title: Generation of Tetraploid Organs in Mice [heart scRNA-seq]

city: Kunming

first: Shu

last: Wei

address: No.17 Longxin Road, Ciba Subdistrict, Panlong District

department: Group of Non-human primates of reproductive and stem cell

institute: Kunming insititute of zoology

summary: Tetraploidy is rare in mammals but common in plants and fish, a phenomenon that offers evolutionary benefits. In mammals, tetraploid cells naturally occur in the liver, heart, and pancreas. Although previous studies have shown that tetraploid embryonic stem cells (4N-ESCs) can contribute to the liver and heart, the extent of their potential for regenerating entire organs remains underexplored. Here, we injected 4N-ESCs into blastocysts which lacked specific organs due to Hhex, Nkx2.5, and Pdx1 deficiencies, successfully generating functional tetraploid livers, hearts, and pancreata, which are smaller than their diploid counterparts. FACS analyses showed significant contributions of 4N-ESCs, with up to 84.3% of liver cells, 79.5% of heart cells, and 43.6%of pancreatic cells being tdTomato-positive. Our results indicate that 4N-ESCs preferentially contribute to the formation of tetraploid livers and hearts, and contribute to the pancreata. These findings highlight the potential of 4N-ESCs for human organ regeneration and suggest a new strategy for addressing organ shortages in clinical settings.

overall_design: This dataset contains transcriptome sequencing data obtained from mouse E18.5 tetraploid liver and heart tissue. Sample information: Species: Mus musculus (Mouse) Tissue: tetraploid Liver and heart Stage: E18.5/p180 Sequencing platform: illumina

first: Guowei

last: Zou

first: Yanyan

first: Shuaipeng

first: Mei

last: Hu

first: Juan

last: Du

first: Jiawen

last: Liu

first: Lin

last: Ran

first: Chikai

last: Zhou

first: Jiangwei


title: Adaptive downregulated liver Recucalcin enhances tolerance defense to intestinal infection by mediating interorgan immunometabolic communication

status: Public on Jun 06 2026

city: Shanghai

first: Yi

last: Yang

state: Xuhui District

address: 320 Yueyang Road, Xuhui District, Shanghai, China

department: Gut Microenvironment and Health Research Group

country: China

institute: Shanghai lnstitute of lmmunity and Infection

type: Expression profiling by high throughput sequencing

summary: The gut-liver communication is vital for coordinating a systemic response to intestinal infection, as the liver plays a crucial role in regulating immune tolerance through metabolic reprogramming. However, the mechanisms underlying gut-liver communication during intestinal infection, and the key factors linking these processes, remain poorly investigated. In this study, we identified that Regucalcin expression in the remote liver/fat body (Drosophila analogous) is downregulated in response to intestinal infection. And this adaptive downregulated liver Recucalcin could enhance tolerance defense by limiting intestinal infection-induced lipid wasting. Mechanistically, we uncovered that the loss of Regucalcin facilitated calcium-dependent Dilp6 secretion and suppressed excessive lipid catabolism through the insulin-PI3K-Akt signaling pathway during intestinal infection. Therefore, our work reveals Regucalcin as a novel mediator that orchestrates the cross-talk between the intestine and the liver/fatbody, thereby modulating metabolic tolerance to intestinal infection.

overall_design: The total RNA was isolated from fat bodies of adult flies with P. entomophila oral infection and control flies (fed with 5% sucrose solution) at 18hpi. Perform three biological replicates of the fly infection. The sequencing was performed using the Illumina NovaSeq 6000 platform at Beijing Novogene Bioinformatics Technology Co., Ltd. Skewer (V0.2.2) was utilized for quality trimming and adapter trimming of the reads. The filtered reads were then aligned to the Drosophila genome using STAR version 2.7.4. Gene expression profiles were generated using StringTie (V2.1.2), and each gene's expression was normalized using DESeq2 (V1.20). Following normalization, a differential expression analysis was conducted.

first: Kaiyan

first: Lei

last: Pan


title: Generation of Tetraploid Organs in Mice [E18.5]

last: Zhang

last: Li

last: Lin


title: Generation of Tetraploid Organs in Mice [liver scRNA-seq]


title: Cardiomyocyte-Specific Smad7 protects the pressure-overloaded heart, inhibiting the TbR1/Smad2/3 cascade [Smad7 knockout]

city: New York

first: Claudio

middle: Diego

last: Humeres

state: New York

address: 2911 PEARSALL AVE

department: Medicine

country: USA

institute: Albert Einstein College of Medicine

summary: Cardiomyocytes are the major effectors of cardiac remodeling under pressure overload, undergoing hypertrophy and contractile dysfunction in response to sustained mechanical stress. These maladaptive changes are orchestrated by transforming growth factor beta (TGF-β), a key mediator of hypertrophic and profibrotic signaling. Smad7, an inhibitory Smad, negatively regulates TGF-β signaling, but its cardiomyocyte-specific role in pathological remodeling is unclear. We hypothesized that Smad7 acts as an endogenous inhibitor of cardiomyocyte dysfunction during pressure overload. To investigate this, we generated cardiomyocyte-specific Smad7 knockout (CMS7KO) mice and subjected them to transverse aortic constriction (TAC). Echocardiography, RNA-sequencing, histological, and molecular analyses were performed. Smad7 expression was upregulated in cardiomyocytes of TAC mouse hearts and in patients with non-ischemic cardiomyopathy. While baseline cardiac function was preserved in CMS7KO mice, TAC induced an increase in systolic and diastolic dysfunction, ventricular dilation, and hypertrophy compared to controls. Histological analysis revealed increased cardiomyocyte size and macrophage infiltration, without significant fibrosis. Transcriptomic profiling showed downregulation of contractile and sarcomeric genes. Cardiomyocyte-specific Smad7 loss enhanced TGF-β/Smad3 and ERBB2 signaling in vivo. In H9c2 cardiomyocyte-like cells, Smad7 knockdown increased TbR1 and Smad3 phosphorylation, confirming a direct inhibitory effect. These findings identify cardiomyocyte Smad7 as a critical regulator of pathological remodeling and a potential therapeutic target in heart failure.

overall_design: Comparison of the transcriptomic profile of whole hearts from cardiomyocyte-specific Smad7 knockout (CMS7KO) and alpha MHC Cre control (ACRE) hearts exposed to a model of transverse aortic constriction for 7 days. Smad7 loss in cardiomyocytes in the whole heart was achieved via Cre-mediated excision of Smad7 driven by the promoter of alpha myosin heavy chain (gene specific of cardiomyocytes). 2 conditions (aMHC Cre Control (ACRE), Cardiomyocyte-specific Smad7 knockout (CMS7KO); 4 independent samples per condition. 8 samples total.

first: Izabela

last: Tuleta

first: Arti

middle: V

last: Shinde

first: Anis

last: Hanna

first: Aadya

last: Deepak

first: Nikolaos

middle: G

last: Frangogiannis


title: Cardiomyocyte-Specific Smad7 protects the pressure-overloaded heart, inhibiting the TbR1/Smad2/3 cascade

overall_design: Comparison of the transcriptomic profile of whole hearts from cardiomyocyte-specific Smad7 knockout (CS7KO) and alpha MHC Cre control (CRE) hearts exposed to a model of transverse aortic constriction for 56 days Smad7 loss in cardiomyocytes in the whole heart was achieved via Cre-mediated excision of Smad7 driven by the promoter of alpha myosin heavy chain (gene specific of cardiomyocytes). 2 conditions (aMHC Cre Control (CRE), Cardiomyocyte-specific Smad7 knockout (CMS7KO); 4 independent samples per condition. 8 samples total.


title: Innate immunocompetent iNSpheroids: A hiPSC-derived 3D model to study the central nervous system captures an early CNS response to rAAV

city: Oeiras

first: Catarina

middle: Monteiro

last: Gomes

state: Lisboa

address: Av. República, Qta. do Marquês

country: Portugal

institute: iBET

summary: Gene therapies using adeno-associated viruses (AAVs) for central nervous system (CNS) disorders face challenges due to host immune responses not represented in classical preclinical models. Here, we present a human-induced pluripotent stem cell (hiPSC)-derived innate immunocompetent 3D CNS model that recapitulates neuroinflammatory hallmarks, serving as a platform for preclinical gene therapy development. Utilizing various scales of stirred-tank bioreactor systems, we produced iNSpheroids composed of neurons, astrocytes, and oligodendrocytes, alongside microglial cells (iMGL) to mimic the neuro-immune axis. These systems enabled large-scale production of iNSpheroids and subsequent miniaturization for co-culture experiments and screening of inflammatory stimuli, while maintaining a highly controlled environment. The iMGL-iNSpheroids demonstrated active neuron-microglia crosstalk and exhibited distinct inflammatory responses to a series of neuroinflammatory factors. iMGL-iNSpheroids mounted a mild and transient response to rAAV9, mediated by the activation of inflammatory pathways (e.g., TNF-via NF-κB activation) in glial cell populations.. This model offers a valuable tool to dissect neuroinflammatory mechanisms, accelerating gene therapy development.

overall_design: iNSpheroid and iMGL were co-culture and subsquently transduced with rAAV9. Samples before and after transduction were collected and processed for snRNA-seq.

middle: M

first: Gabriela

last: Silva

first: Mafalda

last: Aleixo

first: Daniel

last: Simão

first: Stephan

last: Holtkamp

first: Diana

middle: D

last: Lobo

first: Pradeep

last: Harish

first: Lekh

last: Dahal

first: Rui

middle: J

last: Nobre

first: Luís

middle: P

last: Almeida

first: Mark

last: Trautwein

first: Paula

last: Alves

last: Brito


title: Single cell gene expression profiling of triple negative breast cancer organoids

city: Chapel Hill

first: Michael

last: East

state: NC

address: 120 Mason Farm Rd, GMB 4100C

department: Pharmacology

institute: UNC

summary: Triple negative breast cancer (TNBC) is a heterogenous disease driven by aberrant activation of receptor tyrosine kinases and the proliferative MEK-ERK signaling pathway. Heterogeneity in kinase expression levels across two TNBC organoid lines was used in combination with the Atlas of substrate specificities for the human Ser/Thr kinome to predict phenotypic differences between the two organoid lines. Single nucleus RNAseq validated these predictions showing high enrichment of immune and inflammatory signatures within a subpopulation of tumor cells.

overall_design: The Two TNBC patient derived organoid lines NH87TT and NH95TT were profiled using 10X Genomics multiome ATAC + Gene Expression workflows. Single nucleus gene expression is reported herein.

first: Jose

middle: F

last: Olivares-Quintero

first: Gary

middle: L

last: Johnson


title: Ectothermic vertebrates evolved gut-associated germinal center-like structures

city: Wuhan

first: Peng

last: Yang

address: No. 7 Donghu South Road

institute: Institute of Hydrology, Chinese Academy of Sciences

summary: Germinal centers (GCs), specialized microanatomical structures that emerged in endothermic vertebrates, serve as critical hubs for immune surveillance and lymphocyte activation. The constant exposure to foodborne pathogens drives the evolutionary selection for potent gut mucosal immune defenses in vertebrate species. Despite retaining ancestral ectothermic traits including underdeveloped lymph nodes, teleost fish have evolved specialized gut-associated lymphoid tissue capable of generating robust antigen-specific immune responses. How and where ectothermic vertebrates initiate adaptive immunity in the gut remains enigmatic. Through single-cell RNA sequencing (scRNA-seq), we comprehensively mapped the dynamic immune landscape of common carp (Cyprinus carpio) in the gut and head kidney (HK) following Spring Viremia of Carp Virus (SVCV) challenge. Strikingly, lymphocytes within gut exhibited pronounced upregulation of memory-related genes upon secondary viral exposure, oncomitant with robust expression of canonical GC markers in B cells. Furthermore, using FISH, we observed SVCV co-localization with CXCR5⁺ B cells within the lamina propria basement of the gut and perivascular niches of the HK, encircled by a peripheral ring of AICDA⁺/MKI67⁺/CXCR4⁺ B cells. Notably, within these same microanatomical niches, we detected distinct aggregates composed of highly proliferative IgM⁺ B cells undergoing significant apoptosis and antigen (Ag)-specific B cells. Collectively, our findings reveal that teleosts have evolved GC-like structures in the gut, offering novel insights into the evolutionary origins of GCs.

overall_design: 16 samples 2 biological replicates

first: Weiguang

last: Kong


title: Single-cell RNA-seq analysis identifies the atlas of lymph fluid and reveal a sepsis-related T cell subset

city: wenzhou

first: hui

last: wang

address: wenzhou medical university

institute: wenzhou medical university

summary: The lymphoid cycle as the sentinel of immune response, its cell subtypes and immune properties and functions during sepsis are still unclear. This study described a comprehensive picture of immune cells in rat lymph fluid by single-cell RNA sequencing and identified a unique subset of CD4+ T cells (CD4_Icos) in the early state of sepsis, confirming its crucial role in Treg cell production. Transferring with CD4+Icos+ T cells significantly alleviated CLP-induced organ injury, while Icosfl/flCd4-CreERT2 mice showed reduced number of Treg and increased inflammation and mortality risk. Further screening and validation experiments identified Npas2 as an Icos-specific transcription factor that regulates Icos expression and promotes the differentiation of CD4+Icos+ T cells. Clinical results disclosed the negative correlation between the expression of ICOS in CD4+ T cells and SOFA score in septic patients, which affected the prognosis of septic patients. These findings indicated the protective role of CD4+ T cells in sepsis.

overall_design: Polymicrobial sepsis was induced by cecal ligation and puncture (CLP) injury. The lymph fluid collection was performed 24h after sham/CLP surgery. scRNA-seq libraries were constructed using the 10X Genomics 3' Gene expression with feature barcoding HT kit.

first: Hui

last: Wang

first: Jianguang


title: Multimodal characterization of the effects of stimulation on the human brain ex vivo and in vivo.

city: Los Angeles

first: Genevieve

last: Konopka

state: CA

address: 650 Charles Young Drive South, 73-214 CHS

department: Neurobiology

institute: UCLA David Geffen School of Medicine

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The underlying mechanisms of therapeutics using brain stimulation in humans are not understood. In particular, it is unknown how brain stimulation impacts gene expression in acute and chronic temporal periods. Although therapeutic approaches like deep brain stimulation are becoming more widely used, it is impossible to study stimulation-induced genetic changes without tissue samples which at best could be collected post-mortem. To overcome these extremely limiting circumstances, we have implemented a multi-part experimental design involving single cell resolution RNA and ATAC sequencing of human cortex that has been stimulated in several paradigms. In the first, acute human cortex slices are stimulated with a high-density microelectrode array, which allows us to track how neural activity changes after stimulation together with genomic changes. In the second, tissue is collected from neurosurgery patients immediately after direct cortical stimulation in vivo. We have uncovered differentially expressed genes and differentially accessible chromatin regions in both paradigms. We have also determined the impact of stimulation on cell assembly plasticity and celltype-specific changes in firing patterns. Our integrated approach of applying stimulation paradigms in human brain tissue both in vivo and ex vivo has not been completed before.  These results represent a key first step in our quest to understand exactly how brain stimulation supports neural function at the cellular level.

overall_design:
MEA stimulation: Acute slices were prepared from human temporal cortex tissue obtained from temporal lobectomy operations. Slices were stimulated (15 minutes, 300mv) using the MaxwellBiosystems MaxOne microelectrode array. Control slices rested in oxygenated normal artificial CSF and received no stimulation. Nuclei were extracted from flash frozen samples - each sample consisted of 3 to 4 individual slices which were pooled to increase the mass of the tissue to aid in nuclei extraction. Joint snRNA/snATACseq libraries were prepared using the 10x Genomics platform.
In vivo stimulation: Intraoperative stimulation of the premotor cortex was performed at the time of epilepsy surgery. Stimulated tissue and adjacent non-stimulated tissue were resected according to clinical need then flash-frozen in the operating room in separate sample tubes. Nuclei were extracted from flash frozen tissue samples. Joint snRNA/snATACseq libraries were prepared using the 10x Genomics platform.

first: Haley

last: Moore

first: Stefano

last: Berto

first: Ashwinikumar

last: Kulkarni

first: Mantre

last: Dehnad

first: Anne

last: Freelin

first: Bryan

last: Granger

first: Suganya

last: Subramanian

first: Bradley

middle: C

last: Lega


title: The roles of Nudt15 in leukemic and hematopoietic stem cells

first: Zhonghui

last: Zhang

state: Shanghai

address: 381 Nanchen Rd

department: School of Life Sciences

institute: Shanghai University

summary: NUDT15 encodes nucleotide triphosphate diphosphatase that is responsible for metabolizing purine analog drugs, and its genetic mutation results in severe side effects from thiopurine therapy. However, the functions of Nudt15 in leukemic stem cells (LSCs) and hematopoietic stem cells (HSCs) remain unknown. Here we reveal the Nudt15-regulating self-renewal of both mouse LSCs and HSCs. Our data show that Nudt15 negatively regulates murine leukemogenesis and its deficiency prolongs the survival of murine AML recipients by impairing LSC self-renewal, while Nudt15 ablation markedly enhances mouse HSC regenerative potential and self-renewal. Mechanistically, Nudt15 modulates inflammatory signaling in mouse LSCs and HSCs, leading to divergent self-renewal outcomes. Nudt15 depletion inhibits mouse LSC self-renewal by downregulating Ifi30, resulting in elevating intracellular ROS levels. Gata2, a key regulator, is required for Nudt15-mediating inflammatory signaling in mouse HSCs. Collectively, our results present new crucial roles of Nudt15 in maintaining the functions of mouse LSC and HSC through inflammatory signaling and have a new insight into clinical implications.

overall_design: To explore the potential function of Nudt15 on leukemogenesis, we established AML mice by using the MLL-AF9 oncogene. Wild-type and Nudt15KO HSCs were transduced with retroviral particles containing MLL-AF9 and then transplanted into the recipients. LSCs were isolated from the AML recipients and sorted by FACS. To investigate the role of Nudt15 in HSCs, we sorted HSCs from wild-type and Nudt15KO mice by FACS. The LSCs and HSCs were then performed gene expression profiling analysis using data obtained from RNA-seq.


title: Co-transcriptional RNA processing boosts zygotic genes and restrains noncoding transcription

city: Beijing

first: Xu

last: Jingzhao

address: Zhongguancun North Street

department: School of Medicine

institute: Tsinghua university

summary: Transcription decodes protein-coding genes and interprets regulatory information embedded in the genome by generating RNA. In eukaryotes, gene transcription is coupled with RNA processing via the carboxyl terminal domain (CTD) of RNA polymerase (Pol) II to enhance mRNA production. Here we propose that co-transcriptional RNA processing is essential for zygotic gene activation (ZGA), which shifts from noncoding to protein-centered gene expression post-fertilization. Truncating the Pol II CTD in mouse embryonic stem cells disrupts this coupling, halting global mRNA synthesis and causing widespread intergenic transcription. This triggers transcriptional and epigenetic reprogramming and nuclear reorganization towards totipotency, resembling early two-cell embryos before ZGA. Mechanistically, the CTD suppresses noncoding transcription by restraining polymerase activity on chromatin, but facilitates promoter-proximal pausing, transcription directionality, velocity, and elongation efficacy at genes through coupled RNA processing. The evolution of longer CTD lengths enhances gene activity, likely accommodating the increasingly abundant noncoding genome sequences in mammals.

overall_design: To investigate the broad impact of co-transcriptional RNA processing on genome activity, we used a mouse ESC line with an auxin-inducible degron (AID) tag fused to the C-terminal domain (CTD) of endogenous RPB1. Treatment with indole-3-acetic acid (IAA) induced CTD truncation while leaving the catalytic N-terminal domain (NTD) intact. We performed RNA-seq analysis on EU-labeled nascent RNA and total cellular RNA (rRNA-depleted) following IAA treatment and subsequent wash-off to study the effects of CTD truncation and its reversibility.

first: Jingzhao

last: Xu

first: Xiaohua

last: Shen


title: Application of Transcriptomics Dose-Response Modeling to Risk-Based Prioritization of Contaminants Detected in Tributaries of the North American Great Lakes [P. promelas]

city: Duluth

first: Peter

last: Schumann

state: MN

address: 6201 Congdon Blvd

institute: United States Environmental Protection Agency

summary: As part of the Great Lakes Restoration Initiative, a series of chemical monitoring and surveillance efforts have detected approximately 550 chemicals in Great Lakes tributaries. Among these, there were 140 chemicals for which no empirical toxicity data were available to support prioritization. The aim of the present study was to generate transcriptomic points of departure (tPODs) for 10 of these compounds and demonstrate how they could be applied in a screening-level prioritization. Organisms representing three different trophic levels of the aquatic food-web (Pimephales promelas – secondary consumer, Daphnia magna-primary consumer, and R. subcapitata-primary producer). were exposed for 24 h to a ½-log dilution series of nominal exposure concentrations typically ranging from 66.7 to 0.021 µM of each chemical. In addition to observations of apical effects such as survival and morphology, whole body transcriptomic responses to each chemical were evaluated with targeted analysis using TempO-seq for P. promelas and D. magna and non-targeted full RNA-seq for R. subcapitata. Benchmark concentrations (BMCs) were calculated for each gene showing a concentration-dependent expression pattern. The tPOD for each chemical-species combination was defined as the 10th percentile of the BMCs. The tPODs ranged from 0.18 to 10.8 µM for P. promelas and 0.32 to 29 µM for D. magna, with the most potent of the chemicals tested being fipronil carboxamide. For R. subcapitata, the tPODs ranged from 0.04 to 1.77 µM, with gabapentin as the most potent chemical tested. Empirically derived tPODs from these data poor chemicals, as well as tPODs from previously tested data rich chemicals, were compared with concentrations detected in the Great Lakes basin. This work demonstrates the potential utility of emerging ecological high-throughput transcriptomics assays to support timely screening and prioritization of data poor environmental contaminants.

overall_design: RNA-seq was performed using the TempO-Seq protocol on RNA extracted from whole, larval Pimephales promelas that were exposed for 24 h to a ½-log dilution series of nominal exposure concentrations (typically ranging from 66.7 to 0.021 µM) of the following 12 chemicals: 1(2H)-Phthalazinone, cis-nonachlordane, Metolachlor OA, 3,4-Dichlorophenyl isocyanate, Gabapentin, Metribuzin-DA, 2-tert-butyl-4-methoxyphenol, Hydrochlorothiazide, 4-chlorophenyl methyl sulfone, Cetirizine Hydrochloride, Fipronil carboxamide, Fexofenadine. Samples were pooled by treatment concentration within each plate, resulting in n=3 replicates per treatment, each containing five pooled organisms. Each assay included DMSO controls, with final in-well DMSO concentrations never exceeding 0.34% in the exposure plate wells. Additionally, 8 replicates of positive controls were included as exposures to 110 uM of caffeine.

first: Jenna

middle: E

last: Cavallin

first: Kendra

last: Bush

first: Steven

middle: R

last: Corsi

first: Laura

middle: A

last: De Cicco

first: Kevin

last: Flynn

first: Monique

last: Hazemi

first: Erin

last: Maloney

first: Alex

last: Kasparek

first: Daniel

last: Villeneuve


title: Smart-seq2 analyses of ESCs-derived CD144 population transplanting-derived Lin-Sca-1+c-Kit- cells

city: Hangzhou

first: Wei

last: Shan

state: Zhejiang

address: Bone Marrow Transplantation Center, The First Afﬁliated Hospital, School of Medicine, Zhejiang University, No.79 Qingchun Road, Hangzhou, Zhejiang, PR China.

institute: Zhejiang University

summary: Smart-seq2 was further performed to investigate transcriptome characteristics of the in vivo Lin-Sca-1+c-Kit- lymphoid progenitors (ESC-derived Lin-Sca-1+c-Kit-) obtained from the primary recipients and wild-type LSK HSPCs from the bone marrow of C57BL/6 mice (wt-LSK).

overall_design: 3 sample (ESC-derived Lin-Sca-1+c-Kit-)；3 sample (wild-type LSK HSPCs from the bone marrow of C57BL/6 mice)；

first: Pengxu

last: Qian

first: Xiangjun

last: Zeng


title: RNA-seq revealed the anti-pyroptotic effect of suramin by suppressing NLRP3/caspase-1/GSDMD pathway in LPS-induced MH-S alveolar macrophages

city: Ningbo

first: Yuhui

last: Zhu

address: No. 59 Liuting Street, Haishu District

department: Anesthesiology

institute: The First Affiliated Hospital of Ningbo University

summary:
Background:
Acute lung injury (ALI)/acute respiratory distress syndrome (ARDS), acting as one common sepsis-associated organ injury, induces uncontrolled and self-amplifies pulmonary inflammation. Given the lack of clinically effective approaches, the mortality rate of it still remains high. Suramin(SUR) was found to ameliorate sepsis associated ALI in our previous work. However, the underlying mechanism of its protective effects has not been clarified. Pyroptosis, categorized as an inflammatory form of programmed cell death, could aggravate lung inflammatory responses via inducing alveolar macrophages (AM) pyroptosis.
Methods:
MH-S AM cell line was stimulated with or without lipopolysaccharide (LPS) or suramin, and the differential expression genes (DEGs) were excavated using RNA sequencing (RNA-Seq). To identify the regulatory roles of these genes, pyroptosis-related genes (PRGs), GO/KEGG and GSEA analysis were conducted. We also performed WB, qRT-PCR and ELISA to validate the RNA-seq results and further expound the protective effect of suramin.
Results:
624 DEGs were identified between CON and lipopolysaccharide (LPS) groups, and enrichment analysis of these genes revealed significantly enriched pathways that related to immune system and signal transduction. Meanwhile, 500 DEGs were identified in LPS/SUR+LPS group. In addition to the pathways mentioned above, IL-17 pathway and C-type lectin receptor signaling pathway were also enriched. All 6 pathways were connected with pyroptosis. Concurrently, the “DESeq2” R package was used to identify differentially expressed PRGs. Nod1, Nod2, interleukin (IL)-1, IL-6, tumor necrosis factor (TNF), NLRP3 were upregulated under LPS stimulation. Then, in SUR+LPS group, Nod2, IL-6, IL-1, NLRP3 were downregulated. The validation results of WB, qRT-PCR, and ELISA showed: the protein and mRNA expression levels of NLRP3, caspase-1, GSDMD and the concentrations of IL-1, IL-18 were decreased when treated with suramin and LPS.
Conclusion:
Suramin could inhibit NLRP3/caspase-1/GSDMD canonical pyroptosis pathway in LPS-induced MH-S alveolar macrophages.

overall_design: To investigate the relationship between suramin and proptosis in LPS induced sepsis associated ALI, MH-S AM cell line was stimulated with or without lipopolysaccharide (LPS) or suramin.We performed GO/KEGG/GSEA analysis using data obtained from RNA-seq,then clarifed the correlation with proptosis-related genes, and validated by Western Blot, qRT-PCR and ELISA.

first: Haidong

last: Zhou


title: Mapping the unicellular transcriptome of the ascending thoracic aorta to changes in mechanosensing and mechanoadaptation during aging

status: Public on Jun 05 2026

city: New York City

first: Eduardo

last: Esteva

address: 550 1st Ave

institute: NYU Grossman School of Medicine

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

overall_design: Refer to individual Series


title: Active and Passive Mechanical Deficits Precede Spinal Curvature in a Zebrafish Model of Idiopathic Scoliosis

city: Eugene

first: Samuel

last: Bertrand

state: OR

address: 1318 Franklin Blvd

department: IMB

institute: University of Oregon

summary: Idiopathic scoliosis is a common spinal disorder characterized by progressive three-dimensional curvature of unknown cause. Although biomechanical imbalance has long been proposed to contribute to scoliosis, the early physiological states that precede curvature onset remain poorly understood. Here, we investigated this problem using zebrafish uts2r3 mutants, which develop fully penetrant juvenile-onset spinal curvature following disruption of urotensin signaling. Transcriptomic analysis before curvature revealed altered expression of muscle-associated genes, suggesting that Uts2r3 influences axial muscle development or function. However, immunofluorescence, birefringence imaging, and quantitative analysis of myotome morphology showed that mutants lack overt muscle architectural defects or dystrophic pathology. By contrast, direct measurements of isolated larval trunks revealed pre-curvature biomechanical abnormalities: namely, uts2r3 mutants generated reduced active force following electrical stimulation while also exhibiting increased passive resistance to stretch. These findings identify urotensin signaling as a regulator of axial tissue biomechanics during growth and suggest that scoliosis-like curvature can arise from an early imbalance between active force generation and passive tissue stiffness.

overall_design: RNA-seq profiling of whole body wild type and uts2r3 homozygous mutant 28 hpf zebrafish embryos


title: Butyrate kinase (Buk) links branched-chain fatty acid biosynthesis, cold adaptation, and pathogenesis in Listeria monocytogenes

city: Mississippi State

first: Monzur

last: Chowdhury

state: MS

address: 240 Wise Center Dr

department: Comparative Biomedical Sciences, College of Veterinary Medicine

institute: Mississippi State University

summary: The phosphate acetyltransferase Ptb and butyrate kinase Buk constitute a proposed alternative route for short-chain acyl-CoA and branched-chain fatty acid (BCFA) precursor metabolism in Listeria monocytogenes. We constructed in-frame deletion mutants of ptb and buk in L. monocytogenes F2365 and found that Buk, but not Ptb, is required for anteiso-BCFA biosynthesis and cold tolerance. The buk mutant displayed reduced anteiso-BCFAs and a shift in phosphatidylglycerol (PG) composition, indicating substantial membrane remodeling. Functionally, the buk mutant exhibited defects in cell-to-cell spread, intracellular replication, phospholipase activity, LLO production, and in vivo virulence, whereas ptb retained wild-type phenotypes. Transcriptomic profiling revealed coordinated metabolic reprogramming in the buk mutant, characterized by downregulation of branched-chain amino acid (BCAA) biosynthesis and phosphotransferase (PTS) systems, indicating impaired precursor supply and nutrient acquisition, along with compensatory upregulation of central metabolism and redox processes. These findings identify Buk for the first time as a metabolic and virulence determinant in L. monocytogenes.

overall_design: RNA-seq transcriptomic profiling comparing the buk deletion mutant (F2365 delta-buk) with the parent wild-type strain F2365 grown to stationary phase in defined minimal media (MM) at 25 degrees C. Two independent biological replicates were analyzed per condition (wild-type and delta-buk).

first: Seto

last: Ogunleye

first: Matthew

last: Frank

first: Hossam

last: Abdelhamed


title: Mapping the unicellular transcriptome of the ascending thoracic aorta to changes in mechanosensing and mechanoadaptation during aging [old_arch CITE-seq]

summary: Aortic stiffening is an inevitable manifestation of chronological aging, yet the mechano-molecular programs that orchestrate region- and layer-specific adaptations along the length and through the wall of the aorta are incompletely defined. Here, we show that the decline in passive cyclic distensibility is more pronounced in the ascending thoracic aorta (ATA) compared to distal segments of the aorta and that collagen content increases in both the medial and adventitial compartments of the ATA during aging. The single-cell RNA sequencing of aged ATA tissues reveals altered cellular senescence, remodeling, and inflammatory responses accompanied by enrichment of T-lymphocytes and rarefaction of vascular smooth muscle cells, compared to young samples. T lymphocyte clusters accumulate in the adventitia, while the activation of mechanosensitive Piezo-1 enhances vasoconstriction and contributes to the overall functional decline of ATA tissues. These results portray the immuno-mechanical aging of the ATA as a process that culminates in a stiffer conduit permissive to the accrual of multi-gerogenic signals priming to disease development.

overall_design: Ascending thoracic aortas (ATA) were collected from aged (84 ± 4 weeks old, n=3) wildtype mice for single-cell RNA sequencing analysis.

first: Cristobal

last: Rivera

first: Yasmeen

last: Farra

first: Michele

last: Silvestro

first: Steven

last: Medvedovsky

first: Jacqueline

last: Matz

first: Muhammad Yogi

last: Pratama

first: John

last: Vlahos

first: Bhama

last: Ramkhelawon

first: Chiara

last: Bellini


title: Mapping the unicellular transcriptome of the ascending thoracic aorta to changes in mechanosensing and mechanoadaptation during aging [young_arch CITE-seq]

overall_design: Ascending thoracic aortas (ATA) were collected from young (12 ± 1 weeks Young, n=3) wildtype mice for single-cell RNA sequencing analysis.


title: Paired mutation calling and spatial transcriptomics identify cellular neighborhoods associated with neoplastic outcomes in mouse colitis

city: Cambridge

last: Eldridge

address: Robinson Way

department: Cancer Research UK Cambridge Institute

country: United Kingdom

institute: University of Cambridge

summary: In the progression from Inflammatory Bowel Disease to associated cancer, the clonal mutational landscape shifts from selection of mutations in inflammatory genes to selection for cancer-driver mutations. How prevalence and expansion of either type of mutant clones could be impacted by the cellular environments in which they arise, and how this affects the neoplastic outcome of colitis, remains unknown. Here, we combine in vivo lineage tracing, in silico modelling, mutational profiling and spatial transcriptomics in a mouse model of colitis-associated tumorigenesis to capture clone fates associated with chronic inflammation. We identify epithelial- and immune-enriched neighbourhoods and propose a model in which establishment of a reparative tissue environment facilitates tumour initiation by promoting the selection and expansion of pro-oncogenic clones, reducing the span of inflammation-resistant neighbourhoods containing non-oncogenic clones.

overall_design: n=5 Muc2hom mice treated with 200mg/kg ENU intraperitoneally at 8 weeks. Colon tissue was collected at 16 weeks. n=3 Muc2het and n=3 Muc2wt mice treated with 200mg/kg ENU intraperitoneally at 8 weeks, followed by 2% DSS treatment at day 10 post-ENU for 5 days. Colon tissue was collected at day 7 (n=1 Muc2wt, n=2 Muc2het) or day 21 post-ENU (n=1 Muc2het, n=2 Muc2wt). n=4 VillinCreERT; Apc+/- mice were treated with treated with 200mg/kg ENU intraperitoneally at 8 weeks, and with 4mg tamoxifen intraperitoneally at day 30 post-ENU. Colon tissue was collected at humane endpoint. n=3 Muc2het and n=3 Muc2hom mice were aged until humane endpoint before colon tissue collection. All whole-mounted colons were fixed with 4% PFA, and 3-5µm thickness tissue sections were cut for spatial transcriptomics with 10X Visium (FFPE).

first: Elisa

middle: B

last: Moutin

first: Giada

last: Giavara

first: Filipe

last: Lourenco

first: Nefeli

last: Skoufou-Papoutsaki

first: Douglas

last: Winton


title: Driving tumor-associated macrophages to a CXCL9Hi/SPP1Low phenotype eliminates pancreatic cancer

city: Boston

first: Yen

last: Nguyen

state: MA

address: 11 Myrtle St, unit 2

department: Center of Systems Biology

institute: Mass General Brigham

summary: Pancreatic ductal adenocarcinoma (PDAC) remains one of the deadliest cancers, with limited therapeutic options. Recent studies have revealed the complex PDAC microenvironment, which fosters interactions between various cell types that contribute to immunosuppression. Among these, tumor-associated myeloid cells with a CXCL9-low, SPP1-high phenotype are particularly abundant and play a significant role in promoting disease progression. We hypothesized that targeting these cells could reprogram the tumor microenvironment and improve survival outcomes. To test this, we developed a novel myeloid cell-targeting nanoformulation, CANDI470, designed to increase CXCL9 expression and reduce SPP1 levels in tumor-associated myeloid cells. Our results demonstrate that this approach not only enhances immune responses but also leads to remarkable therapeutic efficacy, including cures in murine PDAC models, even when used as a monotherapy. This myeloid cell modulation strategy represents a promising new therapeutic avenue for PDAC, offering hope for improved treatment in this otherwise difficult-to-treat malignancy.

overall_design:
BMDMs were cultured as described. On day 7 after differentiation, CANDI470 or empty CANDI was added to the final concentration of 1 mg/mL. RNA was extracted using Qiagen RNeasy Kit per instructions 12 hours after the treatment. RNA samples were sent to Novogene for RNA integrity testing, mRNA library preparation, and sequencing (NovaSeq X Plus Series, PE150).
NOTE: While the '*control' processed data files contain four control sample data (control_1, control_2, empty_1, empty_2), only one control sample has been submitted and the record will be updated with the remaining three samples data shortly.

first: Yen T. M.

first: Marc

last: Pfefferlé

first: Juhyun

last: Oh

first: Grant

last: G. Simpson

first: Sierra

last: A. Walker

first: Shingo

last: Noguchi

first: Christopher S.

last: Garris

first: Riley J.

last: Deutsch Williams

first: Pratyaksha

last: Wirapati

first: Federico

last: De Stefano

first: Marie

last: Goemans

first: Rui

last: Dai

first: Claudio

last: Vinegoni

first: Carlos

last: Fernández del Castillo

first: Andrew S.

last: Liss

first: Mikael

last: Pittet

first: Ralph

last: Weissleder


title: Baseline interferon signaling in monocytes and antibody-mediated innate activation at injection site shape mRNA vaccine reactogenicity [ATAC-seq]

city: Lausanne

first: Gustavo

middle: Agustín

last: Ruiz Buendía

state: Vaud

address: Amphipôle, Quartier UNIL-Sorge

country: Switzerland

institute: Swiss Institute of Bioinformatics

summary: The local and systemic symptoms that follow vaccination -collectively referred to as reactogenicity- are common, yet the mechanisms underlying individual variability remain poorly understood. Through longitudinal immune profiling of vaccinated individuals and mechanistic studies in mice, we identified key immunological determinants of reactogenicity induced by mRNA vaccines. Systemic adverse events were associated with stronger interferon and pro-inflammatory responses following the second dose of COVID-19 vaccine, which were also correlated with the magnitude of the antigen-specific adaptive responses. This heightened inflammation occurred within 24 hours of vaccination and originated primarily from the injection site and was characterized by enhanced recruitment and activation of myeloid cells, particularly monocytes. Two mechanisms contributed to this response: (1) early interferon production by muscle T cells generated after the first dose and (2) FcγR-dependent chemokine induction by antigen-specific antibodies. Consistently, serum antibody levels prior to vaccination correlated positively with reactogenicity. In addition to this local amplification mechanism, variability in reactogenicity was influenced by the baseline immune state, as individuals with a pre-existing interferon-stimulated gene signature in monocytes, detectable at both transcriptomic and epigenetic levels, were more prone to systemic symptoms. Our findings reveal molecular and cellular mechanisms driving vaccine reactogenicity, providing a framework for the design of less reactogenic vaccines.

overall_design:
ATAC-seq profiling of chromatin accessibility of classical monocytes obtained from control participants with a corresponding reactogenicity score approximately 30 days after a first dose of a Spikevax or Comirnaty COVID-19 mRNA vaccine.

***************************************************************
Raw files for human/patient samples are being made available in EGA (https://www.ebi.ac.uk/ega/) for controlled access to the personally identifiable sequence data.
***************************************************************

first: Natacha

last: Madelon

first: Arnaud

last: Didierlaurent


title: Baseline interferon signaling in monocytes and antibody-mediated innate activation at injection site shape mRNA vaccine reactogenicity [NanoString nCounter dataset]

overall_design: Profiling of gene expression of dLN and muscle samples from mice vaccinated with a prime or booster dose of Spike mRNA COVID-19 vaccine.


title: Comparative transcriptomic analysis of rice under cadmium and selenium nanoparticle treatments

city: Chengdu

first: xiumei

last: luo

address: Shuangliu

department: Institute of Urban Agriculture

institute: Chinese Academy of Agricultural Sciences

summary: This study investigated the role of biosynthesized selenium nanoparticles (SeNPs) derived from Chlorella sorokiniana SZ2-1 in alleviating cadmium (Cd) toxicity in rice (Oryza sativa L. cv. Quan Youde Zhan) under hydroponic conditions.The research focused on evaluating the effects of SeNPs on Cd uptake, translocation, subcellular distribution, selenium speciation, and stress-responsive transcriptional regulation. Rice seedlings were exposed to Cd alone or in combination with different concentrations of SeNPs. Physiological, biochemical, ionomic, transcriptomic, and metabolomic analyses were conducted to elucidate the detoxification mechanisms induced by SeNPs.

overall_design: Rice (Oryza sativa L. cv. Quan Youde Zhan) seedlings were grown hydroponically in Kimura nutrient solution under controlled conditions. After preliminary Cd toxicity screening, 10 mg/L Cd was selected for further experiments. Seedlings were treated with Cd alone or combined with different concentrations of biosynthesized SeNPs (1, 3, and 5 mg/L). Treatments included control (CK), Cd, SeNPs alone, and Cd + SeNPs, each with three biological replicates. Root and shoot samples were collected for analyses of Cd accumulation, selenium speciation, transcriptomics, metabolomics, and physiological responses associated with Cd detoxification.


title: Modification of VE-cadherin signalling by ZEB1 in Lymphatic Endothelial Cells

city: Nottingham

first: Alan

last: McIntyre

address: Biodiscovery Institute

department: Centre for Cancer Sciences

institute: University of Nottingham

summary: Zinc finger E-box-binding homeobox 1 (ZEB1) is a transcription factor primarily known for its regulatory roles in epithelial-to-mesenchymal transition (EMT) and cell fate determination. Recent studies suggest that endothelial ZEB1 signalling promotes blood vessel growth and reduces junctional integrity, although the underlying mechanisms remain unclear. Notably, the role of ZEB1 in the lymphatic vasculature is unknown, and the regulation of lymphatic integrity by VE-cadherin remains poorly defined. Here, using an integrated proteomic and transcriptomic approach, we identify ZEB1-dependent signalling pathways associated with cell–cell junction reorganisation in lymphatic endothelial cells (LECs). Loss of ZEB1 reduced VE-cadherin phosphorylation at pY731 and pY685 and was accompanied by decreased monolayer resistance and impedance, together with increased leukocyte transendothelial migration. ZEB1 knockdown also reduced YES tyrosine kinase expression and altered YAP1 expression and junctional localisation, changes that were associated with reduced VE-cadherin phosphorylation. Silencing YAP1 in HDLECs similarly reduced VE-cadherin phosphorylation and impaired barrier integrity, recapitulating aspects of the phenotype observed following ZEB1 knockdown. Collectively, these findings suggest that ZEB1 contributes to lymphatic endothelial barrier maintenance in association with altered YAP1 and YES signalling.

overall_design: Pooled primary human dermal lymphatic endothelial cells (HDLECs; Promocell) were transfected with 20 nM ON-TARGETplus SMARTpool siRNA (Dharmacon) targeting ZEB1 (n=3 biological replicates: NS_19, NS_20, NS_21) or a non-targeting ON-TARGETplus control pool (n=3 biological replicates: ZEB1_15, ZEB1_16, ZEB1_22). Total RNA was extracted 48 hours post-transfection using the RNeasy Mini Kit (QIAGEN). Libraries were prepared from random hexamer–primed cDNA with NEBNext adaptor ligation (150–200 bp inserts) by Novogene (Hong Kong) and sequenced paired-end on an Illumina platform (NovaSeq 6000) to a target depth of 20 million read pairs per sample.

first: Nada

middle: S

last: Ahmed

first: Joseph

last: Horder

first: Charles

middle: T

last: Cresswell

first: Poppy

last: Harris

first: Amy

last: Lynch

first: Zarah

last: Tabrizi

first: Kathryn

last: Green

first: James

middle: H

last: Hallwood

first: Anton

last: Smith

first: Michael

last: Portelli

first: Alexander

last: Fezovich

first: Christos

last: Spanos

first: David

last: Gardner

first: Sarah

last: Storr

first: Daniel

last: Booth

middle: O

last: Bates

first: Andrew

last: Benest


title: Baseline interferon signaling in monocytes and antibody-mediated innate activation at injection site shape mRNA vaccine reactogenicity [human_RNAseq]

first: Gustavo

last: Ruiz Buendía

overall_design:
RNA-seq profiling of gene expression of whole blood and monocytes (classical and intermediate) obtained from control participants with a corresponding reactogenicity score. Participants were vaccinated with Spikevax or Comirnaty COVID-19 mRNA vaccines.

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

first: Natacha

last: Madelon

first: Arnaud

last: Didierlaurent


title: Targeting KRAS in a TRP53/KRAS mouse and organoid model inhibits Barrett Esophagus to Gastroesophageal Adenocarcinoma progression

city: Freiburg im Breisgau

first: Linus

middle: Rudolf

last: Schoemig

state: Baden-Wuerttemberg

address: Breisacherstr. 66

department: Department of Medicine II, Faculty of Medicine

country: Germany

institute: University of Freiburg - Medical Centre

summary: The lack of experimental systems that faithfully model the genetic and phenotypic progression from Barrett’s esophagus (BE) to gastroesophageal adenocarcinoma (GEAC) has limited mechanistic discovery and preclinical testing. Here, we report a refined L2-IL-1B based mouse model engineered to capture two hallmark alterations of human GEAC: Trp53 loss and elevated KRAS signalling driven by KRAS amplification, modelled through oncogenic KrasG12D activation. This combinatorial genetic approach accelerates malignant transformation and enables controlled, stage-resolved analysis of carcinogenesis at the gastroesophageal junction (GEJ). Parallel murine and human organoid systems recapitulate these in vivo phenotypes and provide a platform for functional interrogation of KRAS amplification, a frequent but understudied driver in GEAC. Using these organoids as treatment avatars in addition to the mouse model, we demonstrate that KRAS dependent growth is selectively vulnerable to combined SHP2 + MEK1/2 or ERK1/2 inhibition, revealing a therapeutically targetable signalling axis. Together, these integrated in vivo and organoid platforms represent a technical advance for modelling BE progression, dissecting KRAS pathway biology, and evaluating targeted strategies for KRAS amplified GEAC.

overall_design: RNA-seq profiling of murine organoids from the refined L2-IL-1B based mouse model.

last: Quante


title: Inherent tissue homeostasis of the juvenile metaphysis provides a foundation for osteosarcoma development [scRNAseq_p21]

city: Tokyo

first: Yasuhiro

last: Yamada

address: 7-3-1 Hongo, Bunkyo-ku

department: Department of Molecular Pathology

country: Japan

institute: University of Tokyo

summary: Osteosarcomas typically arise from the metaphyseal cells of juvenile long bones, in contrast to most cancers that develop in aged individuals. Here, we show that the cyclin-dependent kinase inhibitor p21 is expressed in proliferating osteoblasts within the juvenile metaphysis in response to replication stress. Single-cell RNA sequencing focused on the juvenile metaphysis reveals a hierarchical differentiation trajectory of osteoblast-lineage cells, with active proliferation and DNA damage responses predominantly occurring in immature osteoblasts. We find that proliferation of p21+ osteoblasts is mediated by Hedgehog signaling associated with Indian hedgehog (IHH) expression in the growth plate. Consistently, the number of p21+ osteoblasts is markedly reduced following growth plate maturation or pharmacological inhibition of Hedgehog signaling. Induction of c-Myc—a known driver of replication stress and frequently amplified in early-stage osteosarcoma—enhances osteoblast proliferation specifically in juvenile mice, while concurrently augmenting replication stress responses including p53 activation. This c-Myc-driven proliferation remains dependent on Hedgehog signaling and is not sustained after growth plate maturation. Remarkably, functional inactivation of p53 enables continuous proliferation of c-Myc-induced osteoblasts, independent of IHH expression at the growth plate, leading to rapid and widespread metastasis to the lungs. These findings suggest that intrinsic DNA damage responses to replication stress, together with the spatiotemporal restriction of mitogen signaling, safeguard against oncogenic transformation in osteoblasts. Collectively, we uncover the unappreciated aspects of juvenile metaphyseal tissue homeostasis in mice, which may account for the characteristic age of onset, anatomical specificity, and mutational profile of human osteosarcomas.

overall_design: Analyzing tissue homeostasis in the juvenile metaphysis by scRNA-seq analysis in 3-week-old p21-reporter mice.

first: Masato

last: Saito

first: Sho

last: Ohta

first: Fumie

last: Nakasuka

first: Takuya

last: Yamamoto


title: Distal Enhancer-Insulator Module of GDF6 is Essential for Cochlear Formation [ATAC-seq]

city: Miami

first: Mustafa

last: Tekin

state: Florida

address: 1501 NW 10th Ave

department: Human Genetics

institute: University of Miami

summary: Inner-ear malformations cause congenital hearing loss, and several genes are known to guide inner-ear development. However, the contribution of noncoding regulatory elements remains largely unclear. This study investigates the function of distal enhancer elements in the transcriptional regulation of GDF6, a gene crucial for cochlear development. Using mouse models with targeted deletions, human iPSC-derived ear organoids (IEO), and CRISPR interference (CRISPRi) techniques, we identified a downstream regulatory interval harboring a developmental enhancer required to maintain GDF6 expression during otic epithelial maturation, vital for cochlear morphogenesis. Deletion of this regulatory region or targeting of CRISPRi-based repressors to these regions resulted in decreased GDF6 expression, failure of otic-epithelium development, and prevention of hair cell-like differentiation, reflecting cochlear aplasia observed in patients with corresponding genomic deletions. These findings highlight the essential role of long-range regulatory elements in auditory development and illustrate how their disruption contributes to human deafness.

overall_design: ATAC-seq was performed on control (CD2) iPSC-derived inner ear organoids (IEOs) at Day 8 and Day 13 of differentiation to profile chromatin accessibility at the GDF6 cis-regulatory locus. CD2 is a healthy donor-derived iPSC line used as a control.

first: Mohammad Faraz

last: Zafeer

first: Clemer

last: Abad

first: Havva

last: Ortabozkoyun

first: Memoona

last: Ramzan

first: Guney

last: Bademci


title: Distal Enhancer-Insulator Module of GDF6 is Essential for Cochlear Formation [single-cell multiome]

first: Anthony

last: Griswold

state: FL

address: 1501 NW 10th Ave, BRB 318

summary: Mutations in approximately 30 genes have been linked to cochlear malformations, but the contribution of noncoding regulatory elements remains largely unclear. This study investigates the function of distal enhancer elements in the transcriptional regulation of GDF6, a gene implicated in cochlear development. Using mouse models with targeted deletions, human inner ear organoids, and CRISPR interference (CRISPRi), we identified a downstream regulatory interval harboring a developmental enhancer required to maintain GDF6 expression during otic epithelial maturation and cochlear morphogenesis. To characterize cellular composition and chromatin accessibility changes in patient (166-101) versus control (CA-26) iPSC-derived otic progenitor cells, we performed joint single-nucleus RNA-seq and ATAC-seq (10X Genomics Multiome) on CD271+ enriched populations.

overall_design: Human iPSC lines from a control individual (CA-26; sample CKR0426) and a patient (166-101; sample 166P0426) carrying a ~200 Kb homozygous deletion {Chr8:96,596,661-96,803,788; hg19} downstream of GDF6 were differentiated into early otic lineage cells under 2D conditions. Cells were dissociated with Accutase, negatively selected for TRA-1-81 (pluripotency marker), and positively selected for CD271/p75 (early otic progenitor marker) using magnetic beads (Miltenyi). The CD271-enriched population was used for single-nuclei isolation and processed through the 10X Genomics Chromium-X Multiome (snRNA-seq + scATAC-seq) pipeline, generating paired gene expression and chromatin accessibility libraries from the same nuclei for each sample.

first: Juan

middle: I

last: Young


title: Distal Enhancer-Insulator Module of GDF6 is Essential for Cochlear Formation


title: NAB2::STAT6 Fusion Proteins Drive Nuclear Condensate Formation and Transcriptional Reprogramming in Solitary Fibrous Tumors

first: Felipe

last: Beckedorff

address: 1501 NW 10th Avenue room 731.G , Miami, FL

summary: Solitary fibrous tumor (SFT) is a rare and aggressive sarcoma driven by NAB2::STAT6 gene fusions, yet effective targeted therapies remain unavailable. Here, we report that the NAB2ex4::STAT6ex2 fusion variant forms nuclear condensates via liquid-liquid phase separation (LLPS) in engineered fibroblast models and primary SFT cells. These condensates co-localize with BRD4S and EGR1, key transcriptional regulators, and are functionally active, driving widespread transcriptional reprogramming. Treatment with Mithramycin A, a compound that disrupts EGR1-DNA interactions, dissolves NAB2::STAT6 condensates and reverses their aberrant gene expression and chromatin binding signatures. Our findings uncover a previously unrecognized role for NAB2::STAT6 in condensate-mediated oncogenic signaling and provide a mechanistic rationale for condensate-targeted therapy in SFT.

overall_design: ChIP-seq was performed for EGR1 in Lf and Lf-ns cells treated either with DMSO or 300 nM Mithramycin

first: Yi

last: Li

first: Jose

last: Mondaza-Hernandez

first: Gauthami

last: Pulivendala

first: Fardous

last: Elsenduny

first: Guilherme

middle: M

last: Lavezzo

first: Farhan

last: Vahdat Azad

first: Zikun

last: Zhou

first: Jeremy

last: Warren

first: Paulina

last: Trevino

first: Clark

last: Meyer

first: David

last: Lombard

first: Javier

last: Martin-Broto

last: Moura

first: Heather

middle: N

last: Hayenga

first: Leonidas

last: Bleris


title: Distal Enhancer-Insulator Module of GDF6 is Essential for Cochlear Formation [ChIP-Seq]

first: Mustafa

last: Tekin

overall_design: Examination of CTCF, H3K27ac, and H3K4me1 binding in CD2 induced pluripotent stem cells (iPSCs) using ChIP-seq, by status of WT vs Patient-derived deletion in the cells: WT, Patient

first: Tekin

last: Mustafa

first: Zafeer

last: Mohammad Faraz

first: Ortabozkoyun

last: Havva


title: IBI351, a novel KRASG12C inhibitor, enhances αPD-1 efficacy in KRASG12C mutant lung cancer

city: Guangzhou

first: Shuangli

last: Zhu

state: - Select -

address: Dongfeng East Road

institute: Sun Yat-sen University Cancer Center

summary: The clinical benefit of immune checkpoint inhibitor (ICI) treatments in patients with advanced KRAS mutant non-small-cell lung cancer (NSCLC) is limited.   Here, we found IBI351, a selective KRASG12C inhibitor, significantly enhanced the efficacy of anti-PD-1 antibody (αPD-1) in inhibiting tumor growth in vitro and in vivo.   Mechanistically, IBI351 inhibited STAT3 activity, leading to downregulation of stanniocalcin 1 (STC1). STC1 anchors calreticulin (CRT) to the mitochondrial membrane; its downregulation promoted CRT translocation to the cancer cell surface, increasing the ‘eat me’ signal and enhancing T cell infiltration.  In clinical specimens from KRASG12C mutant NSCLC patients treated with PD-1 inhibitors, low STC1 expression correlated with better treatment response and prolonged survival. Together, these findings demonstrate that IBI351 enhances ICI efficacy by suppressing the STAT3-STC1 axis and promoting CRT-mediated phagocytosis, supporting further clinical evaluation of this combination.

overall_design: To further investigate the mechanism by which IBI351 enhanced anti-tumor effects, we conducted RNA-sequencing analysis on H23 cells treated with IBI351 and untreated controls for 48 h (Control and IBI351)


title: Early macrophage immune responses and pathogenic features of an emerging Mycobacterium wolinskyi

city: Jinan

first: Yuxiao

last: Zhao

state: Shandong

address: Qilu Hospital of Shandong University, 107 Wenhua  Xi Road, Jinan, Shandong 250012, China

institute: Qilu Hospital of Shandong University

summary: Mycobacterium wolinskyi is an emerging rapidly growing mycobacterial species whose pathogenic mechanisms and host response patterns remain poorly understood. In this study, a clinical M. wolinskyi strain, designated QL01, was isolated from an 11-year-old child with a facial skin infection. Whole-genome sequencing revealed multiple features associated with pathogenicity, antimicrobial resistance, and host adaptation, including antimicrobial resistance genes, putative virulence factors, genomic islands, prophages, type VII secretion systems, and mammalian cell entry operons. To investigate the early host response, mouse bone marrow-derived macrophages were infected with M. wolinskyi QL01 and subjected to RNA sequencing. Transcriptomic analysis showed broad induction of inflammatory and immunometabolic programs, with prominent enrichment of the TNF, NF-kappa B, and HIF-1 signaling pathways. These findings provide a genomic and transcriptomic framework for understanding host-pathogen interactions involving M. wolinskyi.

overall_design: RNA-seq profiling of uninfected wild-type bone marrow-derived macrophages and M. wolinskyi QL01-infected wild-type bone marrow-derived macrophages after 6 h infection, with three biological replicates per group.

first: Yiwen

last: Gao

first: Shixuan

last: Wei

first: Weiwei

last: Sun

first: Xiaoli

last: Zhang

first: Enhua

first: Lili

last: Wang

first: Zhihong

last: Wu

first: Hongwei

last: Pan

first: Wei

last: Li


title: Atlas of human gut-associated lymphoid tissue reveals immunomodulatory interactions of B cells

city: London

first: Jo

last: Spencer

state: Kent

address: Guy’s Hospital Campus

institute: King's College London

summary: Gut-associated lymphoid tissue (GALT) is organized lymphoid tissue that responds chronically to antigens, including whole bacteria, sampled from the gut lumen. The ensuing immunoglobulin A (IgA) plasma cell response disseminates to regulate bacterial populations and to mediate intestinal immune homeostasis. GALT has roles in the development of the innate-like marginal zone B cell population and is also associated with a B cell–mediated contribution to ulcerative colitis (UC) severity and response to therapy. Applying integrated multiomics methodologies, we identified key spatially resolved interactions of B cell subsets including broad regulatory features of double negative 2 (DN2) B cells with potential to maintain homeostasis within microbe-rich mucosa. By contrast, GALT in UC is distorted in composition and spatial distribution of B cell subsets that have altered immunomodulatory potential compared to healthy GALT. Thus, we identify interactions of strategically located B cells as mediators of immunological equilibrium in human gut.

overall_design: CITEseq data: FACS sorted B cells from healthy donor human appendix were stained with ADT antibodies. Single cell RNA and ADT libraries generated using the 10X Chromium platform.

first: Michael

last: Pitcher

first: Chiara

last: Dionisi


title: Integrative transcriptomic, network, and genomic analysis of peripheral blood mononuclear cells identifies candidate gene drivers of dupilumab clinical response in atopic dermatitis patients

city: Maribor

first: Martina

last: Krušič

address: Taborska ulica 8

country: Slovenia

institute: Faculty of Medicine

summary: Atopic dermatitis (AD) is among the most common chronic inflammatory diseases. Due to the heterogeneous presentation of AD, patient response to treatment may differ considerably. Therefore, there is a pressing need for biomarkers that could predict response to biological therapies. In line with this, we aimed to identify blood biomarkers that could predict response in patients treated with dupilumab. The present study applied a multi-stage integrative analytical framework combining transcriptomic profiling, functional enrichment, co-expression network analysis, and genomic variant analysis to identify potential biomarkers. Eighteen dupilumab-naïve patients were enrolled in the transcriptomic analysis, with blood samples collected at baseline and after 16–18 weeks of therapy; five patients were identified as non-responders. Additionally, genotyping was performed in 34 patients. We identified a set of candidate genes (RPL18A, RPS28, FAU, MASTL, AURKA, TAF2, BUB1B, and RNF135) and genomic variants that may reflect underlying biological mechanisms influencing therapeutic response. Finally, our study highlighted potential genes that could predict outcome in patients with AD who are treated with dupilumab. Moreover, our study represents an incremental contribution to existing knowledge and opens new avenues for research that may ultimately lead to personalized medicine.

overall_design: Blood samples were collected from dupilumab-naïve patients with atopic dermatitis at week 0 (baseline), prior to the first administration of dupilumab. Follow-up blood samples were obtained 16–18 weeks after treatment.

first: Mario

last: Gorenjak

first: Uroš

last: Potočnik

first: Maruška

last: Marovt


title: Fibroadipogenic Progenitor–Secreted Prostaglandin E2 Coordinates Stem Cell Fate via Autocrine and Paracrine Crosstalk in Healthy and Dystrophic Muscle.

city: Montreal

first: Nicolas A

last: Dumont

state: Quebec

address: 3175 Chem. de la Côte-Sainte-Catherine

country: Canada

institute: CHU Sainte-Justine

summary: Fibroadipogenic progenitors (FAPs) play a key role in skeletal muscle homeostasis and regeneration. They produce extracellular matrix components and secrete cytokines that regulate muscle stem cell function. The number of FAPs and their activity need to be dynamically regulated to avoid their chronic accumulation and overproduction of fibrosis. However, the intrinsic factors by which FAPs control their cell fate decisions remain elusive. Here, we show that FAPs-secreted prostaglandin-E2 (PGE2) functions as a key autoregulatory factor. Using single cell lipidomics and single cell transcriptomics, we show that FAPs are the main cellular source of PGE2 in resting muscle and during regeneration. FAP-secreted PGE2 exerts paracrine effects that maintain the muscle stem cell pool at steady state and stimulate their proliferation post-injury. Moreover, it has autocrine effects that influence FAP fate decisions and promote their apoptosis. Administration of non-steroidal anti-inflammatory drugs that inhibit the prostaglandin-synthesizing enzyme COX2 increases FAPs content post-injury. Using Pdgfrα-CreERT2_Cox2flox mice, we showed that conditional ablation of COX2 specifically in FAPs increases FAPs content, fibrosis, and impairs muscle regeneration, which can be rescued by PGE2 administration. Furthermore, we show that PGE2 production in FAPs is impaired in mouse models of Duchenne muscular dystrophy, and we provide a proof-of-concept that PGE2 administration can reduce FAPs numbers, fibrosis accumulation, and increase muscle strength. Overall, we uncover a novel role for PGE2 beyond its function in inflammation and identify a mechanism by which FAPs intrinsically regulate their own cell fate, revealing therapeutic potential for muscle injury and dystrophic conditions.

overall_design: RNA-SEQ profiling of wt FAPs isolated from mouse muscle treated with vehicle or PGE2 once per day over 2 consecutive days.

first: Thomas

last: Molina

first: Etiene

last: Collette


title: Hierarchy of grammar rules for the language of transcriptional activation domains

city: Indianapolis

first: David

last: Cooper

state: IN

address: 350 PHSB, 4600 Sunset Ave.

institute: Butler University

summary: Transcriptional activation domains (ADs) of eukaryotic gene activators have remained enigmatic for decades as short, consensus-less, extremely variable amino acid sequences that lack a specific structure and interact fuzzily with an uncertain number of targets. Understanding AD sequence grammar is critical for solving the enigma. Using rational design of AD sequences and high-throughput in vivo experimentation combined with bioinformatic analysis and machine learning, we refined grammar rules for AD sequences, calculated the relative importance of each rule, and linked them to the biochemical features essential for biological function. The key feature – redundant representation in the sequence of aromatic and acidic residues - is consistent with the novel idea that ADs function as acidic-hydrophobic surfactants, which is crucial for understanding eukaryotic gene regulation and the function of intrinsically disordered protein regions.

overall_design: DNA-Seq of yeast cell line Y2H Gold containing designed TAD sequences, at baseline and after growth on  growth medium containing antibiotic aureobasidin for up to three days. Five biological replicates were taken at each time point, indicated by biorep barcodes appended to the sequences. Ability to grow on antibiotic-containing media leads to increase in sequence read counts after a certain growth period, demonstrating the functionality of certain TAD sequences

middle: G

first: Bradley

middle: K

last: Broyles

first: Caleb

last: Class

first: Tamara

middle: Y

last: Erkina

first: Alexandre

last: Erkine


title: Transcriptomic differences in Vhl-deficient and wild-type (WT) ventricular cardiac tissue using the Wt1-Cre mouse model (RNA-Seq)

city: Madrid

first: Manuel

middle: J

last: Gomez

state: Madrid

address: Melchor Fernández Almagro, 3

country: Spain

institute: CNIC

summary: RNA-seq was performed on ventricular cardiac tissue isolated from Vhl-floxed/Wt1-Cre mice  and their WT counterparts. This study aimed to characterize the transcriptomic differences in the heart from mice deficient in Vhl in the Wt1 lineage, with the goal of identifying genes regulated by the HIF signaling patway.

overall_design: WT and Vhl-deficient ventricular tissue was obtained upon disection. RNA was extracted using the RNeasy Micro Kit (Qiagen) and sequencing was performed on a NovaSeq 6000 (Illumina).

first: Silvia

last: Martin-Puig


title: Cytotoxic CD39+ tumor-associated NK cells respond to NKG2A blockade in lung cancer (10x Xenium)

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

institute: University of Basel

summary: Natural killer (NK) cell–targeting immunotherapies are emerging, yet the differentiation and functional states of tumor-infiltrating NK cells remain poorly understood. Using matched single-nucleus RNA and ATAC sequencing of samples from patients with non–small cell lung cancer (NSCLC), we resolved the transcriptional and epigenetic landscape of intratumoral NK cells. We identified two tumor-associated NK (taNK) cell subsets marked by expression of ITGAE (CD103) and ITGA1 (CD49a) that display features of tissue residency and dysfunction while preserving cytotoxic function. Trajectory and regulon analyses revealed an inflammation-driven transition from early granzyme K (GZMK)+ NK cells toward an ENTPD1+ (CD39+) effector state characterized by interferon-stimulated gene (ISG) programs. Functional profiling established CD39+ taNK cells as the dominant cytotoxic NK cell population with superior killing capacity that was further potentiated by NKG2A blockade. This study offers mechanistic insights into NK cell differentiation in NSCLC and establishes CD39+ taNK cells as a targetable effector population for immunotherapy.

overall_design: 10X Genomics Xenium spatial transcriptomics on a treatment-naive LUAD patient (LuT-722) was performed comparing tumor core, invasive margin, and adjacent non-tumor lung

first: Wiebke

last: Rackwitz

first: Annalena

last: Brüggemann

first: Carina

last: Pawlow

first: Evgeny

last: Chichelnitskiy

first: Clara

last: Serger

first: Alfred

last: Zippelius

first: Lavinia

last: Neubert

first: Christine

last: Falk


title: Systemic and breast chronic inflammation and hormone disposition promote a tumor-permissive environment for breast cancer in older women (Organoid scRNA-Seq)

city: Pittsburgh

first: Neil

last: Carleton

state: PA

address: 5051 Centre Ave

department: Pharmacology & Chemical Biology

institute: University of Pittsburgh

summary: Estrogen receptor positive (ER+) breast cancer, the most common subtype of breast cancer, is an age-related disease, with the peak incidence of diagnosis occurring around age 70 despite low circulating levels of estradiol. Despite the hormone sensitivity of these age-related tumors, our understanding of the interplay between the systemic and local hormonal disposition and chronic inflammaging is limited. We show that aged F344 rats treated with the DMBA/MPA carcinogen develop more tumors at faster rates than their younger counterparts, suggesting that the aged environment accelerates tumor growth. snRNA-seq of the tumors showed broad local immune dysfunction that was associated with circulating chronic inflammation. Across a broad cohort of specimens from patients with ER+ breast cancer and age-matched donors of normal breast tissue, we observe that even with E1-predominant estrogen disposition in the systemic circulation, tumors in older patients upregulate HSD17B7 expression to convert E1 to E2 in the TME. Age-related accumulation of tumor-associated macrophages serve as signaling hubs that integrate the E2 and chemokine-driven chronic inflammatory signaling in the TME, which polarize TAMs towards a CD206+/PD-L1+, immunosuppressive phenotype. Overall, these findings suggest that the host's chronic inflammation and hormonal disposition shape the local tumor microenvironment and are critical contributors to the age-related nature of ER+ breast cancer development and growth.

overall_design: PDO-296 ER+ breast cancer patient-derived organoids were treated with 7 conditions: Vehicle, E1, E1+fulvestrant (ICI 182,780), E1+HSD17B7 inhibitor, E2, E2+fulvestrant, E2+HSD17B7 inhibitor. Single-cell RNA-seq was performed using the 10x Genomics Chromium Flex (Fixed RNA Profiling) platform. Samples were multiplexed into two pools: Pool 1 (OS01-OS04, Vehicle/E1/E1+ICI/E1+HSD17B7i) and Pool 2 (OS05-OS07, E2/E2+ICI/E2+HSD17B7i). Libraries were sequenced on an Illumina NovaSeq X Plus.

first: Alexander

last: Chang

first: Steffi

last: Oesterreich

first: Adrian

last: Lee


title: Efferocytosis induces proangiogenic function and chromatin remodeling in tumor-associated macrophages [ATAC-seq]

city: Tel Aviv

first: Merav

last: Cohen

address: Chaim Levanon St 55

department: Clinical microbiology and immunology

country: Israel

institute: Tel Aviv University

summary: Macrophages remove apoptotic cells by efferocytosis during immune-surveillance and in the tumor microenvironment (TME). However, the gradual molecular and epigenetic consequences of efferocytosis on the single macrophage are not thoroughly elucidated. Here we introduce Effero-seq, an approach that captures single-cell transcriptomic changes coupled with lysosomal acidification tracked by pHrodo, thus enabling the dissection of molecular dynamics over time following engulfment. Using apoptotic pHrodo-labeled cells as cargo, we defined the effero-score, a gene program gradually upregulated correlatively with pHrodo intensity. In a murine melanoma model, we found that efferocytosis induces a pro-angiogenic function in macrophages with spatial proximity to vascular niches. Moreover, efferocytosis reprograms chromatin accessibility, leading to attenuated macrophage response to IFNγ. In human uveal melanoma, expression of the effero-score is correlated with poor survival. Effero-seq sheds light on the molecular reprogramming induced by efferocytosis in the TME, opening new avenues for understanding macrophage function and developing targeted treatments.

overall_design: We applied Effero-seq in a murine melanoma model by injecting B16 cancer cells subcutaneously into adult mice. Annexin V+ ACs were isolated and stained with pHrodo, before being injected into new mice with viable B16 cells. Then, for 3 replicates we bulk sorted macrophages into bins according to pHrodo intensity - negative, low, intermediate and high. We then performed ATAC-seq on each bin of macrophages.

first: Roi

last: Balaban

first: Ori

last: Moskowitz

first: Maiia

last: Levinson

first: Noam

last: Ofer

first: Alice

last: Raizman

first: Gaya

last: Levi Kitron

first: Eden

last: Aviv

first: Sandra

last: Camargo

first: Lihi

last: Goldman

first: Aviv

last: Leeman

last: Noachas

first: Chen

last: Sharon-Yagol

first: Amir

last: Giladi


title: Genome-wide Discovery of lncRNAs in Mucorales Reveals Essential Roles in EDF Biology

city: Murcia

first: Carlos

last: Lax

address: Facultad de Biología

department: Genetics and Microbiology

institute: University of Murcia

summary: Long non-coding RNAs (lncRNAs) emerged as key regulators across eukaryotes, yet their functions in early-diverging fungal (EDF) pathogens remain largely unknown. Here, we provide the first comprehensive identification and characterization of lncRNAs in the EDF order Mucorales, a threatening and WHO high-priority group of opportunistic human pathogens. In this work, we focus on the two major models of this group: Mucor lusitanicus and the clinically relevant pathogen Rhizopus microsporus. We show that EDF lncRNAs exhibit conserved features, dynamic regulation during host interactions, and integration within critical gene regulatory networks. Despite being distributed preferentially in the inactive compartment of chromatin, we found that their expression is associated with 6mA presence in R. microsporus. Additionally, we also found that the lncRNA can be targeted by both canonical and non-canonical RNA pathways active in these fungi. Comparative genomics revealed a subset of evolutionarily conserved lncRNAs, including two essential lncRNAs for fungal viability (lncRNA2 and lncRNA4). LncRNA4 disruption, even in heterokaryosis, resulted in severely affected growth and filamentation. These results establish lncRNAs as indispensable regulators of fungal physiology and pathogenicity, highlighting their potential as novel antifungal targets.

overall_design: Transcriptomic analysis using RNA-seq to study the impact of lncRNA2 and lncRNA4 deletions on gene expression at both messenger RNA (mRNA) in Rhizopus microsporus. Wild-type strain UM6 and lncRNA2::pyrF and lncRNA4::pyrF mutants  were used. Total RNA was extracted from samples collected after 24 hourr of saprophytic growth  at 30ºC, MMC media. Three biological replicates were performed for each condition.

first: Ghizlane

last: Tahiri

first: Hrant

last: Hovhannisyan

first: Eusebio

last: Navarro

first: Toni

last: Gabaldón

first: Francisco

last: Nicolás

first: Victoriano

last: Garre


title: Identification of highly potent inhibitors capable of blocking VprBP kinase activity and suppressing prostate tumor growth

city: Los Angeles

first: Sungmin

last: Kim

state: CA

address: 1450 Biggy St, NRT 6517

department: Department of Cancer Biology

institute: University of Southern California

summary: VprBP has been recently identified as an oncogenic kinase and a promising drug target in human malignant tumors. Although VprBP can phosphorylate histone H2A and some non-histone proteins, it seems to selectively target specific substrates in a cancer type-dependent manner by an unknown mechanism. Here we report that VprBP is highly expressed in prostate cancer cells and inactivates a group of genes encoding critical regulators of cell growth and proliferation in a manner dependent on its kinase activity toward H2AT120. As an extension of our previous finding of VprBP inhibitor B32B3, we also screened a series of small molecule compounds derived from B32B3 and identified B1486 as a second-generation VprBP inhibitor with much higher efficacy and potency. B1486 is far more effective in blocking VprBP-mediated H2AT120p and reactivating growth regulatory genes, resulting in a significantly lower proliferative capacity of prostate cancer cells. Similarly, B1486 treatment inhibits VprBP kinase activity, modulates H2AT120p-induced gene inactivation, and impairs prostate tumor growth in xenograft mouse models. Together, our findings establish a critical role for VprBP-mediated H2AT120p in oncogenic gene silencing and B1486 as a promising therapeutic strategy for prostate cancer.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for PC3 cells (Control sh and VprBP sh).

first: Woojin

last: An


title: Cytotoxic CD39+ tumor-associated NK cells respond to NKG2A blockade in lung cancer (10X Multiome)

first: DBM Bioinformatics

last: Core Facility

overall_design:
CD56⁺ NK and T cells were sorted from 11 treatment-naive NSCLC patients. Single nulceus RNA and ATAC sequencing was performed using the 10x Multiome protocol. The rds supplementary file contains filtered NK cells only.

***************************************************************
Raw files for human/patient samples are available in EGA (https://www.ebi.ac.uk/ega/) for controlled access to the personally identifiable sequence data.

Studies: EGAS50000001189, EGAS50000001190
Datasets: EGAD50000001695
***************************************************************

first: Clara

last: Serger

first: Lucas

last: Rebuffet

first: Michael

last: Sandholzer

first: Eric

last: Vivier

first: Andrea

last: Romagnani

first: Alfred

last: Zippelius


title: Efferocytosis induces proangiogenic function and chromatin remodeling in tumor-associated macrophages

first: Merav

last: Cohen

overall_design: Single cell transcriptional profiling of macrophages that performed efferocytosis (phago/pHrodo+) and that didn't perform efferocytosis (non-phago/pHrodo-) as well as macrophages which did not receive external apoptotic supplementation (PBS/viable only) in an in-vitro model and in-vivo models of healthy lung and B16 tumors.

first: Roi

last: Balaban

first: Ori

last: Moskowitz

first: Maiia

last: Levinson

first: Noam

last: Ofer

first: Alice

last: Raizman

first: Gaya

last: Levi Kitron

first: Eden

last: Aviv

first: Sandra

last: Camargo

first: Lihi

last: Goldman

first: Aviv

last: Leemann

last: Noachas

first: Chen

last: Sharon-Yagol

first: Amir

last: Giladi


title: Human Endogenous Retroviruses Drive Type-I Interferon Signaling activation in Early Rheumatoid Arthritis

city: Suzhou

first: xinyu

last: zhou

address: No. 199 Ren'ai Road, Suzhou Industrial Park

institute: Soochow University

summary: Substantial reactivation of HERVs was observed in both synovial tissues and PBMCs from early RA patients. Differentially expressed HERVs regulate adjacent ISGs expression by providing cis-regulatory elements. Moreover, excessive cytoplasmic HERVs trigger a type I interferon (IFN-I) response through the dsRNA-RIG-I-IRF3-IFN-I axis. Targeting endogenous retroviruses exhibited potential therapeutic benefits in both CIA mouse models and RA patient-derived ex vivo models. Specifically, the IFN-I inducible HERV.MLT2B2, a novel primate-specific retroelement, acts as a key driver of the antiviral gene IFI44L, establishing a positive feedback loop that amplifies IFN-I signaling.

overall_design: The discovery cohort included six early RA patients, six osteoarthritis (OA) patients, and six healthy controls, from whom PBMCs were isolated for RNA sequencing analysis.


title: Effect of METTL4 knockout on expression and splicing in HeLa S3 cells [Human M4]

city: Pushchino

first: Andrey

middle: Igorevich

last: Buyan

state: Moskovskaya obl.

address: Institutskaya st., 4

country: Russia

institute: Institute of Protein Research

summary: In this work we studied the role of U2 snRNA m6A(m)30 modification introduced by METTL4 methyltransferase on a model of METTL4 knockout human cell line. METTL4 gene inactivation resulted in dysregulation of gene expression and alternative splicing, as well as general decrease in splicing speed and accuracy.

overall_design: We performed high-throughput RNA sequencing of wild-type and METTL4 knockout HeLa S3 cells.

first: Anastasiia

last: Bolikhova

first: Olga

last: Averina

first: Alexander

last: Mazur

first: Petr

last: Sergiev


title: Effect of METTL4 knockout on expression and splicing in HeLa S3 cells [human WT]

overall_design:
We performed high-throughput RNA sequencing of wild-type and METTL4 knockout HeLa S3 cells.
Processed data on this series is identical to GSE299981.


title: Metabolic trade-offs in Neonatal sepsis triggered by TLR4 and TLR1/2 ligands result in unique dysfunctions in neural breathing circuits

first: Michele

middle: Joana

last: Alves

address: 11200 SW 8th Street,  AHC1- 417B

department: Cellular and Molecular Medicine

institute: Florida International University

summary:
Expression of the brainstem tissue and cells in postnatal day 5 pups following sepsis-like model with TLR ligands; TLR4 and TLR1/2
We used gene expression to evaluate the inflammatory pathways activated by either saline (control) LPS or PAM3CSK4 in neonates.

overall_design: CD1 Postnatal day 5 pups were administered with either LPS or PAM3CSK4 and following 3h they were euthanized. For brainstem: 12 samples per group were used to extract the RNA. Total RNA samples (n=4) were pooled into 1. Total of 3 replicates per group. For isolated cells: 10 samples/brainstem of 3 different litters were pooled into 1 sample of isolated cells.

first: Brigitte

last: Browe

first: Ana

middle: C

last: Dias

first: Juliet

last: Torres

first: Giuliana

last: Zaza

first: Suzy

last: Bangudi

first: Jessica

last: Blackburn

first: Wesley

last: Wang

first: Silvio de Araujo

last: Fernandes-Junior

first: Paolo

last: Fadda

first: Amanda

last: Toland

first: Lisa

last: Baer

first: Kristin

last: Stanford

first: Catherine

last: Czeisler

first: Alfredo

last: Garcia 3rd

first: Jose

last: Otero


title: Reconstitution of sex-determination process and testicular environment using mouse pluripotent stem cells

city: Suita

first: Katsuhiko

last: Hayashi

state: Osaka

address: 2-2 Yamadaoka

department: Graduate School of Medicine

institute: The University of Osaka

summary: Proper differentiation of gonadal somatic cells is crucial for sex determination and subsequent production of sex hormone and gametes. A proper reconstitution of the process in culture will provide not only an appropriate tool for fully understanding the process but also creation of gametes in culture, so called in vitro gametogenesis. Here, we report reconstitution of testicular gonadal somatic cells using mouse pluripotent stem cells. The reconstitution recapitulated a trajectory of the sex-determination process in vivo and consequently provide cell types forming seminiferous tubules and adjacent interstitial tissues including steroidogenic cells. Importantly, the reconstituted testicular tissue incorporated pluripotent stem cell-derived primordial germ cells and provided an environment sufficient for differentiation of spermatogonial stem cells. These spermatogonial stem cells can propagated in culture while keeping potential to differentiate into spermatozoa capable of full-term development with in vitro fertilization followed by transplantation into surrogate mothers. With this reconstitution system, embryonic tissues are no longer required to obtain male germ stem cells, encouraging application to other mammalian species. This study contributes to deeper understanding sex determination process and to creating an alternative source of male germ line in culture.

overall_design: After culturing female (XX) or male (XY) mouse embryonic stem cells under testicular (TES) or ovarian (FOS) cell differentiation conditions, Nr5a1-hCD271–positive cells were isolated by fluorescence-activated cell sorting (FACS) and analyzed using single-cell RNA sequencing (scRNA-seq).

first: Hayashi

last: Katsuhiko

first: Nakamura

last: Tomonori

first: Yoshino

last: Takashi


title: Parkinson’s disease microglia induce endogenous α-synuclein pathology in patient specific midbrain organoids.

city: Esch-Belval

first: Elisa

last: Zuccoli

address: 6, Avenue du Swing

department: Luxembourg Centre for Systems Biomedicine

country: Luxembourg

institute: University of Luxembourg

summary: The accumulation of misfolded α-synuclein and the loss of dopaminergic neurons are hallmarks of Parkinson’s disease (PD), contributing to the development of synucleinopathies. Although considerable progress has been made in understanding α-synuclein's role in PD pathology, the precise mechanisms involved remain unclear. Human midbrain organoids (hMOs) have emerged as valuable models for studying PD, yet the lack of microglia limits the ability to investigate neuroimmune interactions. Recent studies show that integrating microglia into hMOs enhances neuronal maturation and functionality. Here, we generated a human midbrain assembloid model by incorporating iPSC-derived microglia into midbrain organoids from healthy control individuals and a PD patient carrying the SNCA triplication (3xSNCA) mutation. Our results show that 3xSNCA microglia alone are sufficient to induce early, endogenous formation of phosphorylated α-synuclein (pS129) pathology in the absence of exogenous fibril seeding. This PD-pathology emerged as early as day 50 of culture and was not observed in models lacking microglia. These findings highlight a critical role for patient-derived microglia in driving α-synuclein pathology and provide a physiologically relevant platform for studying early neuroimmune mechanisms in PD and testing potential therapeutic strategies.

overall_design: Investigating pS129 pathology in Parkinson's Disease patient-derived 3xSNCA microglia integrated into midbrain organoids.

first: Hemry

last: Kurniawan

first: Sonia

last: Sabate-Soler

first: Alise

last: Zagare

first: Isabel

last: Rosety

first: Anna-Sophie

last: Zimmermann

first: Jens C.

last: Schwamborn


title: Inherent tissue homeostasis of the juvenile metaphysis provides a foundation for osteosarcoma development

city: Tokyo

first: Yasuhiro

last: Yamada

address: 7-3-1 Hongo, Bunkyo-ku

institute: University of Tokyo

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

overall_design: Refer to individual Series


title: Inherent tissue homeostasis of the juvenile metaphysis provides a foundation for osteosarcoma development [RNA-seq]

summary: Osteosarcomas typically arise from the metaphyseal cells of juvenile long bones, in contrast to most cancers that develop in aged individuals. Here, we show that the cyclin-dependent kinase inhibitor p21 is expressed in proliferating osteoblasts within the juvenile metaphysis in response to replication stress. Single-cell RNA sequencing focused on the juvenile metaphysis reveals a hierarchical differentiation trajectory of osteoblast-lineage cells, with active proliferation and DNA damage responses predominantly occurring in immature osteoblasts. We find that proliferation of p21+ osteoblasts is mediated by Hedgehog signaling associated with Indian hedgehog (IHH) expression in the growth plate. Consistently, the number of p21+ osteoblasts is markedly reduced following growth plate maturation or pharmacological inhibition of Hedgehog signaling. Induction of c-Myc—a known driver of replication stress and frequently amplified in early-stage osteosarcoma—enhances osteoblast proliferation specifically in juvenile mice, while concurrently augmenting replication stress responses including p53 activation. This c-Myc-driven proliferation remains dependent on Hedgehog signaling and is not sustained after growth plate maturation. Remarkably, functional inactivation of p53 enables continuous proliferation of c-Myc-induced osteoblasts, independent of IHH expression at the growth plate, leading to rapid and widespread metastasis to the lungs. These findings suggest that intrinsic DNA damage responses to replication stress, together with the spatiotemporal restriction of mitogen signaling, safeguard against oncogenic transformation in osteoblasts. Collectively, we uncover the unappreciated aspects of juvenile metaphyseal tissue homeostasis in mice, which may account for the characteristic age of onset, anatomical specificity, and mutational profile of human osteosarcomas.

overall_design: Analyzing transcriptional profiles by RNA-seq in the metaphysis of long bone of 3-week-old and 8-week-old Osx-reporter mice,  3-week-old Osx-reporter with cMyc inducible mice or 3-week-old Osx-reporter with cMyc ant Trp53 inactivation inducible mice.

first: Masato

last: Saito

first: Sho

last: Ohta

first: Fumie

last: Nakasuka

first: Takuya

last: Yamamoto


title: Phenotypic patterns in feline heart failure: a natural model for understanding variable disease severity in humans

city: Utrecht

first: Frank

last: van Steenbeek

state: Select State/Province

address: Yalelaan 104

country: Netherlands

institute: Utrecht University

summary: Cats frequently develop myocardial remodelling, for example, hypertrophic cardiomyopathy, affecting 14.7 percent of domestic cats compared to 0.2 percent of humans, with shared genetic features making them relevant to human disease. Yet features distinguishing clinical outcomes such as heart failure and arterial thromboembolism remain poorly characterized. Using artificial intelligence-based digital pathology and Oxford Nanopore sequencing, we analyzed myocardial tissue from 37 cats grouped by outcome: arterial thromboembolism, congestive heart failure, or no documented cardiac disease. Myocardial fibrosis was significantly higher in cats with arterial thromboembolism, indicating a distinct fibrotic phenotype. Cats with heart failure showed nuclear hypertrophy, while cats with arterial thromboembolism had increased numbers of small, hematoxylin-dense non-myocyte nuclei. Higher fibrosis was associated with downregulation of mitochondrial and cardiac conduction genes, and nuclear size correlated with proteostasis and stress-response pathways. This multimodal framework reveals distinct histological and molecular profiles by outcome, with relevance for translational hypertrophic cardiomyopathy research.

overall_design: Left ventricular biopsies of cats collected post-mortem and analyzed using tissue characterization based on deep phenotyping

first: Talitha C. F.

last: Spanjersberg

first: Alma H.

last: Hulsman

first: Guy C. M.

last: Grinwis

first: Babette

last: Janssen

first: C. Nina

last: van der Wilt

first: Rogier J. A.

last: Veltrop

first: Christian

last: Snijders Blok

first: Claudia

last: Rozendom

first: Paul

last: Besseling

first: Jolanda

last: van der Velden

first: Pim

last: van der Harst

first: Magdalena

last: Harakalova

first: Frank G.


title: Systemic and breast chronic inflammation and hormone disposition promote a tumor-permissive environment for breast cancer in older women (Rat WES)

first: Neil

last: Carleton

summary: Estrogen receptor positive (ER+) breast cancer, the most common subtype of breast cancer, is an age-related disease, with the peak incidence of diagnosis occurring around age 70 despite low circulating levels of estradiol. Despite the hormone sensitivity of these age-related tumors, our understanding of the interplay between the systemic and local hormonal disposition and chronic inflammaging is limited. We show that aged F344 rats treated with the DMBA/MPA carcinogen develop more tumors at faster rates than their younger counterparts, suggesting that the aged environment accelerates tumor growth. snRNA-seq of the tumors showed broad local immune dysfunction that was associated with circulating chronic inflammation. Across a broad cohort of specimens from patients with ER+ breast cancer and age-matched donors of normal breast tissue, we observe that even with E1-predominant estrogen disposition in the systemic circulation, tumors in older patients upregulate HSD17B7 expression to convert E1 to E2 in the TME. Age-related accumulation of tumor-associated macrophages serve as signaling hubs that integrate the E2 and chemokine-driven chronic inflammatory signaling in the TME, which polarize TAMs towards a CD206+/PD-L1+, immunosuppressive phenotype. Overall, these findings suggest that the host’s chronic inflammation and hormonal disposition shape the local tumor microenvironment and are critical contributors to the age-related nature of ER+ breast cancer development and growth.

overall_design: This dataset contains the whole exome sequencing data from the six rat tumors (three tumors from younger rats and three tumors from older rars) that were sequenced as a part of the larger study. In brief, Fischer 344 (F344) rats aged 6-8 weeks old were purchased from Envigo and served as the “young” rats in the study. Aged F344 rats were obtained from the National Institutes of Aging (NIA) Rodent Colonies at 19-21 months old and served as the “older” rats in the study. To investigate the effect of age on tumor incidence and growth, we used a chemical carcinogen model. All rats were surgically implanted with a 50mg MPA pellet in a subcutaneous fashion (90 day continuous release; Innovative Research of America, #NP-161). One week following pellet implant, rats were dosed with a single oral gavage of DMBA (65mg/kg; Thermo Scientific Chemicals, #408181000) dissolved in sesame oil (Thermo Scientific Chemicals, #241002500). All rats recovered fully from pellet implant surgery and tolerated the DMBA dose. Whole exome sequencing (WES) sequencing was done via Azenta Life Sciences on an Illumina 2 x 150bp configuration with a 5x average coverage. Sequencing results were aligned and analyzed using version 3.4.0 of the NF-Core Sarek Pipeline, using Nextflow version 23.10.1, Singularity 3.9.6. Pipeline settings used the Singularity profile, Rnor_6.0 Rat genome, CNVKit and Mutect2 tools, skipped base_recalibrator, WES-only mode with a minimal SLURM config file for the University of Pittsburgh Center for Research Computing High Throughput Computing Cluster. Mutect2.vcf.gz outputs were then annotated using VEP 95. High impact and Moderate Impact mutations as defined by Ensembl were then extracted for analysis. Rat genes were made comparable to human homologs using PyBioMart, and then filtered down to a list of pan-cancer and breast cancer genes (See supplementary information), in cases where multiple gene mutations were found in the same gene, ties were broken by prioritizing greatest impact followed by frequency. Results were then plotted in an Oncoplot. Tumor Mutational Burden was calculated using the whole exome length of the rat genome of 71Mb. K-means clustering was done by selecting all genes affected by moderate and high impact mutations and binarized into a corresponding matrix. Predicted labels were then evaluated to see if the two populations of tumor were distinctly separable based on mutational characteristics. Mutational Signature Analysis was done using SigProfilerAssignment, with context 96 and genome Rnor_6.0.

first: Sanghoon

last: Lee

first: Steffi

last: Oestereich

first: Adrian


title: Inherent tissue homeostasis of the juvenile metaphysis provides a foundation for osteosarcoma development [scRNA-seq]

first: Yasuhiro

last: Yamada

overall_design: Analyzing tissue homeostasis in the juvenile metaphysis by scRNA-seq analysis in 3-week-old and 8-week-old wild-type mice.

first: Masato

last: Saito

first: Sho

last: Ohta

first: Fumie

last: Nakasuka

first: Takuya

last: Yamamoto


title: Systemic and breast chronic inflammation and hormone disposition promote a tumor-permissive environment for breast cancer in older women (All Samples; Human and Rat)

sample_organism:
Homo sapiens
Rattus norvegicus

platform_organism:
Homo sapiens
Rattus norvegicus