title: Cell senescence emerges as a hallmark and therapeutic target of chronic intracellular infection

city: Milano

first: Riccardo

last: Nodari

address: Via F. Sforza

institute: University of Milan

summary: Intracellular pathogens are ideal candidates for modelling the pathophysiology of chronic infection, as they hide within host cells and avoid immune clearance by reshaping cellular fate. This study unveils how the intracellular pathogen Mycobacterium abscessus (Mab) reprograms alveolar macrophages towards a senescent state -a multifaced phenotype marked by proliferative arrest, distinctive morphological shifts, activation of DNA damage signalling cascade, and secretion of senescence-associated secretory phenotype (SASP) factors. Mab-induced DNA damage emerged as the primary driver of senescence, while SASP secretion acts as a molecular broadcaster, propagating secondary senescence in neighbouring, uninfected cells through paracrine signalling. This cascading wave of amplified senescence underscores a detrimental effect on the tissue microenvironment, turning it into a chronic inflammatory niche that facilitates Mab persistence and immune evasion. By leveraging evidence of chronic infection-induced senescence, we prototyped a therapeutic approach where senolytic drugs selectively eradicated senescent cells and significantly reduced bacterial burden, similarly to antibiotics.

overall_design: RNA-sequencing profile of MPI-2 wild type cells following 1 or 5 days of exposure to Mycobacterium abscessus, as well as time matched uninfected controls

first: Edoardo

last: Scarpa

first: Doriana

last: Oliveri

first: Diego

last: Rondelli

first: Carla

last: Chernichero

first: Federico

last: Russo

first: Giorgia

last: Moschetti

first: Anna

last: Griego

first: Marta

last: Zaccaria

last: Di Marco

first: Fabio

last: Saliu

first: Gabriele

last: Marchello

first: Ferdinando

last: Cannella

first: Manuel

last: Albanese

first: Gianluca

last: Cidonio

first: Lara

last: Manganaro

first: Daniela M.

last: Cirillo

first: Raffaele

last: De Francesco

first: Sergio

last: Abrignani

first: Raffaella

last: Di Micco

first: Nicola I.

last: Lorè

first: Loris

last: Rizzello


title: Rapid and functional intestinal regeneration after full-organ transection in zebrafish larvae is regulated by opposing effects of IL-22 and IL-26

status: Public on Jul 14 2026

city: Paris

first: Pedro Pablo

last: HERNANDEZ CERDA

address: 11-13 rue Pierre et Marie Curie, BDD building

country: France

institute: Institut Curie

type: Expression profiling by high throughput sequencing

summary: The intestinal epithelium is among the most regenerative tissues, continuously renewing and repairing after damage. Severe injuries that disrupt all tissue layers, however, pose a distinct challenge, requiring restoration of the epithelium together with its surrounding tissues. Whether and how a vertebrate intestine can restore architecture and function after complete loss of gut continuity remains unknown. Here, we establish a larval zebrafish model of severe intestinal injury, in which full-organ transection disrupts all gut tissue layers. Following injury, the intestine rapidly reattaches, restores lumen continuity, and resumes food transit. This repair process is accompanied by mesenchymal remodeling and restoration of muscle continuity, and is promoted by transient epithelial proliferation. Injury induces a sox17-expressing epithelial progenitor-like state, with localized re-expression of this embryonic gut marker at the wound site. Injury also triggers transient neutrophil and macrophage recruitment to the wound site and broadens the range of epithelial cell types that express il22. STAT3 signaling is required for timely epithelial reattachment and injury-induced proliferation. Loss of IL-22 blunts early repair-associated responses, impairs reattachment, reduces proliferation, and limits lumen restoration. In contrast, loss of IL-26 enhances early epithelial repair programs, accelerates gap closure, and elevates proliferation in a mitosis-dependent manner. Together, these findings establish zebrafish larvae as a tractable vertebrate model for full-organ intestinal regeneration and identify IL-22 and IL-26 as opposing regulators of STAT3-associated repair

overall_design: RNA-seq profiling of dissected guts from 5-day post-fertilization WT zebrafish larva 24 hours after gut transection

first: Medina-Yáñez

last: Ignacio

first: Hernandez

last: Pedro


title: Genome-wide EP300 CUT&Tag profiling in RAW264.7 macrophages treated with LPS and CCS1477

city: Shanghai

first: Panyu

last: Chen

address: 1111 Xianxia Road

department: Department of Gastroenterology, Shanghai Tongren Hospital

country: China

institute: Shanghai Jiao Tong University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: EP300 is an important epigenetic regulator involved in inflammatory gene transcription. CUT&Tag sequencing was performed to characterize genome-wide EP300 occupancy in RAW264.7 macrophages under basal conditions, following lipopolysaccharide (LPS) stimulation, and after treatment with the EP300 inhibitor CCS1477. Corresponding IgG controls were included for each experimental condition.

overall_design: Experimental conditions included untreated control (NC), LPS stimulation for 6 hours, and pretreatment with CCS1477 for 2 hours followed by LPS stimulation in the presence of CCS1477 for 6 hours. For each treatment condition, RAW264.7 cells were independently prepared in three replicates and pooled before CUT&Tag library preparation and sequencing. CUT&Tag was performed using an anti-EP300 antibody, and corresponding IgG controls were included for each treatment condition. Sequencing libraries were generated on the Illumina NovaSeq 6000 platform. Clean reads were aligned to the mm10_gencode reference genome using BWA.

first: Cheng

last: Luo


title: Single-cell RNA sequencing of liver CD45+ immune cells in mouse acute-on-chronic liver failure

summary: Single-cell RNA sequencing was performed on liver CD45+ immune cells isolated from mice subjected to acute-on-chronic liver failure (ACLF). Three experimental groups were included: CCl4-treated control mice, ACLF mice treated with vehicle, and ACLF mice treated with the EP300 inhibitor CCS1477. Male C57BL/6J mice were intraperitoneally injected with carbon tetrachloride (CCl4, 0.2 ml/kg, twice weekly) for 8 weeks. ACLF was induced by administration of a double dose of CCl4 (0.4 ml/kg), followed by intraperitoneal injection of Klebsiella pneumoniae. CCS1477 was administered intraperitoneally 2 hours before bacterial challenge. Liver CD45+ immune cells were isolated 36 hours after K. pneumoniae injection and subjected to BD Rhapsody whole-transcriptome single-cell RNA sequencing.

overall_design: Liver CD45+ immune cells were isolated by enzymatic digestion and fluorescence-activated cell sorting (FACS) from three groups of mice: CCl4-treated fibrotic mice (Fibrosis group), vehicle-treated acute-on-chronic liver failure (ACLF) mice (ACLF_VEH group), and CCS1477-treated ACLF mice (ACLF_CCS group). For each experimental group, liver CD45+ immune cells from three biological replicate mice were individually labeled with BD Sample Tags, pooled for multiplexed library preparation, and demultiplexed using the BD Rhapsody Sequence Analysis Pipeline. Single-cell RNA sequencing libraries were generated using the BD Rhapsody Whole Transcriptome Analysis (WTA) platform and sequenced on the Illumina NovaSeq 6000 platform.

first: Luo


title: Genome-wide H3K27ac profiling of RAW264.7 macrophages treated with LPS and CCS1477

summary: Histone H3 lysine 27 acetylation (H3K27ac) ChIP-seq was performed to investigate genome-wide epigenetic changes in RAW264.7 macrophages following inflammatory stimulation and EP300 inhibition. RAW264.7 macrophages were pretreated with the EP300 inhibitor CCS1477 for 2 hours and subsequently stimulated with lipopolysaccharide (LPS) in the presence or absence of CCS1477 for 6 hours before chromatin immunoprecipitation and sequencing. Genome-wide H3K27ac occupancy was analyzed to characterize changes in chromatin activation associated with inflammatory responses and EP300 inhibition.

overall_design: H3K27ac ChIP-seq was performed in RAW264.7 macrophages under three experimental conditions: untreated control (NC), LPS stimulation for 6 hours, and pretreatment with CCS1477 for 2 hours followed by LPS stimulation in the presence of CCS1477 for 6 hours. RAW264.7 macrophages were subjected to three independent biological experiments under each treatment condition. Cells from the three biological replicates were pooled prior to chromatin immunoprecipitation, and one ChIP-seq library was generated for each experimental condition.


title: A Lactic Acid-Chac1 Axis Regulates Ferroptosis-Associated Cell Death and Tumor Progression

city: chendu

first: lilan

last: he

address: yulin

institute: Sichuan University

summary: Tumor metabolic reprogramming plays a critical role in cancer progression, yet the direct involvement of lactic acid in regulating tumor cell death remains incompletely understood. In this study, we identified lactic acid as a previously underappreciated regulator of tumor cell fate and investigated whether lactic acid induces ferroptosis-associated cell death in tumor cells. Lactic acid suppressed tumor cell viability in a dose-dependent manner across multiple tumor cell lines and triggered cell death with both apoptotic and non-apoptotic features. Transcriptomic analysis revealed significant enrichment of ferroptosis-related pathways, accompanied by glutathione depletion, Gpx4 downregulation, and increased oxidative stress. Pharmacological inhibition using Ferrostatin-1 and genetic modulation of Slc7a11 supported the involvement of ferroptosis in lactic acid-induced cytotoxicity. Mechanistically, we identified Chac1 as an important mediator linking lactic acid-induced metabolic stress to ferroptosis-associated tumor cell death, as Chac1 knockdown attenuated cytotoxicity in vitro while promoting tumor growth and metastasis in vivo. Furthermore, Chac1 deficiency was associated with enhanced metastatic progression, suggesting that suppression of ferroptosis may facilitate tumor progression, at least in part, potentially associated with alterations in tumor immune cell infiltration. Collectively, these findings uncover a previously unrecognized link between lactic acid and ferroptosis, establish Chac1 as a critical regulatory node, and highlight the therapeutic potential of targeting the lactic acid-Chac1-ferroptosis axis in cancer treatment.

overall_design: Bulk RNA-seq was performed on murine LL2 tumor cells. Cells were treated with 20 mM lactic acid added directly to the culture medium for 24 h (two biological replicates) or with an equal volume of PBS for 24 h as the control (two biological replicates). Total RNA was extracted using TRIzol and submitted to a commercial sequencing service for paired-end RNA sequencing.

first: Lilan

last: He

first: Aaron

middle: Q

last: Zhang

first: Rui

last: Wu

first: Shitong

last: Zhong

first: Jiali

first: Bin

last: Shao

first: Siyu

first: Jingyuan

last: Lu

first: Fan

last: Hu

first: Jiayun

last: Yu

first: Hanwen

last: Li


title: HP1α depletion and TGFβ activation exert antagonistic effects on 3D genome organization.

city: Oslo

first: Fabiana

last: Patalano

address: Blindernveien 31

country: Norway

institute: University of Oslo

summary: The three-dimensional (3D) organization of the human genome plays a critical role in regulating gene expression and is frequently disrupted in cancer. However, how key factors like Heterochromatin Protein 1 alpha (HP1α) and Transforming Growth Factor beta (TGFβ) remodel this architecture to drive tumorigenesis remains poorly understood. We investigated the effects of HP1α knockdown and TGFβ treatment on higher-order chromatin structure and gene expression in human mammary epithelial cells. Our findings reveal that HP1α depletion and TGFβ stimulation exert distinct and opposing effects on genome compartmentalization and subcompartmentalization. HP1α knockdown drives a genome-wide shift of chromatin from transcriptionally inactive B compartments to active A compartments. This is accompanied by a stepwise redistribution of A subcompartments toward the most transcriptionally active state (A3), and the upregulation of oncogenic genes involved in EMT and proliferation. In contrast, TGFβ treatment promotes chromatin compaction, increases the proportion of B compartments, and drives a stepwise reduction in active A subcompartments. Our results highlight the differential roles of HP1α and TGFβ in shaping the 3D genome and underscore how precise, stepwise architectural changes contribute to malignant transformation. This study provides critical insight into how chromatin architecture acts as a regulatory layer in breast cancer development.

overall_design: We generated Hi-C and RNA-seq datasets and ChIP-seq  for MCF10A, MCF10A HP1a knockdown, and MCF10 treated with TGFB cell lines to investigate changes in 3D genome conformation and the impact on gene expression. Additionally we generated also  ChIP-seq datasets for  HP1b knockdown, HP1a knockdown HP1b and HP1b knockdown HP1a

first: Oda

last: Hovet

first: Roberto

last: Rossini

first: Maxim

last: Nekrasov

first: Yasmin

last: Dijkwel

first: Bhumika

last: Azad

first: Tatiana

last: Soboleva

first: Rein

last: Aasland

first: David

last: Tremethick

first: Jonas

last: Paulsen


title: Sex-specific differences of amlexanox in a mouse model for atherosclerosis and MASLD

city: Frankfurt

first: Ellen

last: Niederberger

address: Theodor-Stern-Kai 7

department: Institute for Clinical Pharmacology

country: Germany

institute: Goethe-University Frankfurt

summary: Inhibitor‑κB kinase epsilon (IKKε) is a non‑canonical IκB kinase involved in NF‑κB signaling and type I interferon responses. We recently demonstrated sex‑dependent effects of IKKε deletion on atherosclerosis and metabolic dysfunction‑associated steatotic liver disease (MASLD), with male knockout mice showing protection against both diseases, while female mice exhibited exacerbated inflammatory and metabolic disturbances. These divergent outcomes were linked to differential effects on inflammatory pathways and lipid metabolism. To evaluate the therapeutic potential of pharmacological IKKε inhibition, we treated wild type mice with established atherosclerotic plaques and hepatic steatosis - induced by PCSK9 gain‑of‑function and Paigen diet - with the IKKε inhibitor amlexanox. Amlexanox modulated serum lipid levels and altered plaque composition but did not halt plaque progression. In the liver, treatment produced marked sex‑specific effects: male mice exhibited substantial improvement in steatosis, whereas female mice showed worsened lipid accumulation. These outcomes were reflected in pronounced sex‑dependent differences in serum and hepatic lipid and metabolite profiles, indicating regulation of fatty acid and bile-acid metabolism predominantly in males. Protein analyses in liver and adipose tissue further supported opposing metabolic and inflammatory responses between sexes after amlexanox treatment. Collectively, our findings indicate that therapeutic IKKε inhibition with amlexanox does not prevent progression of advanced atherosclerosis in this model but effectively ameliorates MASLD in male mice. In contrast, female mice experience aggravated hepatic lipid deposition. These results underscore the importance of incorporating sex‑specific analyses in metabolic and cardiovascular research and highlight the need to evaluate therapeutic strategies such as amlexanox in both sexes.

overall_design: Total RNA seq of liver samples from mice treated with a PCSK9 gain-of-function virus and a Paigen diet for 8 weeks followed by 8 weeks oral treatment with DMSO (vehicle) or Amlexanox [25mg/kg BW) with ongoing Paigen diet.

first: Eleonora

last: Mungo

first: Tobias

last: Schmid

first: Silvia

last: Kuntschar

first: Sofie

middle: P

last: Meyer


title: Innate immune activation profiles are associated with polarization of the T cell response to recombinant arenaviral vectors

city: Wien

first: Sarah

last: Szaffich

address: Schenk-danzinger-gasse 6/4/17

country: Austria

institute: Hookipa Biotech GmbH

summary: Arenavirus-based vectors are uniquely positioned to generate durable T cell responses against tumors, which remains a central challenge in cancer immunotherapy.  Two members of the arenavirus family, Lymphocytic choriomeningitis virus and Pichinde virus, were genetically engineered to encode a non-oncogenic fusion protein, originating from human papillomavirus 16 E6 and E7. Hereafter, these vectors are referred to as HB-201 and HB-202, respectively. HB-201 alone or in combination with HB-202 elicited strong and durable E6/E7-specific CD8+ T cell responses in HPV 16+ cancer patients . Despite their classification within the same virus family, Lymphocytic choriomeningitis virus and Pichinde virus are phylogenetically distant, which may influence virus-host interactions and the pathways leading to antiviral immune responses. Previous studies showed that both vectors infect and activate professional antigen presenting cells. To elaborate on these findings, this study aimed to characterize in depth the innate immune response to HB-201 and HB-202 by single cell sequencing in an in vitro human PBMCs infection model. We confirmed the preferential infection of antigen presenting cells for both vectors, with HB-201 infecting the cross-priming conventional dendritic cell subset cDC1 more efficiently than HB-202. Furthermore, HB-201 induced stronger type I interferon responses than HB-202, as well as quantitative and qualitative differences in inflammatory response linked to a distinct reshaping of monocyte subsets towards intermediate and non-classical monocytes. Antigen presentation and T cell priming cytokines in dendritic cells appeared to favor antiviral CD8+ T cell responses upon HB-201 infection, whereas a more balanced CD4+ and CD8+ priming profile was observed upon HB-202 infection. Immunogenicity data from patients treated with HB-201 and HB-202 confirmed the in vitro findings with functional differences in early T cell response. Thus, despite their shared origins within the arenavirus family, HB-201 and HB-202 demonstrate distinct differences in early host-virus interaction, potentially resulting in shaping unique T cell responses.

overall_design: PBMCs were infected at a MOI of 1 for 24h, each sample was infected either with HB-201, HB-202 or mock. Because PBMCs contain less than 20% of APCs, we enriched for APCs before scRNAseq by HLA-DR positive selection using magnetic beads to increase the proportion of APCs in the sequencing data.


title: Isolation and Characterization of a Novel Streptomyces murinus Strain with Dual Activities: Biocontrol of Maize Foliar Pathogens and Growth Promotion

city: Hangzhou

first: yuanlin

last: qi

address: No. 666, Wusu Street, Lin'an District

department: Donghu Campus

institute: Zhejiang A&F University

summary: This study evaluated the biocontrol efficacy, growth-promoting potential, and molecular mechanisms of the actinomycete strain FJSM-07, identified via 16S rDNA sequencing as Streptomyces murinus.

overall_design: In vitro assays demonstrated potent broad-spectrum antifungal activity against multiple plant pathogens, yielding the strongest inhibition zones against Bipolaris maydis and Exserohilum turcicum. In pot experiments, FJSM-07 application on two maize cultivars achieved high disease control efficacies exceeding 70% at 7 and 14 days post-treatment, outperforming carbendazim. Furthermore, FJSM-07 significantly enhanced plant agronomic traits, including height, fresh weight, and root length. RNA-Seq identified numerous differentially expressed genes primarily enriched in plant-pathogen interactions and plant hormone signal transduction; significant upregulation of PIN-likes 3 and Aux/IAA family members confirmed activation of the auxin pathway. Metabolomic profiling revealed substantial shifting of metabolites involved in secondary metabolism and amino-acid biosynthesis. Finally, LC-MS profiling of FJSM-07 identified ten major bioactive compounds, including the lipopeptides fengycin and surfactin. Distinctly, S. murinus FJSM-07 serves as an effective dual-action biocontrol agent and biofertilizer for sustainable maize production.

first: Yuanlin

last: Qi

first: Jinai

last: Yao


title: RNA-seq analysis on maize plants treated with Streptomyces sclerogranulatus

summary: In this studies, we sought to isolate and identify a novel Streptomyces sclerogranulatus SM3-7 strain with biocontrol potential and to elucidate the antibacterial secondary metabolites responsible for its antagonistic activity.

overall_design: Susceptible and resistant maize cultivars were inoculated with Streptomyces sclerogranulatus under controlled conditions. At 30 days after treatment, whole-plant tissues were harvested from each group, and total RNA was extracted for transcriptome sequencing (RNA-seq) to profile global gene expression responses


title: Fluoride Alters Gene Expression via Histone H3K27 Acetylation in LS8 Cells

city: Davie

first: Maiko

last: Suzuki

state: Florida

address: 3300 S. University Drive

department: College of Dental Medicine

country: USA

institute: Nova Southeastern University

summary: Excessive fluoride ingestion during tooth development can cause dental fluorosis. Previously, we reported that fluoride activates histone acetyltransferase (HAT) to acetylate p53, promoting fluoride toxicity in mouse ameloblast-like LS8 cells. However, the roles of HAT and histone acetylation status in fluoride-mediated gene expression remain unidentified. Here, we demonstrate that fluoride-mediated histone modification causes gene expression alterations in LS8 cells. LS8 cells were treated with or without fluoride followed by ChIP-Seq analysis of H3K27ac. Genes were identified by differential H3K27ac peaks within ±1 kb from transcription start sites. The levels of mRNA of identified genes were assessed using rea-time PCR (qPCR). Fluoride increased H3K27ac peaks associated with Bax, p21, and Mdm2 genes and upregulated their mRNA levels. Fluoride decreased H3K27ac peaks and p53, Bad, and Bcl2 had suppressed transcription. HAT inhibitors (Anacardic acid or MG149) suppressed fluoride-induced mRNA of p21 and Mdm2, while fluoride and the histone deacetylase (HDAC) inhibitor sodium butyrate increased Bad and Bcl2 expression above that of fluoride treatment alone. To our knowledge, this is the first study that demonstrates epigenetic regulation via fluoride treatment via H3 acetylation. Further investigation is required to elucidate epigenetic mechanisms of fluoride toxicity in enamel development.

overall_design: ChIP-seq of the histome modification H3K27Ac in LS8 cells

first: Chang-Sheng Sam

last: Chang

first: Eiko

last: Kitamura

first: Navi

last: Gill Dhillon


title: Periconoid A, a Novel Ergosterol Derivative from Periconia caespitosa, Induces Apoptosis in Nasopharyngeal Carcinoma Cells Accompanied by the Enrichment of Inflammatory Pathways

city: Haikou

first: Liu

last: Jie

address: hainan university

institute: Hai Nan University

summary: Chemical investigation of marine Conus Literatus endophytic fungus Periconia caespitosa HDYXY-1 led to the isolation and characterization of seven novel compounds, including an oxirane-fused cyclohexanone (1), benzothiazole isomers (2 and 3), rare cyano-bearing phenyl ethers (4 and 5), as well as ergosterol derivatives (8 and 9), along with three known analogs (6, 7, and 10). Their structures were elucidated via NMR, HRESIMS, HRAPCIMS, X-ray diffraction, and ECD/DP4+ calculations. Among them, the ergosterol derivative Periconoid A (8) showed potent cytotoxicity against glioblastoma (LN-229, IC50 = 10.05 μM) and nasopharyngeal carcinoma (NPC; CNE2, IC50 = 5.62 μM) cells. Mechanism studies revealed that Periconoid A (8) triggers mitochondria-dependent apoptosis by modulating the Bax/Bcl-2 ratio, activating caspase-3, and inducing PARP-1 cleavage. Transcriptomic analysis indicated that 8 enriches inflammatory response pathways (TNF, JAK-STAT, and NF‑κB), suggesting an inflammation-associated apoptotic mechanism. Molecular docking confirmed a high binding affinity of Periconoid A (8) for the Bcl‑2 protein (–7.6 kcal/mol) through a dual‑polar anchoring network. ADME prediction indicated favorable druggability with high GI absorption and a PAINS‑free profile. Collectively, these findings establish Periconoid A (8) as a promising lead candidate for anti‑NPC drug development, acting through a mechanism that activates inflammation-associated apoptosis.

overall_design: To elucidate the molecular mechanism underlying the anticancer activity of Periconoid A (8), RNA-seq was performed on CNE2 cells treated with 5.62 μM of the compound 8 (H41) for 48 hours.

first: Jie

last: Liu

first: Jin-Long

last: Huang

first: Jing

last: Wang

first: Run-Qi

first: Tian-Tian

last: Meng

first: Jiao-Lin

last: Bao

first: Ren-Bo

last: Ding

first: Shuai

last: Dong


title: Exploring Platelet-Covered and Naked Circulating Tumor Cells: A Single-Cell Transcriptomic Perspective [scRNA-seq Singleron]

city: Gdansk

first: Krzysztof

last: Pastuszak

state: Pomorskie

address: Debinki 1

department: Translational Oncology

country: Poland

institute: Medical University of Gdansk

summary: Circulating tumor cells (CTCs) and platelets can be collected simultaneously during liquid biopsy; however, their interaction in the form of platelet-covered CTCs (pcCTCs) remains only partially understood. This submission contains single-cell RNA sequencing data generated from PBMC/buffy coat fractions from 29 donors: 12 patients with high-grade serous ovarian carcinoma, 4 non-malignant gynecological controls, 10 patients with breast cancer, and 3 healthy donor controls. The dataset was used to detect and characterize candidate naked CTCs and pcCTCs and to compare their transcriptomic profiles with platelet and cancer-related signatures.

overall_design: Whole blood was collected before ex vivo processing. Ovarian cancer and benign gynecological control samples were processed using 10x Genomics Chromium Next GEM Single Cell 3' chemistry at the Institute of Bioorganic Chemistry PAS, Poznan. Breast cancer and healthy donor samples were processed using the Singleron GEXSCOPE SCOPE-chip micro-well single-cell RNA-seq system. The submission is organized as one GEO Sample row per donor/library. Each sample lists its raw FASTQ files and one Matrix Market feature-barcode matrix triplet as processed data. Ovarian and benign 10x libraries include three lanes of I1/I2/R1/R2 FASTQ files; Singleron breast and healthy libraries include one R1/R2 FASTQ pair.

first: Michal

last: Sieczczynski

first: Marcin

last: Banacki

first: Kamil

last: Langowski

first: Sylwia

last: Lapinska-Szumczyk

first: Anna

last: Samelak-Czajka

first: Paulina

last: Jackowiak

first: Iwona

last: Inkielewicz-Stepniak

last: Supernat

first: Anna Joanna

last: Zaczek


title: Transcriptomic analysis of unwounded skin, vehicle-treated wounds, and brequinar-treated wounds in mice

city: Maebashi

first: Akihiko

last: Uchiyama

state: Gunma

department: Dermatology

country: Japan

institute: Gunma University

summary: Bulk RNA sequencing was performed to investigate transcriptomic changes in unwounded skin, vehicle-treated wounds, and brequinar-treated wounds collected from mice on day 9 after wounding. The study aimed to identify molecular pathways associated with the brequinar-induced pyoderma gangrenosum-like phenotype and to compare gene expression profiles among experimental groups.

overall_design: Bulk RNA sequencing was performed on murine unwounded skin, and on wound tissues collected at day 9 after wounding from vehicle-treated and brequinar-treated mice.

first: Ken

last: Araki

first: Yoko

last: Yokoyama

first: Yohei

last: Morishita


title: Mechanical stiffness-promoted tumor tagging to navigate radiopharmaceuticals: Single-cell RNA sequencing revealed the fate of MSC after tumor homing

city: Beijing

first: Xiujie

last: Yang

address: 38 Xueyuan Road

institute: Peking University

summary: Radiopharmaceutical imaging and targeted radionuclide therapy rely on endogenous molecular targets which are frequently heterogeneous, absent, or lost during cancer progression. We developed SMART, a Stiffness-responsive Mesenchymal stem cell (MSC)-Assisted Relayed tumor-Targeting platform that converts elevated matrix stiffness, a conserved biophysical feature of tumors, into localized expression of synthetic radiopharmaceutical targets. Engineered MSCs sensing stiff tumor microenvironments induced tumor-restricted expression of prostate-specific membrane antigen (PSMA), enabling 68Ga-PSMA-617 positron emission tomography (PET) imaging and 177Lu-AB-PSMA-617 therapy across diverse tumor models. SMART-enabled PET improved detection sensitivity relative to 18F-fluorodeoxyglucose PET, including in brain, lung, and bone metastases. The platform is modular, extendable to targets such as somatostatin receptor 2, and compatible with induced pluripotent stem cell (iPSC)-derived MSCs. SMART therefore decouples radiotheranostic performance from endogenous biomarker status and establishes a generalizable strategy for targeting biophysical hallmarks of cancer.

overall_design: MDA-MB-231 tumor tissues were harvested at days 6 and 9 following MSCYAP-PSMA administration and enzymatically dissociated into single-cell suspensions. Cells from these time points, together with MSCYAP-PSMA from the same batch that were not injected (serving as the day 0 control) were incubated with AF647-conjugated anti-PSMA antibody (clone EPR6253, Abcam) for 1 h. PSMA+ cells were subsequently enriched using anti-AF647 microbeads and LS columns (Miltenyi Biotec, Teterow, Germany) according to the manufacturer’s instructions. For each group, approximately 10,000 cells were processed using the BD Rhapsody Whole Transcriptome Analysis (WTA) pipeline (v1.8) to generate single-cell RNA-seq libraries without a targeted panel. Sequencing reads (FASTQ files) were aligned to the human reference genome (GRCh38) with GENCODE v32/Ensembl 98 annotations, and unique molecular identifier (UMI) count matrices were generated. Low-quality cells, defined as those with fewer than 200 detected genes or with >15% mitochondrial transcripts, were excluded, resulting in a final dataset of 31,669 single cells. Data preprocessing was performed using Scanpy (v1.8) 63. Counts were normalized by total expression per cell (scale factor = 10,000) and log-transformed using pp.log1p. Highly variable genes were identified using pp.highly_variable_genes. Dimensionality reduction was conducted by principal component analysis (tl.pca), followed by graph-based clustering using pp.neighbors. Uniform manifold approximation and projection (UMAP; tl.umap) was used for 2D and 3D visualization. Cluster-specific marker genes were identified using the Seurat FindAllMarkers function (Wilcoxon rank-sum test; P < 0.05 and log2 fold change > 0.5). Cell trajectory inference was performed using Slingshot (v2.0) based on UMAP embeddings, with the “Quiescent MSC” cluster defined as the root for pseudotime analysis. Cell plasticity was quantified using CytoTRACE (v1.0). Cell cycle phases (G1, S, and G2/M) were assigned using Seurat CellCycleScoring. All sequencing and bioinformatic analyses were performed by Genechem (Shanghai, China).

first: Chunhong

last: Zheng

first: Zhaofei

last: Liu


title: Exploring Platelet-Covered and Naked Circulating Tumor Cells: A Single-Cell Transcriptomic Perspective [scRNA-seq 10x_Poznan]

last: Pastuszak


title: Repeated mild spinal cord contusions exacerbate tauopathy development in PS19 mice

city: Godinne

first: Nicolas

last: Debortoli

address: avenue Docteur G. Thérasse, 1

country: Belgium

institute: CHU UCL Namur

summary: Growing evidence indicates that traumatic brain injury constitutes a significant risk factor for the development of age-related tauopathies, yet the consequences of repeated mild spinal cord injuries (rmSCI) remain insufficiently explored. In this context, we developed a mouse model undergoing two successive mild cervical contusions during young adulthood, which do not produce immediate functional motor deficits, thereby mimicking real-life conditions of occupational- or sports-related trauma. rmSCI were induced in PS19 (hTauP301S) mice developing late-onset tauopathy in the brain and in the spinal cord. The consequences of rmSCI were assessed on motor outcomes and tauopathy signature in injured PS19 mice during ageing. rmSCI exacerbated age-dependent motor deficits and significantly increased tau hyperphosphorylation on the pSer422 and pSer202/Thr205 epitopes. Pathological changes, initially confined to the epicenter of the contusions, extended along a caudo-rostral axis reaching the thalamus. While rmSCI did not modify intraspinal tau aggregation, spinal cord-derived protein extracts displayed enhanced seeding activity in vitro. Although causality was not established with tau hyperphosphorylation status, early response towards mild spinal contusions included glial activation and upregulation of interferon-stimulated genes. Together, these data identify rmSCI as a previously underappreciated modifier of tau pathology and disease progression. Moreover, this study provides a novel experimental link between mild central nervous system injuries and exacerbation of tauopathy and suggests the involvement of type I interferon signalling or sustained glial activation. Ultimately, these findings underscore the importance of preventing even mild spinal injuries in individuals at risk of tauopathy.

sample_organism:
Mus musculus
blank sample

platform_organism:
Mus musculus
blank sample

overall_design: Expression profiling of PS19 (hTauP301S) mice with repeated mild spinal cord injuries (rmSCI) for 48h or without rmSCI (sham).

last: Halloin

first: Hélène

last: Collignon

first: Zoé

last: Marlier

first: Kunie

last: Ando

first: Valérie

last: Suain

first: Louise

last: Conrard

first: Margaux

last: Mignolet

first: Lindsay

last: Sprimont

first: Marino

last: Caruso

first: Aurélie

last: Ladang

first: Jonathan

last: Degosserie

first: Karelle

last: Leroy

first: Charles

last: Nicaise


title: Truncating ASXL1 variants rewire cellular metabolism via mitochondrial pyruvate carrier repression

city: Los Angeles

first: Isabella

last: Lin

address: 615 Charles E Young Dr S

institute: University of California Los Angeles

summary: Bohring-Opitz syndrome (BOS, OMIM#605309) is a rare neurodevelopmental disorder caused by heterozygous and truncating variants in ASXL1 (Additional Sex Combs Like 1), a chromatin-associated epigenetic regulator that forms the catalytic PR-DUB complex with BAP1. Truncating ASXL1 variants are also recurrent somatic drivers in myeloid leukemia, yet the metabolic consequences of these mutations remain undefined. Using patient derived dermal fibroblasts, we show that truncating ASXL1 variants drive a Warburg-like metabolic state characterized by increased glycolytic flux, and accumulation of pyruvate and lactate. Stable isotope tracing revealed preservation of glucose-derived carbon incorporation into tricarboxylic acid (TCA) cycle intermediates, suggesting compensatory metabolic adaptation to maintain pyruvate-dependent TCA cycle metabolism. Overexpression of truncating ASXL1 constructs in cell models replicated this phenotype. Mechanistically, truncated ASXL1 shows decreased occupancy at an H3K4me3-marked enhancer upstream of mitochondrial pyruvate carrier 2 (MPC2), together with BAP1 co-recruitment, and selectively reduces MPC1 and MPC2 protein levels through a mechanism that is independent of transcript levels. Pharmacologic inhibition of the MPC reproduces both the metabolic and Wnt signaling phenotypes of BOS cells, while canonical Wnt activation also increases glycolytic flux but without reducing the MPC abundance, implicating that reduced MPC abundance acts upstream of signaling dysregulation. These findings define a previously unrecognized pathway connecting gain-of-function ASXL1 truncation to chromatin-level regulation of mitochondrial pyruvate transport, and identify the MPC as a central mediator of epigenetic-metabolic crosstalk in both a rare developmental syndrome and ASXL1-mutated myeloid malignancies.

overall_design: RNA-seq profiling of wild type HEK293T and Caco-2 cells, and cells transfected with truncating ASXL1 plasmids and full length ASXL1 plasmids

first: Michael

last: Reyes

first: Valerie

last: Arboleda


title: Human ribomes reveal DNA-embedded ribonucleotides as epigenetic modulators of DNA supercoiling

city: Atlanta

first: Francesca

last: Storici

state: GA

address: 950 State Street Nw, Krone Engineering Biosystems Building

department: Biological Sciences

institute: Georgia Institute of Technology

summary: The goal of this study is to analyze distribution and enrichment of ribonucleotide embedment in human genome in various genomic regions of funcitonal relevance and association with gene expression and methylation levels.

overall_design: The libraries are generated using ribose-seq method (2015) using different fragmentation methods to optimize for coverage. The matching fragmentation methods are also applied to genomic DNA of CD4T cells as a reference to study effect on genomic coverage. We conducted RNA-seq for HEK293T RNase H2A wild-type cells and KO genotypes along with Whole genome bisulfite-seq for CD4+T cells derived from 4 patients.

first: D

middle: L

last: Kundnani

first: T

last: Yang

first: P

last: Xu

first: Y

last: Lee

first: M

last: Sun

first: G

last: Newnam

last: Lu

last: Warner

first: F


title: Ciliogenic pancreatopathy reveals a link between ciliopathies and exocrine pancreatic disease

city: Brussels

first: Patrick

last: Jacquemin

address: 75, Avenue Hippocrate bte B1.75.03

institute: de Duve Institute SSS/DDUV

summary: Background Ciliopathies are genetic disorders affecting primary cilia, most commonly affecting the kidney and liver. Although pancreatic cysts have been described in syndromic ciliopathies, the pancreas is not commonly recognized as a target organ. However, several ciliary gene knockout mouse models develop a pancreatic phenotype characterized by acinar atrophy and adipocyte accumulation, hereby called adipopancreatosis, suggesting a link between ciliary dysfunction and pancreatic disease. Objective To investigate whether mutations in ciliopathy-associated genes are associated with pancreatic dysfunction in humans, and to explore the underlying mechanisms. Design We analyzed a cohort of 341 patients with pediatric-onset pancreatic anomalies. In parallel, we generated Nphp3 patient-specific and conditional knockout mouse models to characterize pancreatic alterations at histological, molecular, and cellular levels. In patients, pancreatic fat content was quantified using Dixon-MRI. Results Mutations in HNF1B and NPHP3 were identified in patients presenting both renal ciliopathy and pancreatic dysfunction. Nphp3 mutant and conditional knockout mice developed progressive adipopancreatosis with acinar atrophy and distinct inflammatory profiles. Transcriptomic analyses indicated that the adipocytes displayed a white adipocyte–like gene expression profile and mesothelial-derived fibroblasts were implicated as a likely cellular origin. Additional pathological features included ductal cilium alterations and acinar microcysts. Consistent with the mouse phenotype, Dixon-MRI in patients with HNF1B and NPHP3 mutations demonstrated significantly increased pancreatic fat content. Conclusion We describe a previously unrecognized pancreatic manifestation of ciliopathies, which we term ciliogenic pancreatopathy. Our findings suggest that patients with known ciliopathy-associated mutations should be evaluated for this pancreatic condition during clinical assessments, particularly those with kidney disease, as concomitant exocrine pancreatic insufficiency may further compromise renal function or the outcome of kidney graft.

overall_design: Three adipocyte-containing regions were microdissected from the pancreas of an 8-month-old Nphp3mut1/mut2 mouse and subjected to bulk RNA sequencing following rRNA depletion and strand-specific library preparation.

first: Memoona

last: Rajput

first: Lydie

last: Flasse

first: Esther

last: Porée

first: Alice

last: Serafin

first: Nicolas

last: Papadopoulos

first: Younes

last: Achouri

first: Axelle

last: Loriot

first: Valentine

last: Gillion

first: Nathalie

last: Godefroid

first: Charlotte

last: Bodson

first: Joel

last: Moro

first: Leyre

last: López-Muneta

first: Antonio

last: Garcia de Herreros

first: Cécile

last: Haumaitre

first: Laurent

last: Gatto

first: Meritxell

last: Rovira

first: Amandine

last: Viau

first: Anne

last: Grapin-Botton

first: Sophie

last: Saunier

first: Isabelle

last: Scheers


title: Ciliogenic pancreatopathy reveals a link between ciliopathies and exocrine pancreatic disease [scRNA]

first: Patrick

last: Jacquemin

overall_design: Single-cell RNA sequencing was performed on pancreatic tissue from Sox9CreER;Nphp3^f/f^ mice to characterize pancreatic epithelial and stromal cell populations. Ambient RNA-corrected datasets were analyzed using Seurat for quality control, clustering, cell type annotation, and comparative integration with published ductal and mesothelial reference atlases.

first: Memoona

last: Rajput

first: Lydie

last: Flasse

first: Esther

last: Porée

first: Alice

last: Serafin


title: In vivo DNA damage protection during cell migration across confining embryonic tissue environments

city: Cambridge

first: Elena

last: Scarpa

address: Downing Street

department: Physiology Development and Neuroscience

country: United Kingdom

institute: University of Cambridge

summary: In physiology and in disease, cells often migrate through narrow spaces, such as leukocytes undergoing diapedesis or cancer cells during dissemination. Cultured cells under physical confinement can experience mechanical stress due to deformation of the nucleus. Nuclear deformation leads to loss of nuclear integrity and DNA damage, and it has been proposed to underlie cancer initiation and progression. In vivo, the consequences of physical confinement on physiological cell migration remain poorly understood. Here, we use the zebrafish neural crest as an in vivo model to address how multipotent embryonic cells respond to physical confinement during developmental migration.  By measuring the size of extracellular spaces, we found that the level of tissue scale confinement increases from head to tail along the embryonic antero-posterior axis. Nuclear morphometrics analysis shows that neural crest experience dramatic nuclear deformation during their migration between adjacent tissues, which quantitatively scales with tissue confinement. By using complementary genetic and mechanical strategies to ablate the surrounding tissue, we observe a rescue of nuclear deformation in vivo. Surprisingly, we found that while deformation of the neural crest nucleus causes nucleo-cytoplasmic leakage, it does not cause nuclear envelope rupture or increase DNA damage even upon extreme deformations. Instead, confined migratory neural crest show decreased LaminB2 at the nuclear envelope. By perturbing LaminB2 expression levels, we discover that loss of LaminB2 facilitates fast recovery from deformation, while sustained expression of LaminB2 results in persistently deformed nuclei, highlighting a role for LaminB2 in nuclear shape deformability. Using a photoconversion and RNA-seq approach, we uncover upregulation of a large network of DNA repair genes in confined trunk neural crest, suggesting these stem cells might be resistant to confinement-induced mechanical stresses. In summary, we establish the neural crest as a physiological framework, uncovering dynamic adaptations to tissue confinement in vivo.

overall_design: Transgenic Sox10:H2B-Dendra2 trunk  neural crest cell nuclei were photoconverted and FACS sorted before confined migration (16hpf) or after confined migration (23-24hpf) and processed for  low input bulk RNA-seq (n=20 cells per sample).

first: Zainalabdeen

last: Alhashem

first: Mint R

last: Htun

first: You-Hsuan

last: Liu

first: Hanna-Maria

last: Hakkinen


title: Upf3a-dependent genetic compensation sustains BMP robustness during murine odontogenesis

city: Fuzhou

first: Chensheng

last: Lin

state: Fujian

address: 18 Wulongjiangzhong Avenue, Shangjie Town

department: College of Life Sciences

institute: Fujian Normal University

summary: Homology-dependent genetic compensation response (HDGCR), also known as transcriptional adaptation (TA), represent evolutionarily conserved mechanisms that buffer deleterious mutations through transcriptional upregulation of functionally related genes. However, direct in vivo evidence for HDGCR in mammal species remains limited. Bone morphogenetic protein (BMP) signaling is indispensable for murine tooth development, yet extensive ligand redundancy frequently masks phenotypes in single-gene knockouts, making odontogenesis an ideal organ system to interrogate HDGCR. Here, we generated a conditional Upf3a knockout mouse (Upf3af/f), exhibiting normal survival and tooth development when crossed with Wnt1-Cre mice, for in vivo HDGCR studies. Loss of Upf3a abolished the compensatory upregulation of paralogous Bmp4 following Bmp2 deletion, functionally mimicking a Bmp2/Bmp4 double-deficient state. This disruption promoted proliferation of dental pulp cells and root progenitor cells and inhibited differentiation of odontoblasts, leading to severe defects in dentinogenesis and root development. ChIP-seq revealed that this organ-specific, Upf3a-dependent HDGCR operates independently of H3K4me3 enrichment at the Bmp4 promoter. Collectively, these findings provide in vivo mammalian evidence that Upf3a-dependent HDGCR critically modulates BMP signaling robustness during murine odontogenesis within a defined developmental and tissue context.

overall_design: ChIP-seq profiles of H3K4me3 in PN0 mandibular molar tooth germs from wild-type, Wnt1-Cre;Bmp2f/f, and Wnt1-Cre;Upf3af/f;Bmp2f/f embryos

first: Xi

last: Zheng

first: Lanting

last: Zhang

first: Ying

last: Chen

first: Shunting

first: Yihang

last: Xiang

first: Huan

last: Huang

first: Yanding

first: Xuefeng

last: Hu


title: Early high-frequency spinal cord stimulation modulates the ROS/p38 MAPK/NF-κB and CXCL10/CXCR3 pathways to alleviate neuropathic pain and promote spinal cord injury repair

first: sitong

last: su

address: West District, Majiapu China Rehabilitation Research Center, Fengtai District, Beijing

institute: School of Rehabilitation Medicine, Capital Medical University, Beijing, China

summary: High-frequency spinal cord stimulation (HF-SCS) has been proven to be an effective method for treating neuropathic pain, but its specific mechanism of action in spinal cord injury (SCI) remains unclear. This study aims to explore the therapeutic effect of early HF-SCS in a rat model of SCI and its potential molecular mechanism. The SD rat model of T10 spinal cord contusion was established, and stimulation electrodes were implanted epidurally, followed by HF-SCS treatment (movement threshold 40%, frequency 10,000 Hz). The results showed that HF-SCS significantly attenuated SCI-induced neuropathic pain, facilitated functional recovery, and accelerated axonal regeneration and myelin repair. Further mechanism studies indicated that HF-SCS exerts its neuroprotective effect by down-regulating the ROS/p38 MAPK/NF-κB signaling pathway to reduce microglial activation and decrease the release of pro-inflammatory factors; simultaneously, it inhibits the activation of the CXCL10/CXCR3 axis to alleviate central sensitization. This study suggests that early HF-SCS intervention can improve the functional prognosis after SCI by suppressing neuroinflammation and reducing central sensitization, thereby providing a theoretical basis for the treatment of SCI with HF-SCS.

overall_design: RNA-seq profiling of spinal cord tissues from three groups of Sprague-Dawley rats: sham-operated controls, rats with T10 contusive spinal cord injury (SCI), and SCI rats receiving high-frequency spinal cord stimulation (HF-SCS) treatment. All rats were sacrificed 35 days post-surgery/treatment to investigate transcriptomic mechanisms underlying the analgesic effect of HF-SCS in SCI-induced neuropathic pain.

first: Sitong

last: Su

first: Tao

first: Honghui

last: Lei

first: Yang

last: Yu

first: Caizhi

last: Ma

first: Xinglang

last: Wang

first: Haoyuan

first: Zebin

first: Meiling

last: Cheng

first: Tongtong

last: Qian

first: Fangyong


title: H2A.Z levels control the timing of major events at the maternal-zygotic transition

city: Denton

first: Fanju

last: Meng

state: TX

address: 1155 Union Circle #305220

institute: University of North Texas

summary: Across animals, early embryonic events are temporally tightly coordinated but the underlying mechanisms remain incompletely understood. In Drosophila, both global and nuclear levels of the histone variant H2Av rise progressively during the maternal-zygotic transition (MZT), but whether this increase is functionally important is unknown. We find that increased H2Av dosage expedites specific MZT events: the transition from nuclear cycle (NC) 13 to 14 occurs prematurely as does the turnover of thousands of maternal transcripts; in addition, a subset of genes is precociously expressed in the zygote. Reduced H2Av dosage has reciprocal effects. Comparable transcriptional shifts are observed in zebrafish embryos overexpressing the H2Av ortholog H2A.Z, suggesting H2Av/H2A.Z dosage as a conserved timer of early development. We also examined Jabba mutans which compared to wild type display increased nuclear H2Av levels but reduced cytoplasmic levels. Unexpectedly, nuclear H2Av abundance influences the timing of NC 13 but is not the main driver of transcriptome remodeling. In summary, we find that H2Av/H2A.Z levels are critical timers of early embryogenesis and that – at least in Drosophila – H2Av acts in part by a non-nuclear mechanism.

sample_organism:
Drosophila melanogaster
Danio rerio

platform_organism:
Drosophila melanogaster
Danio rerio

overall_design: RNAseq profiling of wild type, 1x H2Av, 2x H2Av, 4x H2Av embryos at Egg, NC11, NC13, NC14 stages to study genome-wide transcriptional changes

first: Pakinee

last: Phromsiri

first: Xiaolu

last: Wei

first: Claire

middle: E

last: Makowski

first: Noah

last: Reger

first: Duy

middle: K

last: Nguyen

first: Humeira

last: Marzia Alam

first: Yuki

last: Shindo

first: Amanda

last: Amodeo

first: Patrick

middle: J

last: Murphy

middle: W

first: Michael

middle: A

last: Welte


title: Analysis of transcriptional changes associated with acquired resistance to docetaxel in HR+/HER2- breast cancer cell line MCF-7

city: Woluwé

first: Jérôme

last: Ambroise

address: Avenue Hippocrate 54

department: Institut de Recherche Expérimentale et Clinique

institute: Université catholique de Louvain

summary: Resistance to neoadjuvant chemotherapy in HR+/HER2- breast cancers is increasingly recognized as a consequence of tumor cell plasticity rather than fixed genetic alterations. Large-scale genomic analyses comparing tumors before and after chemotherapy have failed to identify recurrent mutations that consistently account for treatment failure. Instead, resistance is thought to arise predominantly through non-genetic, adaptive mechanisms, including the acquisition of gene expression changes that allow cancer cells to survive chemotherapy-induced stress and later re-enter proliferative programs.To uncover transcriptional adaptations to docetaxel, a chemotherapeutic agent used in the NAC clinical setting, we performed bulk RNA-sequencing on parental and docetaxel-resistant MCF-7 cells.

overall_design: Parental (docetaxel-sensitive) and docetaxel-resistant MCF-7 cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM), low glucose, supplemented with GlutaMAX™ and sodium pyruvate (#10567014, Gibco), 10% heat-inactivated fetal bovine serum (FBS; Merck Life Science), and 1% penicillin-streptomycin (Gibco). Cells were maintained at 37°C in a humidified atmosphere containing 5% CO₂. Chemoresistant MCF-7 cells were continuously cultured with 20 ng/mL docetaxel. Total RNA was extracted from subconfluent cells and subjected to bulk RNA-sequencing.

first: Cyril

last: Corbet

first: Martin

last: Michaelis

first: Jindrich

last: Cinatl Jr


title: T-cell Multiomic Analysis Identifies Subsets and Mechanisms of Interaction with Epithelial Cells in Idiopathic Pulmonary Fibrosis

city: Nashville

first: Ana

last: Serezani

state: TN

address: 1161 21st Ave. S, MCN B1320B

department: Medicine

institute: Vanderbilt Medical Center

summary: While T-cell numbers are elevated in IPF lungs, including in fibrotic regions, their contributions to fibrosis, especially beyond inflammation, remain unclear. We used single-cell RNA and protein profiling (CITE-seq) of CD3⁺ T cells from control and fibrotic lungs to investigate molecular pathways involved in T-cell functions in pulmonary fibrosis. This study reveals a previously unrecognized role for MIF/CXCR4/EGFR signaling in T-cell activation. Targeting the epithelial–T-cell axis may provide novel therapeutic strategies to mitigate T-cell-mediated epithelial damage and slow IPF progression.

overall_design: CITE-seq was performed using single-cell suspensions derived from minced lung tissue of control and fibrotic samples.Whole lung cell suspensions (up to 1 million cells) were incubated with an Fc receptor blocking reagent (TrueStain FcX, BioLegend, USA) for 15 minutes, followed by staining with a panel of flow cytometry antibodies [anti-CD45 (APC-Cy7), anti-CD3 (PE-Cy5), and fourteen oligo-conjugated TotalSeq-C human antibodies (BioLegend)] for 30 minutes. Cells were washed three times with PBS containing 1% BSA and stained with a viability dye (Zombie Aqua kit, BioLegend). Up to 25,000 viable CD45⁺CD3⁺ cells were sorted per sample using a BD FACS ARIA and submitted for sequencing on the 10x Genomics Chromium platform. Briefly, 10,000 cells were loaded onto a 10x Chromium single-cell encapsulation chip, and libraries were prepared according to the manufacturer’s instructions. Sequencing was performed on Illumina platforms at a depth of at least 80 million reads per library

first: Julia

last: Bazzano

first: Bruno

middle: D

last: Pascoalino

first: Ludmilla

last: Silva

first: Abigail

last: Dietrich

first: Chase

last: Taylor

first: Taylor

last: Sherrill

first: Carla

last: Calvi

first: Paula

last: Gonzalez-Ericsson

first: Matthew

last: Bacchetta

first: Ciara

last: Shaver

first: Lorraine

last: Ware

first: Margaret

last: Salisbury

first: Luc

last: Van Kaer

first: Nicholas

last: Banovich

first: Jonathan

last: Kropski

first: Timothy

last: Blackwell


title: Integrative transcriptomic analysis reveals Cytip as a novel pro-inflammatory factor which interacting with Lrrfip2 in microglia following

city: Wuhan

first: Yang

last: Zhihao

state: Hubei

address: Shizishan street

department: College of Life Sciences & Technology

institute: Huazhong Agricultural University

summary: In this study, we sought to elucidate the transcriptional landscape of microglia during the acute phase of cerebral I/R injury. By integrating transcriptomic data from an in vivo mouse model of middle cerebral artery occlusion/reperfusion (MCAO/R), with in vitro bulk RNA sequencing of Bv2 microglia subjected to oxygen-glucose deprivation/reperfusion (OGD/R), we identified Cytip (Cytohesin Interacting Protein) as significantly upregulated. Our results demonstrated that CYTIP expression peaked 24 h post-reperfusion and its knockdown markedly attenuated neuroinflammation.

overall_design: control group:Bv2 CON1,Bv2 CON2,Bv2 CON3.  OGD/R group:Bv2 OGD1,Bv2 OGD2,Bv2 OGD3.

first: Zhihao

last: Yang

first: Yuneng

last: Zhou

first: Yiqi

last: Wang

first: Ke

last: Shui

first: Zhiqiang

last: Dong


title: Genetic engineering of carbon monoxide dehydrogenases produces distinct autotrophic phenotypes in Clostridium autoethanogenum

city: Tartu

first: Kaspar

last: Valgepea

state: Tartumaa

address: Nooruse 1

department: Institute of Bioengineering

country: Estonia

institute: University of Tartu

summary: Acetogens are promising microbes for sustainable biomanufacturing but improving acetogen gas fermentation requires efficient conversion of CO and CO2 into fuels and chemicals. Carbon monoxide dehydrogenase (CODH) enzymes couple carbon fixation to energy conservation in acetogens and serve as potential regulatory modules for tuning autotrophic metabolism. Intriguingly, the model-acetogen Clostridium autoethanogenum lost its unique truncation in the bifunctional CODH (acsA), essential for autotrophy, during autotrophic adaptive laboratory evolution while obtaining superior phenotypes. Additionally, protein expression of the monofunctional CODH cooS1 is high and conditionally-regulated in C. autoethanogenum. Here, we genetically engineered CODHs in C. autoethanogenum by replacing the stop codon in acsA with leucine (strain Leu_SNP) or serine (Ser_SNP), and deleting cooS1 (ΔcooS1). Phenotyping in autotrophic batch and chemostat cultures revealed altered growth profiles and significant redistribution of carbon and redox flows in SNP strains, whereas ΔcooS1 showed moderate and condition-dependent effects. Surprisingly, structural modelling identified no conformational differences between wild-type and mutant AcsA proteins. While transcriptomics showed limited transcriptional changes in ΔcooS1, it suggested potential transcriptional adjustments linked to reduced robustness and altered product profile of Leu_SNP. Our results demonstrate the impact of CODHs on autotrophy and offer targets for rational engineering of acetogen cell factories.

overall_design: RNA sequencing of CO- or syngas-grown Clostridium autoethanogenum chemostat cultures with multiple strains; 17 samples in total with various number of biological replicate samples

first: Kurshedaktar

middle: M

last: Shaikh

first: Kristina

last: Reinmets

first: Pratik

middle: R

last: Pawar

first: Clara

middle: V

last: Carneiro


title: HERC4-mediated ubiquitination licenses RIPK1 to initiate TNF-induced cell death

city: Suzhou

first: Haohao

last: Lu

state: Jiangsu

address: No. 100 Chongwen Road, Suzhou Industrial Park

institute: Suzhou Institute of Systems Medicine

summary: TNF can activate both pro-survival and pro-death signaling downstream of tumor necrosis factor receptor 1 (TNFR1). Survival signaling originates from TNFR1-containing membrane-bound Complex I, while death signaling is driven by cytosolic Complex II. RIPK1 is a central component of both complexes, but the molecular switch converting RIPK1 from a pro-survival scaffold in Complex I to a pro-death kinase in Complex II has remained elusive. Here, we identify the E3 ligase HERC4 as the molecular determinant of pro-death signaling. We show that HERC4 binds Complex-I-derived S166-phosphorylated, kinase-active RIPK1 and ubiquitinates it within its death domain. This enables RIPK1 oligomerization and assembly of the apoptosis-inducing RIPK1–FADD–caspase-8-containing Complex IIa and, upon caspase inhibition, formation of the necroptosis-initiating RIPK1–RIPK3-containing necrosome. HERC4 deficiency protects mice from TNF-induced systemic inflammatory response syndrome and acute liver injury. Thus, HERC4 is the link enabling Complex I-derived RIPK1 to initiate death signaling.

overall_design: CRISPR screening in HT-29 cells infected with a ubiquitination-related protein library (Addgene, cat#174592), followed by selection with DMSO (Control) or the combination of TNF, Smac mimetic, and z-VAD (TSZ).

first: Tongde

last: Du

first: Sudan

last: He


title: Targeting ZIP12-mediated Zn2+ signaling as a treatment for pulmonary hypertension

city: LONDON

first: CHIEN-NIEN

last: CHEN

address: Du Cane Road

department: National Heart and Lung Institute

institute: Imperial College London

summary: ZIP12, a membrane bound zinc importer, is upregulated in the remodeled pulmonary arterioles of patients with pulmonary arterial hypertension (PAH). Genetic deletion of its encoding gene, slc39a12, ameliorates the disease in rodent models. We developed a humanized anti-ZIP12 monoclonal antibody, APL-9796, which showed dose-dependent efficacy and improved cardiopulmonary parameters of hypoxia-induced pulmonary hypertension in in humanized Slc39a12 rats. Transcriptomic profiling revealed modulation of pathways including AMPK, PPAR, and PI3K-Akt signaling pathways. ZIP12-driven labile Zn2+ signaling underpins the pathogenesis of PAH.

overall_design: RNA sequencing using lung tissues collected from APL-9796 treated chronic hypoxic rats (n =12 in each group comprising 6 males and 6 females).

first: Chien-Nien

last: Chen

first: Lan

last: Zhao


title: GAS deficient mice display premature aging associated with loss of chromatin organization, derepression of LINE1 elements and induction of inflammation [Cut & Tag]

city: Rochester

first: Francesco

last: Morandini

state: NY

address: 402 Hutchison Hall

institute: University of Rochester

summary: Aging-associated inflammation, or ‘inflammaging” is a driver multiple age-associated diseases. Cyclic GMP-AMP Synthase (cGAS) is a cytosolic DNA sensor that functions to activate interferon response upon detecting viral DNA in the cytoplasm. cGAS is also implicated in induction of inflammaging by responding to endogenous signals such as damaged DNA or LINE1 cDNA which forms in aged cells. While cGAS knockout mice are viable their aging has not been examined. Unexpectedly, we found that cGAS knockout mice exhibit accelerated aging phenotype associated with induction of inflammation and DNA damage signaling. Cells from cGAS knockout mice showed increased overall chromatin accessibility, particularly on LINE1 (L1) transposons and inflammation genes. Transcription of L1 elements was also increased associated with high levels of cytoplasmic L1 DNA and expression of ORF1 protein. Stimulated emission depletion microscopy (STED) showed that cGAS forms nuclear condensates that co-localize with heterochromatin. Taken together these results suggest a previously undescribed role for cGAS at maintaining heterochromatin and repressing L1 elements. We propose that cGAS knockout mice lose heterochromatin, leading to derepression of L1 elements and induction of inflammation resulting in premature aging phenotype.

overall_design: We performed Cut&Tag against H3K9me3, H3k27me3 and IgG on primary lung fibroblasts from 3 WT and 3 cGAS KO mice.

first: John

middle: C

last: Martinez

first: Cheyenne

last: Rechsteiner

first: Lucinda

last: Fitzgibbons

first: Natasha

last: Sieczkiewicz

first: Xiaoyan

last: Liao

first: Weijie

first: Sung Jae

last: Bae

first: Michael

last: Meadow

first: Eric

last: Hillpot

first: Joseph

last: Cutting

first: Victoria

last: Paige

first: Maxwell

last: Zacher

first: Seyed Ali

last: Biashad

first: Matthew

last: Simon

first: Ines

last: Meula-Zarzuela

first: Mario

last: Cordero

last: Sedivy

first: Andrei

last: Seluanov

first: Vera

last: Gorbunova


title: Long-term effects of adolescent risperidone treatment on mouse cortex

city: Philadelphia

first: Hyowon

last: Choi

state: PA

institute: Thomas Jefferson University

summary: Antipsychotics have been increasingly prescribed for children and adolescents. Despite multiple rodent studies showing long-term neurocognitive dysfunction associated with adolescent antipsychotic treatment, there is a lack of understanding of neurobiological underpinnings of these long-term changes. We utilized single nucleus RNA-seq to assess the long-term transcriptomic changes in mouse cortex, 9 weeks after they were treated with risperidone during adolescence. Analysis of the mouse cortex snRNA-seq dataset showed downregulation in voltage-gated and inwardly rectifying potassium channels and genes associated with synaptic structure and function in pyramidal neurons and interneurons. Our findings suggest that adolescent risperidone treatment can cause long-term transcriptomic changes associated with altered excitatory-inhibitory neuronal interactions.

overall_design: C57BL/6J mice were treated with risperidone (4 mg/kg) or saline at post-natal day (PND) 22 for 21 consecutive days, followed by a drug washout period of 43 days. Mice were euthanized at PND90 and their cortical tissues nuclei were isolated for snRNA-seq via 10X Genomics Chromium platform.

first: Laurence

last: Busque

first: Evan

last: Zhang

first: Jonathan

last: Preall

first: Chang-Gyu

last: Hahn

first: Karin

last: Borgmann-Winter


title: Remodeling of the SAMP1/YitFc mouse ileum during chronic ileitis

city: Cleveland

first: Katreya

last: Lovrenert

address: 10900 Euclid Avenue

department: Department of Genetics and Genome Sciences

institute: Case Western Reserve University

summary: Inflammatory bowel disease (IBD) is marked by progressive epithelial, immune, and stromal dysfunction. While human datasets have yielded important insights, they are inherently descriptive and limited in their ability to support in vivo mechanistic interrogation. The SAMP1/YitFc (SAMP) mouse model develops spontaneous ileitis, providing an experimental system that reflects human disease progression while allowing controlled manipulation of pathophysiologic pathways. To understand cell-specific gene expression changes in the diseased ileum, we defined the single nucleus transcriptomes of chronically inflamed SAMP ileum using single nucleus RNA sequencing (snRNA-seq). Whole-ileum snRNA-seq was performed from SAMP (n=4) and AKR (n=3) mice using the gut-optimized CitraPrep protocol, generating 58,349 high-quality nuclei across epithelial, immune, and stromal lineages. We corroborated SAMP-associated changes using immunofluorescence, western blotting, spatial transcriptomics, and integration with human single cell IBD data.  We observed a shift to Th2 response and an expansion of ILC2 and mast cells in SAMP mice compared to AKR. Stromal remodeling in SAMP mice included increased expression of Igf1 in fibroblasts. In addition to observing previously validated Paneth cell expansion, a new expansion of tuft cells and emergence of SAMP-only Pcsk6⁺ crypt enterocytes were observed and confirmed in human Crohn’s patients. Finally, interactome analyses revealed cross-compartment changes in cell-cell signaling, including enterocyte-to-ILC3 communication and enhanced tissue-wide Igf1 signaling. These features mirror known and novel aspects of Crohn’s disease and extend our understanding of disease-associated multicellular networks. This atlas of spontaneous ileitis in SAMP mice provides a high-resolution resource for dissecting conserved and novel mechanisms of chronic inflammation and tissue remodeling. It demonstrates that the SAMP ileum recapitulates key transcriptomic features of human Crohn’s disease, validating it as a translational platform for mechanistic and therapeutic studies.

overall_design: Whole ileum was isolated, flushed with PBS to remove luminal contents, and snap frozen from 20 week old SAMP1/YitFc (n=4) and AKR/J mice(=3). Tissue was stored at -80C until nuclei isolation for snRNAseq.

first: Katherine

last: Letai

first: Paul

last: Tesar


title: Comparative phenotypic characterisation of mutant human bronchial epithelial cells in vitro and in vivo

city: Manchester

first: Carlos

last: Lopez Garcia

state: Greater Manchester

address: Paterson Building, Wilmslow Rd

department: TLCB

institute: CRUK-MI

summary: Development of tractable and robust models of cancer depends on a transparent, detailed and critical evaluation of their advantages and disadvantages for their use in basic and translational cancer research. Specifically, identifying the phenotypic differences of cancer cells in vivo and in vitro is essential to select the most informative experimental setting without compromising the scalability, versatility and cost-effectiveness of research projects. Development of tractable and robust models of cancer depends on a transparent, detailed and critical evaluation of their advantages and disadvantages for their use in basic and translational cancer research. Specifically, identifying the phenotypic differences of cancer cells in vivo and in vitro is essential to select the most informative experimental setting without compromising the scalability, versatility and cost-effectiveness of research projects. Our observations showed similar results in vivo and in vitro regarding the essential components for the transformation of hBECs. We also observe differences in gene expression that suggest an increase in motility in vivo and, importantly, an alternative mechanism of LUSC development that depends on squamous differentiation mediated by epithelial inactivation of NOTCH1.

overall_design: RNA-seq profiling of wild type and mutant human bronchial epithelial cells (hBECs)  in vitro (ALI cultures) and in vivo (xenografts). ALI cultures uploaded in this project were used for batch testing. The ALI culture samples used for the in vivo versus in vitro comparison in the article were uploaded in  Bioproject PRJNA1043668 (Lonza Donor ID 36722) used in Ogden et al.,(2025) (PMID: 40185723); where comparisons between ALI and PDX are featured batch effects were modelled within DESeq2 or removed using limma. Whole-exome sequencing of xenografts generated from mutant hBECs and genotype-matched pre-injection (PI) cell population. Note that the sample labelled 'parental' in the library name and sample title represent pre-injection wild type hBECs. The mutant hBECs harbour up to 5 genetic alterations and genotypes are denominated using a five letter system: T=TP53 knockout; C=CDKN2A knockout; P=PTEN knockout; K=KEAP1 knockout; S=SOX2 overexpression.

last: Lopez-Garcia

first: Robert

last: Sellers


title: To investigate NRF2 activation modulates cellular behaviors on mRNA expression in a human esophageal squamous cell carcinoma cell line (KYSE70 cells)

city: Camden

first: Xiaoxin

middle: Luke

last: Chen

state: NJ

address: 403 Haddon Avenue

institute: Coriell Institute for Medical Research

summary: To study NRF2 activation modulates cellular behaviors in human esophageal squamous cell carcinoma cells.

overall_design: Cultured cells, extracted RNA, RNAseq assay for cell comparision.

first: Xiong

last: Zhaohui

first: Chen

last: Xiaoxin


title: To investigate NRF2 activation modulates cellular behaviors on mRNA expression in a human esophageal squamous cell carcinoma cell line (KYSE450 cells)


title: Human ribomes reveal DNA-embedded ribonucleotides as epigenetic modulators of DNA supercoiling

first: Francesca

last: Storici

institute: Georgia Institute of Technology

type: Methylation profiling by high throughput sequencing

summary: The goal of this study is to analyze distribution and enrichment of ribonucleotide embedment in human genome in various genomic regions of funcitonal relevance and association with gene expression and methylation levels.

overall_design: The libraries are generated using ribose-seq method (2015) using different fragmentation methods to optimize for coverage. The matching fragmentation methods are also applied to genomic DNA of CD4T cells as a reference to study effect on genomic coverage. We conducted RNA-seq for HEK293T RNase H2A wild-type cells and KO genotypes along with Whole genome bisulfite-seq for CD4+T cells derived from 4 patients.

first: Deepali

last: Kundnani

first: Taehwan

last: Yang

first: Penghao

last: Xu

first: Yeunsoo

last: Lee

first: Mo

last: Sun

first: Gary

last: Newnam

first: Yilin

last: Lu

first: Tyler

last: Warner


title: Targeting Regnase-1 unleashes CAR T cell antitumor activity for osteosarcoma and creates a proinflammatory tumor microenvironment [scRNAseq1]

city: Memphis

first: Hongbo

last: Chi

address: 262 Danny Thomas Place

department: Immunology

institute: St Jude Children's Research Hospital

summary: We took advantage of CAR T cells targeting B7-H3 in immune competent osteosarcoma models and evaluated the intrinsic and extrinsic effects of the known negative regulator Regnase-1 (Reg-1).

overall_design: We used 5' scRNAseq (10X Genomics) to compare the transcriptome and TCR sequences of spleen or lung-derived control and Reg-1-deficient CAR T cells, isolated 5 days after CAR T infusion.

first: Adeleye

last: Adeshakin

first: Hao

last: Shi

first: Stephen

last: Gottschalk


title: Targeting Regnase-1 unleashes CAR T cell antitumor activity for osteosarcoma and creates a proinflammatory tumor microenvironment [scRNAseq2]

overall_design: We used 5' scRNAseq (10X Genomics) to compare the transcriptome and TCR sequences of lung-derived CD45+ immune cells, isolated 21 days after control or Reg-1 KO CAR T infusion.


title: The tumor suppressor SMAD4 is a gatekeeper for genome stability

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

institute: Universitaetsmedizin Goettingen

summary: Cancer chromosomal instability (CIN) causes structural and numerical chromosome aberrations and acts as a driver for tumor progression and poor patient outcome. However, the mechanisms driving CIN are incompletely understood. In this study, we identified SMAD4, a key tumor suppressor in colorectal and pancreatic cancers, as a gatekeeper for genome stability. Loss of SMAD4 results in homologous recombination DNA repair defects, DNA replication stress and mitotic errors, resulting in genome instability. SMAD4 acts as part of BMP signaling and ensures genome stability through its transcriptional target inhibitor of DNA binding 3 (ID3). Consequently, abrogation of BMP signaling or ID3 phenocopies the genome maintenance defects induced upon loss of SMAD4. Thus, our study defines SMAD4 as a key suppressor of genome instability in human cancer.

overall_design: To investigate the role of SMAD4 on the transcriptome, RNA sequencing was performed on HCT116 and HT29 colorectal cancer cell lines with or without SMAD4 knockout or SMAD4 re-expression. To identify targets specific to BMP-SMAD4 signaling, HCT116 cells were treated with the selective BMP Type 1 receptor inhibitor K02288.

first: Atmika

last: Paul

first: Holger

last: Bastians

first: Maren

last: Sitte


title: Direct interaction of Vδ7 TCRs with IL17RA drives the differentiation of TH1-like γδT cells

city: Stockholm

first: Taras

last: Kreslavsky

address: Karolinska University Hospital L8:03, Visionsgatan 18

country: Sweden

institute: Karolinska Institutet

summary: Of the three classes of lymphocytes that constitute the adaptive immune system, γδT cells are the only class for which the principles of antigen recognition remain enigmatic. While endogenous γδTCR ligands are thought to regulate γδT cell development, their identities are largely elusive. Here, we identified the cytokine receptor chain IL17RA as a γδTCR ligand that drove the differentiation of Vδ7+ γδT cells with a TH1-like effector program. IL17RA promoted this differentiation through an interaction involving germline-encoded regions of the Vδ7 chain, enabling the selection of cells with a diverse CDR3 repertoire – therefore acting as a non-clonotypic γδTCR ligand. Together with the non-clonotypic mode of γδTCR engagement by butyrophilins, these results suggest that such interactions represent a general biological mechanism shaping the γδT cell compartment.

overall_design: RNAseq profiling of BEKO cells.


title: PFOS caused fertility defects and disrupted spermatogenic gene networks in the male medaka with a transgenerational history of ancestral BPA exposure

city: Columbia

first: Ramji

last: Bhandari

state: MO

address: 1200 University Ave

department: Division of Biological Sciences

institute: University of Missouri

summary: Environmental chemical exposures induce heritable and transgenerational effects in reproductive and metabolic systems. How organisms respond when exposed to contemporary environmental chemicals overlaid upon the transgenerational inheritance of their ancestors’ exposure profiles is currently unknown. Here, we investigated the effects of a second hit of perfluorooctane sulfonate (PFOS) exposure on male reproductive health in medaka fish (Oryzias latipes) with or without a history of ancestral bisphenol A (BPA) exposure. The PFOS exposure occurred in offspring four generations after ancestors’ BPA exposure (10 ug/L) during their embryonic development. Three concentrations of PFOS (0, 0.002, and 0.02 mg/L for 21 days) were tested in two lineages: control lineage with no ancestral history of BPA exposure and BPA lineage whose ancestors were exposed to BPA four generations ago. Our results show that the second hit of PFOS significantly decreases fertility in fish with a pre-existing history of ancestral BPA exposure. RNA sequencing of the testis revealed that PFOS exposure in the BPA lineage caused a significant increase in the number of upregulated genes. In contrast, in the control lineage, it caused downregulation of genes related to cell cycle dysregulation. Differentially expressed genes in the PFOS-exposed BPA lineage fish were related to apoptosis, proteolysis, and cytoskeletal disarrangement. The genes associated with Sertoli cell function and spermatogenesis, mainly associated with locomotion, mitotic cycle, and cell morphogenesis, were significantly dysregulated in the BPA lineage fish. Altogether, the present study found exacerbated fertility defects and significant alterations in the molecular networks associated with Sertoli cell function & spermatogenesis due to the second hit of PFOS in the fish with a history of ancestral BPA exposure, suggesting that a pre-existing history of ancestral environmental chemical exposure can be a contributing factor for adverse health outcomes in the upcoming generations upon exposure to contemporary legacy chemicals.

overall_design:
This study investigated the effects of a second exposure to perfluorooctane sulfonate (PFOS) on male reproductive health in medaka fish, considering whether their ancestors were exposed to bisphenol A (BPA). The PFOS exposure occurred in offspring four generations after ancestors’ BPA exposure (10 ug/L) during their embryonic development. Three PFOS concentrations (0, 0.002, and 0.02 mg/L for 21 days) were tested across two lineages: a control lineage with no ancestral BPA exposure and a BPA lineage with ancestral BPA exposure four generations prior.

RNA sequencing was conducted on biological replicates of testes from both the BPA and control lineages of medaka fish, with three replicates per condition.

first: Seraiah

last: Coe

first: Santosh

last: Anand

first: Sourav

last: Chakraborty


title: Molecular Profiling of the Appendix in Pediatric Inflammatory Bowel Diseases

city: Edmonton

first: John Maringa

last: Githaka

state: AB

address: 5-73 Medical Sciences Building, University of Alberta

department: Biochemistry

country: Canada

institute: University of Alberta

summary: Clinical studies suggest a critical role for the appendix in the pathogenesis of inflammatory bowel diseases (IBD), including Crohn disease (CD) and ulcerative colitis (UC), as indicated by the presence of peri-appendicular patches in UC and the beneficial effects of appendectomy in UC. However, the underlying mechanisms remain unclear. To address this gap, we characterized microbial species, associated patterns, and host-microbiota interactions in the appendix and non-inflamed regions of the colon tissue and mucus from pediatric IBD and non-IBD patients (n=15). Metagenomic analyses revealed an enrichment of Proteobacteria (p-value=0.0061) and reduced bacterial diversity in IBD patients’ appendix compared to controls. Strong correlations between host tissue and mucus microbial pathways of IBD patients highlighted a link between microbial communities and host gene expression, contributing to immune activation and inflammation in the appendix. Our findings thus provide valuable insights and a basis for mechanistic hypotheses regarding the appendix’s role in IBD pathogenesis.

overall_design: Mucus samples from pediatric IBD patients and control non-IBD patients were collected from the appendix, peri-appendicular region, cecum, and ascending colon using sterile swabs immediately after excision. The samples were promptly frozen at -80C for subsequent DNA extraction and whole genome sequencing (SRA BioProject: PRJNA1160849). Appendix tissues preserved in RNA-later were kept at room temperature for 1 hour before being frozen at -80C for DNA and RNA extraction, intended for 16S rRNA (SRA BioProject: PRJNA1160849) and RNA sequencing (this repository) respectively.

first: Nazanin Arjomand

last: Fard

first: Eytan

last: Wine


title: cGAS deficient mice display premature aging associated with loss of chromatin organization, derepression of LINE1 elements and induction of inflammation [RNA-seq]

first: Francesco

last: Morandini

overall_design:
We investigated the transcriptional changes induced by cGAS KO in mouse lung primary fibroblasts.
We performed RNA-seq on cells from 6 cGAS KO mice (3 male, 3 female) and 5 WT mice (3 male, 2 female)

first: John

last: Martinez

first: Cheyenne

last: Rechsteiner

first: Lucinda

last: Fitzgibbons

first: Natasha

last: Sieczkiewicz

first: Xiaoyan

last: Liao

first: Weijie

last: He

first: Sung Jae

last: Bae

first: Michael

last: Meadow

first: Eric

last: Hillpot

first: Joseph

last: Cutting

first: Victoria

last: Paige

first: Maxwell

last: Zacher

first: Seyed Ali

last: Biashad

first: Matthew

last: Simon

first: Ines

last: Meula-Zarzuela

first: Mario

last: Cordero

last: Sedivy

first: Andrei

last: Seluanov

first: Vera

last: Gorbunova


title: cGAS deficient mice display premature aging associated with loss of chromatin organization, derepression of LINE1 elements and induction of inflammation

first: Francesco

last: Morandini

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

overall_design: Refer to individual Series


title: cGAS deficient mice display premature aging associated with loss of chromatin organization, derepression of LINE1 elements and induction of inflammation [ATAC-seq]

overall_design:
We investigated the chromatin accessibility changes induced by cGAS KO in mouse lung primary fibroblasts.
We performed ATAC-seq on cells from 4 cGAS KO mice (2 male, 2 female) and 4 WT mice (2 male, 2 female)

first: John

last: Martinez

first: Cheyenne

last: Rechsteiner

first: Lucinda

last: Fitzgibbons

last: Sieczkiewicz


title: Effects of hepatic mARC1 inhibition in a mouse model of liver fibrosis

city: Riverside

first: Brendan

last: Gongol

state: Ca

address: 900 University Ave

institute: University of California, Riverside

summary: Metabolic-dysfunction associated steatohepatitis (MASH) is defined by increased liver adiposity that is causative to hepatic fibrosis, cirrhosis, and hepatocellular carcinoma.  Despite the high prevalence of the disease, there are currently few treatment options in part because the mechanistic basis causative to hepatic fatty acid biogenesis and accumulation are unresolved.  Recent evidence indicates that enhanced mitochondrial amidoxime-reducing component 1 (mARC1) induction is associated with increased hepatic triglyceride accumulation and reduced plasma triglycerides indicting that it may play an important role in NASH pathogenesis. The goal of this study is to explore the therapeutic potential of mARC1 inhibition on the inhibition or reversal of NASH pathogenesis in a mouse model of diet induced MASH.

overall_design: C57BL/6J mice were fed either a high fat diet in combination with high fructose water or a normal chow diet without high fructose water supplementation for 12 weeks.  Mice were then administered a 10 mg/kg dose of a mARC1 antisense oligonucleotide or a vehicle control Q2W. After 8 weeks, mice were sacrificed and liver tissue was harvested for RNAseq analysis.

first: Erin

middle: S

last: Coyne

first: Yang

last: Liu

first: Stacey

last: Meyers

first: Wendy

last: Blumenschein

first: Saswata

last: Talukdar


title: The heat shock transcription factor, HSF1, facilitates the catalytic engagement of topoisomerase IIb (TOP2B) within the neuronal genome

city: Dallas

first: Lahiri

last: Konada

address: 5225 Fleetwood Oaks Ave, Apt 527

department: Pshychiatry

institute: UTSW Medical center

summary: Topoisomerase II (TOP2) poisons, such as etoposide and doxorubicin, are potent antineoplastic drugs that are used to treat a variety of solid tumors and leukemias. Yet these drugs also cause significant secondary malignancies and toxicity to postmitotic cells. Proliferating mammalian cells express two TOP2 isoforms, TOP2A and TOP2B, while postmitotic cells only express TOP2B. Selectively targeting TOP2A, but not TOP2B, could thus prevent secondary toxicity in postmitotic cells, but such isoform-selective targeting strategies remain elusive. Here we report that the heat shock transcription factor, HSF1, facilitates the catalytic engagement of TOP2B on chromatin. Purified recombinant HSF1 stimulates the DNA cleavage and relaxation activity of purified TOP2B. Using atomic force microscopy, we show that HSF1 also enhances the recycling of TOP2B for subsequent rounds of DNA relaxation. TOP2B co-occupies the genome with HSF1 in both postmitotic and dividing cells, and either the knockdown or inhibition of HSF1 reduces the levels of catalytically engaged TOP2B. Intriguingly, HSF1 neither significantly interacts with TOP2A nor enhances its catalytic activity. Furthermore, pharmacological HSF1 inhibitors protect postmitotic cells from the cytotoxicity of TOP2 poisons without compromising their ability to kill cancer cells, revealing a potential strategy for minimizing the side-effects of TOP2 poison-based chemotherapy.

overall_design: HSF1 ChIP-seq in mouse cortical neruons

first: Thomas

last: Catley

first: Lance

last: Heady

first: Morgan

last: Crewe

first: Ilse

last: Ramirez

first: Laura

last: Wiggins

first: Amir

last: Segev

first: Alice

last: Pyne

first: Ram

last: Madabhushi


title: Single cell RNA-sequencing of H9 human embryonic stem cell-derived cortical organoid slice cultures (ALI-COs) at various timepoints

city: Cambridge

first: Lea

middle: Marion Denise

last: Wenger

address: Robinson Way

department: Clinical Neurosciences

institute: University of Cambridge

summary: scRNA-seq analysis of 100, 150, 290, 360 and 390 day old human cortical organoids grown at the air-liquid interface (ALI-COs). Investigations reveal a gliogenic switch, resulting in two distinct astrocyte populations with different propensities for synapse regulation.

overall_design: Single cell RNA-sequencing data was generated using the 10X Genomics Chromium Single Cell 3' chip and workflow.

first: George

last: Gibbons

first: Kornelia

last: Szebenyi

first: Andras

last: Lakatos


title: Comparative transcriptomics of Nipah virus infection in human and fruit bat cells

city: Lyon

first: olivier

last: reynard

state: Auvergne-Rhône-Alpes

address: 21 avenue Tony Garnier

department: CIRI

institute: INSERM

summary: We used bulk RNA sequencing to investigate the transcriptomic signature of fruit bat and human cells after Nipah virus infection. We have infected immortalized and bat and human cells and collected samples at 0, 8, 24, 48 hours-post-infection (hpi). Positive cells to infection were sorted at 24 and 48hpi. We  also have infected primary bat and human cells and collected samples at 0 and 48hpi. We analyzed inter- and intra-species responses to highlight mecanims allowing bat to control Nipah virus infection.

sample_organism:
Homo sapiens
Pteropus vampyrus

platform_organism:
Homo sapiens
Pteropus vampyrus

overall_design: Bat and human immortalized cell lines were infected with Nipah and RNA samples collected at 0, 8, 24 and 48hours post infection (hpi) in 5 replicates. Bat and human primary cells were infected with Nipah and RNA samples collected at 0 and 48hpi.

first: Claudia

last: Gonzalez

first: Carine

last: Rey

first: Omran

last: Allatif

first: Severine

last: Croze

first: Olivier

last: Reynard

first: Branka

last: Horvat


title: Widespread transmission of DNA supercoiling and selective topoisomerase utilization regulates torsional stress within the neuronal genome [RNA-Seq]

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

summary: DNA supercoiling has the potential to alter gene transcription and chromatin topology, yet how its distribution is regulated on a genome-wide level is poorly understood. Here we utilized psoralen crosslinking and sequencing (TMP-seq) to assess the distribution of underwound DNA at high resolution in postmitotic neurons. We report that supercoiling propagates widely (> 200 kb) from the sites of active RNAPII and that its distribution is constrained by chromosome compartments and by specific nucleosome configurations, including H3K27me3-rich regions and broad distributions of active promoter-related chromatin marks. Underwound DNA does not accrue upstream of expressed genes in postmitotic neurons, which could shield them from cumulative torsional stress. Inhibiting either transcription or TOP1 affect underwound DNA levels genome-wide; however, supercoiling at the boundaries of expressed genes is minimally perturbed, indicating that dynamic supercoiling is not locally confined to sites of RNAPII activity at expressed genes. Surprisingly, TOP1 inhibition elevates supercoiling but stimulates nascent transcription at most genes and other sites of transcription, including enhancers, suggesting that torsional stress generally favors transcription, and that topoisomerase activity is not essential for transcription at most genes. We show that the induction of cryptic transcription within gene bodies, and not supercoiling buildup, could underlie the vulnerability of long neuronal genes to topoisomerase inhibition. These observations illuminate how chromatin organization governs the distribution of torsional stress within the genome and how the interplay of supercoiling and topoisomerases regulates transcription.

overall_design:
We preformed RNA-seq in control samples and obtained normalized read counts

Re-analysis GSE195963: Murine neural stem/progenitor cells DRIP-seq raw data (FASTQ) from Thongtip et al. (2022) were adapter trimmed (TrimGalore 0.6.6), aligned to the GRCm38/mm10 genome using BWA-MEM. Reads per kb per million (RPKM)-normalized bigWig tracks were generated from BAM files containing uniquely mapped reads using deepTools2 Bamcoverage. GRCm38/mm10 NCBI Refseq gene and gene prediction table from UCSC genome browser was used to generate length categories.

first: Lahiri

last: Konada

first: Morgan

last: Crewe


title: Widespread transmission of DNA supercoiling and selective topoisomerase utilization regulates torsional stress within the neuronal genome [TOP2Bcc-seq]

overall_design: TOP2Bcc-seq was used to map catalytically engaged TOP2B in mouse cortical neruons

first: Ilse

last: Ramirez


title: Widespread transmission of DNA supercoiling and selective topoisomerase utilization regulates torsional stress within the neuronal genome [fastGRO-seq]

overall_design: We preformed fastGRO-seq to map nascent RNA following Top 1, Top 2 and RNAPII inhibition.

first: Amir

last: Segev


title: Widespread transmission of DNA supercoiling and selective topoisomerase utilization regulates torsional stress within the neuronal genome


title: Widespread transmission of DNA supercoiling and selective topoisomerase utilization regulates torsional stress within the neuronal genome [TMP-Seq]

overall_design: We preformed TMP-seq to map negatively supercoiled regions in mouse cortical neruons, following Top 1, Top 2 and RNAPII inhibition.


title: The Mest DMR regulates Klf14 imprinting via allele-specific sub-TAD structures

city: Vancouver

first: Louis

last: Lefebvre

state: BC

address: 5.503-2350 Health Sciences Mall

department: Medical Genetics

institute: University of British Columbia

summary: The imprinted gene Mest is regulated by a gametic differentially-methylated region (gDMR) at its promoter CpG island (CGI), retaining oocyte-derived DNA methylation (DNAme) throughout development. The maternally-expressed gene Klf14 is located ~200 kb downstream of Mest. Although its promoter CGI is kept unmethylated in most tissues, maternally-inherited DNAme is paradoxically required for Klf14 expression. Here, we show that Mest and Klf14 reside within the same topologically associating domain (TAD) in mouse embryonic stem cells (ESCs), defined by sites of biallelic CTCF binding at the boundaries. Using allele-specific 4C-seq in F1 hybrid ESCs, we show that CTCF binding to the unmethylated Mest gDMR generates a paternal allele-specific sub-TAD required for Klf14 silencing. These observations, supported by analysis of CRISPR-mediated deletions of the Mest gDMR, define a new role for maternally methylated gDMRs, which are all associated with promoter-proximal functions: our results show they can also exert long-range effects via allele-specific modulation of TAD structures.

overall_design: Allele-specific 4C-seq experiments were performed in reciprocal B6xCAST F1 mESC.

first: Amanda

last: Ha

first: Aaron

middle: B

last: Bogutz


title: Somatic mutations reveal the ontogeny of microglia in human aging [mtscATAC-seq]

status: Public on Jul 13 2026

city: Stanford

first: Julia

last: Belk

state: California

address: 450 Serra Mall

institute: Stanford University

summary: Microglia are the resident macrophages of the central nervous system. In mice, microglia seed the brain during embryogenesis and can be maintained throughout life with minimal input from adult hematopoiesis. The origins of human microglia are less clear, but recent evidence suggests that marrow-derived cells contribute to the human microglial pool in certain individuals. Here, to investigate the ontogeny of human microglia, we develop a method that uses the collection of accumulated somatic mutations which uniquely labels each clone of cells to track the infiltration of marrow-derived cells into the human brain. Applying this method to 20 aged individuals, we find evidence of an influx of marrow-derived cells into the brain in all examined individuals. Single cell analysis, including single cell lineage tracing using mitochondrial DNA variants, demonstrates that these infiltrating cells are similar to microglia and can comprise a large fraction of the microglial pool. Analysis of large-scale sequencing cohorts demonstrates a protective association between most types of clonal hematopoiesis and Alzheimer’s disease. In sum, this work uncovers a widespread influx of myeloid cells into the healthy human brain which contributes to the pool of human microglia and becomes common with aging.

overall_design: mtscATAC-seq was performed on fresh tissue specimens from two research autopsies. mtDNA variants enabled lineage tracing of bone marrow cells to assess the presence/absence and phenotype of bone marrow cells in the human brain.

first: Howard

middle: Y

last: Chang

first: Siddhartha

last: Jaiswal


title: Somatic mutations reveal the ontogeny of microglia in human aging


title: Fatty Acid Binding Protein 5-deficiency impairs alveolar macrophage function and metabolism

city: Denver

first: Fabienne

middle: Sabrina

last: Gally

state: Colorado

address: 1400 Jackson Street, K827

institute: National Jewish Health

summary: Macrophages are large mononuclear immune cells that participate in host protection, not only by phagocytosing foreign or infected cells and initiating inflammatory responses, but also by contributing to the resolution of inflammation. Chronic Obstructive Pulmonary Disease (COPD) is characterized by increased numbers of macrophages in lung tissue, with altered engulfment capabilities. However, the molecular pathways leading to macrophage dysfunction in COPD remain unclear. Using integrated genetics and genomics approaches, we previously identified Fatty Acid Binding Protein 5 (FABP5) as a key target in the resolution of airway inflammation that exhibits decreased expression in COPD patients. The objective is to define the significance of alveolar macrophage FABP5 by comparing the resolution of inflammation in WT and FABP5-/- mice following nontypeable Haemophilus influenzae (NTHi) infection or LPS sterile inflammation. Immune and metabolic responses were analyzed using functional assays, flow cytometry, ELISA, cell metabolic profiling and tracing, as well as ATAC-seq. FABP5-/- mice exhibited impaired efferocytosis, reflected by a reduction of apoptotic cell engulfment by alveolar macrophages. This was accompanied by a reduction in fatty acid uptake and fatty acid b-oxidation, a reduction in mitochondrial respiration, an accumulation of TCA cycle and glycolysis metabolites, and an increased chromatin accessibility for AP-1 family members. FABP5-deficient alveolar macrophages failed to initiate reparative metabolic programming, which is critical for the resolution of inflammation. Our data suggest that increasing FABP5 expression could provide a metabolic switch that facilitates macrophage conversion to a pro-resolving phenotype and restores alveolar macrophage efferocytic functions in the lungs of COPD patients.

overall_design: Eight- to twelve-week-old WT and FABP5-/- mice were anesthetized by isoflurane (3-5%) and then inoculated by oropharyngeal aspiration with 50 µl of 15 µg of LPS from Pseudomonas aeruginosa. Nine-days post-LPS sterile inflammation, mice were sacrificed with an injection of Fatal Plus (2 µl/g of body weight). Lungs were digested and CD45+ cells were enriched using magnetic beads per manufacturer’s instructions (StemCell Technologies) and subjected to scRNA-seq.