title: High-throughput transcriptome sequencing of Curcumol-treated clear cell renal cell carcinoma cells（Curcumol vs Ctrl）

status: Public on Jun 30 2026

city: Hangzhou

first: Yunkai

last: Yang

address: Zhejiang provincial people’s hospital

country: China

institute: Zhejiang provincial people’s hospital

type: Expression profiling by high throughput sequencing

summary: This project was designed to investigate transcriptomic changes induced by Curcumol treatment in clear cell renal cell carcinoma (ccRCC) cells using high-throughput RNA sequencing. Control cells and Curcumol-treated cells were subjected to next-generation transcriptome sequencing to identify differentially expressed genes and Curcumol-associated signaling pathways. This dataset was used to explore the molecular basis by which Curcumol regulates malignant phenotypes and metabolic activity in ccRCC cells, with particular attention to glycolysis-related pathways and downstream regulatory genes.

overall_design: Clear cell renal cell carcinoma ACHN cells were divided into two groups: blank control group (Ctrl) and Curcumol-treated group. Cells in the intervention group were treated with Curcumol at the corresponding effective concentration, while the control group received no drug treatment. All cells were cultured under consistent experimental conditions with independent biological replicates for each group. Total RNA was extracted from each sample for high-throughput transcriptome sequencing. Raw sequencing data were processed for quality control, genome alignment, and gene expression quantification. Differential gene expression analysis and functional enrichment analysis were performed to screen key genes and signaling pathways altered by Curcumol intervention, aiming to explore the molecular mechanism of Curcumol in regulating glycolysis and malignant biological behaviors of ccRCC cells.


title: Environmental Mixture Toxicity of Guanitoxin and Organophosphates in Zebrafish: from Developmental and Neurobehavioral Phenotypes to Transcriptomic Responses

city: Dübendorf

first: Colette

last: vom Berg

address: Überlandstrasse 133

department: Environmental Toxicology

country: Switzerland

institute: EAWAG

summary: Guanitoxin, a neurotoxin produced by cyanobacteria and the only known naturally occurring organophosphate, poses environmental risks comparable to synthetic organophosphate insecticides. Its effects on aquatic organisms, particularly in combination with compounds sharing similar mechanisms of action, remain poorly understood. This study evaluated the developmental toxicity of guanitoxin, alone and combined with the organophosphate insecticides malathion and trichlorfon, in zebrafish (Danio rerio) embryos and larvae at environmentally relevant concentrations. Developmental, neurobehavioral, and molecular endpoints were assessed. All compounds exhibited dose-dependent toxicity, with mixtures significantly enhancing both lethal and sublethal effects. The trichlorfon + guanitoxin combination was particularly potent, causing embryo coagulation, cardiac arrest, hatching failure, and pronounced pericardial swelling. Sublethal effects were consistently observed across mixtures, including edema, craniofacial malformations, muscle disorganization, and strong hypoactivity. Transcriptomic profiling revealed downregulation of genes critical for muscle contraction, synaptic signaling, energy metabolism and oxidative stress. The highest number of differentially expressed genes was observed in the trichlorfon + guanitoxin mixture (1348 genes). Synergistic interactions were observed, with mixture-induced effects exceeding those of individual compounds. Together, these findings demonstrate that guanitoxin, particularly in combination with synthetic organophosphates, poses a significant ecological risk and highlights the importance of considering mixture toxicity in environmental risk assessments.

overall_design: This study investigated the developmental toxicity and transcriptomic responses of zebrafish (Danio rerio) larvae exposed to the cyanotoxin guanitoxin and organophosphate insecticides malathion and trichlorfon, both individually and in combinations. Individual compound dose response curves to derive EC50 values were generated using the following concentration ranges: guanitoxin (7.81–125 mg/L crude extract equivalent; T1–T5), trichlorfon (1.875–30 mg/L; T1–T5), and malathion (0.125–2.0 mg/L; T1–T5). For mixture experiments, ten combinations of equitoxic and non-equitoxic ratios were tested and a set of apical endpoints was measured. For transcriptomics assessment, inidivual exposures and mixtures, which were combined based on their 0.5x EC50 values in equitoxic ratios, were used. All transcriptomic experiments were conducted in triplicate with 20 pooled larvae per replicate.

first: Larissa

last: Souza Passos

first: Melissa

last: von Wyl

first: Elisabeth

last: M.-L. Janssen

first: David

last: Lopez-Rodriguez

first: Ernani

last: Pinto


title: Effects of bile acid exposure on gene expression in oesophageal epithelial cells

city: LEEDS

first: SAFOURA

last: ZAHED MOHAJERANI

state: -- Please select --

address: 7.10, T. C. Miall Building

department: LIRMM

country: United Kingdom

institute: UNIVERSITY OF LEEDS

summary: Gastro-oesophageal reflux disease is highly prevalent in systemic sclerosis (SSc) and may contribute to oesophageal tissue damage. To investigate the molecular effects of reflux-associated injury, human oesophageal epithelial cells (Het1A) were exposed to bile acids and analysed by RNA sequencing. Chronic bile acid exposure induced transcriptional changes associated with innate immune activation, type I interferon signalling, TGF-β responses, epithelial–mesenchymal transition (EMT), oxidative stress, and mitochondrial dysfunction. Differential gene expression profiles were compared with publicly available SSc oesophageal transcriptomic datasets to identify shared disease-associated pathways. These data provide insight into the molecular mechanisms by which bile acid-induced epithelial injury may contribute to oesophageal pathology in systemic sclerosis.

overall_design: Het1A oesophageal epithelial cells were exposed daily for 10 minutes to acidified medium (pH 4.0) containing 100 μM mixed bile acids for 5 days. Control cells received vehicle treatment. RNA was extracted 24 hours after the final exposure and analysed by RNA sequencing.

first: Safoura

last: Zahed Mohajerani

first: Ala

last: Altaie

first: Marco

last: Minerba

first: Kin

last: Man Suen

first: Christopher

last: J Black

first: Lesley-Anne

last: Bissell

first: Monique

last: Hinchcliff

first: John

middle: E

last: Ladbury

first: Natalia

middle: A

last: Riobo-Del Galdo

first: Rebecca

middle: L

last: Ross

first: Francesco

last: Del Galdo


title: KMT2C catalytic activity regulates enhancer H3K4me1 and synaptic gene expression in cortical excitatory neurons [CUT&Tag]

city: Philadelphia

first: Matthew

last: Edwards

state: PA

address: 450 Clinical Research Building

department: Genetics

country: USA

institute: University of Pennsylvania School of Medicine

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Autism spectrum disorder (ASD) is a highly heritable neurodevelopmental condition in which chromatin regulators represent some of the highest-confidence genetic risk factors. KMT2C encodes a COMPASS family histone methyltransferase that deposits H3K4me1 at enhancers, yet how its dysfunction contributes to ASD remains poorly understood. Here, analysis of the SPARK cohort revealed a significant enrichment of ASD-associated variants within the catalytic SET domain of KMT2C. To determine the functional consequences of impaired catalytic activity, we selectively ablated the SET domain in cortical excitatory neurons. Loss of KMT2C catalytic function resulted in robust and persistent downregulation of genes involved in synapse assembly and synaptic signaling across developmental stages and in both sexes. These transcriptional deficits were accompanied by selective reductions in H3K4me1 at associated regulatory elements. Together, our findings demonstrate that KMT2C catalytic activity is required to maintain enhancer-associated H3K4me1 and sustain synaptic gene expression in cortical excitatory neurons.

overall_design: Cut and tag profiling of core histone marks (H3K4me1,H3K4me2,H3K4me3, and H3K27ac) in excitatory(Nex-expressing) neurons from wild-type and Nex-specific Kmt2c knockout mice in both sexes at 18 weeks of age

first: Mingjia

last: Li

first: Thaise

last: Carneiro

first: Yaohao

last: Zhang

first: Zijie

last: Xie

first: Maria

last: Fasolino

first: Marc

last: Fuccillo

first: Zhaolan

last: Zhou


title: Trivalent arsenicals enhance UVA-associated genomic instability in human keratinocyte models

city: Washington

first: Peter

last: Sykora

state: DC

address: 1121 5th Street NW

institute: Amelia Technologies

summary: Inorganic arsenic is a well-established human carcinogen strongly associated with non-melanoma skin cancer, yet its interaction with solar radiation remains incompletely understood. Arsenic-related tumors arise preferentially in sun-exposed regions and frequently exhibit mutational patterns associated with oxidative stress rather than classical ultraviolet B signatures, implicating ultraviolet A (UVA) radiation as a potential co-exposure factor. Here, we evaluated the effects of physiologically relevant concentrations of trivalent arsenicals on UVA-associated genomic instability using keratinocyte models differing in p53 status. A multi-endpoint platform integrating comet assay kinetics, micronucleus analysis, Bliss synergy modeling, and transcriptomic profiling was used to characterize combinational responses. Sub-micromolar arsenicals alone produced minimal cytotoxicity and negligible increases in comet-detectable DNA damage. In contrast, co-exposure with UVA significantly increased chromosomal instability, particularly in p53-deficient and p53-mutant cells, despite limited additional comet signal. Repair kinetics demonstrated efficient lesion resolution in primary keratinocytes, whereas monomethylarsonous acid (MMA(III)) selectively impaired repair progression in p53-mutant HaCaT cells. Transcriptomic analysis identified altered expression of replication- and checkpoint-associated pathways in transformed keratinocytes. Across models, micronucleus formation was disproportionately elevated relative to measurable strand-break induction, indicating a dissociation between initial DNA damage and downstream genomic outcomes. Collectively, these findings support a model in which arsenicals enhance UVA-associated genomic instability by altering the processing and persistence of oxidative DNA damage rather than substantially increasing initial lesion burden.

overall_design: Untreated human keratinocyte models were profiled by RNA-seq to compare baseline gene-expression states across HaCaT, HPV E6/E7-transduced keratinocytes, and NHEK.

first: Scott

last: Rosenthal

first: Elijah

last: Finn

first: Lucia

last: Dussan

first: Vilhelm

last: Bohr

first: Bonnie

last: Carney

first: Cynthia

last: Simbulan

first: Dean


title: Integrative Transcriptomics Identifies Trazodone as a Modulator of Urban Particulate Matter-Induced Neuroinflammation

city: Daejeon

first: Bu-Yeo

last: Kim

address: 1672 Yuseongdae-ro, Yuseong-gu

department: Herbal Medicine Research Division

country: South Korea

institute: Korea Institute of Oriental Medicine

summary: Urban particulate matter (UPM) triggers neuroinflammation through microglial activation, contributing to the progression of neurodegenerative diseases; however, effective therapeutic interventions remain limited. In this study, we investigated the inhibitory effects of trazodone (TZ), a clinically approved antidepressant, on UPM-induced neuroinflammation using transcriptomic analyses.

overall_design: BV-2 murine microglial cell line were pretreated with TZ (1.25, 2.5, and 5 μg/mL) for 1 h, followed by exposure to UPM (50 μg/mL) for 23 h.

first: Soo-Jin

last: Jeong


title: A Rat Embryonic Enteric Nervous System Culture Platform for Modeling Neuronal Subtype Diversity and Network Activity Maturation

city: Seoul

first: Soryung

last: Jung

address: 52, Ewhayeodae-gil, Seodaemun-gu

institute: Ewha Womans University

summary: We present an in vitro culture system of enteric neurons and glia derived from migratory cells isolated from the embryonic rat small intestine. This system gives rise to functional neuronal networks composed of multiple enteric neuronal subtypes and closely integrated with enteric glial cells. Single-cell RNA sequencing identifies diverse neuronal populations, including ChAT-positive excitatory neurons, NOS-positive inhibitory neurons, and VIP-positive interneurons, as well as a glial cell population. Transcriptomic analysis further defines cell type-specific marker profiles and candidate regulators of enteric neuronal and glial development. Electrophysiological recordings demonstrate maturation of spontaneous network activity, with contributions from cholinergic, nitrergic, and VIPergic neuronal populations. Together, these findings establish a tractable in vitro platform for investigating neuronal subtype specification, the emergence of cellular diversity, neuro-glial interactions and functional electrophysiological network organization.

overall_design: Single cells isolated from embryonic rat small intestine (E15) were cultured in enteric glial cell-conditioned medium to promote neuronal and glial maturation. At day 21 in vitro, cells were dissociated with Accutase, and transcriptomic profiles were generated using the 10x Genomics single-cell RNA sequencing platform.

first: Yerim

last: Lee

first: Sanghyuk

first: Jaesang


title: Murine splenic CD45+ Erythroid cells display transcriptomic signatures of antigen-presenting cells [NanoString]

city: Yerevan

first: Roman

middle: Yurievich

last: Perik-Zavodskii

state: Yerevan

address: Khorenatsi 1

department: Research and Development

country: Armenia

institute: PerikLab

summary: To validate the immune programme of murine splenic CD45+ erythroid cells in a bulk format, we profiled Ter-119+ erythroid cells magnetically enriched from the spleens of adult mice under homeostatic conditions and after two models of stress erythropoiesis (acute blood loss and acute hypoxia) using the NanoString nCounter Mouse Immunology v1 panel (561 immunity-related genes). This Series accompanies the single-cell RNA-seq Series GSE313280 and is linked to it as a SuperSeries.

overall_design: Ter-119+ erythroid cells were enriched from spleens of adult male F1 (CBA x C57BL/6) mice under Normal, acute blood loss (ABL) and acute hypoxia (Hyp02) conditions, n=4 per group (12 samples), and profiled on the NanoString nCounter Mouse Immunology v1 panel.

first: Kirill

last: Nazarov

first: Saleh

last: Alrhmoun

first: Olga

last: Perik-Zavodskaia

first: Egor

last: Vasiliev

first: Sergey

last: Sennikov


title: Deubiquitinase USP2 accelerates endothelial glycocalyx degradation in sepsis-induced ALI by stabilizing MTCH2

city: Chongqing

first: Jin

last: Zhang

address: Southeast University

institute: Southeast University

summary: Sepsis remains a major cause of death worldwide. The lung is particularly vulnerable, and sepsis‑induced acute lung injury (ALI) carries high mortality. Endothelial glycocalyx degradation is an early event that promotes vascular leakage and inflammation, but the upstream regulators of this process are poorly understood. Here we identify ubiquitin‑specific protease 2 (USP2) as a critical driver of pulmonary endothelial glycocalyx breakdown in sepsis. USP2 expression was markedly upregulated in lung endothelial cells of septic mice and in LPS-stimulated human endothelial cells. Endothelial‑specific Usp2 knockdown protected against cecal ligation and puncture (CLP)‑induced lung injury, vascular leakage, and glycocalyx degradation. Mechanistically, USP2 directly bound to mitochondrial carrier homolog 2 (MTCH2), an outer mitochondrial membrane protein, and removed K27‑linked ubiquitin chains at lysine 158, thereby stabilizing MTCH2. MTCH2 was required for USP2‑mediated downregulation of syndecan‑1 (SDC1), a core glycocalyx component, and its silencing rescued SDC1 levels in USP2‑overexpressing cells. Endothelial‑specific Mtch2 knockout mice phenocopied the protective effects of USP2 deficiency, including improved survival, preserved glycocalyx structure, and reduced inflammation. These findings uncover a USP2‑MTCH2 axis that links deubiquitination to glycocalyx integrity in the pulmonary endothelium during sepsis. Targeting this interaction may offer a new therapeutic strategy for septic ALI.

overall_design: HUVECs were transduced with lentivirus carrying USP2 cDNA or empty vector control. After transduction, cells were treated with lipopolysaccharide (LPS, 1 µg/mL) for 24 hours. Cells were then harvested, and total RNA was extracted for RNA sequencing.


title: Effects of norepinephrine(NE) and dexamethasone(DEX) exposure on signaling pathways in immortalized primary human trabecular meshwork cells.

city: Fukuoka

first: Keisuke

last: Ikegami

address: Nishi-ku Motooka 744

country: Japan

institute: Kyushu University

summary: Aqueous humor drainage through the trabecular meshwork is regulated in part by hormonal cues, including norepinephrine (NE) and dexamethasone (DEX), and its circadian variation is thought to reflect rhythmic changes in these signals. However, the transcriptional programs and molecular pathways through which NE and DEX influence human trabecular meshwork cells remain incompletely defined. In this study, we performed RNA-seq analysis of immortalized human primary trabecular meshwork cells (abm; T0371) exposed to NE or DEX for 6 hours, with vehicle-treated cells as controls, to identify stimulus-responsive genes and pathways associated with trabecular meshwork function and aqueous humor outflow.

overall_design: Immortalized human trabecular meshwork cells (iHTMC) were treated with norepinephrine (NE; 1 µM), dexamethasone (DEX; 0.1 µM), or vehicle control and analyzed by RNA-seq. Treated cells were collected after 6 hours of exposure, and vehicle-treated control cells were collected at matched time points. Three biological replicates were analyzed for each condition.


title: Ultrafine particulate matter emitted from ships drives inflammation and susceptibility to viral infection

city: Southampton

first: Matthew

last: Loxham

address: Tremona Road

department: Faculty of Medicine, Clinical and Experimental Sciences

institute: University of Southampton

summary: Exposure to ambient airborne particulate matter (PM) has been associated with almost 9 million premature deaths per year worldwide. Ports are essential infrastructure for trade and transport, with over 80% of the world’s international trade volume travelling by sea, yet there is little understanding of the potential health effects of PM from ships. Here, we studied the elemental and toxicological characteristics of size-fractionated PM collected at different areas of a busy European mixed-use port. We found that unregulated ultrafine PM, a PM size fraction <100 nm in aerodynamic diameter, originating from a cruise-ship source, was highly enriched compared to ultrafine PM from other sites in tracers of heavy fuel oil combustion (V and Ni), with Co identified as a novel tracer. In cell models of airway and alveolar epithelium, this cruise ship-associated ultrafine PM was markedly more pro-inflammatory than PM from other sites, while simultaneously reducing expression of a range of genes associated with the innate antiviral response. Investigation of the effects of the three metals found to be enriched in our cruise-ship ultrafine PM showed that these effects could be reproduced by vanadium exposure, which reduced interferon signalling and increased permissiveness to viral infection, facilitating replication of the respiratory viruses rhinovirus-16 and SARS-CoV-2. Our findings suggest that, despite a series of regulations introduced over the last 20 years, cruise ship-associated emissions of PM from heavy fuel oil combustion may exert disproportionate effects on health compared to PM from other sources. In particular, the effects manifest themselves through induction of a response with characteristics of a poor viral infection prognosis. More broadly, current regulations, which neglect PM source- and composition-related variations, and ultrafine PM in general, may need strengthening to better mitigate health effects resulting from exposure to PM.

overall_design: We exposed 16HBE14o- bronchial epithelial cells to (32 ug cm-2) (100 ug mL-1) ultrafine PM collected near a cruise ship terminal in the summer season at Southampton docks. Exposures lasted for 24 h.  In parallel, otherwise identical non-PM medium-only controls were performed. N = 3 biological replicates (separate experiments performed at different times)

first: Natasha

last: Easton

first: Lareb

last: Dean

first: James

last: Parkin

first: Joseph

last: Bell

last: Cooper

first: Robert

last: Ridley

first: Franco

last: Conforti

first: Elizabeth

last: Davies

first: Carmelo

last: Sofia

first: Liam

last: Edgeway

first: Alice

last: Eminton

last: Bray

first: Florentin

last: Bulot

first: Catriona

last: Menzies

first: Agnieszka

last: Michalik

first: Julia

last: Tree

first: Helen

last: Barryman

first: Amanada

last: Horton

first: Serena

last: Chee

first: Christian

last: Ottensmeir

first: Aiman

last: Alzetani

first: Debbie

last: Crans

first: Simon

last: Cox

first: Steven

last: Ossont

first: Flemming

last: Cassee

first: Cornelia

last: Blume

first: Emily

last: Swindle

first: Damon

last: Teagle

first: Mark

last: Jones

first: Donna

first: Gavin

last: Foster


title: Integration of miRNA profiles and clinical data for early risk assessment of bronchopulmonary dysplasia in VLBW and ELBW newborn infants: a discovery study

city: Almaty

first: Iskander

last: Isgandarov

address: Timiryazev 45

country: Kazakhstan

institute: Institute of plant biology and biotechnology

summary:
Bronchopulmonary dysplasia (BPD) is a major complication of preterm birth. This study aimed to identify circulating miRNA biomarkers in peripheral blood of preterm infants for early risk prediction of BPD.
Peripheral blood was collected from 41 very low birth weight (VLBW) and extremely low birth weight (ELBW) preterm newborns (BPD+: n=20; BPD-: n=21) at days 10-14 of life. Total RNA was profiled using the Affymetrix GeneChip miRNA 4.1 Array (GeneTitan instrument, 96-well plate format). RMA normalization and limma differential expression identified candidate miRNA biomarkers. Four miRNAs (hsa-let-7b-5p, hsa-miR-27a-3p, hsa-let-7c-5p, hsa-miR-182-5p) were significantly upregulated in BPD infants.

overall_design: Case-control study. Peripheral blood samples were collected from preterm newborns (gestational age ≤36 weeks) at days 10-14 of life. Cases (n=20): infants diagnosed with BPD. Controls (n=21): preterm infants without BPD. RNA was hybridized to Affymetrix GeneChip miRNA 4.1 Array. RMA normalization applied. Differential expression assessed with limma, adjusted for gestational age and birth weight.

first: Iskandar


title: scRNA and spatial transcriptomics analysis of allele-specific MHC expression in peripheral blood mononuclear cells and tissues of Mauritian-origin cynomologus and Indian-origin rhesus macaques

city: Madison

first: David

middle: H

last: O'Connor

state: WI

address: 585 Science Drive

department: Pathology and Laboratory Medicine

institute: University of Wisconsin-Madison

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

sample_organism:
Macaca fascicularis
Macaca mulatta

platform_organism:
Macaca fascicularis
Macaca mulatta

overall_design: Refer to individual Series


title: KMT2C catalytic activity regulates enhancer H3K4me1 and synaptic gene expression in cortical excitatory neurons [RNA-Seq]

first: Matthew

last: Edwards

overall_design: RNAseq profiling of excitatory(Nex-expressing) neurons from wild-type and Nex-specific Kmt2c knockout mice across 2 time points and in both sexes

first: Mingjia

last: Li

first: Thaise

last: Carneiro

first: Yaohao

last: Zhang

first: Zijie

last: Xie

first: Maria

last: Fasolino

first: Marc

last: Fuccillo

first: Zhaolan

last: Zhou


title: Reversible epiblast regionalisation determines differentiation potential of human PSCs [RNA-Seq]

city: Cambridge

first: Steven

middle: William

last: Wingett

state: Cambs

address: Francis Crick Avenue, Cambridge Biomedical Campus

department: Cell Biology

institute: MRC Laboratory of Molecular Biology

summary: Although the epiblast in the embryo has the capacity to generate all tissues of the body, its in vitro counterparts often exhibit differentiation biases, posing significant challenges for both basic research and translational applications involving pluripotent stem cells (PSCs). The origins of these biases remain incompletely understood. In this study, we identify regional epiblast identity as the hallmark of differentiation competency through fluctuations in repressive and activating histone posttranslational modifications. We present a novel approach to overcome this bias using a chemical chromatin restoration (CHR) treatment. This method restores transcriptional programs, chromatin accessibility, histone modification profiles, and differentiation potential, effectively recapitulating the competent anterior epiblast-like state. Furthermore, we propose that a high bivalency state is a defining feature of the anterior human epiblast and is a characteristic of unbiased PSCs. We suggest that fluctuations in histone modification marks drive epiblast regionalization, ultimately shaping cellular responses to differentiation cues.

overall_design: To assess intrinsic differences in pluripotency state that could predict competency, we analysed the bulk transcriptome of the starting cells of the 5 competent lines (deyz2, H1, H9, hehd1, kolf2) and 6 noncompetent lines (burb1, cuhk2, feec2, fiaj1, HUES8, sojd3).  We also investigated the transcriptome of multiple cell lines before and after chromatin restoration treatment.

first: Magdalena

last: Sutcliffe

first: Eugenia

last: Wong

first: Charles

last: Morris

first: Stachelscheid

last: Harald

first: Stefan

last: Schoenfelder

first: Madeline

last: Lancaster


title: Coordinated response of vascular and glial cells in a pig model of sepsis

city: Phoenix

first: John

last: Fryer

email: jfryer@tgen.org, kolney@tgen.org

address: 445 N 5th St

institute: TGen

summary: Sepsis is a deadly syndrome arising from overactivation of the immune system in response to a pathogen. Severe sepsis can result in sepsis-associated encephalopathy (SAE) that significantly contributes to morbidity and long-term cognitive impairment. Studying the molecular underpinnings of SAE in the human brain is challenging, and rodent models have limited translational applicability due to significant neuroanatomical and immune differences. To bridge this gap, we employed a Yorkshire pig model to investigate changes in the brain cortex during the early stages of SAE using a uropathogenic strain of E. coli to model bacterial sepsis. Bulk RNAseq of cortical brain demonstrated profound global shifts in immune and inflammatory pathways, cytokine signaling, vascular dysfunction, and homeostatic dysregulation. To gain a more granular understanding of the changes in this model, we performed single-nucleus RNA sequencing (snRNAseq) on the same cortical brain tissue. This snRNAseq analysis revealed dramatic alterations in vascular cell populations, accompanied by concomitant glial cell activation. Surprisingly minimal changes were noted in neurons, likely due to the very early nature of this insult. The neurovascular unit, including vascular leptomeningeal cells (VLMCs), mural cells, endothelial cells, astrocytes, and microglia, showed strong upregulation of genes involved in TNF signaling, cellular responses to cytokine stimuli, and cytokine signaling in the immune system. Conversely, downregulated genes were enriched in pathways related to the disruption of metabolic and structural functions, including genes involved in maintaining the blood-brain barrier (BBB). Cell-cell communication analysis also identified significant rewiring of intercellular signaling in the septic brain, with an overall increase in the number and strength of cell to cell interactions in the E. coli pigs compared to saline controls. In saline controls, cell-cell communication was dominated by homeostatic signaling from microglia and astrocytes. In contrast, the septic pigs showed a significant shift toward inflammatory and immune-related signaling pathways, mainly involving microglia and astrocytes, along with the emergence of signaling pathways from mural cells and VLMCs. Our findings reveal that systemic sepsis triggers a rapid shift from homeostatic to inflammatory signaling within the neurovascular unit, driven by the emergence of pro-inflammatory crosstalk between vascular cells, astrocytes, and microglia. This porcine model effectively captures the acute transcriptional landscape of the septic brain, offering a critical window for therapeutic strategies aimed at stabilizing the BBB and preventing long-term cognitive decline in sepsis survivors.

overall_design: Outbred Yorkshire female swine (Sus scrofa domesticus) were randomly selected to receive continuous intravenous (i.v.) infusion of Escherichia coli (E. coli, n = 4) or saline (control, n = 4). Animals were aged 4.5 months and weighed between 74.4 – 86 Kg

first: Kimberly

last: Olney

first: Leslie

last: Thomas


title: hLMR1, a hepatocyte-specific long noncoding RNA that represses amino acid catabolism through pre-mRNA interaction in human liver [ChIRP-seq]

city: St. Petersburg

first: Xiangbo

last: Ruan

state: Florida

address: 600 Fifth Street S

institute: Johns Hopkins University School of Medicine

summary: To investigate the molecular mechanisms underlying hLMR1-mediated gene regulation, Chromatin Isolation by RNA Purification followed by RNA sequencing (ChIRP-RNA-seq) was performed using human liver tissues. Endogenous hLMR1-associated RNA molecules were isolated using biotinylated antisense oligonucleotide probes targeting hLMR1 and subsequently characterized by high-throughput sequencing. This approach was used to identify RNA transcripts physically associated with hLMR1 and to gain insight into the molecular pathways regulated by this human liver-enriched long non-coding RNA.

overall_design: Cryo-pulverized human liver tissues from four male and four female donors were pooled to minimize interindividual variability. Chromatin Isolation by RNA Purification (ChIRP) was performed using two independent sets of biotinylated antisense oligonucleotides spanning the hLMR1 transcript. As a specificity control, an independent oligonucleotide set targeting the abundant human lncRNA LINC01018 was used.

first: Marcos

last: Jaso-Vera

first: Shohei

last: Takaoka

first: Lanuza A.P

last: Faccioli

first: Zhiping

last: Hu

first: Alejandro

last: Soto-Gutierrez


title: A PLURIPOTENT STEM CELL PLATFORM FOR IN VITRO SYSTEMS GENETICS STUDIES OF MOUSE DEVELOPMENT

city: New York City

first: Ragavi

last: Vijayakumar

state: New York

address: 430 E 67th St

department: Developmental Biology

institute: Sloan Kettering Institute

summary: The directed differentiation of pluripotent stem cells (PSCs) from panels of genetically diverse individuals is emerging as a powerful experimental system for characterizing the impact of natural genetic variation on developing cell types and tissues. Here, we establish new PSC lines and experimental approaches for modeling embryonic development in a genetically diverse, outbred mouse stock (Diversity Outbred mice). We show that a range of inbred and outbred PSC lines can be stably maintained in the primed pluripotent state (epiblast stem cells) and establish the contribution of genetic variation to phenotypic differences in gene regulation and directed differentiation. Using pooled in vitro fertilization, we generate and characterize a genetic reference panel of Diversity Outbred PSCs (n = 250). Finally, we demonstrate the feasibility of pooled culture of genetically diverse PSCs as “cell villages”, which can facilitate the differentiation of large numbers for forward genetic screens. These data can complement and inform similar efforts within the stem cell biology and human genetics communities to model the impact of natural genetic variation on phenotypic variation and disease-risk.

overall_design: We converted embryonic stem cells (ESCs) from the 7 of the 8 Diversity Outbred founder strains (129S1/SvImJ, C57BL/6J, NOD/ShiLtJ, NZO/HiLtJ, CAST/EiJ, PWK/PhJ, WSB/EiJ) to epiblast stem cells (EpiSCs) and collected them for RNA-sequencing at low passage. We then performed directed differentiation to definitive endoderm (DE) from these cells. Following 40 hours of differentiation, cells were collected and sorted using magnetic activated cell sorting (MACS) to perform RNA-sequencing on the CXCR4-positive population. We differentiated epiblast stem cells (EpiSCs) from 6 out of 8 the Diversity Outbred founder strains (C57BL/6J, NOD/ShiLtJ, NZO/HiLtJ, CAST/EiJ, PWK/PhJ, WSB/EiJ) and 62 Diversity Outbred lines to telencephalic neural progenitor cells and collected them for RNA-Sequencing at passage 2.

first: Rachel

last: Glenn

first: Thomas

last: Vierbuchen


title: Reversible epiblast regionalisation determines differentiation potential of human PSCs [CUT&Tag]

first: Steven

last: Wingett

overall_design: CUT&Tag was performed to assess histone modifications H3K27me3 and H3K4me3 in human pluripotent stem cells either competent or noncompetent to generate unguided cerebral organoids. Samples were collected from lines before and after chromatin restoration treatment (CHR), and a naturally competent line H9. Two biological replicates were generated from independent experiments for each condition.

first: Magdalena

last: Sutcliffe

first: Eugenia

last: Wong


title: Transcriptomics of the hypothalamus, pituitary gland, liver and adipose tissue of Tan sheep under dietary succinic acid treatment

city: Yinchuan

first: Wenyi

last: Ren

address: 489 Helanshan West Road, Xixia District, Yinchuan City, Ningxia

department: College of Animal Science and Technology

institute: Ningxia University

summary: 24 growing male Tan sheep were assigned to a basal diet or the same diet supplemented with 1% succinic acid for 60 days. Transcriptomic analyses further revealed tissue-specific responses involving neuroendocrine regulation, mitochondrial metabolism, lipid handling, thermogenesis, and adipose lipolysis across the hypothalamic-pituitary-liver-adipose axis.

overall_design: All experimental procedures involving animals were conducted in accordance with the ethical guidelines approved by the Animal Management and Use Committee of Ningxia University (approval no. NXU-2023-420). The feeding trial was conducted at Zhongquan Agriculture and Animal Husbandry Technology Co., Ltd., Yanchi County, Wuzhong City, Ningxia Hui Autonomous Region, China. Animals were maintained under natural photoperiod conditions. Zeitgeber time (ZT) was defined according to the local light-dark cycle, with ZT0 corresponding to natural sunrise and light onset at approximately 06:00, and ZT12 corresponding to sunset and darkness onset at approximately 18:00. Twenty-four healthy 3-month-old male Tan sheep with similar initial body weight (22.59 ± 0.64 kg) were randomly assigned to two dietary treatments, with 12 sheep per treatment. Sheep were housed individually in 2 m x 2 m pens and had free access to feed and water throughout the trial. The experiment included a 10-d adaptation period followed by a 60-d formal feeding period. The control group (CON) received a basal pelleted diet, whereas the SA group received the same basal diet supplemented with 1% SA on a dry matter basis. SA was incorporated into the feed before pelleting. SA (Jiangsu Baiye Biotechnology Co., Ltd., Jiangsu, China) had a purity ≥99.50% on a dry matter basis. Under routine feeding conditions, feed was offered twice daily at 06:00 and 18:00. Refusals were weighed before the morning feeding on the following day, and the offered amount was adjusted to maintain refusals at no less than 5% of the daily feed offered. During the rhythmic sampling week before slaughter, feed was offered at 06:00, 12:00, 18:00, and 24:00, corresponding to ZT0, ZT6, ZT12, and ZT18, respectively, and feed intake was calculated for each time interval.

first: Miao

last: Liu

first: Xiaofeng

last: Xu

first: Lili

last: Zhang


title: HEXB promotes tumor progression of glioblastoma through the HIF1α-CA9 pathway as a therapeutic approach

city: HENAN

first: ZHENG

last: YUAN

address: Jinming Campus, Henan University, Minglun Street, Longting District, Kaifeng, Henan, China

institute: HENAN University

summary: Glioblastoma (GBM) is among the most aggressive and lethal primary malignant brain tumors, notorious for its high recurrence rates. A major challenge in GBM treatment is the paucity of patient-specific therapeutic targets, underscoring the need to identify actionable vulnerabilities that drive GBM progression. Here, through integrative proteomic and transcriptomic profiling of matched GBM tissues and non-tumor tissues adjacent to the tumor from individual patients, we identified the β-subunit of β-hexosaminidase, encoded by HEXB, as a previously underappreciated mediator of GBM progression. Inhibition of HEXB markedly attenuated GBM cell proliferation and tumorigenicity. Mechanistically, HEXB interacted with HIF1α, prevented its ubiquitin-mediated degradation, and promoted its nuclear translocation, thereby enhancing the transcriptional upregulation of CA9, a hypoxia-associated enzyme implicated in glioma progression. Guided by these findings, brain-targeted nanocapsule delivery of HEXB-directed siRNA exerted therapeutic efficacy, as evidenced by robust suppression of GBM cell proliferation and tumor growth, as well as prolonged survival in mice bearing GBM xenografts. This study highlights HEXB as a promising therapeutic target for GBM and supports patient-matched proteotranscriptomic profiling as a feasible strategy for discovering vulnerabilities in GBM precision medicine.

overall_design: To further investigate the downstream signaling pathways regulated by HEXB, GBM4 cells were infected with either control shRNA lentivirus or shHEXB lentivirus. RNA sequencing was subsequently performed to compare the transcriptomic profiles between the control and HEXB-knockdown groups.

first: Zheng

last: Yuan


title: Discovery of Tcf7 regulators with clonally-resolved CRISPR screens identifies Trim28 as a mediator of CD8 T cell differentiation in tumors [CRISPR Screen]

first: Nir

last: Hacohen

state: MA

address: 415 Main Street, Room 6032

department: Cell Circuits Program / Center for Cell Circuits

institute: Broad Institute

summary: Stem-like TCF7+ CD8 T cells sustain anti-tumor responses and support immune checkpoint blockade. We systematically identified regulators of this cell state using genome-wide CRISPR screens in primary T cells in vitro. Using random barcodes to link clonal relationships with guide identity and transcriptional states in single cells, we inferred differentiation trajectories and differentiation rates of CD8 T cells in tumors, while mitigating confounding clonal bias. We found that Trim28-deficient T cells in tumors were enriched in the TCF7+ cell state, depleted in cycling and terminal effector states, and uniquely generating a tissue resident memory (TRM)-like state with increased chromatin accessibility at known TRM loci as well as repeat elements. Despite the increase in TCF7+ CD8 T cells, loss of Trim28 did not improve tumor control, likely because of reduced effector differentiation, highlighting the need for tuning the balance and dynamics of stem-like versus effector states for effective tumor clearance.

overall_design: Pooled sgRNA amplicon sequencing was used to quantify guide abundance across in vitro and in vivo Tcf7-focused CRISPR screen conditions, sorted fractions, input libraries, and control libraries.

first: Schwartz

last: Marc

first: Lue

last: Dillon

first: Mutaher

last: Mohammed

first: McNerney

last: Miriam

first: Olajide

last: Oluwatomisin

first: Mehta

last: Arnav

first: Rowe

last: Jared

first: Park

last: Ryan

first: Dubrot

last: Juan

first: Al’Khafaji

last: Aziz

first: Bakalar

last: Matthew

first: Bi

last: Lynn

first: LaFleur

last: Martin

first: Yates

last: Kathleen

first: Manguso

last: Robert

first: Doench

last: John

first: Sharpe

last: Arlene

first: Pritykin

last: Yuri

first: Hacohen

last: Nir


title: HIV infection exacerbates ischemic brain injury through dysregulating phagocytosis and neuroinflammatory signals in macrophages/microglia via C1ql2

city: Shenzhen

first: Fan

last: Bu

address: 1 Fuhua Road

institute: Shenzhen Traditional Chinese Medicine Hospital

summary: The incidence of human immunodeficiency virus (HIV)-infected individuals is greater, and outcomes are worse following cerebral stroke, despite widespread access to antiretroviral therapy. As the major reservoir of HIV, resident microglia and infiltrative macrophages in the brain can be aberrantly activated by HIV after stroke. However, the underlying reason driving these pathological processes in poststroke brain injury remains unclear. Herein, with the use of ischemia mice and oxygen-glucose deprivation models, we revealed that HIV infection induced a proinflammatory phenotype and impaired the phagocytic clearance of dead/dying neurons by macrophages/microglia, which was accompanied by a marked reduction in complement C1q-like protein (C1ql) 2 in both peri-infarct macrophages/microglia and cerebrospinal fluid. Importantly, these pathological changes, with ischemia-induced neural demyelination, were strongly mitigated by the intracerebral delivery of recombinant C1ql2, which culminated in a reduced infarct volume and neurological deficits poststroke. Notably, delivering recombinant C1ql2 in the presence of gavage antiretroviral drug Biktarvy further promoted functional recovery and rescued tissue loss following chronic ischemia in HIV-bearing mice, underscoring its potential therapeutic relevance. Collectively, these findings reveal a previously unrecognized C1ql2-dependent mechanism through which HIV infection impairs poststroke repair, which highlights C1ql2 restoration as a promising neuroprotective strategy for HIV-infected stroke patients.

overall_design: RNA-seq profiling of mice brain that suffered the following challenge respectively: A. Ischemic stroke (MCAO), B. HIV infection (NDK), C. Antiviral drug treatment.


title: Electromagnetic modulation of the ALS transcriptome: towards a non-drug molecular cure

city: Rostock

first: Andreas

last: Hermann

state: Mecklenburg-Western Pomerania

address: Gehlsheimer Str.20

department: Neurology

country: Germany

institute: University Medical Center Rostock

summary: Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease hallmarked by progressive loss of neuromuscular junctions and cortical and spinal motoneurons (MNs) yielding in muscle paralysis. MNs are particularly vulnerable due to their long axons and high metabolic demands. ALS pathology involves impaired RNA metabolism, protein aggregation, cytoskeletal defects affecting organelle trafficking, and mitochondrial dysfunction, ultimately leading to neurodegeneration. Current treatments only marginally extend survival, calling for alternative therapies. We recently reported beneficial effects of electromagnetic field stimulations driven by alternating currents (ACMS) on axonal regeneration and organelle motility in ALS. Here, we used iPSC-derived spinal MNs from familial ALS patients with FUS mutations to optimize magnetic field parameters regarding frequency, amplitude and duration. Using compartmentalized neuron cultures, we also tested different magnetic field orientations relative to axons. Following ACMS, we assessed axonal organelle trafficking and the nuclear DNA damage response (DDR) by live-cell imaging. Untreated ALS neurons showed clear defects in both assays. Exposure to magnetic AC sine waves above a threshold of 7 mT, applied perpendicular to the axonal plane with an optimal low frequency of 25 Hz, led to a sustained boost of mitochondrial and lysosomal motility for over one week and rehabilitaiton of DDR. These phenotypic improvements correlated with global transcriptomic changes revealed by RNA-sequencing. While untreated mutant and wild-type neurons displayed distinct gene expression profiles, ACMS induced a novel, harmonized profile across all lines. Differential gene expression analysis suggests that ACMS activates extracellular matrix (ECM)-mediated cell adhesion and triggers neurotransmitter receptors, ion channels and kinase signaling pathways, ultimately altering gene transcription and, thereby, motor and microtubule-associated proteins. Our results highlight ACMS as a promising non-invasive, non-pharmacological treatment for neurodegenerative diseases.

overall_design: Spinal motor neurons (MNs) from four healthy human patients (four WT Ctrl lines) and four ALS patient with mutations in the nuclear location sequence (NLS) in the FUS gene (four mutant ALS FUS lines) were iPSC-derived and matured in compartmentalized Zona microfluidic chambers (MFCs) to obtain distal axons separated from the proximal somatodendritic compartment. These eight cell lines included one isogenic pair of Ctrl and mutant FUS MNs. At defined time points, each MFC was treated by alternating magnetic field stimulation (ACMS) and total RNA was extracted (distal and proximal MFC compartments pooled) afterwards at 48 days in vitro (48 DIV) for global RNA-seq to investigate sustained transcriptomic changes in response to ACMS compared to untreated (UT) samples. Each of the eight cell lines was seeded into four biological replicas (i.e., four MFCs: Rep1, Rep2, Rep 3, Rep4), respectively, which were ACMS-treated and compared against four untreated replicas to calculate differentially expressed genes (DEGs). In addition, DEGs were also calculated for isogenic mutant FUS versus Ctrl MNs, both untreated. In essence, for each of the eight cell lines we executed four ACMS-treated versus four untreated biological replicas, summing up to a total of 64 samples resulting in 64 prepared cDNA libraries for RNA-seq. For more details refer to the associated manuscript.

first: Arun

last: Pal

first: Banaja

middle: P

last: Dash

first: Marc

last: Uhlarz

first: Jonas

last: Gronemann

first: Julia

last: Japtok

first: Hannes

last: Glaß

first: Jens

last: Pietzsch

first: Joachim

last: Wosnitza

last: Dahl

first: Richard

last: Funk

first: Thomas

last: Hermannsdörfer


title: Serial Monitoring of Circulating Tumor Cells Reflects Treatment Response Across Systemic Therapies in Unresectable Hepatocellular Carcinoma

city: FUKUI

first: Yosuke

last: Murata

address: 23-3 Matsuoka Shimoaizuki, Eiheiji-cho, Yoshida-gun

department: second Department of Internal Medicine

institute: University of Fukui

summary: Aim: The strategy of systemic therapy for hepatocellular carcinoma (HCC) has drastically changed with the introduction of combination immunotherapy. However, clinically useful biomarkers for evaluating treatment response remain limited. Circulating tumor cells (CTCs) are a form of  liquid biopsy that offers a noninvasive and real-time approach and is expected to serve as a biomarker for treatment monitoring. We investigated the clinical utility of CTCs for treatment response in patients with unresectable HCC undergoing systemic therapies. Methods: We collected peripheral blood samples from 63 patients with HCC, and changes in CTC counts during the clinical course were analyzed in patients treated with atezolizumab plus bevacizumab (Atezo+Bev), single tremelimumab regular interval durvalumab (STRIDE), or lenvatinib. We analyzed the association between CTC counts and treatment response, and compared their clinical utility with conventional biomarkers. Results: Baseline CTC counts were significantly higher in patients with advanced-stage disease. CTC counts were also associated with elevated des-γ-carboxy prothrombin  (DCP) levels, multiple tumors, vascular invasion, and distant metastasis. At response evaluation, CTC counts significantly decreased in responders. In particular, CD90-positive CTC counts also changed in association with treatment response. Receiver operating characteristic analysis showed that changes in CTC counts had a higher predictive value for treatment response (AUC = 0.8371) compared with conventional biomarkers such as alpha-fetoprotein (AFP) and DCP. Patients with decreased CTC counts had significantly longer progression-free survival than those with increased CTC counts. Conclusions: Serial monitoring of CTC counts may serve as a useful biomarker of treatment response in patients with unresectable HCC undergoing systemic therapies.

overall_design: To evaluate the changes in molecular expression of CTCs in patients with HCC treated with Atezo+Bev, STRIDE and lenvatinib. we designed an NGS panel comprising 373 genes associated with stem cell potency, epithelial–mesenchymal transition (EMT), HCC progression, and cancer immunotherapy.

first: Takuto

last: Nosaka

first: Yu

last: Akazawa

first: Tomoko

last: Tanaka

first: Kazuto

last: Takahashi

first: Tatsushi

last: Naito

first: Masahiro

last: Ohtani

first: Yasunari

last: Nakamoto


title: Splice isoforms of the histone variants macroH2A1 differentially regulate hippocampal gene expression and memory formation

city: Mississauga

first: Iva

last: Zovkic

state: ON

address: 3359 Missisauga Road, DV1015 (Zovkic Lab)

department: Psychological and Brain Sciences

country: Canada

institute: University of Toronto Mississauga

summary: Histone variants are critical components of neural chromatin and emerging regulators of long-term memory formation and neural gene expression. We previously showed that deleting the macrodomain-bearing histone macroH2A1 in mouse hippocampus impairs long-term memory. Here, we expand on this finding by discriminating between alternative splice isoforms of mH2A1, mH2A1.1 and mH2A1.2, which bear structurally distinct macrodomains. We characterized the genomic localization of mH2A1.1 and mH2A1.2 using isoform-specific antibodies, and evaluated the effects of isoform-specific knockdown via shRNA on hippocampal transcription and hippocampal-dependent memory.

overall_design: ChIP-seq of mH2A1.1 or mH2A1.2 in adult male mouse hippocampus. RNA-seq of transcriptome after mH2A1.1 or mH2A1.2 knockdown via shRNA in dorsal hippocampus (sugrery targeted to dorsal CA1)

first: Timothy

last: McLean

first: Zhenhong

last: Jin

first: Luca

last: Hategan

first: Samantha

middle: D

last: Creighton

first: Jian Qi

last: Luo

first: Fardad

last: Pirri

first: Tarkan

last: Dahi

first: Laura

last: Neira Diaz

first: Mark

last: Brimble

first: Stephen

last: Winston

first: Brandon

middle: J

last: Walters

middle: B


title: Pan-cancer analysis reveals oncogenic roles of KCNQ3 in tumor progression, immune microenvironment remodeling, and its mechanistic dependence on ERK1/2 signaling in cholangiocarcinoma

city: Bengbu

first: Shuoshuo

last: Ma

state: Anhui

address: NO. 287, Changhuai Road, Longzihu district, Bengbu 233000, Anhui, China;

institute: The First Affiliated Hospital of Bengbu Medical College

summary: Background: Potassium voltage-gated channel subfamily Q member 3 (KCNQ3) is primarily recognized for its function in neuronal excitability; however, its expression patterns, genetic landscape, and functional significance across human malignancies remain largely unexplored. This study aimed to systematically investigate the pan-cancer expression profile, prognostic value, immune regulatory functions, and molecular mechanisms of KCNQ3, with a focused functional validation in cholangiocarcinoma (CHOL). Methods: We integrated multi-omics data from public databases including GTEx, HPA, TIMER2, TISCH2, cBioPortal, SMART, and TIMER3 to comprehensively analyze KCNQ3 expression, genetic alterations, DNA methylation, clinical prognosis, immune infiltration, and pathway enrichment across 33 cancer types. Single-cell RNA sequencing and spatial transcriptomics were employed to dissect KCNQ3 expression at the cellular level. In vitro and in vivo functional experiments, including CCK-8, colony formation, EdU, Transwell, wound healing, flow cytometry, and xenograft models, were conducted in CHOL cell lines (RBE and 9810). RNA sequencing, Western blotting, and pharmacological inhibition were utilized to elucidate the underlying molecular mechanisms. Results: KCNQ3 exhibited tissue-specific expression in normal tissues and was significantly dysregulated across multiple tumor types, with notable upregulation in breast invasive carcinoma (BRCA), cholangiocarcinoma (CHOL), lung adenocarcinoma (LUAD), and thyroid carcinoma (THCA). Single-cell analysis revealed predominant KCNQ3 expression in malignant cells, mono/macrophages, endothelial cells, and myofibroblasts, with spatial transcriptomics confirming elevated expression in malignant regions. Pan-cancer genomic analysis identified copy number amplifications as the predominant alteration, which correlated with worse progression-free survival (PFS, P = 1.709 × 10⁻³) and disease-free survival (DFS, P = 7.350 × 10⁻⁶). Widespread DNA hypomethylation of KCNQ3 was observed across tumors, potentially contributing to transcriptional activation. Elevated KCNQ3 expression was significantly associated with unfavorable overall survival (OS), PFS, disease-specific survival (DSS), and disease-free interval (DFI) in multiple malignancies. Gene set enrichment analysis demonstrated robust positive enrichment of epithelial-mesenchymal transition (EMT), inflammatory response, angiogenesis, and KRAS signaling, coupled with suppression of oxidative phosphorylation. Immune landscape analysis revealed extensive correlations between KCNQ3 and diverse immune cell subsets, immune stimulators, inhibitors, and chemokines, suggesting a role in tumor immune microenvironment modulation. Notably, KCNQ3-high malignant cells exhibited enhanced cell-cell communication with surrounding stromal and immune populations. Functional studies in CHOL demonstrated that KCNQ3 promoted cell proliferation, suppressed apoptosis, and enhanced migration, invasion, and EMT in vitro, while stable knockdown significantly inhibited tumor growth and pulmonary metastasis in vivo. Mechanistically, transcriptomic profiling and pathway analysis identified ERK1/2-MAPK cascade activation as a central mediator of KCNQ3-driven oncogenesis, and pharmacological ERK inhibition substantially reversed the pro-tumorigenic effects of KCNQ3 overexpression. Conclusion: Our pan-cancer analysis establishes KCNQ3 as a prognostic biomarker and functional oncogene across multiple human cancers. KCNQ3 orchestrates tumor progression, immune microenvironment remodeling, and metabolic reprogramming, with its oncogenic effects in cholangiocarcinoma mediated through activation of the ERK1/2 signaling pathway. These findings highlight KCNQ3 as a potential therapeutic target and prognostic indicator in precision oncology.

overall_design: This study employed an integrative strategy combining pan-cancer multi-omics analysis with functional experimental validation. We first systematically analyzed KCNQ3 expression profiles, genetic alterations, DNA methylation status, and prognostic significance across 33 cancer types using public databases including GTEx, HPA, TIMER2, cBioPortal, SMART, and TIMER3. Single-cell RNA sequencing (TISCH2) and spatial transcriptomics were subsequently utilized to dissect the cell-specific expression patterns of KCNQ3. Functional experiments were performed in cholangiocarcinoma cell lines (RBE and 9810) with KCNQ3 knockdown and overexpression models to evaluate effects on proliferation, apoptosis, migration, invasion, and EMT via CCK-8, EdU, Transwell, flow cytometry, and Western blotting assays. Finally, RNA-seq was conducted to identify downstream pathways, and ERK1/2 inhibitor rescue experiments were performed to validate the KCNQ3-ERK1/2 axis, with in vivo tumorigenicity and metastatic potential confirmed through subcutaneous xenograft and tail-vein pulmonary metastasis models.


title: IGF2BP1 fosters an immunosuppressive tumor microenvironment in high-risk neuroblastoma, contributing to their resistance to immunotherapy.

city: Hershey

first: Yuka

last: Imamura Kawasawa

address: 500 University Dr.

department: College of Medicine, Neuroscience and Experimental Therapeutics

institute: Penn State University

summary: Incorporation of the current immunotherapy, GD2-targeting monoclonal antibody into the standard of care has moderately improved clinical outcomes in children with high-risk neuroblastoma (HR-NB), however, the overall survival remains low. More than 50% of patients with HR-NBs are refractory to or eventually develop resistance towards anti-GD2 treatment. HR-NBs in general are known to exhibit low tumor-mutational burden, are immunologically cold and possess an immunosuppressive tumor microenvironment. Understanding the mechanisms of immune evasion may provide novel targets for improving the efficacy of immunotherapies for these immunologically cold HR-NBs. Here, utilizing immunocompetent mouse models of immunologically cold HR-NB, we uncovered a novel function of IGF2BP1 in promoting immune escape of neuroblastoma tumors. We demonstrate that neuroblastoma cell-specific knockdown of IGF2BP1 favorably alters the tumor microenvironment of HR-NBs, turning these “immunologically cold” tumors to an immunogenic type, thereby priming them for anti-GD2 therapy-induced immune responses. Downregulation of IGF2BP1 in NB cells decreased the immunosuppressive T-regulatory and dysfunctional/exhausted CD8 T cells; and promoted the accumulation of effector MHCII+ macrophages at the tumor site. Importantly, knockdown of IGF2BP1 along with anti-GD2 immunotherapy induced a synergistic immunogenic effect and achieved a potent anti-tumor response in HR-NB mouse model, with increased accumulation of effector CD8+ T cells and CD86+ macrophages, but decreased MDSCs in the tumor microenvironment. Thus, disrupting NB cancer cell IGF2BP1-mediated immunosuppression is a potential approach for improving the efficacy of anti-GD2 immunotherapy towards HR-NBs.

overall_design: RNA-seq profiling of control (shNT) and IGF2BP1 knockdown (shIGF2BP1) M1 neuroblastoma cells at day 6 post doxcycline shRNA induction.

first: Mayura

middle: R

last: Dhamdhere

first: Chethana

last: Gowda

last: Imamura

first: Hong-Gang

last: Wang

first: Todd

middle: S

last: Schell

first: Vladimir

last: Spiegelman


title: Pangenome and genome-scale essentiality in the emerging fungal pathogen Candidozyma auris [ATAC-seq]

city: Ann Arbor

first: Ajay

last: Larkin

state: MI

address: 1150 W Medical Center Dr

department: Microbiology & Immunology

institute: University of Michigan

summary: Candidozyma auris is an emerging multi-drug resistant fungal pathogen characterized by high mortality and rapid transmission in healthcare settings, but the genetic drivers of phenotypic variation between strains and the landscape of gene essentiality in this organism remain undercharacterized. Here, we integrate pangenomic analysis with global essentiality screening to establish a foundational understanding of the C. auris genome and identify potential therapeutic targets. We performed pangenome analysis on 695 outbreak strains of C. auris selected to be genetically representative of publicly sequenced genomes. After using BLAST to refine the pangenome, we found that 96.8% of gene families were core, with the remaining high-confidence accessory gene families primarily consisting of gene loss events or clade-specific genes. The high proportion of core genes emphasizes the clonal nature of these outbreak strains, but comparative analysis with the closely related C. haemuli species complex suggested that most of these core genes are functionally dispensible. To examine this hypothesis, we developed a novel insertional mutagenesis approach that leverages the promiscuous integration of linear DNA in the C. auris genome. This global analysis identified 614 high-confidence essential genes. Crucially, nearly one-third of these genes, including the conserved translation initiation factor Sui1, exhibit divergent essentiality patterns compared to the model yeasts Candida albicans and Saccharomyces cerevisiae. These findings highlight organism-specific biology that would be overlooked by orthology alone. By combining pangenomic diversity with functional essentiality, this study provides a comprehensive resource for identifying species-specific determinants of virulence and prioritizing novel targets for antifungal drug development.

overall_design: Logarithmically growing cells were spheroplasted using a preparation buffer and zymolase, then washed in cold sorbitol. Spheroplasts were harvested and tagmented using the ActiveMotif ATACseq (#53150) kit.

first: Joseph

last: Hale

first: Jackson

last: Rapala

first: Rebecca

last: Hurto

first: Guolei

last: Zhao

first: Brynn

last: Elson

first: Lydia

last: Freddolino

first: Evan

last: Snitkin

first: Teresa

last: O'Meara


title: Osteoblasts regulate neutrophil development

city: Gunagzhou

first: Min

last: Xiao

state: Guangdong

address: changgang dong Road

department: Department of Hematology

institute: The Second Afﬁliated Hospital of Guangzhou Medical University

summary: Study on the mechanism of osteoblast regulation of neutrophil development

overall_design: Osteoblasts were isolated from the skulls of mice in the control and knockout groups and then sent for sequencing. cDNA libraries were constructed from cranial osteoblasts of OSX-SphK2 knockout (KO) mice and littermate controls.

last: xiao


title: The relationship between cell surface CD11c and neutrophil transcriptomic profiles

city: Boston

first: Koichi

last: Yuki

address: 300 Longwood Avenue

institute: Boston Children's Hospital

summary: CD11c is traditionally considered as a dendritic cell marker, but we and others reported that it is expressed in other type of cells. We recently reported that CD11c was expressed in the intracellular space of neutrophils and delineated its function. However, we do not know any functional role of cell surface CD11c in neutrophils. We decided to study the role of cell surface CD11c by sorting into CD11c negative/low neutrophils and CD11c high neutrophils.

overall_design: Neutrophils were sorted based on Cell surface CD11c expression profiles into CD11c negative/low neutrophils and CD11c high neutrophils and subjected to RNA seq experiment.


title: CD99 Is a Novel Immunotherapy Target in Diffuse Midline Glioma: Fratricide-Resistant CAR T Cells Enable Durable Tumor Control

city: Denver

first: Sujatha

last: Venkataraman

state: CO

address: 12800 E. Montview Blvd.

department: Department of Pediatrics/Neuro-Onc

institute: University of Colorado Anschutz Medical Campus

summary: Diffuse midline glioma (DMG) is a highly infiltrative brain tumor of the pons and other midline structures with a dismal prognosis. Chimeric antigen receptor (CAR) T cell therapy has shown promise for DMG; however, to date, clinical responses have generally been transient, underscoring the need for strategies that achieve more durable therapeutic benefit. Here, we identify CD99 as a highly and consistently expressed surface antigen in both H3K27M-mutant and histone wild-type DMG, supporting its potential as a pan-DMG therapeutic target. We engineered a second-generation CD99-directed CAR incorporating a single-chain variable fragment targeting a membrane-proximal epitope and a 4-1BB co-stimulatory domain, which demonstrated potent antitumor activity in DMG models. Locoregional delivery resulted in complete tumor regression in orthotopic xenografts. However, endogenous CD99 expression on T cells triggered severe fratricide, limiting expansion and persistence. To overcome this barrier, we generated fratricide-resistant CD99 CAR T cells via CRISPR/Cas9 deletion of CD99, which markedly improved T cell viability and durability, resulting in sustained tumor clearance in aggressive DMG models. Together, these findings establish CD99 as a promising immunotherapeutic target and show that underscoring the target-dependent need for genetic fratricide prevention.

overall_design: As described in Strategy 2 above, the nucleofected T cell population was first transduced with the 10D1-BBz CAR viral supernatant and subsequently expanded for 4 days. On day 5 post-transduction, live singlet T cells were gated and flow-sorted based on CD99 expression using an anti-CD99 antibody (BioLegend, Catalog #371308). Viable CAR positive unedited 10D1 BBz CAR T cells, as well as CRISPR edited 10D1 BBz CAR T cells within the CD99 negative and CD99 low gates, were isolated.  Cells were washed twice with PBS before scRNA-seq.

first: Ilango

last: Balakrishnan

first: Lillie

last: Leach

first: Krishna

last: Madhavan

first: Senthilnath

last: Chetty

first: Dianzheng

first: Breauna

last: Brunt

first: Angie

middle: M

last: Pierce

first: Josh

last: Obrecht

last: Michlin

first: Bridget

last: Sanford

first: Rajeev

last: Vibhakar

first: Mark

last: Kohler


title: Weissella confusa Wc1982 ameliorates hyperlipidemia through gut microbiota remodeling and hepatic PPARα/NF-κB signaling in hamsters

city: Beijing

first: Ruoshi

last: Wang

address: 155 Changbai Road

department: National Institute for Communicable Disease Control and Prevention

institute: Chinese Center for Disease Control and Prevention

summary: This study investigated whether the human feces-derived candidate probiotic Weissella confusa Wc1982 ameliorates high-fat diet-induced hyperlipidemia in Golden Syrian hamsters and characterized the associated hepatic transcriptional responses. Male LVG hamsters received a normal diet, a high-fat diet, or a high-fat diet plus oral Wc1982 (5 × 10^8 CFU/day) for six weeks. Liver RNA sequencing showed that Wc1982 increased expression of genes involved in PPARα-regulated fatty acid uptake, fatty acid oxidation, and ketogenesis, while reducing expression of canonical and non-canonical NF-κB pathway genes and fibrosis-related genes. The dataset contains raw gene-level counts and FPKM-normalized expression values for 18 liver samples.

overall_design: Specific-pathogen-free male Golden Syrian (LVG) hamsters were randomly assigned to three groups (n = 8 per group): normal control (NC), high-fat diet (HFD), and Wc1982. The NC group received normal diet D12102 and oral PBS; the HFD group received high-fat diet D12108C and oral PBS; and the Wc1982 group received high-fat diet D12108C plus oral Weissella confusa Wc1982 at 5 × 10^8 CFU/day. Treatments were administered for six weeks. Liver RNA-seq was performed on six biological replicates per group (18 libraries) using 150-bp paired-end sequencing on an Illumina NovaSeq 6000.

first: Wang

last: Ruoshi

first: Liu

last: Liyun

first: Xu

last: Jianguo


title: CD99 Is a Novel Immunotherapy Target in Diffuse Midline Glioma: Fratricide-Resistant CAR T Cells Enable Durable Tumor Control [RNA-seq]

overall_design: Human donor T cells transduced with either mock vector or the 10D1-BBz CAR construct were co-cultured with BT245-Luc2 tumor cells for 24 hours. Following co-culture, CAR-T cells were isolated using anti-CD45 microbeads. Total RNA was extracted from mock and 10D1-BBz CAR-T cells and subjected to bulk RNA sequencing to characterize transcriptional changes associated with CAR expression following tumor cell exposure.

last: Zhao


title: The resin glycoside Cus-1, a cuscutae extract, ameliorates oligozoospermia via an aquaporin-driven p38 MAPK/SAT1/GPX4 axis that suppresses ferroptosis and restores spermatogenesis

city: Nantong

first: tong

last: peng

address: No. 19 Qixiu Road, Chongchuan District, Nantong City, Jiangsu Province, China**

institute: Nantong University

summary: This study employed 1H-NMR-guided isolation to rapidly pinpoint, purify and elucidate the on-the-map metabolite resin glycosides“Cus-1” from the Cuscuta chinensis Lam. phenotype, and subsequently interrogated its remedial value in a busulfan (BUS)-induced mouse model of oligozoospermia.

overall_design: Perform RNA sequencing analysis on the BUS group and the CUS group

first: Wenbiao

last: Zhou

first: Qinyi

last: Li

first: Mingyang

first: Yao

last: Shi

first: Chenyang

last: Xu

first: Guangtong

last: Chen

first: Lei

last: Zhang


title: A Patient-Derived Xenograft Model Identifies AK1 as a Key Regulator of Metastatic Potential in Primary Triple-Negative Breast Cancer [WES]

city: seoul

first: Dakyung

last: Lee

address: 101 Daehakro

institute: University

summary: Metastasis remains the major cause of mortality in triple-negative breast cancer (TNBC), yet the metastatic potential of primary tumors is difficult to predict at diagnosis. Here, we leveraged patient-derived xenograft (PDX) models as a functional readout of primary tumor metastatic propensity. We first performed integrated genomic and transcriptomic profiling of primary breast tumors and their matched PDX models and found that key driver mutations, recurrent copy number alterations, and molecular subtype features were largely conserved between patient tumors and xenografts. These findings support the utility of matched PDX models as clinically relevant platforms for studying tumor-intrinsic features associated with breast cancer progression. We next focused on TNBC PDX models with reproducible metastatic phenotypes across biological replicates and classified primary tumors into metastatic and non-metastatic groups based on their matched PDX behavior. Single-cell transcriptomic profiling of these tumors revealed that metastatic samples were characterized by hypoxia-associated metabolic reprogramming, with coordinated activation of hypoxia and glycolysis pathways. This metabolic phenotype was associated with poor clinical outcome in independent breast cancer cohorts. Network-based prioritization identified adenylate kinase 1 (AK1) as a candidate regulator of this metastatic program. Functionally, AK1 promoted metastatic potential in primary tumor by supporting glycolytic ATP production, resistance to hypoxic and oxidative stress, and promoting trans-endothelial migration. Together, our findings establish primary tumor–matched PDX models as a clinically relevant discovery platform for metastatic potential, overcoming the challenge that future metastatic events are not readily predictable from primary tumors at diagnosis. Using reproducible PDX metastasis as a functional readout, we identify AK1-mediated metabolic stress adaptation as a key mechanism underlying metastatic potential in primary TNBC.

overall_design: WES profiling of matched patient blood, patient tumor and PDX tissue samples.


title: The distinct expression features between chronic phase and B-lymphoblastic crisis samples from patients with CML

city: Dalian

first: Xuehong

state: Liaoning

address: No. 9 West Section Lvshun South Road, Dalian 116044, Liaoning, China

department: Institute of Cancer Stem Cell

institute: Dalian Medical University

summary: Chronic myeloid leukemia (CML) is a biphasic clonal hematopoietic stem cell disorder driven by the Philadelphia chromosome (Ph)-encoded BCR::ABL1 oncogene. The blast phase (BP) in CML progressed from indolent chronic phase (CP), usually has a dismal outcome. Single-cell RNA sequencing (scRNA-seq) have identified the pretreatment features linked to therapy resistance and disease progression. We performed the scRNA-seq on bone marrow cells derived from paired CML-CP and CML-BLBC samples, and found that CD24 displayed a striking upregulation in CML-BLBC samples when compared with both the CML-CP and Ph+ B-ALL samples, suggesting the potential as a target in the future therapy of patients with CML-BLBC. Therefore, we profiled the BM samples from patients with CML-CP (n = 16), CML-BLBC (n = 8), and de novo Ph+ B-ALL (n = 13) using bulk RNA sequencing to validate the upregulated expressio of CD24 in patients with CML-BLBC.

overall_design:
We profiled the BM samples from patients with CML-CP (n = 16), CML-BLBC (n = 8), and de novo Ph+ B-ALL (n = 13) using bulk RNA sequencing.

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

first: Shuheng

last: Yan


title: Pangenome and genome-scale essentiality in the emerging fungal pathogen Candidozyma auris [insertMutagenesis]

first: Ajay

last: Larkin

overall_design: C. auris cells were transformed through electroporation with a NAT selection marker cassette. Cells were outgrown in YPD post-transformation for approximately 24 hours and harvested by centrifugation. gDNA was isolated through phenol-chloroform extraction, and digested with MSEI. Libraries were constructed using a transposon footprinting-like strategy to capture junctions between the end of the NAT cassette and C. auris gDNA, allowing for insertion site mapping.

first: Joseph

last: Hale

first: Jackson

last: Rapala

first: Rebecca

last: Hurto

first: Guolei

first: Brynn

last: Elson

first: Lydia

last: Freddolino

first: Evan

last: Snitkin

first: Teresa

last: O'Meara


title: Systematic Discovery of Pathogen Effector Functions across Human Pathogens and Pathways

city: Vienna

first: Tomas

last: Pachano

address: Campus-Vienna-Biocenter 1

country: Austria

institute: IMP

summary: Pathogens deploy effector proteins to exploit host cell biology, and most pathogen open reading frames (ORFs) are rapidly evolving and lack functional annotation. We developed the eORFeome, a scalable functional genomics platform encompassing 3,835 effector ORFs from diverse viruses, bacteria, and parasites. High-throughput barcoded screens across NFκB, apoptosis, p53, cGAS–STING and MHC-I pathways revealed functions for hundreds of uncharacterized eORFs, unexpected new activities for known effectors, and distinct pathway-specific functions encoded by single ORFs. Illustrating the power of the approach, we identify HHV6A U14 as a p53 antagonist, HHV7 U21 as a dual-function STING antagonist and MHC-I antigen display inhibitor, and adenoviral 13.6K/i-leader protein as a de novo evolved TAP inhibitor that suppresses MHC-I display. These results establish a general framework for systematic effector annotation, uncover new mechanisms of host–pathogen interaction across kingdoms, and highlight pathogen effectors as a versatile toolkit for rewiring and probing human cellular pathways.

overall_design: The effector ORF BC was PCR-amplified from gDNA of the selected or input samples, followed by next-generation sequencing

first: He

last: Leng

first: Guillaume

last: Dugied

first: Travis

last: Tribble

first: Vincent

last: Loubiere

first: Felix

last: Rauh

first: Yeojin

first: Alexander

last: Schleiffer

first: Veronika

last: Young

first: Benjamin

last: Weller

first: Eleanor

last: Lyons

first: Matthew

last: Hass

first: Leah

last: Kottayan

last: Weirauch

first: Juan

last: Fuxman Bass

first: Hayley

last: Newton

last: Ensminger

first: Pascal

last: Falter-Braun

first: Daniel

last: Schramek

last: Stark

first: Mikko

last: Taipale


title: Short-term toxic effects of Potassium peroxymonosulfate on Chlorella pyrenoidosa: due to its rapid degradation

city: Yang Zhou

first: Yi

last: Du

address: Shuangqiao Street

institute: Yang Zhou University

summary: The widespread use of potassium peroxymonosulfate (PMS) in aquaculture raises concerns about its ecological risks. This study evaluated acute toxicity of PMS to Chlorella pyrenoidosa over 24-96 h to establish a 96 h EC₅₀. Chronic exposure groups (0, 1.70, 3.40, 8.49 mg/L, corresponding to 0, 0.1, 0.2, and 0.5 of the EC₅₀) were cultured for 12 days. Cell growth, oxidative stress, ultrastructure, chlorophyll fluorescence, and transcriptomic genes were measured on days 0, 3, 6, 9, and 12. PMS decomposition products were monitored and correlated with physiological and Biochemical responses. PMS rapid decomposition increased breakdown products, inhibiting algal growth during days 0-3 and causing surface wrinkling, plasmolysis, chloroplast damage, and thylakoid disarray. Oxidative stress rose and growth_x001E_related genes were down_x001E_regulated. After day 6, with the cessation of PMS decomposition and the subsequent reduction in its byproducts, growth recovered, cellular structures were restored, oxidative stress decreased, and ribosome‑related genes were up_x001E_regulated. These findings contribute to the assessment of the potential risks of PMS to C.pyrenoidosa and provide new insights for the application of PMS in aquaculture practices.

overall_design: This study evaluated acute toxicity of PMS to Chlorella pyrenoidosa over 24-96 h to establish a 96 h EC₅₀. Chronic exposure groups (0, 1.70, 3.40, 8.49 mg/L, corresponding to 0, 0.1, 0.2, and 0.5 of the EC₅₀) were cultured for 12 days,each group at least rep 3 times. Cell growth, oxidative stress, ultrastructure, chlorophyll fluorescence, and transcriptomic genes were measured on days 0, 3, 6, 9, and 12.


title: Multinucleated giant cells in human pancreatic cancer are a distinct macrophage population undergoing a DNA damage response and associated to an aggressive tumor microenvironment [RNA-seq]

city: Rozzano

first: Anna Rita

last: Putignano

state: Milano

address: Via Alessandro Manzoni, 56

country: Italy

institute: IRCCS Humanitas Research Hospital

summary: Macrophages constitute a dominant and functionally diverse immune population within the microenvironment of pancreatic ductal adenocarcinoma (PDAC), yet how this heterogeneity contributes to the tumor remains poorly defined. In an institutional cohort of 145 PDAC specimens, we identified a population of multinucleated giant cells (MGCs) of macrophage origin, an entity previously described in chronic inflammation but rarely in cancer. CD68⁺ MGCs were present in 28% of tumors, enriched in squamous, non-glandular regions, and more frequent after neoadjuvant chemotherapy. By integrating spatial transcriptomics and quantitative imaging, we defined the features of these cells, which, compared with MGCs in non-neoplastic inflammatory lesions, lacked canonical polarization markers (HLA-DR, CD163) and displayed a distinctive transcriptional program characterized by upregulation of POLR2K, TUBA8, COX5B, and VDAC1 genes, involved in DNA repair, oxidative stress, and MYC signaling. Spatial analyses revealed activation of hypoxia and extracellular matrix–remodeling pathways in MGC-associated niches, and experimental hypoxia promoted MGC formation in vitro. Consistently, a macrophage MGC gene signature was enriched in the squamous PDAC subtype and correlated with poorer overall survival in TCGA (p = 0.018). Morphometric and immunofluorescence analyses further showed increased 53BP1⁺/Ki67⁺ nuclei and nuclear atypia in MGCs, indicating ongoing proliferation despite DNA damage. Together, these data identify multinucleated macrophages as a previously unrecognized immune cell state shaped by hypoxia and stress signaling, associated with aggressive tumor phenotypes, and potentially exploitable as an immune classifier in pancreatic cancer.

overall_design: Paired-end bulk RNA-seq of FFPE pancreatic tumor tissue from PDAC patients with or without neoadjuvant chemotherapy.

first: AR

first: M

last: Viatore

first: R

last: Polidori

first: F

last: Marchesi

first: A

last: Mantovani


title: Mutual interaction between Schwann cells and CD4+T cells promotes the progression of perineural invasion in colorectal cancer [ATAC-seq]

first: Huayuan

last: Liu

state: Beijing

address: New Student Apartment Building, No. 17, South Panjiayuan, Chaoyang District, Beijing

institute: Chinese Academy of Medical Sciences Cancer Hospital

summary: Background: Perineural invasion (PNI) is a common pathological feature associated with poor prognosis of colorectal cancer (CRC). However, the mechanisms underlying PNI formation and its relationship with CD4+T cells within the tumor immune microenvironment remain unclear. Aims: This study investigated the role of CD4+T cells in the development and progression of PNI in CRC by examining the interactions between Schwann cells (SCs), primary glial cells in peripheral nerves, and CD4+T cells. Methods: Single-cell RNA sequencing, spatial transcriptomics, and multiplex immunohistochemistry were used to profile the characteristics and spatial relationship between SCs and CD4+T cells in PNI CRC tissues. This study established an SCs-CD4⁺T-cells co-culture system and used flow cytometry, transcriptomic sequencing, proteomics, and ATAC-seq to investigate the mechanisms of their interaction. The key findings were validated in mouse models of sciatic nerve invasion and subcutaneous tumor formation. Finally, the origin of PNI was explored by co-culturing SCs with CRC cells.


title: H3K27ac-associated regulatory atlas in foxtail millet and green foxtail validation

city: Xi'an

first: Huiying

last: Shang

address: Cuihua Road No. 17

institute: Xi'an Botanical Garden

summary: This high-throughput sequencing submission contains H3K27ac CUT&Tag data used to build a source-supported regulatory atlas for foxtail millet, Setaria italica, and a single Setaria viridis validation sample used for representative candidate loci. The data support an H3K27ac-associated regulatory map, sequence-model based candidate cis-regulatory region prediction, and conservative candidate-locus prioritization.

sample_organism:
Setaria italica
Setaria viridis

platform_organism:
Setaria italica
Setaria viridis

overall_design: Eight Setaria italica H3K27ac CUT&Tag libraries from stem, leaf, and panicle source samples were analyzed to generate sample-level peak calls, normalized signal tracks, and a nonredundant consensus H3K27ac peak atlas. One Setaria viridis H3K27ac CUT&Tag library was analyzed as single-sample locus-level validation only. Please associate this submission with existing BioProject PRJNA1481790.

first: Fenghua

last: Zhang

first: Kun

last: Wang


title: Effect of PTEN-NEDD8 fusion gene expression at intestine tissues

first: Zhiqiang

last: Peng

address: 38 Life Science Park Road

institute: State Key Laboratory of Medical Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics

summary: Transcriptome analysis of RNAs extracted from intestine tissues of wild type or PTEN-NEDD8 fusion gene heterozygous mice

overall_design: RNA-seq profiling of WT or PTEN-NEDD8 HET at intestine tissues

first: Lingqiang

first: Cuihua


title: Optical Screening Identifies Chemical Modulators of Intracellular α-synuclein Aggregation

city: CAMBRIDGE

first: Jacques

last: Deguine

state: Massachusetts

address: 415 Main Street, 415M-7175 - Xavier lab

department: Immunology Program

institute: Broad Institute

summary: Parkinson’s disease (PD) is a movement disorder characterized by the accumulation of alpha-synuclein aggregates leading to dopaminergic neuron loss in the substantia nigra. While PD has been associated with environmental and microbiome changes, our ability to assess the mechanistic impact of these factors on synuclein aggregation in cells has remained limited. Here, we designed and optimized a high-throughput optical screening system to assess the effect of metabolites and small molecules on synuclein aggregation in cell lines expressing a synuclein-fluorescent protein fusion and treated with pre-formed fibrils (PFFs). Using this assay, we identified several compounds that modulate synuclein aggregate accumulation in cells, including harman, a β-carboline that led to reduced synuclein aggregation. We further investigated the transcriptional effect of harman and PFFs and identified changes in peroxiredoxins as a potential mechanism linking harman to aggregate accumulation. Altogether, this work establishes a pipeline to prioritize small molecules that can impact synuclein aggregate formation.

overall_design: Cells expressing alpha-synuclein or controls were treated with pre-formed fibrils and the aggregation inhibiting compound harman to determine the transcriptional pathways associated with synuclein aggregation.

first: Lily

last: Rothschild

first: Colter

last: Giem

first: Aditya

last: Bajaj

first: Jessica

middle: W

last: Luo

first: Kimberly

last: Carey

first: Ramnik

last: Xavier


title: Sphingosine kinase 2 regulates adipocyte browning and whole-body metabolism

city: Richmond

first: Christopher

last: Green

state: Virginia

address: 1101 E. Marshall St.

institute: Virginia Commonwealth University

summary: Obesity increases circulating levels of the bioactive sphingolipid metabolite sphingosine-1-phosphate (S1P).  Here, we identify adipocyte-expressed sphingosine kinase 2 (SPHK2), an enzyme that produces S1P, as a regulator of adipose tissue browning. Mice with adipocyte-specific deletion of Sphk2 were protected from Western diet-induced obesity concomitantly with elevated energy expenditure and browning of subcutaneous fat and enhanced expression of Ucp1 and key thermogenic genes, resulting in reduced adiposity and hepatic steatosis, improved glucose tolerance and insulin sensitivity. Mechanistically, obesogenic diet promoted nuclear localization of SPHK2 in adipocytes, where it cooperated with transcription factors to suppress the thermogenic transcriptome. Adipocyte SPHK2 was responsible for maintaining homeostatic circulating S1P levels and driving the pathogenic rise of S1P in response to obesogenic diet. Our findings reveal a distinct role of adipocyte SPHK2 in regulation of the thermogenic program important for whole-body metabolic homeostasis and energy expenditure and highlights SPHK2 as a potential therapeutic target for treatment of metabolic disorders.

overall_design: Bulk RNA sequencing was used to profile genome-wide transcriptome changes in male wild-type and adipocyte-specific Sphk2 deleted brown adipose, gonadal white adipose, and subcutaneous white adipose tissue after eighteen weeks on either standard chow diet or a high fat, high sugar Western diet.

first: Ryan

last: Brown

first: Christiane

last: Carter

first: Katarzyna

last: Tyc

first: Sarah

last: Spiegel


title: Multinucleated giant cells in human pancreatic cancer are a distinct macrophage population undergoing a DNA damage response and associated to an aggressive tumor microenvironment [GeoMx DSP]

first: Anna Rita

last: Putignano

overall_design: CD68+ AOIs were collected from PDAC, tuberculosis and scar lesion tissues across 2 runs. PanCK+ AOIs were collected from PDAC tissues in 1 run. All samples profiled with GeoMx DSP WTA panel, NGS readout.

first: AR

first: M

last: Viatore

first: R

last: Polidori

first: F

last: Marchesi

first: A

last: Mantovani


title: Activation of the SRC/MEK/ERK Pathway by Arsenic Disulfide Restores Megakaryopoiesis and Platelet Production in Myelodysplastic Syndrome

city: Shanghai

first: Kexin

last: Hu

address: Middle Zhijiang Road 274

institute: Shanghai Municipal Hospital of Traditional Chinese Medicine

summary: Thrombocytopenia is a common and clinically significant complication of myelodysplastic syndrome (MDS), but effective therapies directly targeting megakaryopoiesis are limited. Sanzi Huangshi Pill (SZHSP), a traditional Chinese medicine formula containing arsenic disulfide (As2S2), has been found to have haematopoietic effects in clinical settings, but the mechanisms involved have yet to be fully explained. In this study, the effects of SZHSP and As2S2 on megakaryocyte differentiation were evaluated in NUP98-HOXD13 transgenic mice and Meg-01 cells. Through haematological analyses, flow cytometry, molecular assays, network pharmacology, RNA sequencing, and pharmacological inhibition studies, we found that SZHSP significantly improved thrombocytopenia in MDS mice, increased the proportion of mature CD41+CD42+ megakaryocytes, and up-regulated the expression of Gata-1, Fog1, and Fli1. In vitro, both SZHSP-containing serum and As2S2 induced megakaryocytic differentiation and increased lineage-associated markers in Meg-01 cells. Transcriptomic analysis and network pharmacology demonstrated the activation of MAPK-related pathways and megakaryopoiesis-associated gene programs, identifying SRC and MAPK signaling as important regulatory nodes. Mechanistic studies further revealed that As2S2 increased the phosphorylation of SRC, MEK, and ERK, and the pharmacological inhibition of SRC significantly reduced the differentiation-promoting effects of As2S2. In conclusion, SZHSP and its major active ingredient As2S2 promote megakaryocyte differentiation and platelet recovery by activating the SRC/MEK/ERK signaling pathway, offering mechanistic evidence for SZHSP as a potential differentiation-based therapeutic approach for MDS-associated thrombocytopenia.

sample_organism:
root
Homo sapiens

overall_design: mRNA profiling by high throughput sequencing to dissect the molecular mechanism by which SZHSP and its active ingredient As₂S₂ promote megakaryocyte differentiation and alleviate thrombocytopenia via activating SRC/MEK/ERK signaling pathway in NUP98-HOXD13 transgenic mice and Meg-01 cells.


title: Discovery of Tcf7 regulators with clonally-resolved CRISPR screens identifies Trim28 as a mediator of CD8 T cell differentiation in tumors [RNA-Seq]

city: Cambridge

first: Nir

last: Hacohen

address: 415 Main Street, Room 6032

summary: Stem-like TCF7+ CD8 T cells sustain anti-tumor responses and support immune checkpoint blockade. We systematically identified regulators of this cell state using genome-wide CRISPR screens in primary T cells in vitro. Using random barcodes to link clonal relationships with guide identity and transcriptional states in single cells, we inferred differentiation trajectories and differentiation rates of CD8 T cells in tumors, while mitigating confounding clonal bias. We found that Trim28-deficient T cells in tumors were enriched in the TCF7+ cell state, depleted in cycling and terminal effector states, and uniquely generating a tissue resident memory (TRM)-like state with increased chromatin accessibility at known TRM loci as well as repeat elements. Despite the increase in TCF7+ CD8 T cells, loss of Trim28 did not improve tumor control, likely because of reduced effector differentiation, highlighting the need for tuning the balance and dynamics of stem-like versus effector states for effective tumor clearance.

overall_design: To test the ability of naive transduced CD8 T cells to respond to an antigen and form functional memory cells and precursors in mice, we used a lymphocytic choriomeningitis viral model (LCMV) model. Competitive transfer experiments were performed using: (1) P14 LCMV-specific CD8 T cells transduced with our naive state-preserving lentiviral transduction method (termed lenti naive); (2) P14 cells transduced and activated with anti-CD3/CD28 stimulation (termed activated condition); (3) P14 cells with no transduction or stimulation (termed fresh). Transfers were mixed freshly isolated naive P14 CD45.1+CD45.2+ CD8 T cells (termed control cells). Recipient mice were then infected with LCMV Armstrong, and splenic T cells were analyzed 7 and 30 days following infection. Bulk RNA-seq samples were collected for samples prior to transfer, 7 days after transfer, and 30 days after transfer. For the samples from 30 days after transfer they were further sorted into central memory (CM) and effector memory (EM) populations.

first: Schwartz

last: Marc

first: Lue

last: Dillon

first: Mutaher

last: Mohammed

first: McNerney

last: Miriam

first: Olajide

last: Oluwatomisin

first: Mehta

last: Arnav

first: Rowe

last: Jared

first: Park

last: Ryan

first: Dubrot

last: Juan

first: Al’Khafaji

last: Aziz

first: Bakalar

last: Matthew

first: Bi

last: Lynn

first: LaFleur

last: Martin

first: Yates

last: Kathleen

first: Manguso

last: Robert

first: Doench

last: John

first: Sharpe

last: Arlene

first: Pritykin

last: Yuri

first: Hacohen

last: Nir


title: Circ_0005406 Promotes Ovarian Cancer Progression through IL-33-Dependent Recruitment of Tumor-Associated Macrophages [Human ovary]

city: Nanjing

first: Xiyi

last: Chen

address: No.123 Mochou Road

institute: Women’s Hospital of Nanjing Medical University

type: Non-coding RNA profiling by high throughput sequencing

summary: Ovarian cancer (OC) is a highly lethal malignancy with limited therapeutic options. Multiple peptides encoded by non-coding RNAs have exhibited critical anti-tumor activities. Through integrated RNC-seq and MeRIP-seq analyses, we identified circ_0005406 as a circRNA with translational potential. This study aims to elucidate the role and mechanism of circ_0005406 in OC progression and evaluate its potential as a therapeutic target. Circ_0005406 was downregulated in OC tissues compared to normal ovarian epithelium. Its overexpression robustly promoted orthotopic tumor growth in mice, despite exerting minimal proliferative effects in vitro. Integrated RNA-seq and co-culture studies revealed that this pro-tumorigenic phenotype was driven by an immunosuppressive microenvironment, characterized by IL-33 upregulation and increased M2 macrophage infiltration. Mechanistically, the m6A reader IGF2BP2 was identified as a central regulator that binds circ_0005406 to enhance its translation and stabilizing IL33 mRNA. Knockdown of IGF2BP2 abrogated macrophage chemotaxis. Besides, circ_0005406 may encodes a nuclear-localized 275-amino-acid peptide. Circ_0005406 promotes OC progression by recruiting M2 macrophages via IL33. Mechanistically, IGF2BP2 acts as a nexus that concurrently boosts circ_0005406 translation and stabilizes IL33 mRNA, a dual action that synergistically drives macrophage infiltration.

overall_design: 6 human surgery specimens, 3 human ovary tissues as control and 3 high-grade serous ovarian cancer tissues.

first: Hongmei

last: Wang

first: Zhenlong

first: Chengjie

last: Xia

first: Xusu

first: Juan

last: Xu

first: Xuemei

last: Jia


title: SMD2 reads pseudouridines to regulate mRNA splicing and promote tumorigenesis [PRAISE-seq]

city: Shanghai, P.R. China

first: weiying

last: meng

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

institute: Tongji University

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

overall_design: PRAISE-seq was employed to map the transcriptome-wide distribution of Ψ in HEK293T cells, using PUS1/PUS7/RPUSD4 triple-knockout (PUS TKO) cells as a negative control.

first: Weiying

last: Meng

first: Moping

first: Shuxia

last: Sun

first: Zhiyan

first: Jiejun

last: Shi


title: Analysis and statistics of mRNA interacting with Tau5-positive microtubule associating protein tau in human hippocampal Alzheimer’s Disease tissue

city: Gainesville

first: John

last: Koren

state: FL

address: 1275 Center Dr

institute: University of Florida

summary: The microtubule associating protien tau, (MAPT, tau) is a primary pathologic factor in a number of neurodegenerative disorders, including Alzheimer's Disease. Tau can interact with RNA. These interactions have been proposed as initiating factors for the formation of the pathological forms of tau noted in diseases. Additionally, it has been suggested that the m6A-methylation state of RNA is a factor in the association of RNA to tau. This study uses enhanced crosslinking immunoprecipitation (eCLIP) techniques to 1) identify, quantify, a sequence the RNA species interacting with the tau protein isolated from Alzheimers disease human hippocampal tissue, 2) identify, quantify, and sequence the methylated RNA in Alzheimer's disease human hippocampal tissue, and 3) to look for associations between the RNAs that interact with tau and RNA methylation status.

overall_design: Tissue from nine donors of ages not associated with sporadic Alzheimer's disease. underwent eCLIP processes to identify and sequence the RNA that were interacting with tau and the RNA that featured m6A methylation. The primary output, in a manuscript under preparation, was to simplify the associated RNA data to a list of their representative genes. These gene lists were then compared for methylation status, tau interaction, and signaling pathways.

last: Koren III

first: Tristyn

middle: N

last: Garza


title: Circ_0005406 Promotes Ovarian Cancer Progression through IL-33-Dependent Recruitment of Tumor-Associated Macrophages

overall_design: 6 orthotopic ovarian cancer xenograft samples (SKOV3 cells injected into nude mouse ovaries), with 3 circ_0005406-overexpressing SKOV3-derived tumors and 3 control group tumors.