title: RNA-seq analysis of sodium butyrate effects on palmitate-induced insulin resistance in HepG2 cells

city: Xining

first: Yinan

state: Qinghai

address: No. 251 Ningda Road

institute: Qinghai University

summary: Objective: Metabolic dysfunction-associated steatotic liver disease (MASLD) is characterized by hepatic insulin resistance (IR) and impaired lipid–glucose metabolism. Sodium butyrate (NaB), a short-chain fatty acid (SCFA), may improve metabolic homeostasis, but its actions in MASLD-related IR remain unclear. This study investigated the therapeutic effects and mechanisms of NaB in palmitate (PA)-induced insulin-resistant hepatocytes and high-fat diet (HFD)-induced MASLD mice. Methods: PA-treated HepG2 cells received NaB (0.5–1.5 mM). Lipid accumulation, glucose uptake, glycogen content, and metabolic gene and protein expression were analyzed using biochemical assays, staining, qPCR, Western blotting, and RNA-seq. In vivo, C57BL/6 mice were fed an HFD for 16 weeks and then treated orally with NaB (200 or 400 mg/kg/day) for 8 weeks. Metabolic phenotypes, liver histology, and major signaling pathways were analyzed. Results: In PA-induced HepG2 cells, NaB dose-dependently decreased triglyceride, total cholesterol, low-density lipoprotein cholesterol, and non-esterified fatty acid levels, while increasing high-density lipoprotein cholesterol, glucose uptake, and glycogen storage. NaB suppressed lipogenesis (↓SREBP1c, ↓FASN), enhanced fatty acid oxidation (↑PGC-1α, ↑PPARα, ↑CPT1A), restored GPR43–CaMKK2–adenosine monophosphate-activated protein kinase (AMPK)α–SIRT1 signaling, and activated PI3K/AKT signaling (↑p-IRS1, ↑p-PI3K, ↑p-AKT, ↑GLUT2), thereby reducing gluconeogenic markers (↓FOXO1, ↓PCK1, ↓G6PC1) and increasing glycogen synthase (↑GS). Transcriptomics confirmed enrichment of PPARα and metabolic pathways. In HFD-fed mice, NaB reduced body weight, improved lipid profiles, alleviated steatosis, improved glucose tolerance and insulin sensitivity, and restored liver glycogen, with greater effects at the higher dose. Conclusion: NaB alleviates hepatic steatosis and IR in MASLD by activating AMPK and PI3K/AKT pathways, promoting fatty acid oxidation, and enhancing glycogen synthesis. NaB may serve as a promising multi-target metabolic modulator for MASLD.

overall_design: Five experimental groups were included: Control, IR, IR + low NaB (IRL), IR + medium NaB (IRM), and IR + high NaB (IRH). Cells were collected at 24 h and 48 h with three biological replicates per group. Differential expression analysis was performed to identify genes associated with NaB-mediated effects on insulin resistance.

first: Ping

last: Jiang

first: Yiwen

first: Ya

last: Wang

first: Yige


title: Next Generation Sequencing of Transcriptomes from Murine Articular Chondrocytes Treated with TGFb1 and BMP2

status: Public on Mar 25 2026

city: St Louis

first: Tiandao

last: Li

state: MO

address: 4444 Forest Park Ave

country: USA

institute: Washington University

type: Expression profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

type: Methylation profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Androgen activity in the male embryonic hindbrain drives lethal PFA ependymoma [mm_MF_Dev_scRNA_batch1]

city: Toronto

first: Michael

middle: D.

last: Taylor

state: Ontario

address: 555 University Ave

department: DSCB

country: Canada

institute: The Hospital for Sick Children

summary: In this study, we examine transcriptional sex differences between developing male and female hindbrain cells and their role in PFA pathogenesis, primarily in the poor prognosis of male patients.

overall_design: Male and female mouse hindbrain structures from 8 developmental stages were processed for single-cell RNA sequencing.

middle: D


title: Next Generation Sequencing of Transcriptomes from Murine Articular Chondrocytes Treated with TGFb1 and BMP2 [MRE-seq]

summary: Murine articular chondrocytes were isolated from femoral heads of 3-week-old wild-type C57BL/6J pups as described (Gosset et al., 2008) with modifications. Following digestion, chondrocytes were harvested and cultured in complete high-glucose Dulbecco’s modified Eagle’s medium (DMEM; Gibco; #31053028) supplemented with 10% fetal bovine serum (FBS; Gibco; #10437), 2 mM L-Glutamine (Gibco; #A2916801), and 1% penicillin/streptomycin. Primary chondrocytes were seeded at a density of 50 x 104 cells/well in 12-well plates and treated with vehicle, 5 ng/ml TGFβ1 (R&D Systems; #240-B-010) and 100ng/ml BMP2 (R&D Systems; #355-BM-010) for 24 hours. Total RNA was then extracted from cell cultures and performed RNA sequencing.

overall_design: DNA metylation of Murine articular chondrocyte treated with TGFb1 and BMP2

first: Jie

last: Shen


title: Impact of ATEVs on transcriptional profile of pancreatic tumor tissues derived from a poorly immunogenic pancreatic cancer cell clone

status: Public on Mar 24 2026

city: Columbus

first: Mengying

last: Hu

state: Ohio

address: 496 W 12th Ave

department: Pharmaceutics and Pharmacology

institute: The Ohio State University

summary: Antigen processing and presentation (APP) is essential for adaptive immunosurveillance. We uncover a mechanism whereby activated T cell-derived extracellular vesicles (ATEVs) drive a positive feedback loop that enhances antigen presentation and immune responses in normal physiology and cancer. ATEV-induced immunogenicity relies on extracellular vesicular double-stranded DNA (EVDNA), which is notably abundant and primarily composed of genomic DNA enriched in immune-related genes, including those encoding APP machinery. Mechanistically, granzyme B (Gzmb) packaged by ATEVs disrupts the nuclear envelope of recipient cells, facilitating intranuclear transfer and subsequent transient expression of EVDNA encoding APP genes. DNase treatment removes most AT-EVDNA, abrogating APP upregulation and thus T cell activation and recruitment to tumors. Notably, ATEVs hold promise as an acellular immunotherapy, restoring APP and synergizing with checkpoint blockade in immunotherapy-refractory tumors. Collectively, our findings uncover a mechanism of transient, non-viral gene delivery by ATEVs which boosts APP and anti-tumor immunity while limiting autoimmunity.

overall_design: Bulk RNAseq profiling of pancreatic tumor tissues derived from an immunogenic pancreatic cancer cell clone (KrasLSL-G12D/+; Trp53LSL-R172H/+; Pdx1-Cre; Rosa26YFP/YFP), after intratumoral injections with PBS or ATEVs in vivo


title: MUC21 is downregulated in oral squamous cell carcinoma and associated with poor prognosis

city: Beijing

first: 唐

last: 伟评

address: 2 Anzhen Rd, Chaoyang District,

country: China

institute: Beijing Institute of Heart Lung and Blood Vessel Diseases

summary: The role of MUC21 in oral squamous cell carcinoma (OSCC) remains unexplored. Microarray data of 10 paired OSCC and  adjacent normal oral mucosae (para-OSCC) from this study and datasets from  GEO and TCGA RNA-seq were analyzed to screen out differentially expressed genes including MUC21 which was further validated by qRT-PCR. the impact of  expression changes of MUC21 on OSCC  was retrospectively studied by clinical data, MUC21 immunohistochemistry data from a cohort of patients. In vitro OSCC cell lines experiments were also conducted to further verify the results.

overall_design: 10 paired tissue specimens (OSCC and para-OSCC oral mucosae) were collected during surgical resection, then directly transfered to total RNA extraction and microarray profiling. All patiens had no previous adjuvant therapy such as radiotherapy and/or chemotherapy.This study was approved by the Medical Ethics Committee of Capital Medical University School of Stomatology (Approval No. CMUSH-IRB-KJ-PJ-2018-04), and written informed consent was obtained from all participants in accordance with ethical guidelines.

first: Lisha

last: Mao

first: Xuejiu


title: H2AC19 acts as a novel regulator of angiogenesis to promote the progression of lung adenocarcinoma

city: Jinan

first: xiaorui

last: liu

address: 107 Wenhua West Road

institute: Qilu hospital of Shandong University

summary: Background: Angiogenesis is a significant character of lung adenocarcinoma (LUAD) and is an important reason leading to high mortality rates of LUAD patients. Identification of potential therapeutic targets for regulating angiogenesis has clinical importance for the treatment of LUAD. Methods: We constructed a prognostic risk model based on hypoxia- and angiogenesis-associated genes using bioinformatics analysis. CRISPR/Cas9-mediated knockout, overexpression and truncation mutants of H2AC19 and patient-derived organoid (PDO) models were used to assess H2AC19 function in LUAD. RNA-seq, ChIP-seq and molecular docking were performed to explore the underlying mechanism. Results: It was found that the level of H2AC19 was increased in human samples with LUAD, which was positively correlated with angiogenesis and clinical stage, negatively correlated with patient prognosis. Knockout of H2AC19 suppressed angiogenesis and tumor growth in vitro and in vivo models, and reduced HUVEC proliferation, migration, and tube formation in LUAD cell/HUVEC coculture model. Mechanistically, H2AC19 promoted angiogenesis, at least in part through p300/EGR1/MMP-1 signaling pathway. Conclusions: Collectively, our findings provide new insights into the pivotal role of H2AC19 in regulating angiogenesis, indicating that H2AC19 might serve as an attractive therapeutic target for LUAD.

overall_design: RNA-seq profiling of wildtype A549 cells and their knockout derivatives sgH2AC19


title: Butyrylcholinesterase alleviates hepatic stellate cell activation via paracrine muscarinic signaling [2W-CCL4-DOX-HSC]

city: Shanghai

first: Tao

last: Le

address: LANXI ROAD 164

institute: Shanghai University of traditional Chinese Medicine

summary:
Background & Aims: Butyrylcholinesterase (BuChE) is an enzyme involved in Alzheimer’s disease (AD), detoxification and depression. While BuChE expression is reduced in liver cirrhosis, its physiological substrate, acetylcholine (ACh), promotes fibrogenic responses in hepatic stellate cells (HSCs). However, the function of BuChE in liver fibrosis and mechanistic link between these two observations is not known.
Methods: BuChE expression and HSC activation were assessed in liver biopsies from patients with liver fibrosis using qPCR and immunostaining. To investigate the functional role of BuChE in fibrogenesis, we employed BucheΔHep, knock-in (BucheKI/KI-Hep) mice, as well as pharmacological inhibition. The inhibitory effect of BuChE on HSC activation was further confirmed using conditioned medium from cells expressing mutant BuChE, in hepatocyte-HSC co-culture experiments, and analyses of recombinant BuChE protein. The release of ACh was measured with patch-clamp and the expression and functionality of its receptor were detected via intracellular Ca2+ influx measurements. The role of the muscarinic acetylcholine receptor 3 (ChRM3) in HSCs was investigated through gain- and loss-of-function experiments, utilizing Chrm3ΔHSC mice and AAV-mediated Chrm3 overexpression driven by the alpha-smooth muscle actin (Acta2) promoter.
Results: Buche mRNA expression in livers and enzymatic activity in serum are downregulated in patients and mouse models with liver fibrosis, and show a negative correlation with F stage and ACTA2 expression. Pharmacological inhibition or depletion of BuChE in hepatocytes results in increased HSC activation and aggravates liver fibrosis in various mouse models, whereas its overexpression exerts the opposite effect, indicating a causative role of BuChE downregulation in liver diseases. BuChE is predominantly expressed in hepatocytes in the liver, which can be reduced by TGFβ treatment. Notably, BuChE enzymatic activity is required to prevent HSC activation and fibrogenesis in homeostatic liver. As consequence of the lost BuChE metabolic activity, levels of released unmetabolized ACh are increased, which acts as DAMP to activate HSCs via ChRM3 signaling. This finding was confirmed using Chrm3ΔHSC mice, which exhibit diminished HSC activation and liver fibrosis. Conversely, ChRM3 overexpression in HSCs is promoting the fibrogenic process.
Conclusion: Hepatocyte injury disrupts BuChE activity, causing local ACh accumulation and subsequent HSC activation via ChRM3 signaling. This novel cholinergic circuit drives fibrosis and represents a promising new target for therapeutic intervention.

overall_design: Overexpression of BUCHE in hepatocytes and modeling of CCL4, isolation of primary hepatic stellate cells

first: Le

last: Tao

first: Nuoya

last: Liu

first: Wei

last: Zhang

first: Zongguo

last: Yang

first: Jianrong

last: Xu

first: Guang

last: Ji

first: Cheng


title: Nimbolide competitively binds to 14-3-3 epsilon with TFEB to promote lipophagy and ameliorate atherosclerosis

city: Hengyang

first: chaochao

last: he

address: 28 West Changsheng Road

institute: University of South China

summary: Atherosclerosis is a chronic inflammatory disease driven by lipid accumulation in the arterial wall, where macrophage foam cell formation represents a key pathological event. Nimbolide (NIM), a natural limonoid with documented anti-inflammatory and lipid-regulatory properties, may offer therapeutic potential, though its effects on atherosclerosis remain poorly characterized.

overall_design: Here, we examined whether NIM attenuates atherosclerotic progression and explored the mechanisms involved. In apoE-/- mice fed a high-fat diet, NIM administration reduced plaque burden, improved serum lipid profiles, and suppressed vascular inflammation. In macrophage foam cells, NIM promoted cholesterol efflux to apoA-I and HDL by upregulating ABCA1 and ABCG1 expression. Transcriptomic profiling pointed to activation of the autophagy-lysosomal pathway, and subsequent experiments confirmed that NIM promotes lipophagy through nuclear translocation of transcription factor EB (TFEB). Using surface plasmon resonance, cellular thermal shift assays, and co-immunoprecipitation, we identified 14-3-3 epsilon as a direct binding target of NIM. NIM competes with TFEB for binding to 14-3-3 epsilon, displacing TFEB from cytoplasmic sequestration, reducing its Ser211 phosphorylation, and enabling nuclear entry. This 14-3-3 epsilon/TFEB axis thus links NIM binding to coordinated activation of lipophagy and cholesterol efflux. These observations suggest that the 14-3-3 epsilon/TFEB axis contributes to NIM-mediated protection against atherosclerosis and may warrant further exploration as a target for cardiovascular intervention.

first: Chaochao

last: He


title: Transcriptomic response of Trichoderma atroviride to different carbon sources

city: Irapuato

first: Manuel

last: Villalobos-Escobedo

state: Guanajuato

address: Km 9.6 Libramiento Norte Carretera Irapuato-León Irapuato

department: Ingeniera Genetica

country: Mexico

institute: cinvestav

summary: RNA-seq analysis of Trichoderma atroviride grown under different carbon source conditions (glucose, xylan, and no carbon). The aim of the experiment is to characterize transcriptional changes associated with carbon source utilization and metabolic adaptation. Three biological replicates were sequenced for each condition using Illumina sequencing.

overall_design: Trichoderma atroviride was initially grown for 48 h in liquid Vogel’s minimal medium supplemented with glucose. Mycelium was then washed with Vogel’s minimal medium lacking a carbon source and transferred to fresh medium containing different carbon conditions (glucose, xylan, or no carbon). Cultures were incubated for 12 hours after transfer, and total RNA was extracted for RNA-seq analysis. Three biological replicates were generated for each condition.

first: Villalobos-Escobedo

last: José M.

first: Huberman

last: Lori B.

first: Skerker

last: Jeff

first: Shi

last: Ran

first: Rico-Ramírez

last: Adriana

first: Adams

last: Catharine

first: Arkin

last: Adam

first: Deutschbauer

first: Glass

last: Louise


title: Influence of lateral compression on epithelium and role of lamin A in this process

city: Tampere

first: Elina

last: Mantyla

address: Arvo Ylpön katu 34

department: Faculty of Medicine and Health Technology

country: Finland

institute: Tampere University Foundation

summary: Intercellular compressive forces during cellular packing and maturation of epithelium are guided by cellular mechanotransduction. In this study, the goal was to identify how lateral compression alters gene expression in the epithelium, and given that nuclear lamina -mediated nuclear mechanics contribute in mechanotransduction, we sought to decipher the role of A-type lamins in this process. We used Madine Darby canine kidney type II (MDCKII) cells as wild-type (WT) cells and established a derivative pre-lamin A knockout (referred here as LMNA KO) cell line. Cells were grown for 3-4 days until an intact monolayer was formed (but which had not reached maturity). We applied our in house developed Brick Strex  cell stretching deviceand cultured cells in this device on a pre-stretched and pre-strained PDMS with 25 % tensile strain, inducing a 20 % lateral compressive strain upon gradual release of the pre-strain. After a 2 h recovery, total cell lysates were made and mRNA was extracted for mRNA-seq.

overall_design: RNA-seq profiling of wildtype MDCKII cells at Day 7 and at 2 h post-reseeding.

first: Sanna

last: Korpela

first: Anna

last: Rekonen

first: Sini

last: Hakkola

first: Jenni

last: Karttunen

first: Anni

last: Pörsti

first: Sanni

last: Erämies

first: Fábio Tadeou

last: Arrojo Martins

first: Roselia

last: Davidsson

first: Markus

middle: J

last: Ojanen

first: Satu

middle: A

last: Hakanen

first: Peipei

last: Wang

first: Joonas

last: Uusi-Mäkelä

first: Alice

last: Anais Varlet

first: Maija

last: Vihinen-Ranta

first: Daniel

middle: E

last: Conway

first: Keijo

last: Viiri

first: Matti

last: Nykter

first: Jan

last: Lammerding


title: Expression data from CD4+CD25- T cells of VAVcreKeapfl/fl mice

city: Aachen

first: Christopher

middle: Thomas

last: Neullens

address: Pauwelsstraße 30, 52074

country: Germany

institute: RWTH Aachen University Medical Faculty

summary: The transcription factor NRF2 regulated oxidative stress responses. Deletion of Keap1 results in constitutive NRF2 activation. We analyzed the consequences of NRF2 activation for gene expression in T cells.

overall_design:
Genome-wide transcriptome analysis for VAVcreKeapfl/fl and WT CD4+CD25- T cells were performed using Gene Chip® Mouse Gene 2.0 arrays

**Submitters state that the complete processed data files were not available due to file loss.**

first: C

first: K

last: Ohl


title: The melanocytic transcriptomic state is independently associated with poor overall survival in long term follow up of patients with metastatic melanoma

city: ANN ARBOR

first: Ziyin

last: Huang

state: MI

address: 3003 S. STATE STREET

institute: University of Michigan

summary: Introduction: Advanced cutaneous melanoma shows substantial heterogeneity in clinical outcomes, even among patients classified within the same clinical stage. Understanding the molecular drivers underlying this heterogeneity is critical for advancing treatment strategies. Previous studies have identified distinct melanoma transcriptomic states - Tirosh et al. and Balderson et al. have agreed on a four-subtype model defining “Undifferentiated/AP1”, “Neural Crest/AP2”, “Transitory”, and “Melanocytic” states. However, their biological and clinical relevance remains unclear. Here we profiled in-transit melanoma (ITM) using digital spatial RNA profiling to associate melanoma transcriptomic states with overall survival (OS) and acral melanoma (AM) status. Methods: Digital spatial profiling (Nanostring GeoMx Whole Transcriptome Atlas) was performed across a tissue microarray constructed from patients with ITM diagnosed from 1990-2020. After filtering poor quality areas of interest (AOIs), we processed the data using noise correction and quantile normalization. We applied Principal Component Analysis (PCA) to define melanoma subtype signatures by ranking genes contributing to each of the first four PCs. We performed gene set enrichment analysis using GSEA with significance defined as an adjusted p-value < 0.05. Association between gene or gene-set expression and overall survival was evaluated using optimal expression cutoffs to define high and low groups, with a minimum group size of 20% to avoid overfitting. Cox proportional hazards models were then used to assess survival differences between groups. Results: We analyzed a cohort of 84 patients (116 AOIs) with ITM passing spatial transcriptomic QC. PCA of transcriptional profiles revealed distinct transcriptional states. The PC1 axis differentiated Transitory from Undifferentiated melanoma, PC2 reflected immune cell infiltration, PC3 corresponded to stromal cells and Neural crest-like melanoma, and PC4 associated with Melanocytic melanoma. We derived gene sets from the PCA results and associated the expression of each gene set with OS. Across a cohort of treatment-naïve ITM, high expression of the melanocytic state conferred a median overall survival difference of 7.59 years and independently associated with poor survival in multivariate analysis. AMs showed higher melanocytic state gene expression compared to non-acral cases. These findings were validated in external datasets, supporting that the melanocytic state predicts poor prognosis. Conclusion: The melanocytic transcriptional state was independently associated with worse overall survival in patients with metastatic melanoma and was enriched in acral melanoma, suggesting that assessment of the melanocytic state may have value for clinical risk stratification.

overall_design: Spatial transcriptomics was performed on the TMA using the Nanostring GeoMx Digital Spatial Profiler (DSP) with the human Whole Transcriptome Atlas (WTA) probe panel. The TMA underwent staining for CD20 (B cells), CD3 (T cells), and DNA to guide region of interest (ROI) selection. ROIs were drawn to maximize tumor content within each tissue spot on the TMA. Full ROIs were profiled without the use of segmentation to avoid inadequate cell counts. The DSP plates were dried down and rehydrated in 10uL nuclease-free water. Libraries were prepared and pooled as specified in the protocol for WTA RNA samples. The final pool was assessed for quality using the Tapestation D1000 assay and Qubit. Sequencing was performed using NovaSeq 6000 S4 flowcell run as 27x8x8x27 bp (Illumina). The GeoMx DSP Analysis Pipeline version 2.3.3.10 performed trimming, alignment, and deduplication of UV-cleaved probe barcodes. A tabulated matrix of probe counts for each AOI was exported from the DSP server for subsequent analysis.

first: Kristen

last: Rhodin

first: Rami

last: Al-Rohil

first: Viviana

last: Geron

first: Arul

last: Chinnaiyan

first: Margaret

last: O'Connor

first: Christina

last: Angeles

first: Smita

last: Nair

first: Matthew

last: Iyer

first: Georgia

last: Beasley


title: An Instructive Neural Interface for Layer-Specific Cortical Repair with Human Brain Organoids

city: Tianjin

first: Xiaohong

last: Li

address: 92 Weijin Road

institute: Tianjin University

summary: Repairing precise neural microcircuitry after cortical injury remains a pivotal challenge. While human brain organoids (hBOs) provide a promising cell source, their therapeutic potential is limited by disorganized integration. Here, we demonstrated that targeted neuromodulation, steered by endogenous narrowband gamma (NBG) rhythms, could instruct the structural and functional integration of hBOs grafts in the injured adult mouse visual cortex. Using a neural interface system, we first promoted general graft-host coupling and then delivered NBG-rhythmic stimulation to specific functional clusters during a critical period of plasticity. This two-phase strategy guided the emergence of layer 4-appropriate molecular and functional properties within the grafts, established bidirectional connectivity with the host visual pathway, and supported the development of advanced visual processing, including direction selectivity in hBOs neurons. Electrophysiologically, graft spiking phase-locked to host NBG oscillations. Our work established a new framework for circuit-level repair, highlighting a synergistic strategy that moves beyond cell replacement to actively direct the assembly of neural grafts.

overall_design: Single-nucleus RNA sequencing was performed on human brain organoids transplanted into the primary visual cortex of Nod-SCID mice at 150 dpt, following either Non-Target or Target neuromodulation.

first: Zhehan

last: Chang


title: Spatial transcriptomics identifies IL-32 as a lipid droplet-associated cytokine linked to tubular injury in human diabetic kidney disease

city: Calgary

first: Justin

last: Chun

state: Alberta

address: 3330 Hospital Drive NW

institute: University of Calgary

summary: Diabetic kidney disease (DKD) is a severe complication of diabetes mellitus and the leading cause of chronic kidney disease worldwide. Among the many drivers of tubular injury, lipid accumulation and inflammation are emerging as major contributors to kidney disease progression, but the molecular link between lipid metabolism and inflammatory signaling remains to be determined. Kidney biopsies from patients with DKD across pathologic classes were labelled for lipid droplets and analyzed by Nile Red spectroscopy. Digital spatial profiling and single-cell spatial transcriptomics were performed on samples from 14 patients representing different DKD classes. RNA scope and immunofluorescence microscopy were used for data validation and characterization. Lipid droplets (LD) were increasingly abundant in advanced stages of DKD, primarily accumulating in the proximal tubules. Single-cell spatial transcriptomics identified several genes—DUSP5, AZU1, COL9A1, HSPB1, and IGFBP7—as highly upregulated in DKD. Remarkably, IL32, which encodes a LD-associated cytokine, was highly enriched in injured proximal tubules. Immunofluorescence confirmed IL-32 localization to LDs predominantly within KIM1 positive tubules in moderate to advanced DKD. Furthermore, injured IL-32 expressing tubules were in close proximity to infiltrating neutrophils and macrophages, immune effectors of non-resolving inflammation and kidney disease progression. IL-32 is a LD-associated cytokine upregulated during tubular injury that represents a potential link between lipid dysregulation, inflammation and progression in human DKD.

overall_design: 14 human patient kidney biopsy samples ranging in DKD classification from non-disease controls to Class IV DKD. The NanoString CosMx spatial molecular imager was used to assay a 1000-plex CosMx Human RNA panel with the addition of kidney-specific genes: APOL1, AQP1, AQP2, CLDN10, EMCN, HAVCR1, LRP2, NOS1, NPHS1, PALMD, PIEZO2, PLVAP, PROM1, PROX1, REN, SCN2A, SH3GL3, SLC12A1, SLC12A3, SLC14A2, SLC26A4, SLC26A7, SLC4A9, SLC5A12, SLC5A2, SLC7A13, SLC8A1, SYN1, UNC5D. Morphology visualization from upfront staining was performed using CD298, B2M, PanCK, CD45, and/or CD68 and DAPI.

first: Kieran

last: Meadows

first: Hyunjae

last: Chung

first: Son

last: Vo

first: Aysa

last: Imanzadeh

first: Heewon

last: Seo

first: Sisay

middle: G

last: Belay

first: Asha

last: Swamy

first: Wulin

last: Teo

first: Kevin

last: Chapman

first: Graciela

last: Andonegui

first: Hallgrimur

last: Benediktsson

first: Peter

middle: K

last: Stys

first: Thang

last: Pham

first: Daniel

last: Muruve


title: Selective Transcriptomic Vulnerability Of Membrane-Integrated Architectures During Neural Tissue Vitrification

city: Kunshan

first: Dominika

last: Wilczok

address: No 8 Duke Avenue

department: Division of Natural and Applied Sciences

institute: Duke Kunshan University

summary: Cryopreservation is essential for long-term storage of biological tissues. Yet, surprisingly, the precise molecular impact of cryopreservation on tissue transcriptomes remains poorly defined. This study provides the first resource of whole-genome transcriptomic changes following cryopreservation. This study used bulk RNA sequencing to examine how preservation method (snap freezing or vitrification) affects transcriptomes in mouse cerebral cortex and hippocampus. This allowed us to separate cryoprotectant-specific changes from cold induced-changes via snap freezing. In a subset of genes, tissues processed under vitrification conditions showed selective under-representation of a small but structurally coherent group of transcripts, with the hippocampus exhibiting greater vulnerability than the cortex. UniProt annotation revealed that affected transcripts were strongly enriched for proteins with membrane-associated, secretory-pathway, and multi-pass topologies, indicating that structurally complex membrane-integrated architectures are disproportionately sensitive to vitrification. Pathway-level analysis using iPANDA further showed that negative preservation scores in vitrified tissue clustered primarily within signal transduction and metabolic pathways, suggesting coordinated pathway-level disruption rather than global transcript loss. Together, these results demonstrate that vitrification conditions induce selective and structured molecular perturbations in neural tissue, defined by the under-recovery of transcripts associated with membrane and secretory pathway organization. This work highlights molecular vulnerability during vitrification and emphasizes the need for transcript-level evaluation when optimizing cryopreservation approaches for neural systems.

overall_design: Murine cerebral cortex and hippocampus in 3 conditions: fresh, snap frozen and vitrified with cryoprotective agents

first: Qian

last: Long

first: Zhuoan

last: Huang

first: Joseph

last: Kangas

first: Yewei

last: Liu

first: Minyan

last: Wang


title: Bulk RNAseq in microglia from wild-type (WT) and Lactamase B (LACTB) enymatic dead (ED) mice (LACTB S162I).

city: Houston

first: Ruben

last: Gomez-Gutierrez

state: TX

address: 1881 East Road

department: Therapeutics Discovery Division

institute: The University of Texas MD Anderson Cancer Center

summary: Our mendelian randomization analysis showed that lower expression of LACTB in myeloid cells might be protective for Alzheimer's Disease. We evaluated how microglial cells from LACTB enzymatic dead mice show transcriptional changes.

overall_design: RNA-seq profiling of microglia (iMGLs) from mice with enzymatic dead Lactamase B (LACTB ED) and wild-type (WT) controls.

first: Jiacheng

last: Ma

first: Kendra

last: Allton

first: Olivia

last: Calderon

first: Yaima

middle: L

last: Lightfoot

first: Morgan

last: McReynolds

first: William

last: Ray


title: Viral SSB-bound ssDNA activates the bacterial anti-phage defense system DARNA

city: Missoula

first: Christopher

middle: Nicholas

last: Vassallo

state: MT

address: 32 Campus Dr.

department: Biological Sciences

institute: University of Montana

summary: To protect themselves against phage infection, bacteria employ diverse defense systems that are typically activated specifically upon infection. However, the mechanisms of activation and self versus non-self discrimination for most systems remain poorly understood. Here, we show that the bacterial immunity protein DARNA, once activated, cleaves a subset of host tRNAs, thereby inhibiting phage propagation. Although phages escape DARNA-mediated defense through mutations in the gene encoding single-stranded DNA-binding protein (SSB), we find that phage SSBs do not directly stimulate DARNA. Instead, DARNA is activated by single-stranded DNA presented by phage SSB, but not by the host SSB. The recognition of an endogenous nucleic acid signal promoted by a viral protein ensures that DARNA can detect and respond to a broad range of viruses while avoiding auto-immunity.

sample_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: RNA sequencing analysis of  MG1655 carrying the DARNA defense system plasmid investigating cleavage of RNA in cells infected with bacteriophage T7 or expressing T7 Gp 2.5 (single-stranded DNA-binding protein).

first: Rugile

last: Puteikiene

first: Arunas

last: Silanskas

first: Jonas

last: Juozapaitis

first: Inga

last: Songailiene

first: Michael T.

last: Laub

first: Giedrius

last: Sasnauskas


title: DGAT1 Drives Racially Divergent Fibroblast Activation via ERK1/2-Dependent Tumorigenic Signaling in Prostate Cancer

city: Shreveport

first: Omar

last: E. Franco

state: LA

address: 1501 Kings Hwy

department: Biochemistry and Molecular Biology

institute: LSU Health Shreveport

summary: Lethal prostate cancer (PCa) disproportionately affects African American (AA) men, who experience a higher incidence and earlier onset compared to Caucasian (Cau) men, reflecting a persistent biological and clinical disparity. Recent studies have implicated raceassociated differences in lipid metabolic reprogramming as key contributors to this disparity. We recently identified carcinoma-associated fibroblasts (CAFs) as a major stromal component that mediates racial disparities in tumor progression. Here, we demonstrate that lipid-laden CAF from AA patients (AACAF) display enhanced protumorigenic properties compared with CAFs from Cau patients (CauCAF). Lipid droplet (LD) biogenesis and storage analysis revealed a robust diacylglycerol O-acyltransferase 1 (DGAT1) enzyme-dependent LD accumulation in AACAF . Ectopic DGAT1 expression in benign fibroblasts induced canonical CAF markers (FAP1 and ⍺SMA) expression linked to fibroblast activation, altered the secretome, and significantly enhanced PCa cells’ growth in vivo. Integrative transcriptomic and secretome analyses identified novel DGAT1- regulated genes involved in CAF linked to metabolism, cell–cell communication, motility, and angiogenesis, mediated mainly through ERK1/2 signaling activation. Pharmacological DGAT1 inhibition suppressed these pathways and elicited racially distinct regulation of tumor-promoting mediators, including BDNF, VEGF, and TSP1. Mechanistic experiments show that functionally, lipid-laden CAF from AA patients exhibit increased fibroblast activation and a secretory phenotype with greater pro-tumor activity compared to CAF from Cau patients. Collectively, these findings reveal that DGAT1 is a pivotal enzymatic regulator of fibroblast activation and lipid-driven remodeling in the PCa tumor microenvironment (TME) of AA men. Targeting DGAT1 represents a promising strategy for disrupting metabolic-stromal crosstalk to mitigate race-associated disparities in PCa progression.

overall_design: RNA-Seq profiling of BHPrS1-WT and DGAT1 overexpressing BHPrS1 cells after three days of culture.

first: Sathyavathi

last: ChallaSivaKanaka

first: Mamatha

last: Kakarla

first: Renee

last: E. Vickman

first: Yana

last: Filipovich

first: Philip

last: Fitchev

first: Md Maksudul

last: Alam

first: Md Niaz

last: Morshed

first: Pooja

last: Talaty

first: Brian

last: T. Helfan

first: David

last: Price

first: Simon

last: W. Hayward

first: Susan

last: E Crawford

last: E Franco


title: Intercellular competition in transposon libraries can influence Tn-seq outcomes

city: GRONINGEN

first: Biwen

last: Wang

state: Groningen

address: Zernikeplein 11

department: Research Centre Biobased Economy

country: Netherlands

institute: Hanze University of Applied Sciences

summary: Here, we used genome wide transposon insertion sequencing (Tn-seq) to measure the fitness of genes in the Gram-positive model system Bacillus subtilis. We tested an alternative fitness calculation method that makes use of the predicted transposon insertion frequency.

overall_design: Preparation of transposon inserted DNA in vitro and transform the Tn-gDNA to BSB1 competent cells to creat a transposon mutant library pool. Grow the transposon mutant library in liquid and solid mediums respectively and then sampled at desired growth conditions for Illumina sequencing.

first: Zihao

last: Teng

first: Tjalling

last: Siersma

first: Frans

last: van der Kloet

first: Leendert

last: W Hamoen


title: Robust generation of distal respiratory airway organoids by an engineered cuboid chip to therapy chronic obstructive pulmonary disease

city: Guangzhou

first: Yin

middle: Jia

last: Xiang

address: Building B, Guangzhou Laboratory, No. 9 XingDaoHuanBei Road, Guangzhou International Bio Island, Guangzhou 510005, Guangdong Province, China

institute: Guangzhou Laboratory

summary: Background Human distal respiratory airway (DRA) cells are located in the smallest conducting airways of the human lung, specifically in the terminal and respiratory bronchioles, and represent a newly discovered cell type. Due to their absence in mice and the limited existing research on these cells, there is an urgent need to establish an in vitro model of human distal respiratory airways to study the role of such cells in respiratory diseases. Results Here, we developed a robust differentiation protocol to derive DRA organoids (DRAOs) from human pluripotent stem cells (hPSCs) and investigated their role in the treatment of chronic obstructive pulmonary disease (COPD). We engineered a cuboid chip-based culture platform, where seeding single-cell suspensions mixed with Matrigel onto the chip increased lung progenitor cell (LPC) spheroid yield by 7.5-fold and upregulated NKX2.1 expression nearly 300-fold. Single-cell transcriptomic analysis further demonstrated that the platform enhanced distal lung-related gene expression. Prolonged culture of LPC spheroids yielded expandable hollow lung organoids. The resulting cells exhibited protein and molecular profiles closely resembling native human DRA cells, with over 70% co-expressing SFTPB and SCGB3A2. Using this method, we demonstrate accelerated production of DRAOs with significantly enhanced structural and functional maturity in 30 days. Furthermore, these DRAOs retain the potential to undergo alveolar differentiation. By exposing these organoids to cigarette smoke extract (CSE), we established a COPD-like model. In addition, DRAOs can survive in COPD mice, repair alveolar structural damage, and alleviate COPD symptoms. Conclusions Our method will facilitate increasingly widespread culture and differentiation of organoids, paving the way for constructing more accurate models of complex organs that mimic in vivo structures and functions. Furthermore, the favorable applicability of DRAOs in cell therapy studies using a mouse model of COPD-related alveolar injury provides critical insights for cell therapy in respiratory diseases.

overall_design: scRNA-seq revealed that the cuboid chip facilitates the generation of distal-LPCs. scRNA-seq revealed that the major cell population within the organoids was lung epithelial cells scRNA-seq revealed that these cells can be classified into 8 distinct populations.

first: Jiaxiang

last: Yin

first: Zirong

last: Bi

first: Tiankai

last: Dai

first: Hao

last: Meng

first: Jiaqi

last: Sun

first: Tao

last: Xu

first: Huisheng

last: Liu


title: Transcriptomics analysis reveals that age affects the survival ability of offspring through an epigenetic mechanism.

city: Kunming

first: Qiu

last: Zhao

state: Yunnan

address: Chenggong

department: State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan

institute: Yunnan University

summary: Using the nematode Caenorhabditis elegans as a model, we show that aging triggers transcriptional activation and repression of a large set of DNA repair genes and peroxisome-related genes, respectively in old worms.

overall_design: Synchronized C. elegans N2 wild-type worms were cultured  until the adult stage. For the experimental group, worms were  cultured  until five-day-old (5P0) stage after reaching adulthood ;while for the control group, they were cultured until one-day-old (5P0) stage after reaching adulthood . 1P0 and 5P0 worms were collected for RNA-seq analysis.

first: Chenggang

last: Zou

first: KeQin

last: Zhang

first: Yicheng

last: Ma

first: XinQian

last: Gong


title: MECOM promotes leukemia progression and inhibits mast cell differentiation through functional competition with GATA2

city: Tokyo

first: Mayuko

last: Nakanishi

address: 4-6-1 Shirokanedai, Minato-ku

country: Japan

institute: The University of Tokyo

summary: MECOM is a transcription factor critical for the maintenance of hematopoietic stem cells (HSCs) and the pathogenesis of myeloid leukemia. Germline mutations clustered in the C-terminal zinc finger domain (ZFD) of MECOM are known to cause MECOM-associated syndromes, involving bone marrow failure and skeletal anomalies. However, the molecular consequences of these mutations and the precise downstream mechanisms of MECOM remain elusive. Here, we demonstrate that the C-terminal ZFD serves as the dominant DNA-binding module of MECOM, and that disease-associated mutations abrogate its DNA-binding capacity. Mechanistically, we reveal that MECOM functionally antagonizes GATA2 via C-terminal ZFD-mediated DNA binding and recruitment of the corepressor CtBP. This repression promotes myeloid leukemogenesis while suppressing mast cell differentiation. Furthermore, we generated a knockin mouse model harboring a C-terminal ZFD mutation, which successfully recapitulated the clinical phenotypes of MECOM-associated syndromes, including reduction of HSCs and B cells. Collectively, our findings define C-terminal ZFD mutations as loss-of-function mutations with impaired DNA binding, uncover the MECOM-GATA2 axis as a key regulatory pathway, and provide a valuable mouse model for understanding MECOM-associated syndromes.

overall_design: RNA-seq profiling of SLAM-LSK (CD150+, CD48-, Lineage-, ScaI+, cKiT+) cells derived from bone marrows of wild type or MecomWT/R751W C57BL6 mice.

first: Kohei

last: Iida

first: Susumu

last: Goyama


title: Deep Invaginations of Nuclear Envelope Coordinate Spatial Organization of Chromatin in Epithelium (Part A: 7d and 2h grown epithelium)

first: Elina

last: Mantyla

summary: Cell nuclei are often used to assess cell health, but how their shapes vary in normal tissues and respond to mechanical forces is not well understood. Here, we describe deep invaginations of the nuclear envelope (DINEs) as common features of epithelial cell nuclei. Our data indicates DINEs in mature epithelium in vitro and in vivo. Our mRNAseq data compiles transcriptional profiling of these DINE-containing, mature epithelium grown for 7 d, and epithelial cells grown for 7 d and then detached and reseeded for 2 h. The data indicates correlation of DINEs with suppression of MAPK-signaling pathways.

first: Sanna

last: Korpela

first: Anna

last: Rekonen

first: Sini

last: Hakkola

first: Jenni

last: Karttunen

first: Anni

last: Pörsti

first: Sanni

last: Erämies

first: Fábio Tadeou

last: Arrojo Martins

first: Roselia

last: Davidsson

first: Markus

last: Ojanen

first: Satu

last: Hakanen

first: Peipei

last: Wang

first: Joonas

last: Uusi-Mäkelä

first: Alice

last: Anais Varlet

first: Maija

last: Vihinen-Ranta

first: Daniel

last: Conway

first: Keijo

last: Viiri

first: Matti

last: Nykter

first: Jan

last: Lammerding

first: Teemu

last: Ihalainen


title: Butyrylcholinesterase alleviates hepatic stellate cell activation via paracrine muscarinic signaling [DDC-OE-BUCHE]

first: Tao

last: Le

summary:
Background & Aims: Butyrylcholinesterase (BuChE) is an enzyme involved in Alzheimer’s disease (AD), detoxification and depression. While BuChE expression is reduced in liver cirrhosis, its physiological substrate, acetylcholine (ACh), promotes fibrogenic responses in hepatic stellate cells (HSCs). However, the function of BuChE in liver fibrosis and mechanistic link between these two observations is not known.
Methods: BuChE expression and HSC activation were assessed in liver biopsies from patients with liver fibrosis using qPCR and immunostaining. To investigate the functional role of BuChE in fibrogenesis, we employed BucheΔHep, knock-in (BucheKI/KI-Hep) mice, as well as pharmacological inhibition. The inhibitory effect of BuChE on HSC activation was further confirmed using conditioned medium from cells expressing mutant BuChE, in hepatocyte-HSC co-culture experiments, and analyses of recombinant BuChE protein. The release of ACh was measured with patch-clamp and the expression and functionality of its receptor were detected via intracellular Ca2+ influx measurements. The role of the muscarinic acetylcholine receptor 3 (ChRM3) in HSCs was investigated through gain- and loss-of-function experiments, utilizing Chrm3ΔHSC mice and AAV-mediated Chrm3 overexpression driven by the alpha-smooth muscle actin (Acta2) promoter.
Results: Buche mRNA expression in livers and enzymatic activity in serum are downregulated in patients and mouse models with liver fibrosis, and show a negative correlation with F stage and ACTA2 expression. Pharmacological inhibition or depletion of BuChE in hepatocytes results in increased HSC activation and aggravates liver fibrosis in various mouse models, whereas its overexpression exerts the opposite effect, indicating a causative role of BuChE downregulation in liver diseases. BuChE is predominantly expressed in hepatocytes in the liver, which can be reduced by TGFβ treatment. Notably, BuChE enzymatic activity is required to prevent HSC activation and fibrogenesis in homeostatic liver. As consequence of the lost BuChE metabolic activity, levels of released unmetabolized ACh are increased, which acts as DAMP to activate HSCs via ChRM3 signaling. This finding was confirmed using Chrm3ΔHSC mice, which exhibit diminished HSC activation and liver fibrosis. Conversely, ChRM3 overexpression in HSCs is promoting the fibrogenic process.
Conclusion: Hepatocyte injury disrupts BuChE activity, causing local ACh accumulation and subsequent HSC activation via ChRM3 signaling. This novel cholinergic circuit drives fibrosis and represents a promising new target for therapeutic intervention.

overall_design: Overexpression of BUCHE in hepatocytes and modeling with DDC

first: Le

last: Tao

first: Nuoya

last: Liu

first: Wei

last: Zhang

first: Zongguo

last: Yang

first: Jianrong

last: Xu

first: Guang

last: Ji

first: Cheng


title: Proteasome alteration between epithelial and hematopoietic cells facilitates positive selection of CD8 T cells

city: Frederick

first: Biraj

last: Shrestha

state: MD

address: 8560 Progress Drive

institute: Frederick National Laboratory

summary: The thymoproteasome, a proteolytic complex uniquely expressed in cortical thymic epithelial cells (cTECs), governs the positive selection of CD8 T cells. It was hypothesized that the thymoproteasome promotes CD8 T cell development by forging a sequential switch between cTECs and medullary antigen-presenting cells (APCs), in which stepwise difference in MHC-I-associated peptides by cTECs and medullary APCs would spare positively selected thymocytes from subsequent negative selection. In this study, we engineered mice ectopically expressing thymoproteasomes in various APCs including medullary TECs (mTECs), eliminating the proposed proteasome switch. Surprisingly, we found that the proteasome switch between cTECs and mTECs was dispensable for thymoproteasome-dependent CD8 T cell development. Instead, we found that ectopic thymoproteasomes in hematopoietic cells impaired CD8 T cell development by hindering cortical positive selection.Our findings reveal that proteasome difference between cTECs and hematopoietic cells facilitates thymoproteasome-dependent positive selection in the thymic cortex.

overall_design: Bulk RNA sequencing profile of CD4-CD8+ T cells sorted from the lymph nodes in WT and BIT mice.

first: Yongmei

last: Zhao

first: Siyuan

last: Ding

first: Alexei

last: Lobanov

first: Xialin

last: Wu

first: Mami

last: Matsuda-Lennikov

first: Yousuke

last: Takahama


title: A single-cell RNA sequencing dataset of cardiac aging in African Turquoise Killifish

city: Rochester

first: Baul

last: Yoon

state: MN

address: ST4-16 150 3rd St SW

institute: Mayo Clinic

summary: Aging is a major contributor to functional decline of the heart and various cardiovascular diseases. Alterations across different cardiac cell types must be tightly orchestrated during normative aging process that has begun to be mapped at the transcriptional level through single-cell RNA-sequencing. However, current rodent models are limited in their capacity to experimentally test large numbers of candidate differentially expressed genes (DEGs). As an attractive alternative, the African Turquoise Killifish (ATK) promises more efficient genetic studies of cardiac aging because it has the shortest lifespan among vertebrates. Despite its experimental advantages, single-cell transcriptomic studies on cardiac aging in ATK have not yet been conducted. Here, we generated the first scRNA-seq profiles of hearts from young and old GRZ strain ATK and demonstrated changes in cellular composition, gene expression, functional pathways, and intercellular communication during cardiac aging.

overall_design: Heart cells were extracted from wild-type week 8 (young) and week 16 (old) GRZ strain African Turquoise Killifish and extracted heart cells were used for scRNA-seq data analysis

first: Yifeng

first: Ping

last: Zhu

first: Yuji

first: Xiaolei


title: Inference of cell-cell communication in human fetal liver from high definition spatial profiling using Renoir

first: Narein

last: Rao

state: Texas

address: 6100 Main St

department: Computer Science

institute: RICE University

summary: We developed Renoir, an algorithm for charting the ligand-target activities across a spatial topology. To validate this method, we generated 10x Genomics Visium HD datasets from human fetal liver samples (13 PCW and 14 PCW) and applied Renoir on these datasets. Renoir identified hepatocyte-macrophage interactions in these samples.

overall_design: Two fetal liver samples (FFPE) were used for the generation of 10x Genomics Visium HD datasets.

first: Ankur

last: Sharma

first: Archita

last: Mishra

first: Jerry

last: Chan

first: Florent

last: Jinhoux

first: Hamim

last: Zafar


title: Xenium spatial transcriptomic profiling of mouse lung following pharmacologic inhibition of lactate transport during fibrotic remodeling

city: Providence

first: William

last: Oldham

state: RI

address: 55 Claverick Street

department: Medicine

institute: Brown University

summary: Lactate transport is an important regulator of cellular metabolism and may contribute to fibroblast activation and extracellular matrix remodeling during pulmonary fibrosis. To define the spatial transcriptional landscape associated with pharmacologic inhibition of lactate transport during fibrotic lung remodeling, we performed spatial transcriptomic profiling of mouse lung tissue using the 10x Genomics Xenium Analyzer. Lung sections from mice with bleomycin-induced pulmonary fibrosis treated with inhibitors of monocarboxylate transport were analyzed using the Xenium Prime 5K Mouse Pan Tissue & Pathways panel to generate cell-resolved spatial gene expression maps. The resulting dataset provides spatially resolved transcriptional profiles across epithelial, stromal, endothelial, and immune compartments of the injured lung, enabling analysis of fibroblast activation states and spatial microenvironments associated with fibrotic remodeling.

overall_design: Pulmonary fibrosis was induced in C57BL/6N mice (10–12 weeks old) by intratracheal administration of bleomycin (1.2 U/kg). Beginning on day 7 after injury, mice received pharmacologic inhibition of lactate transport consisting of the MCT1 inhibitor AZD3965 (100 mg/kg twice daily) and the MCT4 inhibitor VB124 (30 mg/kg once daily) administered by oral gavage. Control animals received vehicle alone. Animals were sacrificed 21 days after bleomycin administration and lungs were harvested. The left lung was inflation-fixed and processed for formalin-fixed paraffin-embedded (FFPE) tissue preparation. Lung sections from eight samples were distributed across two Xenium slides to minimize batch effects. Slides were processed according to the Xenium Prime in situ gene expression workflow and hybridized with the Xenium Prime 5K Mouse Pan Tissue & Pathways panel. Spatial transcript detection and imaging were performed on the 10x Genomics Xenium Analyzer, and transcript coordinates were assigned to segmented cells to generate cell-level gene expression profiles for downstream analysis.

first: David

middle: R

last: Ziehr

first: Fei

last: Li

first: Ce

last: Gao

first: Sean

last: Prell

first: Kevin

middle: S

last: Wei

middle: M


title: Effect of elevated ferrous ion to the gene expression of Desulfovibrio ferrophilus IS5

city: Tsukuba

first: Xiao

last: Deng

state: Ibaraki

address: 1-1 Namiki

institute: National Institute for Materials Science

summary: Microbial extracellular electron uptake (EEU) is central to bioelectrochemical processes and biocorrosion, yet its molecular mechanisms remain incompletely understood. Here, we investigate how excess Fe2+ modulates EEU in Desulfovibrio ferrophilus IS5, a strain that causes severe anaerobic iron corrosion via outer-membrane cytochromes (OMCs)-mediated electron uptake. We show that IS5 grown with elevated Fe2+ exhibits substantially enhanced EEU. This enhancement arises through two complementary mechanisms: (i) increased abundance of functional OMCs via upregulation of a cytochrome assembly protein, and (ii) an additional electron transfer route mediated by FeS nanoparticles precipitated on the IS5 outer membrane. Remarkably, IS5 with low OMCs expression but biosynthesized FeS can rapidly shift to EEU before OMCs induction. These findings suggest that during iron corrosion, when IS5 cells are embedded within thick corrosion crusts and biofilms and face both high Fe2+ concentrations and organic limitation, they exploit OMCs and FeS nanoparticles in parallel to sustain high-rate EEU from iron. This study advances the mechanistic understanding of EEU-driven iron corrosion and highlights a potential avenue for manipulating bioelectrochemical systems.

overall_design: RNA profiling of IS5 grown for 4 days in ferrous-enriched medium (containing 3.6 mM Fe2+) and in standard DSMZ 195c medium (containing 7.6 µM Fe2+). Processed data: cpm_195c_easw.xlsx


first: Yongmei

last: Zhao

address: Post Office Box B

department: Advanced Biomedical Computational Science

institute: Frederick National Labroatory for Cancer Research

overall_design: TCRαβ sequencing profile of CD4-CD8+ cells sorted from the lymph node in WT, β5i-KO, β5t-KO and BITmice.

first: Siyuan

last: Ding

first: Alexei

last: Lobanov

first: Xialin

last: Wu

first: Mami

last: Matsuda-Lennikov

first: Yousuke


title: Pertussis Toxin as well as Staphylococcal superantigen induce glycolysis as the major energy source during CD4+ T cell activation in a human tonsil organoid model

first: Christopher

last: Neullens

address: Pauwelsstraße 30, 52074

institute: RWTH Aachen University Medical Faculty

summary: Bystander activation represents an innate-like mechanism by which T cells, particularly effector and memory subsets, can become activated in the absence of cognate antigen recognition. Using human tonsil organoid cultures as a physiologically relevant model, we investigated bystander activation of CD4+ memory T cells in situ in comparison to superantigen stimulation. Tonsillar T cells were stimulated with pertussis toxin – a component of the childhood pertussis vaccine – in comparison to TSST-1 as the staphylococcal superantigen and assessed for activation status, cytokine expression, RNA expression, and metabolic reprogramming. We observed robust T cell activation and cytokine production as well as transcriptional changes comparable to that elicited by TSST-1. Notably, both bystander- and superantigen-activated T memory cells exhibited a metabolic shift toward glycolysis as the dominant energy pathway. These findings demonstrate the similarities of bystander and superantigen-induced TCR -independent T cell activation and show up pathways to sway bystander activation depending on the immunological context.

overall_design: 3'mRNA Seq. profilling of Tmem (CD4, CD45RO, CD69) sorted T cells treated with Pertussis toxin, TSST-1 or anti-CD3/CD28 for 2 days.

middle: T

first: Christaian

last: Kühne

first: Renske

last: de Jong

first: Anandhi

last: Rajendiran

first: Christoph

last: Kessel

first: Sabrina

middle: B

last: Bennstein

first: Justus

last: Ilgner

first: Miguel

last: Goncalves

first: Sebastian

middle: P

last: Schraven

first: Stephan

last: Hackenberg

first: Dirk

last: Baumjohann

first: Kim

last: Ohl

first: Klaus

last: Tenbrock


title: Differential expression profiles of gemcitabine resistant gallbladder cancer cells and parental cells

city: Chongqing

first: Yunping

last: Hu

address: No.30 Gaotanyan Main Street

institute: The First Affiliated Hospital, Third Military Medical University (Army Medical University)

summary: In order to study the transcriptional changes during the development of gemcitabine resistance in gallbladder cancer cells, we established gemcitabine resistant NOZ cells, named NOZ-R. We then performed RNA sequencing (RNA-seq) to compare transcriptome profiles between NOZ-R and parental NOZ cells.

overall_design: we established a resistant gallbladder cancer cell line, NOZ-R using a stepwise dose-escalation method. We compared the expression profiles between NOZ-R and parental NOZ cells using RNA-seq.

first: Jingrong

last: Zhou

first: Gan

last: Tian


title: Ellagic Acid as a Novel YTHDF Inhibitor Triggers Tumor-Suppressive in Triple-Negative Breast Cancer I

city: nanjing

first: Zhou

last: Jun

state: jiangsu

address: longmiandadao

department: College of life science and technology

institute: China Pharmaceutical University

summary: The m⁶A reader proteins YTHDF1–3 are key post-transcriptional regulators of methylated transcripts and have been implicated in the progression of triple-negative breast cancer (TNBC). Owing to their roles in sustaining malignant phenotypes, YTHDF1–3 are attractive targets for therapeutic intervention. Here, we identify ellagic acid (EA), a naturally occurring polyphenol, as a pan-inhibitor of YTHDF proteins. To investigate the effect of YTHDF inhibition on mRNA stability, we performed RNA lifetime sequencing (RNA lifetime-seq) to profile transcriptome-wide RNA decay dynamics in EA-treated TNBC cells.

overall_design: To investigate the effects of EA on triple-negative breast cancer MDA-MB-231 cells, we treated the cells with varying concentrations of EA for 24 hours before performing subsequent analyses.

first: Jianheng

first: Jun

last: Zhang


title: Tissue tension fosters macrophage-driven lipid peroxidation-induced DNA damage [WES]

city: San Francisco

first: Hugo

last: Gonzalez

address: 513 Parnassus Avenue

department: Anatomy

institute: University of California San Francisco

summary: Tissue tension fosters macrophage-driven lipid peroxidation-induced DNA damage.

overall_design: To explore the association between tissue tension, oxidative stress and DNA damage, we utilized the p53null mammary tumor model, where we orthotopically implanted p53null mammary fragments into the cleared mammary fat pads of wild-type females with soft (non-crosslinked) and stiff (L-ribose crosslinked) collagen 1/ basement membrane (Col1/BM) hydrogels, or we implanted p53null mammary fragments into the mammary fat pads of LysM-Cre GPX4 wild-type (WT) or knockout (KO) mice. Mice were euthanized once tumors reached a maximum diameter of 2 cm, at which point tumor tissue was collected for analysis. RNA and DNA were extracted from the tumors for subsequent RNA sequencing (RNA-seq: GSE299513) and/or whole-exome sequencing (WES).

first: Valentina

last: Opazo-Mellado

first: Mary Kate

last: Hayward

first: Valerie

last: Weaver


title: Elimination of senescent cells with senolytic host-directed therapy reduces tuberculosis progression in mice.

city: Baltimore

first: Somnath

last: Shee

address: 1550 Orleans St, CRB2 Building, Room-176

department: Medicine, Infectious diseases

institute: Johns Hopkins University

summary: By eliciting lung necrosis, which enhances aerosol transmission, Mycobacterium tuberculosis (Mtb) sustains its long-term survival as a human pathogen. In studying the necrotic granuloma lesions unique tocharacteristic of Mtb-infected B6.Sst1S mice, we found that lung myeloid cells display elevated senescence markers including cell cycle arrest proteins p21 and p16, the DNA damage marker γH2A.X, senescence-associated β-Galactosidase activity, and senescence-associated secretory phenotype (SASP) proteins. These same markers were also elevated in Mtb-infected aged wild type (WT) mice but not in young WT mice. Global transcriptomics data revealed activation of pro-survival (PI3K, MAPK) and anti-apoptotic pathways in TNFα- treated and Mtb- infected B6.Sst1S BMDMs. As senescent cells have been postulated shown to be long-lived, non-dividing cells which release tissue damaging signaling molecules, we treated Mtb-infected mice with a cocktail of three senolytic drugs (dasatinib, quercetin, and fisetin) designed to kill senescent cells. Senolytic drug treatment prolonged survival and reduced Mtb lung counts in B6.Sst1S and aged WT mice to a greater degree than young WT mice and concomitantly reduced lung senescence markers. These findings indicate that (1) Mtb infection may induce lung myeloid cells to enter a senescent state and that these cells play a causal role in disease progression, and (2) Senolytics merit consideration for human clinical trials against tuberculosis (TB)Senolytics should be tested in human clinical trials against TB.

overall_design: To compare the gene expression in stressed bone marrow- derived macrophages (BMDMs) from young B6.Sst1S mice (female; 8-12 weeks old) relative to young WT C57BL/6 (B6)- BMDMs, we performed bulk RNA- sequencing on BMDMs subjected to (1) 10 ng/ml TNFα treatment (48 hours only), and (2) Mtb H37Rv (MOI=10; 24 hours) infection only.

first: Wiiliam

last: Bishai


title: Resolving inflammation to promote stem cell-based bone regeneration

city: Bergen

first: Salwa

last: Suliman

address: Årstadveien 19

department: Department of Clinical Dentistry

country: Norway

institute: Faculty of Medicine, University of Bergen

summary: Bone marrow-derived mesenchymal stromal/stem cells (BMSC) are widely studied for their potential in regenerative therapies for bone defects. However, the therapeutic efficacy of BMSC is strongly influenced by interactions with the host immune system, particularly T lymphocyte subsets. Emerging evidence suggests that while some T cells can impair BMSC-mediated bone healing, regulatory T cells (Treg) may enhance it by promoting a balanced immune environment.

overall_design: This study investigates immune-modulatory strategies to optimize BMSC-based bone regeneration, focusing on priming BMSC in vitro with either Treg or Resolvin E1 (RvE1), a specialized pro-resolving lipid mediator known to enhance Treg function and promote inflammation resolution. We assessed the osteogenic potential of these primed BMSC implanted with bicalcium phosphate granules (BCP) in vivo and explored the role of endogenous Treg in mediating regenerative outcomes. Furthermore, we evaluated whether RvE1 could rescue impaired bone regeneration in a Treg-deficient mouse model. The different groups are abbreviation as follows in the uploaded samples: BCP alone (BCP), BCP+MSC (MSC), BCP+MSC+Rve1 (R), BCP+MSC+Treg (T), BCP+MSC in Treg depleted mice (DT), BCP+MSC+Rve1 therapy in Treg depleted mice (DTR).

first: Suliman

last: Salwa

first: Rivas

last: Carla Alvarez

first: Srivastava

last: Aashish

first: Marek

last: Nora

first: Mustafa

last: Kamal

first: Kantarci

last: Alpdogan


title: Resistance to neoadjuvant talazoparib in triple-negative breast cancer mediated by BRN2-induced ATR/STAT3 pathways or Shieldin 2 subclone expansion

first: Jeffrey

last: Chang

address: 6431 Fannin St

institute: University of Texas

summary: Intrinsic and acquired resistance to poly(ADP-ribose) polymerase (PARP) inhibitors (PARPi) remains a major barrier in treating homologous recombination (HR) repair-deficient tumors, including those with germline or somatic BRCA1/2 mutations. Although PARPi are FDA approved for adjuvant treatment of locally advanced or metastatic breast cancer in patients with germline BRCA1/2 mutations, emerging data support their use as monotherapy in the neoadjuvant setting. Promising safety profiles of newer-generation PARPi further support this potential. However, resistance mechanisms specific to the neoadjuvant setting are poorly understood. To address this gap, we leveraged resources from a phase II neoadjuvant clinical trial (NCT03499353), analyzing tumors from patients with germline BRCA1/2 mutant  breast tumors before and after six months of talazoparib monotherapy. Whole-transcriptome analyses were performed on these samples. Additionally, we established orthotopic patient-derived xenograft models from a subset of the patient tumors and conducted whole-exome and whole-transcriptome analysis. This integrative approach revealed both known and novel PARPi resistance mechanisms. In one case, overexpression of BRN2, encoding a transcription factor that plays a critical role in neurogenesis, led to activation of ATR/RAD51 and STAT3 pathways, restoring homologous recombination  (HR) repair. BRN2-driven resistance could be reversed with ATR and STAT3 inhibitors, resensitizing cells to talazoparib. In another, an HR repair proficient tumor subclone lacking Shieldin 2 expression expanded during treatment and accounted for intrinsic resistance. Our findings highlight the need to determine intrinsic and anticipate acquired resistance pathways in treatment-naïve tumors and support combining PARPi with targeted agents to improve outcomes in the neoadjuvant setting.

overall_design:
RNA-Seq profiling of PDX tumors established from breast cancer tumors from patients with germline BRCA mutations, before and after treatment with PARP inhibitor.

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These samples are derived from patient tissue, and we do not have consent to share the raw sequence data in a database that is not controlled  access.
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first: Noor

last: Abdulkareem

first: Yan

last: Jiang

first: Yuan

last: Qi

first: Xuan

last: Liu

first: Xiaomei

first: Shirong

last: Cai

first: Jiansu

last: Shao

first: Sabrina

last: Jeter-Jones

first: Amanda

last: Rinkenbaugh

first: Chun-Chun

last: Cheng

first: Faiza

last: Hancock

first: Jill

last: Schwartz

first: Jennifer

last: Litton

first: Helen

last: Piwnica-Worms


title: Hypoxic regulation of chromatin and gene transcription [ChIP-Seq]

city: Oxford

first: David

middle: Robert

last: Mole

address: Roosevelt Drive, Headington

department: Nuffield Department of Medicine

country: United Kingdom

institute: University of Oxford

summary: Pan-genomic analysis of normoxic and hypoxic histone trimethylation by ChIP-seq in cancer cell lines using a Drosophila spike-in normalisation control.

overall_design: Genome-wide assays of histone trimethylation in PC3 and HCT-116 in normoxia and 0.5% hypoxia for 16 hours using a Drosophila spike-in normalisation control

first: Jessica

last: Kindrick


title: Beneficial impact of acquired AmpC β-lactamases on bacterial fitness and pathogenicity: a new paradigm

city: RENNES

first: Charlotte

last: Michaux

address: 2 avenue du Pr Leon Bernard

department: Inserm

country: France

institute: University of Rennes

summary: The study investigated the impact of acquired AmpC β-lactamases on global gene expression and cellular physiology in Enterobacterales. Isogenic Escherichia coli MG1655 strains carrying empty vector (p0) or plasmids encoding CMY-2, CMY-42, or CMY-145 β-lactamase variants were grown to mid-log phase in minimal M9 medium with kanamycin. Total RNA was extracted in three biological replicates, ribosomal RNA was depleted, and strand-specific libraries were sequenced. Reads were mapped to the E. coli K-12 reference genome and differential expression analysis was performed. Comparative transcriptomics revealed large gene expression changes associated with AmpC variant production, including consistent deregulation of genes involved in flagellar biosynthesis, motility, and additional metabolic functions. These RNA-seq data provide a transcriptomic framework to understand how distinct AmpC variants differentially reshape bacterial regulatory networks beyond β-lactam resistance.

platform_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: RNA-seq profiling of wild-type Escherichia coli MG1655 with or within expression of different β-lactamase variants.

first: Otávio Hallal

last: Ferreira Raro

first: Andrea

last: Endimiani

first: Jorge

last: Lariosf

first: Claudia

last: Aldeia

first: Edgar

last: Campos-Madueno

first: Dimitri

last: Vanhecke

first: Patrice

last: Nordmann

first: Vincent

last: Cattoir

first: Laurent

last: Poirel


title: An Optimised Translating Ribosome Affinity Purification (TRAP) Protocol for Low-Abundance Drosophila tissues

city: Cambridge

first: Alex

last: Whitworth

address: Hills road

department: MRC MBU

institute: University of Cambridge

summary: Localised protein translation, from subcellular localised mRNAs, has emerged as an important process of spatially-restricted cellular changes. This is especially important in cells with extremely elaborated architectures such as neurons. We present a highly sensitive TRAP protocol optimised for the specific isolation of ribosome-bound mRNAs in Drosophila from limited input samples, which enabled the isolation of axonal mRNAs from larval and adult (leg) motor neurons. RNA-seq revealed a set of axonally translated transcripts, including mRNAs encoding multiple ribosomal and mitochondrial proteins. Notably, these are among the types of transcripts found in axons of other species, indicating that axonal translation is conserved in Drosophila. Our optimised low-input TRAP method will allow the study of local translation to be explored in conjunction with Drosophila genetic manipulations, facilitating in-depth investigation of axonal translation across genetic backgrounds, developmental stages, and experimental conditions such as models of human disease. Moreover, it can be used for rare or genetically challenging genotypes and can be adapted to other tissues and model systems that may benefit from a sensitive TRAP protocol.

overall_design: Translating Ribosome Affinity Purification (TRAP) was used to identify neuronal mRNAs from Drosophila heads and axonal mRNAs from adult legs and larval motor neurons expressing Flag-GFP-RpL10 under DIP-γ-GAL4 (adult neurons) or OK371-GAL4 (larvae). Control genotype was UAS-Flag-GFP-RpL10/+. Three biological replicates were performed per condition (two for leg control).

first: Leonor

last: Miller-Fleming

first: Wing Hei

last: Au


title: Hypoxic regulation of chromatin and gene transcription

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

overall_design: Refer to individual Series


title: Comparative single cell genomics of facial signaling centers of avian and murine embryos [ME11_scATAC-seq]

city: Plön

first: Stella

last: Kyomen

address: August-Thienemann-Strasse 2

institute: Max Planck Institute for Evolutionary Biology

summary: Morphogens are crucial in craniofacial development, directing cellular processes that shape facial features in vertebrates. In this study, we used single-cell RNA and ATAC sequencing to investigate the genomic regulation underlying species-specific morphogen expression in mouse and chicken embryos. We identified unique expression patterns of morphogens and receptors across facial prominences in both species and predicted cellular communication between cell populations involved in facial development. Our analysis revealed highly specific morphogen expression, predominantly originating from spatially segregated regions known as signaling centers. By examining the chromatin landscape, we uncovered species-specific regulatory elements and accessibility patterns that control gene expression and facial morphogenesis. We validated candidate enhancers in vivo, demonstrating that their activity correlates with the expression of morphogen ligands in the embryonic face. This study underscores the complex and species-specific regulation of facial morphogenesis, offering insights for comparative genomics across vertebrates with distinct facial morphologies.

overall_design: Single-cell ATAC-seq of facial prominences from wild type mouse embryos (embryonic stage E11.5).

first: Louk

last: Seton


title: Hypoxic regulation of chromatin and gene transcription [ChIP-seq]

first: David

last: Mole

middle: D


title: Ellagic Acid as a Novel YTHDF Inhibitor Triggers Tumor-Suppressive in Triple-Negative Breast Cancer II

first: Zhou

last: Jun

summary: The m⁶A reader proteins YTHDF1–3 are key post-transcriptional regulators of m⁶A-modified transcripts in mammalian cells, and have emerged as critical contributors to the pathogenesis of triple-negative breast cancer (TNBC). Given their role in promoting tumorigenic phenotypes, YTHDF1–3 represent promising therapeutic targets. In this study, we identified ellagic acid (EA), a natural small molecule, as a pan-inhibitor of YTHDF proteins. To investigate the translational consequences of YTHDF inhibition, we performed ribosome profiling (Ribo-seq) to assess the global impact of EA on mRNA translation in TNBC cells.

first: Jianheng

last: Zhou

first: Jun

last: Zhang


title: Nanopore-based sequencing of active DNA replication reveals key principles of metazoan replication fork progression and origin usage

city: Nashville

first: Jared

last: Nordman

state: TN

address: 465 21st Ave S

institute: Vanderbilt University

summary: Balancing replication fork progression and origin usage is essential to maintain genome stability, but measuring replication fork progression rates and origin usage throughout the genome has been challenging. Here, we use nanopore sequencing combined with DNAscent to measure replication fork progression together with origin and termination site usage with single-molecule precision throughout the Drosophila genome with nearly full genome coverage. We find that replication fork progression rates are not uniform throughout the genome. Rather, fork progression is slowest in euchromatin, and this is not correlated with active transcription. Replication origins are also influenced by chromatin, but the exact position of initiation is highly variable and are often several kilobases away from ORC binding sites. Termination sites lack any chromatin or sequence motifs and appear nearly random throughout the genome. By measuring DNA replication dynamics at near full genome coverage, our work reveals key principles of metazoan replication dynamics.

overall_design:
Drosophila S2 Cell cultures are labeled with thymidine analogue EdU and chased with BrdU. Extracted uHMW gDNA is sequenced using Nanopore Sequencing and replication forks are identified using DNAscent.

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Raw data not included because SRA does not support upload in pod5 format.
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first: Dongsheng

last: Han

first: Cole

last: Shepherd

first: Mary Lauren

last: Benton


title: Comparative single cell genomics of facial signaling centers of avian and murine embryos [HH22_scATAC-seq]

overall_design: Single-cell ATAC-seq of facial prominences from wild type chicken embryos (embryonic stage HH22).


title: Spatial analysis revealed localization of osteblastogenesis-inhibitory factors in Giant Cell Tumor of Bone

city: Chuo-ku

first: Masaki

last: Shimada

state: Kumamoto

address: 1-1-1 Honjo

department: Department of Orthopaedic Surgery

institute: Kumamoto University

summary: Giant cell tumor of bone (GCTB) is an intermediate malignant tumor characterized by osteolytic lesions. Although surgical resection is the mainstay of treatment, the postoperative recurrence is frequently seen, and the tumor can arise in surgically challenging locations such as the pelvis. GCTB tumor cells are not giant cells, but rather stromal cells surrounding giant cells. However, currently available pharmacological therapies are limited to indirect inhibition of bone resorption by giant cells. The mechanisms underlying the marked osteolysis and the insufficient osteogenesis—despite the usual reactive stimulation of bone formation—remain poorly understood. In this study, we employed spatial transcriptomic approaches to visualize gene expression within the tumor microenvironment of GCTB. The resulting data, integrated with immunohistochemical analyses, revealed region-specific cellular distributions and characteristic gene expression patterns, providing new insights into the survival strategies of this tumor.

overall_design: The 5 µm section of the formalin-fixed paraffin-embedded (FFPE) tumor block was placed on a standard glass slide. Deparafinization, H&E staining and imaging were performed. After decrosslinking was conducted, probe hybridization and ligation were also performed.

first: Takeshi

last: Miyamoto


title: Cord-derived iNKT cells are enriched with human NKT10 and exert the immunosuppressive function through the interaction with NRP1 [RNA-seq]

city: Houston

first: Jin Seon

last: Im

address: 7455 Fannin St

department: HBM

institute: MD Anderson Cancer Center

summary: Invariant Natural Killer T (iNKT) cells are a unique subset of T lymphocytes that recognize glycolipid antigens presented by the non-polymorphic MHC class I-like molecule CD1d through a semi-invariant T cell antigen receptor. In mice, this receptor consists of the invariant Vα14Ja18 (TRAV11+TRAJ18+) chain paired with Vβ8, Vβ7, or Vβ2, while in humans, it comprises Vα24Ja18 (TRAV10+TRAJ18+) paired with Vβ11. Upon activation, iNKT cells modulate adaptive immunity by promoting either immune suppression or inflammation through the production of Th1- and Th2-type cytokines. They also enhance adaptive T and B cell responses via the CD40-CD40L feedback loop with antigen-presenting dendritic cells (DCs). iNKT cells exhibit phenotypic and functional heterogeneity, with subsets including CD4+ and CD4- populations, as well as functionally distinct NKT1 (Th1), NKT2 (Th2), NKT10 (Th10), and NKT17 (Th17) cells. The developmental pathways and immunological roles of murine iNKT cells are well characterized, highlighting their functional plasticity in immune modulation. The NKT10 subset, in particular, has been studied in various murine models and demonstrated a regulatory function within CD4+ iNKT cells. These cells are enriched in specific NKT10 signature markers, including IL-10, NRP1, and PD-1, which define their immunoregulatory properties. Despite these findings in mice, the phenotype and function of IL-10-producing human iNKT cells remain poorly characterized, and their regulatory role in human diseases is not well understood. Here, we aim to characterize human NKT10 cells derived from cord blood iNKT cells and explore their therapeutic potential in bone marrow transplantation.

overall_design: The freshly-expanded iNKT cells from adult donor and cord blood at resting status were stained for following surface markers: CD3, iNKTCR, CD4, and Live/Dead Fixable 620, followed by FACS-sorting for CD4+iNKTCR+CD3+ or CD4-iNKTCR+CD3+ cells from adult-derived iNKT cells and CD4+iNKTCR+CD3+ from cord-derived iNKT cells. Total RNA was extracted from adult and cord iNKT cells, then submitted for RNA sequencing.


title: CTHRC1 promotes bone metastasis in prostate cancer

city: Toon

first: Yuichiro

last: Sawada

address: Shitsukawa

institute: Ehime Univercity

summary: Prostate cancer causes a high frequency of bone metastases. The purpose of this study was to identify molecules that regulate prostate cancer bone metastasis as potential therapeutic and/or prognostic targets in prostate cancer, using integrative genome-wide data. Based on the biological characterization of prostate cancer cell lines and integrated big data analysis of clinical samples, we identified CTHRC1 as a candidate gene that regulates prostate cancer bone metastasis. The knockdown of CTHRC1 suppressed cell migration and cell adhesion, but not cell proliferation, in vitro and in vivo. In a mouse tibia xenograft model, CTHRC1 knockdown markedly suppressed metastatic growth of prostate cancer cells in the bone microenvironment. CTHRC1 also promoted in vitro osteoclast differentiation. The analysis of 343 human prostate cancer biopsy samples showed that CTHRC1 expression was positively correlated with bone metastasis, indicating that CTHRC1 could be a useful predictive marker for bone metastasis. Our findings illustrate the clinical relevance of CTHRC1 and demonstrate that CTHRC1 plays an important role in prostate cancer bone metastasis. CTHRC1 may be useful for predicting prostate cancer bone metastasis and may lead to the development of new methods for the prevention and treatment of metastasis.

overall_design: mRNA profiles of sh Control PC3-Luc cells and two CTHRC1 knockdown PC3-Luc cells were generated by deep sequencing, in triplicate, using NovaSeq6000.

first: Yuuki

last: Imai


title: Cellular stress-induced eccrine gland dysfunction as a potential mechanism in acquired idiopathic generalized anhidrosis

city: Hamamatsu

first: Tetsuya

last: Honda

address: 1-20-1 Handayama, Chuo-ku

institute: Hamamatsu University School of Medicine

summary: Acquired idiopathic generalized anhidrosis (AIGA) is a rare disorder characterized by systemic anhidrosis or hypohidrosis of unknown etiology. Corticosteroid pulse therapy is widely used for its treatment. We analyzed skin lesions from AIGA patients before and after corticosteroid pulse therapy through single-cell RNA sequencing analyses.

overall_design: Biopsies were taken from anhidrotic skin areas before corticosteroid therapy and from adjacent sweat-recovered areas after therapy.

first: Reiko

last: Kageyama

first: Keiko

last: Sakamoto

first: Satoshi

last: Nakamizo

first: Masahiro

last: Nakagawa

first: Kenji

last: Kabashima

first: Keisuke

last: Nagao


title: Elimination of senescent cells with senolytic host-  directed therapy reduces tuberculosis progression in mice

first: Somnath

last: Shee

overall_design: To compare the gene expression in stressed bone marrow- derived macrophages (BMDMs) from young B6.Sst1S mice (female; 8-12 weeks old) relative to young WT C57BL/6 (B6)- BMDMs, we performed bulk RNA- sequencing on BMDMs subjected to 10 ng/ml TNFα pretreatment (18 hours), followed by Mtb H37Rv (MOI=10; 24 hours) infection in the continued presence of TNFα.

first: Wiiliam

last: Bishai


title: An Artemisia scoparia extract and rosiglitazone have distinct but overlapping effects on adipocyte function.

city: Baton Rouge

first: Jacqueline

last: Stephens

address: 6400 Perkins Road

institute: Louisiana State University

summary: The effects of the PPAR-gamma agonist rosiglitazone (ROSI) on adipocyte gene expression have been extensively studied. Like ROSI, both SCO and a bioactive derivative, capillartemesin 7 (CAP7) inhibit lipolysis induced by the inflammatory cytokine TNF-alpha; they appear to do so through PPARg-dependent mechanisms that are overlapping but not identical to those engaged by ROSI. To compare the transcriptional effects of SCO, CAP7, and ROSI, we performed a comparative gene expression profiling analysis of RNA-seq data from fully differentiated adipocytes that were treated with DMSO vehicle, SCO, CAP7, or ROSI, in the presence or absence of TNFa. Gene ontology and pathway analyses were performed to provide guidance for developing additional hypotheses to investigate mechanism of action underlying the ability of SCO and CAP7 to reduce TNFa-induced lipolysis and affect overall adipocyte function.

overall_design: Fully differentiated 3T3-L1 adipocytes were treated with DMSO vehicle, SCO, CAP7, or the PPARgamma agonist, rosiglitazone (ROSI), in the presence or absence of TNFa. Four replicates per condition were included. ROSI was used as control to compare specific affects on PPARgamma target gene expression.

first: Anik

last: Boudreau

first: Allison

middle: J

last: Richard

first: Lindsey

last: Yoo


title: RbFox2 is a RhoBTB1-Cullin-3 Target in Vascular Smooth Muscle Regulating Arterial Stiffness through the Cytoskeleton

city: Wauwatosa

first: Ibrahim

last: Vazirabad

state: Wisconsin

address: 8915 W Connell Ave

department: Physiology

institute: Medical College of Wisconsin

summary: The RhoBTB1-Cullin3 (CUL3) pathway in smooth muscle cells (SMCs) controls the ubiquitination of target proteins and through this blood pressure (BP) and arterial stiffness. We performed proximity labelling coupled with mass spectrometry to identify RhoBTB1 interacting partners in A7R5 SMCs. We identified 59 proteins which bound to the C-terminal half of RhoBTB1, the region identified as essential for its adapter function to deliver substrates to CUL3. We examined one of these proteins in detail - RbFox2. Co-immunoprecipitation validated the interaction of RbFox2 with RhoBTB1. Expression of RbFox2 was elevated in response to inhibition of the ubiquitination-proteasomal pathway, CUL3-deficiency, and RhoBTB1 inhibition by either siRNA or angiotensin II (ANG). RbFox2 was ubiquitinated in a RhoBTB1- and CUL3-dependent manner suggesting it is regulated through the RhoBTB1-CUL3-dependent ubiquitin-proteasome pathway. Inhibition of RbFox2 impaired the actin cytoskeleton in A7R5 cells and in primary SMC from RbFox2Flox mice and decreased the levels of globular and filamentous actin. ANG increased BP and arterial stiffness of RbFox2Flox mice, but the progression of arterial stiffness was halted after SMC-specific RbFox2 deletion despite a continued rise in BP. We conclude that RhoBTB1 and its target RbFox2 is an important regulator of arterial stiffness through its actions to regulate the cytoskeleton.

overall_design: A7R5 cells were grown in Dulbecco’s modified Eagle medium supplemented with 5% fetal bovine serum and 1% penicillin–streptomycin and maintained at 37°C with 5% CO2. The A7R5 cells were transfected with RbFox2 siRNA and matched scrambled control siRNA.

first: Gaurav

last: Kumar

first: Nisita

last: Chaihongsa

first: Daniel

last: Brozoski

first: Daria

last: Golosova

middle: Y

first: Ko-Ting

last: Lu

first: Kelsey

last: Wackman

first: Ravi

last: Singh

first: Curt

last: Sigmund


title: Killer cell immunoglobulin-like receptors delineate distinct phenotypes and functions in human γδ T cells [RNA-seq]

city: Ottawa

first: Alexandre

last: Blais

state: ON

address: 451 Smyth Road

institute: University of Ottawa

summary: Killer cell immunoglobulin-like receptors (KIRs) are a diverse family of HLA class I-specific receptors that shape immune responses, primarily through NK cells. Beyond NK cells, subsets of T cells, notably γδ T cells, express KIRs, but their roles remain unclear. Here, we demonstrate that KIR⁺γδ T cells are significantly more abundant in CMV-seropositive healthy adults, particularly within the Vδ2⁻ subset. These cells exhibit a TEMRA phenotype, are predominantly CD16⁺CD57⁺, hallmarks of a highly differentiated state, and express multiple NK cell-associated receptors. KIR+γδ T cells display enhanced cytotoxic potential, with higher levels of granzyme B and perforin than their KIR- counterparts. Using Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) and transcriptional analyses, we show that KIR- and KIR+ γδ T cells reveal distinct molecular signatures, with KIR+γδ T cells transcriptionally and epigenetically aligning with terminally differentiated effector memory T cells, while KIR- cells retain a naïve-like phenotype. These findings suggest that CMV infection drives the differentiation of γδ T cells into potent, KIR-expressing cytotoxic effectors. This adaptive mechanism may bolster immune defense while maintaining self-tolerance, highlighting a previously unappreciated role for KIRs in shaping γδ T cell immunity.

overall_design: Peripheral blood KIR- and KIR+ γδ T cell subsets from healthy adult humans were separately sorted using flow cytometry. Total RNA was then extracted and subjected to short-reads high-throughput sequencing. Six biological replicates for each subset were profiled.

first: Mahya

last: Razmi

first: Yeganeh

last: Almasi

first: Marilee

last: Larrivée

first: Jonathan

last: Angel

first: Zakia

last: Djaoud


title: The pleuroparenchymal fibroelastosis atlas reveals aberrant cell states and their zonation as an alternate roadmap to lung fibrosis

city: Hannover

first: Jonas

last: Schupp

address: Carl-Neuberg-Str. 1

department: Respiratory Medicine

institute: Hannover Medical School

summary: Single-nuclei RNA-sequencing (snRNA-seq) using the 10x Genomics Flex technology was performed in peripheral lung tissues from  PPFE patients undergoing lung re-transplantation, and from  healthy control lungs.

overall_design: Lung tissue from PPPFE patients vs control lungs

middle: C

first: Justet

last: Aurelien

first: Lena

last: Leiber

first: Ruwisch

last: Jannik

first: Cazes

last: Aurelie


title: Killer cell immunoglobulin-like receptors delineate distinct phenotypes and functions in human γδ T cells [ATAC]

overall_design: Peripheral blood KIR- and KIR+ γδ T cell subsets from healthy adult humans were separately sorted using flow cytometry. ATAC-seq libraries were then prepared using the OMNI-ATAC protocol descibed by Corces et al (Nature Methods, 2017). Six biological replicates for each subset were profiled.


title: eIF4E2 Deficiency Drive Cisplatin Resistance in NSCLC

city: nanjing

first: Zhou

last: Jun

address: longmiandadao

institute: China Pharmaceutical University

summary: Cisplatin resistance remains a major obstacle in treating non-small cell lung cancer (NSCLC). Mechanistic insights into the translational control of cisplatin resistance remain sparse. This study identifies eIF4E2 as a critical translational regulator whose downregulation elevates DNA repair capacity and drives cisplatin resistance.

overall_design:
Ribosome profiling was performed on:
(i) PC9 parental cells (PC9/Nor) and their cisplatin-resistant derivative (PC9/DDPr) (each with two biological replicates);
(ii) PC9 cells with eIF4E2 knockdown, comprising:
- A knockdown cohort transduced with two distinct shRNAs targeting eIF4E2 (representing two independent biological replicates)
- A control cohort transduced with non-targeting shScramble (two independent biological replicates).
Matched Input RNA and ribosome-protected footprints (RPFs) from all eight samples were subjected to high-throughput sequencing.

first: Xianrong

last: Lin

first: Rui

last: Zhang

first: Wenjun

last: Tao

first: Jun


title: Tissue tension fosters macrophage-driven lipid peroxidation-induced DNA damage [RNA-seq]

city: San Francisco

first: Hugo

middle: A

last: Gonzalez

address: 513 Parnassus Avenue

institute: University of California San Francisco

summary: Using RNAseq and WES, we explore differences in the transcriptional and mutational landscapes between soft and stiff p53null mammary tumors

overall_design: To explore the association between tissue tension and DNA damage, we utilized the p53null mammary tumor model, where we orthotopically implanted soft (non-crosslinked) and stiff (L-ribose crosslinked) collagen 1/ basement membrane (Col1/BM) hydrogels with p53null mammary fragments into the cleared mammary fat pads of syngeneic wild-type females. Mice were euthanized once tumors reached a maximum diameter of 2 cm, at which point tumor tissue was collected for analysis. RNA and DNA were extracted from the tumors for subsequent RNA sequencing (RNA-seq) and whole-exome sequencing (WES; GSE318365), respectively.

first: Mary Kate

last: Hayward

first: Valerie

last: Weaver


title: Evidence for coordinate epigenomic roles for CTCF and histone H3.3 in K27M diffuse midline gliomas [ChIP-seq]

city: Sacramento

first: Paul

last: Knoepfler

state: CA

address: 2425 Stockton Blvd, Room 633

department: Cell Biology and Human Anatomy

institute: University of California Davis

summary: In this study we identified and characterized key chromatin domains in diffuse midline glioma cells, looking at well known types of domains including super enhancers, bivalent domains, and H3K4me3 broad domains as well as the chromatin states identified by chromHMM. In this context, we identified a key role for CTCF in maintaining H3K27me3 levels at bivalent domains, and demonstrated that the H3.3K27M mutation affects both CTCF localization and H3K27me3 at these regions. We further characterized a functional interaction between H3.3 and CTCF in diffuse midline glioma cells, finding that the H3.3K27M mutation affects CTCF localization, leading to an expansion of CTCF-bound domains including a large number of ectopic CTCF binding sites found in H3.3K27M but not WT cells. We also found that CTCF knockdown increases cell viability in H3.3K27M cells, and affected the expression of a set of genes highly enriched in active chromatin states and likely important for some of the oncogenic properties of these cells. Together, our results identified complex chromatin domains defined by combinations of epigenetic modifications, which may have implications for designing therapy regimens that include multiple epigenetic drugs to more effectively target the numerous changes in chromatin observed in glioma cells with H3.3K27M. We also defined an important role for the structural protein and transcription factor CTCF in influencing the epigenetic landscape and transcriptome in the context of the H3.3K27M mutation in diffuse midline glioma cells.

overall_design: H3K4me3 ChIP-seq was performed in duplicate in DIPG Line XIII cells.

first: Rachel

last: Klein


title: Hypoxic regulation of chromatin and gene transcription [RNA-seq]

first: David

last: Mole

summary: Pan-genomic analysis of poly-adenylated transcript levels in normoxic and hypoxic cancer cell lines

overall_design: PolyA RNA-seq analysis of gene expression in PC3 and HCT-116 incubated in 21% oxygen and 0.5% oxygen for 16 hours

first: Jessica

last: Kindrick


title: Comparative single cell genomics of facial signaling centers of avian and murine embryos [HH22_scRNA-seq]

first: Stella

last: Kyomen

overall_design: Single-cell RNA-seq of facial prominences from wild type chicken embryos (embryonic stage HH22).

first: Louk

last: Seton


title: Baicalin maintained redox balance and inhibited PI3K/AKT pathway via binding with AKT to ameliorated LPS induced cardiac injury

city: wuxi

first: Zhixuan

state: Jiangsu

address: North Hospital, No. 200 Huihe Road, Binhu District

institute: Jiangnan University

summary:
Purpose The aim of this study was to investigate the effects of baicalin on septic cardiomyopathy and to elucidate the underlying mechanisms involved. Specifically, this study sought to determine the effects of baicalin on septic cardiomyopathy induced by AC16 cells and LPS in C57BL/6J mice and its underlying mechanisms.
Methods: Echocardiography, histological staining, immunoblotting, qPCR, ELISA, RNA-seq, network pharmacology and molecular docking were performed. Changes in cardiomyocytes after LPS injection in mice were observed. The targets of baicalein  in septic cardiomyopathy were screened using molecular docking and molecular dynamics, and the pathway of baicalein action was further elucidated by using RNA-seq and network pharmacology.
Results: LPS stimulation induced apoptosis, an inflammatory response and oxidative stress in cardiomyocytes. In vivo experiments revealed that baicalin treatment attenuated septic myocardial injury, as evidenced by enhanced cardiac functional parameters, preservation of myocardial structure, and reduced inflammatory/apoptotic responses, and RNA-seq analyses revealed that the Pi3k/AKT signaling pathway was activated after the administration of baicalin, which was verified both in vitro and in vivo; this indicated that the protective effects of baicalin were related to the findings in vitro and in vivo, suggesting that the protective effect of baicalin is related to the activation of the PI3K/AKT pathway. Molecular docking studies revealed that baicalin inhibited cardiomyocyte inflammation and cardiomyocyte apoptosis, thereby ameliorating sepsis-induced cardiac injury, which may be related to the PI3K/Akt pathway.
Conclusion: Baicalin activates the PI3K/AKT pathway and protects against sepsis-induced cardiac injury by binding with AKT.

overall_design: In this experiment, mice were divided into three groups: the blank group, the LPS group, and the LPS + baicalin group. After one week of adaptive feeding, the mice were randomly assigned to the blank group, LPS group, and baicalin administration group (100 mg/kg), with 8 mice in each group. The baicalin group was gavaged with the corresponding dose of baicalin, while the blank group and LPS group were gavaged with an equal amount of distilled water. After 14 days of continuous administration, both the LPS group and the baicalin group received a single intraperitoneal injection of 10 mg/kg LPS to establish a mouse model of septic cardiomyopathy, while the blank group received an equal volume of saline. Seventy-two hours after LPS injection, anesthesia was induced using 1%-1.5% isoflurane for cardiac ultrasound examination. The mice were then euthanized, and blood and cardiac tissue were collected for transcriptomic sequencing to explore the mechanism of action of baicalin in LPS-induced septic cardiomyopathy.Transcriptomics for differential gene analysis

first: Qiusheng

last: Shen

first: Xin

last: Gu

first: Xiaodong


title: Comparative single cell genomics of facial signaling centers of avian and murine embryos [ME11_scRNA]

overall_design: Single-cell RNA-seq of facial prominences from wild type mouse embryos (embryonic stage E11.5).