title: Single-cell sequencing-based technology reveals differences in four animal models of pulmonary fibrosis

status: Public on Apr 30 2025

city: Jinan

first: zhao

last: shan

address: No. 16369, Jingshi Road

country: China

institute: Affiliated Hospital of Shandong University of Traditional Chinese Medicine

type: Expression profiling by high throughput sequencing

summary: Pulmonary fibrosis is a progressive interstitial lung disease characterised by a progressive loss of lung function. It can occur as a result of occupational or medical exposures, genetic defects, trauma or acute lung injury leading to fibroproliferative acute respiratory distress syndrome, or it can occur in an idiopathic manner. The pathogenesis of each form of pulmonary fibrosis remains unclear. A variety of animal models have been developed to better understand the pathogenesis of pulmonary fibrosis. It has been shown that animal models of pulmonary fibrosis rely heavily on severe adverse effects induced by a variety of drugs, such as bleomycin, amiodarone, lipopolysaccharide and silica. The construction of animal models plays a key role in our understanding of the molecular mechanisms underlying the pathogenesis of PF, in outlining patient-specific pathology and in developing therapeutic strategies. However, the differences between models of pulmonary fibrosis induced by different drugs have rarely been investigated. Therefore, in this paper we performed single-cell sequencing analysis of animal models constructed from four drugs. The characteristics of the changes in the number of epithelial cells and macrophages and their functional enrichment in each model were summarised, and it was deduced that the model induced by lipopolysaccharide was mainly focused on the inflammatory damage stage of pulmonary fibrosis, the model induced by amiodarone on the regeneration stage of persistent failure, and the model induced by bleomycin and silica on the fibrotic stage of pulmonary fibrosis.

overall_design: Our experiments were divided into: control group (C), bleomycin group (BLM), lipopolysaccharide group (LPS), amiodarone group (AM), and silica group (SIO2). Five rats in each group were given free choice of sterile food and water and maintained on a 12-hour light/dark cycle

first: Shan

last: Zhao

first: Weibin

last: Qian

first: Xinrui

last: Cai


title: Therapeutic base editing alleviates restrictive cardiomyopathy

city: Xihu District, Hangzhou

first: Xing

last: Chang

state: Zhejiang

address: No.18 Shilongshan Road Cloud Town

department: School of Life Sciences

institute: Westlake University

summary: Restrictive cardiomyopathy (RCM) is a severe cardiac disorder characterized by impaired ventricular filling and diastolic dysfunction, with mutations in sarcomeric proteins representing major causative factors. Mutations of TNNI3 gene (e.g. p.R192H) constitute major genetic causes of RCM, particularly affecting pediatric patients and being associated with poor prognosis. Here, we demonstrate that adenine base editor (ABE) is able effectively correct RCM-causing mutation and alleviate RCM in a murine model. We first developed a novel murine model harboring the Tnni3R193H mutation that recapitulates the hallmark features of human RCM. Importantly, targeted delivery of ABE via adeno-associated virus (AAV) achieved efficient and precise correction of the Tnni3R193H mutation in adult RCM mice, leading to significant improvement of cardiac functions. Our findings establish base editing as a therapeutic strategy for RCM and highlight its broader potential for treating genetic cardiomyopathies in clinical settings.

overall_design: RNA sequencing (RNA-seq) was employed to identify RNA off-target effects induced by ABE8e treatment in vivo. Untreated mice were included as a control group to serve as mock treatment for comparison, ensuring a baseline for evaluating the specificity and potential off-target impacts of the ABE8e intervention

first: Chong

first: Xiulin

last: Zhang

first: Geng

last: Li


title: Generation of a biliary tract cancer cell line atlas identifies molecular subtypes and therapeutic targets

city: Boston

first: Vindhya

last: Vijay

state: MA

address: 185 Cambridge Street

country: USA

institute: MGH Cancer Center/ Harvard Medical School

summary: Biliary tract cancers (BTCs) are aggressive malignancies encompassing intrahepatic and extrahepatic cholangiocarcinoma, gallbladder carcinoma, and ampullary carcinoma. Here, we report integrative analysis of 63 BTC cell lines via multi-omics and genome-scale CRISPR screens. We identify widespread EGFR dependency in BTC, alongside dependencies selective to anatomic subtypes. Additionally, we delineate strategies to overcome therapeutic resistance, with combined EGFR inhibition potentiating targeting of KRAS-mutant and FGFR2-fusion-driven models, and SHP2 inhibition effective in the latter context. Clustering RNA/protein expression and dependencies data revealed functional relationships transcending single-gene alterations, with biliary, squamous, or dual biliary/hepatocyte lineage signatures stratifying BTC models. These subtypes exhibit distinct dependency profiles— including cell fate transcription factors GRHL2, TP63, and HNF1B, respectively— and demonstrate prognostic significance in patient samples. Potential subtype-specific targetable vulnerabilities include Integrin-a3 and the detoxification enzyme UXS1. This cell line atlas reveals therapeutic targets in molecularly-defined BTCs, unveils disease subtypes, and provides a resource for therapeutic development.

overall_design: RNASeq profiling of newly developed and established patient-derived biliary tract cancer cell lines.

first: Vijay

last: Vindhya

first: Karisan

last: Negin

first: Vazquez

last: Francisca

first: Getz

last: Gad

first: Bardeesy

last: Nabeel


title: Glioblastoma quiescent cells hijack astrocyte-derived mitochondria to drive activation and malignancy

city: Hefei

first: Li

last: Wang

address: No. 443, Mount Huangshan Road, Shushan District

institute: University of Science and Technology of China

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Quiescent tumor cell subpopulations at the invasive margin of glioblastoma (GBM) can drive therapeutic resistance, tumor dissemination, and recurrence through phenotypic plasticity. However, the mechanisms underlying their activation remain unclear. This study reveals that reactive astrocytes regulate this critical process via mitochondrial transfer. Specifically, Shmt2 enzyme in astrocytic mitochondria catalyzes one-carbon metabolic products, which significantly promote synthetic metabolic reprogramming and activation of quiescent GBM cells through intercellular mitochondrial transfer. Mechanistic analyses show that tumor cells acquiring astrocytic mitochondria exhibit two key features: (1) Enhanced one-carbon metabolism drives global hyperactive anabolic metabolism through YTHDC1-mediated transcriptional pause release of ribosomal genes; (2) Acquisition of immune-evasive phenotypes and mesenchymal/astrocyte-like characteristics. Genetic experiments further demonstrate that inhibiting astrocytic mitochondrial serine catabolic enzyme SHMT2 or blocking mitochondrial transfer markedly suppresses quiescent GBM cell activation and tumor progression. These findings elucidate a novel mechanism by which astrocytes in the tumor microenvironment drive GBM malignancy through metabolic symbiosis.

overall_design: Glioma was digested and dissociated single-cell suspensions were loaded to scRNA-seq. U87 cells from co-culture system of various groups were sorted using Fluorescence-activated cell sorting (FACS) and analyzed using CUT&Tag seq.

first: Hongrui

last: Zhu

first: Qingsong

last: Hu


title: The foam cell-derived exosomes exacerbate ischemic white matter injury via transmitting metabolic defects to microglia

city: Wuhan

first: Hang

address: Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology 1095 Jiefang Avenue 430030 Wuhan China

institute: Tongji hospital

summary: Experimental atherosclerosis was established by feeding Apoe KO mice a western diet(WD) for 14 weeks and experimental cerebral ischemia was established by bilateral carotid artery stenosis (BCAS). RNA-seq was perfomed to investigate the potential gene regulation of AS-Exos-dependent changes of microglia in the corpus callosum after BCAS.

overall_design: Transcriptional profiles of microglia sorted from Sham mice, BCAS mice, BCAS mice treated with ND-Exos, and BCAS mice treated with WD-Exos.

first: Luoqi

last: Zhou

first: Sheng

last: Yang

first: Wei

first: Daishi

last: Tian

first: Chuan

last: Qin


title: Lysine Methylpropionylation, a Hybrid Post-Translational Modification Mediated by p300/PCAF Couples Metabolic Dynamics with Protein Function

city: Shanghai

first: Liu

last: Fangfang

address: No. 555, Zuchongzhi Road, Pudong New Area, Shanghai, China

institute: Shanghai Institute of Materia Medica, Chinese Academy of Sciences

summary: Lysine alkylation and acylation serve as crucial links between cellular metabolism and a wide range of biological functions. However, hybrid modifications that combine features of both alkylation and acylation remain largely unexplored. Here, we report the discovery and in-depth characterization of lysine methylpropionylation (Kpm), a hybrid post-translational modification (PTM) defined by the propionylation of monomethyllysine residues. Genome-wide chromatin immunoprecipitation coupled with transcriptomic profiling revealed that Kpm exhibits distinct genomic distribution compared to canonical Kac and Kpr, with preferential enrichment at promoters of genes involved in metabolic pathways. Together, our findings establish Kpm as a dual-feature PTM that integrates metabolic cues with both chromatin regulation and non-histone protein function, offering a mechanistic framework for understanding metabolism-proteome crosstalk.

overall_design: ChIP-seq of Kpm, Kac, and Kpr modifications in wild-type and PCCB-knockdown HepG2 cells.

first: Fangfang

last: Liu

first: Runhua

last: DU

first: Xinlong

last: Guo

first: He

last: Huang


title: Eosinophils but not mast cells exert anti-tumorigenic activity, without being predictive markers of the long-term response to Bacillus Calmette-Guérin (BCG) therapy in patients with bladder carcinoma.

city: Jerusalem

first: Francesca

last: Levi-Schaffer

address: Kalman Ya'akov Man Street

country: Israel

institute: The Hebrew University of Jerusalem

summary: Bacillus Calmette-Guerin (BCG) therapy is an established immunotherapy for non-muscle invasive bladder cancer (NMIBC); however, the response variability of patients remains a challenge, necessitating insight into immune cell function. Previous studies established that a preexisting Th2 immune microenvironment correlates with a positive BCG therapy outcome. Therefore, in this study, we explored the role of mast cells (MCs) and eosinophils in bladder cancer as a potential predicting tool for BCG immunotherapy response.  Methods: We investigated the effect of MCs and eosinophils on bladder cancer cell viability together with their chemotactic migration towards cancer cells in vitro. The effect of BCG on these immune cells was also evaluated. Moreover, we performed an orthotopic model of bladder cancer in MC- and eosinophil-deficient mice. Finally, to evaluate whether these immune cells predict the therapy response, 26 patient biopsies pre-BCG treatment were analyzed for MC and eosinophil numbers in the tissue and 11 among them were sequenced for gene expression. Results: Eosinophils, but not MCs, reduced bladder cancer cell viability in vitro and inhibited tumor growth in vivo. However, addition of BCG did not increase these effects in vitro. Patient biopsy analysis and mRNA sequencing showed that neither cell type predicted long-term therapy responsiveness. Gene expression analysis suggested that extracellular matrix and epithelial-to-mesenchymal transition factors could influence BCG therapy outcomes. Conclusion: Even though eosinophils exhibit anti-tumorigenic effects in bladder cancer, neither MCs nor eosinophils were predictive of the long-term BCG therapy response. However, our findings implicate that matrix-related factors may modulate BCG therapy responses.

overall_design: RNA seq profiling of tumor bladder biopsies from patients prior BCG treatment. Samples were divided in responders and non responders group to the BCG treatment, based on clinical observation two years after last BCG inoculation

first: Ilan

last: Zaffran

first: Yara

last: Zoabi

first: Vladimir

last: Yutkin

first: Shmuel

last: Ruppo


title: Pre-existing allergic inflammation alters both innate and adaptive immune responses in mice co-infected with influenza virus

city: Groningen

first: Barbro

middle: N

last: Melgert

address: Antonius Deusinglaan 1

department: Molecular Pharmacology

country: Netherlands

institute: University of Groningen

summary: Introduction: Asthma, a chronic airway disease, is marked by allergic inflammation, hyperresponsiveness, and tissue remodeling. Influenza infections in asthma patients can cause severe exacerbations, though the underlying mechanisms remain unclear. This study investigated how pre-existing allergic inflammation affects immune responses to influenza infection in mice exposed to house dust mite (HDM). Methods: Mice were repeatedly exposed to HDM, followed by infection with influenza A virus, and were sacrificed three days post-infection. Plasma was analyzed for HDM-specific immunoglobulins, while lung tissue was used for immune cell flow cytometry and RNA sequencing analysis. Results: HDM exposure induced allergic inflammation, evidenced by more HDM-specific IgE, IgG1, IgG2, eosinophils, neutrophils, Th1, and Th17 cells compared to controls. Upon influenza infection, the effects of HDM and influenza co-infection interacted, showing fewer Th1 cells and regulatory T cells and more Th2 cells compared to mice exposed to influenza virus alone. Interestingly, RNA-seq analysis revealed less upregulation of Th1-related genes and antiviral pathways in co-exposed mice, suggesting impaired Th1 immunity and antiviral responses. Conclusion: Pre-existing allergic inflammation significantly altered immune responses in mice coinfected with influenza, revealing underdeveloped antiviral responses as early as three days post-infection. These findings may explain the increased susceptibility of patients with asthma to severe viral diseases.

overall_design: The data  are the result of 3 independent experiments with each 3-6 mice per experimental group. Mice were anesthetized with isoflurane and intranasally exposed to either saline or 62.5 µg of whole culture house dust mite (HDM) extract (Dermatophagoides pteronyssinus, 15G10, Citeq, Groningen, The Netherlands, containing an endotoxin level of 1.65 × 10^7 EU/gram) in saline. The animals were exposed to saline or HDM three times per week for 24 days and a single, nasal administration of 20 units of 50% tissue culture infectious dose of H3N2 influenza A virus Hong Kong (HK) X31 or saline on day 21 and were separated into 4 groups: saline/saline, HDM/saline, saline/influenza, HDM/influenza, with 11-16 mice in each group when combining the three independent experiments. On day 24, which was one day after the final HDM exposure and three days after the X31 challenge, mice were sacrificed by cardiac exsanguination.


title: Single-nucleus and spatial transcriptome identify brain landscape of gene regulatory networks associated with behavioral maturation in honeybees

city: shenzhen

first: CNSA

last: CNGB

address: BGI

institute: BGI

summary: Animal behavior is linked to the gene regulatory network (GRN) coordinating gene expression in the brain. Eusocial honeybees, with their natural behavioral plasticity, provide an excellent model for exploring the connection between brain activity and behavior. Using single-nucleus RNA sequencing and spatial transcriptomics, we analyze the expression patterns of brain cells associated with the behavioral maturation from nursing to foraging. Integrating spatial and cellular data uncovered cell-type and spatial heterogeneity in GRN organization.

overall_design: Single-nucleus expression profiling by high-throughput sequencing of 10-day-old nurse bees and 21- to 23-day-old forager bees.

first: Xiaohuan

last: Mu

first: Jie

last: Ma

first: Qun

first: Zijing

last: Zhang

first: Yating


title: Trichostatin A Treatment Has Little Impact on Nuclear compartments in Cells Depleted of H3K9me, H3K27me3, and uH2A [Hi-C]

city: Saitama

first: Kei

last: Fukuda

state: Japan

address: 2-1 Hrosawa, Wakoshi

country: Japan

institute: RIKEN

summary: In the mammalian nucleus, heterochromatin is segregated from transcriptionally active euchromatic regions (A compartments), forming large, condensed, and inactive nuclear compartments (B compartments). However, the mechanisms underlying its spatial organization remain incompletely understood. We previously demonstrated that simultaneous depletion of H3K9 methylation, H3K27me3, and H2A monoubiquitination in immortalized mouse embryonic fibroblasts (iMEFs) leads to heterochromatin weakening and alterations in nuclear compartments. However, the overall pattern of A/B compartments remains largely preserved even under these conditions, suggesting the involvement of unknown factors. Since histone deacetylation is a key factor in transcriptional repression, we investigated the impact of histone deacetylase (HDAC) inhibition on nuclear compartments by treating cells depleted of H3K9 methylation, H3K27me3, and H2A K119 monoubiquitylation (H2AK119ub/uH2A) with the HDAC inhibitor Trichostatin A (TSA). We performed Hi-C analysis to assess the nuclear compartment changes. Our results showed that, although TSA treatment globally increased H3K27ac levels, the difference in H3K27ac enrichment between A/B compartments remained evident, and nuclear compartments were minimally affected. These findings suggest that factors other than HDACs maintain nuclear compartmentalization when repressive chromatin modifications are depleted.

overall_design: Hi-C analysis of H3K9me/H3K27me3/uH2A-depleted immortalized mouse embryonic fibroblasts treated with TSA

first: Yoichi

last: Shinkai


title: ANTXR2 Deficiency Promotes Cellular Senescence and Chondroid Differentiation in Hyaline Fibromatosis Syndrome Fibroblasts

city: Cologne

first: Alvise

last: Schiavinato

address: Joseph-Stelzmann Str. 52

country: Germany

institute: Center for Biochemistry

summary: Mutations in anthrax toxin receptor 2 (ANTXR2) cause hyaline fibromatosis syndrome (HFS), a rare genetic disorder marked by subcutaneous nodules filled with amorphous hyaline extracellular material. In addition to these nodules, HFS patients exhibit gingival hypertrophy, joint contractures, osteolytic lesions, and, in severe cases, intractable diarrhea. The mechanisms by which ANTXR2 regulates extracellular matrix (ECM) composition and connective tissue homeostasis remain incompletely understood. Here, we show that dermal fibroblasts from HFS patients exhibit hallmarks of cellular senescence, chondroid differentiation  and abnormal ECM deposition. Additionally, HFS dermal fibroblasts are refractory to matrix metalloproteinase (MMP) 2 and 9 activation, potentially explaining phenotypic similarities between HFS and disorders caused by loss-of-function mutations in MMP genes. These findings underscore the essential role of ANTXR2 in maintaining dermal fibroblast identity and connective tissue homeostasis, laying the groundwork for novel therapeutic interventions for HFS.

overall_design: RNA-seq profiling of primary human dermal fibroblasts from a healthy donor (CTRL #1), a Hyaline Fibromatosis Syndrome (HFS) patient (HFS #1), and a second healthy donor transfected with either a non-targeting control siRNA (siCTRL) or two independent siRNAs targeting ANTXR2 (siANTXR2_a and siANTXR2_b). All conditions were performed in biological triplicates.


title: Bulk RNA-seq of Kupffer cells from Hepa1-6_EV (empty vector) and Hepa1-6_EpoOE (overexpression) HCC-bearing C57BL/6 mice

city: Palo Alto

first: David Kung-Chun

last: Chiu

state: CA

address: 3373 Hillview Ave, Rm 260

institute: Stanford University

summary: Successful cancer immunotherapy requires a patient to mount an effective immune response against tumors, however many cancers evade the body’s immune system. To investigate the basis for treatment failure, we examined spontaneous mouse models of hepatocellular carcinoma (HCC) with either an inflamed T-cell-rich or non-inflamed T-cell-deprived tumor microenvironment (TME). Our studies reveal that erythropoietin (EPO) secreted by tumor cells determines tumor immunotype. Tumor-derived EPO autonomously generates a non-inflamed TME by interacting with its cognate receptor EPOR on tumor-associated macrophages (TAMs). EPO signaling prompts TAMs to become immunoregulatory via NRF2-mediated heme depletion. Removing either tumor-derived EPO or EPOR on TAMs leads to an inflamed TME and tumor regression independent of genotype, due to augmented antitumor T-cell immunity. Thus, the EPO/EPOR axis functions as an immunosuppressive switch for anti-tumor immunity.

overall_design: Kupffer cells (KCs) were isolated by FACS from liver tissues of Hepa1-6_EV (KC_EV) and Hepa1-6_EpoOE (KC_Epo) HCC-bearing mice at day 18 post-implantation. KC_EV and KC_Epo were analyzed with flow cytometry and subjected to bulk RNA-seq.

first: Edgar G

last: Engleman


title: On target: Transcriptomic analysis of 12 human iPSC-derived cell phenotypes shows precision in an extensive pharmacological investigation [set 1]

city: Cardiff

first: Frank

last: Wessely

address: Maindy Road

department: UK DRI

country: United Kingdom

institute: Cardiff University

summary: The specificity of action of a pharmaceutical compound to a particular target cell type is desirable to mitigate undesired effects in off target cell types. However, drug screening strategies necessarily employ cell lines that aim to represent but are potentially poor surrogates for the target cell phenotype. In this study, we addressed whether transcriptomic similarity between cell phenotpyes is predictive of their drug response. Thus, we differentiated  hiPSC from three individuals into twelve different distinct  phenotypes (cardiomyocytes, smooth muscle cells, hepatocytes, renal proximal tubular cells, podocytes, cortical neurons, dopaminergic neurons, neural progenitor cells, nociceptors, astrocytes, macrophages and endothelial cells). We exposed these cells and the MCF-7 cancer cell line with 12 compounds (Taxol (Paclitaxel) (0.04 µM), 17-AAG (Tanespimycin) (0.2 µM), Bardoxolone methyl (CDDO-Me) (0.2 µM), Rapamycin (Sirolimus) (0.2 µM), Tunicamycin (0.2 µM), Vorinostat (0.2 µM), A-366 (1 µM), A-971432 (1 µM), Compound 81 (1 µM), Rosiglitazone (1 µM), Thiamet-G (1 µM), Lithium chloride (5000 µM)) for 7 hours. Analysis of the RNAseq profiles revealed that the impact of drug treatment varies significantly among different cell types. Despite some compounds showing consistent effects across various cell types, there was no clear correlation between transcriptomic similarity and the magnitude of response to the same drug. These findings underscore that accurate predictions of drug responses necessitate employing the most representative models of the target cell types involved.

overall_design: iPSC-derived cell types (3 differentiations per cell line) as well as undifferentiated iPSCs and MCF-7 breast cancer cells were exposed to 12 small molecule tool compounds in 0.1% DMSO (dimethyl sulfoxide). After seven hours of incubation, cell lysates were collected from which total RNA was extracted and used for 3’ mRNA-seq library preparation (Lexogen QuantSeq). Libraries were sequenced on an Illumina HiSeq 4000 system to obtain drug-induced gene expression data.

first: Anja

last: Wilmes

first: Rory

last: Bowden

first: Sally

middle: A

last: Cowley

first: Paul

last: Jennings

first: Caleb

last: Webber

first: Zameel

last: Cader


title: Mycoplasma bovis nucleomodulin MbovP202 modulates DNA methylation in BoMac cells

first: Doukun

last: Lu

address: Huazhong Agricultural University

institute: National Key Laboratory of Agricultural Microbiology

type: Methylation profiling by high throughput sequencing

summary: We identified a novel M. bovis nucleomodulin, MbovP202, which functions as a 5-methylcytosine-specific DNA methyltransferase that localizes to the nucleus of the bovine macrophage cell line (BoMac). Whole genome bisulfite sequencing (WGBS) demonstrated  that MbovP202 increases methylation at mCATG sites  and mCG sites. Integrated analysis of WGBS and RNA-Seq data revealed that genes with promoter hypermethylation and concomitant down-regulated expression were predominantly enriched in metabolic and inflammatory pathways.

overall_design: Whole genome bisulfite sequencing was used to profile DNA methylation in BoMac (empty vector control) and BoMacMbovP202 cells (stable monoclonal cell lines expressing MbovP202)

first: Aizhen

last: Guo


title: Designed NGF mimetics with reduced nociceptive signatures in neurons

city: Seattle

first: Research

middle: Scientific

last: Computing

state: WASHINGTON

address: 818 Stewart Street

department: Research Scientific Computing

institute: Seattle Children's Research Institute

summary: The clinical use of Nerve Growth Factor (NGF) for neural regeneration has been hampered by pain sensitization side effects. NGF signals through the receptor tyrosine kinase TrkA and the co-receptor p75NTR; We sought to overcome this limitation by de novo design of a TrkA agonist that does not bind p75. We designed homodimeric TrkA engaging constructs that bring together two TrkA subunits in a variety of geometrics, and identified those eliciting the strongest signaling. The resulting designed agonists are able to stimulate transdifferentiated neurons and neuroblastoma cell lines, leading to outgrowth of neurites and neuronal differentiation, with considerably reduced transcription of inflammation and pain related genes. Although detailed in vivo characterization will be required to fully understand their therapeutic potential, these agonists are promising candidates for inducing neural regeneration with reduced pain side effects.

overall_design: RNA-seq profiling of SY5Y cells was performed between ag231 and PBS; and between ag237 and PBS.

first: Thomas

last: Schlichthaerle

first: Aerin

last: Yang

first: Damien

last: Detraux

first: David

last: E. Johnson

first: Chloe

last: J. Peach

first: Natasha

last: I. Edman

first: Catherine

last: Sniezek

first: Charles

last: A. Williams

first: Sonali

last: Arora

first: Neerja

last: Katiyar

first: Irene

last: Chen

first: Ali

last: Etemadi

first: Andrew

last: Favor

last: Lee

first: Connor

last: Kubo

first: Brian

last: Coventry

first: Buwei

last: Huang

first: Nathan

last: Ennist

first: Lukas

last: Milles

first: Banumathi

last: Sankaran

first: Alex

last: Kang

first: Stacey

last: Gerben

first: Hannah

last: Nguyen

first: Devin

last: K. Schweppe

first: Nobuhiko

last: Hamazaki

first: Asim

last: K. Bera

first: Babak

last: Negahdari

first: Lance

last: Stewart

first: Nigel

last: W. Bunnett

first: Jessica

last: E. Young

first: Christopher

last: K. Garcia

first: Hannele

last: Ruohola-Baker

first: Julie

last: Mathieu

first: Siobhan

last: Pattwell

last: Baker


title: On target: Transcriptomic analysis of 12 human iPSC-derived cell phenotypes shows precision in an extensive pharmacological investigation [set 2]

first: Frank

last: Wessely

first: Anja

last: Wilmes

first: Rory

last: Bowden

first: Sally

last: Cowley

first: Paul

last: Jennings

first: Caleb

last: Webber

first: Zameel

last: Cader


title: Plasma levels of microRNA let-7c-5p may predict the risk of acute chest syndrome in patients with sickle cell disease

city: Chicago

first: Eric

middle: C

last: Beyer

state: IL

address: 900 E 57th St

department: Pediatrics

institute: University of Chicago

type: Non-coding RNA profiling by high throughput sequencing

summary: Acute Chest Syndrome (ACS) is one of the most severe complications of Sickle Cell Disease (SCD). While the pathogenesis of ACS is incompletely understood, endothelial damage and microvascular occlusion are critical components. Our previous studies have implicated small extracellular vesicles in the plasma of subjects with SCD in induction of endothelial dysfunction. We hypothesized that microRNAs contained within these small EVs could be responsible for the endothelial damage. Sequencing of the microRNAs in small EVs from the plasma of SCD subjects revealed that several miRNAs were differentially expressed between subjects with or and without ACS history, including let-7c-5p.

overall_design:
RNASeq profiling of micro RNAs in small extracellualr vesicles isolated from the plama of human subjects with sickle cell disease

***************************************************************
Raw files for human/patient samples were not submitted to GEO due to concerns about submitting personally identifiable sequence data for open access.
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first: James

last: Fan

first: Joanna

last: Gemel

first: Gabrielle

last: Lapping-Carr


title: Effect of neurotensin on fed and fasted mouse livers

city: Lexington

first: Moumita

last: Banerjee

state: Kentucky

address: 760 Press Avenue

department: Markey Cancer Center

institute: University of Kentucky

summary: Neurotensin(NTS), a gut hormone, is known to impact whole body energy metabolism. Here we investigated the impact of neurotensin on the liver in fed (ad libitum) and fasted (22h) female mice livers from NTS wild type (WT) and knockout (KO) mice. Our goal was to investigate the regulation of energy metabolism pathways in the liver that are regulated by neurotensin, specifically lipid uptake and mitochondrial metabolism.

overall_design: RNAseq profiling of livers from NTS WT and KO mice that were either fed (ad-libitum) or fasted for 22h. There were 3 mice in each group.

first: Jing

last: Li

first: Mark

last: Evers


title: Adamantane-Quinoxalone Hybrids: Precision Chemotypes and Their Molecular Mechanisms in Acute Myeloid Leukemia

city: Delhi

first: Jaidev

last: Sharma

state: Delhi

address: Indraprastha Institute of Information Technology, Okhla Industrial Estate, Phase III, near Govind Puri Metro Station, New Delhi, Delhi 110020

department: Computational Biology

country: India

summary: Acute myeloid leukemia (AML) is an aggressive blood cancer with poor prognosis, particularly when diagnosed late. Approximately 10–15% of AML cases are linked to a specific chromosomal abnormality, t(8;21), which drives the rapid proliferation of myeloid cells and contributes to disease onset. Despite advances in understanding AML biology and treatment protocols, clinical outcome for t(8;21) AML has not improved. Most patients with this subtype continue to receive standard, non-specific chemotherapies used for other AML subtypes. This one-size-fits-all approach harms both cancerous and healthy cells, emphasizing the urgent need for targeted therapies. In this study, we report the discovery of a precision chemotypes based on a quinoxalone-tethered adamantane framework. Developed using a metal- and light-free protocol, the compound selectively inhibits the proliferation of t(8;21) AML cells and induce cell death by disrupting growth and metabolic pathways, as demonstrated through bioassays, RNA sequencing, and proteomic analysis. Importantly, the compound spares other leukemic and solid cancer cells, demonstrating its specificity and potential as a precision therapy for t(8;21) AML.

overall_design: Transcriptional profiling was performed in Kasumi-1 cell line. Kasumi-1 cell lines were treated at its  IC50 dose with 3j  for 24 hours and untreated control was also maintained.

first: Sangita

middle: D

last: Shinde

first: Ambika

last: Chamoli

first: Sai

last: Shweta

first: Vibhor

last: Kumar

first: Amit

last: Mandoli

first: Dinesh


title: Transcriptome analysis of bacterial blight susceptible and resistant rice lines

city: Hyderabad

first: Ramesh

middle: Venkata

last: Sonti

state: Telangana

address: Habsiguda

institute: CSIR-Centre for Cellular and Molecular Biology

summary:
Rice-Xanthomonas oryzae is an economically important pathosystem owing to the loss caused by bacterial blight disease. Understanding the moleulcar dynbamics that occur during rice-Xoo interaction is crucial for understanding disaease susceptible and resistance mechanisms.
SM210, harbors the resistance alleles xa5, xa13, and Xa21 and is resistant against Xoo. Transcriptome analysis of Xoo-treated. SM210 and SM, its parent variety, indicated different pathways that are altered in these varieties after Xoo treatment.

overall_design: Xoo strain BXO43 was cultured overnight on peptone-sucrose (PS) media. 60-day-old rice plant leaves were clip-inoculated with scissors dipped in water or Xoo (O.D. = 1.0) (Kauffman, 1973). After 24hr a 2mm leaf piece from the site of clip-inoculation was collected and frozen immediately into liquid nitrogen. 15 such leaf pieces were collected for each treatment in each set.

first: P

middle: S

last: Rao

first: Kamal

last: Malukani

first: Hitendra

last: Patel


title: Hyperbaric Oxygen Promotes Both the Proliferation and Chemosensitization of Glioblastoma Cells by Inhibiting HIF1α/HIF2α-ABCG2

city: Chongqing

first: Sheng

last: Gong

address: Jinzhou Avenue, Liangjiang New District, Department of Neurosurgery, Chongqing General Hospital, Chongqing University, Chongqing 401147, China

institute: Chongqing University

summary: Hyperbaric oxygen enhances glioma chemosensitivity, but the mechanism remains unclear. Hypoxia is common in gliomas, and as the main effector molecules of hypoxia, HIF1α and HIF2α promote the malignant progression by inhibiting cell apoptosis and maintaining stemness. ABCG2 is a marker protein of tumor stem cells and drug efflux transporter protein. This study aims to reveal the detailed mechanism of hyperbaric oxygen promote both proliferation and chemosensitization. Under hyperbaric oxygen and hypoxic conditions, we investigated the differences in cell cycle, proliferation, apoptosis, LDH release, and the expression of proteins and mRNA. We also conducted studies on transcriptional regulation and performed in vivo experiments. It revealed that under hypoxic conditions, HIF1α, HIF2α, and ABCG2 are highly expressed, and both HIF1α and HIF2α promote ABCG2 expression. After hyperbaric oxygen treatment, the expression of HIF1α, HIF2α, and ABCG2 decreased, both cell proliferation and chemosensitivity increased. After knocking out HIF1α and HIF2α, cell proliferation and chemosensitivity increased, but the expression of stem cell marker proteins decreased. ChIP‒qPCR revealed that HIF1α and HIF2α target the ABCG2 promoter. Gain- and loss-of-function experiments suggested that ABCG2 can promote the expression of stem cell marker proteins, inhibit cell apoptosis, and promote tumor progression. This study confirmed that hyperbaric oxygen can inhibit ABCG2 expression through HIF1α and HIF2α, thereby promoting the proliferation and chemosensitization of gliomas.

overall_design: The experiments were divided into control, HIF1α knockout, HIF2α knockout, and dual HIF1α/2α knockout groups. The mRNA-seq was used to compare each knockout group with the control group after U-87MG cells were cultured in hypoxic conditions (1%O2)for 72 hours.

first: Pan

last: Wang

first: Bin

last: Liao

first: Lu

last: Zhao

last: Wu


title: Targeting Glucose Metabolism: Synergistic Strategies to Enhance Apoptosis and Immune Activation in Hepatocellular Carcinoma Treatment

city: Hsinchu City

first: YenNhi

middle: Ngoc

last: Ta

address: No. 101, Sec. 2, Guangfu Rd., East District

department: Institute of Biomedical Engineering

country: Taiwan

institute: National Tsing Hua University

summary: Exploiting the dependency of cancer cells on glycolysis offers a promising avenue to enhance therapeutic strategies for hepatocellular carcinoma (HCC). In our study, we employ glucose oxidase (GOx) as a glucose metabolism modulator to deplete glucose within the tumor microenvironment, initiating reactive oxygen species (ROS)-mediated endoplasmic reticulum (ER) stress and regulating both death receptor and mitochondrial apoptosis pathways, subsequently sensitizing HCC cells to DOX- induced apoptosis. DOX, co-formulated with GOx in nanoparticle (GOx-DOX-NP), not only substantially reduces tumor volume and increases number of apoptotic cells in tumors, but also acts as an immunogenic cell death (ICD) inducer, stimulating anti-tumor immunity. This effect further improves the immunotherapy. In conclusion, our findings underscore the potential of integrating glucose metabolism modulation with apoptosis-based therapies and immunotherapy for more effective liver cancer treatment.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for murine HCC tumors with or without treatment of GOX-DOX nanoparticles

first: Yunching

last: Chen

first: Yen-Nhi Ngoc


title: Arabidopsis GH3.10 conjugates jasmonates

city: Goettingen

first: Ivo

last: Feussner

address: Justus-von-Liebig-Weg 11

department: Dept. for Plant Biochemistry

institute: University of Goettingen

summary: Jasmonates regulate plant development and defence. In angiosperms, the canonical bioactive jasmonate is jasmonoyl-isoleucine (JA-Ile), which is formed in Arabidopsis thaliana by JAR1 and GH3.10. In contrast to other jasmonate biosynthesis or perception mutants, however, gh3.10 jar1 knockout lines are still fertile. Therefore we investigated whether further jasmonates and GH3 enzymes contribute to regulation of fertility.  This study found JAR1 and GH3.10 are the only contributors to JA-Ile biosynthesis in Arabidopsis and identified a number of JA conjugates as potential bioactive jasmonates acting in the absence of JA-Ile. However, their contribution in regulating fertility is yet to be conclusively determined. Transcriptomic analysis did not identify further GH3 enzymes with increased transcription rate in flowers of gh3.10 jar1 plants.

overall_design: RNA was prepared from flowers of Col-0 wild type and gh3.10 jar1-1, gh3.10 jar1-11  and gh3.10 jar1-12  double mutants. Flower material was harvested from flower stages 13 to 15 and pooled (Smyth et al. 1990). Samples are from one experiment with three independent biological replicates.

first: Benedikt

last: Ni

first: Moritz

last: Klein

first: Ben

middle: M

last: Hoßbach

first: Kirstin

first: Ellen

last: Hornung

first: Cornelia

last: Herrfurth

first: Mats

last: Hamberg


title: Evolution of Mycobacterium tuberculosis transcription regulation is associated with increased transmission and drug resistance [IDAP-seq]

city: Boston

first: Peter

last: Culviner

address: 677 Huntington Ave

department: IID

institute: Harvard School of Public Health

summary: Mycobacterium tuberculosis (Mtb) has co-evolved with humans for thousands of years leading to variation in clinical virulence, transmissibility, and disease phenotypes. To identify bacterial contributors to this phenotypic diversity, we developed new RNA-seq and phylogenomic analysis tools to capture hundreds of Mtb isolate transcriptomes, link transcriptional variation to genetic variation, and find associations between variants and epidemiologic traits. Across 274 Mtb clinical isolates, we uncovered unexpected diversity in expression of virulence genes which could be linked to known and previously unrecognized regulators. Surprisingly, we found that many isolates harbor variants associated with decreased expression of EsxA (Esat6) and EsxB (Cfp10), which are virulence effectors, dominant T cell antigens, and immunodiagnostic targets. Across >55,000 isolates, these variants associate with increased transmissibility, especially in drug resistant Mtb strains. Our data suggest expression of key Mtb virulence genes is evolving across isolates in part to optimize fitness under drug pressure, with sobering implications for immunodiagnostics and next-generation vaccines.

overall_design: To identify binding of Rv0042c (slfR) transcription factor, slfR was purified and added at a 300 nM final concentration to an in vitro binding reaction with sheared Mycobacterium tuberculosis gDNA (IDAP-Seq). Enrichment of genomic regions was compared to a control reaction where no protein was added.

middle: H

first: Sarah

last: Fortune


title: H3F3A K27M Mutations Drive a Repressive Transcriptome by Modulating Chromatin Accessibility, Independent of H3K27me3 in Diffuse Midline Glioma [RNA-seq]

city: Austin

first: James

last: Robinson

state: MN

address: 801 16th Ave NE

department: The Hormel Institute

institute: University of Minnesota

summary: Heterozygous histone H3.3K27M mutation is a primary oncogenic driver of Diffuse Midline Glioma (DMG). H3.3K27M inhibits the Polycomb Repressive Complex 2 (PRC2) methyltransferase complex, leading to a global reduction and redistributing of the repressive H3 lysine 27 tri-methylation.  This rewiring of the epigenome is thought to promote gliomagenesis. We established novel, isogenic DMG patient-derived cell lines that have been CRISPR-Cas9 edited to H3.3 WT or H3.3K27M alone and in combination with EZH2 and EZH1 co-deletion, inactivating PRC2 methyltransferase activity of PRC2 and eliminating H3K27me3. RNA-seq and ATAC-seq analysis of these cells revealed that K27M has a novel epigenetic effect that appears entirely independent of its effects on PRC2 function.  While the loss of the PRC2 complex led to a systemic induction of gene expression (including HOX gene clusters) and upregulation of biological pathways, K27M led to a balanced gene deregulation but having an overall repressive effect on the biological pathways. Importantly, the genes uniquely deregulated by the K27M mutation, independent of methylation loss, are closely associated with changes in chromatin accessibility, with upregulated genes becoming more accessible. Notably, the PRC2-independent function of K27M appears necessary for tumorigenesis as xenografts of our H3.3K27M/EZH1/2 WT cells developed into tumors, while H3.3/EZH1/2 KO cells did not. We demonstrate that K27M mutation alters chromatin accessibility and uniquely deregulates genes, independent of K27 methylation. We further show the mutation's role in altering biological pathways and its necessity for tumor development.

overall_design: We established novel, isogenic DMG patient-derived cell lines including SF8628 cell line that have been CRISPR-Cas9 edited to H3.3 WT or H3.3K27M alone and in combination with EZH2 and EZH1 co-deletion, inactivating PRC2 methyltransferase activity of PRC2 and eliminating H3K27me3. RNA-seq and ATAC-seq analysis were carried out in these modified cell lines.

first: Suraj

last: Bhattarai

middle: P


title: Evolution of Mycobacterium tuberculosis transcription regulation is associated with increased transmission and drug resistance [RNA-seq]

overall_design: Clinical isolates from Vietnam and Peru were grown to the same OD in rich media. RNA-Seq libraries were captured to compare in vitro transcriptomes across clinical isolates to determine if transcriptional regulation plays a role in disparate phenotypes between Mtb clinical isolates.


title: Trichostatin A Treatment Has Little Impact on Nuclear compartments in Cells Depleted of H3K9me, H3K27me3, and uH2A [ChIP-Seq]

first: Kei

last: Fukuda

overall_design: ChIP-seq profiles of H3K27ac in immortalized mouse embryonic fibroblasts

first: Yoichi

last: Shinkai


title: An activation of interleukin-17C signaling drives cancerogenesis of endometriosis

city: 广州市

first: bo

last: Yao

state: 广东省

address: 广州市天河区黄埔大道西601号暨南大学医学楼

institute: 暨南大学

summary: Endometriosis -associated ovarian carcinoma (EAOC) is mostly malignant transformation from endometriomas.  However, the endometriosis cancerogenesis remains to be established.  Using spatial transcriptomic of human specimens of normal, endometriomas and EAOC, activation of Interleukin-17C (IL-17C) signaling is identified, with higher IL-17 receptor E (IL-17RE) expression in endometriotic cells, to be associated with cancerogenesis and which has no previous association with EAOC.  Elevated IL-17C concentration is found in peritoneal fluid in women with ovarian cancer and IL-17RE-overexpressed endometriosis mice.  In particular, IL-17C knockout reduces peritoneal fluid IL-17C concentration and inhibits ectopic lesion growth in endometriosis mice.  Besides, the role of IL-17C in the endometriosis cancerogenesis was investigated by blocking the IL-17C/IL-17RE, modulating IL-17RE and neutralizing IL-17C in endometriotic cells, endometrial organoids and endometriosis mice.  These data defined peritoneal fluid-mediated endometriosis cancerogenesis through IL-17C regulation and suggests that IL-17C/IL-17RE can thus potentially serve as novel targets for with high IL-17C.

overall_design: Normal endometrium, endometriosis, and endometriosis associated ovarian cancer were analyzed by spatial transcriptomics


title: Effect of Gpr85 constitutive deficiency on gene expression of the adult zebrafish cerebral gpr85-expressing cells.

city: bruxelles

first: Romain

last: DARCHE-GABINAUD

address: 808 route de lennik

department: IRIBHM, Jacques E. Dumont

country: Belgium

institute: Université libre de bruxelles

summary: We investigated the transcriptomic changes caused by Gpr85 constitutive depletion focusing on the cerebral cells naturally expressing gpr85.

overall_design: scRNAseq experiment on zebrafish dissociated and cell sorted gpr85-expressing cells from a control versus a Gpr85 knock out adult brain.

last: Darche-Gabinaud

first: Isabelle

last: Pirson

first: Anne

last: lefort

first: Frédérick

last: Libert


title: MAVS Orchestrates a Potent IFN-independent Antiviral Immunity by 2 Preserving Mitochondrial Integrity

first: Krishnan

middle: Harnivas

last: Harshan

address: Uppal Rd, IICT Colony

department: Infectious Diseases Group

institute: CSIR-CCMB

summary: Viruses target mitochondria, critical for antiviral defense and metabolism, to evade immunity. While mitochondrial antiviral-signaling protein (MAVS) is known for its regulation of type I interferon (IFN) signaling, we discover that its overarching primary role is safeguarding mitochondrial integrity against virus- and toxin-induced mitophagy. This function is critical in enacting a potent, IFN/NF-κB-independent antiviral response. Using SARS-CoV-2 (CoV-2) infection model, where disruption of MAVS aggregation and induction of mitophagy were observed, we demonstrate that functional MAVS prevents CoV-2-induced mitophagy and restricts viral replication without engaging type I or III interferon (IFN), and NF-κB pathways. Employing MAVS-knockout and MAVS:IFNAR1 double-knockout cells, and inhibition studies, our results further establish MAVS as a critical protector against virus- and chemical mitotoxin-induced mitophagy. Loss of MAVS results in increased mitochondrial membrane depolarization, reduced oxidative potential, and increased PINK1-dependent mitophagy leading to elevated viral replication-all reversed by MAVS supplementation. The IFN-independent antiviral immunity generated by MAVS-driven mitochondrial safeguarding conferred robust protection against mitophagy-inducing viruses, such as CoV-2 and JEV, but not DENV, which does not trigger mitophagy. By facilitating the mitochondrial integrity, MAVS governs the overall innate antiviral immunity- integrating IFN-dependent and IFN-independent mechanisms- and energy metabolism in the host cells. Thus, the regulation of these central functions makes MAVS a prime target for subverting host defenses and cellular energy homeostasis. These insights underscoring MAVS’s wider role in sustaining mitochondrial homeostasis positions it as a promising target for antiviral strategies.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Experiment 1: RNA-Seq profiling of Huh7 cells upon overexpression of MAVS or Interferon alpha (IFN-α), in uninfected or CoV-2 infected conditions for 24 hours at an MOI of 1. Appropriate  Empty Vector and Vehicle controls are included.  Experiment 2: RNA-Seq profiling of Mouse Embryonic Fibroblasts (MEFs) isolated from WT and MAVS KO mice in uninfected and CoV-2 infected conditions at an MOI of 1 for 12, 24 and 48 hours.

first: Vishal

last: Sah

first: Poojitha

last: Potharaju


title: 6-phosphogluconate dehydrogenase blockade in T Cells mitigates acute graft-versus-host disease while preserving graft-versus-tumor activity

city: Buffalo

first: Jianmin

last: Wang

state: NY

address: Elm and Carlton Streets

department: Bioinformatics and Biostatistics

institute: Roswell Park Comprehensive Cancer Center

summary: T cells undergo significant metabolic reprogramming after allogeneic hematopoietic cell transplantation (allo-HCT). However, the influence of metabolic pathway reprogramming on altering the severity and mortality of acute graft-versus-host disease (aGvHD), a critical allo-HCT complication, remains unclear. Through single-cell RNA sequencing (scRNA-seq) of allogeneic T cells isolated from the spleen of GvHD mice, we uncovered that 6-phosphogluconate dehydrogenase (6PGD), the second major rate-limiting enzyme in the oxidative pentose phosphate pathway, is upregulated and activated during allo-HCT. Clinical and histopathological analyses revealed that 6PGD deficiency in donor T cells significantly mitigates aGvHD severity and mortality in murine models of acute GvHD. An in vitro assay using murine and human T cells and an in vivo murine GvHD model showed that in the absence of an intact 6PGD pathway, donor T cell proliferation was reduced. Metabolic analyses confirmed that blocking 6PGD activity shifted T cell metabolism from glycolysis to oxidative phosphorylation (OXPHOS), as evidenced by isotope-labeled metabolic tracing and Seahorse assays. Pharmacological inhibition of 6PGD with 6-aminonicotinamide (6AN) demonstrated similar efficacy as the infusion of donor 6PGD deficient T cells in reducing aGvHD severity in allogeneic aGvHD and humanized xenogeneic GvHD models. Importantly, 6PGD inhibition preserved the graft-versus-tumor (GvT) effect by promoting the generation of a small subset of effector T cells with potent anti-tumor activity. From these findings we propose 6PGD as a promising therapeutic target for alleviating aGVHD the beneficial GvT effects.

overall_design: Splenic donor T cells (CD45+, H2kb+, H2kd-, TCRβ+) were harvested, sorted on day +7 and day +14 and examined for T cell clusters using single cell RNA sequencing (scRNA seq).

first: Saeed

last: Daneshmandi

first: Hemn

last: Mohammadpour


title: DNA methylation profiling of colonic epithelium from chronically SIV infected rhesus macaques

city: San Antonio

first: Mahesh

last: Mohan

state: Texas

address: 8715 West Military Road

department: Host Pathogen Interaction Program

institute: Southwest National Primate Research Center

summary: HIV and pathogenic SIV infection are characterized by gastrointestinal mucosal damage and immune dysfunction that is not reversed by combination anti-retroviral therapy (cART). Increasing evidence points to the contribution of aberrant epigenetic changes to the pathogenesis of gastrointestinal diseases. Nevertheless, the role of epigenetic mechanisms in HIV/SIV-induced gastrointestinal mucosal dysfunction remains understudied. Using reduced-representation bisulfite sequencing, we identified HIV/SIV infection in combination anti-retroviral therapy (cART)-naive rhesus macaques (RMs) to induce marked hypomethylation throughout promoter-associated CpG islands (paCGIs) in genes related to inflammatory response (NLRP6, cGAS), cellular adhesion and proliferation in colonic epithelial cells (CEs). Moreover, low-dose delta-9-tetrahydrocannabinol (THC) administration reduced NLRP6 protein expression in CE by hypermethylating the NLRP6 paCGI and blocked polyI:C induced NLRP6 upregulation in vitro. In cART suppressed SIV-infected RMs, NLRP6 protein upregulation associated with significantly increased expression of necroptosis-driving proteins; phosphorylated-RIPK3(Ser199), phosphorylated-MLKL(Thr357/Ser358), and HMGB1. Most strikingly, supplementing cART with THC effectively reduced NLRP6 and necroptosis-driving protein expression to pre-infection levels. These findings for the first time demonstrate that NLRP6 upregulation and ensuing activation of necroptosis promote HIV/SIV-induced gastrointestinal mucosal dysfunction and that epigenetic modulation using phytocannabinoids represents a feasible therapeutic modality for alleviating HIV/SIV-induced gastrointestinal inflammation and associated comorbidities.

overall_design: Colonic epithelium DNA methylation profiles of uninfected control (n=5) and chronically SIV-infected rhesus macaques that were treated with vehicle (n=7) or delta-9-tetrahydrocannabinol (THC) (n=6) were generated by reduced representation bisulfite sequencing


title: SAMHD1 Knockout iPSC model enables high lenti-viral transduction in myeloid cell types

city: San Francisco

first: Scot

last: Federman

address: 499 Illinois St

department: Biochemistry

institute: UCSF

summary: Recent advances in functional genomics tools have ushered in a new era of genetic editing to identify molecular pathways relevant to developmental and disease biology. However, limited model systems are available that adequately mimic cell states and phenotypes associated with human disease pathways. Here, we quantitatively analyzed the founder population bottleneck effect and demonstrated how the population changes from induced pluripotent stem cells (iPSCs) to hematopoietic stem cells and to the final induced macrophage population. We then engineered SAMHD1 knockout (KO) iPSC and characterized the iPSC line with RNA Seq, and induced macrophages from two distinct protocols with functional analysis. We then generated SAMHD1 KO CRISPR-dCAS9 KRAB iPSC through lenti-viral transduction aiming to increase the efficiency of lentiviral mediated gene transfer. We demonstrated increased lenti-viral transduction efficiency in induced macrophage, as well as microglia induced with two distinct protocols. This model allows for efficient gene knock down, as well as large-scale functional genomics screens in mature iPSC-derived macrophages or microglia with applications in innate immunity and chronic inflammatory disease biology. These experiments highlight the broad applicability of this platform for disease-relevant target identification and may improve our ability to run large-scale screens in iPSC-derived myeloid model systems.

overall_design: To investigate the transcriptomic differences between WT and SAMHD1 KO iPSC and WT and SAMHD1 KO iMacrophage, we established SAMHD1 KO iPSC cell line through CRISPR KO stratergy. We then performed gene expression profiling analysis using data obtained from RNA Seq of WT iPSC, SAMHD1 KO iPSC, WT iMacrophage and SAMHD1 KO iMacrophage with duplicates. Comparative gene expression profiling analysis of RNA-Seq data for iPSCs between WT and SAMHD1 KO, as well as iMacrophage between WT and SAMHD1 KO

first: Huinan

last: Li

first: Maliha

last: Afroze

first: Gunisha

last: Arora

first: Kaivalya

last: Shevade

first: Yeqing

last: Yang

first: Phuong

last: Nguyen

first: Rustam

last: Esanov

first: Laralynne

last: Przybyla

first: Adam

last: Litterman

first: Shawn

last: Shafer


title: RNA Sequencing Analysis of Human Non-Small Cell Lung Cancer Cell Line A549 in Dormancy Induction and Osteoclast-Activated States

city: Shanghai

first: yuzhen

last: Du

address: West Huanhu Road 3, No.222

department: Laboratory Medicine

institute: Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

summary: When lung adenocarcinoma cells metastasize to the bone microenvironment, they often enter a dormant state. These dormant cells can be reactivated after bone microenvironment remodeling and reemerge as metastatic disease, posing challenges for the treatment and prognosis of lung adenocarcinoma. In the bone microenvironment, it is primarily osteoclasts that activate dormant lung adenocarcinoma cells. However, the specific mechanism by which osteoclasts contact dormant lung adenocarcinoma cells and promote their proliferation remains unclear. In this experiment, dormant lung adenocarcinoma cells were induced through in vitro culture and treated with osteoclast-conditioned medium for 24 hours to obtain osteoclast-activated lung adenocarcinoma cells. RNA-seq was performed on both dormant and activated lung adenocarcinoma cells to analyze the specific mechanism of the transition from dormancy to activation in lung adenocarcinoma cells following osteoclast interaction.

overall_design: In this experiment, dormant A549 cells and A549 cells activated by osteoclast conditional medium were collected, with three samples for each condition, totaling six samples for transcriptome sequencing. The goal was to compare the differential genes during the transition from dormancy to activation in lung adenocarcinoma cells.

first: Xingyu

last: Liu

first: Rong

last: Qiu

first: Pengcheng

last: Gui

first: Lirong

last: Wei

first: Yue

last: Lu

first: Yan

last: Deng

first: Yang

last: Xue

first: Yingyang

last: Su

first: Qin

last: Huang

first: Yuzhen


title: Comparative Transcriptome Analysis of PBMCs in Cats Diagnosed with and Recovered from FIPV

city: Jeongeup-Si

first: Ju Young

last: Lee

address: 30 Baekhak 1 Gil,

country: South Korea

institute: Korea institute of toxicology

summary: Background Feline infectious peritonitis is a viral disease caused by feline coronavirus an enveloped virus with a single-stranded RNA genome that is approximately 30 kb long. Although FCoV generally causes mild symptoms, approximately 5 % of cases progress to death in cats worldwide. FCoV shares certain virological features with severe acute respiratory syndrome coronavirus 2 that causes COVID-19, indicating that common therapeutic strategies may be applicable. GS-441524 the parent drug of remdesivir and a competitive inhibitor of nucleoside triphosphates in viral RNA synthesis is a well-known treatment for FIP. However, comparative transcriptome and gene ontology analyses of normal (Normal), FIP-diseased (FIPD), and FIP-recovered (FIPR) cats have not yet been conducted. Results  In this study, we compared the mRNA expression profiles of peripheral blood mononuclear cells from Normal, FIPD, and FIPR cats to identify immunological alterations. We identified 715 (FIPD/Normal) and 1,164 (FIPR/FIPD) differentially expressed genes with statistical significance. These data were input into the bioinformatics program. As a result, the analysis revealed statistically significant and contrasting patterns of canonical pathways of neutrophil degranulation and interleukin-8 (IL-8) signaling pathways. Additionally, we observed that kruppel-like factor 6 (KLF6)  and nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) were upstream molecules of IL-8, promoting neutrophil activation and function. Conclusions This study identified immunological alterations in PBMCs of Normal, FIPD, and FIPR cats. KLF-6 and NF-κB were found to regulate IL-8-mediated neutrophil activation.

overall_design: To compare DEG profiles of PBMCs between normal cats, FIP diseased cats and FIP recovered cats.

first: Ju-young

first: Hyeong-ryeol

last: Cho

first: Hong-geun

last: Oh

first: Jeong-ho

last: Hwang


title: Analysis of gene expression change between HCC827 SC and HCC827 shCEACAM6

city: Hsinchu

first: Ming-Yi

last: Zheng

address: College of Life Science, No. 101, Section 2, Kuang Fu Road

department: college of life science and medicine

institute: NATIONAL TSING HUA UNIVERSITY

summary: CEACAM family proteins have been extensively studied as cell adhesion molecules, yet the biological and clinical significance of CEACAM6 remains relatively unexplored. Our research identifies a significant increase in CEACAM6 expression in lung adenocarcinoma, particularly correlating with EGFR mutation status. In EGFR-mutated lung cancer cells, CEACAM6 knockdown induced apoptosis and reduced p-ERK1/2 signaling downstream of EGFR. Treatment with EGFR-tyrosine kinase inhibitors (TKIs) decreased CEACAM6 levels, leading to TKI-resistant lung cancer cells that exhibited reduced p-ERK1/2 and increased epithelial-mesenchymal transition (EMT) characteristics. Co-immunoprecipitation assays revealed an interaction between CEACAM6 and EGFR. Although CEACAM6 expression was lost in EGFR-TKI resistant cells, its re-expression stabilized EGFR and increased sensitivity to EGFR-TKIs. TGF-? treatment, which induced EMT, also decreased CEACAM6 expression and improved EGFR-TKI resistance. Further analysis showed that EGFR-TKI resistant lung cancer cells had lower H3K27ac epigenetic modification levels at the CEACAM6 locus than EGFR-TKI sensitive cells. Treatment with HDAC1/2 inhibitors in EGFR-TKI sensitive cells reduced CEACAM6 expression, induced EMT and TGF-?-ligand/receptor gene expression, and enhanced EGFR-TKI resistance. These data highlight the crucial role of CEACAM6 in maintaining oncogenic EGFR signaling and its regulation by cytokine stimulation and epigenetic modification, influencing EGFR-TKI sensitivity. Our findings underscore CEACAM6's potential as a valuable biomarker in EGFR-driven lung adenocarcinoma and its intricate involvement in EGFR-related pathways.

overall_design:
We collected total RNA from both HCC827 SC and HCC827 shCEACAM6 and examined mRNA expression profile, comprehensively.
HCC827 cells transduced with lentiviral particles encoding scramble control (SC) or shCEACAM6.

first: Yu-Ting

last: Chou


title: Targeting the RBM39-MEK5 axis synergizes with bortezomib to inhibit the malignant growth of multiple myeloma

first: Hua

last: Yan

address: 197 Ruijin 2nd Road

institute: Ruijin Hospital

overall_design: To investigate the function of RBM39 in multiple myeloma, we knock down RBM39 with shRNA in H929 and MM1S cell line. We also treated MM1S cells with the RBM39 inhibitor indisulam. We then performed gene expression profiling analysis using data obtained from RNA-seq of H929 and MM1S cell lines. We also performed RNA immunoprecipitation (RIP) using an anti-RBM39 antibody in MM.1S cells and then performed RIP-seq to identify RNA targets of RBM39.

first: Yingli

last: Wu

first: Jia

first: Zilu

last: Zhang

first: Wenbin

last: Xu


title: A Super Enhancer derived enhancer RNA acts together with CTCF/Cohesin in trans to regulate erythropoiesis

city: Bethesda

first: Bingning

last: Xie

address: 50 South Drive

institute: NIDDK

summary: Enhancer RNAs (eRNAs) function in diverse modes and increasing studies have shown that they play important roles in normal development and disease. However, their role in erythropoiesis is not fully understood. We analyzed published RNA-seq and Promoter Capture Hi-C data from mouse fetal liver cells and embryonic stem cells to identify enhancer RNAs in erythroid cells with long-range interactions. We discovered an erythroid-specific enhancer RNA (CpoxeRNA) transcribed from an enhancer region upstream of Cpox, an enzyme important for heme synthesis. CpoxeRNA is crucial for erythropoiesis, as knockdown of CpoxeRNA results in impaired enucleation and cell proliferation during terminal erythropoiesis. CpoxeRNA interacts with cohesin and acts both in cis and in trans to regulate erythroid genes. Thus, we have identified a trans-acting eRNA, CpoxeRNA, as an important regulator of terminal erythropoiesis.

overall_design: ChIRP-seq of CpoxeRNA in differentiate MEL cells

first: Ann

last: Dean


title: Rapamycin Immunomodulation Utilizes Time-Dependent Alterations of Lymph Node Architecture, Leukocyte Trafficking, and Gut Microbiome

city: Baltimore

first: yang

last: song

state: MD

address: HSF-3, 3rd Floor; 670 W Baltimore St.

department: Department: Institute for Genome Sciences

institute: University of Maryland in Baltimore

summary: Transplant recipients require lifelong, multimodal immunosuppression to prevent rejection by reducing alloreactive immunity. Rapamycin, a mechanistic target of rapamycin (mTOR) inhibitor, is known to modulate adaptive and innate immunity, while the full spectrum of its immunosuppressive mechanisms remains incompletely understood. Given the broad expression of mTOR, we investigated the understudied effects of rapamycin on lymph node (LN) architecture, leukocyte trafficking, and the gut microbiome and metabolism after 3, 7, and 30 days of rapamycin treatment, to characterize the early, intermediate, and late changes. Rapamycin significantly reduced CD4+ T cells, CD8+ T cells, and regulatory T (Treg) cells in peripheral LNs, mesenteric LNs, and the spleen over time. Rapamycin induced early pro-inflammation transition to pro-tolerogenic status, by modulating the LN laminin α4:α5 expression ratios (La4:La5) through LN stromal cells laminin α5 expression and by adjusting Treg numbers and distribution. Additionally, rapamycin significantly altered gut microbiota composition and metabolic functions, shifting the Bacteroides to Firmicutes ratio and increasing amino acid bioavailability in the gut lumen. These effects were evident by 7 days and became most pronounced by 30 days in naïve mice, with notable changes as early as 3 days in allogeneic splenocyte-stimulated mice. These findings reveal a novel mechanism of rapamycin action through time-dependent modulation of LN architecture and gut microbiome, which orchestrates changes in immune cell trafficking, providing a new framework for understanding and optimizing immunosuppressive therapies.

overall_design: the intestinal transcriptome of days 7 and 30 of female C57BL/6 mice between 8 and 14 weeks of age were used.

first: Bing

last: Ma

first: Jonathan

last: S Bromberg

first: Yang

last: Song


title: Genome-scale knockout simulation and clustering analysis of drug-resistant breast cancer cells reveal drug sensitization targets

city: Daejeon

first: Hyun Uk

last: Kim

address: 291, Daehak-ro, Yuseong-gu

institute: KAIST

summary: Anticancer chemotherapy is an essential part of cancer treatment, but the emergence of resistance remains a major hurdle. Metabolic reprogramming is a notable phenotype associated with the acquisition of drug resistance. Here, we develop a computational framework that predicts metabolic gene targets capable of reverting the metabolic state of drug-resistant cells to that of drug-sensitive parental cells, thereby sensitizing the resistant cells. The computational framework performs single-gene knockout simulation of genome-scale metabolic models that predicts genome-wide metabolic flux distribution in drug-resistant cells, and clusters the resulting knockout flux data using uniform manifold approximation and projection. From the clustering analysis, knockout genes that lead to the flux data near that of drug-sensitive cells are considered drug sensitization targets. This computational approach is demonstrated using doxorubicin- and paclitaxel-resistant MCF7 breast cancer cells. Drug sensitization targets are further refined based on proteome and metabolome data, which generate GOT1 for doxorubicin-resistant MCF7, GPI for paclitaxel-resistant MCF7, and SLC1A5 as a common target. These targets are experimentally validated where inhibiting their expression results in increased sensitivity of drug-resistant cells to doxorubicin or paclitaxel. Taken together, the computational framework predicts drug sensitization targets in an intuitive and cost-efficient manner and can be applied to overcome drug-resistant cells associated with various cancers and other metabolic diseases.

overall_design: RNA-seq profiling of parental (drug-sensitive), doxorubicin-resistant, and paclitaxel-resistant MCF7 cells.

first: JinA

last: Lim

first: Hae Deok

last: Jung

first: Soo Young

last: Park

first: Moonhyeon

last: Jeon

first: Da Sol

first: Ryeongeun

first: Dohyun

last: Han

first: Han Suk

last: Ryu

first: Yoosik


title: Barcoded viral tracing identifies bi-directional immunosuppressive astrocyte-glioblastoma cross-talk

first: Zhaorong

last: Li

address: 60 Fenwood Road

institute: Dana Farber Cancer Institute

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

overall_design: Refer to individual Series


title: RNA-Seq analysis among dps-disrupted mutants in Deinococcus geothermalis

city: Seoul

first: Sung-Jae

last: Lee

address: Kyungheedae-ro 26, Dongdaemun-gu

department: Biology

institute: Kyung Hee University

summary: Transcriptomic analysis was performed in Deinococcus geothermalis wild-type and three mutants including dgeo_0257, dgeo_0281, and double knockout (DK) mutants. dgeo_0281 is a major Dps-coding gene and dgeo_0257 is a novel Dps candidate. Thus, to detecte physiological functions of both Dps-encoded genes, each gene-disrupted mutant and DK mutant was constructed and performed RNA-Seq analysis. This result support better understanding for Dps roles in radiation resistant bacterium through up-regulated and down-regulated genes profile.

overall_design: Experimental strains were cultivated to OD600 of 2.0 as an early exponential growth phase in TGY culture medium. The optical density was nomalized to 1.0 value with 0.9% saline and continuously cultivated for 1 hour present or absent of 50 mM H2O2. Then samples were centrifuged and discarded supernatant. The pellets were applied RNA preperation using manufacturing protocols.

first: Hyun Hee

first: Eunjung

last: Shin

first: Yujin


title: BRD9 functions as a methylarginine reader to regulate AKT-EZH2 signaling

city: Charleston

first: Wenjian

last: Gan

state: SC

address: 173 Ashley Ave, BSB507

institute: Medical University of South Carolina

summary: Arginine methylation is a common posttranslational modification that is catalyzed by a family of protein arginine methyltransferases. Recognition of methylarginine marks by effector proteins (“readers”) is a critical link between arginine methylation and various cellular processes. We recently identified methylation of AKT1 at Arg391 by PRMT5, but the reader for this methylation has yet to be characterized. Here, we show that BRD9, a reader of acetylated lysine, unexpectedly recognizes Arg391-methylated AKT1 through an aromatic cage in its bromodomain. Disrupting the methylarginine reader function of BRD9 suppresses AKT activation and tumorigenesis. RNA-sequencing data shows that BRD9 and AKT co-regulate a hallmark transcriptional program in part through EZH2-mediated H3K27 trimethylation. Lastly, we find that inhibitors of BRD9 and EZH2 display synergistic effects on inhibition of cell viability and tumor growth. Together, our study demonstrates that BRD9 serves as a methylarginine reader to promote AKT-EZH2 oncogenic signaling and combined inhibition of BRD9 and EZH2 is a potential strategy for cancer therapy.

overall_design: RNA seq profiling of MDA-MB-231 cell treated with DMSO, I-BRD9, or Ipatasertib (AKT inhibitor) for 16 hours

first: Shasha

last: Yin

first: Bcharles

last: Brobbey

first: Lauren

last: Ball

first: Tian-min

last: Fu

first: Daniel

last: Sprague


title: Sex-specific transcriptional differences in Gulf War Illness patients under stressful conditions

city: Fort Lauderdale

first: Lubov

last: Nathanson

state: Florida

address: 3321 College Ave.

department: INIM

institute: Nova Southeastern University

summary: Background Gulf War Illness (GWI) is a severely debilitating condition with chronic symptoms affecting up to 30% of the veterans deployed to the 1990-91 Persian Gulf War. The symptoms associated with GWI include fatigue, musculoskeletal/joint pain and disturbances of multiple organ systems. The mechanisms of GWI are unknown, although the symptoms suggest that GWI is most likely caused by a combination of genetic predisposition and it’s interaction with environmental factors such as exposure to toxic chemicals. Objectives This research project aims to assess how sex differences in individuals with GWI impact their response to stress, specifically through an exercise challenge. Additionally, it highlights the importance of considering sex differences in the diagnosis and treatment of GWI. Methods We utilized RNA-seq to examine the differential gene expression (GE) in peripheral blood mononuclear cells of 24 female GWI patients, 20 male GWI patients, and 40 healthy controls (HC) who were matched in for sex, age, and BMI. We evaluated the gene expression changes at three time points: T0 (baseline), T1 (at maximal exertion), and T2 (4 hours into recovery after T1). To ensure consistency, we excluded genes located on the sex chromosomes and performed separate analyses for men and women. Our focus was to compare the response to exercise within each group (GWI patients and HC) between different time points. Results In the male GWI cohort, pathways associated with immune system process, particularly IL-12, and natural killer cell cytotoxicity were activated during exercise. The female GWI patients exhibited less significant changes in gene expression than men. During the recovery period, male GWI patients demonstrated distinct alterations in the regulation of innate immune responses. On the other hand, female GWI patients showed significant changes in genes related to regulation of intracellular signal transduction. These functional pathways and differentially expressed genes identified in this project provide valuable insights into the sex-specific pathophysiology of GWI. Conclusion The identification of sex-specific biomarkers and therapeutic targets in GWI holds great potential for understanding the distinct onset and progression of this disease in different sexes.

overall_design: Comparative gene expression analysis of RNA-seq data for female and male GWI patients and matching female and male controls undergoing exercise challenge

first: Frank

last: Joshua

first: Tehrani

last: Lily

first: Gamer

last: Jackson

first: Van Booven

last: Derek

first: Rossman

last: Raquel

first: Edelstein

last: Abraham

first: Uppalati

last: Sadhika

first: Reuthebuck

last: Ana

first: Pangeni

last: Rajendra

first: Klimas

last: Nancy G.

first: Nathanson

last: Lubov


title: The 9p21.3 coronary artery disease risk locus drives vascular smooth muscle cells to an osteochondrogenic state

city: Madison

first: Valentina

last: Lo Sardo

state: Wisconsin

address: 1111 Highland avenue

department: Cell and Regenerative Biology

institute: University of Wisconsin-Madison

summary: Background. Genome-wide association studies have identified common genetic variants at ~300 human genomic loci linked to coronary artery disease (CAD) susceptibility. Among these genomic regions, the most impactful is the 9p21.3 CAD risk locus, which spans a 60 kb gene desert and encompasses ~80 SNPs in high linkage disequilibrium. Despite nearly two decades since its discovery, the role of the 9p21.3 locus in cells of the vasculature remains incompletely resolved. Methods. We differentiated induced pluripotent stem cells (iPSCs) from risk and non-risk donors at 9p21.3 into vascular smooth muscle cells. We performed single-cell transcriptomic profiling, including co embedding and comparison with publicly available human arterial datasets. We conducted functional characterization using migration and calcification assays and confirmed our findings on iPSC-VSMCs derived from additional donors. Finally, we used overexpression of ANRIL followed by gene expression analysis. Results. We demonstrated that iPSC-VSMCs harboring the 9p21.3 risk haplotype preferentially adopt an osteochondrogenic state and show remarkable similarity to fibrochondrocytes from human artery tissue. The transcriptional profile and functional assessment of migration and calcification capacity across iPSC VSMCs lines from multiple donors concordantly resemble an osteochondrogenic state. Importantly, we identified numerous transcription factors driving different VSMC state trajectories. Additionally, we prioritized LIMCH1 and CRABP1 as signature genes critical for defining the risk transcriptional program. Finally, overexpression of a short isoform of ANRIL in non-risk cells was sufficient to induce the osteochondrogenic transcriptional signature. Conclusions. Our study provides new insights into the mechanism of the 9p21.3 risk locus and defines its previously undescribed role in driving a disease-prone transcriptional and functional state in VSMCs concordant with an osteochondrogenic-like state. Our data suggest that the 9p21.3 risk haplotype likely promotes arterial calcification, through altered expression of ANRIL, in a cell-type specific and cell autonomous manner, providing insight into potential risk assessment and treatment for carriers.

overall_design: single-cell RNA sequencing of iPSC-derived VSMC of four genotypes at the 9p21.3 locus: homozygous risk, homozygous non-risk, and complete knockouts of the 9p21.3 CAD risk region in both backgrounds.

first: Elsa

last: Salido

first: Carolina

last: de Medeiros Vieira

first: José

last: Verdezoto Mosquera

first: Rohan

last: Zade

first: Parth

last: Parikh

first: Shraddha

last: Suryavanshi

first: Clint

middle: L

last: Miller


title: Mutant IDH disables p53 tumor suppression [RNA-seq]

city: Chapel Hill

first: John

middle: P.

last: Morris IV

state: NC

address: 450 West Drive, 32-048 Lineberger Comprehensive Cancer Center

department: Pharmacology, Lineberger Comprehensive Cancer Center, UNC School of Medicine

institute: University of North Carolina at Chapel Hill

summary: p53 prevents tumor initiation and progression by adapting cell fate via transcriptional regulation of target gene networks. Here, we find that cancer associated mutations in isocitrate dehydrogenase (IDH) can uncouple p53 activity from tumor suppression by perturbing chromatin states that determine target gene expression. Mutant IDH impairs tumor regressions and promotes outgrowth of cancer cells with transcriptionally active, wild type p53 in a mouse model of liver cancer where restoration of p53 activity results in tumor clearance. Mutant IDH alters p53 target gene expression through the oncometabolite 2-hydroxyglutarate (2-HG), an inhibitor of alpha-ketoglutarate (KG) dependent chromatin remodeling enzymes, without preventing p53 accumulation or global genomic binding. Rather, mutant IDH alters chromatin accessibility landscapes that dictate target gene expression. Mutant IDH interferes with the expression of pro-apoptotic p53 targets, including the death ligand receptor Fas that enables p53 dependent liver tumor regressions. Pharmacological inhibition of mutant IDH in TP53 wildtype cholangiocarcinoma cells, a tumor type where p53 and IDH mutations are mutually exclusive, potentiates p53 target gene expression and sensitizes cells to Fas ligand and chemotherapy induced apoptosis.  Therefore, we implicate disruption of p53 target gene regulation as a reversable, oncogenic feature of cancer associated IDH mutations.

overall_design: To examine how 2-HG alters gene expression coordinated by p53 in human cancer cells, we performed RNA-seq on RBE cholangiocarcinoma cells treated with the mutant IDH1 inhibitor AG-120 to block production of 2-HG in combination with the MDM2 inhibitor Nutlin to activate p53.

first: Cole

last: Martin

first: William

last: Sullivan

first: Jacqueline

last: Brinkman

first: Deena

last: Scoville

first: Jossie

last: Yashinskie

first: Sha

last: Tian

first: Riccardo

middle: E

last: Mezzadra

first: Yu-Jui

last: Ho

first: Richard

last: Koche

first: Timour

last: Baslan

first: Jesse

last: Raab

first: David

last: Corcoran

first: Lydia

middle: W

last: Finley

first: Scott

last: Lowe


title: Lrtm1 - A Novel Sensor of Insulin Signaling and Regulator of Metabolism and Activity

city: Boston

first: Jonathan

last: Dreyfuss

state: MA

address: 1 Joslin Pl

department: Bioinformatics & Biostatistics Core

institute: Joslin Diabetes Center

summary: Insulin regulates glucose uptake and metabolism in muscle via the insulin receptor. Here we show that Lrtm1 (Leucine Rich Repeats and Transmembrane Domains 1), a protein of unknown function enriched in insulin-responsive metabolic tissues, senses changes in insulin signaling in muscle and serves as a regulator of metabolic response. Thus, whole-body Lrtm1 deficient mice exhibit reduced fat mass, increased lean mass, and enhanced glucose tolerance and insulin sensitivity compared to control mice, under both chow and high fat diet conditions. Lrtm1 whole-body deficiency also affects dopamine signaling in the brain leading to hyperactivity. The improvements in glucose and insulin tolerance, but not the behavioral or body composition changes, are also observed in skeletal muscle-specific Lrtm1 knockout mice. The effects are independent of the classical insulin receptor-Akt signaling. Thus, Lrtm1 senses changes in insulin receptor signaling and serves as a novel post-receptor regulator of metabolic and behavioral activity.

overall_design: The tibialis anterior muscle from 6-month-old Lrtm1 flox control and Lrtm1 ko mice that had a C57BL/6 background after a 3-h fast were studied by RNA-sequencing, n=4 per group.

first: Yingying

last: Yu

first: C

middle: R

last: Kahn


title: Heritable states influence stem cell fates upon acquisition of cancer mutations [Second]

city: Barcelona

first: Daniel

last: Fernandez-Perez

state: Choose State

address: Carrer Baldiri Reixac 12

department: Aging and Metabolism

country: Spain

institute: IRB Barcelona

summary: Tumors with the same driver mutations can display a striking variation in their progression and treatment response, but the origins of this variation are still unclear. In this study, we use state-fate analysis to unveil that heritable stem cell states can influence how individual cells respond to the acquisition of the same cancer mutation. We develop a new methodological pipeline, single-cell Tracking of Recombinase Activation And Clonal Kinetics, and apply it to hematopoietic stem cells carrying Cre/Flp-conditional leukemia alleles. Tracking the gene expression changes and expansion kinetics of a common set of stem cell clones, with and without the same myeloid leukemia mutations, we unveil a striking heterogeneity in the malignant fates of diverse stem cells. First, we define that heritable clonal states persist in expansion cultures and cause the selection of a small group of clones with a specific fitness signature. Then, using mouse models of the most frequent initiating mutations, we define that these pre-existent stem cell states influence the mutation-induced changes in expansion, fate, and malignant  gene expression programs. Initiating driver mutations increase the survival probability of clones with low fitness through enhancing their stemness programs. Surprisingly, the fate of high-fitness stem-cell clones is sometimes reversed, producing more mature leukemias, yet still carrying markers of their cell of origin. We further validate these HSC-of-origin signatures in bulk and single-cell RNAseq datasets from cancer patients. Our findings suggest that aggressive premalignant clonal expansions arise from low-fitness stem cells more frequently than previously expected.

overall_design: LARRY single-cell RNA-seq tracing experiment. 2 different timepoints (D6, D30) and 4 different conditions (WT, Dnmt3a-mut, Npm1-mut, Dnmt3a-Npm1-mut), 2 biological replicates per timepoint and condition.

first: Indranil

last: Singh

first: Alejo

last: Rodriguez-Fraticelli


title: Lipoprotein Lpp and L, D-transpeptidases regulate the master regulator of virulence AggR in EAEC

city: Charlottesville

first: Araceli

last: Santiago

state: VA

address: 409 Lane Road

department: Pediatrics

institute: University of Virginia

summary: This study demonstrates that Lpp (Braun’s lipoprotein), and L, D-transpeptidases are required for AggR activation. We found that deletion lpp in EAEC resulted in the downregulation of more than 100 genes involved in transport, metabolism, and virulence. Among those genes, fourteen transcriptional factors, including AggR, were differentially expressed in 042Dlpp.

overall_design: RNA was extracted from EAEC 042 derivatives in duplicates (042-1, 042-3, lpp-1, and lpp-2) grown in DMEM-HG


title: RNF26 promote the proliferation and metastasis of colorectal cancer cells via Wnt pathway

city: Beijing

first: Yalan

last: Lu

address: No. 5 Panjiayuan Nanli, Chaoyang District

department: Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences (CAMS) & Comparative Medicine Center

institute: Peking Union Medical College (PUMC)

summary: Colorectal cancer (CRC) is the third most common malignant tumor in the world. Identification of key genes for prediction and treatment of disease course and prognosis is urgent to reduce morbidity and mortality of CRC patients. Although dysregulated Ring finger protein 26 (RNF26) expression has been detected in several tumors, the potential regulatory effect of RNF26 on CRC remains uncertain. Here we evaluated the expression of CRC using multiple online platforms, and demonstrated that RNF26 upregulation was consistently observed in CRC relative to normal tissues and correlated with unfavorable prognosis. Then, we provide direct evidence that RNF26 acts as a driver of CRC progression by showing that constructed overexpression cell lines. We analyzed the impact of altering RNF26 level on CRC cell viability and metastasis phenotypes in HCT116 and HCT15 modified cell lines. The results showed that RNF26 overexpression promote cell proliferation, migration, and invasion in vitro, and multiple organ distant metastasis in vivo. Moreover, Wnt signaling pathway was common enriched in these modified cell lines. Therefore, we assumed that RNF26 significantly increased CRC proliferation and metastasis through the RNF26/Wnt axis. These data strongly suggest that RNF26 overexpression may be an effective biomarker to monitor and a prospective therapeutic target to treat CRC.

overall_design: Four cell types: HCT116_control, HCT116_OV_RNF26, HCT15_control, HCT15_OV_RNF26, with 3 replicates for each cell type.


title: Clinical utility and biological function of Transfer RNA-derived small RNAs in Patients with Acute Coronary Syndrome [RNA-seq]

city: 武汉

first: yi

last: he

address: 武汉市蔡甸区同济医院科研大楼

institute: 华中科技大学附属同济医院

summary: Acute coronary syndrome (ACS) is one of the leading causes of death worldwide. Aberrant expression of Transfer RNA-derived small RNAs  (tsRNA)  contributed to various human disease. However, the clincal utility and biological function of tsRNA in ACS are largely unknown. High throughput sequencing revealed a landscape of novel sncRNAs in the human PBMCs. tsRNAs represented a characteristic expression pattern in responding to acute coronary syndrome;  tRF-Gly-GCC-06 and tRF-Lys-CTT-02 were significantly up-regulated in patients with unstable angina(UA) and acute myocardial infarction(AMI). Both of the two tRFs demonstrated reasonable diagnostic accuracy for ACS detection. tRF-Gly-GCC-06 and tRF-Lys-CTT-02 upregulation were independent predictors of an increased risk of ACS. Both of the two tRFs expression levels show a significantly positive correlation with Gensini score.Our study identified novel tsRNA alterations  associated with ACS and provided potential clinical  biomarkers and therapeutic targets.

overall_design: Gene expression analysis of RNA-seq data from THP-1 cells with overexpression of tRF-Gly-GCC-06 . Samples were collected 24 hours post-transfection of THP-1 cells with tRF-Gly-GCC-06 mimics.


title: Genome-wide DNA methylation profiles of well-differentiated liposarcomas (WDLPS), dedifferentiated liposarcomas (DDLPS), and normal adipose tissues II

city: Maebashi

first: Naoko

last: Hattori

state: Gunma

address: 3-39-15 Showa-mach

department: Institute for Molecular and Cellular Regulation

institute: Gunma University

summary: Liposarcoma (LPS) is the most common soft-tissue sarcoma in adults, and well-differentiated LPS (WDLPS) and dedifferentiated LPS (DDLPS) are the most frequent subtypes.  These LPSs are considered to develop due to disturbances in the process of adipogenic differentiation of mesenchymal stem cells.  However, the molecular mechanism of the disturbances remains unclear.  Here, we aimed to identify the mechanism and take its advantage in therapy.

overall_design: Genomic DNA from peripheral blood mononuclear cells, the cell lines from liposarcomas (93T449, 94T778, LP6, and LPS12), and dedifferentiated liposarcoma cell lines (LP6 and LPS12) treated with 5-aza-dC and rosiglitazone were extracted. After bisulfite conversion, DNA was hybridized to the Infinium Human MethylationEPIC BeadChip v1.0 (PBMC and cell lines) or Infinium Human MethylationEPIC BeadChip v2.0 (LP6 and LPS12 treated with mock, 5-aza-dC, and 5-aza-dC and rosiglitazone).

first: Satoshi

last: Yamashita

first: Toshikazu

last: Ushijima


title: BMDM from Young and Aged Mice Treated with β-glucan

city: Nashville

first: Margaret

middle: Ann

last: Mcbride

state: Tennessee

address: 1211 Medical Center Drive

department: Anesthesiology

institute: Vanderbilt University Medical Center

summary: Advancing age significantly heightens the incidence and severity of infection, with individuals aged 65 and above, accounting for 65% of sepsis cases. The decline in immune response with age, termed “immunosenescence”, heightens vulnerability to infection and sepsis. This prompts exploration of strategies to enhance infection resistance by modulating the aging immune system. Innate immune training, referred to as “trained immunity” or “innate immune memory”, emerges as a potential strategy. We investigated the impact of 𝛽-glucan induced innate immune training on aged mice (18–20 months old), compared with a group of young mice (10–12 weeks old). We found that 𝛽-glucan augmented host’s resistance to infection. This enhancement was characterized by preservation of body temperature during infection, improved leukocyte recruitment, augmented bacterial clearance, and decreased cytokine production both in blood and infection sites. Furthermore, trained macrophages displayed heightened metabolic capacity and improved antimicrobial functions such as enhanced phagocytosis and respiratory burst. RNA-seq analysis underscored a distinctive gene expression pattern induced by trained immunity in macrophages, consistently observed in both young and aged groups. Our results suggest that immune training can be effectively induced in aging individuals, providing valuable insights into potential strategies for enhancing infection resistance in the elderly.

overall_design: Bone marrow-derived macrophages from WT C57BL/6 mice were treated with β-glucan, lipopolysaccaride (LPS), vehicle  (normal saline (NS)), or multiple treatments in sequence. We then performed gene expression profile analysis from 3 biological replicates per treatment at multiple timepoints. The effects on the transciptome were compared between groups.

last: McBride

first: Edward

last: Sherwood


title: Analysis of extracellular vesicles (Evs) miRNAs in ovarian cancer

city: Bologna

first: Gloria

last: Ravegnini

state: BO

address: via irnerio 48

department: PHARMACY AND BIOTECHNOLOGY

country: Italy

institute: UNIVERSITY OF BOLOGNA


title: The influence of the geroprotective cytokine on the transcriptome of young and old mesenchymal stem cells

city: Moscow

first: Liya

last: Kondratyeva

address: Ulitsa Miklukho Maklaya, 16/10

country: Russia

institute: Institute of bioorganic chemistry of the Russian Academy of Sciences

summary: Increasing longevity and the growing elderly population necessitate a deeper understanding of aging mechanisms to prolong productive life and improve treatments for age-related diseases linked with cellular senescence. Mesenchymal stem cells (MSCs) are crucial for maintaining tissue homeostasis, but their physiological changes during senescence are not well understood. Growth differentiation factor 11 (GDF11) has emerged as a potential rejuvenation factor, enhancing MSC viability, mobility, and angiogenic functions, which improves outcomes in ischemic models and cardiac repair. This study aims to identify transcriptomic changes in young and senescent MSCs influenced by GDF11, highlighting its potential in MSC-based therapies.

overall_design: To evaluate transcriptomic changes induced by the potential geroprotective factor GDF11, we performed RNA sequencing on four groups of samples: 'young' MSCs (MmC-/GDF11-) and senescent MSCs (MmC+/GDF11-) without the addition of GDF11, as well as 'young' (MmC-/GDF11+) and senescent MSCs (MmC+/GDF11+) with the addition of GDF11. After 10 days of incubation, indexed cDNA libraries for Illumina sequencing were prepared from the samples, and the resulting cDNA library mix was subjected to NovaSeq 6000 sequencing.  The RNA sequencing data was further processed with HISAT2 (GRCh38/hg38 was used as the reference genome), featureCount (GENCODE V38 was used as the reference transcriptome).

first: Diana

last: Matveeva

first: Maria

last: Ezdakova

first: Marina

last: Utkina

first: Andrey

last: Ratushnyy


title: Heritable states influence stem cell fates upon acquisition of cancer mutations [Third]

first: Daniel

last: Fernandez-Perez

overall_design: LARRY single-cell RNA-seq tracing experiment. Npm1c-HSCs (Npm1c-HSCs generated fom Flt3Cre-Tdt+ -Flt3pos- or Flt3Cre-Tdt- -Flt3neg-) were transplanted to 7 different recipient. LSKs from bone marrow were profiled after 1 month of transplant.

last: Singh


title: Mutant IDH disables p53 tumor suppression [CUT&RUN]

first: John

last: Morris IV

overall_design: To determine whether Mutant IDH perturbs p53 genomic occupancy, we performed CUT&RUN for p53 in NPsh cells harboring IDH2-WT or IDH2-R172K following restoration of p53.

first: Cole

last: Martin

first: William

last: Sullivan

first: Jacqueline

last: Brinkman

first: Deena

last: Scoville

first: Jossie

last: Yashinskie

first: Sha

last: Tian

first: Riccardo

last: Mezzadra

first: Yu-Jui

last: Ho

first: Richard

last: Koche

first: Timour

last: Baslan

first: Jesse

last: Raab

first: David

last: Corcoran

first: Lydia

last: Finley

first: Scott

last: Lowe


title: Gene expression profile at a single-cell level of CD45+ cells from the livers of mice hepatocellular carcinoma (HCC).

city: Minneapolis

first: Adam

last: Herman

address: 117 Pleasant St SE

department: Minnesota Supercomputing Institute

institute: University of Minnesota

summary: We used droplet-based scRNA-seq to profile the gene expression of magnetically-sorted CD45+ T cells from the livers of helathy mice and mice with HCC.

overall_design: Two million liver CD45+ cells from each mouse were individually labeled with cell multiplexing oligos (CMOs, 10X Genomics) to allow for the multiplexing of individual samples prior to pooling and gel bead-in-emulsion (GEM) preparation. Separate gene expression and CMO libraries were created and sequenced in a Novaseq S4 chip (2 x 150bp PE).

first: Haiguang

last: Wang

first: Xavier

last: Revelo


title: SGLT2 inhibitor upregulates myocardial genes for oxidative phosphorylation and fatty acid metabolism in Gαq mice (genotype x timepoint)

first: Boston University

last: Microarray and Sequencing Resource

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

summary: Background. Mitochondrial dysfunction with decreased ATP production and increased release of reactive oxygen species (ROS) is a hallmark of the failing heart. Although SGLT2 inhibitors have been shown to improve myocardial metabolism in the failing heart, independent of diabetes, the mechanism of this effect is not clear.  Objectives. Our goal was to test the effect of the SGLT2 inhibitor ertugliflozin on mitochondrial gene expression and function in myocardium and isolated mitochondria from non-diabetic mice with dilated cardiomyopathy due to cardiac-specific over-expression of Gαq. Methods. Gαq and wild-type (WT) littermates 4 weeks of age were treated for 16 weeks with or without the SGLT2 inhibitor ertugliflozin (ERTU) formulated in the chow (0.5 mg/g chow).  Results. From weeks 4 to 20, Gαq mice developed progressive cardiac hypertrophy, dilation, contractile dysfunction, myocyte apoptosis and interstitial fibrosis – all of which were prevented by ERTU treatment. Isolated cardiac mitochondria from Gαq mice had decreased maximal ATP production and increased ROS release - both of which were normalized by ERTU. In isolated beating hearts from Gαq mice, contractile reserve and high energy phosphates measured simultaneously by 31P NMR spectroscopy were decreased - and both were improved by ERTU. In Gαq mice, marked suppression of myocardial gene programs for oxidative phosphorylation and fatty acid metabolism was reversed by ERTU. Conclusions. The SGLT2 inhibitor ERTU corrected the expression of myocardial gene programs for oxidative phosphorylation and fatty acid metabolism, thereby leading to increased production of ATP, decreased release of mitochondrial ROS, and amelioration of the consequences of mitochondrial dysfunction on myocardial structure and function.

overall_design: Wild-type mice or animals with cardiac-specific over-expression of Gαq (dilated cardiomyopathy model) were fed a control chow diet and were sacrificed at 4 weeks or 20 weeks of age. 4 representative left ventricular cardiac tissue samples per group were assessed, for a total of 16 samples, and gene expression was profiled by RNAseq.

first: Dominique

last: Croteau

first: Wilson

last: Colucci