study, by analyzing the effects at different times, the spatiotemporal regulation and molecular mechanism of PBM on astrocytes were deeply explored. The results showed that PBM significantly attenuated LPS-induced upregulation of inflammatory factors and mitochondrial dysfunction in astrocytes under LPS stimulation for 4 hours and 24 hours. RNA-seq analysis showed that the JAK-STAT pathway played an important role in the early stage of astrocyte inflammatory response. PBM can promote the expression of Socs3 by activating Stat5a translocation to the nucleus, further inhibit the overactivation of the JAK-STAT inflammatory signaling pathway, and thus alleviate astrocyte inflammation. Taken together, this study provides new insights into the molecular mechanism of the potential application of PBM in the treatment of neuroinflammation.

overall_design: The RNA-seq data of primary astrocytes treated with PBM at 4 hours and 24 hours after LPS stimulation were collected respectively for gene expression profiling analysis.

first: Wenjing

last: Chen

first: Xiaotong

last: Gu

first: Shengnan

last: Wu


title: tRF-394 has the potential to be a RNA-based therapy for H. pylori-infected gastric cancer

city: Nanjing

first: Han

state: Jiangsu

address: #300 Guzhou Road, Gulou District

institute: Nanjing Medical University

summary: HGC-27 GC cells were stimulated with Helicobacter pylori-lipopolysaccharide (Hp-LPS). PANDORA-seq sequencing was employed to elucidate the potential roles of these relatively uncharacterized novel small non-coding RNAs (sncRNAs) in Hp-infected gastric cancers. RNA-seq was performed to identify diffferentially-expressed gene in Hp-infected gastric cancers.

overall_design: PANDORA-Seq profiling of the GC cells after stimulated by H. pylori LPS compared with  H. pylori-negative controls.


title: NF-κB-dependent redistribution of the GR cistrome recruits GR to inflammatory gene loci and correlates with reduced repression by glucocorticoid [RNAP2_ChIPseq]

city: Calgary

first: Alex

last: Gao

state: Alberta

address: 3330 Hospital Dr NW

department: Physiology and Pharmacology

country: Canada

institute: University of Calgary

summary: While ligand-activated glucocorticoid receptor (GR) binds DNA to activate transcription, glucocorticoids, including budesonide, reduce inflammatory gene expression, yet recruit GR to many such gene loci. In epithelial cells, the inflammatory cytokine, interleukin-1β (IL1B), activates NF-κB to induce gene expression and co-treatment with budesonide produces nanoscale GR-RELA nuclear co-localization. Such co-stimulation orchestrated reciprocal genome-wide redistribution of GR and RELA binding regions (GBRs and RBRs, respectively) relative to each mono-treatment to produce widespread GBR RBR overlap. This correlated with increased RNA polymerase-2 presence and required NF-κB for GR cistrome remodeling. Mapping transcription start sites to the nearest GBR or RBR both revealed associations with upregulated, but not repressed, genes. Importantly, RBR proximity to budesonide upregulated genes and GBR proximity to IL1B-upregulated genes correlated with attenuated repression on co-treatment. As this occurred on a background of glucocorticoid-induced repression, GR presence at specific IL1B-induced gene loci may reduce, or protect, from an otherwise prevalent glucocorticoid induced repression.

overall_design: To understand the impact of NF-κB on GR cistrome redistribution, A549 cells were infected with Ad5-GFP (control), or Ad-IκBαΔN (NF-κB inhibitor) before no treatment, or treatment with IL1B, budesonide, or both for 1h. ChIP was performed using RNAP2 antibody, and sequenced using Illumina NovaSeq 6000.

first: Mahmoud

last: Mostafa

first: Robert

last: Newton

first: Amandah

last: Necker-Brown


title: Phenotypically Anchored Transcriptomics of Diverse Agrichemicals Revealed Congruent Pathways and Unique Gene Expression Signatures

city: Corvallis

first: Robyn

middle: Leigh

last: Tanguay

state: OR

address: 28645 East Hwy 34

department: Environmental and Molecular Toxicology

institute: Oregon State University

summary: Transcriptomic data for 48 hour post-fertilization (hpf) wildtype zebrafish developmentally exposed to 45 different agrichemicals.

overall_design: mRNA sequencing was performed on four biological replicates of the five collected for each treatment. Collections of 8 animals performed over 28 different days with a single day match control collected to form a global control dataset compared to treated samples.The samples underwent PrepX Robotic RNA PolyA enrichment combined with NEBNext UltraII Directional RNA Library Prep/Illumina Stranded mRNA library preparation. Samples were split between three P3 flow cells (1.2 billion reads per run) and a P2 (400 million reads per run), and samples were sequenced usii an Illumina NextSeq 2000 (100 bp single end) resulting in 20 million read counts for each sample.

first: Lindsey

last: St Mary

first: Ryan

last: McClure

first: Lisa

last: Truong

first: Katrina

last: Waters

first: Steven

last: Carrell

middle: L


title: NF-κB-dependent redistribution of the GR cistrome recruits GR to inflammatory gene loci and correlates with reduced repression by glucocorticoid

summary: While ligand-activated glucocorticoid receptor (GR) binds DNA to activate transcription, glucocorticoids, including budesonide, reduce inflammatory gene expression, yet recruit GR to many such gene loci. In epithelial cells, the inflammatory cytokine, interleukin-1β (IL1B), activates NF-κB to induce gene expression and co-treatment with budesonide produces nanoscale GR-RELA nuclear co-localization. Such co-stimulation orchestrated reciprocal genome-wide redistribution of GR and RELA binding regions (GBRs and RBRs, respectively) relative to each mono-treatment to produce widespread GBR_x0002_RBR overlap. This correlated with increased RNA polymerase-2 presence and required NF-κB for GR cistrome remodeling. Mapping transcription start sites to the nearest GBR or RBR both revealed associations with upregulated, but not repressed, genes. Importantly, RBR proximity to budesonide_x0002_upregulated genes and GBR proximity to IL1B-upregulated genes correlated with attenuated repression on co-treatment. As this occurred on a background of glucocorticoid-induced repression, GR presence at specific IL1B-induced gene loci may reduce, or protect, from an otherwise prevalent glucocorticoid_x0002_induced repression.

overall_design: To understand transcriptional interactions between GR and NF-κB, mammalian airway epithelial (A549) cells were not stimulated or treated with IL1B, budesonide, or both for 1, 2, 6, 12, and 24h before harvesting for RNA sequencing.


title: SMD2 reads pseudouridines to regulate mRNA splicing and promote tumorigenesis [RIP-Seq]

city: Shanghai, P.R. China

first: weiying

last: meng

address: 1239 Siping Road, Shanghai, P.R. China

institute: Tongji University

summary: Pseudouridines (Ψ) in mRNA are linked to alternative splicing, but their regulatory mechanisms remain unclear due to the lack of identified reader proteins. Here, we identify SMD2, a core spliceosomal component, as a direct Ψ reader. Using in vitro and ex vivo assays, we show that SMD2 preferentially binds Ψ over unmodified uridines. SMD2 collaborates with PUS family enzymes to regulate alternative splicing by binding Ψ near exon-intron boundaries, modulating the splicing of numerous pre-mRNAs. Notably, the gene encoding SMD2, SNRPD2, is overexpressed across multiple cancers and is essential for tumor cell proliferation through the maturation of key transcripts. These findings uncover a direct mechanistic link between Ψ and spliceosomal function, establishing SMD2 as a critical regulator of Ψ-mediated splicing and a potential cancer therapeutic target.

overall_design: Using RNA-Pull-Down technology, it was identified that the pseudouracil modification might have an interaction relationship with the SMD2 protein (gene name SNRPD2). We knocked out the pseudouracil modification enzyme PUS7 and the SNRPD2 gene in HEK293T cells through CRISPR-Cas9 technology (n=3). Meanwhile, the SMD2-RIP experiment was combined to explore its internal interaction relationship. Furthermore, we simultaneously conducted a CRISPR-Cas9 knockout similar to that in the SNRPD2 cancer high-expression CHOL cell line to investigate the specific functions of the interaction relationship between SNRPD2 and pseudouracil modification in cancer.

first: Weiying

last: Meng

first: Moping

last: Xu

first: Shuxia

last: Sun

first: Zhiyan

first: Jianhuang

last: Xue

first: Jiejun

last: Shi


title: Bulk RNA sequencing for gene expression profiling of iPSC-derived liver sinusoidal endothelial cells treated with Antithymocyte globulin compared with normal rabbit IgG

first: Shuntaro

last: Kawamura

summary: Antithymocyte globulin (ATG) is a widely used immunosuppressive agent, yet its off-target vascular effects remain a clinical challenge in part due to a lack of relevant human models. To elucidate the effects of ATG on liver sinusoidal endothelial cells, we performed bulk RNA-seq analysis of iPSC-derived liver sinusoidal endothelial cells (iLSECs) exposed to ATG or normal rabbit IgG (rIgG) for 4 or 24 hours. We here report that ATG induces a proinflammatory program in iLSECs, characterized by upregulation of chemokines and prothrombotic factors. While minimal differences were observed at 4 hours, expression patterns clustered separately at 24 hours between rIgG- and ATG-treated cells. At 24 hours, ATG upregulated gene expressions, including chemokines such as CCL2, CXCL1, and CXCL5, as well as prothrombotic mediators SPP1 and SERPINE1, with downregulation of the vasoprotective gene NOS3. Gene set enrichment analysis identified that the gene set "Overview of Proinflammatory and Profibrotic Mediators" was significantly enriched in ATG-treated iLSECs at 24 hours compared to rIgG controls. This dataset provides critical insight to uncover the direct mode of action of ATG on LSEC beyond its immunosuppressive function.

overall_design: RNA-seq profiling of iLSECs differentiated from iPSCs for 14 days. Cells were treated with vehicle control, normal rabbit rIgG as antibody control, or ATG, and harvested at baseline (0 h), 4 h, and 24 h post-treatment.

first: Yosuke

last: Yoneyama

first: Norikazu

last: Saiki

first: Takanori

last: Takebe


title: Transcriptomic profiling of cardiac lymphatic endothelial cells in autoimmune myocarditis

city: Tsu

first: Kazuaki

last: Maruyama

state: Mie

address: 2-174, Edobashi

institute: Mie University, Graduate school of medicine, Department of Pathology and Matrix Biology

summary: This study investigates how cardiac lymphatic endothelial cells (LECs) respond to VEGF-C stimulation during autoimmune myocarditis in mice. The tissue from mouse hearts 3 weeks after disease induction and analyzed via bulk RNA sequencing. VEGF-C treatment significantly altered immune-related gene expression, particularly in macrophage regulatory pathways, highlighting lymphatic immunomodulation in myocarditis.


title: SMD2 reads pseudouridines to regulate mRNA splicing and promote tumorigenesis [RNA-Seq]


title: Bulk RNAseq profiling of Streptococcus pneumoniae EF3030 and Influenza A virus (A/California/07/2009(H1N1))    mono/coinfection in the mouse lungs.

city: Baltimore

first: Adonis

last: D'Mello

state: Maryland

address: Health Science Facility III, 670 W Baltimore St 3rd floor

institute: IGS- University of Maryland Baltimore

summary: To investigate the host-pathogen interactions of Streptococcus pneumoniae EF3030 (NZ_CP035897) and Influenza A virus (A/California/07/2009(H1N1))    in the mouse lung. We generated monoinfections and coinfections of C57BL/6 mice, as well as mock infection controls, and harvested whole mouse lung homogenates.

overall_design: We performed gene expression profiling analysis using bulk RNA-seq. K-means clustering of normalized gene expression values was used to identify true mock/coinfected cohorts of samples (mock infected, EF3030 infected, pH1N1 infected, and EF3030+pH1N1 coinfected), as some mice cleared infections over time. As such, with a focus on EF3030 infected and EF3030+pH1N1 coinfected groups, samples that did not fit into these 2 group clusters were labeled "inconclusive_infection".

first: Jessica

middle: R

last: Lane

first: Hervé

last: Tettelin

first: Carlos

last: Orihuela


title: Influenza A virus modulation of Streptococcus pneumoniae infection using ex vivo transcriptomics in a human primary lung epithelial cell

summary: Nanostring validation of deep sequencing of cDNA from Streptococcus pneumoniae EF3030 bacteria and normalized human broncial epithelial cells (nHBEC), together, and after coincubation with Influenza A virus pH1N1. (Accession:GSE225108)

sample_organism:
Streptococcus pneumoniae
Homo sapiens
Influenza A virus

overall_design: Cross platform validation of specific Streptococcus pneumoniae EF3030 genes from deep RNAseq samples (Accession:GSE225108). [HB indicates Human+Bacteria, HIB indicates Human+Influenza+Bacteria]


title: Deficiency of the Collagen Endocytic Receptor MRC2 Accelerates Mouse Lung Fibroblast Proliferation

city: Madison

first: Lynn

last: Schnapp

state: WI

address: 1685 Highland Ave, Suite 5000

department: Medicine

institute: University of Wisconsin-Madison

summary: Mannose receptor C type 2 (MRC2) is highly expressed in the lung and is the major endocytic receptor for the internalization and degradation of collagen in mesenchymal cells. Using Mrc2 knockout (KO) mice, we previously showed that MRC2 is required for efficient clearance of collagen in bleomycin-induced fibrosis. However, MRC2 also interacts with various cell-surface receptors and ligands beyond collagens, indicating that MRC2 may have additional, previously unrecognized functions in fibroblasts. To uncover novel pathways regulated by MRC2, we took an unbiased approach to compare the transcriptomic profile of MRC2-deficient lung fibroblasts to WT after in vitro culture.

overall_design: RNA-seq profiling of cultured Mrc2 knockout versus wild-type mouse lung fibroblasts

first: Shota

last: Yamamoto

first: Carole

last: Wilson

first: Melissa

middle: A

last: Krueger

first: Sina

last: Gharib


title: NF-κB-dependent redistribution of the GR cistrome recruits GR to inflammatory gene loci and correlates with reduced repression by glucocorticoid [GR_RELA_ChIPseq]

first: Alex

last: Gao

overall_design: To understand interactions between the GR and NF-κB cistromes, A549 cells were not treated, or treated with NS, IL1B, budesonide, or both before ChIP was performed using GR and RELA antibodies, and sequenced using Illumina NovaSeq 6000.

first: Mahmoud

last: Mostafa

first: Robert

last: Newton

first: Andrew

last: Thorne

first: Akanksha

last: Bansal


title: Novel variants in the splicing factor gene SF3B1 are associated with neurodevelopmental disorders

city: BREST

first: Delphine

last: Bernard

address: 22 avenue Camille Desmoulins

country: France

institute: UMR1078 - Université de Bretagne Occidentale

summary: SF3B1 is an essential and ubiquitous splicing factor that plays a pivotal role in the early steps of pre-mRNA splicing. Recurrent somatic missense mutations in SF3B1 are frequent in cancers, but no constitutional variant has been reported so far. We describe here a cohort of 26 individuals with neurodevelopmental disorders, harbouring SF3B1 constitutional heterozygous variants that appeared mostly de novo. Patients present with a global developmental delay, associated with variable neurological and facial dysmorphic traits. A dichotomy may emerge between patients harbouring predicted loss of function (n=9) and missense variants (n=17), the latter being associated with a more severe and syndromic phenotype, including heart and gastrointestinal anomalies. We focused on de novo SF3B1 missense variants, which were largely distinct from those reported in cancer. Functional complementation assays show that de novo SF3B1 missense variants did not cause a loss of function of the protein. Targeted and genome-wide analysis of RNA splicing reveal that they affect canonical and alternative splicing more moderately than somatic variants, and subtly modify the splicing of many transcripts, some of which are involved in neurodevelopmental disorders. SF3B1 joins the short list of U2 snRNP components involved in both cancer and neurodevelopmental disorders.

overall_design: RNA-seq profiling of K562 cells stably expressing wild type or variant SF3B1 (K700E, E722K, P780L, N829S) upon induction with 2 microg/mL of doxycycline for 7 days (in RPMI, 10% FBS, 2mM Gln). Biological independent replicates (n=3) were realised for each condition. RNA sequencing was performed by Novogene on an Illumina NovaSeq platform, using a 150-bp paired-end sequencing strategy.

first: Kevin

last: Uguen

first: Tiffany

last: Bergot

first: Solène

last: Chapalain

first: Marie-Pier

last: Scott-Boyer


title: A Novel Microprotein, MUCP1, Mediates Succinate Transport and Promotes Colorectal Cancer Progression by Modulating Glutamine Metabolism

city: Philadelphia

first: Junjie

last: Nie

state: PA

address: 4119 Powelton Avenue

institute: university of Pennsylvania

summary: Metabolic reprogramming is a hallmark of colorectal cancer (CRC) progression, yet the molecular mechanisms governing this process remain largely unresolved. And the translational roles of numerous long non-coding RNAs (lncRNAs) have been largely overlooked, despite their protein products being essential in cancer progression. This study identifies MUCP1, the microprotein encoded by lncRNA MUC20-OT1, as a central regulator of metabolic processes in CRC. Positioned on the mitochondrial outer membrane, MUCP1 is vital for the export of succinate, a key oncometabolite. Acute depletion of MUCP1 causes succinate accumulation, Tricarboxylic acid cycle (TCA) instability, and disruptions in glutamine metabolism. Cancer cells lacking MUCP1 show decreased H3K4me3 modifications on genes crucial for glutamine metabolism, driving further metabolic imbalance.  Sustained MUCP1 deficiency ultimately triggers metabolic reprogramming, emphasizing the role of this microprotein in linking mitochondrial metabolism to epigenetic regulation and presenting it as a promising therapeutic target in CRC.

overall_design: This RNA-seq dataset examines the transcriptomic impact of MUCP1 overexpression in SW480 colorectal cancer cells. The experiment includes two groups: control (LV-NC) and MUCP1-FLAG overexpression. RNA was extracted from biological replicates of both groups for sequencing, with the aim of identifying differentially expressed genes influenced by elevated MUCP1 levels. Comparative gene expression analysis and pathway enrichment studies were conducted to assess changes, particularly in metabolic and signaling pathways.

first: Shukui

last: Wang


title: Augmenting AMPA receptor signaling following spinal cord injury increases ependymal-derived stem/progenitor cell (epNSPC) migration and promotes functional recovery

city: Toronto

first: Laureen

last: Hachem

state: Ontario

address: 60 Leonard Ave

institute: University of Toronto

summary: Using lineage tracing in adult mice, we demonstrate that pharmacological blockade of AMPARs reduces epNSPC proliferation and migration after cervical SCI. Similarly, knocking out AMPAR subunits in Foxj1+ ependymal cells and their progeny abolishes glutamate-mediated AMPA currents and impairs the migration of epNSPCs after SCI. Augmenting AMPAR signaling with ampakines maintains the acute maturation reversal  of epNSPCs into the chronic injury period, enhances ependymal-glial cell contacts, which may contribute to the spatial distribution and migratory pattern of activated ependymal cells, ameliorates the decrease in corticospinal tract excitability subacutely after SCI, and improves long-term neurobehavioral recovery. Together this work uncovers a neurotransmitter receptor-dependent  mechanism of epNSPC activation following injury, which may be targeted to harness the regenerative potential of the spinal cord.

overall_design: Single nucleus RNA sequencing

middle: D

first: Homeira

last: Moradi Chameh

first: Gustavo

last: Balbinot

first: Andrea

last: Mothe

first: Alain

last: Pacis

first: Rui Tong

last: Geng Li

first: Taufik

last: Valiante

first: Wei

last: Lu

first: Charles

middle: H

last: Tator

first: Michael

middle: G

last: Fehlings


title: Detection and monitoring of translocation renal cell carcinoma via plasma cell-free epigenomic profiling

city: Boston

first: Karl

last: Semaan

state: MA

address: Brookline Ave 450

institute: Dana-Farber Cancer Institute

type: Methylation profiling by high throughput sequencing

summary: Translocation renal cell carcinoma (tRCC) is an aggressive fusion-driven subtype of kidney cancer that is frequently misdiagnosed due to morphologic overlap with other kidney cancer subtypes. Conventional liquid biopsy assays targeting DNA alterations are suboptimal for use in tRCC due to its paucity of genomic changes. We demonstrate the utility of cell-free chromatin profiling to noninvasively detect and monitor tRCC with high accuracy, a method that could have applicability to other genomically quiet cancers.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for histone modifications H3K27ac, and H3K4me3, methylated immunoprecipitation and high-throughput sequencing (MeDIP-seq), and low pass whole genome sequencing on cell-free DNA.

first: Simon

last: Garinet

first: Toni

middle: K

last: Choueiri

first: Matthew

last: Freedman

first: Sylvan

middle: C

last: Baca

first: Srinivas

last: Viswanathan


title: Highly multiplexed mRNA quantitation with CRISPR-Cas13

city: Princeton

first: Cameron

last: Myhrvold

state: NJ

address: Washington Street, Moffett, 161

department: Molecular Biology

institute: Princeton University

summary: RNA quantitation tools are often either high-throughput or cost-effective, but rarely are they both. Existing methods can profile the transcriptome at great expense or are limited to quantifying a handful of genes by labor constraints. A technique that permits more throughput at a reduced cost could enable multi-gene kinetic studies, gene regulatory network analysis, and combinatorial genetic screens. Here, we introduce quantitative Combinatorial Arrayed Reactions for Multiplexed Evaluation of Nucleic acids (qCARMEN): an RNA quantitation technique which leverages the programmable RNA-targeting capabilities of CRISPR-Cas13 to address this challenge by quantifying over 4,500 gene-sample pairs in a single experiment. Using qCARMEN, we studied the response profiles of interferon-stimulated genes (ISGs) during interferon (IFN) stimulation and flavivirus infection. Additionally, we observed isoform switching kinetics during epithelial-mesenchymal transition. qCARMEN is a simple and inexpensive technique that greatly enhances the scalability of RNA quantitation for novel applications with performance similar to gold-standard methods.

overall_design: RNAseq profiling of U2OS cells treated with IFN-beta for 0 hours, 4 hours, or 8 hours.

first: Brian

last: Kang

first: Alexandra

last: Bell

first: Jiayu

last: Zhang

middle: P

last: Schwoerer

first: Aaron

middle: E

last: Lin

first: Amy

middle: N

last: Nelson

first: Emily

last: Schoeman

first: Andrew

last: Guo

first: Alexander

last: Ploss


title: Circadian Reprogramming by Timed Sodium Intake Reveals Transcriptional Pathways of Daily Salt Handling in the Colon.

city: Tokyo

first: Kenichiro

last: Kinouchi

address: 35 Shinanomachi, Shinjuku-ku

institute: Keio University School of Medicine

summary: ChIP-seq was performed to investigate the genome-wide occupancy of the circadian clock and mineralocorticoid receptor in the colon.

overall_design: male C57BL/6 mice were subjected to ad libitum normal chow diet. Chromatin immunoprecipitation with BMAL1 or MR antibody followed by deep sequencing was performed using the colon tissue harvested at ZT12.

first: Takuto

last: Torimitsu

first: Hiroshi

last: Itoh


title: Effect of NUDT21 knockdown on gene expression in MUTZ-1 and SKM-1 myelodysplastic syndrome cells

city: Taiyuan

first: Shuo

last: Li

state: Shanxi Province

address: No.382, Wuyi Road, Taiyuan, Shanxi Province, China

department: Second Clinical Medical College

institute: Shanxi Medical University

summary: During mRNA maturation, splicing, capping and polyadenylation are its three main steps. And polyadenylation is the last key step in mRNA maturation, where the 3' end of pre-mRNA is cleaved and polyA sequence is added, which plays an important role in the stability of mRNA and its cellular function. NUDT21, which we report here, is a key regulator involved in polyadenylation in mRNA maturation and plays an extremely important role in variable polyadenylation. And we found that NUDT21 was highly expressed in MDS cells and that NUDT21 had a significant effect on the biological functions of MDS cells, especially in the transformation of MDS into AML. Therefore, our data report a specific gene profile of MDS cell lines after NUDT21 knockdown, which provides a new biomarker for clinical judgement of whether the disease has progressed in MDS patients, and provides new ideas on whether NUDT21 downstream regulatory genes, such as XAF1, may be new targets for MDS therapy.

overall_design: To investigate the role of NUDT21 in the transformation of myelodysplastic syndromes, we established MUTZ-1 and MUTZ-1 cell lines in which NUDT21 was knocked down by shRNA. We then performed gene expression profiling of the RNA-seq data of these two cells and knockdown models.Comparison of RNA-seq data of MUTZ-1 and SKM-1 cells and their KD derivatives (shNUDT21)Gene Expression Profiling

first: Peichun

first: Hongwei

last: Wang

first: Fanggang

last: Ren


title: Senescence of tumor-specific Non-Classic Monocytes Facilitates Immune Suppression and Prostate Cancer Progression through Tumor and Host Immune Interactions

city: Birmingham

first: Runhua

last: Liu

state: AL

address: 1720 2nd Avenue South

institute: University of Alabama at Birmingham

summary: Prostate cancer remains a leading cause of cancer-related mortality in men, with metastatic cases presenting significant therapeutic challenges due to genetic alterations that drive disease progression and immune evasion. While localized prostate cancer generally has favorable outcomes, metastatic disease is associated with much poorer survival rates. This study investigates the role of specific tumor-associated senescent non-classical monocytes (NC-Mo) in MYC amplification and PTEN deletion-mediated lethal prostate cancer progression, focusing on tumor-host immune interactions. Key genetic alterations, such as MYC amplification and PTEN deletion, lead to tumor cell apoptosis via mitochondrial Complex I dysfunction, driven by metabolic reprogramming characterized by increased glycolysis and arginine biosynthesis. A specific subtype of Ly6cLowCD43LowCXCR2+ NC-Mo is activated by the phagocytosis of apoptotic tumor cells and damage-associated molecular patterns (DAMPs) through TLR4 activation, promoting their differentiation into a senescent phenotype.TLR4 activation further induces NC-Mo to secrete TNF-α, which stimulates intra-tumor endothelial cells to produce G-CSF, circulating to the bone marrow and promoting the transition of classical monocytes into NC-Mo. Once senescent, NC-Mo secrete more TGF-β1, which enhances CXCL5 secretion from tumor cells, mainly via the AKT/PI3K pathway, creating a feedback loop that recruits more peripheral NC-Mo into the tumor microenvironment (TME). Additionally, IL-18 secreted by senescent NC-Mo suppresses T cells and NK cells, weakening both adaptive and innate immune responses in the TME. Targeting NC-Mo and key pathways, such as TLR4, CXCL5-CXCR2, and IL-18-IL18R, reduce immune suppression and inhibit tumor progression. These findings provide insights into how MYC/PTEN dysfunction accelerates prostate cancer progression through specific tumor-associated senescent NC-Mo, offering novel therapeutic opportunities.

overall_design: Based on Hi-Myc and Pten cKO mice model, we explore the mechanisms promoting prostate cancer progression and metastasis.

first: Chao

first: Haiyan

last: Yu

first: Chen

last: Huang

first: YanFeng

first: Lizhong


title: Exercise Training-induced Extracellular miR-136-3p Modulates Glucose Uptake and Myogenesis through Targeting of NRDC in Human Skeletal Muscle

city: Stockholm

first: Mutsumi

last: Katayama

address: Solnavägen 9

country: Sweden

institute: Karolinska Institutet

summary:
We identified several exercise training-responsive miRNAs within exosome-rich EVs in serum, including miR-136-3p. In human myotubes, miR-136-3p enhanced glucose uptake and targeted the nardilysin convertase (NRDC) gene.
To search miR-136-3p and NRDC relating function in human myotubes, we performed transcriptome analysis.

overall_design: We used microarrays to detail the global regulation of gene expression by miR-136-3p and NRDC.

first: Anna

last: Krook


title: The Parkinson’s disease associated LRRK2-G2019S variant restricts serine metabolism leading to microglia inflammation and dopaminergic neuron degeneration

city: Belval

first: Matthieu

last: Gobin

address: 6, avenue du Swing

country: Luxembourg

institute: LCSB

summary: A mounting body of evidence reveals that inflammation is a major hallmark in the pathophysiology of Parkinson’s disease (PD). Notably, microglia are key players in orchestrating neuroinflammatory signalling pathways in the brain. However, the molecular mechanisms underlying the microglial response in the dopaminergic neuron degeneration remain unclear. In this study, we investigated the role of the PD-associated LRRK2-G2019S variant in microglial neurotoxicity that potentially drives the loss of dopaminergic neurons. Using PD patient-specific induced pluripotent stem cell-based models, we showed that microglia harbouring the LRRK2-G2019S mutation exhibited increased activation markers, phagocytic capacity, and secretion of inflammatory cytokines such as TNF-α. This was linked to metabolic dysregulation, including higher levels of glycolysis and a reduction in serine biosynthesis. These overactivated microglia drove dopaminergic neuron degeneration in a 3D midbrain organoid model. Intriguingly, addressing the PD associated metabolic disturbances reduced the inflammatory state of the microglia and reversed neuronal loss. These findings reinforce the immunometabolic control of microglia to preserve dopaminergic neuron integrity and its pivotal role in PD pathogenesis.

overall_design: Bulk RNAseq from iPSC-derived microglia of 4 Healthy and 4 PD patients carrying mutations in the LRRK2-G2019S gene

first: Henry

last: Kurniawan

first: Sarah L.

last: Nickels

first: Alise

last: Zagare

first: Elisa

last: Zuccoli

first: Enrico

last: Glaab

first: Jens

last: Schwamborn


title: Transcriptome analysis of γδT cells with/without PERK knockdown

first: Prithvi

last: Sinha

address: 3400 Civic Center Bvld

institute: University of Pennsylvania

summary: The global RNA expression was assayed in PERK knockdown and control γδT cells exposed to a immunosuppressive mixed cell environment.

overall_design: γδ T cells were activated and expanded from the PBMCs of healthy donors. Cells were transduced lentivirally with shControl or shPERK constructs. Cells were then incubated in an invitro TME system comprising of myeloid , endothelial and tumor cells for 48 hours and sorted out magnetically using CD3 microbeads. RNA was isolated and analyzed by RNAseq.

first: Lin

last: Zhang

first: Xinye

last: Zhao

first: Yi

last: Fan


title: Oxidative phosphorylation in kidney-resident macrophages of type 2 diabetic kidney disease

city: Hwasung

first: Peong Gang

last: Park

address: Dongtansibumhanbi-gil 38, 215-502

country: South Korea

institute: Ajou University School of Medicine

summary: The research aims to elucidate the immunopathology associated with kidney resident macrophages in diabetic kidney disease, and to establish the basis for the development of therapeutics utilizing this understanding.

overall_design: single-cell RNA data of immune cell for induced type 2 DKD

first: Haein

last: Yoon

first: Seung Seok

last: Han


title: LINC01419 role as HCV induced HCC

city: Iksan

first: Ju-Hee

last: Yang

institute: Jeon-buk national university

summary: LINC01419 showed upregulation in the HCC cell lines than the PHH. In particular, LINC01419 was confirmed to have high expression in Huh7.5, which has high HCV infectivity.  LINC01419-silenced Huh7.5 significantly inhibited of cell proliferation, migration, and invasion. In vivo, we performed LINC01419 silencing by siRNA in the xenograft model. These results showed that the tumor weight and growth were suppressed in the LINC01419 downregulated group.

overall_design: To investigate the LINC01419 function in HCV induced HCC we analyzed Huh7.5 cell lines which LINC010419 gene has been knocked down by siRNA.


title: Rapid Disease Progression of Myelodysplastic Syndrome is Reflected in Transcriptomic and Functional Abnormalities of Bone Marrow MSCs

city: Singapore

first: Zhiyong

last: Poon

address: Outram Road

country: Singapore

institute: SGH

summary: Current investigations of MDS-MSCs rely heavily on the clinical international prognostic scoring system (IPSS) or revised IPSS (IPSS-R) of MDS to classify them into either the low- or high-risk categories. This approach, however, suffers from shortcomings, as it is based on assessments of the hematopoietic parameters and may not capture important biological changes or predictors in MDS-MSCs during disease progression. Herein, to focus the investigation on discovering unique characteristics and dominant effects of MDS-MSCs in conditions of fast vs slow transforming disease, we retrospectively examined and selected MDS BM samples from these two patient categories: those with transformation to AML in less than 2 years (MDSfast) or after 2 years (MDSslow) following sample collection.

overall_design: Mesenchymal stromal cells were derived from bone marrow aspirate and cultured for 1 passage before RNA extraction for bulk sequencing.

first: Hein

last: Than


title: Comparing Transcriptomes of human Alpha Beta and Gamma Delta T cells

summary: The global RNA expression was assayed in Alpha Beta (ABT) and Gamma Delta T (GDT) cells isolated and expanded from de-identified healthy volunteer donors

overall_design: ABT and GDT cells were activated and expanded from the PBMCs of healthy donors. RNA was isolated and analyzed by RNAseq.

first: Duo


title: Extracellular matrix glycation epigenetically regulates brain aging and neurodegeneration in the in vitro aged neurovascular model

city: Seoul

first: Minjeong

last: Jang

state: Asia/Oceania

address: 75, Nowon-ro, Nowon-gu, Seoul, Republic of Korea

institute: Korea Institute of Radiological and Medical Sciences (KIRAMS)

summary: Advanced glycation end-products (AGEs) accumulate in brain tissue with as we age, co-localizing with amyloid β and tau in the brains of elderly and Alzheimer’s disease patients. However, the link between increased AGE levels, aging, and neurodegeneration remains unclear. To explore the effect and mechanism of AGEs on the brain, we developed a neurovascular (NV) model that reflects features of an aged brain by integrating an AGE-anchored matrix.  Notably, we discovered that targeting AGE and its receptor could attenuate AGE-mediated neurodysfunction through the histone-modifying enzyme, KMT2A, in neurons within an aged NV model.

overall_design: To investigate the AGE-mediated neurodegenerative mechanism, neuronal cells differentiated from neural progenitor cell lines (ReNcell) were 3D cultured in collagen and Matrigel hydrogel, and provided aged conditions by using soluble AGE and AGE-anchored glycated matrix. We developed RAGE-depleted and -overexpressed ReNcells using shRNA and CRISPR/Cas9, respectively, for further clear mechanistic validation.

first: Hong Nam

last: Kim


title: Phenotypic impact of individual conserved neuronal microexons and their regulators in zebrafish

city: Barcelona

first: Manuel

last: Irimia

state: Barcelona

address: 88 Dr. Aiguader

department: MELIS

country: Spain

institute: Universitat Pompeu Fabra - Centre for Genomic Regulation

summary: Microexons show remarkable neuronal switch-like regulation and evolutionary conservation and they can impact protein-protein interactions and other molecular functions. Neuronal microexons are regulated in a tightly coordinated manner by the splicing factors Srrm3 and Srrm4. Depletion of Srrm3/4 in mice causes dramatic neurological phenotypes and their misregulation is associated with human disease. However, which microexon targets are associated with these phenotypes and how individual microexon deletions could impact neurodevelopment, physiology and behavior is unknown. To address this question, we generated zebrafish KO lines for 18 individual microexons and characterized their phenotypes at multiple levels, together with srrm3/4 mutant lines.  We found that, while mutation of the regulators, specially srrm3, shows multiple alterations in neuritogenesis, locomotion and social behavior, the impact of deleting of individual microexons was usually mild or non-existing. Nonetheless, for various microexons, we identified neuritogenesis defects (evi5b, vav2, itsn1, src) and social defects (vti1a, kif1b). In addition, microexon deletions led to transcriptomic alterations that are likely compensatory. Overall, our data suggest that the defects caused by srrm3/4 depletion are due to a cumulative effect of multiple small impacts that can individually be well tolerated by zebrafish.

overall_design: We deleted individual microexons in zebrafish using CRISPR-Cas9 with a double guide-RNA strategy. Stable mutant lines were generated for each microexon deletion, and rise to the F2 generation. To generate RNA-seq data, we cross two adult heterozygous individuals, and genotyped 5 dpf larva through fin clipping.  Larve of WT or DEL (homozygous deletion) genotype were grouped together, RNA extracted and submitted for  polyA-selected stranded RNA-seq.  A similar approach was taken for the mutant of the regulators. All fish had a HuC:GFP background.

first: Laura

last: Lopez-Blanch

first: Cristina

last: Rodriguez-Marin

first: Jon

last: Permanyer


title: liver isolated single cell RNAseq v1

city: Jerusalem

first: Eithan

last: Galun

address: Hadassah Ein Kerem

institute: Hadassah Medical Organization

summary: Chronic liver inflammation and fibrosis are central to liver diseases, including the most prevalent metabolic-dysfunction-associated steatohepatitis (MASH), chronic autoimmune liver diseases and liver cancer. However, the mechanism orchestrating the co-occurrence of liver inflammation and fibrosis, both tightly associated with liver diseases, remains elusive. Here, we show that the hepatocyte derived, miR-122 regulates both, liver inflammation and fibrosis, through independent pathways, and that miR-122 is involved in tuning innate and adaptive hepatic immune responses. In parallel, we show that decrease of miR-122 is associated with liver fibrosis in advance or together with liver inflammation. We show that miR-122 regulates liver tolerance, and its absence attenuates bacterial and parasitic infections, and thus functions as a liver immune rheostat. As such, miR-122 presents a therapeutic target.

overall_design: RNA from single cells isolated from livers of miR-122 knock out mouse and wild type control from the same founder at the age of 2 weeks.

first: Maytal

last: Gefen

first: Shanny

last: Layani

first: Emma

last: Klahr

first: Zohar

last: Shemuelian

first: Johannes

last: Brandi

first: Thomas

last: Jacobs

first: Christiane

last: Steeg

first: Lorenz

last: Adlung

first: Christoph

last: Kilian

first: Merav

last: Ordan

first: Oren

last: Gordon

first: Nathalie

last: Abudi

first: Rinat

last: Abramovitch

first: Yuval

last: Nevo

first: Sharona

last: Elgavish

first: Hadar

last: Benyamini

first: Jonathan

last: Monin

first: Elina

last: Zorde Khvalevsky

first: Nofar

last: Rosenberg

first: Aurelia

last: Markezana

first: Dayana

last: Yaish

first: Adi

last: S. Yehezkel

first: Alina

last: Simerzin

first: Mila

last: Rivkin

first: Osher

last: Amran

first: Daniel

last: S. Goldenberg

first: Amnon

last: Peled

last: Axelrod

first: Jacob

last: Rachmilewitz

first: Samuel

last: Huber

first: Nicola

last: Gagliani

last: Schramm

first: Sören

last: Weidemann

last: Herkel

first: Antonella

last: Carambia

first: Rifaat

last: Safadi

first: Abed

last: Halila

first: Asraf

last: Imam

first: Daniela

last: Heide

first: Jenny

last: Hetzer

first: Stefan

last: Rose-John

first: Mathias

last: Heikenwälder

first: Hilla

last: Giladi


title: Oligoastrocytoma consisting of IDH-mutant 1p/19q-codeleted oligodendroglioma and IDH-wildtype astrocytoma

city: Hidaka

first: Mitsuaki

middle: Shirahata

last: Shirahata

state: Saitama

department: Neurosurgery/Neuro-oncology

institute: Saitama Medical University International Medical Center

summary: Oligoastrocytoma (OA) was formerly defined as a mixed glioma exhibiting histological features of both astrocytoma and oligodendroglioma. However, OA has been shown to be attributable to either glioma-type based on its molecular characteristics and was excluded from the glioma classification with the introduction of the integrated diagnosis. Nevertheless, some cases showing genetic features of both oligodendroglioma and astrocytoma have been reported since the integrated diagnosis era, and whether OA exists as a glioma-type remains controversial. All previously reported cases were mixed gliomas with and without 1p/19q-codeletion in the lineage of isocitrate dehydrogenase (IDH) mutant gliomas. Herein, we described a 33-year-old man with a progressive headache. Magnetic resonance imaging showed a large left frontal lobe tumor composed of a cystic component with contrast-enhancing walls and a non-contrast-enhancing solid component. The patient underwent a gross total removal of the tumor. Histologically, the cystic and solid components showed oligodendroglioma and astrocytoma morphology, respectively. Immunohistochemically, IDH1-R132H staining was positive in the cystic component and negative in the solid component. Sanger sequencing confirmed the IDH1-R132H mutation and the C228T mutation in the telomerase reverse transcriptase promoter (TERTp) region in the cystic component, while both IDH1/2 and TERTp were wildtype in the solid component. Fluorescence in situ hybridization revealed 1p/19q-codeletion in both areas. The integrated diagnosis led to the diagnosis of oligoastrocytoma consisting of IDH-mutant 1p/19q-codeleted oligodendroglioma and IDH-wildtype astrocytoma. Furthermore, deoxyribonucleic acid (DNA) extracted separately from each area of formalin-fixed paraffin-embedded specimen revealed a distinct methylation profile. On the other hand, the global DNA copy-number analysis derived from the microarray data showed similar copy-number profiles including 1p/19q-codeletion for both sites. This is the first report of a dual-genotype oligoastrocytoma with IDH-mutant 1p/19q-codeleted oligodendroglioma and IDH-wildtype astrocytoma. This extremely rare case provides profound insight into the process of acquiring genetic abnormalities in the development of glioma.

overall_design: The objective of this study was to identify the methylation profile of each site exhibiting oligodendroglioma morphology and astrocytoma morphology, which are components of oligodendrocytoma, a mixed glioma. DNA was extracted separately from each site of formalin-fixed paraffin-embedded　specimens and subjected to DNA microarray analysis.


title: Adoptive transfer of membrane-restricted IL-12-TCR T cells promotes antigen-spreading and elimination of antigen-negative tumor variants

city: Bethesda

first: Jay

last: Berzofsky

state: MD

address: Building 41 Room D702D

department: Center for Immuno-Oncology

institute: National Cancer Institute

summary: Adoptive T-cell therapy has shown promising results with high response rates and frequent complete responses in B-cell malignancies, offering hope for its application to a broad spectrum of cancers. However, a significant portion of patients with solid tumors experience primary or secondary resistance to this treatment modality. Known resistance mechanisms to this therapy include tumor heterogeneity and target antigen loss resulting from defects in antigen processing and presentation machinery. Constitutively expressed membrane-anchored interleukin-12 (caIL-12) has demonstrated low systemic exposure and antitumor activity in multiple preclinical adoptive T-cell treatment models. In this study, we assess the therapeutic impact of caIL-12 on target antigen-negative variants within a heterogeneous tumor. Target antigen-positive tumors were generated by engineering OVA-SIINFEKL peptide to B16 melanoma (B16-U-OVA), while B16 tumors served as antigen-negative variants. C57BL mice bearing heterogeneous tumors were treated with OT-I TCR-T cells engineered with or without caIL-12. Our results demonstrated that TCR-T cells (OT-I) could effectively deliver caIL-12 to the B16-U-OVA tumor sites and induce robust tumor control and survival benefits even in mice bearing OVA-negative B16 tumor variants. CaIL-12 was found to exert its effect on OVA-negative B16 variants within heterogeneous tumors primarily by activating endogenous antitumor CD8 T cells via antigen spreading. In addition, antigen spreading induced by OT-I-ca12 resulted in controlling OVA-negative tumors implanted at distant sites. This therapeutic effect required antigen-specific TCR-T cells and caIL-12 to co-localize at the tumor site, along with endogenous CD8 T cells capable of recognizing shared tumor antigens. These findings highlight the potential of caIL-12 to address challenges of antigen escape and tumor heterogeneity that may limit the efficacy of T-cell therapy against solid tumors.

overall_design: The mice bearing 80%B16-U-OVA/20%B16 were treated with OT-I-control or OT-I-caIL12 T cells. On day 8 post treatment, the tumors were resected and isolated T cells  by Pan T cell isolation kit.  Three replicates from each treatment were barcoded with 5' total-seq hashing antibodies and pooled for single cell seqeunce.

first: Ling

last: Zhang

first: Scott

last: Norberg

first: Farrah

last: Karimipour

first: John

middle: S

last: Davies

first: Alex

last: Kuznetsov

first: Wiem

last: Lassoued

last: Nurnett

first: Philip

last: Homan

first: Margaret

last: Cam

first: Andrew

last: Sinkoe

first: Ping

last: Xue

first: James

last: Gulley

first: Christian

last: Hinrichs


title: TFF3 drives Hippo dependent EGFR-TKI resistance in lung adenocarcinoma

city: Shenzhen

first: Shuwei

state: State...

address: Shenzhen,Guangdong province,China

institute: Tsinghua university

summary: Intrinsic and acquired resistance represent major obstacles to optimize outcomes in epidermal growth factor receptor (EGFR) tyrosine kinase inhibitor (TKI) targeted therapy in lung adenocarcinoma (LUAD). Hence, a deeper understanding of EGFR-TKI resistance mechanisms in LUAD will potentially assist in formulating strategies to delay or overcome such resistance. Herein, it was observed that trefoil factor 3 (TFF3) is a crucial mediator of the LUAD EGFR-TKI response. TFF3 conferred intrinsic resistance to EGFR inhibition in LUAD by promotion of EGFR activation. TFF3 expression was also increased in acquired EGFR-TKI resistant LUAD, accompanied by reduced EGFR activation. YAP, a key mediator of the Hippo signaling, was positively regulated by TFF3 by post-transcriptional mechanisms and was responsible for acquired EGFR-TKI resistance mediated by TFF3. Inhibition of TFF3 by a small molecule inhibitor not only enhanced EGFR-TKI sensitivity in LUAD cells but also restored the sensitivity of acquired EGFR-TKI resistant LUAD cells to EGFR-TKIs in vitro and in vivo. These findings demonstrate a pivotal function of TFF3 in mediating EGFR-TKI resistance in LUAD and may offer a potential therapeutic mechanism for delaying or overcoming resistance to EGFR-TKIs.

overall_design: To determine the potential singaling pathways responsible for the acquired  EGFR-TKI resistance in lung adenocarcinoma (LUAD), 4 pairs of parental and acquired EGFR-TKI resistant LUAD cells were performed RNA-sequencing

first: YanQin

last: Tan

first: Xi

first: Basappa

last: Basappa

first: Tao

last: Zhu

first: Vijay

last: Pandey

first: Peter

last: Lobie


title: Transcriptome sequencing of THP1 cells infected with Brucella

city: shihezi

first: runhui

last: qiu

state: xinjiang

address: No. 221 bei Si Lu

institute: shihezi university

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

summary: Brucella was infected at 1 MOI and cell samples were collected twelve hours later.

overall_design: To investigate the effect of Brucella infection on the differences in mRNA expression in THP1 cells, we infected THP1 cells, with Brucella 1 moi for 24 h, with 3 replicates per group, extracted total RNA, and analyzed it by high throughput sequencing

first: Qiu

last: Runhui


title: The function and mechanisms of hsa_circCDKN2B-AS_012 on tumor suppression of Colorectal cancer

city: Beijing

first: wanru

last: ma

address: No.1 Dahua Road, Dongcheng District

institute: Beijing hospital

summary: Circular RNAs (circRNAs) are a class of non-coding RNAs with a covalently closed loop structure, which plays crucial roles in regulating tumor development and progression. However, the detailed molecular mechanism of circANRIL in CRC is not fully understood. Real-time quantitative PCR was used to examine the expression of circ86591 in cells. RNA pull-down, mass spectrometry, RNA immunoprecipitation and western blotting were applied to investigate the possible molecule mechanisms of circ86591 and its binding proteins. RNA-sequencing, gain-of-function and loss-of function experiments were performed to find tumor-suppressive effect and the relevant signaling pathways of circ86591.

overall_design: To investigate the relevant signaling pathways of circ86591 in the regulation of cell proliferation, we established LOVO cells transfected with ASO-nc or ASO-circ86591 and HCT116 cells infected with ADV ctrl and ADV circ86591.


title: USP13 dictates RAN turnover and vulnerability to ferroptosis in diffused large B cell lymphoma (DLBCL)

city: Chongqing

first: Liu

last: Xiang

address: Tiansheng Street

institute: Southwest University

summary: Diffuse large B-cell lymphoma (DLBCL), the most common type of non-Hodgkin lymphoma, is an aggressive form of lymphoma. It accounts for 40% of non-Hodgkin's adult lymphoma cases worldwide. The current standard treatment for DLBCL is CHOP. The poor prognosis of patients with DLBCL is related to the development of genetic mutations that lead to chemotherapy resistance. This topic mainly explores whether Spautin-1 can improve the sensitivity of DLBCL to chemotherapy drugs and the mechanism of synergistic effect.

overall_design: To investigate  the regulation of  DLBCL cell line genes by small molecule inhibitors Spautin-1, we established a dosing model for DLBCL cell lines. We then performed gene expression profiling analysis using data obtained from RNA -seq. Comparative gene expression profiling analysis of RNA-seq data for SU-DHL-2 cells and its dosing group(Spautin-1,10 μM, 36 h).

first: Boheng

last: Li

first: Xuan

last: Qiao

first: Xingmeng

last: Yang

first: Yuanhao

last: Diao

first: Qiuxiang


title: RNA-seq analysis of NK-92 cells expressing Vaccinia virus (VACV) poxin (encoded by the B2R gene)

city: Daejeon

first: In-Hwan

last: Jang

address: 125, Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea

department: Immunotherapy Research Center

institute: Korea Research Institute of Bioscience and Biotechnology

summary: Transcriptional profiling of Poxin-NK-92 cells compared to control cells.

overall_design: Bulk RNA-seq of experiment: ctrl-NK-92, Poxin-NK-92 (A stable cell line was established by lentiviral infection, and positive cells were selected using fluorescence-activated cell sorting (FACS)). Samples were derived from total RNA extracted from 24 hours cultured NK-92 cells.

first: Ling-Zu

last: Kong

first: Tae-Don

last: Kim


title: Transcriptional alteration in the treatment of MDA-MB-231 cells using SFN and/or ZA

city: Pittsburgh

first: Shivendra

middle: V.

last: Singh

address: 5117 Centre Avenue, UPMC HCC Research Pavilion Suite 2.32A

institute: University of Pittsburgh

summary: We report differential gene expression changes by sulforaphane (SFN) and/or zoledronic acid (ZA) in MDA-MB-231 human breast cancer cell line

overall_design: Examinine the transcriptome regulated by SFN and/or ZA in the MDA-MB-231 human breast cancer cell line

middle: V


title: whole liver RNAseq

first: Eithan

last: Galun

overall_design: Whole liver RNA was extracted form liver of miR-122 KO mice and WT controls from the same founder background at the ages of 2 weeks, 3 weeks and 6 weeks. Gene expression of miR-122 KO mice was compared to WT control mice at each age respectively

first: Maytal

last: Gefen

first: Shanny

last: Layani

first: Emma

last: Klahr

first: Zohar

last: Shemuelian

first: Johannes

last: Brandi

first: Thomas

last: Jacobs

first: Christiane

last: Steeg

first: Lorenz

last: Adlung

first: Christoph

last: Kilian

first: Merav

last: Ordan

first: Oren

last: Gordon

first: Nathalie

last: Abudi

first: Rinat

last: Abramovitch

first: Yuval

last: Nevo

first: Sharona

last: Elgavish

first: Hadar

last: Benyamini

first: Jonathan

last: Monin

first: Elina

last: Zorde Khvalevsky

first: Nofar

last: Rosenberg

first: Aurelia

last: Markezana

first: Dayana

last: Yaish

first: Adi

last: S. Yehezkel

first: Alina

last: Simerzin

first: Mila

last: Rivkin

first: Osher

last: Amran

first: Daniel

last: S. Goldenberg

first: Amnon

last: Peled

last: Axelrod

first: Jacob

last: Rachmilewitz

first: Samuel

last: Huber

first: Nicola

last: Gagliani

last: Schramm

first: Sören

last: Weidemann

last: Herkel

first: Antonella

last: Carambia

first: Rifaat

last: Safadi

first: Abed

last: Halila

first: Asraf

last: Imam

first: Daniela

last: Heide

first: Jenny

last: Hetzer

first: Stefan

last: Rose-John

first: Mathias

last: Heikenwälder

first: Hilla

last: Giladi


title: SGSS05-NS3 as a potent SETD8 inhibitor that activates p53 pathway in Neuroblastoma

city: Rome

first: Veronica

last: Veschi

address: Viale Regina Elena, 291

country: Italy

institute: “La Sapienza” University of Rome

summary: Purpose: The intergration of genetic and chemical screens identified SETD8 as a new druggable target in neuroblastoma tumor. The goal of this study is to evaluate the transcriptome profiling (RNA-seq) of Neuroblastoma cell lines after genetic and pharmacological inhibition of SETD8. Methods: mRNA profiles of NB cells after genetic and pharmacological inhibition of SETD8 were generated by deep sequencing in duplicate with Ilumina HiSeq2500 using Illumina TruSeq V4. The sequence reads were analyzed with software Trimmomatic, STAR and edgeR to determine the differetially expressed genes. qRT–PCR validation was performed using SYBR Green assays. Results:  About 60 million sequence reads per sample were mapped to the human genome (hg19).  Approximately 10% of the transcripts showed differential expression between the control and the treated samples, with a fold change ≥1.5 and p value <0.05. Altered expression of 12 genes was confirmed with qRT–PCR, demonstrating the high degree of sensitivity of the RNA-seq method. Hierarchical clustering of differentially expressed genes uncovered several as yet uncharacterized genes that may contribute to SETD8 function.  Conclusions: Our study identifies SETD8 as a new therapeutic target in Neuroblastoma tumor. RNA-seq transcriptome analyses and functional studies revealed that SETD8 ablation rescued the proapoptotic and cell-cycle arrest functions of p53 through reactivation of the p53 canonical pathway by decreasing p53k382me1.

overall_design: mRNA profiles of Neuroblastoma cells after genetic and pharmacological inhibition of SETD8 were generated by deep sequencing in duplicate with Ilumina HiSeq2500 using Illumina TruSeq V4.

first: Carol

middle: J

last: Thiele

first: Chunhua

last: Yan

first: Ying

last: Hu


title: DNA cytosine methylation suppresses meiotic recombination at the sex-determining region (H3K27ac ChIP-seq)

city: Shanghai

first: Xiuqi

last: Gui

address: 320 Yue Yang Rd

institute: Shanghai Institute of Nutrition and Health

summary: In sexual organisms, random meiotic recombination between homologous chromosomes is vital to maximize genetic variation among offspring. The sex-determining region (SDR), however, does not undergo recombination, as required for the maintenance of distinct alleles. The contribution of epigenetic versus genetic mechanisms to suppress recombination in SDRs and how the suppression mechanisms evolve remain poorly understood. Here we describe the mechanistic control of meiotic recombination at the mating-type locus (MT) in the green alga Chlamydomonas reinhardtii. We identify a maintenance DNA methyltransferase, DNMT1, mutation of which leads to the depletion of 95% of 5-methylcytosines (5mCs) in the nuclear genome. While the 5mC deficiency causes no discernible alteration in haploid vegetative growth or sexual differentiation, the dnmt1 homozygotes display substantially reduced spore viability and 4-progeny-tetrad frequency. Strikingly, in dnmt1 homozygotes, anomalous meiotic recombination takes place at MT, generating haploid progenies with mixed mating-type harboring both plus and minus markers. Although the repressive histone methylation H3K9me1 at MT is lost concurrently in dnmt1 strains, loss of histone methylation alone by gene deletion of the responsible histone methyltransferase SET3p does not lead to anomalous recombination at MT. Thus, DNA methylation, rather than histone modification, mediates the recombination suppression at MT in C. reinhardtii. This finding suggests that in early eukaryotes, which likely lacked histone-based chromatin modification, DNA methylation may have been co-opted to suppress meiotic recombination between alleles responsible for separate sexes.

overall_design: Chromatin immunoprecipitation sequencing (ChIP-seq) for histone modifications H3K27ac in WT, dnmt1 and set3 strains.

first: Tong

last: Ge


title: miR_122 Knockout mice

first: Eithan

last: Galun

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

overall_design: Refer to individual Series


title: liver isolated single cell RNAseq v2

overall_design: RNA from single cells isolated from livers of a miR-122 knock out mouse and wild type control from the same founder at the ages of 2 weeks, 3 weeks and 6 weeks.

first: Maytal

last: Gefen

first: Shanny

last: Layani

first: Emma

last: Klahr

first: Zohar

last: Shemuelian

first: Johannes

last: Brandi

first: Thomas

last: Jacobs

first: Christiane

last: Steeg

first: Lorenz

last: Adlung

first: Christoph

last: Kilian

first: Merav

last: Ordan

first: Oren

last: Gordon

first: Nathalie

last: Abudi

first: Rinat

last: Abramovitch

first: Yuval

last: Nevo

first: Sharona

last: Elgavish

first: Hadar

last: Benyamini

first: Jonathan

last: Monin

first: Elina

last: Zorde Khvalevsky

first: Nofar

last: Rosenberg

first: Aurelia

last: Markezana

first: Dayana

last: Yaish

first: Adi

last: S. Yehezkel

first: Alina

last: Simerzin

first: Mila

last: Rivkin

first: Osher

last: Amran

first: Daniel

last: S. Goldenberg

first: Amnon

last: Peled

last: Axelrod

first: Jacob

last: Rachmilewitz

first: Samuel

last: Huber

first: Nicola

last: Gagliani

last: Schramm

first: Sören

last: Weidemann

last: Herkel


title: A plastidial lipoyl synthase LIP1p plays a crucial role in phosphate homeostasis in Arabidopsis.

city: Zhe jiang

first: Shenghong

last: Ge

address: No. 2318, Yuhangtang Road, Hangzhou, Zhejiang, China

institute: Hangzhou Normal University

summary: Phosphate (Pi) homeostasis is important for plant growth and adaptation to dynamic environment, which requires the precise regulation of phosphate transporter (PHT) trafficking from endoplasmic reticulum to plasma membrane. LIPOYL SYNTHASE 1p (LIP1p) is known as a key enzyme in plastids to catalyze lipoylation of pyruvate dehydrogenase complex for de novo fatty acid synthesis. It is unknown whether this process is involved in regulating Pi homeostasis. Here, we demonstrate a new role of LIP1p in controlling Pi homeostasis by regulating PHT1 trafficking. We recovered a weak mutant allele of LIP1p in Arabidopsis that accumulates much less Pi and has enhanced expression of phosphate starvation induced genes. Lipidomics analysis revealed that LIP1p mutation alters lipid profile and compromises vesicle trafficking of PHT1 to the plasma membrane to impair Pi uptake. Beside phosphorus, the homeostasis of a series of mineral nutrients was also perturbed in lip1p mutant. Our findings provide powerful genetic evidences to support the linkage between lipoylation and ion homeostasis in plant.

overall_design: Total RNAs were extracted from 8-day-old seedlings under HP or LP conditions using a RNeasy Plant Mini Kit (Qiagen, R415102) according to the instruction manual. Three biological replicates were performed for each genotype. The genes that were up-regulated or down-regulated with a twofold or higher change with an adjusted P value of ≤0.05 were regarded as DEGs. Venn diagrams were created using Venny (2.1.0). GO enrichment analysis was performed using clusterProfiler (v.4.0.5)(Yu et al., 2012).

first: Mingguang

last: Lei


title: Multi-omics based dynamic molecular changes characterization in EV-A71-infected mice elucidating potential therapeutic targets

first: wanjun

last: Peng

address: No.5, Panjiayuan Nanli,Chaoyang District, Beijing

institute: Institute of Laboratory Animal Science

summary: To explore the mechanisms underlying the pathogenesis of EV-A71 infection and to identify new therapeutic opportunities, we performed comprehensive proteogenomic characterization of the muscle tissue of BALB/c mice infected with EV-A71, including transcriptomic, proteomic and phosphoproteomic data. Our results showed that phagosome, complement and coagulation cascade pathway-related molecules were activated, and the expression of cell growth-related molecules was downregulated. Time course analysis revealed dynamic changes in the expression of the genes, and cluster analysis revealed different trends. Additionally, we mapped the global phosphorylation profiles to dysregulated kinases, predicting 32 drugs corresponding to 27 kinases. We found that kinase inhibitors have antiviral activity in vitro; vandetanib, nintedanib and dasatinib can inhibit virus replication in mice to some extent. Our multiple -omics dataset represents a useful resource for researchers seeking to better understand and identify candidate therapeutic drugs for treating EV-A71 infection.

overall_design: The differentially expressed genes at different time points (0, 2 and 5 dpi) after EV-A71 infection were compared.


title: A disrupted compartment boundary underlies abnormal cardiac patterning and congenital heart defects

city: San Francisco

first: Benoit

last: Bruneau

state: CA

address: 1650 Owens St

institute: Gladstone Institutes

summary: Failure of septation of the interventricular septum (IVS) is the most common congenital heart defect (CHD), but mechanisms for patterning the IVS are largely unknown. We show that a Tbx5+/Mef2cAHF+ progenitor lineage forms a compartment boundary bisecting the IVS. This coordinated population originates at a first- and second heart field interface, subsequently forming a morphogenetic nexus. Ablation of Tbx5+/Mef2cAHF+ progenitors cause IVS disorganization, right ventricular hypoplasia, and mixing of IVS lineages. Reduced dosage of the CHD transcription factor TBX5 disrupts boundary position and integrity, resulting in ventricular septation defects (VSDs) and patterning defects including Slit2 and Ntn1 misexpression. Reducing NTN1 dosage partly rescues cardiac defects in Tbx5 mutant embryos. Loss of Slit2 or Ntn1 causes VSDs and perturbed septal lineage distributions. Thus, we identify essential cues that direct progenitors to pattern a compartment boundary for proper cardiac septation, revealing new mechanisms for cardiac birth defects.

overall_design: We deployed single cell RNA sequencing (scRNAseq) to discover novel Tbx5-sensitive cues that are essential for compartment boundary regulation of IVS patterning during heart development. We microdissected the interventricular septum (IVS), left ventricular (LV) and right ventricular (RV) tissue from 4 control embryos and 3 mutant embryos and processed them using the 10X Genomics kit.

first: Irfan

last: Kathiriya

first: Kavitha

last: Rao