title: Effect of Molidustat on organotypic cultures of hamster cerebellum

city: Lyon

first: Pierre-Olivier

last: Vidalain

address: 21 Avenue Tony Garnier

country: France

institute: CIRI

summary: Airborne RNA viruses from the Paramyxoviridae family include major human pathogens, in particular measles virus (MeV) and Nipah virus (NiV), which is on the blueprint list of WHO due to its high lethality rate and critical risk of emergence. Although an effective vaccine provides protection against MeV, this is not the case for NiV. Besides, there is no cure to treat MeV- or NiV-infected patients despite the risk of developing acute respiratory infections and lethal encephalitis. To identify host-targeting antivirals against these viruses, a library of metabolic modulators has been screened against MeV. Results showed that Molidustat, Daprodustat and Roxadustat, three pharmacological inducers of hypoxia-inducible factors (HIFs), have inhibitory effects on MeV infection both in vitro and ex vivo in organotypic cultures of hamster cerebellum. In addition, we showed that Molidustat inhibits NiV infection in this ex vivo model. Taken together, our results provide evidence that pharmacological induction of the hypoxia response pathway has inhibitory effect on MeV and NiV, suggesting that HIF-inducing drugs are of potential interest for treating these infections.

overall_design: RNAseq profiling of ex vivo organotypic cultures of hamster cerebellum treated for 24h with DMSO alone or Molidustat at 25 microM

first: Lola

last: Canus

first: Eva

last: Ogire

first: Cyrille

last: Mathieu


title: ATAC-seq time course (in parallel to mRNA-seq time course), of control or GRH-1 depleted C. elegans larvae sampled at 20oC

status: Public on Sep 17 2025

city: Basel

first: Dimos

last: Gaidatzis

address: Maulbeerstrasse 66

department: Computational Biology

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The goal of these experiments were to evaluate how dynamic changes to gene expression (mRNA-seq) and chromatin accessibility (ATAC-seq) were affected by the acute depletion of the transcription factor GRH-1. To do so, we employed a strain that incorporated an auxin-inducible degron at the endogenous grh-1 locus (Meeuse et al., 2023, EMBO J). We can thereby acutely deplete GRH-1 in growing larvae. Based on linear modeling incorporating ATAC-seq dynamics and ChIP-seq data, we hypothesized that GRH-1 depletion should affect accessibility at a specific set of chromatin regions and expression of a specific set of genes.

overall_design: ATAC-seq was performed on nuclei isolated from larval C. elegans (HW2434 strain - grh-1::degron::3xFLAG), treated with either EtOH or 250 uM Auxin, and collected in a time course spanning 12-13 hours of development. Synchronized L1 animals were grown at a density of 1 animal/uL in liquid culture (S-Basal + OP50 at OD600=2.8) for 20-21 hours before splitting the culture to treat half the animals with EtOH, and the other half with 250 uM Auxin. Every hour following treatment, 14000 animals were collected for ATAC-seq. Nuclei were prepared from frozen animal pellets by douncing similar to a previosuly established protocol (Daugherty et al., 2017, Genome Res.). Library was sequenced using NovaSeq S1 2x50bp Paired-end reads.

first: Maike

last: Graf-Landua

first: Stephen P

last: Methot

first: Michaela

last: Woelk

first: A Alexander T

last: Smith

first: Helge

last: Großhans


title: The biological function of GYS1 and p53 in ovarian clear cell carcinoma cell line.

city: Guangzhou

first: Haoyu

last: Liang

address: Sun yat-sen Cancer center

country: China

institute: Sun yat-sen Cancer center

type: Expression profiling by high throughput sequencing

summary: Ovarian cancer (OC) is a highly fatal and refractory malignancy affecting women, with platinum resistance remaining a major clinical dilemma. Ovarian clear cell carcinoma (OCCC) frequently exhibits increased platinum refractoriness than the other OC subtypes, accompanied by heightened glycogen that engenders clear-cell morphology and wild-type p53. However, their roles in platinum resistance are unclear. Here, we investigated whether glycogen promotes OCCC platinum resistance, and found that GYS1 as a rate-limiting enzyme in glycogen synthesis is clinically associated with poor prognosis and chemoresistance in OCCC. GYS1 is a rate-limiting enzyme in glycogen synthesis, which is clinically associated with poor prognosis and chemoresistance in OCCC. Mechanistically, p53 promotes GYS1 breakdown via upregulating RNF144a, while GYS1 enhances reversed ubiquitination and degradation toward p53 by competitively bound to the USP14, forming a positive feedback circuit. Under platinum stress the accumulated glycogen is mobilized by p53/GYS1 feedback circuit, which fueling energetic NADPH production, hence gaining disulfidptosis invulnerability and increased platinum resistance in OCCC. Collectively, our study identifies glycogen as a contributor to OCCC platinum resistance and elucidates the underlying mechanisms, highlighting a crucial p53/GYS1 positive feedback loop.

overall_design: To investigate the the biological function of GYS1 in ovarian clear cell carcinoma cell  line TOV21G, we knock down GYS1 in TOV21G for RNA-seq.

first: Ru

last: Deng


title: Tcf1 and Lef1 transcription factors underpin the inception of T cell fate

city: Nutley

first: Haihui

last: Xue

state: NJ

address: 123 Metro Boulevard, Bldg. 123, Rm. 5527

department: Center for Discovery and Innovation

country: USA

institute: Hackensack University Medial Center

summary: The goal of this study is to resolve the heterogeneity of transcriptomic and chromatin accessibility (ChrAcc) landscape in DN1 thymocytes harboring ETPs. Comparison of molecular features between ETPs with non-ETP DN1 cells predicted contribution by Tcf/Lef family transcription factors, and pre-thymic ablation of Tcf1 and Lef1 impaired ETP formation. Single cell analysis of the factor-targeted ETPs revealed that they converged on Notch1 or Notch pathway effector molecules including Hes1 and Hhex, to support their transcriptional activation.

overall_design: Bone marrow (BM) LSK cells were sorted from CreER+ WT or  CreER+ Tcf7-floxed, Lef1-floxed mice and seeded on OP9-DL1 monolayers for culture. The cells were treated with 4-OH tamoxifen during days 3-5 culture and cKit+ DN1 cells were sorted on day 7 of culture for bulk RNA-seq and ATAC-seq analysis.

first: Zhao

last: Xin

first: Hu

last: Sheng'en

first: Zang

last: Chongzhi

first: Xue

last: Hai-Hui


title: Transcriptomic profiling of activated-HSCs/myofibroblasts of CCl4-injured mouse liver by NanoString GeoMX DSP.

city: Austin

first: Ningling

last: Kang

state: Minnesota

address: 801 16th AVE NE

department: tumor microenvironment and metastasis

institute: the Hormel Institute

summary: To study whether targeting Cd274/PD-L1 of activated-HSCs/myofibroblasts by Cre/loxP approach in mice altered the transcriptome of activated-HSCs/myofibroblasts so as to influence liver fibrosis induced by CCl4

overall_design: Two months old Cd274+/+Col1A1Cre mice and two months old Cd274F/FCol1A1Cre mice were subjected to liver injury by intraperitoneal CCl4 injection. Cryo-sections of their livers were fixed with formalin, hybridized with the NanoString mouse whole transcriptome atlas, followed  by immunofluorescence staining with anti-desmin to label activated-HSCs/myofibroblasts, and SYTO 13 for cell nuclei. Regions of Interest (ROIs) were selected for data requisition and analysis. Activated-HSCs/myofibroblasts (Desmin+ CD45-) within a ROI were collected for transcriptomic profiling. Segments 1-5 were ROIs from Cd274+/+Col1A1Cre livers and 6-10 were from  Cd274F/FCol1A1Cre livers. 18 sequencing data were generated for activated-HSCs/myofibroblasts due to dual-indexing primers-based sequencing.

first: Kang

last: Ningling

first: Bai

last: Bing


title: A protective role of SRC-1 against aging associated cognitive decline

city: Houston

first: Jonathan

middle: Carter

last: Bean

state: TX

address: 1100 Bates Ave

department: Pediatrics

institute: Baylor College of Medicine

summary: The mechanisms underlying dementia, including Alzheimer’s Disease (AD), associated with aging remain elusive.  Our RNA sequencing analysis (RNA-Seq) revealed that the loss of steroid receptor coactivator-1 (SRC-1) leads to alterations in gene expression signatures that are commonly associated with neurodegenerative diseases, including AD. Consistent with previous findings, our research indicates that SRC-1 deficiency diminishes the neural plasticity of the hippocampal CA1 neurons. Cognitive behavior tests demonstrate that both SRC-1-KO mice and mice with a humanized SRC-1 mutation (SRC-1L1376P) displayed early signs of contextual memory impairment at just 6 months of age, in contrast to the typical aging-associated memory decline observed in wild type mice at 18 months of age. These results suggest a protective role of SRC1 against aging-associated cognitive decline. To further explore the molecular mechanism, we reanalyzed publicly available spatial RNA-Seq data of both young and aged mouse brains. We found a synchronous decline in SRC-1 and S100 calcium-binding protein A6 (S100A6), an AD associated gene, in both the hypothalamus and hippocampus of aged brain. Notably, our RNA-Seq data highlighted S100A6 as one of the most profoundly inhibited genes in SRC-1-KO mice. We also identified S100A6 and S100A11 as potential AD-associated genes that are downstream targets of SRC-1, offering novel perspectives on the protective role of SRC1 against cognitive decline due to aging.

overall_design: Hypothalamus from mice with SRC-1 gene deletion and control mice were isolated, RNA extracted, and RNA-sequencing was performed.

middle: C

first: Yongjie

last: Yang

first: Hari

middle: K

last: Yalamanchili

first: Chunmei

last: Wang


title: BubR1 Insufficiency Recapitulates Changes Associated with Age-Related Cardiac Pathologies

city: Omaha

first: Brian

last: North

state: NE

address: 2500 California Plaza

department: Biomedical Science

institute: Creighton University School of Medicine

summary: Aging is a major risk factor for cardiovascular diseases, including heart failure, and contributes to pathological changes such as hypertrophy, fibrosis, and cellular senescence in the heart. BubR1, a critical regulator of the spindle assembly checkpoint, has been linked to various aging phenotypes, though its specific role in the heart remains largely unexplored. In this study, we examined the effects of BubR1 insufficiency in hypomorphic mice, revealing significant cardiac hypertrophy, fibrosis, and increased markers of cellular senescence. Transcriptomic analysis demonstrated that BubR1 insufficiency triggers molecular changes in the heart similar to those seen in aged hearts. Likewise, comparisons with end-stage heart failure patients showed that BubR1 deficiency mirrors transcriptomic alterations characteristic of heart failure. Importantly, our results indicate that heart failure is associated with reduced BubR1 levels, which also naturally declines with age in the heart. Our findings suggest that BubR1, traditionally known for its mitotic functions, plays a crucial role in maintaining the structure and function of the post-mitotic heart.

overall_design: To investigate the transcriptomic profiles between 16 weeks  wildtype and BubR1 hypomorphic hearts

first: Renju

last: Pun

first: Aliya

middle: L

last: Haas

middle: J


title: Transcriptome analysis the ARPE19 cells with the plasma from cigarette exposure or quit smoking rats

city: Shanghai

first: Qingjian

last: Ou

address: Siping Rd

department: Medical

institute: Tongji University

summary: We aim to explore the expression of mRNA in ARPE19 which treated with cigarette exposed rat plasma or stop exposed rat plasma.

overall_design: ARPE19 cells treated with the plasma from the rats in normal group, cigarette exposure group and  stop exposure group. Then the total RNA of these groups were analysed with RNA sequencing.

first: Tingting

last: Cui


title: Profiling linkage-specific ubiquitin chain functions reveals a key role of K29-linked ubiquitylation in epigenome integrity

city: Copenhagen

first: Anja

last: Groth

address: Blegdamsvej 3B

country: Denmark

institute: Novo Nordisk Foundation Center for Protein Research

summary: Linkage-specific ubiquitin (Ub) chains dictate the functional outcome of many critical Ub-dependent signaling processes. However, the functions and targets of several poly-Ub topologies remain poorly understood due to a lack of tools for their specific detection and manipulation. To remedy this knowledge gap, we applied a cell-based Ub replacement strategy enabling specific, conditional abrogation of each of the seven lysine-based Ub chain types in human cells to comprehensively profile global ubiquitylation changes resulting from disabling formation of individual Ub chain types. Focusing on K29-linked ubiquitylation, we found that this linkage type is enriched among chromatin-associated proteins, and that the H3K9me3 methyltransferase SUV39H1 is a prominent cellular target of this modification. We demonstrate that K29-linked ubiquitylation is essential for the proteasomal degradation of SUV39H1 despite its extensive modification by K48-linked ubiquitylation, and that K29-linked ubiquitylation of SUV39H1 is catalyzed and reversed by TRIP12 and TRABID, respectively. Importantly, preventing K29-linked ubiquitylation of SUV39H1 markedly increases H3K9me3 levels, but not other histone marks. Collectively, our Ub replacement cell line panel and datasets provide valuable resources for illuminating cellular functions of linkage-specific ubiquitylation processes and reveal a key role for K29-linked ubiquitylation in epigenome integrity.

overall_design: Quantitative chrommatin immunoprecipitation DNA- sequencing (qChIP-seq) for H3K9me3

first: Javier

last: Arroyo-Gómez

first: Nazaret

last: Reverón-Gómez


title: GPNMB is a potential biomarker for arthroplasty aseptic loosening stages

city: Hannover

first: Andrea

last: Hoffmann

address: Stadtfelddamm, 34

department: Orthopedic Surgery

country: Germany

institute: MHH

summary: Background: Endoprosthesis loosening is the major cause of arthroplasty failure. Currently, radiography and histo-pathological classification of the periprosthetic membrane are used retrospectively for diagnosis. Prospective options for early diagnosis and prevention of loosening are not available. In order to approach this challenge, the study presented here aimed to identify molecular biomarkers in single-centre prospectively collected cell and plasma samples from patients. Methods: Four patient cohorts (primary and revision arthroplasty of hip or knee) were defined. Aseptic loosening of implants was assessed by the standardised approach of the Knee Society Total Knee Arthroplasty Roentgenographic Evaluation and Scoring System (KSRESS) which is based on radiolucent lines. Synovial fluid, bone marrow, and blood were collected from a total of 96 patients. Bulk RNA-sequencing (RNA-seq) of mesenchymal stem cells (MSCs) isolated from the bone marrow of patients was performed for 28 samples. The data was analysed by bioinformatic tools. Quantitative real-time PCR served to validate and extend RNA-seq data. Western blots were performed for molecular differentiation. ELISAs were used to quantitate selected protein targets. Results: RNA-seq of MSCs identified glycoprotein non-metastatic melanoma protein B (GPNMB) as significantly upregulated in the cells from revision patients compared to patients with primary implantations. The protein encoded by this gene is plasma membrane-standing; its extracellular domain may be cleaved and secreted. In synovial fluid plasma, the soluble GPNMB protein exhibited increased levels in patients undergoing revision surgery compared to patients subjected to primary arthroplasty. No significant differences were observed in bone marrow plasma and blood plasma. The molecular species detected by Western blotting were similar in the plasma fractions of synovial fluid, bone marrow and blood. Conclusions: The use of GPNMB as a biomarker may be of prime importance for early detection of implant loosening, ahead of radiographic failure demonstration. Translational potential of this article: GPNMB has the potential to act as a prospective and quantitative parameter to assess different stages of implant loosening. Radiography and histo-pathological classification of the periprosthetic membrane, on the contrary, are used retrospectively for diagnosis and are subjective measures, performed mainly at the end of a full loosening process.

overall_design: Four patient cohorts (primary and revision arthroplasty of hip or knee) were defined. Bulk RNA-sequencing (RNA-seq) of mesenchymal stem cells (MSCs) isolated from the bone marrow of patients was performed for 28 samples.

first: Patrik

last: Schadzek


title: Regulation of ILC2s by Brg1

first: Ju

last: Qiu

address: 320 Yueyang Road

institute: Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

summary: The chromatin status fluctuates with effector and memory group 2 innate lymphoid cell (ILC2) responses. How this intricate coordination affects allergic lung inflammation remains unclear. Here, we report that during papain-induced lung inflammation, the expression of chromatin remodeler Brg1 is upregulated by IL-33 in ILC2s, accompanied with more open chromatin regions having increased accessibility. Brg1 expression is also upregulated in asthma patients’ ILC2s. Ablating Brg1 constrains ILC2 expansion and ameliorates both acute and alarmin-rechallenged secondary lung inflammation. Mechanistically, Brg1 imprints the chromatin landscape favoring aerobic glycolysis, the metabolic process reinforced in effector and memory ILC2s, to facilitate ILC2 expansion. Particularly, Brg1-augmented Hif1a enhancer accessibility is a sustained epigenetic signature in memory ILC2s inherited from effector ILC2s, and Hif1a enhances effector and memory ILC2 responses. Pharmacological inhibition of Brg1, rather than dexamethasone treatment, in acute phase is sufficient to alleviate secondary lung inflammation, highlighting Brg1 as a promising therapeutic target.

overall_design: Refer to individual Series

first: Jupei

last: Tang

first: Hanxiao

last: Sun

first: Jinxin


title: mRNA-seq time course (in parallel to ATAC-seq time course), of control or GRH-1 depleted C. elegans larvae sampled at 20oC [RNAseq_GRH1degron]

first: Dimos

last: Gaidatzis

overall_design: mRNA-seq of RNA isolated from larval C. elegans (HW2434 strain - grh-1::degron::3xFLAG), treated with either EtOH or 250 uM Auxin, and collected in a time course spanning 12-13 hours of development. Synchronized L1 animals were grown at a density of 1 animal/uL in liquid culture (S-Basal + OP50 at OD600=2.8) for 20-21 hours before splitting the culture to treat half the animals with EtOH, and the other half with 250 uM Auxin. Every hour following treatment, 2000-5000 animals were collected for RNA prep. RNA was isolated with Trizol and the Direct-zol RNA microprep kit (R2062, Zymo Research) including DNase treatment. Libraries were prepared according to the Illumina Stranded mRNA-seq protocol. Library was sequenced using NovaSeq SP 2x56bp Paired-end reads.

first: Gaidatzis

last: Dimos

first: Graf-Landua

last: Maike

first: Methot

last: Stephen P

first: Woelk

last: Michaela

first: Smith

last: A Alexander T.

first: Großhans

last: Helge


title: Mitochondrial Ferritin Inhibition Aggravates Pacing-induced Ventricular Arrhythmias after Myocardial Infarction by Promoting Cardiomyocytes Ferroptosis

first: chang

middle: yu

last: chen

address: yishan Rd 600#

institute: shanghai sixth people's hospital

summary: Our findings suggest that FtMt serves as a protective function in myocardial infarction by limiting infarct size, reducing the incidence of ventricular arrhythmias, and inhibiting ferroptosis both in vivo and in vitro. Our results also indicate that FtMt could be a promising therapeutic target for myocardial infarction.

overall_design: The RNA sequencing results of mice cardiac tissue from Sham and MI groups showed that differently expressed genes enriched in “ferroptosis”

first: Chang

last: Yuchen

first: Li

last: Shuai

last: Jingbo

first: Wang

last: Xiaoqing


title: Exploring the Functional Role of Programmed Death-Ligand 1 (PD-L1) in the  Castration-Resistant Prostate Cancer Using Transcriptomic Sequencing

city: Dalian

first: lin

last: zhong

state: Liaoning

address: West Section Lvshun South Road

institute: Dalian Medical University

summary: Prostate cancer is one of the principal malignancies threatening human health, and the development of castration resistance often constitutes a major cause of treatment failure in its management. To elucidate the potential association between programmed death-ligand 1 (PD-L1) and castration resistance in prostate cancer, we analyzed the expression levels of PD-L1 in both primary prostate cancer tissues and castration-resistant prostate cancer (CRPC) specimens as well as in corresponding cell lines. Our findings revealed that, compared to adjacent non-cancerous tissue, PD-L1 expression was unexpectedly lower in primary prostate cancer but notably elevated in CRPC tissues and cells. In CRPC cell lines where PD-L1 was knocked down, a significant suppression of proliferation and metastatic potential was observed. Historically, research has primarily focused on extracellular signaling pathways involving PD-L1 while neglecting its intracellular signaling functions. Based on this background and our preliminary results, employing next-generation sequencing technology, we investigated the impact of PD-L1 knockdown on intracellular signaling pathways in castration-resistant cells. The results demonstrated that PD-L1 knockdown led to alterations in gene expression within several signaling pathways, including those involved in cell surface interactions, regulation of natural killer cell activity, and sodium channel regulatory activity. More intriguingly, PD-L1 knockdown also appeared to induce changes at the level of alternative splicing in multiple genes. This study provides a theoretical basis for understanding the intracellular signaling mediated by PD-L1 and offers valuable insights into the mechanisms underlying castration resistance in prostate cancer.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for BCPAP cells with PD-L1 knockdown or not

first: Lin

last: Zhong

first: Pengxin

last: Zhang

first: Jun

last: Mao

first: Lianhong

last: Li


title: Retinoid X Receptor as a Mediator of Post Stroke Recovery by Reversing Age-Associated Phenotypes of Microglia/Hematogenous Macrophages

first: Shun-Ming

last: Ting

address: 6431 Fannin

department: Neurology

institute: The University of Texas Health Science Center at Houston

summary: After stroke, microglia/blood-derived macrophages, together MF, clear dead cells and cellular debris in the infarcted brain through phagocytosis as an essential part of the repair/recovery process. However, the phagocytic capability of MF declines with age. Furthermore, aged MF become overactivated in response to stroke, enhancing secondary brain injury. Now, demonstrate that by reversing the age-related dysfunctions in MF through activating the retinoid x receptor (RXR), the recovery after stroke in the aged brain could be improved. Using RNA sequencing, we compared the transcriptomes between MF isolated from the brains of young and aged mice. We observed higher levels of pro-inflammatory genes and lower levels of phagocytosis-facilitating genes (Cd206, Cd36) expressed by aged MF. Meanwhile, the treatment with RXR agonist bexarotene (BEX) reversed the signature genes of microglia aging in the aged MF. With the in vivo phagocytosis model, we showed that BEX enhanced the phagocytic ability of aged MF. Using mouse MCAo stroke model, we established that BEX improved sensorimotor and cognitive recovery after MCAo in a myeloid-RXRa-specific and -dependent manner. In conclusion, we showed that activating RXRa partially restores age-related MF dysfunctions and that RXRa deficiency in MF limits the therapeutic effect of RXR in improving post-stroke recovery in the aged brain

overall_design: RNA-seq profiling of microglia/macrophages isolated from young (2-4 months old) and aged (18-20 months old) mice in response to RXR agonist bexarotene (BEX). The RNA-seq profiling of microglia/macrophages isolated from aged mice at Day3 after ischemic stroke (MCAo) treated with vehicle or BEX is also included.

first: Jaroslaw

last: Aronowski

first: Xiuron

last: Zhao

first: Guanghua

last: Sun

first: Xian

last: Chen


title: Analyze the transcriptional signature of kidney glomerular cells in mice

city: Firenze

first: Giulia

last: Carangelo

address: Viale Pieraccini 6

country: Italy

institute: University of Florence

summary: Podocytes and podocyte progenitors are interdependent components of the kidney's glomerular structure, with podocytes forming the glomerular filtration barrier and progenitors being key players in podocyte regeneration during pathophysiological processes. Both cell types are subjected to constant mechanical forces, whose alterations can initiate podocytopathy and worsen glomerular injury.

overall_design: Transcriptional signature of glomeruli isolated from wild type  mice.

first: Maria

middle: E

last: Melica

first: Benedetta

last: Mazzinghi

first: Laura

last: Lasagni


title: Single-cell multiome profiling reveals pancreas cell type-specific gene regulatory programs of type 1 diabetes progression [snATAC-seq]

city: La Jolla

first: Rebecca

last: Melton

address: 9500 Gilman Dr

institute: University of California, San Diego

summary: Genomic changes in the pancreas across stages of type 1 diabetes (T1D) progression are poorly understood. In this study, we performed single nucleus RNA-seq and ATAC-seq in whole pancreas samples obtained from non-diabetic, autoantibody-positive, and T1D organ donors. Genomic profiles from 480,154 cells were mapped to 18 pancreatic cell types and sub-types, and we identified altered abundance of beta, delta, immune, and exocrine sub-type cells in T1D progression. Beta, delta, acinar, stellate, and other cell types had marked gene expression changes in both autoantibody-positive and recent-onset T1D together with key epigenomic drivers of altered cell type-specific gene activity. Combining cell type-specific changes in T1D progression with genetic association data revealed cellular pathways of T1D risk, including antigen presentation and interferon signaling in beta cells and metabolism in acinar cells. We identified changes in predicted cell signaling in the pancreas in T1D, including immune-beta signals associated with increased disease risk.  Finally, we observed several ligands with altered signaling to beta cells in T1D that had protective effects on beta cell regulation in vitro. These results revealed genomic changes in the pancreas driving T1D risk and progression, observations that form the basis for future therapeutic targets for disease intervention.

overall_design: Multi-modal profiling of 32 pancreatic donors including non-diabetic auto-antibody negative, non-diabetic auto-antibody positive and type 1 diabetic individuals form the nPOD biorepository. 10X snATAC-seq was performed for 30 donors across 32 libraries. 10X snRNA-seq was performed for 32 donors across 33 libraries. Paired 10X multiome: RNA + ATAC sequencing was performed for 8 donors across 8 libraries.

first: Kyle

last: Gaulton


title: Single-cell multiome profiling reveals pancreas cell type-specific gene regulatory programs of type 1 diabetes progression [snRNA-seq]


title: Rapid evolution of gene expression patterns in flowering plants

city: Würzburg

first: Alexander

last: Gabel

address: Josef-Schneider-Str. 2 / D15

institute: Helmholtz Institute for RNA-based Infection Research

summary: Phenotypic differences between species are largely driven by changes in both protein-coding sequence and gene expression. The evolutionary history of angiosperms (flowering plants) is characterised by a highly accelerated rate of diversification, which Darwin referred to as an "abominable mystery". Here we show, by analysing the transcriptomes from eight organs across seven species, that angiosperm protein-coding gene expression patterns evolve rapidly: within 45 million years, expression levels of orthologous genes diverged so strongly that they are more similar between different organs within a species than between what are considered homologous organs from different species. This finding differs from previous observations in mammals, which demonstrated that organ-dependent gene expression levels are largely conserved. Among the angiosperm organs, meristems and leaves show the highest degree of expression conservation, whereas stamen and pollen transcriptomes diverge rapidly. Examining changes in the expression level of functionally related genes, we found low rates for those involved in key cellular, metabolic and developmental processes. In contrast, particularly high rates were observed for genes that are involved in the response to endogenous and external stimuli, presumably reflecting an adaptive response of flowering plants to ever-changing environments. Our work reveals that the evolution of gene expression progresses at different rates in angiosperms and mammals, and provides a comprehensive resource to perform cross-kingdom comparative studies of transcriptome evolution.

sample_organism:
Arabidopsis thaliana
Medicago truncatula
Brachypodium distachyon
Tarenaya hassleriana
Arabidopsis lyrata
Eutrema salsugineum
Capsella rubella

overall_design: We identified and quantified the expression of novel coding and non-coding RNA transcripts/genes of seven land plant genomes based on deep, organ-specific, ribo-depleted developmental RNA-Seq data.

first: Christoph

last: Schuster

first: Hajk-Georg

last: Drost

first: Ivo

last: Grosse

first: Ottoline

last: Leyser

first: Elliot

middle: M

last: Meyerowitz


title: Single-cell multiome profiling reveals pancreas cell type-specific gene regulatory programs of type 1 diabetes progression [multiome]


title: Analyze the transcriptional signature of human primary culture of CD133+ CD24+ renal progenitor cells

summary: Podocytes and podocyte progenitors are interdependent components of the kidney's glomerular structure, with podocytes forming the glomerular filtration barrier and progenitors being key players in podocyte regeneration during pathophysiological processes. Both cell types are subjected to constant mechanical forces, whose alterations can initiate podocytopathy and worsen glomerular injury. Despite this, the specific mechanosensors and mechanotransduction pathways involved in their response to mechanical cues remain only partially explored. The role of Piezo1 silencing is studied in this dataset. In this dataset we analyzed 3 primary cell culture treated with LNA scramble or LNA Piezo1 Gapmer.

overall_design: 3 primary cell culture were transfected with LNA scramble or LNA Piezo1 Gapmer antisense oligonucluotide.

first: Roberto

last: Semeraro


title: C. elegans display antipathy behavior towards food after contemporaneous integration of nutritional needs and dietary lipid availability. [neuronal]

city: Los Angeles

first: Sean

middle: Patrick

last: Curran

state: CA

address: 3715 McClintock Ave #350

department: Geronotology

institute: University of Southern California

summary: Organisms utilize sophisticated neurocircuitry to select optimal food sources within their environment. Methylobacterium is a lifespan-promoting bacterial diet for C. elegans that drives faster development and longevity, however after ingestion, C. elegans consistently choose any other food option available.  A screen for genetic regulators of the avoidance behavior toward Methylobacterium identified the AWB and AWC sensory neurons and the odr-1 guanylate cyclase expressed exclusively in those four ciliated neurons as mediators of the antipathy response. Metabolic profiling of the Methylobacterium diet reveals a macromolecular profile enriched in saturated fats and here we show that C. elegans sense and integrate signals related to the type of ingested lipids that subsequently cues food-related behaviors. Moreover, disruption of endogenous lipid metabolism modifies the intensity of antipathy toward Methylobacterium which suggests that the current state of lipid homeostasis influences food preference. Enhanced expression of the sphingolipid degradation enzyme Saposin/spp-9 enhances antipathy behaviors and activation of the sphingosine rheostat and more specifically modulation of the bioactive lipid mediator sphingosine-1-phosphate (S1P) acts as a signal to promote avoidance of Methylobacterium. Taken together, our work reveals that C. elegans modify food choices contemporaneously based on the availability of dietary lipids and the ability to metabolize dietary lipids.

overall_design: For neuronally-enriched RNAseq, we used PY2417 oyls44[odr-1::RFP+lin(+)] to see AWB and AWC neuronal gene expression changes in response to either OP50 or Methylobacterium.

first: Nicole

last: Stuhr

first: Carmen

last: Ramos

first: Chris

middle: D

last: Turner

middle: A

last: Soukas

middle: P


title: C. elegans display antipathy behavior towards food after contemporaneous integration of nutritional needs and dietary lipid availability. [whole animal]

overall_design: For whole animal RNAseq, we asked whether or not gene expression changes between WT and odr-1lf mutants raised on OP50 or Methylobacterium (Red).


title: Effect of miR-628-3p overexpression on gene expression in HCC cells

city: Chongqing

first: Lele

last: Liu

address: Yuzhong District Shiyou Road Street

institute: Chongqing Medical University

summary: In order to investigate the effect of miR-628-3p overexpression on the occurrence and development of HCC, we added miR-628-3p mimics to Huh7 cells, and constructed MHCC97H cells with stable overexpression of miR-628-3p. Then, The RNA-seq data of Huh7 mimic NC/mimics cells and MHCC97H Vector/pGreen-628 cells were subjected to gene expression profiling

overall_design: RNA-seq data of Huh7 miR-628-3p mimic transfected cells and control cells (HUh7-MN/HUh7-M), MHCC97H miR-628-3p overexpression cells and empty vector control cells (P-97H/ p-97H-628) were analyzed for gene expression profiling

first: Jie

last: Xia


title: Neddylation regulate the development of glutamatergic neurons

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

institute: Universitaetsmedizin Goettingen

summary: The development and function of synapses is orchestrated by a plethora of regulatory mechanisms hierarchically controlling gene expression to protein function. Expanding the proteome, protein post-translational modification are additional key events in neu-rons. In such context, the modification of protein with ubiquitin-like modifier (Ubls) such as the SUMOs, but also other Ubls like NEDD8, have been revealed as major steps in regulating neuronal development and synaptic transmission, either by directly acting lo-cally at synapse or via nuclear-mediated mechanism and the regulation of gene expres-sion.  In the present work, we focus on NEDD8 and characterized neuronal morphology, synap-tic transmission and the transcriptional landscape of NEDD8 deficient hippocampal au-taptic neurons. While we observed no major alteration in neuronal morphology, NEDD8-deficient neurons have a decreased pool of ready-releasable synaptic vesicles. This de-fect was likely caused by an imbalance in the expression of vGLUT1/vGLUT2 and de-creased endophilin1 level. Indeed, transcriptome analysis revealed profound defects in the expression of key transcriptional regulators determining glutamatergic neurodevel-opment, indicating that NEDD8 foster the expression of glutamatergic cell fate.

overall_design: We generated a nedd8 conditional knock-out. We cultured primary hippocampal neurons and infected these neurons with either an RFP-expressing virus (as control) or a CRE-expressing virus to ablate NEDD8 expression. After 12 days in culture, RNA were extracted from these culture and their transcriptome was analyzed.

first: Josefa

last: Torres

first: Zehra

last: Vural

first: Maksims

last: Fiosins

first: Fritz

last: Benseler

first: Christan

last: Rosenmund

first: Stefan

last: Bonn

first: Silvio

last: Rizzoli

first: JeongSeop

last: Rhee

first: Nils

last: Brose

first: Marilyn

last: Tirard


title: Gene Expression Profile of Radiation Therapy Resistant BRAFV600E Pediatric Gliomas

city: San Antonio

first: Hanzhou

last: Wang

address: 8403 Floyd Curl Drive, MSC 7784

institute: UT Health San Antonio

summary: Inhibitors of the MAPK pathway (MAPKi) have shown significant activity in treatment of childhood BRAF-activated brain tumors. However, for tumors harboring BRAFV600E mutations, the drugs are rarely curative, and patients can become refractory to treatment. Combining MAPKi with low dose X-ray therapy (XRT) has the potential to improve the cure rate, but development of XRT resistance poses a major challenge.  To understand the mechanisms of radiation resistance in BRAFV600E type pediatric low-grade gliomas, radiation resistance models were developed by using BT-40 pediatric low-grade glioma (PLGG) PDX model harboring BRAFV600E mutation. RNA sequencing was performed to determine the gene expression profile of primary tumors and resistant tumors.  Each tumor tissue was transplanted to 3 scid mice respectively. When tumor volume reach ~0.3~0.6 cm3, tumor tissue (from three mice, triplicates) were collected  and were snap-frozen in liquid nitrogen. RNA was isolated and applied to subsequent 100bp paired read sequencing run with Illumina NovaSeq 6000 platform at 100 bp paired-end module.

overall_design:
Each tumor tissue was transplanted to 6-8 weeks old female scid mice.  Tumor tissue were harvested when tumor size reach 0.3~0.6cm^3, RNA was isolated and applied to subsequent 100bp paired read sequencing run with Illumina NovaSeq 6000 platform at 100 bp paired-end module.
BT40: Classified as PDX, primary. This sample group represents the primary model of pediatric glioma without any treatment.
BT40X: Classified as PDX, X-radiation therapy resistant. This group includes samples from the primary model that have been exposed to radiation therapy and have exhibited resistance.

first: Fuyang

last: Li

first: Kathy

last: Bondra

first: Zhao

last: Lai

first: Peter

last: Houghton

first: Yidong

last: Chen


title: TLR4-dependent fibroblast-monocyte axis in tumor-draining lymph nodes contributes to metastasis in triple-negative breast cancer

first: Angela

last: Riedel

state: Bavaria

address: Josef-Schneider-Straße 2

department: Mildred-Scheel-Nachwuchszentrum (MSNZ) für Krebsforschung

institute: University Hospital Würzburg

summary: Triple-negative breast cancer (TNBC) is the most aggressive form of BC and despite improvements in neoadjuvant treatment with immune checkpoint blockade (ICB) targeting PD-1, response rates vary, and patients relapse with metastatic disease. Using human samples and mouse models, we show that myeloid cells, particularly monocytes, increase in aggressive TNBC draining lymph nodes (TDLN) showing T-cell suppressive capacity via PD-L1 and iNOS. Tumor-induced TLR4 ligands reprogrammed TDLN fibroblastic reticular cells (FRCs) through TLR4 activation to induce the recruitment of monocytes via CCL2 and CCL7 in vascularized and T-cell areas. Indeed, monocytes expressing the receptor of CCL2/7 CCR2 home to and colocalize with FRC-rich niches. The local inhibition of this recruitment axis at the TDLN site, either through CCR2 or TLR4 inhibition, in combination with PD-1 blocking, resulted in reduced LN and distant lung metastasis in mouse models. A subset of TNBC patients with worse survival was stratified using TLR4 ligands, including TNC, S100A9, and FN1. Our results thus demonstrate a novel mechanism through which metastatic TNBC tumors reprogram the TDLN-niche to facilitate PD-L1-mediated immune evasion that precedes and drives metastasis. We thereby provide an opportunity to improve the efficacy of ICB in TNBC patients and to use the TDLN or our primary tumor signature as predictive biomarkers.

overall_design:
Axillary lymph nodes of 8 weeks old female BALB/C mice were sorted to analyze different cell populations from breast cancer mice (4T1 model, 67NR model) and control mice (naive). A minimum of 3 mice were analyzed for each condition.
Cell types analyzed in breast cancer tumor mice: T-cells, myeloid cells and stromal cells (endothelial cells and fibroblasts)
Cell types analyzed in control (naïve): T-cells, myeloid cells, stromal cells (endothelial cells and fibroblasts), B-cells and NK cells

first: Greta

last: Mattavelli

first: Moutaz

last: Helal

first: Anna

last: Frank

first: Emily

last: Riemer

first: Saskia-Laureen

last: Herbert

first: Kilian

last: Mielert

first: Tanja

last: Schlaiß

first: Jonathan

last: Swietlik

first: Laura

last: Kindl

first: Marion

last: Krafft

first: Emilia

last: Stanojkovska

first: Ute

last: Albert

first: Murilo

last: Delgobo

first: Arpa

last: Aintablian

first: Manfred

middle: B

last: Lutz

first: Felix

last: Meissner

first: Gustavo

last: Ramos

first: Thordur

last: Oskarsson

first: Leo

last: Rasche

first: Andreas

last: Rosenwald

first: Achim

last: Wöckel


title: Enhancing Retromer Complex Stability Ameliorates Synaptic Dysfunction in a Mouse Model of Alzheimer's Disease

city: Linköping

first: David

last: Ramonet

address: US campus - BKV floor 10

department: BKV

country: Sweden

institute: University of Linköping

summary: Synaptic dysfunction is an early  hallmark of Alzheimer’s disease, characterized by the disruption of synaptic transmission and plasticity. Central to these processes is endosomal trafficking, mediated by the retromer complex, which orchestrates the movement of vesicle contents for recycling to the plasma membrane, return to the Golgi, or degradation. Variants of VPS35, the cargo recognition component of the retromer complex, have been linked to neurodegenerative diseases, including Parkinson’s disease (PARK17, D620N mutation) and Alzheimer’s disease (L625P mutation). While substantial research has focused on Parkinson's, the role of VPS35 in Alzheimer’s has been less explored. This study investigates the acute neuroprotective effects of retromer-stabilizing compounds in the 5xFAD mouse model of Alzheimer’s. Our results reveal that stabilization of the retromer complex not only mitigates pathogenic Aβ production mechanisms but also compensates for early synaptic dysfunction and microglial activation. Specifically, we observed significant modulation of genes involved in long-term potentiation and a reduction in abnormal retromer-associated cargos.  These findings highlight the potential of retromer stabilisation as atherapeutic strategy to address fundamental pathological pathological processes in Alzheimer's disease.

overall_design: To investigate the pathophysiological changes in AD that can be targeted by retromer stabilization, we delivered two tool compounds (R55 and R33) and vehicle intracranially by sterotaxic microinjection to one hemisphere of 5xFAD transgenic mice. To verify the effects of the surgery, the other hemisphere was used. We collected RNA from the cortex of both hemispheres, built a library and performed RNAseq.


title: Cryptic splice sites generate heterogeneous EZH2 isoforms with distinct functions in embryonic development [RNA-seq]

city: Shenzhen

first: Zhihua

last: Wang

address: No. 12, Langshan Road, Xili Street, Nanshan District, Shenzhen

department: Shenzhen Key Laboratory of Cardiovascular Disease

institute: Fuwai Hospital Chinese Academy of Medical Sciences, Shenzhen

summary: A novel Ezh2 variant was identified, we named Ezh2b, which is lost 27-nt region in the end of exon3, has different functions on embryonic development in mouse compared to Ezh2 with 27-nt region (namely as Ezh2a). Here, we apply transcriptome sequencing to explore the underlying molecular mechanisms.

overall_design: The embryonic fibroblasts (MEF) were isolated from Ezh2amut, Ezh2bmut and respective littermate wild-type control mice. The MEFs  were cultured in DMEM high-glucose medium . DMEM supplemented with 10% fetal bovine serum (FBS, Gibco, USA), 100 U/mL penicillin, and 100 μg/ml streptomycin. Utilizing the Hyperactive® Universal CUT&Tag Assay Kit for Illumina (TD903), we performed CUT&Tag experiments as follows: MEFs were harvested at room temperature and incubated with ConA Beads for 10 minutes. They were then incubated with anti-EZH2 (CST, 5246),  anti-H3K27me3 (CST, #9733) antibodies overnight at 4°C. On the next day, the samples were incubated with a secondary antibody at room temperature for 1h, followed by incubation with pA/G-Tnp for 1h.  After DNA purification with the MinElute kit, and the PCR was performed to amplify the library for 12 cycles and libraries were purified with the MinElute kit. Amplified  libraries were sequenced on the Illumina Novaseq 6000 platform.

first: Ningning

last: Guo

first: Qingqing

last: Yan

first: Qiuxiao

first: Hongchao

last: Zhan

first: Jian

last: Lv

first: Yu

last: Fang

first: Jiajie

last: Li

first: Junmei

first: Xiao

last: Ma


title: Ablation of hematopoietic stem cell derived adipocytes reduces tumor burden in a syngeneic mouse model of high grade serous carcinoma

city: Aurora

first: Andrew

last: Goodspeed

state: CO

address: 12801 E 17th Ave, Mail Stop 8303

institute: University of Colorado Anschutz Medical Campus

summary: Introduction: The purpose of this study is to examine the influence of hematopoietic stem cell derived adipocytes (HSCDAs) on the proliferation and metastasis of high-grade serous carcinoma (HGSC), the most common and aggressive type of ovarian cancer. HSCDAs begin as myeloid cells that traffic to adipose tissue and differentiate a highly inflammatory subtype of adipocytes. HSCDAs accumulate within visceral adipose depots. HSCDA production is increased in ovariectomized mice, suggesting that HSCDAs are likely to extensively accrue in postmenopausal patients. We hypothesize that HSCDAs promote HGSC progression and establish a pro-tumoral niche within peritoneal adipose tissues such as the omentum. Methods: We sorted and differentiated primary human adipocyte precursors into HSCDAs and CMAs and examined cytokine secretion in adipocyte conditioned media by ELISA. We incubated human HGSC cells (PEO1, OVCAR4, and OVCAR8) in conditioned media and assayed proliferation. We incubated conditioned media on PEO1 ovarian cancer cells and analyzed protein expression and phosphorylation by reverse phase protein array (RPPA). Finally, we implanted mouse ID8 HGSC cells into syngeneic HSCDA Deficient (experimental) and Proficient (control) mice. We compared tumor size and intraperitoneal spread. We also measured the adipokine milieu of ascites fluid by ELISA, tumor transcription by RNA-Seq, and immune infiltration by IHC. Results: HSCDA cells secreted elevated amounts of IL-6 and IL-8. In proliferation assays, HGSC lines showed varying growth rates in HSCDA or CMA media. RPPA showed that PEO1 cells incubated in HSCDA media upregulated markers of epithelial to mesenchymal plasticity (EMP) and pro-survival phosphoprotein signaling. Conversely, PEO1 cells in HSCDA media downregulated multiple tumor suppressors. Finally, we observed that ablation of HSCDAs in mice reduced tumor burden. RNA-Seq of bulk omentum tumor from HSCDA Deficient mice had higher TLR and IFN signaling, and lower fatty acid oxidation pathway expression than Proficient mice. Densities of dendritic cells (DC) and natural killer (NK) cells was reduced in tumors in HSCDA Deficient mice, and spatial analysis showed fewer DCs, NKs, and B-cells near tumor cells in HSCDA Deficient mice. Conclusion: Our data suggest that HSCDAs can promote HGSC survival and plasticity while downregulating tumor suppressors, and also may alter the peritoneal adipose immune and metabolic environment to promote HGSC progression.

overall_design:
To examine the effect of hematopoietic stem cell derived adipocytes (HSCDAs) on ovarian cancer progression and metastasis in vivo, we generated female mice that are Proficient (CONTROL GROUP) or Deficient (EXPERIMENTAL GROUP) for HSCDA production. The mice are generated by bone marrow transplant from DONOR mice that have an Adiponectin promoter with a reporter gene (for CONTROL Proficient) or an Adiponectin promoter with an Attenuated Diphtheria Toxin (DTA, for EXPERIMENTAL Deficient) into RECIPIENT C57BL6 mice that have had their bone marrow ablated by x-ray irradiation. The HSCDA Proficient mice can make both mesenchymal and HSC derived adipocytes. The HSCDA Deficient mice can only make mesenchymal adipocytes.
We waited six weeks for the mice to recover from bone marrow transplant, and then implanted ovarian cancer cells by intraperitoneal injection. The cells are ID8 Tp53-/-, Brca2 -/-. After 39 days, all mice were sacrificed and tumor burden was assessed. Bulk omentum tumors were homogenized and RNA-Seq was performed on CONTROL/Proficient (N=4) and EXPERIMENTAL/Deficient (N=4) tumor RNA.

first: Elizabeth

middle: R

last: Woodruff

first: Courtney

last: Bailey

first: Joanne

last: Maltzahn

first: Timothy

last: Sullivan

first: Meher

last: Boorgula

first: Dwight

last: Klemm

first: Benjamin

middle: G

last: Bitler

first: Zachary

last: Watson


title: Cryptic splice sites generate heterogeneous EZH2 isoforms with distinct functions in embryonic development [CUT&Tag]

first: Zhihua

last: Wang

first: Ningning

first: Qingqing


first: Angela

last: Riedel

overall_design:
Axillary lymph nodes of 8 weeks old female BALB/C mice were OCT embedded and cutted to perform spatial  analysis (Visium_10X_genomics) of  different cell populations from breast cancer mice (4T1 model, 67NR model) and control mice (naive).  2 mice were analyzed for each condition.
All axillary lymph node cell types were spatially analyzed. LNs were stained for immunoflurescence with anti-mouse CD3, anti-mouse CD11b and anti-mouse Collagen I.

first: Greta

last: Mattavelli

first: Moutaz

last: Helal

first: Anna

last: Frank

first: Emily

last: Riemer

first: Saskia-Laureen

last: Herbert

first: Kilian

last: Mielert

first: Tanja

last: Schlaiß

first: Jonathan

last: Swietlik

first: Laura

last: Kindl

first: Marion

last: Krafft

first: Emilia

last: Stanojkovska

first: Ute

last: Albert

first: Murilo

last: Delgobo

first: Arpa

last: Aintablian

first: Manfred

last: Lutz

first: Felix

last: Meissner

first: Gustavo

last: Ramos

first: Thordur

last: Oskarsson

first: Leo

last: Rasche

first: Andreas

last: Rosenwald

first: Achim

last: Wöckel


first: Angela

last: Riedel

overall_design: Fibroblastic reticular cells (cell line) were treated with conditioned media (CM) from either control cells (CCM, FRC cell line) or tumor cells (TCM, 4T1 and 67NR cell lines)

first: Greta

last: Mattavelli

first: Moutaz

last: Helal

first: Anna

last: Frank

first: Emily

last: Riemer

first: Saskia-Laureen

last: Herbert


title: Transcriptomic landscape of human stromal cells upon therapy-induced senescence and/or senotherapeutic intervention with PQQ

first: Yu

last: Sun

address: 320 Yueyang Rd, Life Sciences Building A #1508

department: Shanghai Institute of Nutrition and Health

institute: Chinese Academy of Sciences

summary: In higher eukaryotes, cellular senescence represents a significantly conserved stress response triggered by acute or chronic damage signals. In humans, senescent cells can accumulate in multiple tissues and organs at different rates, from 2- to 20-fold when comparing young (<35 years) to old (>65 years) healthy donors. The pathogenic role of cellular senescence in the vast majority of age-related diseases can be explained by the senescence-associated secretory phenotype (SASP). Pyrroloquinoline quinone (PQQ) is a water-soluble vitamin-like compound exhibiting strong antioxidant capacity, and was first discovered to function as a cofactor for oxidoreductases in bacteria. The effects of PQQ largely rely on its radical-scavenging activity, which has been demonstrated to be 7.4-fold higher than that of vitamin C. However, the specific mechanism underlying its antioxidant function remains largely unclear. Although PQQ cannot be synthesized in mammals, it is available in foods such as milk, vegetables and meat, making it an ideal agent for alleviating oxidative stress-induced diseases. The purpose of this study was to investigate whether PQQ exerts certain effects on cellular senescence-associated phenotypes, specifically the SASP. We profiled the influence of PQQ on the transcriptome-wide expression of human stromal cells that were made senescent by genotoxicity in vitro. Together, this is the first report to determine the possibility of using PQQ as a source of antioxidant senomorphics for senescence-modulation and explore its potential in anti-aging pipelines, particularly pharmacological development for future geriatric medicine.

overall_design: High-throughput RNA-seq examination of genome-wide transcriptional alterations of human stromal cells that underwent treatment by the chemotherapeutic agent bleomycin and/or exposure to PQQ.

first: BIrong

last: Jiang


title: Complete stranded RNA profiling during early mouse gonad development

city: Hong Kong

first: Wai-Yee

last: Chan

address: Rm 123, LKS integrated Biomedical Sciences Building

department: School of Biomedical Sciences

institute: The Chinese University of Hong Kong

summary: The sexual dimorphism in mouse gonads becomes evident at around E12.5 followed by initiation of germ cell development. Previous research has been focusing on protein-coding genes. Accumulating evidence has been showing the active involvement of various ncRNAs in development. However, we are still far from having a complete picture of the RNA regulatory networks in early gonadal development. In this study, we performed sequoia complete stranded RNA-Seq using pooled total RNAs from mouse male and female gonads at E11.5, E12.5, E13.5, and E14.5, respectively. By adding poly(A) tails and unique molecular identifiers (UMI) to all stranded RNAs, we were able to quantify short- and long-stranded RNAs with or without poly(A) tails in one preparation for each time point. This is the first profiling of complete stranded RNAs during early mouse gonad development, specifically emcompassing critical stages such as sex determination and initiation of germ cell development. with this advanced sequencing technique, we aim to gain a comprehensive understanding of RNA landscape and regulatory networks involved in these critical developmental processes.

overall_design: Embryos were collected from pregnant C57BL/6J wild-type mice at E11.5, E12.5, E13.5 and E14.5. The XX and XY gonads were dissected and pooled together in equal numbers for total RNA extraction with Trizol reagent, followed by SEQuoia Complete Stranded RNA-Seq. Each time point contained at least 6 embryos. Long RNA and small RNA expression profiles were compared across the four-time points.

first: Fanghong

last: OU

first: Zhangting

last: WANG

first: See

middle: W

last: CHAN

first: Kai

last: MIU

first: Jinyue

last: LIAO

first: Hoi

last: SUN


title: MiRNA expression profile after overexpression of LOC102163816 in porcine granulosa cells

city: Changchun

first: Caomeihui

last: Shen

address: No. 5333 Xi'an Road, Lvyuan District

institute: Jilin University

type: Non-coding RNA profiling by high throughput sequencing

summary: Sequencing of miRNA expression profiles after overexpression of LOC102163816 in pig granulosa cells

overall_design: Porcine granulosa cells are collected from the vector control group and the overexpression group. Then miRNA sequencing and differential analysis were performed.


title: PPARg acetylation governs mammary adenocarcinoma tumor growth via acetylated residues that determine DNA sequence-specific binding

city: Wynnewood

first: Xuanmao

last: Jiao

state: PA

address: 100 E Lancaster Ave, LIMR R234

department: Pennsylvania Cancer and Regenerative Medicine Research Center

institute: Baruch S. Blumberg Institute

summary: Peroxisome proliferator-activated receptorg (PPARg), which is expressed in a variety of malignancies, governs biological functions through transcriptional programs. Defining the molecular mechanisms governing selection of canonical versus non-canonical PPARg binding sequences may provide the opportunity to design regulators with distinct functions and side effects.  PPARg is acetylated at multiple residues including K268/293 in mouse Pparg2 and the conserved lysine residues (K154/155) in mouse Pparg1.  Herein, the PPARg acetylated residues K154/155 were shown to be essential for growth control, and the induction of transcriptional modules governing growth factor signaling, cellular apoptosis and autophagy. The K154/155 residues determined the selection of genome wide DNA binding sites, altering the selection from canonical to non-canonical (C/EBP) DNA sequence specific binding. The gene signature reflecting the acetylation-dependent genomic occupancy provided predictive value in patient survival outcome. Pparg1 participates in ErbB2-induced tumor growth and inflammation and represents a relevant target for therapeutic coextinction.

overall_design: Chromatin immunoprecipitation DNA-sequencing (CHIP-Seq) was used to determine how PPARg K154/155Q acetylation deficeint mutant influences the binding of PPARg to genomic DNAs. The flag tagged wild PPARg and PPARg K154/155Q mutant were stable tranfected into NeuT transformed MCF10A cells respectively. Anti-flag IP were used to pull down wildtype PPARg or PPARg K154/155Q mutant bound DNA.

first: Lifeng

last: Tian

first: Joanna

last: Achinger-Kawecka

first: Susan

last: Clark

first: Richard

last: Pestell


title: Compartment Specific Mechanical Loading of Bi-Layered Osteochondral Micro-Tissues in a Joint-on-Chip System suggests routes for Osteoarthritis pathogenesis investigation

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

institute: University of Basel

summary: In this work we engineered an osteochondral unit (OCU) on-chip model where osteoarthritis (OA) phenotype is recapitulated through the application of hyper-physiological mechanical loading. After a functional and biological validation of the device, we aimed to better characterize the diversity of the human articular chondrocytes (hACs) population present in our in vitro model and identify subpopulations responsible for the pathological loading response. As a method, we applied single-cell RNA sequencing (scRNA-seq) to hACs from both on-chip single cultures and co-cultures with bone marrow derived mesenchymal stromal cells (bmMSCs), i.e. in osteochondral construct, and either exposed or not to cyclic mechanical loading.

overall_design:
Single cell RNA-seq (scRNA-seq) was performed on hACs after 21 days of culture on-chip (i.e. 14 days of static maturation and 7 days of mechanical stimulation, with constructs cultured statically for 21 days used as controls). hACs were cultured either in a single culture (in cartilaginous constructs) or in a co-culture with bmMSCs (in osteochondral constructs).
***Submitter states that raw files are not provided due to data sensitivity***

first: Andrea

last: Mainardi

first: Anastasiya

last: Börsch

first: Paola

last: Occhetta

first: Robert

last: Ivanek

first: Martin

last: Ehrbar

first: Lisa

last: Krattiger

first: Philipp

last: Oertle

first: Marco

last: Loparic

first: Ivan

last: Martin

last: Rasponi

last: Barbero


title: CAR-T cells shape the immunological potential of the tumor microenvironment

city: Boston

first: Julia

last: Frede

address: 450 Brookline Ave.

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary: CAR-T cells lose effectiveness over time and subsequent lines of immunotherapy become increasingly less potent. Investigating patients from two independent clinical trials at single cell resolution, we demonstrate that CAR-T cell treatment drives bystander CD8+ T lymphocytes along the differentiation path, which initially supports a clonal anti-tumor immune response, but ultimately results in terminal exhaustion, reduced potential for self-renewal and sustained depletion of the tumor-reactive T cell repertoire. The immune environment changes orchestrated by CAR-T cells result in reduced immune capacity, which could potentially diminish responses to other immunotherapies, such as response to checkpoint blockade. We describe the transcriptional modules that regulate plasticity of the T lymphocytic compartment and identify Tim3/Gal9 and CD27/CD70 as two crucial interactions of the cell-cell communication network that regulates immune capacity. The ability of the CAR-T cells to shape a regulatory immune microenvironment may explain why repeated immunotherapies become increasingly less successful, even when targeting distinct antigens. Our studies provide a framework for assessing and manipulating the ‘mileage’ of the immune system as a predictive marker and a therapeutic opportunity.

overall_design:
Single cell expression profiles of 4 patients with relapsed/refractory multiple myeloma (RRMM) treated with BCMA-directed CAR-T cells profiled with 10X Genomics technology (5' expression profiling) and single cell expression profiles of T cells and CAR-T cells isolated from RRMM 24 patients treated with BCMA-directed CAR-T cells profiled with plate-based scRNA-Seq (Smartseq2).
Submitter declares that the raw data is not provided due to patient privacy concerns.

last: Poller

first: Kayleen

last: Shi

first: Hannah

last: Stuart

first: Noori

last: Sotudeh

first: Claire

last: Havig

first: Klothilda

last: Lim

first: Caroline

last: Wiggers

first: Eugene

middle: Y

last: Cho

first: Tushara

last: Vijaykumar

first: Johannes

last: Waldschmidt

first: Monica

middle: S

last: Nair

first: Praveen

last: Anand

first: Valeriya

last: Dimitrova

first: Anna

last: Montanaro

first: Nikhil

last: Munshi

first: Kenneth

last: Anderson

first: Nathan

first: Shari

last: Kaiser

first: Marc-Steffen

last: Raab

first: Noopur

last: Raje

first: Birgit

last: Knoechel

first: Jens

last: Lohr


title: LKB1 regulates adipose tissue ILC2 function through regulating mitochonrial

city: Shanghai

first: Youqin

last: Zhang

address: No. 280, Chongqing South Road

institute: NewsMORE+  Shanghai Institute of Immunology

summary: Our study represents LKB1 defects lead to the loss and dysfunction of adipose tissue ILC2s.And we found that LKB1 regulate ILC2s homeostasis and cytokines function in a cell-intrinsic manner.In high-diet-fed mice,LKB1 in ILC2s protects against metabolic disturbances and fat fibrosis.LKB1 deficient in ILC2 impaired the oxidative phosphorylation and led to mitochondria loss though more mitophagy.

overall_design: mRNA profiles of VAT ILC2s  from 14-week old wild-type male mice fed with normal diet(ND) or high-fat-diet(HFD) for 8 weeks starting at 6 weeks old

first: Lei

last: Shen

first: Jiping

last: Sun


overall_design: mRNA profiles of VAT ILC2s  from 8-week old R5/+(WT) and R5/+Stk11f/f(KO) male mice


title: Lobe-less, a long noncoding RNA that regulates Drosophila mushroom body morphogenesis

city: Sapporo

first: Masanao

last: Sato

state: Hokkaido

address: Kita 9 jo Nishi 9 chome, Kita-ku, Sappro

country: Japan

institute: Hokkaido University

summary:
Investigation of the effects of lol mutation on Drosophila transcriptome.  w[1118] was used as the control strain.
The lol mutation used in this study were further described in Inagaki et al.

overall_design: A triplicated DNA microarray experiments were performed using total RNA from whole body or head of mutants (males or females were sorted), with three independent samples for each experiment. Same analysis was done for the control w[1118] strain.  The DNA microarray was designed for 16,637 transcripts with 8 probes per transcript based on flybase build DM5.7 (07/05/22)

first: Sachi

last: Inagaki

first: Yuji

last: Kageyama


title: Specialized enteric glial cells coordinate intestinal motility [MERSCOPE]

status: Public on Sep 16 2025

city: Cleveland

first: Marissa

last: Scavuzzo

state: OH

address: 2109 Adelbert Rd

department: Genetics

institute: Case Western Reserve University

summary: Enteric glia are the predominant cell type in the enteric nervous system yet their identities and roles in gastrointestinal function are not well classified. Using an optimized single nucleus RNA-sequencing method, we identified distinct molecular classes of enteric glia and defined their morphological and spatial diversity. Our findings revealed a functionally specialized class of enteric glial cells that we call “hub cells.” Hub cells retain dual functionality: they generate neurons and glia and act as force transducers to regulate intestinal physiology. Deletion of the mechanosensory ion channel PIEZO2 from adult enteric glial hub cells, but not other subtypes of enteric glia, led to defects in intestinal motility and gastric emptying in mice. These results provide insight into the multifaceted functions of different enteric glial cell subtypes in gut health and emphasize that therapies targeting enteric glia could advance the treatment of gastrointestinal diseases.

overall_design: MERSCOPE imaging of duodenum and colon processed and imaged simultaneously from 2 biological replicates

first: Paul

last: Tesar


title: Role of CD5 signalling for pro-inflammatory Th17 response in multiple sclerosis

city: Mainz

first: Matthias

last: Klein

address: Langenbeckstrasse 1

department: Inst. for Immunology

institute: University Medical Center Mainz

summary: This study aimed to assess the role of the CD5-CK2-STAT3 signalling axis in human pro-inflammatory Th17 cells. Blockade of CD5 reduced production of IL-17A, IFN-γ and GM-CSF by Th17-polarised cells without affecting proliferation. In comparison, blockade of its intracellular interaction partner CK2 exerted partly similar effects with a decrease in IL-17A and GM-CSF production but also impaired T cell proliferation. Both blocking agents resulted in a decreased phosphorylation of the downstream signalling molecule STAT3. The CD5 targeting treatment was able to abolish cytotoxic effects caused by Th17-polarised cells. Transcriptomic and proteomic analysis showed that CD5 expression correlates with an inflammatory immune profile in MS in serum as well as CSF.

overall_design: Single cell analysis from Csf of RRMS and NIND patients

first: Stefan

last: Bittner

first: Katrin

last: Pape

first: Tobias

last: Bopp


title: RNA-seq of THP-1 and U937 exposed to enamel matrix derivative.

city: Vienna

first: Reinhard

last: Gruber

address: Sensengasse 2a

country: Austria

institute: Medical University Vienna

summary: Enamel matrix derivatives (EMDs) treat periodontal defects and gingival recession, a process where macrophages are believed to contribute to the clinical outcome.  However, the present findings are heterogeneous, raising the need for standardized bioassays to better understand and monitor EMD activity in vitro. To this aim, we have conducted THP-1 and U937, both widely established monocytic cell lines, as bioassays in EMD research. To understand their differential response to EMD, we employed an RNA-seq approach to identify changes in the genetic signatures of THP-1 and U937 cells. When applying a threshold of 1.5 log2 fold-change and a significance of 2.0-log10, we could identify 5/37 and 30/23 up-and-down-regulated genes in THP1 and U937 cells, respectively. In THP-1, the upregulated genes included S100A8, S100A9 and CD38; downregulated gene included ADM, CD48, IL24, MMP1, and PDGFB. In U937, most striking was the increase of alpha subunit integrins ITGA1, ITGA2, ITGA6, and the decrease of genes including OLR1, CCL1, CCL4L2, CCL8, IL21R, MMP7, PDGFB and MMP25. We further show that the TGF-β receptor type I kinase inhibitor SB431542 blocked the expression changes of S100A8, S100A9, CD38, ITGA2, ITGA6, and OLR1 but failed to reverse PDGFB. These data serve as a primer for developing macrophage bioassays to measure EMD activity in the context of TGF-β signaling.

overall_design: We proposed using THP-1 and U937, both widely established monocytic cell lines, as bioassays in EMD research. Both cell lines have different origins, as THP-1 is a leukemia cell line, and U937 originates from the pleural effusion of a patient with histiocytic lymphoma. Differentiated THP-1 and U937 cells were then exposed to 300 µg/mL EMD. In the indicated experiments, 10 µM of the TGF-β receptor I kinase inhibitor SB431542 was used. To understand their differential response to EMD, we employed an RNA-seq approach to identify changes in the genetic signatures of THP-1 and U937 cells.

first: Panahipour

last: Layla

first: Xiaoyu

last: Huang


title: Oncogenic MAPK signalling induces epithelial cell state change and therapeutic resistance in vivo [scRNA-Seq]

city: Glasgow

first: Kathryn

last: Gilroy

address: Garscube

country: United Kingdom

institute: CRUK Scotland Institute

summary: The colorectal epithelium is a rapidly renewing tissue, with a remarkable capacity to regenerate following injury. In colorectal cancer (CRC), this regenerative capacity can be co-opted to drive epithelial plasticity. Activation of oncogenic MAPK signalling in CRC is common, with mutations frequently found in both KRAS (40-50%) and BRAF (10%), alongside other mechanisms of EGFR pathway upregulation. Nonetheless, inhibition of this pathway is often linked to rapid therapeutic resistance in patients. Given the recent development of KRAS inhibitors and the licensing of BRAF+EGFR inhibitor combinations we have investigated mechanisms of resistance to these agents in complex mouse models of CRC. Here we show that MAPK signalling supports the regenerative/revival stem cell phenotype in vivo, while its inhibition leads to rapid remodelling of both Kras and Braf mutant mouse models to a high Wnt activity canonical stem cell phenotype marked by expression of Lgr5. This results in acute therapeutic resistance in Kras driven, and delayed resistance in Braf driven models. Importantly, where therapeutic MAPK targeting is applied in the presence of a single regenerative epithelial population, such as early metastatic disease, or where plasticity is restrained, for example through Wnt pathway restriction, a marked impact on tumourigenesis is observed. Modelling of an BRAF and RNF43-mutant patient population, clinically super-responders to BRAF/EGFR inhibitor therapy, demonstrates excellent response to therapy due to restricted epithelial plasticity, highlighting the criticality of cellular plasticity in therapeutic response. Together, our data provide clear insight into the mechanisms underpinning resistance to targeting oncogenic MAPK signalling in CRC. Moreover, we demonstrate that strategies that aim to restrict epithelial plasticity or corral into or intervene when tumours are in a regenerative cell fate may improve efficacy of MAPK targeting agents in CRC.

overall_design: Mice were induced with a single 70uL injection of 100uM 4-OH tamoxifen into the colonic submucosa. When an established tumour was identified on colonoscope (beginning weekly two weeks post injection), mice were placed on a treatment regime. Mice were treated twice  daily with MRTX1133 IP AM and PM (MRTX1133 100uL 7.5mg/kg) or vehicle (100uL10% hydroxpropyl beta cyclodextrin in 50mM citrate buffer ph5) for 4 days and sampled two hours post AM dose on the fourth day.

first: Mark

last: White

first: Megan

last: Mills

first: Laura

last: Millett

first: Andrew

last: Campbell

first: Owen

last: Sansom


title: Rate Limiting Enzymes in Nucleotide Metabolism Synchronize Nucleotide Biosynthesis and Chromatin Formation [RNA-Seq]

city: Chicago

first: SHASHANK

last: SRIVASTAVA

state: IL

address: 303 E Superior St, SQE Lab 7-400

institute: Northwestern University

summary: Fundamental cellular processes including replication, transcription, and repair rely on both an adequate nucleotide supply and sufficient availability of new histones. Chromatin disassembly and reassembly is crucial to maintain genome stability, and is regulated by the orderly engagement of histones with a series of histone chaperones that guide newly synthesized histones from ribosomes to DNA. Although the synthesis of nucleotides and the histone proteins are the two major biosynthetic processes to complete the formation of chromatin, our knowledge about the coordination of these processes is limited. Phosphoribosyl pyrophosphate synthetases (PRPSs) catalyze the rate-limiting step in the nucleotide biosynthesis pathway. PRPS enzymes form a complex with PRPS-associated proteins (PRPSAPs). In the present study, we discover that PRPS-PRPSAP enzyme complex are part of the histone chaperone network involving HSP70/90, NASP, HAT1/RBBP7 and importin-4 to regulate chromatin assembly. We show PRPS enzymes are essential not only for nucleotide biogenesis, but together with PRPSAP also play a key role in the heterodimerization of H3-H4 and posttranslational modification of nascent histones, early steps in the process of histone maturation. Depletion of PRPS proteins leads to limited histone availability and therefore to impaired chromatin assembly. Our discovery bridges nucleotide metabolism and chromatin regulation and provides first evidence on how nucleotide biogenesis and chromatin dynamics work in synchrony.

overall_design: To evaluate the transcriptomic changes in response to PRPS1 or PRPSAP1 depletion. We treated  HEK293T-PRPS1-HA-dTAG-PRPSAP1-V5-BromoTag cells with DMSO, dTAG47 (to deplete PRPS1) or AGB1 (to deplete PRPSAP1) for 24 hours and RNA seq was conducted.

first: Shashank

last: Srivastava

first: Daniel

last: Foltz


title: Oncogenic MAPK signalling induces epithelial cell state change and therapeutic resistance in vivo [RNA-Seq]

overall_design: Bulk RNAseq expression data from treated and untreated mouse small intestine and colon tumours, with genetic modifications in combinations of the genes Apc, Kras, Braf, p53, Alk5, Notch1, Bcl9, Bcl9l and Rnf43.

first: Rosalin

last: Simpson


title: Transposable elements as catalysts of genome evolution in Drosophila virilis

city: Moscow

first: Alexander

middle: Pertovich

last: Rezvykh

state: Moscow

address: Vavilova, 32

department: Russian Academy of Sciences

country: Russia

institute: Engelhardt Molecular Biology Institute

summary: Transposable elements (TEs) drive genomic innovation, but their dynamics in non-model species remain unclear. Herein, we integrated multiomics data to explore TE dynamics in Drosophila virilis, an important model for repetitive DNA research. By combining computational predictions with manual curation, we identified 100 TE families and delineated three temporal waves of TE mobilisation: recent activity, speciation-associated divergence, and ancient invasions. TEs in D. virilis dynamically colonise euchromatin and heterochromatin, contradicting the idea that heterochromatin is just a passive dump for degenerate repeats. Most TE families are prevalent across all analyzed D. virilis strains, while certain DNA transposons and retroelements exhibit strain-specific expansion, suggesting different TE activity and silencing across populations. Nonetheless, there is substantial evidence for extensive horizontal transfer of TEs among close relatives, demonstrating that the D. virilis species group function effectively as TE “ecosystem”. Epigenetic profiling revealed H3K9me3 spreading from TEs represses adjacent genes in a distance-dependent manner, influenced by insertion length and genomic context, affecting developmental and metabolic genes. We also discovered the first polymorphic inversion in D. virilis, likely linked to retrotransposons. Our findings illuminate TEs as catalysts of genomic innovation, influencing gene regulation and evolutionary trajectories, providing a framework for studying TE dynamics across species.

overall_design: RNA-seq, ChIP-seq and long-read genomic sequences of various strains of Drosophila virilis

first: Sergei

last: Funikov


title: Targeting HIF-2α in glioblastoma reshapes the immune infiltrate and enhances response to immune checkpoint blockade

city: Lausanne

first: Felipe

last: Espinoza

address: Rue du Bugnon 7

department: Department of Biomedical Sciences

institute: University of Lausanne

summary: Glioblastoma (GBM) is an aggressive primary brain tumor with dismal clinical prognosis and resistance to current therapies. GBM progression is facilitated by the tumor microenvironment (TME), with an immune infiltrate dominated by tumor-associated microglia/macrophages (TAMs) and regulatory T cells (Tregs). The TME is also characterized by hypoxia and the expression of hypoxia-inducible factors (HIFs), with HIF-2α emerging as a potential regulator of tumor progression. However, its role in GBM immunosuppression remains unknown. Here, we investigate HIF-2α and the use of the HIF-2α inhibitor PT2385 to modulate the TME in the immunocompetent GL261 mouse GBM model. PT2385 administration in vivo decreased tumor volume and prolonged survival of tumor-bearing mice, without affecting GL261 viability in vitro. Notably, HIF-2α inhibition alleviated the immunosuppressive TME and synergized with immune checkpoint blockade (ICB) using αPD-1 and αTIM-3 antibodies to promote long-term survival. Comprehensive analysis of the immune infiltrate through single-cell RNA sequencing and flow cytometry revealed that combining PT2385 with ICB reduced numbers of pro-tumoral macrophages and Tregs while increasing numbers of microglia, with a corresponding transcriptional modulation towards an anti-tumoral profile of these TAMs. In vitro, deletion of HIF-2α in microglia impeded their polarization towards a pro-tumoral M2-like profile, and its inhibition impaired Treg migration. Our results show that targeting HIF-2α can switch an immunosuppressive TME towards one that favors a robust and sustained response to ICB based immunotherapy. These findings establish that clinically relevant HIF-2α inhibitors should be explored not only in malignancies with defects in the HIF-2α axis, but also in those exhibiting an immunosuppressive TME that limits immunotherapy responsiveness.

overall_design: Brain tumors (GL261-bearing brains) were harvested at day 21 post-implantation and tumor infiltrating leukocytes (CD45+ DRAQ7-) were sorted by fluoresence-activated cell sorting FACS, and analyzed for scRNA-seq

first: Felipe I

first: Paul R

last: Walker


title: Rate Limiting Enzymes in Nucleotide Metabolism Synchronize Nucleotide Biosynthesis and Chromatin Formation [ATAC-Seq]

overall_design: ATAC seq-To evaluate the nucleosome positioning by measuring the fragment size, in response to dTAG47 mediated depletion  of PRPS1, for 24 h in HEK293T cells.


title: Runx, Tcf/Lef, and Tle factors underpin the inception of T cell fate

city: Nutley

first: Haihui

last: Xue

address: 123 Metro Boulevard, Bldg. 123, Rm. 5527

department: Center for Discovery and Innovation

institute: Hackensack University Medial Center

summary: The goal of this study is to resolve the heterogeneity of transcriptomic and chromatin accessibility (ChrAcc) landscape in DN1 thymocytes harboring ETPs. Comparison of molecular features between ETPs with non-ETP DN1 cells predicted contribution by Runx and Tcf/Lef family transcription factors, and pre-thymic ablation of Runx1/3, Tcf1/Lef1, or their common Tle/Groucho cofactors invariably impaired ETP formation. Single cell analysis of the factor-targeted ETPs revealed that these three sets of factors converged on Notch1 or Notch pathway effector molecules including Hes1 and Hhex, to support their transcriptional activation by acting on shared and distinct regulatory elements. Furthermore, Runx and Tcf/Lef deficiency caused thymic expansion of myeloid and B cells, respectively, while loss of Tle/Groucho factors resulted in broader diversion to multiple non-T lineages

overall_design: Cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq) was performed on sort-purified Lin–TCRb–CD8–CD44hiCD25– DN1 cells from WT, Tcf1−/−, Tcf1−/−Lef1−/−, Runx1−/−Runx3+/–, Tle1+/–34–/– mice. scATAC-seq was performed on DN1 cells from WT, Tcf1−/−Lef1−/−, Runx1−/−Runx3+/–, or Tle1+/–34–/– mice were sort-purified.

first: Zhao

last: Xin

first: Hu

last: Sheng'en

first: Zang

last: Chongzhi

first: Xue

last: Hai-Hui


title: Self-Limiting AAV-Mediated FGF7 Expression Promoters Re-epithelialization and Accelerates Cutaneous Wound Healing

city: shanghai

first: Xinhua

middle: hong

last: Liao

state: shanghai

address: No. 333 Nanchen Road

institute: shanghai university

summary: The skin serves as a vital barrier against external damage. Severe wounds, particularly chronic ones, compromise this barrier, which can result in infection, pain, disfigurement and life-threatening complications. However, there are limited pharmacological interventions that can substantially enhance wound healing. Gene therapy offers a promising strategy by enabling the sustained local expression of therapeutic factors. In this study, we demonstrate that the AAV-DJ vector efficiently delivers genes to dermal cells, where transgene expression exhibits a self-limiting profile characterized by robust expression during wound healing, followed by a rapid decline after cell proliferation and wound closure. Furthermore, we show that AAV-mediated delivery of the fibroblast growth factors Fgf1, Fgf2 and Fgf7 (KGF) significantly accelerates wound closure, with Fgf7 having the most pronounced effect. Mechanistically, dermally expressed FGF7 promotes keratinocyte proliferation and migration in a paracrine manner, thereby enhancing re-epithelialization. Furthermore, the downstream factor SFN (Stratifin, 14-3-3σ) was identified as a partial mediator of the pro-healing effects of FGF7. Taken together, these results demonstrate the efficacy and safety of AAV-mediated gene delivery in promoting wound healing and provide a foundation for extending gene therapy applications to other skin disorders.

overall_design: SD rats were injected with AAV-Fgf7 or control virus in the left and right ears, respectively. Three days later, tissues at the injection sites were harvested and subjected to RNA-seq by Novogene.

first: Hongzhi

last: Song

first: Zi-Ling

last: Tang

first: Xiao-Yang

last: Tan

first: Zi-Hua

last: Ge

first: Leslie

last: Zhang

first: Jun-Feng

last: Han

first: Ming-Hui

last: Liu

first: Xin-Hua


title: Effect of depletion of PERK on gene expression in T cells after polyclonal or allogeneic stimulation

city: Milwaukee

first: Qiao

middle: cheng

last: Cheng

state: Wisconsin

institute: Medical College of Wisconsin

summary: PERK differentially regulates T cell allogeneic and anti-tumor responses. To further elucidate the mechanism, we performed transcriptomics analyses via bulk RNA sequencing on WT and PERK-deficient T cells after polyclonal or allogeneic stimulation. We here report that endoplasmic reticulum-associated degradation (ERAD)-associated genes, including Sel1l and Erlec1, were significantly increased in PERK conditional knock out (cKO) compared with WT T cells upon allogeneic but not polyclonal stimulation. SEL1L-HRD1 axis plays a central role in ERAD pathway, we also observed that PERK binds to SEL1L in activated human T-cell line. By using PERK-/-SEL1L-/- mice, we eluciated that PERK regulates T-cell allogeneic responses and GVHD induction through SEL1L-mediated ERAD pathway.

overall_design: RNA-seq profiling of wildtype or PERK-deficient T cells after stimulation with  anti-CD3 and anti-CD28 antibodies for 3 days or allogeneic antigen presenting cells (APCs) for 4 days.

first: Hee-Jin

last: Choi

first: Yongxia

last: Wu

first: Xue-Zhong

last: Yu


title: Targeting SUV39H2 Exon Skipping Reversing CDK4/6 Inhibitor Resistance in Breast Cancer [RNAseq]

city: yangzhou

first: Yu

last: Shiyi

state: Jiangsu

address: hanjiang district jiangyangzhonglu136, Hanjiang district, Jiangyangzhonglu 136

institute: yangzhou university

summary: Breast cancer, the most prevalent malignancy among women, is predominantly estrogen receptor-positive (ER+), with ER+ cases accounting for 80% of the total. The combination of CDK4/6 inhibitors and endocrine therapy has become the standard treatment for advanced ER+ breast cancer. However, around 30% of patients exhibit intrinsic resistance, while others eventually develop acquired resistance leading to recurrence and metastasis. Here, we identified reduced exon 2 skipping of SUV39H2 in CDK4/6 inhibitor-resistant breast cancer cells, leading to increased SUV39H2 protein expression and consequent elevation of H3K9me3 levels, collectively suppressing the p53 pathway and promote resistance. Subsequently, we designed antisense oligonucleotides (ASOs) to modulate SUV39H2 exon skipping, which successfully reduced SUV39H2 levels and H3K9me3 modifications, thereby reactivating p53 target genes and restoring drug sensitivity in vitro and in vivo.Our results demonstrate that SUV39H2 serves as both a potential biomarker and therapeutic target for CDK4/6 inhibitor-resistant breast cancer, highlighting its clinical translational value.

overall_design: RNAseq in MCF7-ABER, MCF7-PALR and MCF10A cells treated with antisense oligonucleotides (ASO) targeting SUV39H2 or control (Ctr). Meanwhile, RNAseq in MCF7-ABER cell treated with RAD21 overexpression or pcDNA3 (Ctr)

first: Shiyi

first: Yawen

last: Yang


title: Targeting Siglec-10/α3β1 Integrin Interactions Enhances Macrophage-Mediated Phagocytosis of Pancreatic Cancer

first: Pratima

last: Saini

address: 300 E. Superior Street

summary: Tumor-associated macrophages (TAMs) in the pancreatic ductal adenocarcinoma (PDAC) tumor microenvironment (TME) exhibit immunosuppressive phenotypes and impaired phagocytic activity, facilitating tumor progression and immune evasion. Here, we identify integrin α3β1, composed of ITGA3 and ITGB1 subunits, as a sialylated glycoprotein ligand for Siglec-10, an inhibitory glyco-immune checkpoint receptor highly expressed on TAMs in PDAC. The interaction between Siglec-10 on TAMs and α3β1 on PDAC cells suppresses macrophage-mediated phagocytosis, thereby promoting immune evasion. Consistently, disrupting Siglec-10 interactions with monoclonal antibodies significantly enhances macrophage phagocytosis of PDAC cells and alleviates myeloid cell-mediated inhibition of T cell proliferation and activation in vitro. In both a PDAC xenograft mouse model engrafted with human macrophages and a human Siglec-10 transgenic mouse model, targeting Siglec-10 with monoclonal antibodies reduces PDAC tumor growth. These findings suggest that the Siglec-10 interactions are key mediators of TAM-driven immune evasion in PDAC and highlight the therapeutic potential of targeting these interactions to restore anti-tumor immunity in PDAC.

overall_design: RNA-seq profiling of tumor-associated macrophages (TAMs) isolated from NSG mice co-injected with human TAMs and either isotype control or Siglec-10 antibody.

first: Mohamed

last: Abdel-Mohsen


title: Thimerosal Inhibits Tumor Malignant Progression Through Direct Action and Enhancing the Efficacy of PD-1-Based Immunotherapy

city: GuangZhou

first: Zeng

last: Jun Xiang

address: No. 1023–1063 South Shatai Road, Baiyun District

institute: The Southern of Medical University

summary: Background: Thimerosal is a mercury-containing preservative widely used in vaccines.. This study aimed to investigate its potential antitumor effects and mechanisms in solid malignancies, particularly colorectal cancer and melanoma. Methods: A combination of in vitro and in vivo approaches was employed. Cell proliferation, apoptosis, migration, and invasion were assessed using Cell Counting Kit-8 (CCK-8), colony for-mation, ATP viability, Western blotting, flow cytometry, wound-healing and transwell assays. Sub-cutaneous, lung metastases, and Azoxymethane/Dextran Sulfate Sodium Salt (AOM/DSS)-induced colitis-associated colorectal cancer (CRC) models were established to examine antitumor efficacy and safety. The functional role of mercury ions was validated using structural analogues. Mechanistic studies included RNA sequencing, Western blot, and immunohistochemical analysis of CD8+ T cell infiltration. The synergistic effect with programmed cell death protein 1 (PD-1) antibodies therapy was also evaluated. Results: Thimerosal potently inhibited tumor growth (with IC50 values ranging from 0.1 to 1 µM in vitro) and significantly prolonged survival without overt toxicity in vivo. Mechanistically, mercury ions were critical functional sites mediating Thimerosal’s antitumor effects. Specifically, Thimerosal inhibited the phosphorylation of Janus kinase 1(JAK1) and signal transducer and activator of tran-scription 3(STAT3). Furthermore, Thimerosal enhanced the infiltration of CD8+ T cells into the tumor microenvironment and synergistically augmented the efficacy of PD-1 antibody therapy. Conclusion: Thimerosal exerts dual antitumor roles by direct JAK1/STAT3 inhibition and immune modulation via CD8+ T cell recruitment. It represents a promising repurposed drug and immuno-therapeutic adjuvant for CRC and melanoma.

overall_design: Based on the provided background, the experimental design was structured to comprehensively evaluate thimerosal's antitumor potential. It utilized a combination of in vitro assays (CCK-8, colony formation, flow cytometry, wound-healing, transwell) on cancer cell lines and in vivo models (subcutaneous, lung metastasis, and AOM/DSS-induced CRC) in mice to assess efficacy and safety. The role of mercury ions was specifically tested using structural analogs. Mechanistic studies involved RNA sequencing, western blotting to analyze the JAK1/STAT3 pathway, and immunohistochemistry to quantify CD8+ T cell infiltration. Finally, the synergistic effect of thimerosal with anti-PD-1 therapy was investigated.

first: Ping

last: Wang

first: Yan-Han

last: Chen

first: Ze-Tao

last: Zhan

first: Jun-Xiang

last: Zeng

first: Yuan

last: Lin

first: Tao

first: Wei-Jie

last: Zhou


title: O-antigen Deficiency Sparks Metabolic Shifts That Blunt ROS-Mediated Killing by Meropenem

city: Beijing

first: Jiangqing

last: Huang

address: No 3, 1st Beichen West Road, Chaoyang District

institute: Chinese Academy of Sciences

summary: Carbapenem-resistant Klebsiella pneumoniae (CRKP) poses a major global health threat, particularly in healthcare-associated infections. While carbapenemase- and porin-centered mechanisms are well characterized, how subinhibitory carbapenem exposure selects noncanonical adaptive routes remains unclear. Here, we show that subinhibitory meropenem promotes O_x001E_antigen loss in K. pneumoniae, predominantly mediated by insertion sequences (IS), thereby enhancing carbapenem resistance. O_x001E_antigen deficiency rewires metabolism under meropenem pressure, especially glycine, serine, and threonine pathways, dampening reactive oxygen species (ROS) accumulation and limiting oxidative killing; exogenous glycine restores ROS production and meropenem susceptibility. Genomic surveys reveal widespread O_x001E_antigen loss in K. pneumoniae, largely driven by IS, and also in Escherichia coli, and O_x001E_antigen–deficient mutants confirm its role in promoting carbapenem resistance. Importantly, this adaptation entails a trade-off: it improves survival under carbapenem pressure but increases serum susceptibility, destabilizes the capsule, attenuates virulence in murine infection models, and confers collateral sensitivity to aminoglycosides. These findings uncover a previously unrecognized route to carbapenem resistance that links O_x001E_antigen remodeling to metabolic rewiring, offering conceptual and therapeutic leverage points.

overall_design: RNA-seq of Klebsiella NK01067 and its ΔwbbM mutant with and without 8 μg/L meropenem.

first: Dawei

last: Wei


title: Disruption of Pre-Bötzinger Complex neuropeptidergic tonality controls fear and metabolic response

city: New York

first: Prashant

last: Rajbhandari

state: New York

address: 1468 Madison Ave, Annenberg 18-10

institute: Icahn School of Medicine at Mount Sinai

summary: Stress profoundly impacts systemic metabolism, yet the central circuits linking stress responses to peripheral metabolic regulation remain poorly defined. Here, we identify the preBötzinger complex (preBötC), a brainstem breathing rhythm generator, as a key stress-responsive hub coordinating metabolic adaptations. Using viral tracing, we show that preBötC neurons project to brown adipose tissue and liver, and that a subset of these projection neurons expresses the pituitary adenylate cyclase–activating polypeptide (PACAP) receptor PAC1R, positioning PACAP signaling as a critical modulator of this circuit. Whole-brain c-Fos mapping revealed robust preBötC activation under stress, while spatial transcriptomics demonstrated altered neuronal metabolic circuitry in preBötC following PAC1R ablation. PAC1R knockdown in preBötC combined with stress resulted in blunted respiratory rhythmicity, reduced sympathetic innervation, and suppression of energy expenditure and lipid metabolic pathways in brown fat, while reprogramming hepatic transcriptional networks toward amino acid metabolism and gluconeogenesis. These findings define a unique neuropeptidergic brainstem–periphery circuit integrating stress, respiration, and metabolism.

overall_design: RNA-seq was performed on BAT and liver isolated from Ctrl (AAV-GFP) or Cre (AAV-Cre) preBötC-injected Adcyap1r1^flox/flox mice subjected to SEFL.


title: Targeting SUV39H2 Exon Skipping Reversing CDK4/6 Inhibitor Resistance in Breast Cancer [CUT&Tag]

overall_design: CUT&Tag-seq in MCF7-ABER cells treated with antisense oligonucleotides (ASO) targeting SUV39H2 or control (Ctr)


title: Transcriptional Response to Non-Steroidal Anti-Inflammatory Drugs and Tryptophan Supplementation

city: Philadelphia

first: Nicholas

last: Lahens

address: Smilow Center for Translational Research 10-110 3400 Civic Center Blvd, Bldg 421

department: ITMAT

institute: University of Pennsylvania

summary: Non-steroidal anti-inflammatory drugs (NSAIDs) are popular choices for the mitigation of pain and inflammation; however, they are accompanied by adverse effects in the gastrointestinal and cardiovascular systems. We compared the effects of placebo, naproxen, a traditional NSAID, and celecoxib, a cyclooxygenase (COX)-2 inhibitor, in the plasma of healthy volunteers. We found a decrease in tryptophan and kynurenine levels in the plasma of those volunteers treated with naproxen. Based on these findings we treated mice with control, celecoxib, or naproxen diets, and examined their effects on the heart and jejunum transcriptomes. Additionally, we tested if tryptophan treatment rescued the transcriptional effects of naproxen treatment.

overall_design: RNA-Seq profiling of heart or jejunum tissue from female C57BL/6 mice following three weeks of treatment with celecoxib, naproxen, tryptophan, naproxen + tryptophan, or control. Celecoxib and naproxen treatments were provided through diet, while tryptophan treatment was administered through intraperitoneal injection. Tissue samples were collected and sequenced in four different experimental batches with 5-8 mice per combination of treatment and experiment. The first experimental batch collected from heart tissue of mice treated with control or naproxen diets also included 5 male mice per treatment.

first: Soumita

last: Ghosh

middle: F

first: Kayla

last: Barekat

first: Soon-Yew

last: Tang

first: Katherine

middle: N

last: Theken

first: Emanuela

last: Ricciotti

first: Arjun

last: Sengupta

first: Robin

last: Joshi

first: Weiming

last: Hu

first: Frederic

last: Bushman

first: Aalim

last: Weljie

first: Tilo

last: Grosser

first: Garret

last: FitzGerald