title: Establishment and Characterization of Three Canine Ameloblastoma Cell Lines with Genomic and Transcriptomic profiles

city: Davis

first: Stephanie

last: Goldschmidt

address: one shields ave

department: VSR

institute: UC-Davis

summary: Establishment of canine acanthomatous ameloblastoma (CAA) cell lines has profound importance in pre-clinical in vitro testing. The goal of this study was to develop, authenticate, and characterize three CAA cell lines. Cell lines were developed with standard cell culture techniques from dogs with naturally occurring CAA. Each cell line was authenticated as canine with a validated PCR panel. Epithelial cell origin was confirmed with pan-CK flow cytometry. Next generation DNA and RNA sequencing characterized features of the cell lines and compared them to the parent tumor. We confirmed that all cell lines maintained mutations seen in the parent tumors including a missense HRAS mutation and RTK-RAS pathway upregulation across all samples. Other common mutations (2/3 cell lines and their parent tumors) included ADGRA3, DNAH7, F10, KIAA1671, OGFR, SLC6A17, SNX7, SPTBN5, TENM4, and YEATS2.

overall_design: We compared the transcriptional profiles from our parent tumors and established cell lines to historical transcriptomic analysis of CAA and healthy gingiva. We confirmed the same canonical CAA molecular features of primary tumors across studies with distinct clustering from healthy gingiva. Further, we documented that the cell lines maintained upregulated genes that are seen within in vivo CAA across both studies including upregulated GPC4 and ETV5 as well as gene sets associated with the presence of epithelial-mesenchymal transformation, KRAS, Pi3K-AKT signaling, and hedgehog signaling pathways. Thorough characterization of the mutational and transcriptional profiles of the established cell lines, especially in context to how they differ from the parent tumors, sets the platform for translational in vitro testing.

first: Natalia

last: Vapniarsky

first: John

last: Mcpherson

first: Daniel

last: York

first: Rob

last: Rebhun

first: Maria Soltero

last: Rivera

first: Abraham

last: Morales

first: Christine

last: Ly


title: Pseudomonas putida KT2440 gene expression comparison of ethanol growth with lanthanum chloride or oxide.

status: Public on Jul 01 2026

city: Berkeley

first: Nathan

last: Good

state: CA

address: 111 Koshland Hall

department: Plant and Microbial Biology

country: USA

institute: UC-Berkeley

type: Expression profiling by high throughput sequencing

summary: The physiological impact of lanthanum solubility on Pseudomonas putida KT2440 was assessed using RNA-seq transcriptomics. Differential gene expression analysis was applied to samples of P. putida KT2440 grown in minimal media with ethanol where lanthanum was added in the highly soluble chloride or poorly soluble oxide form.

overall_design: RNA-seq transcriptomics comparison of Pseudomonas putida KT2440 grown on ethanol with lanthanum chloride or oxide.

first: Trinity

middle: K

last: Reimer

first: Cecilia

last: Martinez-Gomez


title: Small Extracellular Vesicles Secreted from Cardiomyocytes Targeting Microglial Activation and Hypothalamic Inflammation Aggravate HFpEF

city: Wuhan

first: Lintong

last: Men

address: Huazhong University of Science and Technology  1095 Jiefang Avenue

country: China

institute: Tongji Hospital Tongji Medical College

type: Non-coding RNA profiling by high throughput sequencing

summary: Background: Heart failure with preserved ejection fraction (HFpEF) is increasingly acknowledged as a major public health concern due to its complex pathophysiology that involves neuroinflammation and sympathetic activation. The crosstalk between the heart and hypothalamic microglia in HFpEF, particularly the role of small extracellular vesicles (sEVs), remains insufficiently explored. Methods and Results: We constructed a HFpEF model in mice by combining a long-term high-fat diet with the nitric oxide synthase inhibitor L-NAME. These mice exhibited activation of microglia and hypothalamic inflammation. Microglia depletion with PLX3397 suppressed sympathetic activity and improved cardiac dysfunction in HFpEF. sEVs derived from the myocardium of HFpEF mice induced a pro-inflammatory M1 phenotype in microglia, leading to hypothalamic inflammation and sympathetic activation. Intraperitoneal injection of the sEVs biogenesis inhibitor GW4869 reversed these changes in HFpEF mice. Similar pathological changes were observed in BV2 microglia treated with sEVs isolated from palmitic acid-treated HL-1 cardiomyocytes. Bioinformatic and RT-qPCR analyses revealed a notable upregulation of miR-200c-3p in sEVs derived from both HFpEF myocardial tissue and palmitic acid- treated HL-1 cardiomyocytes, as well as in microglia. Cardiomyocyte-specific miR-200c-3p sponge inhibited microglial activation, hypothalamic inflammation and sympathetic activation in HFpEF mice. Conversely, miR-200c-3p mimic exacerbated pro-inflammatory responses in BV2, while miR-200c-3p inhibitor prevented the transition to a pro-inflammatory phenotype. The anti-inflammatory protein DUSP1 was validated as a potential downstream target of miR-200c-3p in microglia. Conclusions: Our study reveals that HFpEF prompts cardiomyocytes to release sEVs enriched with miR-200c-3p, leading to hypothalamic inflammation and evoking sympathetic outflow, which in turn exacerbates cardiac dysfunction. Focusing on sEV-mediated communication between cardiomyocytes and microglia may offer a new therapeutic approach for HFpEF.

overall_design: To establish the HFpEF model, 8-week-old male C57BL/6J mice were randomly assigned to a two-hit protocol combining a high-fat diet (60% fat, Research Diets, Cat#D12492) with the nitric oxide synthase inhibitor L-NAME (0.5 g/L, Merck, Cat#51298-62-5) in drinking water, and maintained on the corresponding diets and drinking water for 12 weeks. Control male mice received standard chow diet. Mouse cardiac tissue was minced to 1×1×1 mm pieces and digested in DMEM (Wuhan Promoter Biological CO., LTD, Cat#KGL1211-500) containing Type II collagenase (Biosharp, Cat#9001-12-1) at 37°C in a constant temperature water bath for 1 hour. All tissue fragments with supernatants were centrifuged at 300 g for 10 minutes. The supernatants centrifugation at 2000 g for 20 minutes, and then collected and filtered through a 0.22 μm filter (Merck, Cat#SLGP033R), followed by ultracentrifugation (Optima XPN-100, Beckman Coulter, Brea, CA, USA) at 10000 g for 30 minutes. Next, the collected supernatants ultracentrifuged at 100000 g for 70 minutes. The sEVs were washed in 56 mL of sterile PBS and re-centrifuged at 100000 g for another 70 minutes. The final pellet was resuspended in 100 µL of sterile PBS.


title: PRMT1 knockdown transcriptome profiling in MDA-MB-231 M3 cells

city: nanjing

first: li

last: shang

address: longmian road 101

institute: nanjing medcial university

summary: RNA-seq was performed to profile transcriptomic changes caused by PRMT1 knockdown in the human MDA-MB-231 M3 breast cancer bone-metastatic cell line. Control cells and siPRMT1-treated PRMT1 knockdown cells were analyzed in three biological replicates per group.

overall_design: Six RNA-seq libraries were generated from MDA-MB-231 M3 cells: three control biological replicates (A_1, A_2, A_3) and three siPRMT1 PRMT1-knockdown biological replicates (C_1, C_2, C_3). Libraries were sequenced as paired-end 150 bp reads on an Illumina NovaSeq 6000 platform.


title: Expression of glia-associated genes and emergence of glial lineages in Xenopus laevis suggests divergence in the regulation of gliogenesis

city: Houston

first: Amy

last: Sater

state: Texas

address: 3455 Cullen Blvd, SR2 421F

department: Biology and Biochemistry

institute: University of Houston

summary: Although glia are essential for the development and maintenance of the vertebrate central nervous system, the elucidation of glial development lags behind that of neuronal differentiation. We have examined the emergence of glial lineages in Xenopus laevis. Single-cell transcriptomics shows that by stage 40, following the completion of primary neurogenesis, the central nervous system includes astrocytes and oligodendrocyte precursors, as well as proliferating neural progenitors expressing glast and other genes associated with glial functions. These analyses also reveal clusters of GABAergic neurons, glutamatergic neurons, and immature neurons. Our results establish a time course for early astroglial functions and the differentiation of astrocyte and oligodendrocyte lineages.

overall_design: Isolates of brain and trunk spinal cord were prepared from Xenopus laevis embryos at st. 40; cells were dissociated and used to prepare libraries for scRNA-sequencing.

first: Mahmoud

last: Alhomouz

first: Christina

last: Ulrich

first: Heithem

last: El-Hodiri


title: The intracellular domain of the epilepsy protein PCDH19 regulates spine density in cortical neurons in vivo via Xlr genes.

city: Leioa

first: Sylvia Adriana

last: Newbold

state: Bizkaia

address: Science Park of EHU, Sede building

country: Spain

institute: Achucarro Basque Center for Neuroscience

summary: Mosaic mutations in the X-linked cell adhesion molecule Protocadherin 19 (PCDH19) lead to epilepsy with cognitive impairment, whereas complete absence of functional protein, although possibly linked to autistic features, does not elicit any seizures. It is believed that mosaic expression of PCDH19 leads to defective neuronal communication, but whether further roles beyond cell adhesion are critical for PCDH19 function in the cortex is currently unknown. We confirm that the proteolytic processing of PCDH19, previously described in hippocampal neurons, also takes place in mouse cortical neurons in vivo and show that nuclear transport of its intracellular domain is mediated by importins. RNAseq analysis further indicates that the intracellular domain of PCDH19 leads to broad transcriptomic changes. Finally, we use in utero electroporation to provide the first in vivo data about the role of this cleaved intracellular domain in upper layer cortical neurons of male and female mice, where it reduces spine density through an increase in Xlr gene expression without affecting overall dendritic morphology. Our results suggest that PCDH19 could act as an activity sensor in a synapse to nucleus signalling pathway involved in synaptic homeostasis.

overall_design: RNAseq analysis of E14 mESC-derived cortical neurons at day in vitro (DIV8) and DIV12, from control neurons (WT) and neurons overexpressing the cytoplasmic domain of PCDH19 (19ICD-OE).  For each genotype samples were obtained from three independent differentiations.

first: Victoria

last: Becerra-Espinosa

first: Jaime

last: Fabra-Beser

first: Ian William John

last: Fox

first: Cristina

last: Llinares-Benadero

first: Elizaveta

last: Stebleva

last: Gil-Sanz

first: Isabel

last: Martinez-Garay


title: Interaction between PRDM14 and CBFA2T2 supports pluripotency and proliferation in germ cell tumors

city: Farmington

first: Ching

middle: C

last: Lau

state: CT

address: 10 Discovery Drive

institute: The Jackson Laboratory for Genomic Medicine

summary: Background/Objectives: Germ cell tumors (GCTs) are thought to arise from primordial germ cells that fail to appropriately differentiate and instead retain pluripotency programs. PRDM14 is a key regulator of pluripotency and primordial germ cell specification and is aberrantly expressed in multiple GCT subtypes. However, the role of PRDM14 in GCT malignancy remains unclear. In this study, we investigated whether PRDM14 functions in GCTs through CBFA2T2, a transcriptional corepressor previously identified as a PRDM14‑interacting partner in pluripotent stem cells and developmental models. Methods: To determine the presence and level of PRDM14 and CBFA2T2 in GCT, a panel of GCT lines were assessed for RNA and protein expression and interaction. Then, to better understand the biological effects of PRDM14 and CBFA2T2 within GCT, PRDM14 and CBFA2T2 knockdowns were employed. Results: We show that PRDM14 and CBFA2T2 are expressed across GCT cell lines, colocalize predominantly in the nucleus, and cooperate as a complex in GCT cell lines. Knockdown of either PRDM14 or CBFA2T2 resulted in reduced expression of key pluripotency genes and a significant impairment of cell proliferation, indicating a shared role in maintaining an undifferentiated, proliferative state. Transcriptomic analysis following PRDM14 or CBFA2T2 depletion revealed extensive overlap in differentially expressed genes and convergent alterations in developmental and metabolic signaling pathways. Conclusions: Together, these findings suggest that PRDM14 and CBFA2T2 form a functional complex that sustains pluripotency and proliferation in GCT cells. This supports a model in which persistence of germline regulatory mechanisms contributes to GCT malignancy, highlighting this interaction as a potential therapeutic vulnerability.

overall_design: RNA-seq profiling of embryonal carcinoma cell lines NEC8/NCCIT, and their siRNA knockdowns of PRDM14 and CBFA2T2.

first: Deana

middle: L

last: Wood

first: Aaron

middle: M

last: Taylor

first: Jody

middle: T

last: Lombardi

first: Patrick

last: Ng

first: Joanna

middle: J

last: Gell


title: A comparative analysis of the immunotranscriptomic features of DENV-1, -3, and -4 human challenge models

city: Syracuse

first: Celine

last: Hardy

address: 750 East Adams Street

institute: SUNY Upstate Medical University

summary: Three different dengue human challenge models (DHIM) have been performed and provide an invaluable tool for studying the early virologic and immunologic features of dengue infection. In this work, we performed a comparative analysis of DHIM-1, DHIM-3, and DHIM-4 studies to determine shared and unique features of the transcriptional response to infection. We identify a conserved transcriptional signature across all three DHIMs which is correlated with RNAemia. In order to validate the association of viral dose these signatures in vitro, we then exposed primary human PBMC to DENV-1 or DENV-3 at varying titers and performed bulk RNA sequencing.

overall_design: Peripheral blood mononuclear cells (PBMC) were isolated from a healthy human donor. Cells were inoculated with DENV-1 45AZ5 or DENV-3 CH53489 at 0 (uninfected control), 1 X 10^2, 10^3, or 10^4 PFU (triplicate for each condition).

first: Céline

middle: S

first: Adam

last: Waickman


title: scRNA-seq of immune cells during targeted therapy-induced tumor regression and targeted therapy tolerant residual melanoma

city: Ithaca

first: Andrew

last: White

state: NY

address: 930 CAMPUS RD

institute: Cornell University

summary: Single-cell RNA sequencing (scRNA-seq) was performed to profile immune cell states in BRAF-mutant melanoma during targeted therapy-induced tumor regression and therapy-tolerant residual disease. CD45⁺ tumor-infiltrating immune cells were isolated from immunocompetent melanoma models treated with BRAF/MEK inhibitors and analyzed by scRNA-seq using the 10x Genomics Chromium platform. Comparative single-cell transcriptomic analysis revealed dynamic remodeling of the tumor immune microenvironment during treatment, including distinct macrophage and NK cell populations associated with therapeutic response and tolerance. Macrophage–NK cell crosstalk and cytokine signaling pathways were found to orchestrate immune activation during tumor regression, whereas immunosuppressive macrophage subsets and reduced NK effector signatures characterized the tolerant state. This dataset provides a comprehensive immune cell–level resource to investigate innate immune dynamics and intercellular communication mechanisms underlying targeted therapy efficacy and resistance in melanoma.

overall_design: Single-cell suspensions were generated from melanoma tumors, followed by CD45⁺ cell enrichment. Samples were submitted to the Cornell University BRC Genomics Core Facility (RRID: SCR_021727), where they were processed on a Chromium X instrument using the Chromium Next GEM Single Cell 3’ High Throughput RNA-Seq Assay v3.1 Dual Index protocol (10x Genomics, CG000416, RevC). Sequencing data were processed with Cell Ranger using the mouse GRCm39 reference genome. All downstream analyses were performed in Seurat v5.1.0. Raw data were merged and filtered (nFeature_RNA > 200, < 8000), with exclusion of contaminating non-immune cells such as fibroblasts and melanoma cells, resulting in 41,588 CD45⁺ immune cells. Integration and scaling were performed using IntegrateData and ScaleData. Dimensionality reduction was achieved through PCA, and clustering and visualization were conducted using UMAP on the top 50 principal components. Differentially expressed genes (avg_log2FC > 1) were identified using FindAllMarkers, visualized via heatmaps (DoHeatmap) and dot plots (DotPlot). Macrophage functional scoring was calculated using AddModuleScore with previously published gene signatures, and CellChat was used to infer cell–cell communication and ligand–receptor interactions.

first: Chia-Hsin

last: Hsu

first: Keng-Jung

last: Lee

first: Jingyi

last: Chen

first: Leanne R.

last: Donahue

first: Jianping

last: Lin

first: Danielle

last: Kacaj

first: Richard M.

first: Zhong-Yin

last: Zhang

first: Andrew C.


title: swiss cheese is essential for maintaining spermatogenesis and the proper functioning of biological barriers in Drosophila

city: St. Petersburg

first: Artem

middle: Evgenevich

last: Komissarov

address: Kotelnikova Alley 2a

country: Russia

institute: PNPI

summary: Functional changes in PNPLA6 (Patatin-like phospholipase domain-containing protein 6), caused by gene mutations or organophosphate inhibition, alter the levels of various phospholipids. In humans, this leads to organophosphorus compound-induced delayed neurotoxicity (OPIDN) syn-drome and several rare diseases. In this study, we analyze the role of the swiss cheese gene (sws), an ortholog of PNPLA6, in Drosophila melanogaster spermatogenesis. We show that mutation in sws affects membrane remodeling during spermatid individualization, as well as spermatid coiling during the late stages of spermatogenesis. Furthermore, the sws1 mutation induces transcriptome changes in the testes. We also demonstrate that sws gene is essential for the proper functioning of important biological barriers in Drosophila.

overall_design: RNA-seq analysis was performed to evaluate the transcriptional profile changes in testes of 5-day-old Drosophila melanogaster sws1 mutants compared to wild-type controls

first: Elena

middle: V

last: Ryabova

first: Ekaterina

middle: A

last: Ivanova

middle: E

middle: U

last: Bolobolova

first: Natalia

last: Dorogova

first: Elizaveta

last: Slepneva

first: Evgenia

last: Latypova

first: Irina

last: Ogneva

first: Svetlana

last: Sarantseva


title: Analysis of murine pancreatitis tissues and KPC PDAC tumours

status: Public on Jul 02 2026

city: CAMBRIDGE

first: Giulia

last: Biffi

state: Cambridgeshire

address: Cancer Research UK, Robinson Way

country: United Kingdom

institute: University of Cambridge

summary: We investigate the pancreatitis tissues from carulein-induced mice and PDAC tumours from KPC genetically engineered mice.

overall_design: 10 samples in total - 4 KPC GEMM; 6 Pancreatitis

first: Wenlong

last: Li

first: Muntadher

last: Jihad


title: Local control of Cre-regulated genetic modeling in vivo using wireless implantable optoelectronics [Spatial transcriptomics]

city: Chicago

first: Jalees

last: Rehman

state: IL

address: 900 S. Ashland Ave. MBRB 2072, Mailcode 669

department: Biochemistry and Molecular Genetics

institute: UIC

summary: Effective modeling of chronic human diseases in vivo requires precise spatiotemporal regulation of molecular processes at defined tissue locations. Optogenetic and optoelectronic tools can provide such control but targeting internal organs such as the lungs remain challenging. To address this, we developed E-LightR-Cre recombinase, enabling precise, spatially restricted gene activation with no dark-state activity and robust blue-light responsiveness. To achieve local activation of E-LightR-Cre in specific organ sites, we engineered wireless, fully implantable optoelectronic devices enabling focal illumination of murine lungs with no discernible organ damage. The size of activated area is controlled by modulating light intensity and duration. Using implanted optoelectronic devices, we activated E-LightR-Cre in a selected area of mouse lungs and achieved local regulation of targeted genes. Light-regulated expression of oncogenic KRas-G12D mutant in mouse lungs induced local formation of oncogenic lesions. These results show that our protein engineering and adaptable optoelectronic approaches enable facile application of optogenetic tools for locally controlled disease modeling in vivo.

overall_design: Spatial transcriptomic analysis was performed on mouse lung tissue sections collected from two mice, 8 weeks after E-LightR-Cre delivery and localized Low_power µ-ILED activation in LSL-kRASG12D mice. H&E-stained sections containing pathologist-identified neoplastic lesions and adjacent normal tissue regions were analyzed per sample for each condition, followed by pseudobulk differential expression, Gene Ontology enrichment, and ssGSEA-based pathway activity analyses.

first: Trisha

last: Bansal

first: Varsha

last: Sreekanth

first: Andrei

last: Karginov


title: Local control of Cre-regulated genetic modeling in vivo using wireless implantable optoelectronics

overall_design: To assess the ability of E-LightR-Cre to induce specific signaling and oncogenic transformation in a locally illuminated population of cells, we generated reporter constructs that express membrane targeted tdTomato flanked by loxP sites and followed by GFP-tagged wild-type KRas or G12D mutant. GFP-tagged wild type KRas or its oncogenic mutant (G12D) will be expressed only in cells where E-LightR-Cre is activated.  Using the optoelectronic device µ-ILEDs, we induced expression of GFP-KRas-G12D or GFP-KRas-WT in a local population of HEK293T cells lacking intrinsic KRas mutations. Cells transfected with unmodified mTmG reporter construct served as a negative control. After 6 hours of local illumination followed by 18 hours of incubation in the dark, GFP-positive cells were observed in the illuminated regions, while GFP-negative/tdTomato-positive cells remained at the non-illuminated periphery. To evaluate the effect of oncogenic KRas, GFP-positive and GFP-negative cells from each group were sorted using fluorescence-activated cell sorting (FACS), and total RNA was extracted from the sorted cells for bulk RNA sequencing analysis.


title: RNA-seq profiling of liver and lung of CLP mice(6h)

city: Gent

first: Steven

last: Timmermans

address: Technologiepark 71

country: Belgium

institute: VIB-UGent

summary: An RNA-seq of mouse liver and lungs 6 hours after CLP or sham to investigate differenial gene expression and functional effects.

overall_design: RNA-seq profiling of mouse lung and liver 6 hours after Sham or CLP surgery (n=3/group).

first: Marah

last: Heyerick

first: Louise

last: Nuyttens

first: Robin

last: Van Loke

first: Elise

last: Moens

first: Nikita

last: Gerebtsov

first: Helena

last: Aegeter

first: Bart

last: Lambrecht

first: Domien

last: Vanneste

first: Thomas

last: Marichal

first: Jolien

last: Vandewalle

first: Claude

last: Libert


title: Limited Immune-Mediated Efficacy of Anti-PD-L1/VEGF in EGFR-TKI-Naïve Egfr-Mutant Lung Cancer with Non-Inflamed Tumor Microenvironment

city: Okayama

first: Shuta

last: Tomida

state: Okayama

address: 2-5-1 Shikata-cho, Kita-ku

department: Center for Comprehensive Genomic Medicine

country: Japan

institute: Okayama University Hospital

summary: Patients with EGFR-mutated lung cancer show limited response to immune checkpoint inhibitors. In this study, we found that anti-PD-L1/VEGF combination therapy failed to activate tumor immunity in a syngeneic Egfr-mutant lung cancer mouse model. Unlike the combination of paclitaxel (PTX) and anti-PD-L1, the combination of PTX and anti-VEGF enhanced anti-tumor effects and altered the tumor microenvironment (TME), showing potential to activate anti-tumor immunity. To investigate these mechanisms, we profiled the transcriptomes of tumors treated with PTX and/or anti-VEGF. The data suggested a potential trend where the combination of PTX and anti-VEGF therapy might be associated with a modest increase in natural killer (NK) cell populations within the TME.

overall_design: Total RNA was extracted from subcutaneous Egfr-mutant lung tumors harvested from C57BL/6J mice on day 8 post-treatment with PBS (control), paclitaxel (PTX), anti-PD-L1, and/or anti-VEGF antibodies. RNA-seq was performed to evaluate treatment-induced changes in gene expression profiles and the tumor immune microenvironment.

first: Atsuko

last: Hirabae

first: Kadoaki

last: Ohashi


title: THBS1 Induces Dysfunction of Ovarian Granulosa Cells in Patients with Polycystic Ovary Syndrome by Activating the TGF-β/Smad Pathway

city: Lanzhou

first: Jiajing

last: He

address: No. 1 Dong Gang Xi Road, Chengguan District

department: The Reproductive Medicine Center

institute: The First Hospital of Lanzhou University

summary: To investigate the role of thrombospondin-1 (THBS1) in polycystic ovary syndrome (PCOS) pathogenesis and its mechanism in regulating granulosa cell (GC) function.

overall_design: Follicular fluid and granulosa cells from 21 PCOS patients and 21 age-matched non-PCOS controls were analysed for THBS1 expression and clinical correlations. A dehydroepiandrosterone (DHEA)-induced PCOS rat model with adeno-associated virus serotype 9 (AAV9)-mediated THBS1 knockdown was used to assess phenotypic changes. The KGN human granulosa-like cell line was employed to evaluate THBS1 overexpression effects on proliferation, apoptosis, and steroidogenesis. Mechanistic studies included RNA sequencing with Gene Set Enrichment Analysis (GSEA), co-immunoprecipitation, molecular docking against the latent TGF-β1 crystal structure (PDB 9VJJ), molecular dynamics simulation, an active/total TGF-β1 ELISA, and pharmacological TGF-β receptor inhibition.


title: EZH1/2 inhibition improves immunotherapy response through MHC Class II de-repression and neutrophil reprogramming

city: Lexington

first: Avery

middle: R

last: Childress

state: KY

address: 800 Rose Street

department: Toxicology and Cancer Biology

institute: University of Kentucky

summary: Squamous cell carcinoma of the lung is a difficult-to-treat cancer with high prevalence in the US, and particularly in Kentucky.  The goals of this work were to test if the EZH1/2 inhibitor valemetostat improves anti-PD1 responses in squamous cell lung cancer models, and to develop ex vivo models to test immunotherapy drug combinations. We found that valemetostat produced augmented anti-tumor responses to anti-PD1 therapy through up-regulation of tumor cell specific Major Histocompatibility Complex Class II (MHC Class II), and a shift towards activated CD8+ T cells . Neutrophils predominated in these tumors regardless of therapy, but examination of bone marrow revealed that valemetostat treated mice and mice that rejected tumors both had more mature neutrophils.  Likewise, Ezh2 knock-out mice produced neutrophils that were more apoptotic, less migratory, and less able to produce extracellular nets, but had similar ability to kill bacteria as Ezh2-WT neutrophils. To test tumor responses to differing neutrophil populations, we engineered three-dimensional air-liquid interface cultures with tumoroids, lung mesenchymal cells, and T cells, with and without bone marrow containing neutrophils and myeloid progenitors from distinct donors.  Bone marrow from tumor-naïve and mice with actively growing untreated tumors boosted tumoroid growth, while bone marrow from tumor-rejected and mice with tumors treated with valemetostat was anti-tumor.  MHC Class II blockade lowered the ability of bone marrow to boost tumor growth and reduced the ability of valemetostat with anti-PD1 to reduce tumoroid growth.  Patient samples revealed a strong negative correlation between EZH2 and MHC Class II, suggesting that targeting EZH2 activity could lead to marked increase in MHC Class II and improve treatment responses in lung squamous cell carcinomas.

overall_design: Looked at Neutrophils from mice treated with or without an epigentic inhibitior EZH2 and how that altered both their maturation as well as downstream markers

first: Dave-Preston

last: Esoe

first: Xiulong

last: Song

first: Yindan

last: Lin

first: Daniel

last: Plaugher

first: Tanner

last: DuCote

first: Ryan

last: Goettl

first: Kassandra

last: Naughton

first: Erika

last: Skaggs

first: Jinpeng

last: Liu

first: Zhonglin

last: Hao

first: Alber

last: Fliss

first: Daisuke

last: Honma

first: Todd

last: Burus

first: Feitong

last: Lei

first: Bin

last: Huang

first: Ellen

last: Beswick

first: Christine

middle: F

last: Brainson


title: Single-cell transcriptomics identifies ergothioneine as a mitochondrial protector to prevent AKI-to-CKD progression

city: WuHan

first: Zhipu

last: Qian

address: DongHu road ,No.115

institute: WuHan university

summary: This study investigates the role and mechanism of ergothioneine (EGT) in mitigating the progression of acute kidney injury (AKI) to chronic kidney disease (CKD). Using a cisplatin-induced mouse model of the AKI-to-CKD transition with EGT intervention, we combined histopathological examination, biochemical assays, and single-cell RNA sequencing (scRNA-seq) to demonstrate that EGT may significantly improve renal function parameters and attenuate renal injury and fibrosis. scRNA-seq analysis revealed that EGT may restore the expression of mitochondrial function-related genes in renal tubular epithelial cells, enhance oxidative phosphorylation and electron transport chain activity, thereby potentially promoting mitochondrial homeostasis. Furthermore, our in vitro experiments confirmed the protective effects of EGT on mitochondria in injured renal tubular epithelial cells, including reducing reactive oxygen species (ROS) generation, restoring diminished mitochondrial membrane potential, and increasing ATP production. These findings elucidate a mechanism by which EGT might delay AKI-to-CKD progression through multi-cellular coordination aimed at improving mitochondrial function, offering a promising therapeutic strategy for kidney diseases.

overall_design: We conduct this experiment to investigate how ergothioneine play the role in the process of acute kidney injury(AKI) to chronic kidney disease(CKD). The ergothioneine is used to treat the AKI to CKD model which was constructed by cisplatin, and a blank control group and a model group were set up accordingly. Subsequently, single-cell sequencing was conducted on the kidney tissues of the mice, with the aim of identifying and uncovering the relevant mechanisms for their treatment.Finally, we discover the possible therapeutic mechanism of ergothioneine

first: Jiaxin

last: Peng

first: Ling

last: Chen

first: Jing

first: Mingzhang

last: Han


title: RNA sequencing was conducted to profile gene expression changes in mouse tumor tissues following treatment with a bacteria-mediated nanozyme (BCHT).

city: Chengdu

first: Susu

last: Xiao

address: No.37 Guoxue Alley, Wuhou District

institute: West China Hospital, Sichuan University

summary: This study primarily investigates alterations in immune regulatory gene expression.

overall_design: Mouse tumor tissues without any treatment served as the control group, whereas tumors treated with the bacteria-mediated nanozyme were used as the experimental group. RNA sequencing was conducted to identify differential gene expression between the two groups.

first: Chenqian

last: Feng

first: Yuanxiang

last: Wang

first: Nianyong

first: Bo

first: Gang

last: Guo


title: Analysis of murine normal pancreatic organoids, pancreatitis-derived organoids, and PDAC organoids in complete media and of pancreatitis-derived organoids, and PDAC organoids cultured alone or cocultured with pancreatic stellate cells in reduced media

first: Giulia

last: Biffi

summary: We investigated the differences between murine normal pancreatic organoids (N), pancreatitis-derived organoids (P), and PDAC organoids cultured in completed media (i.e., mCPLT). We also studied the crosstalks between P and PDAC organoids and PSCs when they are cocultured together (i.e., cocx) or in monoculture (i.e., monocx) in reduced media.

overall_design: 75 samples: complete media: 5 N, 10 P, and 5 PDAC samples; reduced media monoculture: 4 PSCs, 10 P, and 7 PDAC; reduced media coculture: 10 PSCs (cultured+P), 7 PSCs (cultured+PDAC), 10 P and 7 PDAC.

first: Wenlong

last: Li

first: Muntadher

last: Jihad


title: Inflammatory Monocytes Constrain YAP-Induced Cell Proliferation [scRNA-seq immune]

city: Pittsburgh

first: Shuchang

last: Liu

state: PA

address: 203 Lothrop Street

institute: University of Pittsburgh

summary: YAP and its paralog, TAZ are transcriptional co-activators of the Hippo pathway that regulate cell growth. Their structural distinctiveness suggests important independent functional differences. To investigate this further, we generated YAP- and TAZ-predominant clones in the liver and followed their long-term behavior. YAP clones rapidly de-differentiate cells into a stem cell-like state with inflammatory immune cell recruitment followed by their clearance. In contrast, TAZ clones promote an anti-inflammatory immune environment resulting in their long-term maintenance, massive organ growth and increased mortality. YAP clones recruit inflammatory blood-derived monocytes, which if inhibited permits YAP clonal growth. Consistent with these results, YAPHigh colorectal cancer (CRC) patients had a 67% 5-year survival rate, while TAZHigh CRC patients did not survive to 5 years. Similar trends were seen in hepatocellular carcinoma patients. These findings underscore the importance of understanding the intrinsic differences in YAP and TAZ biology as independent drivers of disease.

overall_design: Immune cells were sorted from LATS KO or YAP-Tg after 2 weeks of treatment. The experiment was done in duplicate.

first: Serrena

last: Singh

first: Nareh

last: Tahmasian

first: Jia-Jun

first: Wenjia

first: Lucas

last: Haas

first: Yingdong

last: Zhu

first: Magdalena

last: Griswold

first: Nina

middle: N

last: Brodsky

first: Silvia

first: Brian

last: Kalish

first: Dean

last: Yimlamai


title: Transcriptomic profiling of BAZ1A-AS1 and BAZ1A knockdown in human vascular smooth muscle cells and rhabdomyoblasts

city: Augusta

first: David

last: Kim

state: GA

department: Vascular Biology Center

institute: Augusta University

summary: BAZ1A-AS1 is a novel human-specific long non-coding RNA upregulated during neointima proliferation in human saphenous veins. To elucidate the transcriptional programs regulated by BAZ1A-AS1 and its cis-regulatory gene BAZ1A, we performed bulk RNA-seq on human saphenous vein smooth muscle cells (HSVSMCs) with BAZ1A-AS1 knockdown (LNA gapmeR ASO) and rhabdomyoblast (RD) cells with BAZ1A knockdown (siRNA) under UV exposure. Differential expression analysis revealed convergent suppression of proliferative, inflammatory, and stress-response transcriptional programs across both knockdowns, supporting a shared regulatory axis.

overall_design: Bulk RNA-seq of HSVSMCs transfected with negative control ASO (NC-ASO) or BAZ1A-AS1 ASO (AS1-ASO), n=3 per group. Bulk RNA-seq of RD cells transfected with scrambled siRNA (siScram) or BAZ1A siRNA (siBAZ1A) under UV exposure, n=3 per group.

first: Brandee

last: Goo

first: Hong

last: Shi

first: Neal

last: Weintraub

first: Ha Won


title: HCN4 gain-of-function mutation increases intrinsic heart rate and limits maladaptive remodeling under pressure overload

city: Munich

first: Stefanie

last: Fenske

address: Butenandtstr. 7

department: Department of Pharmacy - Center for Drug Research

country: Germany

institute: Ludwig-Maximilians-Universität München

summary: Introduction: Gain-of-function (GOF) mutations in the cardiac pacemaker channel HCN4 have been associated with inappropriate sinus tachycardia in human patients. Chronic tachycardia is generally associated with adverse cardiac remodeling and cardiomyopathy, but whether enhanced HCN4 activity can induce or modulate such remodeling remains unknown. We aimed to investigate the influence of an HCN4 gain-of-function mutation on cardiac function and structure under baseline and pressure overload conditions. Methods and Results: We generated HCN4(Y527F) knock-in mice (HCN4F) carrying a GOF mutation in the C-Linker of HCN4 channels, which shifts their activation curves to more positive potentials. Electrophysiological recordings confirmed increased channel availability at physiological membrane potentials. Telemetric ECGs and in vivo electrophysiological studies revealed an elevated mean and intrinsic heart rate, faster sinus node and atrioventricular conduction in HCN4F mice, but no spontaneous arrhythmias. In HCN4F mice, the heart rate histogram was truncated at lower heart rates, indicating fewer low-rate intervals and more frequent periods of elevated heart rate, while maximal heart rates remained comparable between the two phenotypes. Histological analysis did not reveal structural changes consistent with tachycardia-induced cardiomyopathy. Cardiac morphology, fibrosis, and contractility were indistinguishable between genotypes up to 12 months of age. Following transverse aortic constriction, both WT and HCN4F mice developed left ventricular hypertrophy, but HCN4F hearts exhibited less chamber dilatation, smaller left ventricular lumen, and preserved systolic function compared to WT. Gene expression and RNA-sequencing analyses revealed activation of a typical hypertrophic gene program in both genotypes, but distinct remodeling signatures. Discussion: The HCN4(Y527F) gain-of-function mutation increases intrinsic heart rate without inducing structural or functional deterioration. Under pressure overload, it even confers protection against maladaptive dilatation and contractile dysfunction. These findings challenge the concept that persistent inappropriately elevated heart rate is necessarily detrimental and suggest that enhanced HCN4 activity may facilitate adaptive cardiac responses to stress.

overall_design: For RNA-seq, RNA isolated from left ventricular tissue was used and sequenced on an Illumina platform; the same RNA samples were also employed for qPCR analyses. In total, 16 samples were analyzed, comprising four biological replicates per group (WT-Sham, HCN4F-Sham, WT-TAC, and HCN4F-TAC). Differential gene expression analysis (TAC versus Sham and WT versus HCN4F) was conducted using DESeq2. P-values and log2-fold changes were calculated using the Wald test. Genes with an adjusted p-value < 0.05 and an absolute log2-fold change > 1 were considered significantly differentially expressed.

first: Konstantin

last: Hennis

first: Julia

last: Rilling

first: Linh

last: Pham

first: Rene

last: Rötzer

first: Chiara

last: Piantoni

first: Yakun

last: Wu

first: Nicolas

last: Auerbach

first: Jürgen

last: Groher

first: Daniela

last: Kruck

first: Stefan

last: Koplitz-Weißgerber

first: Christian

last: Gruner

first: Andreas

last: Scharr

first: Verena

last: Mehlfeld

first: Martin

last: Biel

last: Wahl-Schott


title: CAGE transcription start site mapping in Hydra viridissima

city: Baltimore

first: Alex

last: Bortvin

state: MD

address: 3520 San Martin Dr

department: Embryology

institute: Carnegie Institution

summary: Cap Analysis of Gene Expression (CAGE) in aposymbiotic and green/symbiotic Hydra viridissima clone 2 to map transcription start sites at single-nucleotide resolution. 19,892 TSS clusters were shared between conditions.

overall_design: Two conditions (aposymbiotic and green/symbiotic), one sample each, paired-end Illumina sequencing.

first: Alexander

last: Gimelbrant


title: Intestinal Villus-on-Chip with Dynamic Magnetic Actuation for Identifying EGR1 as IBD Therapeutic Target

city: Chongqing

first: longli

last: peng

address: kaizhou

institute: Chongqing University

summary: The pathogenesis of inflammatory bowel disease (IBD) is closely related to the mechanical microenvironment of the intestine, but existing in vitro models lack the key physiological feature of dynamic intestinal villus oscillation. Here, a magnetic intestinal villus chip (IVC) was constructed using a dual-channel microfluidic structure and embedded with biomimetic intestinal villi (BioVilli) membranes. The magnetically driven BioVilli replicated physiological villus oscillation (8 - 10°, 0.15 Hz), while controllable fluid perfusion applied physiological fluid shear stress at the intestinal vascular interface. This platform uniquely integrated structural fidelity, rhythmic mechanical actuation, and multicellular interactions into a single system. We found that through the IVC system, mechanical signals mediated by FOXO1 could enhance barrier integrity, absorption function, and epithelial cell proliferation. Under inflammatory stimulation, by replicating pathological villus oscillation (>12°, 0.15 Hz), the IVC system realistically reproduced the characteristics of IBD, revealing that the imbalance of EGR1 caused by inflammatory stress is a key factor in the pathogenesis of IBD. Spatial transcriptomic analysis of clinical IBD tissues confirmed that the downregulation of EGR1 expression is associated with metabolic dysregulation and barrier dysfunction, and pharmacological inhibition of EGR1 can alleviate inflammation and promote barrier repair, thereby establishing it as a promising therapeutic target. This work sets a new benchmark for intestinal chip technology and opens up new avenues for mechanism-based drug discovery for IBD.

overall_design: RNA-seq profiling of Caco-2 cells from NOS, VOS, and IBD-VOS groups (with 4 biological replicates per group). All samples were performed on Illumina high-throughput RNA sequencing.

first: Shun

last: Yao

first: Wang

first: Tian

last: Tian

first: Gaoxing

last: Luo

first: Jun

last: Deng


title: ATAC-seq chromatin accessibility profiling in Hydra viridissima

type: Genome binding/occupancy profiling by high throughput sequencing

summary: ATAC-seq in aposymbiotic and green/symbiotic Hydra viridissima clone 2 to map open chromatin regions. Four samples (two conditions x two biological replicates) were sequenced on Illumina NextSeq, aligned with Bowtie2, and peaks called with MACS3.

overall_design: Two conditions (aposymbiotic and green/symbiotic), two biological replicates each, paired-end Illumina 2x50 bp sequencing.


title: Total RNA-seq of aposymbiotic and symbiotic Hydra viridissima

summary: Total RNA sequencing of aposymbiotic (algae-free) and green/symbiotic Hydra viridissima clone 2 to characterize gene expression differences between symbiotic states. Paired-end reads were trimmed with fastp, aligned to Carnegie v1 (JBWVZK000000000) with STAR, and quantified with featureCounts using BRAKER3 gene annotations.


title: Metabolic inhibition of glutamate-cysteine ligase increases dendritic cell-mediated anti-tumor immunity in melanoma

city: Innsbruck

first: Patrizia

last: Stoitzner

address: Anichstraße 35

department: Department of Dermatology, Venereology and Allergology

country: Austria

institute: Medical University of Innsbruck

summary: Metabolic competition and nutrient restriction in the tumor microenvironment (TME) shape the immune infiltrate in tumors and subsequently tumor immunity. In this study we used the transgenic melanoma mouse model tg(Grm1)EPv, which spontaneously develops melanoma due to the ectopic expression of the metabotropic glutamate receptor 1 (Grm1) in melanocytes to investigate if aberrant glutamate metabolism drives tumor formation, and affects immune cell function.  LC-MS/MS-based metabolomic analyses and RNA sequencing revealed changes in glutaminolysis, a glycolytic shift (Warburg effect), and reduced ATP levels in advanced tumors compared with tumor free tissue, suggesting respiratory chain dysfunction. These metabolic changes in the TME are advantageous for the tumor cells and unfavorable for immune cells, such as dendritic cells (DC). Indeed, flow cytometry analysis of myeloid subsets during tumor progression showed a decline in tumor-infiltrating conventional type 2 dendritic cell (cDC2) and macrophages, alongside an increase in neutrophil and monocyte populations in advanced lesions. Interference with glutaminolysis using L-buthionine sulfoximine (BSO), an inhibitor of the glutamylcysteine synthetase depleting cellular glutathione levels, induced immunogenic cell death, namely ferroptosis, in an tg(Grm1)EPv -derived cell line in vitro. Therefore, we evaluated the combination of this inhibitor with immunotherapy as a promising new approach for the treatment of tumors in the tg(Grm1)EPv mouse model. We observed that tumor growth could be delayed in vivo when BSO was combined with a therapy regimen boosting DC numbers and activation. This knowledge can drive the design of novel therapeutic strategies for cancer patients involving potential modification of tumor glutamate metabolism.

overall_design: RNA-seq profiling of early-stage melanoma and skin and infiltrating immune cells of the tg(Grm1)Epv mouse strain after treatment with control (PBS), BSO, DC boost or BSO DC boost combination treatment

first: Sophie

last: Dieckmann

first: Irene

last: Rigato

first: Francesca

last: Finotello


title: Indole-3-acetic acid alleviates palmitic acid-induced lipid accumulation and endoplasmic reticulum stress via sirtuin 3 in primary bovine hepatocytes

city: Changchun

first: Qi

last: Dandan

address: 吉林省长春市绿园区新竹路1977号吉林大学动物医学学院

institute: JILIN UNIVERSITY

summary: Ketotic cows experience severe negative energy balance, in which an increase in circulating non-esterified fatty acids (NEFA), particularly palmitic acid (PA), is a primary cause of liver damage. Although reports indicate that the endogenous tryptophan metabolite indole-3-acetic acid (3-IAA) can protect the liver of non-ruminant animals, its role in mitigating lipotoxicity-induced damage to bovine hepatocytes remains unclear. In this study, ketotic cows showed higher serum β-hydroxybutyrate and NEFA, lower 3-IAA and glucose concentrations, and increased hepatic triacylglycerol (TG) content, which was negatively correlated with serum 3-IAA. In primary bovine hepatocytes, treatment with 200 μmol/L 3-IAA improved cell viability, reduced cytotoxicity, and alleviated PA-induced lipid metabolic disorders and endoplasmic reticulum stress (ERS). RNA sequencing indicated that 3-IAA regulated pathways related to lipid metabolism and ERS. Mechanistically, 3-IAA attenuated PA-induced lipid accumulation, downregulated sterol regulatory element-binding protein 1 (SREBP-1) protein and acetyl-CoA carboxylase α (ACACA) or fatty acid synthase (FASN) mRNA, and concurrently increased peroxisome proliferator-activated receptor α (PPARα) and carnitine palmitoyltransferase 1A (CPT1A) protein abundance and CPT1A mRNA, suggesting reduced lipogenesis and enhanced fatty acid oxidation. In parallel, 3-IAA alleviated ER swelling and suppressed ERS at both the protein and gene levels by reducing the protein abundance of phosphorylated protein kinase R-like endoplasmic reticulum kinase (P-PERK), phosphorylated inositol-requiring enzyme 1α (P-IRE1α), and cleaved activating transcription factor 6 (ATF6) with gene expression of glucose-regulated protein 78 (GRP78), CCAAT/enhancer-binding protein homologous protein (CHOP), and spliced X-box binding protein 1 (sXBP1). Notably, 3-IAA increased sirtuin 3 (SIRT3) mRNA and protein expression in PA-treated hepatocytes, whereas SIRT3 knockdown partially abolished its protective effects. Collectively, these findings indicate that 3-IAA mitigates PA-induced lipid accumulation and ERS via a SIRT3-dependent pathway in bovine hepatocytes, and suggest that 3-IAA may act as an endogenous regulator of hepatic homeostasis in ketotic cows.

overall_design: RNA sequencing was used to assess the effects of 3-IAA on PA-induced lipotoxicity in bovine hepatocytes isolated from fasted, healthy 1-day-old female calves.

first: Dandan

last: Qi

first: Chenchen

last: Zhao

first: Guiying

last: Li

first: Jinxia

first: Menglin

last: Liu

first: Fanrong

last: Kong

first: Enzhu

first: Jie

last: Gao

first: Wenqi

last: Liao

first: Akos

last: Kenez

first: Wenwen

first: Yuxiang

last: Song

first: Xiliang

last: Du

first: Guowen

first: Xinwei

first: Lin

last: Lei


title: Linking molecular responses to organismal outcomes under complex contaminant stress: a systems biology approach for predictive ecotoxicology

city: Cologne

first: Philipp

last: Antczak

address: Robert-Koch-Strasse 21

department: Center for Molecular Medicine Cologne

institute: University Hospital Cologne

summary: Ecological risk assessments have traditionally relied on simplified models that expose single species to individual chemicals under controlled laboratory conditions. However, real-world ecosystems are subject to multiple, interacting stressors, particularly from anthropogenic sources, that challenge the predictive power of these conventional approaches. To address this gap, we investigated the effects of coal ash, a complex mixture of heavy metals, on the freshwater invertebrate Daphnia magna. We quantified both suborganismal (transcriptomic) and individual-level (survival, growth, reproduction) responses to coal ash exposure. These data were integrated into a Dynamic Energy Budget (DEB) model to simulate physiological modes of action (pMoAs). Using machine learning, we identified gene sets predictive of DEB state variables and prioritized differentially expressed genes to determine the most plausible bioenergetic disruption. This study demonstrates a scalable framework for linking molecular perturbations to organismal outcomes, offering a mechanistic basis for assessing the ecological impact of complex chemical mixtures. Our approach advances predictive ecotoxicology by moving beyond chemical-specific assays toward integrative, systems-level models that better reflect environmental realities.

overall_design: RNAseq of whole Daphnia magna individuals exposed to coal ash across multiple timepoints and concentrations.

first: Louise

last: Stevenson

first: Andre

last: Gergs

first: Lea

last: Rahlfes

first: Ferdinand

last: Pfab

first: Paul

last: Pickhardt

first: Teresa

last: Mathews

first: Natalia

last: Garcia-Reyero

first: Cheryl

last: Murphy

first: Roger

last: Nisbet


title: Single-cell transcriptomic analysis of SP11-treated MOLT4 cell line and untreated control.

city: Bengaluru

first: Bibha

last: Choudhary

state: Karnataka

address: Biotech Park, GN Ramachandran Rd, Electronics City Phase 1, Electronic City,

country: India

institute: Institute of Bioinformatics and Applied Biotechnology

summary: We used single-cell RNA sequencing with the 10x Genomics platform to study the effect of SP11 treatment in a MOLT4. The goal was to examine tumor heterogeneity, identify potential treatment-resistant cell populations, and assess changes in the intercellular communication. This dataset provides an overview of how SP11 impacts tumor biology at single-cell resolution.

overall_design: MOLT4 cells  were treated with the SP11 at 0.8µM concentration, along with untreated controls. Cells were collected after 48h and processed for single-cell RNA sequencing using the 10x Genomics platform.

first: Shahana

last: MV

first: Yash

last: Chindarkar


title: Comparative transcriptomic points of departure analysis of pesticides in human Caco-2 and Hep G2 cells.

city: Sainte-Anne-de-Bellevue

first: Niladri

last: Basu

state: Quebec

address: 21,1111 Lakeshore Blvd, Apt #2

country: Canada

institute: McGill University

summary: Transcriptomic data capture early molecular perturbations and can be used to derive transcriptomic points of departure (tPODs) as potential alternatives to apical points of departure (PODs) from animal studies. This study aimed to derive tPODs for 19 pesticides of environmental concern using two human cell lines relevant to oral exposure, Caco-2 and Hep G2, and to compare the results with in vivo toxicity data and regulatory thresholds. tPODs were successfully obtained for all pesticides, ranging from 0.032 to 880 µM. Pathway analysis indicated more stress-related responses in Caco-2 cells, whereas more metabolic pathways were identified in Hep G2 cells. Following mass balance modeling and in vitro-in vivo extrapolation, tPODs were converted to human administered equivalent doses (t-AEDs). In Hep G2 cells, approximately 70% of t-AEDs were within one order of magnitude of corresponding PODs from chronic animal studies, suggesting moderate concordance. Transcriptomic reference values (t-TRVs) were derived from t-AEDs to compare with regulatory thresholds. Although correlations were weak, the overall trends suggest that short-term in vitro tPODs may provide conservative estimates relative to apical endpoints. Overall, this workflow demonstrates the potential of in vitro transcriptomics to generate quantitative and mechanistic data to support chemical screening and prioritization in risk assessment.

overall_design: Caco-2 and Hep G2 cell lines were exposed to 19 pesticides at various concentrations to investigate cytotoxicity and transcriptomics effects.

first: Ke

last: Xu

first: Krittika

last: Mittal


title: Knockdown of C3 in HDF cells

city: Kuning

first: Runzi

last: Zheng

state: Yunnan

address: No. 727, Jingming South Road, Chenggong District

institute: Kunming University of Science and Technology

summary: Knockdown of C3 in senescent cells to see if it can cause changes in the senescent cells

overall_design: HDF cells were added with transfection reagent. In addition, C3 siRNA was added to the HDF cells. Using ionizing radiation to induce HDF aging was referred to as IR-HDF. IR-HDF was then added with the transfection reagent, and the transfection reagent and C3 siRNA were added to the IR-HDF cells.

first: Yonghan

last: He

first: Jing

last: Liu


title: A polyphenol-rich extract recovered from an industrial byproduct regulates the intestinal microbiota and restricts enteric parasite infection

city: Frederiksberg C

first: Andrew

last: Williams

address: Dyrlægevej 100

country: Denmark

institute: University of Copenhagen

summary: Dietary polyphenols have shown potential in limiting inflammation during noncommunicable diseases. However, interaction of polyphenols with the immune system and gut microbiome during enteric infections are not well defined. Moreover, efficient methods to recover high-value polyphenols from industrial processes are limited. Here, we describe the recovery of a polyphenol-rich extract from a byproduct of protein-producing biorefineries. The extract was modified to allow incorporation into a semi-synthetic mouse diet. During infection with the intestinal nematode Heligmosomoides polygyrus, mice fed the polyphenol-enriched diet had significantly lower parasite burdens and enhanced mast cell–related gene expression in the jejunum, potentially accelerating worm expulsion. Effects on the gut microbiome were dependent on infection status. In uninfected animals, the extract significantly reshaped the gut microbiome by expanding a broad range of short-chain fatty acid (SCFA)-producing bacteria. However, during H. polygyrus infection, its modulatory effect on the microbiome was markedly diminished concomitant with an extensive increase in the abundance of the Lactobacillaceae and Enterobacteriaceae families in infected mice. However, the extract reduced the relative abundance of Clostridiaceae during infection, suggesting a role in restoring gut homeostasis by counteracting parasite-induced expansion of potentially pathogenic bacteria. Collectively, these findings demonstrate that byproducts from the biorefining industry can be repurposed as functional food components with the potential to limit enteric infection and inflammation.

overall_design: Six-week-old C57BL/6 JOlaHsd female mice (n = 36; Envigo) were housed in ventilated cages. Upon arrival, the mice were evenly divided into four groups in a 2 x 2 study design to receive either an ad libitum control SSD diet or a clover diet, with or without H.polygyrus infection. Each group contained three cages, with three animals per cage. All animals were provided with their respective diets upon arrival and were infected with approximately 300 H. polygyrus L3 larvae via oral gavage after an 11-day acclimatization period. Mouse weights were measured upon arrival and 14-days post infection (Supplementary Figure S2). Mice were euthanized by terminal dislocation at 15 days post infection.


title: Toward More Translational Tumor Models: Breast dECM-Based 3D Systems Capture Native Microenvironmental Cues

city: New Orleans

first: Elizabeth

middle: Carol

last: Martin

state: LA

address: 1430 Tulane Avenue

department: Medicine

institute: Tulane University

summary: Current 3D tumor models for aggressive breast cancers inadequately recapitulate the native tumor microenvironment (TME), leading to poor translational potential. There is a critical need for models capable of mimicking the unique biochemical signals present in the TME. To address this gap, breast tissue and a patient derived xenograft tumor were decellularized and processed to produce breast tissue and tumor decellularized ECM (dECM). Decellularized breast tissue histology confirmed complete cellular removal and maintained extracellular matrix (ECM). Further, DNA content was significantly reduced and ECM composition (POSTN, COLI, FN1) retained. Breast dECM was incorporated (0, 5, 10, and 20 µg/mL) with triple negative breast cancer cell lines to form spheroids. Imaging and histology demonstrated that cells in low dECM (5 and 10 µg/mL) formed compact singular spheres while higher dECM concentrations (20 and 50 µg/mL) resulted in cells concentrated on the outer edge of the sphere and irregular sphere circularity. RNA-sequencing of cells seeded in dECM demonstrated gene changes mediated by both dECM inclusion in spheroids and the composition of dECM. High-density tumor dECM enhanced genes associated with metastasis while high-density breast dECM enhanced tumor suppressors and anti-metastasis genes. These findings indicate dECM as a translational model with enhanced TME inclusion.

overall_design: 2.4 million MDA-MB-231 cells were mixed with no dECM, 10 μg/mL of breast adipose dECM, 20 μg/mL of breast adipose dECM, 10 μg/mL of Tu-BcX-4IC PDX tumor dECM, or 20 μg/mL of Tu-BcX-4IC PDX tumor dECM. The cells mixed with the dECM were then seeded in an AggreWell 400 24 well plate (Stem Cell Technologies, Vancouver, BC, Canada) that was prepped with Anti-Adherence solution (Stem Cell Technologies, Vancouver, BC, Canada) in accordance with the manufacturer’s protocol and grown overnight to form 1200 3D spheroids containing about 2000 cells. After 4 days of culture, spheroids were pelleted for  total RNA using Quick RNA Miniprep Kit (Zymo Research, Irvine, California) according to the manufacturer’s protocol. RNA samples were shipped on dry ice to Plasmidsaurus (Louisville, KY, USA) for RNA sequencing.

first: Jorge

last: Belgodere

first: Katherine

last: Hebert

first: Matthew

last: Burow


title: YKL-40 alleviates the TNF-α-Induced chondrocyte injury in osteoarthritis in vitro

city: weifang

first: Zhuozheng

last: Li

state: shandong

address: 7166 Baotong West Street

institute: shandong second medical university

summary: Background: Osteoarthritis (OA) is a degenerative joint disease with high global prevalence, and YKL-40 is an important factor related to the pathological process of OA. Increased levels of YKL-40 exert a protective influence against TNF-α-induced apoptosis in chondrocytes, thereby enhancing chondrocyte survival and activation, while counteracting TNF-α-driven expression of specific inflammatory mediators such as S100A8/A9.This study aims to evaluate the role and molecular mechanism of YKL-40 on chondrocytes in OA and provide a potential therapeutic avenue requiring further validation. Materials and methods: A meta-analysis compared serum YKL-40 and TNF-α levels between OA patients and healthy controls. In vitro experiments examined the effects of YKL-40 on TNF-α-induced OA chondrocytes, assessing proliferation, differentiation, apoptosis, and inflammatory pathways. Results: Meta-analysis revealed significantly elevated serum levels of YKL-40 and TNF-α in osteoarthritis (OA) patients compared to healthy controls. In vitro, TNF-α (10 ng/mL) induced extracellular matrix (ECM) degradation in chondrocytes, significantly reducing glycosaminoglycan (GAG) and type II collagen content. This degradation was effectively rescued by YKL-40 (100 ng/mL). RNA sequencing identified differentially expressed  genes in TNF-α-treated chondrocytes, enriched in pathways like IL-17 and NF-κB signaling. YKL-40 treatment reversed the expression of key genes altered by TNF-α. Crucially, these differentially expressed genes (including S100A8/A9, ISG15, CDSN, BAAT, PTPN4, NPTX1, SMARCA1) were validated in independent OA cartilage and synovium GEO datasets. Protein-protein interaction (PPI) networks highlighted central genes within treatment groups. Western blotting confirmed YKL-40 counteracted TNF-α-induced NF-κB pathway activation (reduced p65 and IκBα phosphorylation) and modulated key targets (S100A8/A9, ASB7, ZFPM2), consistent with qRT-PCR data. Conclusion: YKL-40 is a promising biomarker and therapeutic target for OA. Its interplay with TNF-α provides a molecular basis for novel therapies targeting chondrocyte dysfunction, guiding future translational research.

overall_design:
Eight sexually mature male New Zealand White rabbits (Jinan Pengyue Experimental Animal Breeding Co., Ltd.) aged 3-4 months (weighing approximately 4.5-5.5 kg) were selected for chondrocyte isolation in this experiment. The experimental rabbits were euthanized by excessive carbon dioxide (CO₂) inhalation. Briefly, rabbits were euthanized via CO₂ inhalation in accordance with AVMA guidelines . Animals were placed in a transparent euthanasia chamber prefilled with 70–80% CO₂. This study strictly followed this standard, delivering at a flow rate of 30-40% of the chamber volume per minute to ensure rapid coma . Continuous exposure for 5 minutes to confirm death. And by checking if breathing has completely stopped. Verify the absence of vital signs by auscultating cardiac activity and evaluating corneal reflexes. Instant confirmation of death. This protocol minimizes animal distress while preserving scientific rigor in accordance with AVMA guidelines. The lower limbs were dissected and the rabbit's knee joints were collected. The knee joints were washed several times in sterile PBS to remove most of the blood and lint, and then the tissues were immersed in 75% alcohol for 10 min. After disinfection was completed, the knee joint tissues were transferred into an ultra-clean table. The hyaline cartilage on the surface of the joint was scraped off with a sterile blade, and the scraped cartilage was soaked in PBS to keep it moist, and the cartilage tissue was cut with sterile tissue scissors (the tissue fragments were less than 1 mm3), and the tissue fragments were processed with type II collagenase, and the digesting time was more than 2 h, which could be changed according to the digestion of the tissues. Primary chondrocytes were obtained by centrifugation, and were maintained in DMEM/F12 supplemented with 10% FBS and 1% penicillin/streptomycin at 37°C under 5% CO₂. The articular chondrocytes extracted from each experimental rabbit were cultured in 25 cm² flasks and subsequently passage into 6-well plates at a density of 2×105 cells/cm² for experiments. Chondrocytes under study were categorized into four groups: 1) Control Group: normal chondrocytes (Group C), 2) TNF-α Group: TNF-α-induced osteoarthritic cells (10 ng/mL, 24 h, Group T), 3) YKL-40 Group: normal chondrocytes treated with YKL-40 (100 ng/mL, 24 h, Group Y), and 4) Therapeutic Intervention Group:  Cells pre-treated with TNF-α (10 ng/mL, 24 h) followed by YKL-40 (100 ng/mL, 24 h) (Group Y-T).

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first: zhuozheng

last: li

first: yun

last: sun

first: yongfang

last: xie

first: Zexin

last: Hong

first: Zemin

last: Dou

first: Tingting

last: Feng

first: Guohui

last: Wang


title: Galectin-1 Fuels Monocyte-Driven Hyperinflammation and Represents a Novel Therapeutic Target in Myeloproliferative Neoplasms [scRNA-Seq]

city: Saint Louis

first: Stephen

last: Oh

state: MO

address: Room 8834, 320 S. Euclid Ave, CSRB building

institute: Washington University School of Medicine in St. Louis

summary: Here, we performed a single-cell RNA sequencing analysis using primary bone marrow mononuclear cell (BMMC) samples from essential thrombocythemia (ET) and healthy individuals (HI).

overall_design: CD34+ and CD14+ cells were sequentially isolated from the same individual utilizing Miltenyi magnetic beads. Positive selection was performed according to the manufacturer's protocol. The isolated cell populations were subsequently counted and mixed to generate a controlled, heterogeneous sample for single-cell RNA sequencing.

first: Fan

last: Di Paola


title: Single-cell transcriptomic analysis of SP11-treated DLA lymphoma mouse model

first: Bibha

last: Choudhary

summary: We used single-cell RNA sequencing with the 10x Genomics platform to study the effect of SP11 treatment in a DLA lymphoma mouse model. The goal was to examine tumor heterogeneity, identify potential treatment-resistant cell populations, and assess changes in the tumor microenvironment and immune cell infiltration. This dataset provides an overview of how SP11 impacts tumor biology at single-cell resolution.

overall_design: A DLA lymphoma mouse model was established by tumor cell transplantation. Mice were treated with the SP11 drug, along with untreated controls. Tumor tissues were collected after treatment and processed for single-cell RNA sequencing using the 10x Genomics platform.

first: Shahana

last: MV

first: Yash

last: Chindarkar


title: Galectin-1 Fuels Monocyte-Driven Hyperinflammation and Represents a Novel Therapeutic Target in Myeloproliferative Neoplasms [RNA-Seq]

summary: To investigate the effects of galectin-1 on monocyte gene expression, magnetic bead-enriched CD14+ human monocytes from MPN patients ( n = 5) were incubated with vehicle or recombinant Galectin-1 (5 μg/mL) for 7 hours. Cell pellets were collected for RNA-seq analysis.

overall_design: Gene expression profiling analysis of human primary monocytes

last: He


title: USP22 Suppresses Trophoblast Cell Necroptosis in Preeclampsia by Stabilizing KAT2A-Mediated Histone Acetylation at the SFRP1 Promoter

city: Fuzhou

first: dan

middle: li

last: he

address: College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian  Medical University, Fuzhou 350122, Fujian, China

institute: Fujian  Medical University

summary: This study investigates the role of USP22 in trophoblast necroptosis and preeclampsia (PE). USP22 expression was significantly downregulated in PE placental tissues, accompanied by elevated necroptosis markers RIPK1, RIPK3, and MLKL. A hypoxic HTR-8/SVneo trophoblast cell model recapitulated the PE microenvironment, where necroptosis was confirmed as the dominant death modality. USP22 knockdown exacerbated necroptotic signaling, while USP22 overexpression restored H3K9ac and H3K27ac levels and suppressed necroptosis. RNA-seq identified 1,186 differentially expressed genes upon USP22 knockdown, including marked repression of the Wnt antagonist SFRP1. Mechanistically, USP22 directly interacted with KAT2A and stabilized it via selective removal of K48-linked polyubiquitin chains, sustaining KAT2A-dependent histone acetylation at the SFRP1 promoter to maintain SFRP1 transcription. SFRP1 restoration in USP22-deficient trophoblasts reduced cell death and decreased p-MLKL/MLKL ratio. The L-NAME rat PE model confirmed coordinated downregulation of USP22, KAT2A, SFRP1, and histone acetylation in vivo.

overall_design: Hypoxic HTR-8/SVneo trophoblast cells were used as a preeclampsia (PE) model. Two groups were compared: control vector transfection (Control, n=6) and USP22 knockdown (USP22_KD, n=6) under hypoxia (1% O2, 5% CO2, 94% N2, 48h).

first: Lidan

last: HE

first: Feng

last: ZHAN

first: Shan

last: ZHENG

last: LIN


title: YAP Promotes Microtubule Growth to Facilitate Sarcomere Disassembly in Adult Cardiomyocytes

city: CINCINNATI

first: Shijie

last: Zhang

state: OH

address: 3333 Burnet Ave, T4.325

department: Heart institute

institute: Cincinnati Children's hospital medical center

summary: BACKGROUND: Mature mammalian cardiomyocytes (CMs) develop compact sarcomeric structures that inhibit proliferation. Consequently, CMs must dedifferentiate to a fetal-like state, which is accompanied by sarcomere disassembly, to enable successful cytokinesis. However, the regulation and coordination of CM dedifferentiation, cell cycle progression, and sarcomere reorganization remain unclear. METHODS: We generated adenovirus and adeno-associated virus (MyoAAV) vectors expressing YAP5SA and YAP5SA-S94A under Xon control for LMI070-inducible protein expression. We also developed MyoAAV-cTnT-Tuba1b-shRNA-miR30 for cardiomyocyte-specific knockdown (KD) of Tuba1b. These tools were used to investigated cardiomyocyte dedifferentiation, proliferation, and sarcomere disassembly. We also performed Cleavage Under Targets and Release Using Nuclease (CUT&RUN) to map the genome-wide binding sites of YAP5SA and YAP5SA-S94A, in combination with RNA sequencing to identify YAP target genes. In addition, time-course live-imaging analysis was used to evaluate microtubule and sarcomere dynamics in adult cardiomyocytes. RESULTS: We show that microtubule expression and network density decline with cardiac maturation. Overexpression of YAP5SA, a constitutively active YAP mutant, promotes microtubule growth by stabilizing the microtubule dynamics, leading to CM dedifferentiation, cell cycle re-entry and sarcomere disassembly. In contrast, colchicine blocks these processes and significantly attenuates YAP-induced cardiac regeneration. Live imaging reveals a distinct mode of sarcomere disassembly driven by enhanced microtubule polymerization, where microtubule plus-ends directly interact with α-actinin and displace α-actinin fragments, thereby facilitating sarcomere breakdown. Furthermore, the YAP-S94A mutation, which disrupts the YAP and TEAD interaction, significantly reduces YAP5SA-induced microtubule growth, sarcomere disassembly, and cell cycle activity. Mechanistically, CUT&RUN combined with RNA-seq identified direct YAP targets, including Ajuba and Tuba1b, which are critical for microtubule growth. CM-specific KD of Tuba1b attenuates YAP-driven sarcomere disassembly. CONCLUSIONS: These findings identify microtubule networks as an essential regulator modulating CM dedifferentiation and sarcomere reorganization, which is critical for CM cytokinesis and cardiac regenerative repair.

overall_design: RNA-seq profileing of neonatal rat cardiomyocytes wirh YAP5SA and YAP5SA-S94A overexpression. CUT&RUN of YAP from neonatal rat cardiomyocyte with overexpressing of GFP, YAP5SA and YAP5AP-S94A. Two different YAP antibodies were used.

first: Zhiyuan

last: Chen

last: Liu


title: RNA sequencing data of Drosophila melanogaster intestinal stem cells across different age groups, with overexpression of E374A (ADAR mutant) and knockdown of Zn72d and ADAR

city: Chengdu

first: Qian

address: No. 37 Guoxue Lane, Wuhou District, Chengdu, Sichuan Province, China

institute: Sichuan University

summary: Maintaining tissue homeostasis necessitates the presence of stem cells capable of self-renewal and differentiation. However, stem cell functionality is known to deteriorate with age, although the precise mechanisms involved remain elusive. In this study, we reveal that adenosine deaminase acting on RNA (ADAR) curbs intestinal stem cell (ISC) proliferation via an RNA editing mechanism during gut regeneration and aging in Drosophila, mice, and humans. Notably, the absence of ADAR in Drosophila ISCs elicits an elevation in Insulin-MAPK signaling activities, ultimately resulting in ISC over-proliferation. Our further findings reveal that this ADAR activity is mediated by zinc-finger protein at 72D (Zn72D), an RNA-binding protein known to govern ADAR editing in vivo. This investigation provides valuable insights into the role of ADAR-mediated editing in the regulation of stem cell function during tissue regeneration and aging. Moreover, it underscores the importance of appropriate editing regulation in delaying the onset of natural aging processes.

overall_design: RNA-seq of Drosophila intestinal stem cell enterocytes from young and aged flies, with midgut-specific overexpression of ADAR(E374A) and RNAi-mediated knockdown of Zn72d and ADAR


title: Protein landscape of the chromatin domains in the malaria parasite Plasmodium falciparum

city: Nijmegen

first: Martijn

middle: van den

last: Broek

address: Geert Grooteplein 24, route 846

department: Molecular Biology

country: Netherlands

institute: Radboud university - RIMLS Science

summary: Epigenetic regulation is essential for development and adaptation across eukaryotes. However, a comprehensive overview of the molecular framework of chromatin-mediated regulation, particularly in non-model organisms, is lacking. Here, we present a systematic proteomic characterization of the chromatin domains in P. falciparum, an ancient human pathogen with unique genome composition and epigenetic blueprint. We adapted and systematically employed three proximity-labelling approaches to provide a high-confidence and comprehensive proteome of heterochromatin, euchromatin and (peri)centromeric chromatin comprised of 214 proteins, including both expected and new chromatin components. Characterization of 20 proteins validated our approach and i) uncovered a protein influencing parasite transmission, ii) defined complexes relevant for histone variant exchange and chromatin-RNA interactions and iii) provided evidence for the so far believed to be absent spindle assembly checkpoint and the corresponding Bub1-like kinase. This study hence offers a reference proteome of the chromatin domains and a resource to uncover novel chromatin biology.

overall_design: This experiment was used to evaluate the effects of mislocalization of centrosome interacting candidate 4 (CIC4), which was identified in this study. Using single-cell RNA sequencing control parasites were compared to parasites with mislocalized (KS) CIC4. Changes in transcriptomic profile were investigated and changes in chromosome presence, determined by counting the number of genes expressed from a chromosome per parasite.

first: Gala

last: Ramón Zamorano

first: Sheila

last: Mainye

first: Jessica

last: Kimmel

first: Inge

last: de Krijger

first: Abhishek

last: Kanyal

first: Vendula

last: Horáčková

first: Jonas

last: Gockel

last: van den Broek

first: Yangyang

last: Guo

first: Michaela

last: Petter

first: Max

last: Graser

first: Andrés

last: Guillén Samander

first: Michiel

last: Vermeulen

first: Tobias

last: Spielmann

first: Richárd

last: Bártfai


title: Exercise training does not mitigate high-phosphate diet induced mitochondrial dysfunction in skeletal muscle

city: Columbus

first: Kedryn

last: Baskin

address: 460 W 12th Ave

department: Physiology and Cell Biology

institute: The Ohio State University

summary: Inorganic phosphate (Pi) consumption is two-to-three-fold higher than the recommended daily allowance for adults due to its use as a preservative and flavor enhancer in processed foods. We reported previously that mice fed high-Pi diet (HPD) for 12 weeks exhibited reduced VO2max, altered metabolic gene expression, and mitochondrial dysfunction in skeletal muscle. Exercise is a common intervention for metabolic diseases as it improves metabolic flexibility and mitochondrial function, so we tested the hypothesis that exercise training reverses the negative consequences of HPD. Male mice were fed HPD for five weeks to induce muscle mitochondrial dysfunction and were subsequently subjected to HPD and voluntary exercise training for nine weeks. Serum, urine, and fecal Pi were increased within one day of HPD feeding which was sustained throughout the study. No differences in food intake, body weight, or body composition were detected between NPD- and HPD-fed mice, in either sedentary or exercised trained groups. Trained HPD- and NPD-fed mice performed similarly in forced exercise tests, but mitochondrial respiration was significantly decreased in skeletal muscle from trained HPD-fed mice. RNA sequencing revealed unique differentially expressed genes in HPD-fed sedentary versus exercise trained, compared to NPD-fed sedentary versus exercise trained muscle. These data indicate that voluntary exercise training restores exercise capacity of HPD-fed mice but does not completely restore muscle gene expression or mitochondrial function. Thus, HPD-induced skeletal muscle dysregulation is not fully reversible with exercise and highlights the importance of considering both healthy diet and exercise as part of a healthy lifestyle.

overall_design:
Bulk RNA-seq profiling of 40-week old male mouse gastroc plantaris whole muscle. Dietary and voluntary exercise interventions were used, with a 14 week high phosphate diet and 9 week wheel cage running protcol. Data has been compared to previously published high phosphate sedentary mouse sequencing data of the same design. Previously published normal and high phospate diet sedentary mouse RNA-Sequencing data was sourced from GSE120958 and reanalyzed to ensure consistency between software versions and genome builds.

***************************************************************
The table below lists GEO accessions reused/reanalyzed for this study.
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title: Blood-circulating memory-phenotype CD4+ T cells rapidly accumulate in ischemic organs to exacerbate tissue injury in an innate manner: Gene expression in ischemic intestinal tissue

city: Sendai

first: Kosuke

last: Sato

state: Miyagi

address: 2-1 Seiryo-machi, Aoba-ku

institute: Tohoku University

summary: Memory-phenotype (MP) CD4+ T lymphocytes develop from peripheral naïve precursors via self-recognition at homeostasis. While previous studies revealed their innate immune function in infectious and autoimmune contexts, functional significance of MP cells in ischemia remains unclear. Ischemia-reperfusion injury (IRI) is induced by acute occlusion of organ-feeding arteries and subsequent reperfusion where innate immunity plays an important role. Here we show that blood-circulating MP lymphocytes rapidly infiltrate to the gut in the absence of antigen recognition during intestinal IRI. This MP migration is directed by α4β7 that binds to vascular MAdCAM-1, with the latter expression immediately upregulated by ischemia-induced TNF-α. Moreover, gut-accumulating MP cells respond to IL-12 to produce IFN-γ in an innate manner to orchestrate neutrophils, thereby exacerbating tissue injury. Furthermore, such innate MP responses are operative in hepatic IRI as well. Together our results reveal an essential innate function of blood-circulating MP CD4+ T lymphocytes that rapidly accumulate in ischemic organs to contribute to pathogenesis of IRI.

overall_design: Ischemia was induced in the small intestine of C57BL/6 mice by clamping the superior mesenteric artery (SMA) for 45 minutes with a microvascular clamp, followed by removal of the clamp to allow reperfusion. Small intestinal lamina propria cells were obtained at 6 h post reperfusion (IRI-6h). The sham surgical procedure was performed using the same method as described above, except for clamping of the SMA (Sham-6h). The lamina propria cells were further enriched for live CD11b- cells by using Dead Cell Removal Kit and CD11b Microbeads (Miltenyi Biotec). The cells were then fixed for 19 hours at 4 °C with Chromium Next GEM Single Cell Fixed RNA Sample Preparation Kit (10x Genomics), and analyzed by single-cell RNA sequencing. Live CD11b- cells were pooled from 3 mice per each group. Data of purified CD4+ cells are available in GSE284458.

first: Takeshi

last: Kawabe


title: 4-1BBL signaling aids B cell activation but limits proliferation during experimental malaria

city: NORTH CHICAGO

first: Rahul

last: Vijay

address: 3333 GreenBay Road, BSB 2.450

department: Microbiology and Immunology

institute: Rosalind Franklin University

summary: Several costimulatory and coinhibitory signaling axis have been reported to modulate anti-Plasmodium immune response, albeit the precise role of 4-1BB:4-1BBL axis has yet to be investigated. Here, we show that while complete loss of 4-1BB resulted in heightened parasite burden, impaired germinal center (GC) responses and memory B cell (MBC) recall. The absence of 4-1BBL however, minimally affected parasite load or GC responses, while disrupting humoral immune memory. Strikingly, therapeutic blockade of 4-1BBL early during infection derailed both humoral effector and memory response phenocopying 4-1BB-/- data, an effect that was absent when 4-1BBL was blocked at effector timepoints. Importantly, 4-1BBL blockade any timepoint during the course of infection invariably compromised MBC recall even when the GC response remained intact. Our results indicate that 4-1BBL signaling is required for optimal B cell activation but, its absence, paradoxically leads to expansion of a highly proliferative cell population while shrinking the MBC population. Our study highlights the pivotal role of 4-1BBL signaling in governing B cell responses during Plasmodium infection.

overall_design: Rag1-/- mice (CD45.2) were sub-lethally irradiated (450 rads) and transferred with 10 million cells containing an equal mixture of WT (CD45.1) along with 4-1BB-/- (CD45.2) and 4-1BBL-/- (CD45.1/.2) cells. At 6 weeks post transfer mice were checked for reconstitution by flow cytometry and at 8 weeks post transfer, reconstituted mice were infected with Plasmodium yoelii. On 21 days post infection, the spleens were harvested and single cell suspensions were stained with CITE-seq antibodies (ADTs) and fluorescently-labeled antibodies. Total B cells were flow sorted. scRNA-seq (GEX), CITE-seq (ADT) and V(D)J sequencing libraries were prepared according to the manufacturer’s protocol for Chromium GEM-X Single Cell 5’ Reagent Kit v3 with Feature Barcode technology and V(D)J amplification for mouse B cells (10X Genomics).

first: Carolina

last: Caloba

first: Alexandria

last: Sturtz

first: Laney

last: Thumser

first: Allen

last: Minns

first: Scott

last: Lindner

first: Tania

middle: H

last: Watts

first: Noah

last: Butler


title: ALDH1 inhibitor, DIMATE, Preserves Immune Function While Inducing Immunogenic Remodelling in AML

city: Lyon

first: Céline

last: BAIER

address: 655 Allée des Parcs

country: France

institute: Advanced Biodesign

summary:
DIMATE Preserves Immune Cells in AML
Our study provides a comprehensive characterization of the immuno‑pharmacological effects of DIMATE, a selective ALDH1 inhibitor currently evaluated in the First‑in‑Human ODYSSEY trial. We show that DIMATE preserves the core functions of circulating immune populations—including PBMCs, T cells, NK cells, and phagocytes—while inducing a coordinated pro‑inflammatory and ER‑stress response in AML cells that culminates in the exposure of ecto‑calreticulin, a canonical hallmark of immunogenic cell death (ICD).

overall_design: HL60 cell line has been treated of not with DIMATE 10µM during 6h

first: Baier

last: Céline

first: Costello

last: Régis

first: Colle

last: Julien


title: Regular aerobic exercise can effectively ameliorate the skeletal muscle and mitochondrial function impairments caused by bves deficiency in zebrafish

city: Changsha

first: Wanwan

last: Cai

state: Hunan

address: Lushan South Road

institute: Hunan Normal Universit

summary: The Popeye domain-containing protein 1 (Popdc1), also known as Bves, plays a crucial role in maintaining skeletal muscle homeostasis, with its variants leading to limb-girdle muscular dystrophy type 25. Skeletal muscles of patients with the homozygous missense variant of Bves exhibit impaired membrane trafficking, while skeletal muscle fibers in bvesS191F homozygous mutant zebrafish are significantly reduced and disorganized. However, the mechanism by which the absence of bves induces skeletal muscle atrophy remains unclear. In this study, we discovered a novel mechanism whereby Bves deficiency drives skeletal muscle atrophy by disrupting mitochondrial structure and function. Our findings indicate that bves knockout leads to a significant decrease in the swimming ability of zebrafish, atrophy of skeletal muscle tissue, loss of cell membrane localization signals, and abnormalities in mitochondrial structure and function. An 8-week intervention of regular aerobic exercise, the symptoms of skeletal muscle atrophy in bves knockout zebrafish were significantly alleviated, and the expression levels of genes and proteins related to mitochondrial were effectively rescued. These findings establish a connection between Bves deficiency-induced disruption of mitochondrial structure and function and the onset and progression of skeletal muscle tissue atrophy symptoms, thereby laying a molecular foundation for exercise rehabilitation strategies in atrophic myopathy.

overall_design: Compare the transcriptome differences of skeletal muscle tissue among the WT control group, bves KO knockout group, and bves KO-EX knockout exercise group.

first: Wanbang

last: Zhou

first: Xiushan

last: Wu

first: Junrong

last: Lei

first: Song

first: Kang

last: Sun

first: Haochen

last: Wang

first: Jiao

last: Xu

first: Qiong

first: Xiuyan

last: Li

first: Zhilong

last: Zhang

first: Jisheng

first: Yongqing

first: Zhigang

last: Jiang

first: Xianchu

last: Liu

first: Wuzhou

last: Yuan

first: Lan

last: Zheng


title: RNA-seq analysis of FDX2-inducible knockout (FDX2-iKO) ES2 ovarian carcinoma cells under normoxic and hypoxic conditions

city: Natori

first: Nobuhiro

last: Tanuma

address: 47-1 Noda-yama, Medeshima-shiode

institute: Miyagi Cancer Center Research Institute

summary: This dataset provides RNA-seq profiles of human ES2 ovarian carcinoma cells harboring a doxycycline-regulated, inducible knockout of the FDX2 gene (FDX2-iKO ES2 cells). In this Tet-off system, FDX2 expression is maintained in the presence of doxycycline, while FDX2 knockout is induced upon doxycycline withdrawal. Cells were cultured under normoxic (20% O₂) or hypoxic (3% O₂) conditions, with or without doxycycline. The aim of this study was to define the transcriptional consequences of FDX2 loss under varying oxygen levels. Raw read counts and processed data are provided to facilitate comparative expression analyses.

overall_design:
FDX2-inducible knockout (FDX2-iKO) ES2 ovarian carcinoma cells were cultured under four experimental conditions:
(A) 20% O₂ with doxycycline (+Doxy, FDX2 expression maintained)
(B) 20% O₂ without doxycycline (–Doxy, FDX2 knockout induced)
(C) 3% O₂ with doxycycline (+Doxy, FDX2 expression maintained)
(D) 3% O₂ without doxycycline (–Doxy, FDX2 knockout induced)
Each condition included three biological replicates (n = 3).
Total RNA was isolated, poly(A)-enriched libraries were prepared, and sequencing was performed on the MGI DNBSEQ-T7 platform (150 bp reads).
Gene expression was quantified using STAR and featureCounts, and read counts were normalized using DESeq2.
For samples A1 and A2, one of the paired-end FASTQ files was lost during transfer; count data are included, but the corresponding raw FASTQ files are unavailable.


title: Hepatocytes promote liver metastasis of pancreatic cancer by providing exogenous serine

city: New York

first: Jason

middle: Rodencal

last: Terrell

state: NY

address: 530 1st Avenue

institute: NYU Langone Health

summary: The liver is the major site of metastasis for pancreatic ductal adenocarcinoma (PDAC). In this work, we describe a mechanism wherein serine sythensis is essential for PDAC liver metastasis. To describe this, we knocked out Phgdh in mouse KPC cells and then co-cultured the cells with mouse hepatocytes.

overall_design: RNA-seq of cancer cells (HY19636) either WT or KO for Phgdh, either co-cultured with hepatocytes or monocultured.

first: Koelina

last: Ganguly

first: Keisuke

last: Yamamoto

last: Rodencal

first: Alec

last: Kimmelman


title: Spatial transcriptomic analysis of human iPSC-derived hemanoids at day 16 and day 28

city: Graz

first: Afrim

last: Avdili

address: Auenbruggerplatz 48

department: Blood Group Serology and Transfusion Medicine

institute: Medicl University of Graz

summary: Human induced pluripotent stem cell (iPSC)-derived hemanoids provide a three-dimensional model to study early hematopoietic development in vitro. To characterize the spatial organization and transcriptional dynamics of this system, we performed spatial transcriptomic profiling of FFPE hemanoids at day 16 and day 28 of differentiation using the 10x Genomics Visium Spatial Gene Expression platform (Visium v1 chemistry). This dataset captures the identification and spatial distribution of hematopoietic cells within the three-germ-layer-derived hemanoid environment.

overall_design: Human iPSC-derived hemanoids were generated via directed differentiation toward hematopoietic lineages. Organoids were collected at day 16 and day 28, sectioned, and processed for spatial gene expression analysis using the 10x Genomics Visium v1 platform. Libraries were prepared according to the manufacturer’s protocol and sequenced to generate spatially resolved gene expression profiles for each developmental stage.

first: Isabel

last: Dorn


title: Differential gene expression induced by doxorubicin in tumor-bearing and non–tumor-bearing mice

city: 蚌埠市

first: aonan

last: yu

state: 安徽省

address: 龙子湖区

institute: 蚌埠医科大学

summary: Doxorubicin-related cardiotoxicity is a major concern in cancer therapy and is influenced by drug dose, administration regimen, and host condition. While chemotherapy occurs under tumor-bearing conditions in clinical practice, most experimental studies evaluate cardiotoxicity in non–tumor-bearing models, which may alter cardiac responses to doxorubicin.

overall_design: Through high-throughput sequencing, gene expression differences induced by doxorubicin under tumor-bearing and non–tumor-bearing conditions were investigated.

first: Aonan

last: Yu

first: Mengxiao


title: Analysis of ER stress-induced three-dimensional enhancer network in wild-type and transcription facotr-knockout HCT116 cells [HiChIP]

city: Seoul

first: Hyoung-Pyo

last: Kim

address: Yonsei-ro 50-1

department: Department of Tropical Medicine

country: South Korea

institute: Yonsei University College of Medicine

summary: Integrative analysis of transcriptome, enhancer landscape and transcription factor binding, and three-dimensional genome structure in wild-type and transcription factor-knockout cells folloowing tunicamycin treatment

overall_design: HiChIP for histone modification and transcription factor in DMSO- and tunicamycin (Tm)-treated wild-type and transcription factor–knockout cells (biological replicates)

first: Jung-Sik

last: Joo

first: Mikyoung

last: kim


title: Effect of TAPIR on mNSCs in self-renewing conditions

city: Planegg

first: Anna

last: Danese

address: Grosshaderner strasse 9

institute: Ludwig Maximilians University

summary: Cellular translation rates are hypothesized to impact various cellular processes. Changes in rRNA expression levels are often implicated in diseases. This study reports a novel approach using a CRISPR activation (referred to as TAPIR) to manipulate rRNA levels. Induction of rRNA stimulates protein synthesis and cell proliferation, amongst others

overall_design: Bulk RNA-seq based transcriptome analyses of mNSCs grown in self-renewing conditions (GF) either with TAPIR (gRNA) or without (control) treatment. Additional RIBo-seq

first: Maximilian

last: Wiesbeck

first: Luisa

last: Egert

first: Stefan

last: Stricker


title: Senescence dynamics define therapeutic windows for Duchenne muscular dystrophy in DBA/2-mdx mice

city: San Diego

first: Pura

last: Muñoz-Cánoves

state: CA

address: 5510 Morehouse Dr

institute: Altos Labs

summary: Duchenne muscular dystrophy (DMD) is a severe X-linked disorder marked by progressive muscle degeneration and regeneration, inflammation and fibrosis. Cellular senescence has emerged as a potential driver of chronic muscle damage, yet its temporal dynamics and therapeutic relevance remain unclear. We analyzed senescent cell burden in skeletal and cardiac muscle of the DBA/2-mdx mouse model, which closely mimics many features of human DMD. The senolytic combination of dasatinib and quercetin (D+Q) was administered during early or late disease phases to evaluate the impact of senescent cell clearance. Skeletal muscle strength was measured by grip strength and ex vivo force assays, while cardiac function was assessed by echocardiography. Fibrosis and senescence markers were quantified histologically, and bulk RNA sequencing (RNA-seq) was used to identify transcriptional changes associated with senolysis.

overall_design: Bulk RNA-seq was performed on tibialis anterior (TA) and heart harvested from DBA/2-mdx mouse model treated with either vehicle control or the senolytic combination of dasatinib and quercetin (D+Q). For the TA, treatments were administered twice a week for two months, starting at 3 months of age and ending at 5 months of age. For the heart, treatments were administered twice a week for four months, starting at 12 months of age and ending at 16 months of age.

first: Aina

last: Calls-Cobos

first: Aida

last: Beà-Tàrrega

first: Andrés

last: Cisneros-Fernandez

first: Megan

last: Rommelfanger

first: Silvia

last: Campanario

first: Mercedes

last: Grima-Terrén

first: Ignacio

last: Ramírez-Pardo

first: Victoria

last: Moiseeva

first: Vera

last: Lukesova

first: Eva

last: Andrés

first: Grace

last: Chou

first: Yuewen

last: Zheng

first: Nasun

last: Hah

first: Albert

last: Blasco-Roset

first: Ana

last: Planavila

first: Carolina

last: Soler-Botija

first: Antoni

last: Bayés-Genís

first: Eusebio

last: Perdiguero

first: Antonio

middle: L

last: Serrano


title: Analysis of ER stress-induced three-dimensional enhancer network in wild-type and transcription facotr-knockout HCT116 cells [RNA-Seq]

first: Hyoung-Pyo

last: Kim

overall_design: RNA–seq in DMSO- and tunicamycin (Tm)-treated wild-type and transcription factor–knockout cells (biological replicates)

first: Jung-Sik

last: Joo

first: Mikyoung

last: kim


title: Analysis of ER stress-induced three-dimensional enhancer network in wild-type and transcription facotr-knockout HCT116 cells [Hi-C]

overall_design: Hi-C in DMSO- and tunicamycin (Tm)-treated wild-type and transcription factor–knockout cells (biological replicates)


title: Analysis of ER stress-induced three-dimensional enhancer network in wild-type and transcription facotr-knockout HCT116 cells [ChIP-Seq]

overall_design: ChIP–seq for histone modification and transcription factors in DMSO- and tunicamycin (Tm)-treated wild-type and transcription factor–knockout cells (biological replicates)


title: Transcriptomic profiling of GATA4 Knock-Out in cardiac, lung, and tail tip fibroblasts

first: Jethro

middle: WANG

last: Zih-Shuo

state: Ohio

address: 460 W 12th Ave.

department: Department of Surgery

institute: Ohio State University

summary: Fibroblasts from different anatomical origins exhibit distinct phenotypic properties. In this study, we aimed to determine the cell-type-specific transcriptional responses to GATA4 overexpression. We performed bulk RNA-seq on cardiac fibroblasts (CF), lung fibroblasts (LF), and tail tip fibroblasts (TTF) transduced with either Ad-GFP (control) or Ad-Cre (GATA4 KO). The goal is to delineate the general versus source-specific GATA4 regulatory networks.

overall_design: Bulk RNA-seq was performed on 6 distinct fibroblast samples: Lung Fibroblasts (LF), Cardiac Fibroblasts (CF), and Tail Tip Fibroblasts (TTF), each transduced with either Ad-GFP (control) or Ad-Cre (GATA4 KO). n=1 per group.

middle: W

first: Zhentao

last: Zhang

first: Hua

last: Zhu


title: Analysis of ER stress-induced three-dimensional enhancer network in wild-type and transcription facotr-knockout HCT116 cells [ATAC-Seq]

overall_design: ATAC-seq in DMSO- and tunicamycin (Tm)-treated wild-type cells  (biological replicates)


title: Genome writing to dissect consequences of SVA retrotransposon disease X-Linked Dystonia Parkinsonism [DNA-seq]

first: Weimin

address: 435 E 30th street

department: Institute for Systems Genetics

summary: Human retrotransposon insertions are often associated with diseases. In the case of the neurodegenerative X-Linked Dystonia-Parkinsonism disease, a human-specific SINE-VNTR-Alu subfamily F retrotransposon was inserted in intron 32 of the TAF1 gene. Here, we genomically rewrote a portion of the mouse Taf1 allele with the corresponding 78-kb XDP patient derived TAF1 allele. In mESCs, the presence of the intronic SVAs—rather than the hybrid gene structure—reduces hyTAF1 levels. This leads to transcriptional downregulation of genes with TATA box enriched in their promoters and triggering apoptosis. Chromatin and transcriptome profiling revealed that intronic SVAs are actively transcribed, forming barriers that likely impede transcription elongation. In mice, neuronal lineage TAF1 humanization resulted lethality of male progeny within two months. XDP male mice had severe atrophy centered on the striatum—the same affected brain region in XDP patients. Lastly, CRISPRa-mediated activation of hyTAF1 restored mESC viability, suggesting boosting TAF1 transcription as a therapeutic approach.

sample_organism:
Mus musculus
synthetic construct

platform_organism:
Mus musculus
synthetic construct

overall_design: Two types of DNA samples are included: 1. TAF1 delivery vectors. 2. Captured genomic DNAs from engineered mESCs containing delivered TAF1 variants.

first: Ran

last: Brosh

first: Jef

last: Boeke


title: Genome writing to dissect consequences of SVA retrotransposon disease X-Linked Dystonia Parkinsonism [CUT&Run]

overall_design: CUT&RUN experiment for converted_dSVA_F, converted_dSVA_D and converted_dSVA_F&D mESCs, wild type as control.