title: Digital twins for in vivo metabolic flux estimations in patients with brain cancer

city: Ann Arbor

first: Wajd

last: Al-Holou

address: 1500 E Medical Center Dr

institute: University of Michigan

summary: Recent advancements in metabolic flux estimations in vivo are limited to preclinical models, primarily due to challenges in tissue sampling, tumor microenvironment heterogeneity, and non-steady state conditions. To address these limitations and enable flux estimation in human patients, we developed two machine learning-based frameworks. First, the digital twin framework integrates first-principles stoichiometric and isotopic simulations with convolutional neural networks to estimate fluxes in patient bulk samples. Second, the 13C-scMFA framework combines patient scRNA-seq data with 13C-isotope tracing, allowing single-cell-level flux quantification. These studies allow quantification of metabolic activity in neoplastic glioma cells, revealing frequently elevated purine synthesis and serine uptake compared to non-malignant cells. Our models also identify metabolic heterogeneity among patients and mice with brain cancer, in turn predicting treatment responses to metabolic inhibitors. Our frameworks advance in vivo metabolic flux analysis, may lead to novel metabolic therapies, and identify biomarkers for metabolism-directed therapies in patients.

overall_design: Tumor brain tissues from brain cancer patients were analyzed using scRNA-seq.

first: Baharan

last: Meghdadi

first: Wajd N.

first: Andrew J.

last: Scott

first: Anjali

last: Mittal

first: Ningning

last: Liang

first: Sravya

last: Palavalasa

first: Abhinav

last: Achreja

first: Alexandra

last: O'Brien

first: Kathy

last: Do

first: Zhe

last: Wu

first: Jiane

last: Feng

first: Nathan R.

last: Qi

first: Vijay

last: Tarnal

first: Sriram

last: Venneti

first: C. Ryan

last: Miller

first: Jann N.

last: Sarkaria

first: Weihua

last: Zhou

first: Theodore S.

last: Lawrence

first: Costas A.

last: Lyssiotis

first: Daniel R.

last: Wahl

first: Deepak

last: Nagrath


title: Lipid restriction in Familial Hypolipidemia 2 amplifies type I interferon response and suppresses IL-1beta production in a prenylation-dependent fashion

status: Public on Nov 28 2025

city: Rome

first: Valerio

last: Licursi

address: via degli Apuli, 4

department: c/o Dept. Biology and Biotechnologies "C. Darwin", Sapienza University of Rome

country: Italy

institute: Institute of Molecular Biology and Pathology (IBPM), National Research Council (CNR)

type: Expression profiling by high throughput sequencing

summary: Familial Combined Hypolipidemia (FHBL2) is a genetic disorder caused by loss-of-function mutations in the Angiopoietin-like 3 (ANGPTL3) gene. FHBL2 subjects exhibit hypolipidemia and protection from cardiometabolic diseases. Here, we explored the hypothesis that immunometabolic events contribute to this phenotype.  In FHBL2 subjects, circulating leukocytes exhibited lower content of intracellular lipids, together with a spontaneous type I IFN signature. Higher sensitivity to IFN stimulation was observed in FHBL2 monocytes ex vivo, as well as and in healthy monocytes deprived of lipids in vitro. Lipid restriction reduced mitochondrial metabolism and activated the mevalonate and isoprenoid synthetic pathway. Of note, a prenylation inhibitor reverted the high IFN response in lipid-deprived monocytes. Lipid restriction equaled IFN in repressing, in a prenylation-dependent fashion, the production of the inflammatory and proatherogenic cytokine IL-1. In summary, we uncovered a novel immunometabolic mechanism linking lipid deprivation in monocytes, isoprenoid synthesis, enhanced IFN response, and IL-1 control. This circuit may provide an immunometabolic basis for the protection from atherosclerotic diseases in hypolipidemic subjects.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for PBMC of FHBL2 Homozygous patients (Angptl3 p.s17*/p.s17*) and control patients

first: Silvia

last: Piconese

first: Alessandra

last: Pinzon Grimaldos

first: Marcello

last: Arca


title: Paired Vascular-Parenchymal Single Nuclei Sequencing Reveals Perturbed Endothelial-to-Mesenchymal Transition in Alzheimer’s Disease

city: Cardiff

first: Gabriel Mateus

last: Bernardo Harrington

address: 52 Maindy Road

country: United Kingdom

institute: UK Dementia Research Institute at Cardiff University

summary: The neurovascular unit (NVU) plays a crucial role in maintaining brain functions by integrating vascular cells, neurons, and glia to ensure metabolic support and blood-brain barrier integrity. While vascular dysfunction has been implicated in Alzheimer's disease (AD), the specific contributions of various vascular cell types remain understudied, partly due to challenges in isolating these cells from post-mortem tissue. In this study, we analyzed prefrontal cortex tissue from AD patients and control subjects using single-nuclei RNA sequencing to create a high-resolution atlas capturing major vascular and parenchymal cell types. Our findings reveal distinct associations between AD risk and gene expression profiles specific to pericytes, perivascular fibroblasts, and activated microglia. Functional analyses indicate that these genes converge on amyloid-related pathways, suggesting that perivascular compartments and immune modulators play significant roles in the early stages of AD pathobiology. Additionally, we identified a new endothelial-mesenchymal transition population that is diminished in AD, indicating a potential disruption in endothelial plasticity that may contribute to vascular dysfunction. Key ligand-receptor interactions between vascular and parenchymal cell types, such as ANGPT2, were found to be markedly dysregulated, highlighting potential targets that could drive NVU breakdown in AD. These findings provide a comprehensive framework for evaluating NVU cells in human disease and underscore novel links between vascular dynamics and AD pathogenesis. The study offers valuable insights into disease mechanisms and suggests new therapeutic avenues aimed at protecting and restoring the brain's neurovascular interface.

overall_design: Post-mortem pre-frontal cortex from 20 controls and 20 AD brain donors were collected from The Oxford Brain Bank. Vasculature and parenchyma fractions were sequenced seperately, giving 2 samples from each donor for a total of 80 samples. 3 donors were excluded in QC and of the remaining 37 donors, 23 were female and 14 were male with a median age of 87 (range 48-101).

first: Jimena

last: Monzón-Sandoval

first: Gabriel

last: Rocha

first: Lara

last: Robinson

first: Michal

last: Rokicki

first: Joanne

last: Morgan

first: Ngoc-Nga

last: Vinh

first: Hannah

last: Sleven

first: Quenten

last: Schwarz

first: Caleb

last: Webber

first: Zameel

last: Cader


title: Bacillus mojavensis postbiotics: transcriptomic and anticancer effects in colon cancer cells

city: Puebla

first: Elizabeth

last: Bautista-Rodriguez

state: Puebla

address: 11 poniente 2316

department: Ingenieria en Biotecnología

country: Mexico

institute: Universidad Popular Autonoma del Estado de Puebla

summary: Probiotics have been shown to exert antiproliferative effects on colon cancer cells. While these effects are often attributed to microbiome regulation, they may also result from bioactive metabolites produced by probiotic bacteria. In the present study, we investigated the impact of a cell-free extract, hereafter referred to as a postbiotic, derived from Bacillus mojavensis, a strain isolated from aguamiel (a traditional Mexican beverage). The antiproliferative activity was evaluated in SW480 human colon cancer cells using MTT and crystal violet assays, while antimigratory effects were assessed through a wound-healing assay. In addition, the ability of the postbiotic to counteract inflammatory proliferation was evaluated in SW480 cells treated with lipopolysaccharide (LPS). Biosafety was confirmed using peripheral blood mononuclear cells (PBMCs) from healthy donors. The results demonstrated that treatment with 25 or 50 µg/mL of B. mojavensis postbiotic reduced the viability of more than 75% of SW480 cells and significantly inhibited cell migration after 24 h. Moreover, the postbiotic decreased LPS-induced proliferation without exerting any cytotoxic effect on PBMCs, underscoring its selectivity toward malignant cells. To elucidate the underlying mechanisms, transcriptomic profiling was performed, revealing extensive modulation of oncogenes and tumor suppressors, with enrichment of PI3K–Akt, MAPK, apoptosis, and cytokine receptor pathways. In conclusion, postbiotics from B. mojavensis isolated from aguamiel exhibit selective anticancer activity by inhibiting proliferation, migration, and inflammation-induced growth in colorectal cancer cells. Transcriptomic findings further support these effects.

overall_design: Two conditions assay. MRS control vs BM.  Biological replicates. 2 control. 2 treated with B. mojavensis postbiotic. independently grown and harvested. One replicate per array

first: María

middle: A

last: Trujillo-López

first: Cristina

last: Muñoz-Olivos

first: Miguel

last: Garduño-Vargas

first: Jose

middle: M

last: Sánchez-López

first: Verónica

last: Martínez-Ortiz

first: Beatriz

last: Pérez-Armendáriz

first: Elie

middle: G

last: El-Kassis


title: Pseudopaline-mediated zinc uptake by Pseudomonas aeruginosa drives clinically relevant phenotypes and infection outcomes

city: Braunschweig

first: Nicolas

middle: Oswaldo

last: GOMEZ

state: Lower Saxony

address: Inhoffenstraße 7

country: Germany

institute: Helmholtz Center for Infection Research

summary: Biological metals are vital trace elements required by metalloproteins, which are involved in virtually every cellular, structural and catalytic function of the bacterial cell. Bacterial pathogenesis involves a tug-of-war between the host’s nutritional immunity sequestering essential metals and the invading pathogens that deploy adapted high-metal affinity uptake strategies such as metallophores, in order to efficiently circumvent these defence mechanisms. Pseudopaline is a metallophore produced and secreted by Pseudomonas aeruginosa to acquire zinc when the bioavailability of this metal is severely restricted, as in the presence of a strong metal chelator such as EDTA, or during infections when the nutritional immunity of the host is active. We show that when facing strong metal chelation, the general Znu zinc uptake pathway becomes ineffective and only the pseudopaline pathway is capable of supplying the bacteria with the necessary zinc to maintain their growth, establishing that the pseudopaline pathway is the last-resort pathway for the bacteria to acquire zinc under such restricted growth conditions. Based on this statement, the present study explores the pleiotropic role of pseudopaline-mediated zinc acquisition on clinically relevant phenotypes such as biofilm formation and associated antibiotic tolerance, as well as its capacity to determine infection outcomes using cell-culture and murine models. The expression of pseudopaline-dependent phenotypes in such a diversity of biological contexts demonstrates the essentiality of this specific metal uptake system for P. aeruginosa pathogenicity during infection. We therefore identify this machinery as a promising therapeutic target for P. aeruginosa’s infections.

overall_design: Pseudomonas aeruginosa UCBPP-PA14 mutant strains were planktonically cultured in MCM media for 10h (RNA seq experiment).

first: Lola

last: Bosc

first: Thomas

last: Sécher

first: Geneviève

last: Ball

first: Deborah

last: Le Pennec

first: Mathilde

last: Tribout

first: Moly

last: Ba

first: Yingjie

last: Bai

first: Laurent

last: Ouerdane

first: Erdmann

last: Jelena

first: Pascal

last: Arnoux

first: Yann

last: Denis

first: Xiaoguang

last: Lei

first: Christophe

last: Bordi

first: Nathalie

last: Heuzé-Vourc’h

first: Susanne

last: Häussler

middle: O

last: Gomez

first: Romé

last: Voulhoux


title: Determinants of long-term response to patritumab deruxtecan (HER3-DXd) in breast cancer patient-derived xenografts

city: Barcelona

first: Andreu

last: Òdena

state: Please Select

address: C/ Natzaret, 115-117 CELLEX CENTER

country: Spain

institute: VHIO

summary: Purpose: Novel antibody-drug conjugates (ADCs) have shown potent antitumor activity across multiple cancer types. Here, we aimed to identify potential determinants of response to patritumab deruxtecan (HER3-DXd), a HER3-directed ADC linked to a potent topoisomerase I inhibitor (TOP1i) payload, in breast cancer (BC) patient-derived xenograft (PDX) models. Experimental Design: The antitumor activity of HER3-DXd was assessed in 31 BC PDXs and classified according to tumor growth inhibition and duration of response. We analyzed the sensitivity to HER3-DXd according to the molecular characteristics of the PDX models, the sensitivity to the TOP1i irinotecan, and prior patient treatments. The biological effects following treatment with HER3- DXd were assessed and associated to treatment response. Results: Fourteen out of 31 (45%) PDXs exhibited a profound and sustained response to HER3-DXd. Basal-like PAM50 intrinsic subtype was associated with long-term response, across HER3/ERBB3 expression levels. We also observed a positive association between HER3-DXd and irinotecan sensitivity in the PDXs, as well as short-lasting antitumor response in models derived from patients with prior repeated exposure to chemotherapy. HER3-DXd showed sustained activity in BRCA1/BRCA2-mutated PARPi-resistant PDX models. Long-term responders exhibited persistent DNA damage and lacked early transcriptional activation of the G2/M cell cycle checkpoint to allow for DNA repair and R-loop resolution, in parallel resulting in immune pathways activation. Conclusions: HER3-DXd exhibited potent antitumor activity in breast cancer PDX models, including those with BRCA1/BRCA2 alterations and PARPi resistance. Notably, characteristics linked to long-term response were primarily associated with the TOP1i payload activity.

overall_design: This study includes RNA-seq profiling of 10 BC PDX models, both untreated and treated with HER3-DXd (3 mg/kg) at 24 hours (24h) and 7 days (7d). Baseline RNA-seq profiling was also performed for all 31 BC PDX models in the cohort.

first: Eloi

last: Casals

first: Anna

last: Esteve-Codina

first: Violeta

last: Serra


title: Embryonic lineage-specific iPSC-derived mesenchymal stem/stromal cells exhibit different morphology and intrinsic functions

city: Kyoto

first: Makoto

last: Ikeya

address: 53 kawahara-cho, shogoin

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

country: Japan

institute: Kyoto University

summary: Mesenchymal stem/stromal cells (MSCs) have great potential in regenerative medicine owing to their multilineage differentiation capacity. However, tissue-derived MSCs (tMSCs) exhibit inconsistent characteristics. Although induced pluripotent stem cell (iPSC)-derived MSCs (iMSCs) are a potential solution, the effect of different embryonic lineages on their properties remains unknown. We generated MSCs from human iPSCs via five lineage-specific routes: cranial neural crest, trunk neural crest, paraxial mesoderm (somite), lateral plate mesoderm, and limb mesenchyme. All types met established MSC criteria yet differed in morphology, proliferation, and differentiation capacity. Somite-, cranial neural crest–, and limb mesenchyme–derived MSCs showed higher osteogenic potential, whereas somite-derived MSCs also showed high chondrogenic potential but were prone to hypertrophy. Limb mesenchyme–derived MSCs showed the highest adipogenic potential. Transcriptomic profiles indicated distinct clusters within iMSCs. Despite variances, a high correlation level existed between iMSCs and tMSC. Therefore, iMSCs are potential alternatives to tMSCs in regenerative medicine.

overall_design: RNA-seq profiling was performed on five lineage-specific induced mesenchymal stem cell (iMSC) populations at passage 5 and their corresponding intermediate progenitors (cranial neural crest, trunk neural crest, somite, lateral plate mesoderm, and limb mesenchyme) expanded to passage 4, together with the parental iPSCs and tissue-derived MSCs derived from adipose tissue, bone marrow, dental pulp, and fibro/adipogenic progenitor (FAP) cells.

first: Linh

last: Nguyen

first: Souta

last: Motoike

first: Denise

last: Zujur

first: Keiko

last: Yoshizawa

first: Yasuhiro

last: Takashima

first: Akiyoshi

last: Uezumi

first: Kazuhiro

last: Furuhashi

first: Shoichi

last: Maruyama

first: Yonghui

last: Jin

first: Junya

last: Toguchida

first: Hidetoshi

last: Sakurai


title: Glycolytic heterogeneity drives metabolic-targeted therapy in PDAC

city: Naples

first: Ugo

last: Chianese

address: via Luigi De Crecchio

department: Department of Precision Medicine

institute: Universita degli Studi della Campania Luigi Vanvitelli

summary: Background: Pancreatic ductal adenocarcinoma is classically characterized as a glycolytic tumor. However, the extent and implications of metabolic heterogeneity within PDAC remain poorly defined. This study aimed to determine whether glycolytic activity follows a consistent expression pattern across PDAC patients and to explore how metabolic diversity influences therapeutic vulnerability. Methods: We employed spatial transcriptomics in six, ex vivo, primary human PDAC specimens, complemented by single-cell and bulk RNA sequencing, to map glycolytic heterogeneity in PDAC. Patient-derived cell models, representative of distinct glycolytic phenotypes, were used to assess metabolic and antiproliferative responses to glycolytic pathway inhibition. A comprehensive multi-omics strategy—including metabolomics, proteomics, and lipidomics—was integrated through a robust bioinformatics pipeline to dissect pathway-specific variations and integromics. Results: PDAC tumors displayed marked glycolytic heterogeneity, with distinct transcriptional profiles that preserved cell identity and spatial organization. These glycolytic patterns correlated with clinical outcomes, highlighting their potential prognostic value. Functional studies strengthen differential sensitivity to metabolic inhibitors in models with opposite glycolytic activity, demonstrating both the therapeutic relevance of PDAC glycolytic stratification and highlighting the potential of metabolic targeting. Conclusions: Our findings uncover a clinically relevant metabolic heterogeneity in PDAC, offering a novel stratification framework based on glycolytic profiling. This approach may allow the selection of patients for tailored metabolic therapies, advancing precision oncology in pancreatic cancer.

overall_design: Pancreas samples have been acquired from patients with pancreatic ductal adenocarcinoma diagnosis, having a grade between 2-3, T and N, respectively, between 2-3 and 0-1.

first: Chiara

last: Papulino

first: Gerardo

last: Saggese

first: Ahmad

last: Ali

first: Marianna

last: Ciotola

first: Enza

last: Lonardo

first: Mirko

last: Cortese

first: Gregorio

last: Favale

first: Annabella

last: Di Mauro

first: Danila

last: La Gioia

first: Valentina

last: Golino

first: Eduardo

last: Sommella

first: Pietro

last: Campiglia

first: Renato

last: Franco

first: Fortunato

last: Ciardiello

first: Ferdinando

last: De Vita

first: Vincenzo

last: Carafa

first: Lucia

last: Altucci

first: Rosaria

last: Benedetti


title: A mutation mimicking post-translational acetylation of CRP at Lysine 52 creates a multitude of novel binding sites that activate transcription

city: Boston

last: Santos

state: MA

address: 300 Longwood Ave

country: USA

institute: Boston Children's Hospital

type: Genome binding/occupancy profiling by high throughput sequencing

summary: As a model in the field of bacterial transcription, the structure and function of the cAMP receptor protein (CRP), a global transcription factor, has been exhaustively studied.  These studies have demonstrated three contacts between CRP and RNA polymerase, of which only two were thought to activate transcription in the wild-type protein.  Here we provide evidence that post-transcriptional acetylation of V. cholerae CRP engages activating region 3 leading to the hundreds of novel CRP binding sites that activate transcription of genes involved in uptake and catabolism of specific carbon sources, virulence, and biofilm formation.  This establishes CRP activating region 3 as a critical mediator of association both with DNA and RNA polymerase in WT CRP.

overall_design: Chromatin immunoprecipitation followed by sequencing (ChIP-seq) was performed to assess the genome-wide occupancy of V5-tagged CRP variants in Vibrio cholerae during exponential growth in LB medium at 27 °C with shaking at 200 rpm. Parallel RNA-seq was carried out under the same growth conditions to quantify global transcript abundance and determine transcriptional changes associated with CRP activity and its acetyl-mimicking variants. Both assays were performed in biologically relevant strains and conditions to enable direct comparison between chromatin occupancy and gene-expression profiles.

first: Jacob

last: Gibson

first: Pallabi

last: Basu

first: Michael

last: Gebhardt

first: Simon

last: Dove

first: Paula

last: Watnick


title: Determinants of long-term response to patritumab deruxtecan (HER3-DXd) in breast cancer patient-derived xenografts [NanoString]

first: Andreu

last: Òdena

summary: Purpose: Novel antibody-drug conjugates (ADCs) have shown potent antitumor activity across multiple cancer types. Here, we aimed to identify potential determinants of response to patritumab deruxtecan (HER3-DXd), a HER3-directed ADC linked to a potent topoisomerase I inhibitor (TOP1i) payload, in breast cancer (BC) patient-derived xenograft (PDX) models.  Experimental Design: The antitumor activity of HER3-DXd was assessed in 31 BC PDXs and classified according to tumor growth inhibition and duration of response. We analyzed the sensitivity to HER3-DXd according to the molecular characteristics of the PDX models, the sensitivity to the TOP1i irinotecan, and prior patient treatments. The biological effects following treatment with HER3-DXd were assessed and associated to treatment response.  Results: Fourteen out of 31 (45%) PDXs exhibited a profound and sustained response to HER3-DXd. Basal-like PAM50 intrinsic subtype was associated with long-term response, across HER3/ERBB3 expression levels. We also observed a positive association between HER3-DXd and irinotecan sensitivity in the PDXs, as well as short-lasting antitumor response in models derived from patients with prior repeated exposure to chemotherapy. HER3-DXd showed sustained activity in BRCA1/BRCA2-mutated PARPi-resistant PDX models. Long-term responders exhibited persistent DNA damage and lacked early transcriptional activation of the G2/M cell cycle checkpoint to allow for DNA repair and R-loop resolution, in parallel resulting in immune pathways activation.  Conclusions: HER3-DXd exhibited potent antitumor activity in breast cancer PDX models, including those with BRCA1/BRCA2 alterations and PARPi resistance. Notably, characteristics linked to long-term response were primarily associated with the TOP1i payload activity.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: 109 tumors samples from 31 breast cancer PDXs were sequenced. Untreated samples (CNTL) for each PDX model were used for baseline analysis, including PAM50 characterization (n=1-4 for each PDX model) and to identify differentially expressed genes according to HER3-DXd response (Relapsed vs Non-relapsed). Treated samples (U3) with a single dose of HER3-DXd 10mg/kg were collected at 24 hours (24h) and 7 days (7d) after administration (n=1 for each timepoint and PDX model). Based on gene expression, Proliferation Score was calculated for each sample, and subsequent comparison among untreated and treated samples was conducted.

first: Violeta

last: Serra

first: Fara

last: Brasó-Maristany

first: Aleix

last: Prat


title: Placental Exosomal miR-24-1-5p in LPS-Induced Inflammation

city: Hangzhou

first: Yongqing

last: Zhang

state: Zhejiang

address: 1st, xueshi Road,hangzhou,zhejiang

department: Obstetrics and gynecology

country: China

institute: women's hospital school of medicine, zhejiang university

type: Non-coding RNA profiling by high throughput sequencing

summary: Intra-amniotic infection (IAI) is associated with substantial maternal and neonatal risks, yet the immunoregulatory role of the human placenta remains incompletely understood. We established an in vitro IAI model by co-culturing term human placental explants with lipopolysaccharide (LPS) and monitored temporal changes in inflammatory cytokines. Prolonged LPS exposure induced an early pro-inflammatory phase followed by an anti-inflammatory phase characterized by decreased TNF-α/IL-10 and IL-1β/IL-1Ra ratios. Placenta-derived exosomes (Pd-Exos) were isolated from culture supernatants and subjected to miRNA sequencing, which identified miR-24-1-5p as a key upregulated miRNA in Pd-Exos from LPS-treated explants (1-LPS-Pd-Exos). After uptake by THP-1–derived macrophages, exosomal miR-24-1-5p targeted TNFAIP8, promoted macrophage apoptosis, and suppressed TNF-α and IL-1β expression, thereby contributing to placental endotoxin tolerance.

overall_design: Term placental explants from uncomplicated elective cesarean deliveries were cultured ex vivo either in complete medium (control) or in complete medium supplemented with 1 μg/mL LPS. After 18 h of culture, placenta-derived exosomes (Pd-Exos) were isolated from the supernatants of four control explants and four matched LPS-treated explants (1-LPS-Pd-Exos). Total exosomal RNA was extracted and subjected to small RNA library preparation and high-throughput miRNA sequencing. Differential expression analysis was performed between Pd-Exos and 1-LPS-Pd-Exos to identify miRNAs associated with placental endotoxin tolerance.

first: Lejun

last: Li

first: Luping

last: Chen

first: Tiantian

last: Fu

first: Guohui

last: Yan

first: Zhaoxia

last: Liang

first: Meihua

last: Sui

first: Danqing


title: RNA promotes nucleation and oncogenic activity of chromatin-associated condensates [ChIP-Seq]

city: Philadelphia

first: Liling

last: Wan

state: PA

address: 421 Curie Blvd

department: Cancer Biology

institute: University of Pennsylvania

summary: Aberrant chromatin-associated condensates have emerged as drivers of gene dysregulation in cancer, yet the mechanisms regulating their formation and function remain poorly understood. Mutations in the histone acetylation reader ENL, recurrent in leukemia and Wilms tumor, drive oncogenesis by inducing condensate formation at selective target loci. Here, we show that RNA promotes the nucleation, chromatin engagement, and oncogenic activity of ENL mutant condensates. Mutant ENL binds RNA via a conserved basic patch within the YEATS domain, and this interaction enhances condensate formation in vitro and in cells.  Acute displacement and reassembly experiments demonstrate that interactions with local RNA transcripts facilitate condensate nucleation efficiency at endogenous target loci. Partial disruption of RNA binding preferentially impairs chromatin occupancy of ENL mutants at condensate-permissive loci, leading to reduced transcriptional bursting and target gene expression. In mouse models, disrupting RNA binding  compromises mutant ENL-driven gene expression and malignant self-renewal, halting disease progression and prolonging survival. These findings uncover a previously unrecognized role of RNA in promoting the formation and oncogenic function of chromatin-associated condensate.

overall_design: To determine the role of RNA in modulating pathogenic chromatin-associated condensates.

first: Krista

last: Budinich

first: Xinyi

last: Yao

first: Chujie

last: Gong

first: Lele

last: Song

first: Michelle

middle: C

last: Lee

first: Qinglan

first: Sylvia

last: Tang

first: Kaeli

last: Mathias

first: Yiman

last: Liu

first: Son

last: Nguyen

first: Eric

middle: F

last: Joyce

first: Yuanyuan

first: Haitao


title: RNA promotes nucleation and oncogenic activity of chromatin-associated condensates [RNA-Seq]

last: Li


title: Tissue-specific restriction of transposon-derived regulatory elements safeguards cell-type identity [ATAC-seq]

city: Lausanne

first: Evarist

last: Planet

state: Vaud

address: Route Cantonale

country: Switzerland

institute: EPFL

summary: Transposons, or transposable elements (TEs) have extensively reshaped the cis-regulatory landscape of mammalian genomes, yet the mechanisms that govern their context-specific activity remain incompletely understood. KRAB zinc finger proteins (KZFPs), a large family of transcription factors specialized in TE recognition, are known repressors of TE-derived regulatory activity through TRIM28-mediated H3K9me3 deposition. Here, we expand this paradigm by uncovering noncanonical relationships between TEs and KZFPs. By generating a comprehensive epigenomic map of KZFP-bound TEs, we find that the regulatory activity of ancient mammalian L2/MIR elements is broadly delineated by KZFP binding patterns, despite low H3K9me3 enrichment. We further dissect this relationship by investigating the function of ZNF436, a non-canonical KZFP, highly expressed during in vivo human fetal heart development. Using loss-of-function approaches, we show that ZNF436 preserves cardiomyocyte function by promoting cardiac gene expression while restricting the activation of alternative lineage programs. Mechanistically, ZNF436 recruits specialized SWI/SNF chromatin remodeling complexes to limit the accessibility of L2/MIR-derived enhancers, many of which are active in non-cardiac tissues. These findings reveal a noncanonical, TRIM28-independent role for KZFPs in shaping cell-type-specific regulatory landscapes and emphasize the importance of repressing alternative regulatory programs alongside activating lineage-specific ones to safeguard cell identity.

overall_design: Profiling the gene expression, histone mark and accessibility changes in d15 hESC-derived cardiomyocytes in control and ZNF436 KD condition.

first: Danica

last: Milovanovic


title: Tissue-specific restriction of transposon-derived regulatory elements safeguards cell-type identity [RNA-Seq]


title: amplicon sequence analysis of iPSC-derived iNKT cells and primary iNKT cells

first: Shin

last: Kaneko

state: Kyoto

address: 53 shogoin Kawaharacho Sakyo-ku

summary: 20282 gene expressions of iPSC-derived iNKT cells and primary iNKT cells  were acquired by amplicon-seq and compared their gene expression similarity

overall_design: Examination of mRNA expression from iPSC-derived iNKT cells differentiated using 2D or 3D culture methods and primary iNKT cells

first: Sara

last: Shiina

first: Tatsuki

last: Ueda

first: Shoichi

last: Iriguchi

first: Yasushi

last: Uemura


title: Determinants of long-term response to patritumab deruxtecan (HER3-DXd) in breast cancer patient-derived xenografts.

first: Andreu

last: Òdena

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

overall_design: Refer to individual Series


title: Tissue-specific restriction of transposon-derived regulatory elements safeguards cell-type identity [CUT&Tag]


title: RNA promotes nucleation and oncogenic activity of chromatin-associated condensates [CLAP-seq]

first: Liling

last: Wan

first: Krista

last: Budinich

first: Xinyi

last: Yao

first: Chujie

last: Gong

first: Lele

first: Michelle


title: Stage-specific Epigenetic Priming Amplifies Gene Activation During Lineage Commitment [Micro-C]

city: Freiburg

first: Asifa

last: Akhtar

address: Stuebeweg 51

department: Chromatin Regulation

institute: Max Planck Institute of Immunobiology and Epigenetics

summary: Neural progenitor cells exhibit developmental plasticity, as they are able to commit to different developmental trajectories in response to external stimuli. How these decisions are stabilized at the molecular level remains a highly active area of research. One way to stably integrate external stimuli into cell fate decisions is through epigenetic marks. H4K16ac represents a unique epigenetic mark, as it modulates chromatin compaction and is the only known active histone modification that is transmitted intergenerationally. The deposition of H4K16ac is mediated by the evolutionarily conserved MSL acetyltransferase complex (MSLc), via its catalytic subunit MOF, and mutations in its components have been linked to neurodevelopmental disorders. To dissect the role of the MSLc, we employed a multi-pronged strategy combining both chronic and acute depletion models. Deletion of the MSLc structural backbone Msl1 in vivo resulted in embryonic lethality by E10, and single-cell multi-omics analysis revealed a systemic disruption in lineage commitment within the neuroectoderm. To distinguish primary molecular functions from secondary developmental consequences, we complemented this with a rapid degradation system in vitro, coupled to directed differentiation into two distinct neural lineages. We found that the MSLc facilitates accessibility at regulatory elements in the early stages of lineage commitment during neurogenesis. We observe a significant decrease in enhancer-promoter contacts in a specific subset of neurodevelopmental genes. In the absence of MSLc this gene group fails to reach adequate gene expression levels upon differentiation, resulting in abnormal morphology. Intriguingly, MSLc loss later on during differentiation does not phenocopy this. Our work reveals MSLc-mediated gene priming as a crucial mechanism potentiating the transcriptional activation of neurodevelopmental gene programs. Our study describes a new mode of epigenetic regulation which cements initial cell fate decisions and provides molecular insights into MSLc-associated developmental disorders.

overall_design: Genome wide analysis of 3D chromatin interactions in NPCs and Day7 Neurons. Cells underwent directed in vitro Neuronal differentiation in presence or absence of MSL1 (Auxin treatment during Day0-7 of differentiation).

first: Arion

last: Foertsch

first: Ward

last: Deboutte

first: Janine

last: Seyfferth


title: Stage-specific Epigenetic Priming Amplifies Gene Activation During Lineage Commitment [Multiome]

overall_design: Single-cell multiome datasets were generated from a single E9.5 embryo either WT or homozygous Msl1 KO Genotype. Three biological repicates were independently prepared.

first: Laura

last: Arrigoni


title: Stage-specific Epigenetic Priming Amplifies Gene Activation During Lineage Commitment [RNA-Seq]

overall_design: WT vs KO experiments: Global transcriptomic differences in a chronic MSL1 depletion model (MSL1 KO) during Neuronal differentiation. WT vs dN experiments: Global transcriptomic differences in a chronic MSL1 truncation model (dN-MSL1-F) during Neuronal differentiation. MSL1-AID experiments: Global transcriptomic differences in response to MSL1 depletion via the additin of Auxin to the cell culture medium. MSL1 depletion was carried out either in short term, like 24h MSL1 depletion in NPCs, or throughout entire stages of the directed in vitro differentiation (Auxin treatment: Day0-7, Day7-14 or Day0-14 during Neuronal differentiation or Day0-3 during Astrocyte differentiation). At least three replicates were sequenced per condition.


title: Stage-specific Epigenetic Priming Amplifies Gene Activation During Lineage Commitment [4C]

overall_design: Analysis of locus specific 3D chromatin interactions at genes which showed MSLc primed transcriptomic signatures. Cells underwent directed in vitro Neuronal differentiation in presence or absence of MSL1 (Auxin treatment during Day0-7 of differentiation).

last: Seyffert


title: CDK9 is a Dependency in GATA-3 driven and MCL-1 independent T-cell Lymphomas [ChIP-seq]

first: Chenguang

last: Wang

state: Michigan

address: 1500E Medical Center Dr, Room 4411

department: Department of Internal Medicine

summary: The transcription factor GATA-3 is a proto-oncogene in subsets of mature T cell lymphomas (TCL). CDK9 is a transcriptional regulator that, by phosphorylating paused RNA polymerase II (RNAPII), enables efficient transcriptional elongation. Therefore, we were motivated to examine the extent to which CDK9 is required for controlling transcription and expression of GATA-3 and its target genes. A pharmacologic strategy, using the selective CDK9 inhibitor AZD4573, was utilized to identify CDK9 dependent transcripts. Traveling ratios, defined as the ratio of RNAPII bound at promoter to RNAPII bound within the gene body, were determined by RNAPII ChIP-seq in cell treated with AZD4573 (or vehicle control). CDK9 dependent genes were defined as those with increased traveling ratio and decreased transcripts. MCL-1 dependency was determined in these cell lines by BH3 profiling. The extent to which CDK9 inhibition transcriptionally reprograms TCL was further examined in complementary ex vivo and in vivo studies using primary TCL specimens and GEM and PDX models

overall_design: ChIP-seq and RNA-seq of human T cell lymphoma cells treated with CDK9 inhibitor AZD4573

first: Ryan

last: Wilcox


title: A Natural Cyclic Peptide Enhances Cytotoxic Th9 Differentiation and Antitumor Immunity (ATACseq)

city: Guangzhou

first: yang

last: zhou

address: South Shatai Road, Baiyun District

institute: Southern Medical University

summary: Adoptive cell therapy (ACT) relies on durable and functional T cells to mediate tumor clearance. Th9 cells are a metabolically fit CD4⁺ T cell subset with strong persistence but limited cytotoxicity. Here, we identify Endomelipaneptide A (EpA), a cyclic peptide from Ganoderma lucidum–associated endophytic fungi, as a potent enhancer of Th9 differentiation. EpA promotes a cytotoxic Th9 phenotype with enhanced mitochondrial function and metabolic fitness.

overall_design: Naïve CD4+ T cells were isolated from splenocytes of C57BL/6J, and were cultured in RPMI 1640 medium containing 10% FBS, 1% penicillin-streptomycin and 0.1% β-Mercaptoethanol. Naïve CD4+ T cells were differentiated under plate-bound anti-CD3 (Bioxcell, 17A2, 5 μg/mL) and soluble anti-CD28 (Bioxcell, 37.51, 1 μg/mL) conditions with specific cytokines for Th9 differentiation: IL-4 (peprotech 400-04,10 ng/mL), TGF-β (EPOTO Biotech, 1 ng/mL), anti-IL-12 (Bioxcell, C17.8, 5 μg/mL), and anti-IFN-γ mAbs (Bioxcell, XMG1.2, 10 μg/mL). After the initial 3-day culture, cells were continue culture: IL-4 (10 ng/mL), TGF-β (1ng/mL). Th9 cells on day 4 were analyzed by ATACseq.

first: Wenli

last: Zhao

first: Yang

last: Zhou

first: Yuyang

last: Chen

first: Enguang

last: Bi


title: Stage-specific Epigenetic Priming Amplifies Gene Activation During Lineage Commitment [ATAC-Seq]

overall_design: WT vs MSL1 KO experiments: Global changes in chromatin accessibility in response to chronic MSL1 depletion (MSL1 KO) at different timepoints of the directed in vitro Neuronal differentiation. MSL1-AID experiments: Global changes in chromatin accessibility in response to acute MSL1 depletion in NPCs or prolonged MSL1 depletion throughout the directed in vitro Neuronal differentiation (Auxin treatment from Day0-Day7 of Neuronal differentiation).


title: Stage-specific Epigenetic Priming Amplifies Gene Activation During Lineage Commitment [RELACS]

overall_design: Genome wide patterns of multiple active and repressive histone marks in steady state NPCs in ctrl or MSL1 depleted conditions (24h Auxin treatment). Three replicates were sequenced per condition.


title: Stage-specific Epigenetic Priming Amplifies Gene Activation During Lineage Commitment [CUT&Run]

summary: Precise regulation of epigenetic marks is critical for proper lineage commitment throughout neurodevelopment. Mutations in members of the MSL acetyltransferase complex (MSLc), specific for H4K16ac, are associated with neurodevelopmental disorders in humans. However, the precise gene targets and enzymatic contributions of the MSLc during neural differentiation remain unclear. Through single-cell multi-omics analysis, we demonstrate that Msl1 deletion leads to severe neurodevelopmental defects, culminating in embryonic lethality by E10.5. Using a rapid depletion system, we uncoupled acute transcriptional effects from epigenetic memory and found that MSLc-mediated gene priming is responsible for faithful upregulation of crucial neurodevelopmental gene programs. The priming of the MSLc target genes is limited to the initial stages of differentiation following neuronal induction, where the MSLc facilitates chromatin accessibility at regulatory regions to, allowing for selective enhancer-promoter interactions and subsequent gene activation. Our study identifies the MSLc as a crucial epigenetic regulator during neurodevelopment, providing molecular insights into MSLc-associated developmental disorders.

overall_design: Neural progenitor cells exhibit developmental plasticity, as they are able to commit to different developmental trajectories in response to external stimuli. How these decisions are stabilized at the molecular level remains a highly active area of research. One way to stably integrate external stimuli into cell fate decisions is through epigenetic marks. H4K16ac represents a unique epigenetic mark, as it modulates chromatin compaction and is the only known active histone modification that is transmitted intergenerationally. The deposition of H4K16ac is mediated by the evolutionarily conserved MSL acetyltransferase complex (MSLc), via its catalytic subunit MOF, and mutations in its components have been linked to neurodevelopmental disorders. To dissect the role of the MSLc, we employed a multi-pronged strategy combining both chronic and acute depletion models. Deletion of the MSLc structural backbone Msl1 in vivo resulted in embryonic lethality by E10, and single-cell multi-omics analysis revealed a systemic disruption in lineage commitment within the neuroectoderm. To distinguish primary molecular functions from secondary developmental consequences, we complemented this with a rapid degradation system in vitro, coupled to directed differentiation into two distinct neural lineages. We found that the MSLc facilitates accessibility at regulatory elements in the early stages of lineage commitment during neurogenesis. We observe a significant decrease in enhancer-promoter contacts in a specific subset of neurodevelopmental genes. In the absence of MSLc this gene group fails to reach adequate gene expression levels upon differentiation, resulting in abnormal morphology. Intriguingly, MSLc loss later on during differentiation does not phenocopy this. Our work reveals MSLc-mediated gene priming as a crucial mechanism potentiating the transcriptional activation of neurodevelopmental gene programs. Our study describes a new mode of epigenetic regulation which cements initial cell fate decisions and provides molecular insights into MSLc-associated developmental disorders.


title: CDK9 is a Dependency in GATA-3 driven and MCL-1 independent T-cell Lymphomas [RNA-seq]


title: A Natural Cyclic Peptide Enhances Cytotoxic Th9 Differentiation and Antitumor Immunity

overall_design: Naïve CD4+ T cells were isolated from splenocytes of C57BL/6J, and were cultured in RPMI 1640 medium containing 10% FBS, 1% penicillin-streptomycin and 0.1% β-Mercaptoethanol. Naïve CD4+ T cells were differentiated under plate-bound anti-CD3 (Bioxcell, 17A2, 5 μg/mL) and soluble anti-CD28 (Bioxcell, 37.51, 1 μg/mL) conditions with specific cytokines for Th9 differentiation: IL-4 (peprotech 400-04,10 ng/mL), TGF-β (EPOTO Biotech, 1 ng/mL), anti-IL-12 (Bioxcell, C17.8, 5 μg/mL), and anti-IFN-γ mAbs (Bioxcell, XMG1.2, 10 μg/mL). After the initial 3-day culture, cells were continue culture: IL-4 (10 ng/mL), TGF-β (1ng/mL). RNAex Pro RNA Reagent was used to obtain total RNA of Th9 cells on day 4 for RNAseq.


title: Chromatin Accessibility and Gene Expression Dynamics Suggest Immune-Modulatory Effects of Vitamin D3 In Vivo [ATAC-seq]

city: Olsztyn

first: Maciej

last: Rybiński

state: Warmian-Masurian Voivodeship

address: Trylińskiego 18

country: Poland

institute: Institute of Animal Reproduction and Food Research of the Polish Academy of Sciences.

summary: Vitamin D3 is a key micronutrient known to support innate immunity and modulate adaptive responses, with in vitro studies suggesting involvement of epigenetic mechanisms. However, in vivo evidence for such regulation remains limited. In this proof-of-principle study, we investigated genome-wide epigenomic and transcriptomic responses to vitamin D₃ in a high responder (n=1) from the VitDHiD intervention trial. The participant received monthly oral boluses of 80,000 IU vitamin D3 over three months. Peripheral blood mononuclear cells were collected at baseline (day 0) and at 24 and 48 hours post-supplementation (days 1 and 2) for ATAC-seq and RNA-seq profiling. ATAC-seq revealed over 3,500 regions with increased chromatin accessibility, mainly at gene promoters, indicating a strong epigenomic response. Motif enrichment analysis identified immune-regulatory transcription factors, but not VDR (vitamin D receptor) motifs, suggesting indirect or cooperative regulation. RNA-seq identified 380 vitamin D target genes with time-dependent expression changes, including DUSP6 and FOS. Functional enrichment highlighted pathways related to innate immunity and interferon signaling. Integrative analysis linked 306 differentially expressed genes to nearby vitamin D-sensitive chromatin regions, including both promoters and enhancers. Many of these overlapped with VDR binding sites and promoters of neighboring non-target genes, indicating potential long-range regulatory interactions. Redundancies in regulatory elements were observed among closely located genes sharing enhancers and promoters. These findings provide in vivo evidence that vitamin D3 modulates chromatin accessibility and gene expression, supporting its role as an epigenetic regulator of immune function and highlighting its potential in personalized nutrition and immune health.

overall_design: ATAC-seq libraries of PBMCs obtained from a healthy individual before (day 0) as well as 24 hour (day 1) and 48 hours (day 2) after taking a vitamin D3 bolus (80.000 IU) in three biological repeats

first: Rybiński

last: Maciej

first: Carlberg

last: Carsten


title: Chromatin Accessibility and Gene Expression Dynamics Reveal Immune-Modulatory Effects of Vitamin D3 In Vivo [RNA-Seq]

summary: Vitamin D₃ is a key micronutrient known to support innate immunity and modulate adaptive responses, with in vitro studies suggesting involvement of epigenetic mechanisms. However, in vivo evidence for such regulation remains limited. In this proof-of-principle study, we investigated genome-wide epigenomic and transcriptomic responses to vitamin D₃ in a high responder (n=1) from the VitDHiD intervention trial. The participant received monthly oral boluses of 80,000 IU vitamin D₃ over three months. Peripheral blood mononuclear cells were collected at baseline (day 0) and at 24 and 48 hours post-supplementation (days 1 and 2) for ATAC-seq and RNA-seq profiling. ATAC-seq revealed over 3,500 regions with increased chromatin accessibility, mainly at gene promoters, indicating a strong epigenomic response. Motif enrichment analysis identified immune-regulatory transcription factors, but not VDR (vitamin D receptor) motifs, suggesting indirect or cooperative regulation. RNA-seq identified 380 vitamin D target genes with time-dependent expression changes, including DUSP6 and FOS. Functional enrichment highlighted pathways related to innate immunity and interferon signaling. Integrative analysis linked 306 differentially expressed genes to nearby vitamin D-sensitive chromatin regions, including both promoters and enhancers. Many of these overlapped with VDR binding sites and promoters of neighboring non-target genes, indicating potential long-range regulatory interactions. Redundancies in regulatory elements were observed among closely located genes sharing enhancers and promoters. These findings provide in vivo evidence that vitamin D₃ modulates chromatin accessibility and gene expression, supporting its role as an epigenetic regulator of immune function and highlighting its potential in personalized nutrition and immune health.

overall_design: RNA-seq libraries of PBMCs obtained from a healthy individual before (day 0) as well as 24 hour (day 1) and 48 hours (day 2) after taking a vitamin D3 bolus (80.000 IU) in three biological repeats


title: Splice isoform-perturbation coupled to single cell transcriptome profiling reveals functions of microexons in neurogenesis and autism-linked pathways [snRNA-Seq]

city: Toronto

first: Steven

last: Dupas

address: 160 College St.

country: Canada

institute: University of Toronto

summary: A major challenge of biomedical research is to assign functions to the myriad alternative RNA and protein isoforms. This challenge is particularly relevant to the mammalian nervous system, which produces complex repertoires of alternative splicing events. Here, we describe CHyMErA-seq, a platform that couples systematic deletion of exons to a single cell transcriptomics read-out, and apply this method to investigate a critical program of brain-specific microexons. Perturbation of microexons during neurogenesis reveals convergent roles in the temporal regulation of gene expression programs that direct signalling pathways and morphogenesis. We further observe microexons, including those in the Bin1, Clasp1, Gfra1, Med23, Ptprf and Ralgapb genes, that are required for the correct timing of autism-linked gene expression. Collectively, we describe a flexible system for isoform-resolution perturbation at a single cell level, together with insights into the roles of microexons in the developmental timing of neurogenesis transcriptomic signatures linked to brain disorders.

overall_design: Single-nuclear expression profiling of pooled CRISPR screen for deletion of conserved alternative exons.

first: Guillermo

last: Parada

first: Jack

last: Diayang Li

first: Kevin

last: Brown

first: Jason

last: Moffat

first: Benjamin

last: Blencowe


title: Cardiopulmonary bypass activates classical monocytes via shear-mediated activation of Store-Operated Calcium Entry [scRNA-seq]

city: Seattle

first: Weiming

last: Li

state: WA

address: 4032 8th ave ne

department: Center for developmental biology and regenerative medicine

institute: Seattle children's research institute

summary: Patients undergoing cardiac surgery face significant inflammation induced by exposure to cardiopulmonary bypass (CPB), contributing to heightened morbidity and mortality. The molecular and cellular mechanisms that underpin this inflammatory process remain unknown. To address this knowledge gap, we conducted snRNA/ATAC sequencing to profile transcriptional and chromatin changes on circulating leukocytes from neonatal CPB patients. Classical monocytes become more prevalent after CPB, showing dysregulation of numerous inflammatory genes and significant changes in chromatin accessibility, highlighting their role in CPB-associated inflammation. The proinflammatory cytokine Interleukin 8 (IL8 or CXCL8),  is significantly induced by CPB, with its promoter accessibility to the AP-1 transcription factor significantly increased. A genome-wide CRISPR screen using IL8 gene as a readout in non-adherent monocytic cells identified two genes, non-erythroid spectrin (SPTAN1) and RAF1, as novel effectors of hemodynamic stress. We further found that SPTAN1 and RAF1 activate store-operated calcium entry (SOCE) under CPB conditions, leading to elevated IL8 expression. We propose a novel shear stress-responsive pathway consisting of SPTAN1/RAF1/SOCE signaling. Drug treatment experiments offer a potential therapeutic approach to alleviate CPB-induced inflammation. Together, these findings provide novel insights into the pathogenesis of CPB-associated inflammation, enhancing our understanding of sterile inflammation and how non-adherent cells sense shear stress at molecular level.

overall_design:
Sorafenib, BVD-523, CM-4620 drugs treat PBMCs from three donors.
single cell RNA sequencing using 10x Flex kit.

first: Lan N.

last: Tu

first: Lance

last: Hsieh

first: Julian R.

last: Smith

first: Yi-Ting

last: Yeh

first: Anothony

last: Sinyagin

first: Majid

last: Ghassemian

first: Andrew

last: Timms

first: Lyubomyr

last: Bohuta

first: Christina

last: Greene

first: Juan Carlos

last: del Alamo

first: Ram

last: Savan

first: Vishal

last: Nigam


title: Splice isoform-perturbation coupled to single cell transcriptome profiling reveals functions of microexons in neurogenesis and autism-linked pathways [RNA-seq]

first: Steven

last: Dupas

overall_design: RNA-seq of mouse embryonic stem cells and in vitro differentiated neurons for dCasRx-RBM25 mediated exclusion or exclusion of a target exon in Camta1, Clasp, Ptk2 or Ptprf in duplicate, or Cas9 mediated deletion of Gfra1 homozygous deletion clones or wild type clonal cell lines.

first: Guillermo

last: Parada

first: Jack

last: Diayang Li


title: Mechanism of FABP4 promoting medulloblastoma growth

city: 合肥市

first: 林贵

last: 顾

state: 安徽省

address: 安徽省合肥市蜀山区梅山路安徽医科大学基础医学院

institute: 安徽医科大学

summary: Our results showed that FABP4 knockdown inhibits medulloblastoma cell proliferation, migration, and elevates the ROS and MDA levels, resulting in tumor cell apoptosis.

overall_design: Medulloblastoma cell line DaoY was infected with shFABP4  and pLKO ctrl virus. RNA from these cells was collected and subjected to RNA-seq analysis.

first: Xuanming

last: Shi


title: Antitumor effect of combining STING agonist (ADU-S100) and Doxorubicin versus Doxorubicin alone or control vehicle in mouse sarcoma cell line (WEHI-164)

city: Goyang

first: Wonyoung

last: Choi

state: Gyeonggi

address: 323 Ilsan-ro, Ilsandong-gu

country: South Korea

institute: National Cancer Center

summary: Doxorubicin treatment induces the expression of proinflammatory cytokines through the activation of the STING pathway. Our study demonstrates that the combined administration of the STING agonist ADU-S100 significantly enhances the antitumor efficacy of doxorubicin in a syngeneic mouse model of sarcoma using the WEHI-164 cell line.

overall_design: RNA-seq profiling was performed on CD45+ cells magnetically sorted from dissected tumors treated with: 1) ADU-S100 and doxorubicin, 2) doxorubicin alone, and 3) the control.

first: Gi Yeon

last: Lee

first: Sun-Young

last: Kong


title: DOT1L inhibition exerts anti-tumor effects through activating interferon signaling in breast cancer cells

city: Sapporo

first: Hiromu

last: Suzuki

state: Hokkaido

address: S1, W17, Chuo-ku

department: Department of Molecular Biology

institute: Sapporo Medical University

summary: DOT1L, a histone H3 lysine 79 (H3K79) methyltransferase, is a potential therapeutic target in various malignancies. In the current study, we aimed to clarify the antitumor effect of DOT1L inhibition in breast cancer. Treatment with DOT1L inhibitors (SGC0942, EPZ-5676) suppressed proliferation and induced cell cycle arrest and apoptosis in estrogen receptor (ER)-positive/HER2-negative cancer cells (MCF7) as well as in ER-negative/HER2-positive cancer cells (SKBR3). Transcriptome and epigenome analysis revealed that DOT1L inhibition activated transcription of a number of interferon (IFN)-related genes (IRGs) in both cell lines. Our data suggest that the anti-breast cancer cell effect of DOT1L inhibition is mediated multiple mechanisms including activation of innate immune signaling.

overall_design: Gene expression microarray analysis was performed in breast cancer cells treated with DMSO, SGC0946 or EPZ-5676 for 6 to 12 days.

first: Kazuya

last: Ishiguro


title: Postprandial changes to systemic metabolism imprint durable changes to T cell immunity [ATAC-seq]

city: Pittsburgh

first: Greg

last: Delgoffe

address: 5051 Centre Avenue, 4051

department: Microbiology and Immunology

institute: University of Pittsburgh

summary: Systemic nutrient availability waxes and wanes with dietary input. Here we show that short periods of fasting and refeeding have long-lasting effects on T cell immunity. Human or murine T cells from fed hosts have higher metabolic capacity than those from fasted hosts ex vivo and show better/superior metabolic phenotype and immune response/functions in vitro and in vivo settings of virus infection or tumor model. Serum or chylomicrons enriched from lymphatics of fed mice restores the metabolic and immune functions of fasted T cells. Fed T cells had heightened mTORC1-dependent translation of key immunologic and metabolic genes independent of their epigenetic and transcriptional status. mTORC1 inhibition during the fed period mitigates the postprandial benefit of fed T cells over fasted cells. Our data highlight the need to consider diet content and timing as key factors in immune cell analysis, vaccination strategies, and the generation of cellular therapies.

overall_design: Mice were fasted or fed for overnight (<12 h) and T cells purified. Ex vivo or activated T cells were subjected to epigenetic study/ transcriptomic and translatome studies. For human, blood collected in fasted condition (called as 'Pre') and again after 6 hour of having meal (called as 'Post').  Pre and post ex vivo or activated T cells subjected to transcriptome and translatome studies.

first: Alok

last: Kumar

first: Isha

last: Mehta


title: Postprandial changes to systemic metabolism imprint durable changes to T cell immunity [RNA-seq]


title: Prostaglandin E2-EP2/EP4 signaling induces the tumor-infiltrating Treg phenotype for tumor growth [iTreg]

first: Ryuma

last: Matsuura

address: 53 Kawara-cho, Shogoin, Sakyo-ku, Kyoto City,

summary: Foxp3+ regulatory T cells (Tregs) heavily infiltrate malignant tumors and restrict anti-tumor immunity. These tumor-infiltrating Tregs (TI-Tregs) adopt a distinct phenotype by expressing a unique set of genes including those encoding various co-stimulatory and co-inhibitory molecules. This TI-Treg gene expression signature is conserved in TI-Tregs across species and the types and stages of tumors, suggesting the presence of a common inducing mechanism or mechanisms in tumor microenvironment (TME). However, identity of such a mechanism remains elusive. Here, we show that prostaglandin E2 (PGE2) produced in TME directly acts on its receptor EP2/EP4 on Tregs to induce the TI-Treg phenotype. Indeed, PGE2 added to TCR-activated Tregs induces a set of genes, many of which are included in the reported TI-Treg signature genes, in both induced Tregs (iTregs) and naturally occurring Tregs (nTregs), in a manner dependent on EP2 and EP4 via cAMP-PKA pathway. This is not limited to phenotypic changes, as EP4 agonist-treated Tregs exhibit potent suppressive activity to CD8+ T cells and strongly inhibit their proliferation and survival. Consistently, selective loss of EP2 and EP4 in mouse Tregs and pharmacological inhibition of EP2 and EP4 reduce expression of those genes in Tregs infiltrating LLC1 mouse syngeneic tumor, and significantly delay the tumor progression. In human FOXP3+iTregs, the expression of Treg signature genes, FOXP3, CD25 and CTLA4 as well as a typical TI-Treg signature gene, 4-1BB are significantly upregulated by PGE2-EP4 signaling. Furthermore, analysis of scRNA-seq of nasopharyngeal cancer patients demonstrates preferential expression of the TI-Treg signature genes in Tregs infiltrating the PTGS2hi tumor group compared to the PTGS2lo tumor group. These findings suggest that PGE2-EP2/EP4 signaling is one of the molecular mechanisms inducing the TI-Treg phenotype in TME.

overall_design: mRNA profiles of Foxp3+ iTreg and nTreg treated in vitro with PGE2 and an EP4 agonist, respectively, and tumor-infiltrating Treg sorted ex vivo from LLC1 tumor-bearing control mice and Treg-specific EP2/EP4 KO mice.

first: Shuh

last: Narumiya


title: A-to-I RNA editing prevents an inflammation-mediated lipodystrophy in adipose tissue

city: Singapore

first: Jia

last: Li

address: 8 College Road

country: Singapore

institute: Duke-NUS

summary: RNA editing is a post-transcriptional mechanism that alters the specific nucleotide sequences of RNA to enhance the diversity of gene products. However, the biological function of RNA-editing in different cell types remained poorly understood. In this study, we delineated a comprehensive RNA editome across brown, visceral and subcutaneous adipose tissues from both human and mouse. The edited genes in two species are significantly overlapped and highly enriched for RNA metabolism and lipid metabolism pathways. Using an adipose tissue-specific Adar1 knockout mouse model, we demonstrated that the deficiency of A-to-I editing, through an enhanced formation of double strand RNA (dsRNA) structures, resulted in an inflammation-mediated lipodystrophy which can be fully rescued by deleting Ifih1, a sensor for dsRNA structures. Taken together, our study has addressed a new and fundamental question about the function of RNA editing in adipose tissue.

overall_design: Editing and gene expression analysis in adipose related samples.

first: Dan

last: Xu

first: Lei

last: Sun


title: Normal murine fibroblasts from the colon

city: Paris

first: Noémie

last: Robil

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

country: France

institute: GenoSplice technology

summary:
In the  colon, a single-layered epithelium lines the crypts, which descend into the underlying mucosa. Surrounding the crypts lies a large network of fibroblasts with diverse functions, including extracellular matrix (ECM) production and stem cell  maintenance. However, functional diversity of those cells remains unexplored.
To address  fibroblast heterogeneity in colon homeostasis, we conducted single-cell RNA sequencing on epithelium-stripped colonic mucosal samples of aSMACre:mTmG-reporter mouse. We found 6 clusters of  fibroblasts.

overall_design: Experiment was done on the tissue from colon isolated from an αSMACre:mTmG mouse, injected 5 consecutive days with Tamoxifen (50 mg/kg) and analyzed 2 days after.

first: Aleksandra

last: Chikina

first: Neda

last: Glisovic

first: Sonia

last: Lameiras

first: Danijela

last: Matic Vignjevic


title: Prostaglandin E2-EP2/EP4 signaling induces the tumor-infiltrating Treg phenotype for tumor growth [TITreg]

city: Kyoto

institute: Kyoto University


title: Prostaglandin E2-EP2/EP4 signaling induces the tumor-infiltrating Treg phenotype for tumor growth [nTreg]


title: Extensive remodelling of XIST regulatory networks during primate evolution [WGS]

first: Claire

last: Rougeulle

address: 35 rue Hélène Brion

institute: Université Paris Cité

type: Genome variation profiling by high throughput sequencing

summary: Unravelling how gene regulatory networks are remodelled during evolution is crucial to understand how species adapt to environmental changes. We addressed this question for X-chromosome inactivation, a process essential to female development that is governed, in eutherians, by the XIST lncRNA and its cis-regulators. To reach high resolution, we studied closely related primate species, spanning 55 million years of evolution. We show that the XIST regulatory circuitry has diversified extensively over such evolutionary timeframe. The insertion of a HERVK transposon has reshuffled XIST 3D interaction network in macaque embryonic stem cells (ESC) and XIST expression is maintained by the additive effects of the JPX lncRNA gene and a macaque specific enhancer. In contrast, JPX is the main contributor to XIST expression in human ESCs but is not significantly involved in XIST regulation in marmoset ESCs. None of these entities are however under purifying selection, which suggests that neutrally evolving non-coding elements harbour high adaptive potentials.

sample_organism:
Callithrix jacchus
Macaca mulatta

platform_organism:
Callithrix jacchus
Macaca mulatta

overall_design:
Whole genome sequencing of two female embryonic stem cell lines from macaque (rhESC-LYON1) and marmoset (CMES-40)

Re-analyzed Sample GSM4610404 was submitted to GEO previously in GSE152259.

first: Cazottes

last: Emmanuel


title: MHC II-restricted neoantigen vaccine reverses immune microenvironment and overcomes resistance to immune checkpoint inhibitors in cold tumors

city: Nanjing

first: Chun

last: Lu

address: No. 8 Xuefu Road, Pukou

institute: Nanjing University

summary: Cold tumors are resistant to immune checkpoint inhibitors (ICIs) due to their poor T cell infiltration and immunosuppressive tumor microenvironment (TME). While the role of CD4+ T cell response in anti-tumor immunity has been emphasized, it remains unclear whether the MHC II-restricted neoantigen vaccines targeting CD4+ T cell can reverse the immune microenvironment and overcome resistance to ICIs. Here we observed an enrichment of immune inflammation-related signaling pathways in TME following administration of MHC II-restricted neoantigen vaccines, indicating their potent role in reversing immunosuppressive TME. An increase in the tumor infiltration of CD4+ T cells and CD8+ T cells, an enhancement of their effector functions, and a tendency towards exhaustion were observed, providing prerequisites for the effectiveness of ICI treatment. Furthermore, NicheNet analysis indicated an enrichment of the inhibitory immune checkpoint signaling axis PVR-TIGIT following vaccination. The combination of the vaccines and TIGIT blockade exhibited synergistic anti-tumor efficacy. Mechanistically, the combination therapy promoted the differentiation of CD8+ T cells into effector memory phenotypes while delaying their exhaustion. Our study demonstrates that MHC II-restricted neoantigen vaccines can remodel the inhibitory TME with insufficient T cell infiltration and synergistically inhibit tumor growth with TIGIT antibody, providing a novel strategy for treating cold tumors.

overall_design: B16F10 tumor bearing mice were subcutaneously injected with two doses of saline, M44 vaccine (50 µg M44 peptide formulated with 20 μg CpG) or M44 vaccine and TIGIT antibody on day 2 and 8, and tumors were collected by euthanizing on day 10. CD45 (TIL) MicroBeads (Miltenyi Biotec, #130-110-618, DE) were used for isolating the CD45+ immune cells for scRNA-seq (n=6 mice per group, mixed sample detection).

first: Xueru

last: Song


title: NFATc1 and NFATc2 regulate glucocorticoid resistance in pediatric T-cell acute lymphoblastic leukemia through modulation of cholesterol biosynthesis and the WNT/β-catenin pathway

city: padova

first: silvia

last: bresolin

state: padova

address: via giustiniani 3

department: department of women's and children's health

institute: università di padova

summary: he glucocorticoid (GC) resistance onset in pediatric T-cell Acute Lymphoblastic Leukemia (T-ALL) patients remains one of the biggest challenges in current cancer treatment. The mechanisms driving this resistance are still not fully understood, making it difficult to predict patient outcomes and to develop effective therapies. Our study uncovered critical insights into the biological processes underlying GC resistance, offering potential breakthroughs for future treatments. Building on our previous research on LCK kinase hyperactivation in GC-resistant T-ALL patients, we have now delved deeper into the LCK downstream NFAT transcription factor family's contribution to GC resistance. We discovered that, even at the time of diagnosis, GC resistant T-ALL patients exhibit an intrinsic low glucocorticoid receptor (GR) activity coupled with high NFATc1 and NFATc2 ones. This dysregulation creates a roadblock to effective GC therapy. Indeed, in the absence of either NFATc1 or NFATc2, the normal transcriptional activity of GR is restored, re-sensitizing the leukemia cells to dexamethasone treatment both in vitro and in vivo. This suggests that NFATc1 and NFATc2 are central to driving GC resistance, as they directly regulate crucial pathways like cholesterol biosynthesis and WNT/β-catenin signaling. The identification of NFAT transcription factors as key players in leukemia therapy resistance offers a promising target for future therapeutic strategies, potentially transforming the way we approach treatment for these challenging conditions or autoimmune disorders where glucocorticoids are a cornerstone of treatment.

overall_design: Gene expression was measured using Affymetrix platform in P12-ICHIKAWA and TALL-1 cell lines treated or not with 1µM dex for 12 hours.

first: Silvia

last: Bresolin

first: Valentina

last: Serafin


title: RNA sequencing of fresh tumor tissues from B16F10 tumor bearing mice treated with saline or M44 vaccine

summary: To further reveal the immune regulatory effects of MHC II-restricted vaccines on TME, bulk RNA sequencing (bulk RNA-seq) was performed to analyze the overall immune signal transformation. Differential gene expression analysis recognized a total of 1695 upregulated and 343 downregulated genes on the M44 vaccination. Specifically, a higher expression of CD74, H2-Ab1, H2-Eb1, H2-Aa was observed in the vaccinated group, indicating the active MHC class II antigen processing and presentation in tumors. The ssGSEA method was used to quantify RNA-seq data of each sample and the GO_BP (Biological Process of Gene Ontology) term scores were calculated. The results indicated that the majority of the terms within high ssGSEA scores were related to both adaptive and innate immune-related processes.We then sorted the top 300 differently upregulated genes to generated pathway enrichment analysis and clustered the pathways into 20 categories based on functional relevance. Interestingly, the majority of categories were related to the activation of antitumor immune response, such as “inflammatory response” “leukocyte activation” “antigen processing and presentation” “leukocyte migration” and “phagocytosis”. Moreover, immune infiltration estimations showed increased infiltration levels of T cells, CD8+ T cells, NK cells, memory B cells and monocytes/macrophages.

overall_design: B16F10 tumor bearing mice were subcutaneously injected with two doses of saline or M44 vaccine (50 µg M44 peptide formulated with 20 μg CpG) on day 2 and 8, and tumors were collected by euthanizing on day 10 (n=5 mice per group) . Fresh tumor tissues were processed for bulk RNA-seq to reveal the immune regulatory effects of MHC II-restricted vaccines on tumor microenvironment.


title: Differential gene expression between the hippocampus of WT and SNAT3 (Slc38a3)-conditional knockout mice

city: Haifa

first: Inna

last: Radzishevsky

address: Oren 13

department: Biochemistry

country: Israel

institute: Inna Radzishevsky

summary: The main goal of this study was how the brain obtains glutamine during the early postnatal period, when the expression of glutamine synthetase is low. We found that early postnatal mice maintain their brain glutamine levels by importing glutamine from the blood. We identified the Slc38a3 transporter as a primary transendothelial glutamine transporter at brain capillaries. Mice with selective knockout of Slc38a3 (Slc38a3-cKO) in endothelial cells exhibit a significant decrease in the influx of glutamine and histidine through the BBB at postnatal day 11 (P11). This is accompanied by a significant decrease in brain glutamine and histidine levels, along with secondary reductions in essential amino acids that are not substrates of Slc38a3. Slc38a3-cKO mice also exhibit postnatal/progressive microcephaly, similar to that observed in patients with mutations in Slc38a3. Slc38a3-cKO mice exhibit behavioral deficits, metabolic impairments, and synaptic alterations at P11.

overall_design: RNA-seq profiling of hippocampi isolated from 11-day-old wild-type mice and mice with selective knockout of Slc38a3 (Slc38a3-cKO) in endothelial cells

first: Herman

last: Wolosker


summary: The glucocorticoid (GC) resistance onset in pediatric T-cell Acute Lymphoblastic Leukemia (T-ALL) patients remains one of the biggest challenges in current cancer treatment. The mechanisms driving this resistance are still not fully understood, making it difficult to predict patient outcomes and to develop effective therapies. Our study uncovered critical insights into the biological processes underlying GC resistance, offering potential breakthroughs for future treatments. Building on our previous research on LCK kinase hyperactivation in GC-resistant T-ALL patients, we have now delved deeper into the LCK downstream NFAT transcription factor family's contribution to GC resistance. We discovered that, even at the time of diagnosis, GC resistant T-ALL patients exhibit an intrinsic low glucocorticoid receptor (GR) activity coupled with high NFATc1 and NFATc2 ones. This dysregulation creates a roadblock to effective GC therapy. Indeed, in the absence of either NFATc1 or NFATc2, the normal transcriptional activity of GR is restored, re-sensitizing the leukemia cells to dexamethasone treatment both in vitro and in vivo. This suggests that NFATc1 and NFATc2 are central to driving GC resistance, as they directly regulate crucial pathways like cholesterol biosynthesis and WNT/β-catenin signaling. The identification of NFAT transcription factors as key players in leukemia therapy resistance offers a promising target for future therapeutic strategies, potentially transforming the way we approach treatment for these challenging conditions or autoimmune disorders where glucocorticoids are a cornerstone of treatment.

overall_design: Gene expression was measured using Affymetrix platform in RPMI-8402 cell line transduced with a second generation lentiviral plasmids containing  a short hairpin RNA (ShRNA) NFATc2  expression cassette (named, Sh143) or a control ShRNA sequence (ShRNA CNTR), treated or not with 10µM  Dex for 12 hours.


overall_design: Gene expression was measured using Affymetrix platform in TALL-1 cell line transduced with a second generation lentiviral plasmids containing  a short hairpin RNA (ShRNA) NFATc1  expression cassette (named, Sh335) or a control ShRNA sequence (ShRNA CNTR), treated or not with 1µM Dex for 12 hours.


title: NFATc1 and NFATc2 control glucocorticoid resistance in pediatric T-cell acute lymphoblastic leukemia by regulating cholesterol biosynthesis and WNT/ꞵ-catenin pathway

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

overall_design: Refer to individual Series


title: Extensive remodelling of XIST regulatory networks during primate evolution [ATAC-Seq]

overall_design: Chromatin accessibility in primed rhesus ESCs studied by ATAC-seq on primed rhESCs replicates.

first: Charbel

last: Alfeghaly


title: Boron deficiency stress treatment in sweet orange

city: kunming

first: xiuyao

last: yang

state: yunnan

address: Southwest Forestry University, 300 Bailong Road, Qingyun Street, Panlong District, Kunming, Yunnan Province, China

institute: Southwest Forestry University

summary: Transcriptome sequencing of boron deficiency stress treatment in sweet orange

overall_design:
Sweet orange histocultures were transferred to MS nutrient solution with adequate boron concentration of
0.25 mg/L as control and set boron stress concentration of 0.01 mg/L, respectively
control and treated histocultures were placed in the histoculture chamber at 25°C for 25 days and sweet orange leaves were collected in three biological replicates


title: Extensive remodelling of XIST regulatory networks during primate evolution [Cut & Run]

sample_organism:
Macaca mulatta
Homo sapiens

platform_organism:
Macaca mulatta
Homo sapiens

overall_design: CUT&RUN for H3K4me3, H3K4me1 and H3K27ac histone modifications and for CTCF in primed rhesus ESCs and for H3K4me1 and H3K27ac histone modifications in primed human ESCs. Two independent replicates were analysed.


title: Leukemic Cells Hijack Stromal Bioelectricity to Reprogram the Bone Marrow Niche via CaV1.2-Dependent Mechanisms

summary: Mesenchymal stromal cells (MSCs) are key components of the tumor microenvironment (TME), influencing leukemia progression through poorly understood mechanisms. Here, the bioelectrical properties of MSCs derived from pediatric acute myeloid leukemia (AML) patients (AML-MSCs) are investigated, identifying a significant depolarization of their resting voltage membrane potential (Vmem, -14.7 mV) compared to healthy MSCs (h-MSCs, -28.5 mV), accompanied by downregulation of Calcium channel, voltage-dependent, L type, alpha 1C subunit1.2 (CaV1.2) L-type calcium channel expression. AML-MSCs display increased spontaneous calcium oscillations, suggesting altered ion homeostasis. Notably, h-MSCs exposed to AML blasts undergo a similar Vmem depolarization (-11.8 mV) and CaV1.2 downregulation, indicating that leukemic cells actively reprogram MSCs. Functionally, Vmem depolarization in h-MSCs promotes a pro-leukemic phenotype, whereas hyperpolarization of AML-MSCs restores a normal behavior. CaV1.2 over-expression by lentiviral vectors in AML-MSCs shifts the Vmem toward hyperpolarization and partially reverses their leukemia-supportive properties, in part through CaV1.2 transfer via tunneling nanotubes. These findings reveal that AML blasts impose a bioelectrical signature on MSCs, modulating ion channel activity to sustain a leukemic niche. Targeting this electrical reprogramming through CaV1.2 restoration represents a potential strategy to re-establish homeostasis in the bone marrow microenvironment.

overall_design: Gene expression was measured using Affymetrix platform in AML-MSCs transduced with the CaV1.2 gene by a third generation lentivirus.

first: Martina

last: Pigazzi

first: Maddalena

last: Benetton


title: Copper inhibits ATR and synergizes with PARP inhibitors (DTP model RNA-seq and Ola-ATRi-EC cGAS-STING RNA-seq)

city: Beijing

first: Yabing Nan

last: Yabing Nan

address: 17 Panjiayuan Nanli, Chaoyang Diistrict

institute: Cancer Hospital Chinese Academy of Medical Sciences


title: Innate immune and metabolic signaling retain damaged mitochondria at cell membranes for mitoxyperilysis

city: Memphis

first: Thirumala-Devi

last: Kanneganti

address: 262 Danny Thomas Place

institute: St. Jude Children's Research Hospital

summary: Innate immune activation coupled with metabolic disruptions play critical roles in many diseases, often leading to mitochondrial dysfunction and oxidative stress that drive pathogenesis. However, mechanistic regulation under these conditions remains poorly defined. Here, we report a distinct lytic cell death mechanism induced by innate immune signaling and metabolic disruption, independent of caspase activity and previously described pyroptosis, PANoptosis, necroptosis, ferroptosis, and oxeiptosis. Instead, mitochondria undergoing BAX/BAK1/BID-dependent oxidative stress maintained prolonged plasma membrane contact, leading to local oxidative damage, a process we termed mitoxyperiosis. This process then caused membrane lysis and cell death, mitoxyperilysis. mTORC2 regulated the cell death, and mTOR inhibition restored cytoskeletal activity for lamellipodia retractions to mobilize mitochondria away from the membrane, preserving integrity. Activating this pathway in vivo regressed tumors in an mTORC2-dependent manner. Overall, our results identify a lytic cell death modality in response to the synergism of innate immune signaling and metabolic disruption.

overall_design: To evaluate the expression profiles in bone marrow derived macrophages under different stimulations (media, CS, LPS, LPS+CS and LPS+CS+Torin), BMDMs were stimulated as indicated for 9hours and RNA was extracted by trizol and subject to sequencing.

first: Yaqiu

last: Wang


title: ARID1A recruits TRIM28 for the essential remodeling of heterochromatin independent of SWI/SNF

city: Shanghai

first: Nestor

last: Zhang

address: Dongchuan Road

institute: Shanghai Jiao Tong University


title: Disease-related p63 DBD mutations impair DNA binding by distinct mechanisms and varying degree [RNA-seq]

city: Naples

first: Dario

last: Antonini

address: Strada Vicinale Cupa Cintia, 21

department: Department of Biology

institute: University of Naples "Federico II"

summary: The transcription factor p63 shares a high sequence identity with the tumour suppressor p53 which manifests itself in high structural similarity and preference for DNA sequences. While mutations in the DNA binding domain of p53 cause cancer, mutations in the p63 DNA binding domain result in developmental syndromes affecting lip/palate, skin and limbs. For p53 the effect of mutations has been studied in great detail, enabling the identification of several mechanisms by which mutations inhibit high affinity binding of p53 to DNA. In this study we provide a similar detailed investigation of all currently known mutations in the p63 DNA binding domain by measuring the transcriptional activity, DNA binding affinity, zinc binding capacity and thermodynamic stability. Some of the mutations we have further characterized with respect to their ability to convert human dermal fibroblasts into induced keratinocytes, to elicit changes in the transcriptional program similar to those observed by wild type p63, and to bind regulatory regions in the genome. The data demonstrate that no mutation globally destabilizes and unfolds the domain. Several mutations affect the DNA binding affinity by disturbing the interaction between the DNA binding domains, thereby disrupting p63 ability to bind DNA as a tetramer cooperatively. These mutations retain partial DNA binding capacity which correlates with a milder patient phenotype.

overall_design: p63 binding occupancy was assessed by ChIP-seq with anti-p63 antibodies in BJ-Human Fibroblast expressing KLF4 alone (empty) or ΔNp63α WT (or p63 mutants) and KLF4

first: Christian

last: Osterburg

first: Marco

last: Ferniani

first: Ann-Sophie

last: Frombach

first: Ludovica

last: D’Auria

first: Susanne

first: Rebecca

last: Lotz

first: Frank

last: Löhr

first: Sebastian

last: Kehrloesser

first: Huiqing

last: Zhou

first: Caterina

last: Missero

first: Volker

last: Dötsch


title: Disease-related p63 DBD mutations impair DNA binding by distinct mechanisms and varying degree [ATAC-seq]

overall_design: Chromatin accessibility was assessed by ATAC-seq in BJ-Human Fibroblast expressing KLF4 alone (empty) or ΔNp63α WT and KLF4


title: Extensive remodelling of XIST regulatory networks during primate evolution [Capture Hi-C]

first: Claire

last: Rougeulle

sample_organism:
Macaca mulatta
Pan troglodytes

platform_organism:
Macaca mulatta
Pan troglodytes

overall_design: capture HiC in primed rhesus ESCs and chimpanzee iPSC. Two independent replicates were analysed.

first: Cazottes

last: Emmanuel

first: Villacorta

last: Laura


title: Disease-related p63 DBD mutations impair DNA binding by distinct mechanisms and varying degree


title: Disease-related p63 DBD mutations impair DNA binding by distinct mechanisms and varying degree [ChIP-seq]


title: Copper inhibits ATR and synergizes with PARP inhibitors (RNA-seq)

first: Yabing Nan

last: Yabing Nan

summary: This study unveils copper targeting ATR signaling, synergizing with PARPi to suppress ovarian cancer.

overall_design: RNA-seq of ES-2 derived drug-adaptive cells and parental cells

first: Yabing


title: Tumor cell intrinsic RIG-I activation is sufficient to drive immune mediated tumor rejection

city: Portland

first: sudarshan

last: anand

address: 2720 S Moody Ave

department: CDCB

institute: oregon health & science university

summary: Tumor microenvironment (TME) is key in cancer development. Rencently strategies focus on activation of the innate immune response to enhance the immunesurveillance. Here, we analyse how activation of the nucleic acid sensor RIG-I modifies the tumor cells transcriptome.

overall_design: CT26 Tumors N=3 RIG-I agonist treated cells; N=3 Control agonist treated cells. E0771 N=2 RIG-I agonist treated cells; N=2 Control agonist treated cells

first: Fraile-Bethencourt

last: Eugenia

first: Khou

last: Sokchea

first: Sudarshan

last: Anand


title: Circulating small extracellular vesicle-based miRNA classifier for follicular thyroid carcinoma: a multicenter diagnostics study

city: Chengdu

first: Genpeng

last: Li

state: AA

address: Guoxuexiang 37

institute: West china hospital

summary: Discrimination between follicular thyroid carcinoma (FTC) and follicular thyroid adenoma (FTA) prior to surgery remains a major challenge in clinical practice. To evaluate the feasibility of circulating small extracellular vesicle (sEV)-associated and cell-free RNAs for non-invasive detection of FTC. The diagnostic properties of sEV long RNAs, cell-free long RNAs, sEV miRNAs, and cell-free miRNAs were compared for the detection of FTC.

overall_design: 21 FTC plasma samples and 20 FTA plasma samples were collected. EV long RNAs, cell-free long RNAs, EV miRNAs, and cell-free miRNAs were pairwise detected. Cell-free small and long RNA libraries were not prepared for two participants (FTA-14 and FTA-19) due to the limited plasma samples.

first: Hongke

last: Wang


title: Sensitive and unbiased genome-wide profiling of base-editor-induced off-target activity with CHANGE-seq-BE [gRNA sequencing for ABE targets]

status: Public on Nov 27 2025

first: Shengdar

last: Tsai

state: TN

address: 262 Danny Thomas Pl

department: Department of Hematology

institute: St Jude Children's Research Hospital

summary: To identify potential contaminating gRNAs, we adapted a gRNA sequencing assay based on an established SMARTer smRNA sequencing technology. We evaluated five research-grade gRNAs from three synthetic gRNA manufacturer suppliers (A, B and C). We detected the presence of contaminating gRNAs in CBLB and CIITA gRNAs from supplier A (batch 1), with frequency ranging from 0.09% to 2.71%.

overall_design: guide-RNA (gRNA) sequencing of commerically synthesized gRNAs from multiple manufacturers (suppliers A, B, and C) using modified SMARTer smRNA-seq technology.

first: Varun

last: Katta

first: Yichao


title: Prior High Fiber Intake Impinges on the Cellular Responses of Mesenteric Adipose and Intestinal Tissues to Subsequent High Fat Feeding [16s rRNA-seq]

city: Huddinge

first: Zhi

last: Peng

state: Stockholm

address: Blickagången 16

department: MedH

country: Sweden

institute: Karolinska Institutet

summary: Obesity, characterized by its chronic, recurrent and progressive nature, has become one of the most serious public health problems. As living standards improve, plant-based diet composed of whole grain and vegetable is gradually replaced by high-fat food of animal origin in daily life. The resulting increase in caloric intake is one of the major causes of obesity. In white adipose tissue, excessive calorie intake promotes adipocyte hypertrophy and hyperplasia, increases immune cell infiltration around dysfunctional adipocytes and causes rearrangement of adipocyte subpopulations. In intestinal tissue, obesity development is associated with activation of the gut microbiota to process indigestible dietary polysaccharides into short-chain fatty acid (SCFA) for intestinal absorption. At the cellular level, a high-fat/high-sugar diet induces excessive proliferation and differentiation of intestinal stem cells, leading to onset of intestinal maladaptation and obesity development. In addition, several studies have shown that a high-fat diet (HFD) can affect the enteric nervous system in multiple aspects, including neuronal density, expression of glial cell marker proteins, and ganglion size. A recent study shows that enteric glial cells play a key role in maintaining the homeostasis of the intestinal stem cell niche.

overall_design: We collected fecal samples from the two diet groups at the three time points for 16S sequencing to compare the temporal dynamics of the gut microbiome.

first: Meng

last: Xie


title: Hsp70-Bim interaction mediated mitophagy as a potential therapeutic target for CML stem cells

city: Dalian

first: Ting

last: Song

address: No.2 LingGong Road, GanJingZi District, Dalian, Liaoning, China

institute: Faculty of Medicine, Dalian University of Technology

summary: In chronic myeloid leukemia (CML), disease persistence in patients is maintained by leukemic stem cells (LSCs), which drives tyrosine kinase inhibitor (TKI) resistance. Autophagy has been proposed as a potential therapy to eradicate CML LSCs. Here, using a small-molecule inhibitor of Hsp70 (heat shock protein 70)-Bim (Bcl-2-interacting mediator of cell death) interaction, S1-10, we demonstrate that Hsp70-Bim is a target for CML stemness maintenance. Hsp70-Bim is driven by Bcr-Abl and mediates particularly stronger mitophagy in CML LSCs than differentiated CML cells and HSCs. The more selective mitophagy regulation of Hsp70-Bim than ULK1 (unc-51-like autophagy activating kinase 1) is illustrated. Pharmacological inhibition of Hsp70-Bim blocks mitophagy, leading to differentiation of CML LSCs, loss of quiescence, and loss of LSC self-renewal potential. In the patient-derived xenograft (PDX) CML models, S1g-10 reduces the number of LSCs by more than 80% after two weeks of injection, without obvious toxicity on normal red blood cells.

overall_design: RNA-seq analysis of human primary CML CD34+ cells treated with Hsp70-Bim inhibitor S1g-10 (1 μM) versus Vehicle (DMSO) for 24 hours.

first: Yang

first: Hong

last: Zhang

first: Zhiyuan

last: Hu

first: Fangkui

last: Yin

first: Zhichao


title: Gene expression changes in mouse skin after exposure to SspA and house dust mite extract

city: Charlestown

first: Jin Mo

last: Park

address: 149 Thirteenth Street

department: Cutaneous Biology Research Center

institute: Massachusetts General Hospital

summary: The skin reprograms its gene expression during dermatitis. This transcriptome profiling examines dermatitis-associated gene expression changes in the skin of mice epicutaneously treated with the Staphylococcus aureus protease SspA, also known as protease V8, and house dust mite extract (HDM). Treatment with SspA and HDM combination results in skin disease in mice that closely resembles atopic dermatitis. The genes whose expression changes in this dermatitis model include cytokines, chemokines, and other molecular mediators of intercellular communication in inflamed skin.

overall_design: RNA was isolated from mouse skin left untreated or treated with SspA (staphylococcal protease V8) and HDM. Isolated RNA was subjected to RNA sequencing for gene expression profiling.

first: Toshimi

last: Yoshida

first: Yanek

last: Jiménez-Andrade


title: Cetacean single-nucleus RNA-sequencing positions the cardioprotective gene FHL2 as a target for advancing pig-to-human heart xenotransplantation

city: BeiJing

first: Yue

address: North Lishi Road

institute: Fuwai Hospital, Chinese Academy of Medical Sciences

summary: Damage to the heart, an organ core to the circulation of oxygen and nutrients to the body, significantly reduces lifespan. A heart transplant from human donors (allografts) has been possible for the last four decades, but there is a severe shortage of donor hearts. While transplants from other species (xenografts) are now possible, post-transplant dysfunction limits their success. Herein, we employed a learn-from-nature approach to identify genes that underlie improved cardiac performance. We generated and compared cetacean (the rough-toothed dolphin, Steno bredanensis), bama pig, and human myocardial transcriptomes to identify cellular and molecular features underlying the exceptional resilience of the cetacean heart. The cetacean myocardium exhibits a distinct cell type gene expression signature, marked by a broad and elevated expression of FHL2 (four and a half LIM domains 2) by cardiomyocytes. Overexpression of FHL2 in a mouse model of cardiac failure alle viated pressure overload-induced cardiac dysfunction (hypertrophy). Our bioinspired study provides proof of principle for improved heart function through cardiomyocyte-targeted overexpression of a single gene as a promising candidate for gene editing to enhance pig-human xenotransplant success.

sample_organism:
Homo sapiens
Sus scrofa
Steno bredanensis

overall_design: The snRNA-seq data from three human hearts, two pig hearts, and  two technical replicates of the hearts of one whale heart were compared.


title: Transcriptomic analysis of STUB1 knockdown in HEK293 cells under normal and heat-shock conditions

city: Chapel Hill

first: Jonathan

last: Schisler

state: NC

address: MBRB, Rm 2340C

department: McAllister Heart Institute

institute: The University of North Carolina at Chapel Hill

summary: Poly-A selected mRNA-seq was performed on HEK293 cells stably expressing either shRNA targeting STUB1 (shSTUB1 / shCHIP) or non-targeting control shRNA (shCTL). Biological triplicates were collected under basal conditions (37°C) and after acute heat shock (42°C for 30 minutes) to investigate the role of the STUB1/CHIP co-chaperone/E3 ligase in the cellular heat-shock response and proteostasis. This dataset supports the RNA-seq component of the study examining biochemical and clinical implications of STUB1 mutations in spinocerebellar ataxia type 48 (SCA48).

overall_design: 12 samples total: 4 experimental conditions (shControl 37°C, shControl 42°C 30 min, shSTUB1 37°C, shSTUB1 42°C 30 min) × 3 independent biological replicates. Libraries were multiplexed (6-plex per lane) and sequenced single-end 50 bp on an Illumina HiSeq 2500.

first: Sarah

last: Ronnebaum


title: The Phosphate-Specific Transport System Gene pstA1 Contributes to Rifampin Tolerance in Mycobacterium tuberculosis

city: Baltimore

first: Petros

last: Karakousis

state: MD

address: 1550 Orleans Street

department: Medicine

institute: Johns Hopkins University School of Medicine

summary: This study investigates the role of the phosphate-specific transport system gene pstA1 in rifampin tolerance in Mycobacterium tuberculosis. We constructed a pstA1 deletion mutant (ΔpstA1) and demonstrated that it exhibits enhanced rifampin susceptibility compared to wild-type H37Rv. To explore the molecular mechanisms underlying this phenotype, we performed RNA-seq transcriptomic analysis comparing wild-type and ΔpstA1 strains grown in standard Middlebrook 7H9 broth under exposure to sub-inhibitory rifampin (7.5 ng/ml, 1/4 MIC) for 30 or 60 minutes. The analysis revealed substantial transcriptional reprogramming in ΔpstA1, providing insights into how loss of PstA1 function leads to increased rifampin susceptibility.

overall_design: RNA-seq profiling of wild-type Mycobacterium tuberculosis H37Rv and ΔpstA1 strains with and without rifampin treatment. Strains were cultured in Middlebrook 7H9 broth and sampled at three timepoints: untreated control (0 min), 30 minutes after sub-inhibitory rifampin exposure (7.5 ng/ml), or 60 minutes after rifampin exposure. Three biological replicates per strain per condition.

first: Carina

last: Danchik

first: GV Anoushka

last: Chinmayi

first: Gi Yong

last: Lee

first: Joel

middle: S

last: Bader

first: Hyungjin

last: Eoh


title: Identification of Blood-Brain Barrier Injury-Related Biomarkers in Cerebral Infarction Using Transcriptomic Analysis

city: Macao Special Administrative Region of China

first: GAO

middle: SHAN

last: SHAN

address: MACAU UNIVERSITY STREE

country: Macau

institute: MACAU UNIVERSITY

summary: Background: Cerebral infarction leads to blood-brain barrier (BBB) disruption, exacerbating brain injury through edema, inflammation, and neuronal death. Although BBB damage is a critical event in stroke pathology, the underlying molecular mechanisms and reliable biomarkers remain poorly understood. This study aimed to identify key biomarkers associated with BBB injury following cerebral infarction using an in vitro model and transcriptomic approaches. Human cerebral microvascular endothelial cells (hCMEC/D3) were subjected to oxygen-glucose deprivation (OGD) and OGD/reoxygenation (OGD/R) to simulate ischemic and reperfusion injury. Cell viability, inflammatory cytokines, LDH release, and angiogenesis were assessed. Transcriptomic sequencing, weighted gene co-expression network analysis (WGCNA), and random forest algorithms were employed to identify differentially expressed genes and key biomarkers. OGD treatment significantly increased IL-1β, IL-6, TNF-α, and LDH levels, which were partially reversed by OGD/R. Transcriptomic analysis identified 1229 and 800 differentially expressed genes respectively in OGD and OGD/R comparisons. Enrichment analysis highlighted ribosome, endoplasmic reticulum, and mitochondrial pathways. Six core genes were screened, including RPS7, RPL36A, RPS9, RSL24D1, RPL41, and OSTC, all of which were upregulated under OGD and normalized after reoxygenation. We identified novel ribosome-related genes as potential biomarkers of BBB injury in cerebral infarction. These findings enhance our understanding of BBB pathophysiology and offer new targets for diagnostic and therapeutic strategies in ischemic stroke.

overall_design: The cells were then divided into three groups: one group served as the control group, and the other two groups underwent OGD treatment and OGD/R treatment, respectively. In the OGD treatment, the hCMEC/D3 cells were cultured in normal DMEM medium to 80% confluence, then switched to glucose-free medium and incubated in an anaerobic chamber (95% N₂ and 5% CO₂) for 4 hours. For the OGD/R treatment, the cells from the OGD condition were transferred to a normal incubator (21% O₂ and 5% CO₂) and treated with normal medium for 16 hours to induce reoxygenation.

first: Chuyu

last: Liu