title: A transcriptional atlas of endothelial cell zonation along the pulmonary vascular tree

status: Public on Jan 06 2026

city: San Fransisco

first: Cristina

last: Alvira

state: CA

address: 555 Mission Bay Blvd South

institute: University of California, San Fransisco

summary: Background: The pulmonary vasculature exists as a series of branching vessels that are on gradients of size, oxygenation and pressure. Single cell transcriptomics have provided key insights into the different populations that make up the vasculature but the transcriptomic gradients remain largely undescribed.  Methods: We applied a method of endothelial enrichment and deep single cell RNA sequencing to create a high resolution, transcriptomic dataset from the developing mouse lung.  We developed an analytical framework to assign vessel-size scores and categorize individual endothelial cells (EC) and mural cells along a continuum of vessel sizes. We delineated a continuum of proximal arterial through distal venous EC states by uncovering transcriptional signatures associated with vessel size, spanning micro- to macrovascular zones. Our data recapitulated previously established zonally defined signaling axes, including Cxcl12 and Cxcr4 in arterioles, and identified localization of disease relevant markers such as Esr2. This vessel-size informed framework was robust across species and revealed how spatial EC heterogeneity underlies key processes in lung development and injury.  Results: We generated a robust endothelial cell enriched scRNAseq dataset from the neonatal mouse lung, with deep sequencing coverage. Within this dataset, we defined transcriptomic signatures of macrovascular populations– pulmonary artery (PAEC) and vein (PVEC) endothelial cells– as well as for the microvascular capillary 1 (Cap1) population, incorporating canonical markers genes (e.g. Eln, Vwf, Tmem100, Scn7a). Many of these markers exhibited gradient -like expression patterns extending from arteries or veins toward Cap1, while others displayed polarized expression throughout the Cap1 cluster itself, with subsets exhibiting either artery- or vein-associated signatures. This analytical framework was successfully applied to published human lung datasets across developmental stages, demonstrating cross-species and temporal relevance. Conclusions: By linking scRNA-seq profiles with tissue context, we reconcile molecular signatures with anatomical structure of the pulmonary vasculature, enabling assignment of each individual cell to vessels with defined size. These findings provide a comprehensive transcriptional map of pulmonary endothelial cells and associated mural populations across the vascular continuum, offering valuable insights into spatial inferences and mechanistic insights within single cell RNA sequencing data sets that may help pave the way for targeted therapeutic strategies to treat pulmonary vascular diseases and expansion to tissues outside the lung.

overall_design: At birth, neonatal C57BL-6 (Charles River) mice were housed in room air (normoxia; N) or 80% O2 (hyperoxia; H) for 72hr before euthanasia (N=6 per exposure; 3M 3F). Followed by 10x 3' v4 scRNA-seq.

first: Stefanie

last: Sveiven

first: Carsten

last: Knutsen

first: Fabio

last: Zanini

first: David

last: Cornfield


title: Single-cell data for FGFR3-driven gene regulatory network analysis reveals a pro-tumoral role for p63 in luminal bladder tumors

city: Gif-sur-Yvette

first: Lilia

last: Estrada Virrueta

address: 1, Avenue de la Terrasse

country: France

type: Expression profiling by high throughput sequencing

summary: FGFR3 (Fibroblast Growth Factor Receptor 3) is one of the most frequently altered genes in bladder cancer, primarily through activating mutations that drive oncogenesis and are enriched in luminal tumors. However, the underlying gene regulatory network (GRN) remains poorly characterized. Here, we inferred an FGFR3-mutated GRN using a bottom-up bioinformatics approach, integrating transcriptomic data from bladder cancer cell lines, FGFR3-mutated tumors, and FGFR3-perturbation experiments in human and mouse models. Using CRISPR-Cas9 screen public data, we identified transcription factors (TFs) from this GRN that regulate the viability of FGFR3-mutated cells, with a focus on p63 (TP63). We showed that FGFR3 activation upregulates p63 in patient-derived xenografts and cell lines, while single-cell RNA sequencing revealed heterogeneous p63 activation associated with basal differentiation. Functional studies, including TP63 knock-down in FGFR3-dependent in vitro and in vivo models and RNA-seq along with p63 ChIP-seq, demonstrated that p63 directly promotes cell proliferation and migration, and uncovered a positive feedback loop between FGFR3 and p63. Together, these findings identified p63 as a pro-tumorigenic regulator in FGFR3 mutated tumors despite their luminal differentiation and provide a detailed FGFR3-driven GRN, offering insights into FGFR3-induced oncogenic dependency and potential strategies to circumvent resistance to FGFR inhibitors.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: MGH-U3 and RT112 cells were treated with DMSO or 100 nM erdafitinib for 38 h and  patient‐derived tumor xenografts (PDXs) from the F659 model bearing FGFR3 mutations were sequenced via single-cell RNA-seq. PDXs from F659 models, harboring an FGFR3‐S249C mutation, were obtained as detailed in the publication attached (PMID: 29463565), they were generated by engrafting tumor tissues directly obtained from patients. Fresh tumors were used for single-cell RNA-seq analysis. The sequencing output was processed using Cell Ranger from 10x Genomics.

first: Isabelle

last: Bernard-Pierrot

first: Xiang-Yu

last: Meng

last: Estrada-Virrueta

first: Guerric

last: Gilbert

first: Helene

last: Neyret-Kahn


title: Small nucleolar RNA Snora61 drives self-renewal of small intestinal stem cells via initiation of Lgr5 transcription

city: Beijing

first: Jiacheng

last: He

state: Beijing

address: No.15 DaTun Road

country: China

institute: IBP

summary: Intestinal epithelium relies on intestinal stem cells (ISCs) for rapid and precise tissue replenishment to maintain gut normal function. The self-renewal maintenance of ISCs is finely regulated by multiple stemness factors and signaling pathways. However, the transcription mechanisms of some key stemness factors remain poorly understood. Here we identified that small nucleolar RNA Snora61 is highly expressed in ISCs. Snora61 is mainly distributed in the nucleoplasm. Snora61 knockout impairs ISC self-renewal and intestinal regeneration. Mechanistically, Snora61 binds to the promoter region of Lgr5 gene and engages with RNA-binding protein RBMX to recruit HMGB2 onto Lgr5 promoter, leading to Lgr5 transcription and expression. Snora61 promotes the self-renewal of small intestinal stem cells, which in turn enhances the proliferation of downstream differentiated cells, thereby contributing to the maintenance of intestinal homeostasis. Conversely, Snora61 knockout causes reduced LGR5 expression. Deletion of Lgr5 with Snora61 displays more severely impaired ISC self-renewal and intestinal regeneration. Our findings reveal a novel regulatory mechanism of Lgr5 transcription underlying ISC self-renewal maintenance.

overall_design: ChIRP-seq of Snora61 in ISCs


title: Humanized and Charge-Optimized CSPG4-Specific CAR-T Cells Show Enhanced Efficacy Against Head and Neck Squamous Cell Carcinoma

city: shanghai

first: wang

last: zhitong

state: shanghai

address: No. 138, Fenyang Road, Xuhui District

department: Otorhinolaryngology

institute: Eye & ENT Hospital

summary: Chimeric antigen receptor (CAR) T cell therapy for head and neck squamous cell carcinoma (HNSCC) is hampered by the lack of a robust tumor antigen and a suitable CAR design.CSPG4 is highly expressed in HNSCC clinical samples and cell lines, correlating with poor prognosis. Its knockout markedly reduced tumor cell proliferation in vitro and in vivo, validating CSPG4 as an attractive CAR target. First‑generation CSPG4.CAR‑T cells bearing the murine scFv 763.74 showed potent in vitro cytotoxicity but failed to control tumor growth in vivo due to excessive tonic signaling and early exhaustion. By humanizing the scFv framework to reduce positive_x001E_charge residues and immunogenicity, we generated CAR_x001E_T cells with low tonic signaling, diminished exhaustion and differentiation, enhanced tumor_x001E_specific killing, and prolonged in vivo persistence, resulting in superior antitumor activity in both xenograft and PDX models.

overall_design: We confirmed CSPG4’s expression and oncogenic role via qPCR and immunohistochemistry on primary HNSCC specimens, and by CRISPR‑mediated knockout in cell lines and xenografts. To optimize CAR design, we grafted the murine scFv 763.74 CDRs onto a human antibody framework engineered to minimize surface positive‑charge patches and immunogenic epitopes. Humanized CSPG4.CAR‑T cells were then evaluated for tonic signaling, exhaustion marker expression, proliferation, and cytotoxicity in vitro, as well as for antitumor efficacy and persistence in cell‑line xenograft and patient‑derived xenograft (PDX) models.

first: Jian

last: Chen

first: Xiang

last: Xu

first: Shizhen

last: Qiu

first: Zhitong

last: Wang

first: Haopeng


title: Prenatal diisononyl phthalate exposure induces the development of  pulmonary dysplasia in offspring

city: Shuozhou

first: Dan

last: Li

state: Shanxi

address: No. 11, Changning Street

institute: Shanxi College of Technology

summary: As a widely used plasticizer, Diisononyl phthalate (DINP) has been considered an emerging environmental pollutant. Epidemiological evidence shows that prenatal DINP exposure is linked to an increased risk of lung diseases in offspring and adults. However, little is known about their relationship at the molecular level. We exposed pregnant mice to DINP (100 mg/kg/day) by intragastric administration throughout gestation. On postnatal days (PNDs) 21 and 42 offspring were sacrificed and the lungs were collected. We found that prenatal DINP exposure significantly caused hypoalveolarization on PND 21 in male offspring, which was reversed during postnatal development. Moreover, prenatal DINP exposure significantly caused pulmonary fibrosis on PND 42 in male offspring. However, neither of these changes were observed in female offspring. KEGG enrichment showed that differentially expressed genes (DEGs) in the lungs of male offspring were closely associated with the calcium signaling and IL-17 signaling pathways. Importantly, decreased Htr4 expression might contribute to hypoalveolarization, and the elevated Il-17a expression might be responsible for prenatal DINP exposure-induced pulmonary fibrosis in male offspring. Our results demonstrated that prenatal DINP exposure had a persistent impact on the lung development of the offspring, including early-stage reduced alveolarization and later-stage fibrosis.

overall_design: Six-week-old ICR mice (30 females and 15 males) were used in our study. One male mouse and two female mice per cage were mated. Female mice with positive vaginal plug were considered pregnant, and the day at which the positive plug was detected was regarded as GD0.5 of gestation. Pregnant mice were randomly divided into the control (n=7) and DINP-exposed groups (n=6), and they were exposed to DINP (100 mg/kg bw, dissolved in corn oil) or corn oil by intragastric administration once every days, starting at GD0.5 and continuing throughout gestation.Lung issues were collected from male offspring on postnatal days (PNDs) 21 and 42. for mRNA sequencing. RNA-seq profiling of 3-CM2, 3-CM6, 3-CM7,3-DM5, 3-DM6, 3-DM7, 6-CM5, 6-CM6, 6-CM7, 6-DM6, 6-DM7, 6-DM8.

first: Chengyu

last: Zhao

first: Fu

first: Yao

last: Yuan

first: Sihan

last: Zhang

first: Yuanyuan

last: Tian

first: Meiqiong

last: Wu


title: Transcriptomic profiling of TGF-β–stimulated primary mouse cardiac fibroblasts

city: Nanjing

first: Zhenyang

last: Su

address: No.300 GuangZhou Road

institute: the First Affiliated Hospital of Nanjing Medical University

summary: Primary cardiac fibroblasts were isolated from neonatal C57BL/6J mouse hearts and stimulated with TGF-β1 in vitro to induce a profibrotic phenotype. Bulk RNA sequencing was performed on fibroblasts treated with TGF-β for 48 hours and on matched untreated controls to characterize transcriptional programs associated with TGF-β–driven fibroblast activation. Differential expression and gene ontology analyses were used to identify pathways related to extracellular matrix remodeling, TGF-β signaling, and DNA damage responses. These data support mechanistic studies on CRABP2–MRE11–MRN–dependent regulation of cardiac fibroblast activation and fibrosis.

overall_design: Primary cardiac fibroblasts were obtained from 1-day-old C57BL/6J mice and cultured under standard conditions. Cells were divided into 2 groups: (1) untreated controls and (2) cells treated with recombinant TGF-β1 (10 ng/mL) for 48 hours. For each condition, independent biological replicates of fibroblasts isolated from different litters were processed. Total RNA was extracted using TRIzol, and sequencing libraries were prepared using a standard poly(A)-enriched mRNA protocol and sequenced on an Illumina platform. Raw reads were aligned to the mouse reference genome (mm39), and differential gene expression was assessed between TGF-β1–treated and control fibroblasts.


title: Aptamer-modified 5-fluorouracil encapsulated metal-organic framework nanodrugs for enhanced therapy of colorectal cancer via peroxidative induced cell death

city: Guangzhou

first: Guangzhao

last: Lyu

state: Guangdong

address: 651 Dongfengdong Rd

department: Colorectal Surgery

institute: Sun Yat-Sen University Cancer Center

summary: Colorectal cancer (CRC) remains one of the most devastating malignancies worldwide. 5-Fluorouracil (5-FU) is a widely used therapeutic agent in CRC treatment. Here, we report a PTK-7–targeted, MOF-based nanodrug (AFZC) comprising Sgc8 aptamer, 5-FU, and Cu-doped ZIF-8. AFZC was synthesized via stepwise loading and surface functionalization and rigorously characterized by SEM/TEM. Targeting specificity was confirmed in PTK-7–positive colorectal cancer cells: Cy5-Sgc8 showed strong internalization in CRC cells but negligible uptake in normal epithelial cells. Functionally, AFZC suppressed proliferation and lowered 5-FU IC₅₀ across multiple CRC lines, with enhanced apoptosis versus 5-FU alone. Patient-derived organoids demonstrated greater growth inhibition with AFZC than with 5-FU. Transcriptomic profiling of AFZC-treated CRC cells highlighted pro-apoptotic remodeling with upregulation of NECTIN4 and NCF2, and concordant increases by Western blot alongside caspase cleavage. In vivo, AFZC achieved superior tumor control over 5-FU or ZIF-8 in CRC xenografts and a PDX model. No toxicity was found in histopathology of major organs or in liver/renal function markers at the treatment dosage. Collectively, AFZC couples selective PTK-7 targeting, catalytic activity, and sustained drug release to potentiate 5-FU efficacy with a favorable toxicity profile, supporting its translational promise in CRC.

overall_design: Colon cancer cell lines HCT116 and SW620 were treated with AFZC and 5FU at their respective IC50 doses for 24 hours. After the treatment, cellular RNA was collected for RNA-seq. Bulk RNA was extracted following standard protocols and subjected to high-throughput sequencing on the Illumina platform.

last: Lv

first: Rongxin

first: Duanping

last: Sun


title: Comparative transcriptomic analysis of Raw264.7 cells cultured on hydroxyapatite doping with Mg2+ versus Trio-Active bone scaffold

city: Shanghai

first: Jiren

last: Yan

state: Shanghai

address: 600 Yishan Road, Xuhui District, Shanghai

institute: Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

summary: Comparative transcriptomic analysis of Raw264.7 cells cultured on hydroxyapatite doping with Mg2+ (HA/Mg) versus Trio-Active bone scaffold (TABS)

overall_design: Raw264.7 cells were cultured with HA/Mg scaffolds or TABS for 3 days under standard conditions, with four replicates per group.

first: Linyang

last: Chu


title: Blood-based epigenetic instability linked to human aging and disease [cardiogenic_shock]

city: Toronto

first: Sagi

last: Abelson

state: ON

address: 661 University Avenue

country: Canada

institute: Ontario Institute for Cancer Research

type: Methylation profiling by genome tiling array

summary: The abundance, dynamics, and context-dependent heterogeneity of DNA methylation, where a pattern considered abnormal in one cell type may be normal in another, complicate the identification of early methylation changes that drive or signal disease development. This complexity can obscure early markers of increased disease risk, making it challenging to detect and intervene in disease processes at their inception. Here, we report 31,744 CpG sites exhibiting highly consistent methylation profiles in the blood of young, healthy individuals. We assess alterations at these epigenetically stable loci in 8,886 individuals across 29 diverse cohorts, including those with hematological cancers (n = 3,159), cardiovascular complications (n = 2,788), and healthy controls (n = 2,939). Our findings reveal methylation pattern disruption in myeloid and lymphoid malignancies, correlating with clonal burden dynamics and mutation frequency throughout leukemia treatment. In non-cancer cohorts, we observe that methylation levels at epigenetically stable loci become increasingly variable with age, a shift linked to higher cardiovascular disease risk and lower survival rates. This study highlights DNA methylation instability as a blood-based biomarker for both hematological cancer and cardiovascular disease and uncovers a mechanistic link between methylation dynamics and the expansion of maladaptive hematopoietic clones.

overall_design: Peripheral blood samples from 64 cardiogenic shock patients were analyzed using the Infinium MethylationEPIC array. The cohort consisted of patients with clonal hematopoiesis defined by DNMT3A/TET2 mutations (n=29) and those without clonal hematopoiesis (n=35).

first: Filio

last: Billia


title: Blood-based epigenetic instability linked to human aging and disease [MDS_CML]

overall_design: Diagnosis samples from 57 MDS patients (bone marrow) and 69 CML patients (65 bone marrow, 4 peripheral blood) were analyzed using the Infinium MethylationEPIC array.

first: Dennis

last: Kim

first: Jae-Sook

last: Ahn


title: Comparative transcriptomic analysis of HUVECs cultured on hydroxyapatite doping with Mg2+ versus Trio-Active bone scaffold

summary: Comparative transcriptomic analysis of HUVECs cultured on hydroxyapatite doping with Mg2+ (HA/Mg) versus Trio-Active bone scaffold (TABS)

overall_design: HUVECs were cultured with HA/Mg scaffolds or TABS for 3 days under standard conditions, with four replicates per group.


title: Comparative transcriptomic analysis of MC3T3-E1 cells cultured on hydroxyapatite doping with Mg2+ versus Trio-Active bone scaffold

summary: Comparative transcriptomic analysis of MC3T3-E1 cells cultured on hydroxyapatite doping with Mg2+ (HA/Mg) versus Trio-Active bone scaffold (TABS)

overall_design: MC3T3-E1 cells were cultured with HA/Mg scaffolds or TABS for 3 days under standard conditions, with four replicates per group.


title: Multifaceted B-cell response to transient HIV viraemia in elite controllers

city: London

first: Laura

middle: E

last: McCoy

address: Pears Building, Rowland Hill Street

country: United Kingdom

institute: University College London

summary: Chronic HIV infection drives B-cell dysfunction associated with the accumulation of tissue-like memory (TLMs) and activated memory B cells (MBCs) but decline in resting memory B cells. TLM origin and the mechanisms driving their expansion in HIV infection remain unclear. To elucidate this, we performed single-cell RNA/BCR sequencing of PMBCs enriched for B cells from an elite HIV controller pre-, during and post-viral blip. This provided a new insight into multifaceted functional B-cell response to transient HIV viraemia as likely happens during the early phase of anti-retroviral therapy cessation, highlighting the TLM heterogeneity and the contribution of innate-like B cells which might have important clinical implications for anti-HIV vaccine and therapy design.

overall_design: scRNA/BCR/CITE-seq profiling of PBMCs enriched for B cells obtained from an elite HIV controller (no anti-viral treatment) at three different timepoints (pre, during and post viral blip).

first: Ondrej

last: Suchanek

first: Luke

last: Muir

first: Peter

last: Thomas


title: Blood-based epigenetic instability linked to human aging and disease [longitudinal_AML]

overall_design: Longitudinal samples from 14 AML patients were analyzed using the Infinium MethylationEPIC array. Bone marrow was sampled from four patients at four different time points, and peripheral blood was sampled from another ten patients at three different time points.

first: Steven

middle: M

last: Chan

first: Mark

middle: D

last: Minden


title: Rhythmic nephron formation in the developing kidney

city: Philadelphia

first: Alex

last: Hughes

state: PA

address: 390 Towne Building 220 S. 33rd Street

country: USA

institute: University of Pennsylvania

summary: The mammalian kidney achieves massive parallelization of function by exponentially duplicating nephron-forming niches during development. Each niche caps a tip of the ureteric bud epithelium (the future urinary collecting duct tree) as it undergoes branching morphogenesis, while nephron progenitors within niches balance self-renewal and differentiation to early nephron cells. Nephron formation rate approximately matches branching rate over a large fraction of mouse gestation, yet the nature of this apparent pace-maker is unknown. Here we correlate spatial transcriptomics data with branching ‘life-cycle’ to discover rhythmically alternating signatures of nephron progenitor differentiation and renewal across Wnt, Hippo/Yap, retinoic acid (RA), and other pathways. Our data bring temporal resolution to the renewal vs. differentiation balance in the nephrogenic niche and inform new strategies to achieve self-sustaining nephron formation in synthetic human kidney tissues.

overall_design: We ran duplicate 10x Xenium Prime 5k assays on embryonic kidney cortical en face slices from human week 17 and 20 and mouse E15, 17, and 18. Note: Raw and processed filenames should be edited to remove sample prefix (e.g. "E15s1") and placed in a directory with the same name as "library name". "cell_feature_matrix" and "morphology_focus" sub-directories should be populated according to file descriptions. Once complete, "experiment.xenium" can be opened in Xenium Explorer software.

first: Samuel

last: Grindel

first: Sachin

last: Davis


title: Transcriptomics analysis of Pichia pastoris strains engineered for enhanced branched-chain amino acids production

city: tianjin

first: cancan

last: Dong

address: No. 32, West Seventh Road, Tianjin Airport Economic Zone

institute: Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences

summary: Transcriptomics analysis revealed that Ilv3 gene overexpression regulates the metabolic networks of branched-chain amino acid synthesis, the TCA cycle, methanol assimilation, and carbon‑nitrogen co‑utilization in Pichia pastoris. This study compared the global gene expression differences between the wild‑type and engineered strains under methanol induction.

overall_design: RNA-Seq analysis of P. pastoris control strain (HTX-33) and engineered strain (HTX33-ILV3) grown in minimal medium with 0.5% methanol. Three biological replicates per strain.

first: Cancan

first: Kai

last: Hong

first: Fan

last: Wu

first: Youyan

last: Rong

first: Yanfeng

last: Wang

first: Le

last: Gao

first: Xin

first: Jian

last: Zhang


title: Rhythmic nephron formation in the developing kidney [E17_NZC_scRNAseq]

overall_design: single cell RNA-sequencing of isolated nephrogenic zone cells from pooled E17 wild-type CD1 kidneys.


title: 9-PAHSA orchestrates TCR-T cell fate to boost anti-tumor immunity [ATAC-seq]

city: Hangzhou

first: xiaozhen

last: zhang

state: province

address: 79 Qingchun Road

institute: The first affiliated hospital, zhejiang university school of medicine

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We identify the endogenous lipid 9-PAHSA as a potent enhancer of T cell anti-tumor function and stemness, validated in murine models and a clinical trial. Mechanistically, we identify ICAM2 as a direct surface sensor for 9-PAHSA and delineate a downstream signaling axis whereby the ICAM2-Ezrin-mTORC2 cascade drives FOXO1 O-GlcNAcylation at S318, facilitating its nuclear translocation to enact a stem-like transcriptional program. Translating this discovery, we engineered armored human TCR-T cells with potentiated ICAM2 expression, which achieve superior tumor control through their enhanced intrinsic efficacy and a remarkable ability to ignite a coordinated and durable host anti-tumor immune response. Our work establishes a new paradigm of metabolite-sensing in T cell biology and provides a compelling therapeutic strategy to potentiate cellular immunotherapy for intractable cancers.

overall_design: The experiment was designed to identify genome-wide changes in open chromatin landscape induced by 9-PAHSA treatment. For each condition (vehicle control and 9-PAHSA treated), three independent biological replicates were analyzed.

first: Xiaozhen


title: Rhythmic nephron formation in the developing kidney [E18_stroma_bulkRNAseq]

overall_design: RNA-seq of nephrogenic stroma isolated from pooled E18 wild-type CD1 mouse kidneys. Conditions include stroma subject to 18 hours of culture on PDMS substrates incubated in low or high concentration fibronectin solutions to promote low or high adhesion, respectively. Samples include low and high adhesion conditions from 3 litter-matched replicates.


title: Rhythmic nephron formation in the developing kidney [E14_shRNA_bulkRNAseq]

overall_design: RNA-seq of E14 wild-type CD1 kidneys transduced with AAV2 carrying cag driven mir30 shRNA knockdown cassettes an upstream mCherry transduction reporter prior to culturing for 72 hours in a 3D-culture format. Knockdown conditions include shRNA sequences targeting the Mylk gene (Mylk-shRNA), the Rock1 and Rock2 genes (Rock1/2-shRNA), or a scrambled negative control (scramble-shRNA). Samples include FACS enriched mCherry-negative and mCherry-positive fractions of cells isolated from pooled kidneys. Kidneys for each replicate come from the same litter.


title: Self-Feedback Synaptic Networks Program In Vivo Stem Cells Multi-differentiation and Repair

first: Rong

last: Bao

address: 600 YISHAN ROAD

institute: Department of Orthopaedics Shanghai Jiao Tong University Affiliated Sixth People

summary: Stem cell therapy is rapidly advancing as a transformative approach in regenerative medicine. Due to self-renewal capabilities and plenipotentiary differentiation potential—with low risk of immune rejection—stem cells (SCs) offer the possibility of regenerating specific damaged tissues and organs. Traditional strategies to guide directed SC differentiation primarily includeinduction factors, microenvironment simulation, gene editing, and material scaffolding. Current approaches are capable of inducing the directed differentiation of SCs into a single lineage for tissue repair. However, tissue repair constitutes a complex process including tissue healing and vascular regeneration. Thus, these methods exhibit significant limitations regarding in vivo precision, the efficiency of inducing multi-directional differentiation, real-time monitoring capabilities and biosafety caused by animal-derived products. In contrast, functional stimulation (FS) with external interventions (namly electrical signals in this research) in SCs differentiation presents unique advantages: it offers in vivo modulation, possesses the potential to guide multi-lineage differentiation, high-resolution dynamic sensing of the microenvironment, and maintains excellent bio-compatibility. Consequently, FS is regarded as one of the most promising technological pathways for achieving precise in vivo stem cell-based tissue repair. Despite the evident advantages of FS, existing technologies have largely failed to integrate and improve the above advantages to achieve the multicellular synergistic differentiation and in vivo controllability required for complex process of tissue regeneration. The root cause lies in the inability of current methods to satisfy the core requirements of in vivo repair: 1) the regulation of SCs differentiation is inherently multidimensional, involving the synergistic action of parameters such as voltage, frequency, and waveform, while existing low-dimensional parameter screening strategies fail to cover this complex differentiation lineage; 2) during the repair process, the bioimpedance of the injury micro-environment evolves dynamically due to changes in repair degree, micro-environmental composition, and ion migration, leading to stimulation deviations, while current devices only senses changes in bioimpedance without further regulation; 3) complex injury situations require the induction of distinct differentiation endpoints (e.g. cells that regenerate defective tissues and endothelial cells that form new blood vessels) at specific locations, while existing technologies remain unable to achieve simultaneous repair of multiple tissues. Therefore, there is an urgent need for a spatiotemporally customized, multi-dimensional FS technology capable of dynamically sensing micro-environmental changes and performing self-feedback regulation to replace current static, single-mode stimulation paradigms. To address these challenges, we developed a neuromorphic closed-loop system integrated with deep learning algorithms—a Self-Feedback Synaptic Network(SFSN) capable of real-time bio-computation and multi-dimensional functional stimulation. Utilizing an implantable 1-kb synaptic array, the system senses biological signals and delivers customized stimulation based on the dynamic state of the tissue micro-environment. achieved high-dimensional, precise control over rat bone marrow mesenchymal stem cells (rBMSCs) differentiation into multiple lineages. By mapping the closed-train synaptic network weights onto the implantable 1-kb synapse array, the system performs in-situ hardware inference. This approach successfully guides hydrogel-delivered SCs toward target lineages at precise injury sites—such as fibroblasts, osteoblasts, and tenocytes—while simultaneously promoting endothelial differentiation in regions requiring vascular ingrowth to support site-specific vascularization, ultimately achieving integrated regeneration of structural and functional tissue with in vivo controllability.

overall_design: There are 7 groups: Control; SFSN-FB (Fibroblasts), SFSN-Ot (osteoblasts), SFSN-EC (endothelial cells), SFSN-TC (tendon cells), SFSN-Neu (neuron-like cells) and SFSN-Adipo( adipocytes).


title: CSF3 Promotes TMEM74 Expression and Enhances Autophagy via the p65/NF-κB Signaling Pathway to Drive Colorectal Cancer Progression

first: Junfeng

last: Xu

address: Fuxing Road No.28

institute: Senior Department of Gastroenterology, Chinese PLA General Hospital

summary:
CSF3 is overexpressed in CRC, correlating positively with poor patient prognosis.We want to find out the specific sets of genes are down-regulated.
We used microarrays to detail the global programme of gene expression between HCT116 cells with Ctrl and CSF3 and identified distinct classes of down-regulated genes during this process.

overall_design: HCT116 cells with Ctrl and CSF3 were cultured in RPMI-1640 containing 10 % fetal bovine serum (FBS) and 1% Penicillin-Streptomycin (P/S) and  selected for RNA extraction and hybridization on Affymetrix microarrays.

first: Xinyan

last: Liu


title: Histone lactylation maintains bovine early embryo development via regulating embryonic genome activation [scRNA-Seq]

city: Hefei

first: Wenjie

last: Yu

address: No.130 West Changjiang Road

institute: Anhui Agricultural University

summary: Early embryo loss is an important factor affecting the reproductive capacity of cattle. Recent studies have revealed that during the process of the embryonic genome activation (EGA), epigenetic modification, such as, histone lactylation modification remodeling is crucial for early embryonic development. However, the effect and mechanism of histone lactylation modification on bovine early embryo development remain unknown. In this study, we found that histone lactylation, including pan Kla, H3K9la, and H3K18la were mainly located in nuclear, and were significantly decreased from 8-cell to morula stage as well as increased from morula to blastocyst stage in bovine IVF embryos. Decreased or increased levels of histone lactylation by GSKA or NaLa supplementation inhibited bovine early embryo development and blastocyst lineage differentiation. Furthermore, combined with scRNA-Seq data and EU straining revealed that reduction of histone lactylation levels altered expression of genes associated with DNA transcription and RNA polymerase activity, thereby impairing the process of EGA. Importantly, NMN rescued the inhibitory effects of GSKA supplementation in bovine EGA and early embryonic development. Altogether, these results indicated that histone lactylation maintains bovine early embryo development via regulating EGA process. These findings provide theoretical references for addressing early embryo loss and thereby enhancing the reproductive capacity of cattle.

overall_design: Utilizing single-cell RNA sequencing technology, we conducted an in-depth investigation into how histone lactylation modification affects bovine embryonic genome activation

first: Yi

last: Xia

first: Wenzhuo

first: Zhiyuan

last: Yang

first: Zhengqiu

first: Xinqi

last: Gan

first: Mengya

first: Beibei

last: Zhou

first: Yunsheng

last: Li

first: Yunhai

first: Zubing

last: Cao


title: Single-cell insights into trophoblast heterogeneity and adaptive dysfunction in selective fetal growth restriction

first: Yan

last: Bi

address: 910 Hengshan Road, Xuhui District

institute: International Peace Maternity and Child Health Hospital, Shanghai Jiao Tong University

summary: Selective fetal growth restriction (sFGR) in monochorionic twins reflects placental dysfunction, but trophoblast adaptation mechanisms remain unclear. Using single-cell RNA sequencing of three MCDA twin pairs, we reveal villous cytotrophoblasts (VCT) in growth-restricted placentas shift from TP63/SOX6-expressing barrier phenotypes to metabolically stressed YY1/RELA-activated states, with upregulated glycolysis/mitochondrial dysfunction and downregulated adhesion pathways. Trajectory analysis shows diminished syncytial precursors, suggesting impaired fusion capacity. Immune profiling identifies depleted TREM2+ Hofbauer macrophages and expanded interferon-responsive NK cells. Cell-cell interaction mapping demonstrates enhanced IFNG-IFNGR1-STAT1 signaling between VCT_LDHA and immune cells, alongside weakened VCT_TP63-stromal crosstalk. This study defines a maladaptive triad of metabolic stress, inflammation, and structural disintegration in sFGR, contributing to sFGR pathogenesis.

overall_design: We conducted single-cell RNA sequencing (scRNA-seq) of three pairs of MCDA twin pregnancies discordant for fetal growth (sFGR_Smaller and sFGR_Larger placental territories). A total of six placental samples were processed using the 10x Genomics Chromium platform to characterize cellular heterogeneity and microenvironmental remodeling.

first: Jiawen

first: Yanlin


title: Transposase-assisted in situ capture of recombination DSB hotspots (TAID-seq) [CUT&Tag]

first: Caoling

state: Anhui

address: 96 Jinzhai Road

department: Department of Life Sciences and Medicine

institute: University of Science and Technology of China

summary: Genome-wide profiling of the meiotic recombination initiation sites – DNA double-strand break (DSB) hotspots – is essential for understanding the evolution of species of variable origins in sexually reproducing organisms, and to provide the mechanistic insights into recombination, genetic engineering, and plant or animal breeding. While current high-throughput sequencing approaches are powerful tools for detecting DSB hotspots, revealing remarkable mechanisms underlying meiotic recombination, they are often time-consuming, labor-intensive, and, in some occasions, practically impossible owing to large sample inputs. Herein, we present Transposase-assisted in situ capture of recombination DSB hotspots (TAID-seq), an approach that leverages both RNA:DNA hybrids and D-loop intermediates at DSB sites. TAID-seq enables the rapid and efficient genome-wide capture of meiotic DSB hotspots. Compared with existing approaches, the TAID-seq workflow requires as few as 50,000 testicular cells, sequencing depths as low as 8 million (M) reads, and can be completed in under 1.5 days. We show that TAID-seq can recapitulate the global recombination DSB landscape in mice and humans. TAID-seq is compatible with archived frozen tissues, and revealed significant difference in the DSB hotspot patterning in human individuals. Further extended applications of TAID-seq strategy will likely unravel the genome-wide recombination DSB landscapes between sexes, populations, and in more rare species, while also illuminating rules and mechanisms underlying spatiotemporal regulation of recombination in health and disease.

overall_design: Extract cells/cell nuclei from fresh/frozen testis samples of mice and humans and perform CUT&Tag

first: Jianqiang


title: Transposase-assisted in situ capture of recombination DSB hotspots (TAID-seq) [TAID-seq]

overall_design: Extract cells/cell nuclei from fresh/frozen testis samples of mice and humans and perform TAID-seq


title: Transposase-assisted in situ capture of recombination DSB hotspots (TAID-seq) [KAS-seq]

overall_design: Extract cells from fresh testis samples of mice and humans and perform KAS-seq


title: An ERF transcription factor StPti5, a novel regulator of endophyte community maintenance in potato

city: Madrid

first: Jose M.

last: Franco-Zorrilla

state: Madrid

address: Darwin, 3

department: Plant Molecular Genetics

country: Spain

institute: Centro Nacinal de Biotecnologia-CSIC

summary: We have recently identified an ethylene response factor, StPti5, as a susceptibility factor that negatively regulates immune response to diverse pathogens. Here, we investigated the processes involved in colonisation of potato with beneficial organisms.  RNA-seq showed that at the time of Bacillus subtilis biofilm establishment, immune responses in interacting roots were attenuated, and complex transcriptional network was triggered, with ethylene signalling being a central module and StPti5 strongly induced. Interestingly, the response is intensified if plants are inoculated by two antagonistic B. subtilis strains.  While StPti5 is not involved in the establishment of biofilm on roots, we show that bacterial abundance increases in shoots of StPti5-silenced plants. Remarkably, root colonization by the arbuscular mycorrhizal fungus Rhizophagus irregularis was also higher in the StPti5-silenced plants.  StPti5 is involved both in suppressing defence against harmful and limiting colonisation with beneficial microbes. Such mechanistic understanding of plant–microbe interaction paves the way for sustainable crop management.

overall_design: DAP-seq experiments

first: Franco Zorrilla

last: José Manuel

first: Álvarez

last: Eva

first: Gruden

last: Kristina

first: Levak

last: Valentina


title: Multi-omics analysis of early reperfused ischemic heart reveals ERRβ/γ activation protects against acute myocardial infarction injury [CUT&Tag]

first: Li

last: Shen

state: Zhejiang Province

address: 866 Yuhangtang Road

institute: Life Sciences Institute, Zhejiang University

summary: In the present study, the induction of AMI in rats was achieved by ligating the left anterior descending coronary artery (LAD) for a duration of one hour (early time reperfusion, defined as ETR) or six hours (late time reperfusion, and defined as LTR), followed by reperfusion. Sham-operated rats served as controls for the experiment. Bulk tissue transcriptomic sequencing, metabolomic profiling, and single-nucleus RNA sequencing were performed to analyze the transcriptome and metabolome of the ischemic hearts. TF motif analysis was used to predict the potential transcriptional factor. In addition, we investigated the role of ERRβ and ERRγ in vitro using neonatal rat ventricular myocytes (NRVMs) subjected to hypoxia/reoxygenation (H/R). We administered the ERRβ/γ agonist GSK4716 to rats to assess its therapeutic effects on AMI injury, and compared the protective mechanism with fenofibrate.Bulk tissue transcriptomic and metabolomic profiling demonstrated that the protective effect of ETR on AMI is mediated by two major parts of FAO and dedifferentiation. Single-nucleus RNA sequencing revealed four distinct cardiomyocyte subpopulations (CM1-CM4), and ETR attenuated AMI injury by preserving a greater number of sub-injured CM2 and immature-like CM4. In addition, ERRβ/γ was found to regulate the expression of FAO and immature cardiomyocyte signature genes in vivo and in vitro. Notably, pretreatment with the ERRβ/γ agonist GSK4716 significantly enhanced the protective effect of ETR on AMI by activating FAO and immature CM genes. CONCLUSIONS: The findings indicate that the protective effect of early time reperfusion is associated with preserved FAO and dedifferentiation. Activation of ERRβ significantly enhances these protective effects, highlighting the therapeutic potential of ERRβ activation in ameliorating AMI injury. These findings suggest that targeting the ERRβ pathway may provide an effective strategy for the treatment of AMI.

overall_design: CUT&Tag of ERRβ in the cardiomyocytes collected from the sham rats.

first: Yun

last: Gao

first: Fei

last: Huang

first: Yuan

last: Zhang

first: Jiuxiao

last: Zhao


title: Ovarian Tumor FAK Inhibition Releases Omega-3 Fatty Acids Stimulating GATA6 Peritoneal Macrophage CXCL13 Production Enhancing Immunotherapy

city: La Jolla

first: Dwayne

middle: G

last: Stupack

address: 3855 Health Sciences

department: Obstetrics and Gynecology

institute: UC San Diego Moores Cancer Center

summary: Genetic or pharmacolgic inhibition of Focal Adhesion Kinase in the murine KMF tumor model is compared to the growth of untreated tumors and with  those treated with first line or second line chemotherapies.  Impact upon the tumor subpopulations and immune compartment is evaluated via scRNAseq..

overall_design: KMF cells were seeded at 5 million per C57bl/6 mouse IP and mice were untreate or were treated serially with standard of care chemotherapy (platinum + taxane) or pegylated doxorubicin.  Alternatively, mice were treated with an inhibitor of FAK (VS4718) or with cells deficient in FAK expression(KO) of catalytic activity(KD, Kinase dead).

first: Duygu

last: Ozmadenci

first: David

last: Schlaepfer

first: James

last: Lee


title: EnChAMP-seq genomic localization and footprinting of RNA Pol II and NELF-A

city: Ithaca

first: Abdullah

last: Ozer

state: NY

address: 526 Campus Road

department: Molecular Biology and Genetics

institute: Cornell University

summary: RNA Polymerase II (Pol II) transcription is highly regulated at two early steps in the transcription cycle: 1) Pre-Initiation Complex (PIC) assembly with its coupled initiation, and 2) promoter-proximal pausing with its controlled release. Here, we developed an optimized biochemical purification method that captures endogenously tagged chromatin-bound Pol II complexes under native conditions at these rate-limiting steps. We then identified a large set of Pol II interactors by mass spectrometry and determined the footprints of these assemblies on promoters with high resolution. Many well-known and new or understudied factors were identified as associated with the PIC and promoter proximal paused complexes, indicating that despite decades of efforts, these rate-limiting steps of the transcription cycle are far from being completely understood. The new and understudied factors  implicate novel mechanisms of regulation that will need to be characterized  to fully understand Pol II regulation.

overall_design: EnChAMP-seq analysis of endogenously tagged GFP (control), GFP-RPB1 and NELFA-GFP HCT116 derived cell lines with replicates under no drug, +500nM NVP-2 for 1h, or +1uM Triptolide for 20min conditions.

first: Jin Joo

last: Kang

first: Yuliang

last: Tang

first: Yugandhar

last: Kumar

first: Michael

last: DeBerardine

first: Haiyuan

last: Yu

first: John

middle: T

last: Lis


title: Transcriptomic analysis of Methanothermobacter marburgensis under different nickel concentrations

city: Hachioji

first: Shunsuke

last: Nomura

state: Tokyo

department: Microbial Protein Structure Group

country: Japan

institute: Max Planck Institute for Terrestrial Microbiology

summary: To investigate how Methanothermobacter marburgensis adapts to nickel limitation, we performed transcriptomic profiling under 50 nM and 5000 nM nickel conditions. RNA-seq revealed differential expression of hydrogenase-related genes, suggesting a shift in methanogenic electron flow under nickel limitation, with increased reliance on [Fe]-hydrogenase and associated pathways.

overall_design: In this study, Methanothermobacter marburgensis was cultivated under 50 nM and 5000 nM nickel conditions. Total RNA from three biological replicates per condition was sequenced using strand-specific RNA-seq. Differential expression analysis focused on hydrogenase systems involved in methanogenesis and their transcriptional response to nickel availability.

first: Seigo

last: Shima


title: KMT2A is a prerequisite of malignant transformation during IDH-mutant gliomagenesis [RNA-Seq]

city: Heidelberg

first: Sevin

last: Turcan

address: Im Neuenheimer Feld 420

country: Germany

institute: University Hospital Heidelberg

summary: Background: IDH1R132H is the defining mutation of low-grade gliomas (LGGs), inflicting broad epigenetic rewiring that leads to malignant transformation. Recent studies demonstrated that cell fate change from astrocyte to LGG is accompanied by redistribution of H3K4 methylation. By modulating H3K4-methyltransferase KMT2A in a conditionally IDH1R132H-expressing human astrocyte model system, we sought to define requirements of IDH1R132H dependent gliomagenesis and identify novel therapeutic targets. Methods: Using KMT2A inhibitor MM-102, we targeted H3K4me3 in IDH1R132H -expressing astrocytes, profiling L1CAM expression, proliferation, clonogenicity, invasion and migration, transcriptional and translational changes. Findings were validated in patient-derived IDH1R132H glioma lines with shRNA-mediated knockdown. Epigenetic transformation was characterized with CUT&Tag and MethylationEPIC. Downstream targets were assessed utilizing siRNAs. Results:  KMT2A inhibition significantly decreased L1CAM expression and led to broad transcriptional downregulation, including LGG marker genes. Analyses of transcriptomics and proteomics pointed to altered lipid metabolism and migratory capacity. Phenotypic characterization showed impaired invasion, migration and proliferation. We observed significantly reduced deposition of H3K4me3 at promoters of DEGs and enhanced global DNA methylation. We identified SCD as putative KMT2A-dependent effector whose knockdown reduced clonogenicity. In patient-derived models, KMT2A suppression impaired viability and spheroid growth in vitro; however, in an orthotopic TS603 model, knockdown shortened survival, indicating stage- and context-dependent effects. Conclusions: Disrupting KMT2A-mediated H3K4me3 reshapes the epigenome and attenuates LGG-relevant programs and phenotypes in vitro, supporting a strong role in tumor initiation. In vivo, the TS603 survival result highlights context-dependent maintenance and motivates cautious, microenvironment-aware therapeutic exploration of the KMT2A axis and downstream targets such as SCD.

overall_design: RNA-seq profiling of immortalized IDH1R132H human astrocytes treated with KMT2A shRNA resp. scrambled control


title: Natural daylight during office hours improves glucose control and whole-body substrate metabolism

city: Geneva

first: Andrew

last: Biancolin

address: Rue Michel-Servet 1

country: Switzerland

institute: University of Geneva

summary: Chronic lack of daylight is increasingly considered as a risk factor for metabolic diseases, such as type 2 diabetes (T2D). In a randomized cross-over design (NCT05263232), 13 individuals with T2D were exposed to natural daylight facilitated through windows vs. constant artificial lighting during office hours for 4.5 consecutive days. Continuous glucose monitoring revealed that participants spent more time in the normal glucose range and whole-body substrate metabolism shifted towards a greater reliance on fat oxidation upon daylight. In vitro assessment of the muscle clock displayed a phase advance after daylight exposure. Multi-omic analyses revealed daylight-induced differences in serum metabolites, lipids and monocyte transcripts. Our findings suggest that natural daylight exposure during office hours has a positive metabolic impact in individuals with T2D and could potentially support the treatment of metabolic diseases.

overall_design: Blood monocyte RNA-seq from blood samples taken from patiens with T2D after natural light exposure compared to those after artificial light exposure.


title: High-glucose environment impairs keratinocyte migration and proliferation through the ROS/Akt/ETV4 signaling pathway

first: Hongfeng

last: Chang

address: jixi road number 218

institute: The First Affiliated Hospital of Anhui Medical University

summary: Impaired diabetic wound healing compromises patient quality of life, with keratinocytes playing a pivotal role in the wound repair process. This in vitro study investigated the role of ETS variant transcription factor 4 (ETV4) in keratinocyte migration/proliferation in high glucose (HG) environments to assess whether ETV4-mediated signaling is involved in dysfunctional wound repair. Western blotting showed that ETV4 expression was downregulated in human keratinocytes cultured in HG. ETV4 knockdown using small interfering RNA suppressed keratinocyte migration/proliferation. Intervention with the reactive oxygen species (ROS) scavenger tempol or the Akt activator SC79 restored ETV4 expression and rescued impaired migration/proliferation. Tempol also restored Akt phosphorylation levels. Matrix metalloproteinase-14 (MMP14) was identified in transcriptome sequencing/bioinformatic analyses as a downstream target of ETV4. HG-suppressed MMP14 expression was reversed by tempol or SC79. Specific inhibition of MMP14 attenuated keratinocyte migration/proliferation in HG. This study reveals a critical role for the ROS/Akt/ETV4/MMP14 signaling axis in HG-induced keratinocyte dysfunction, suggesting potential therapeutic targets for diabetic wound healing.

overall_design: This dataset contains transcriptomic profiles of immortalized human keratinocytes (HaCaT) cultured under high glucose conditions following ETV4 knockdown. RNA sequencing was performed using the Illumina platform to investigate how ETV4 suppression modulates gene expression in a diabetic-like microenvironment.The experimental design compared two groups: high glucose control (HG) and ETV4-knockdown under high glucose (HG+siETV4).

first: Bing

last: Shen

first: Qiu

last: Zhang


title: KMT2A is a prerequisite of malignant transformation during IDH-mutant gliomagenesis [CUT&Tag]

overall_design: CUT&Tag profiling  of immortalized IDH1R132H human astrocytes treated with MM-102 resp. mock for H3K4me3, H3K4me1, HeK27me3 and H3K27ac.


title: Modulating AP-1 enables CAR-T cells to establish an intratumoral stem-like reservoir and overcomes resistance to PD-1 blockade

city: Seattle

first: Shivani

last: Srivastava

state: WA

address: 1100 Fairview Ave N

institute: Fred Hutchinson Cancer Center

summary: CAR-T therapy has shown limited synergy with PD-1/PD-L1 blockade, but the mechanisms underlying resistance remain unclear. PD-1⁺TCF1⁺ stem-like T cells mediate responses to PD-1/PD-L1 blockade and are maintained by MHC-dependent interactions with DCs in tumor-draining lymph nodes (dLN). Because CAR-Ts recognize intact antigen, not peptide-MHC, their activation is confined to tumors, potentially preventing maintenance of this critical subset. In ROR1⁺ lung cancer models, ROR1-targeting CAR-Ts rapidly down-regulated TCF1, became exhausted, and were not enhanced by PD-L1 blockade. Overexpression of the AP-1 transcription factor c-Jun, but not BATF, enabled formation of PD-1⁺TCF1⁺ reservoirs in tumors, not dLN, but did not prevent exhaustion, as PD-1 induced post-transcriptional c-Jun down-regulation. Remarkably, PD-L1 blockade restored c-Jun levels, dramatically increased CAR-Ts, and enabled near-complete ROR1+ tumor clearance. These findings identify PD-1 as a suppressor of c-Jun and reveal that MHC-independent CAR-Ts can be engineered to establish intratumoral stem-like reservoirs that overcome resistance to PD-1 blockade.

overall_design: Bulk RNA-seq profiling of ROR1 CAR-T and cJun.ROR1 CAR-T cells sorted 5 days after infusion from KP-ROR1 lung tumor–bearing mice treated with either vehicle (PBS) or anti–PD-L1 checkpoint blockade immunotherapy.

middle: J

last: Snyder


title: Single-cell transcriptomic profiling of lung interstitial macrophages in bleomycin-induced pulmonary fibrosis in Spp1-EGFP reporter mice

city: Tokyo

first: Kohsuke

last: Shirakawa

address: 35 Shinanomachi, Shinjuku-ku

department: Cardiology

institute: Keio University School of Medicine

summary: This study aimed to characterize the transcriptomic landscape of Spp1-expressing interstitial macrophages (IMs) in the lungs of a bleomycin-induced pulmonary fibrosis mouse model using single-cell RNA sequencing (scRNA-seq). We utilized Spp1-EGFP knock-in reporter mice, in which EGFP marks Spp1-expressing cells. Pulmonary fibrosis was induced by intratracheal administration of bleomycin. Lung  cells were isolated, and Spp1-EGFP⁺ SiglecF⁻ CD11b⁺ interstitial macrophages were enriched by flow cytometric sorting. Approximately 10,000 viable sorted cells were processed for single-cell transcriptome profiling using the Chromium Next GEM Single Cell 3' Reagent Kits v3.1 (10x Genomics), and libraries were sequenced on a DNBSEQ-G400 platform. This dataset provides a high-resolution view of the cellular states and gene expression profiles of interstitial macrophages during lung fibrosis.

overall_design: To investigate the transcriptional states of interstitial macrophages (IMs) during pulmonary fibrosis, Spp1-EGFP knock-in reporter mice were used. Pulmonary fibrosis was induced by intratracheal administration of bleomycin (3 μg/g body weight). Mice were anesthetized with 1.0–1.5% sevoflurane during the procedure. Seven days after bleomycin administration, mice were sacrificed, and lung and peripheral blood cells were harvested. Lungs were enzymatically digested using type I collagenase, and immune cells were isolated using a Percoll density gradient. Spp1-EGFP⁺ SiglecF⁻ CD11b⁺ IMs were sorted via flow cytometry on a BD FACSAria III instrument. Sorted cells were pooled, counted, and loaded into a Chromium Controller (10x Genomics) for single-cell capture and library preparation. Libraries were constructed using Chromium Next GEM Single Cell 3' Reagent Kits v3.1, and sequenced with a DNBSEQ-G400 sequencer (MGI Tech) with paired-end 150-bp reads, generating ~350 million reads per sample. The Cell Ranger pipeline was used for data processing including alignment, barcode processing, and gene expression quantification.


title: A therapeutic antisense oligonucleotide encompassing 2′-O-methoxyethyl modification triggers unique perturbation of the transcriptome

city: Ames

first: Ravindra

middle: N

last: Singh

state: IA

address: 2034 Veterinary Medicine

department: Biomedical Sciences

institute: Iowa State University

summary: Antisense oligonucleotides (ASOs) are short nucleic acids that act by annealing to complementary target RNA or DNA sequences. It is currently unknown how the transcriptome-wide off-target effects of different ASO chemistries targeting the same sequence differ. Nusinersen, the first FDA-approved treatment for spinal muscular atrophy (SMA), is an ASO that restores Survival motor neuron 2 (SMN2) exon 7 splicing by binding to the intronic splicing silencer N1 (ISS-N1) element in intron 7. We tested the transcriptome-wide off-target effects in SMA patient fibroblasts of three ASOs targeting ISS-N1: F18OMe, a 2'-O-methyl (OMe) ASO incorporating a phosphorothioate backbone, F18MOE, a 2'-O-methoxyethyl (MOE) ASO incorporating a phosphorothioate backbone, and F20PMO, a phosphorodiamidate morpholino (PMO) ASO. Using minigenes, we showed that skipping of POLR2H exon 2 and seven other exons is triggered by direct annealing of F18MOE to target exonic sequences, and the chemistry-specific effects of F18MOE on exon skipping are primarily due to enhanced mismatch tolerance of MOE. We confirmed that reduction of ASO length and mixed MOE/OMe chemistry are both effective strategies for mitigation of off-target effects. Our findings will be instructive for future design of ASO therapies for SMA as well as other diseases treatable by ASOs.

overall_design: GM03813 SMA patient cells were treated by nucleofection with ASOs targeting Intronic Splicing Silencer N1 incorporating three types of modifications: phosphorothioate backbone with 2'-O-Methyl modificaiton, phosphorothioate backbone with 2'-methoxyethyl modification, and phosphorodiamidate morpholino chemistry. RNA was isolated by TRIzol 24 hours after nucleofection and sequenced by Illumina sequencing

first: Eric

middle: W

last: Ottesen

first: Wren

middle: A

last: Murzyn

first: Robert

middle: L

last: Kaas

first: Keaton

last: Bertrand

first: Jessica

last: Payne


overall_design: CUT&Tag for the histone modificiations H3K4me3 and H3K27me3 in ROR1 CAR-T, cJun.ROR1 CAR-T, and BATF.ROR1 CAR-T cell infusion products.


title: Transcriptomic analysis of BPA alternative chemicals in primary human mammary epithelial cells

city: Ottawa

first: Matthew

last: Meier

state: Ontario

address: 251 Sir Frederick Banting Driveway

department: Health Canada

institute: Government of Canada

summary: Some everyday consumer products contain endocrine disruptors like bisphenol A (BPA) and its replacements. To date, most in vitro chemical screening to evaluate these compounds has been accomplished using immortalized cell lines, which differ significantly from human tissues. Our goal was to test BPA and select alternatives previously screened in breast cancer cells for toxicological potency and mechanism of action in human mammary epithelial cells (HMECs). HMECs from three human donors were exposed to BPA and four alternative chemicals (in concentration response format from 0.001 – 50 µM) for 48 h and global transcriptomic changes were quantified. Transcriptomic biomarker analysis was employed to explore chemically induced estrogen receptor alpha (ERα) activation and alterations in stress response pathways. Benchmark concentration (BMC) analysis was applied to gene expression data to derive transcriptomic points of departure (tPODs) to compare chemicals for potency. Pathway and upstream regulator analysis was applied among the genes fitting BMCs. All chemicals had tPODs within an order of magnitude of each other. Bisphenol AF (BPAF) was the most potent, followed by tetramethyl bisphenol F (TMBPF), bisphenol C (BPC), 4,4’-bisphenol S (BPS), and BPA. None of the chemicals activated the ERα active biomarker. Some stress response biomarkers were activated at high exposure concentrations. Genes fitting BMCs clustered chemicals into two groups, with one group (BPAF and TMBPF) primarily inhibiting expression patterns and the other (BPC, BPS, and BPA) mostly activating. These data suggest that the BPA alternatives tested have similar toxicological potencies in HMECs and oppositely enrich cancer related gene sets.

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design:
To determine the effects of BPA and alternative chemicals on human mammary epithelial cells (HMECs), we exposed HMECs from three biological donors to BPA and four alternative chemicals.
After chemical exposure, samples underwent TempO-Seq library building and NextGeneration sequencing.
Gene expression data underwent benchmark concentration modeling to derive transcriptomic points of departure to compare toxicological potency and compare mechanism of action by doing upstream regulator and biological pathway analysis.

first: Geronimo

last: Matteo

first: Andrea

last: Rowan-Carrol

first: Lauren

last: Bradford

last: Williams

first: Christopher

last: Corton

first: Carole

last: Yauk

first: Ella

last: Atlas


title: Bulk RNA sequencing to investigate transcriptional profiles of lung macrophage subpopulations isolated from wild-type C57BL/6J and Spp1-EGFP knock-in reporter mice subjected to intratracheal administration of bleomycin or PBS.

overall_design: Spp1-EGFP knock-in mice and wild-type C57BL/6J mice were intratracheally administered bleomycin (3 μg/g body weight) or PBS as control. At day 7, 14, or 30 post-administration, mice were euthanized, and lung tissues were harvested. Lung single-cell suspensions were prepared by enzymatic digestion and mechanical dissociation, followed by red blood cell lysis and Percoll density gradient centrifugation. Alveolar and interstitial macrophages were isolated by flow cytometry based on SiglecF and CD11b expression. In Spp1-EGFP knock-in mice, both EGFP⁺ and EGFP⁻ subsets were sorted. Total RNA was extracted from each population, and cDNA libraries were prepared using polyA selection. Sequencing was performed on an MGISEQ-2000RS platform with 150-bp paired-end reads. Raw reads were processed and mapped to the GRCm38 mouse reference genome using HISAT2, and gene-level quantification was conducted with featureCounts. Differentially expressed genes were identified using DESeq2, and downstream analyses included hierarchical clustering, PCA, and gene ontology enrichment using Metascape.


title: Embryo-derived proteins (PDI, CAPG, PSAT1) are highly conserved among placental mammals and alter the transcriptome of endometrial epithelial cells (bovine and human)

city: Leeds

first: LeedsOmics

last: UoLeeds

state: West Yorkshire

address: Clarendon Way

department: Cross-faculty

institute: University of Leeds

summary: Pregnancy establishment in mammals requires a complex sequence of events, including bi-lateral embryo-maternal communication, leading up to implantation. This is the time when most pregnancy loss occurs in mammals (including humans and food production species) and dysregulation in embryo-maternal communication contributes to pregnancy loss. Embryo-derived factors modify the function of the endometrium for pregnancy success. We hypothesise that these previously unexplored conceptus-derived proteins may be involved in altering the function of the endometrium to facilitate early pregnancy events in mammals with different early pregnancy phenotypes. Here, we show that protein disulphide-isomerase (PDI) is a highly conserved protein among mammals, and provide evidence for a species-specific roles for PDI in endometrial function in mammals with different implantation strategies. We show how PDI alters the endometrial transcriptome in human and bovine in vitro in a species-specific manner, and using a microfluidic approach we demonstrate that it alters the secretome capability of the endometrium.  We also provide evidence from in vitro assays using human-derived cells that MNS1, a transcript commonly downregulated in response to PDI in human and bovine endometrial epithelial cells, may be involved in the attachment phase of implantation. We propose that the trophoblast-derived protein PDI, is involved in supporting the modulation of the uterine luminal fluid secreted by the endometrium to support conceptus nourishment, and also in the process of embryo attachment to the uterine lumen for pregnancy success in mammals.

sample_organism:
Homo sapiens
Bos taurus

platform_organism:
Homo sapiens
Bos taurus

overall_design: Recombinant protein production Recombinant bovine PDI (rbPDI), PSAT1 (rbPSAT1), and CAPG (rbCAPG) was produced at the Newcastle University Protein and Proteome Analysis centre using an E. coli pET3A expression vector system and subsequent purification steps. Recombinant ovine IFNT (roIFNT) was kindly gifted by Professor Fuller Bazer for this study, produced in P.pistoris to >80% purity. All recombinant proteins were eluted/purified into PBS and stored at -80C prior to use. Primary bovine endometrial cell culture Primary bovine endometrial epithelial cells (bEECs) and primary bovine endometrial stromal cells (bESCs) were isolated by enzymatic digestion from late-luteal phase uterine tracts (n=3). bEECs and bESCs were maintained in complete bovine medium (RPMI 1640 [Gibco, Massachusetts, US], 10% charcoal-stripped FBS [PAA Cell Culture Company, UK], 1% antibiotic antimycotic solution [ABAM, Sigma-Aldrich, Missouri, USA]). bESCs at a concentration of 150,000 cells per well (n=5) and bEECs at a concentration of 300,000 cells per well (n=5) were plated into separate 6-well plates in 2 mL complete bovine medium. All cultures were maintained at 37C/5% CO2 in a humidified incubator. At 70% confluence bEECs and bESCs were treated with one of the following for 24 hr: (1) Media control, (2) Vehicle control (PBS only), (3) 1000 ng/ml rbPDI, 4) 1000ng/mL rbPSAT1, 5) 1000ng/mL rbCAPG, or (6) 1000 ng/ml rbPDI/CAPG/PSAT1 combined with 100 ng/ml roIFNT. Human endometrial cell culture Ishikawa (ECACC 99040201, passage 10) immortalised human endometrial epithelial cells (hEECs) were plated in biological technical triplicate at 300,000 cells per well in a 6 well plate, in 2 mL complete human medium (DMEM/F12 [Gibco, Massachusetts, US], 10% FBS [PAA Cell Culture Company, UK], 1% Glutamine SStreptomycin PPenicillin [Gibco, Massachusetts, US]). The three replicates were from three different flasks of passage 10 cells, which had been split from a single flask of passage 9 Ishikawa cells. All cultures were maintained at 37 C/5% CO2 in a humidified incubator. At 70% confluence hEECs were treated with one of the following for 24 hours: (1) Media control, (2) Vehicle control (PBS only), (3) 1000ng/mL rbCAPG (4) 1000 ng/ml rbPDI, or (5) 1000 ng/ml rbPSAT1. RNA extraction and sequencing Following treatment cells were washed with PBS, lysed in 400µL mirVana lysis solution from mirVana RNA extraction kit (Invitrogen, St. Louis, US) and snap frozen. RNA was extracted from the cell pellets using the MirVana RNA extraction kit (Invitrogen, St. Louis, US) as per manufacturer’s protocol. Genomic DNA removal was carried out using the DNA free kit (Thermo Fisher Scientific, Massachusetts, US) as per the manufacturer’s protocol. RNA libraries were sequenced at the NGS Facility at the University of Leeds where they were prepared and sequenced as per their standard protocols using the Illumina TruSeq Stranded Total kit according to manufacturer’s guidelines. The RNA libraries were sequenced using the Illumina NextSeq 500 machine (Illumina, California, USA) with a single end 75 bp length read. RNA sequencing data processing was conducted as follows. Briefly, statistical test for differential gene expression was conducted via DESeq2 with the cut-offs such as log2FoldChange >1 (or <-1) and padj <0.05. For principal component analysis (PCA) plotting of each group of samples, both protein-coding genes and long non-coding RNAs (lncRNAs) with RPKM value ≥ 1 in at least one sample were used and subsequently log2(RPKM+1) transformation and a quantile normalisation were applied. Overrepresentation enrichment analysis of differentially expressed protein-coding gene sets was executed using WebGestalt for gene ontology terms and KEGG pathways. For gene ontology terms, biological process non-redundant datasets were chosen as functional database, and for both types of analyses, significance level was determined by FDR <0.05. Venn diagram analysis was performed using Venny.

first: Haidee

last: Tinning

first: Alysha

last: Taylor

first: Dapeng

last: Wang

first: Anna

last: Pullinger

first: Ruth

last: Sutton

first: Irene

last: Malo Estepa

first: Georgios

last: Oikonomou

first: Miguel

last: Velazquez

first: Paul

last: Thompson

first: Achim

last: Treumann

first: Peter

last: Ruane

first: Mary

last: O'Connell

first: Niamh

last: Forde


first: Shivani

last: Srivastava

summary: This SuperSeries is composed of the SubSeries listed below: GSE310249 and GSE310250

overall_design: Refer to individual Series

first: Andrew

last: Snyder


title: Neofunctionalization of a P-type ATPase enables fluconazole efflux in Candida auris

city: Beijing

first: Yabing

last: Song

state: Beijing

address: Chaoyang District

department: Institute of Microbiology

institute: Chinese Academy of Sciences

summary: Candida auris is an emerging fungal pathogen known for its high resistance to fluconazole, the most commonly prescribed antifungal. However, the genetic regulators of fluconazole susceptibility remain insufficiently understood in C. auris. Using a pooled screen of piggyBac (PB) transposition mutants, we identify significant enrichment of mitochondrial genes whose inactivation causes reduced fluconazole susceptibility. Genome-wide genetic interaction analysis of a representative mitochondrial gene-deleted mutant, pet309Δ, implicates that mitochondrial dysfunction reduces fluconazole susceptibility by enhancing Cdr1 efflux activity post-transcriptionally and through the vacuolar calcium pump homolog Cdt1. We further demonstrate that Cdt1, beyond its canonical calcium-pumping function, mediates fluconazole efflux, evidenced by its fluconazole-induced, calcineurin-dependent plasma membrane localization and dependence on ATP hydrolysis. Additionally, Cdt1 accelerates the evolution of fluconazole resistance, and its transcript levels correlate with susceptibility across clinical isolates. Our findings define a novel role for Cdt1 in fluconazole efflux in C. auris.

overall_design: mRNA profiles of pet309Δ and WT cells.

first: Jiaxin

last: Gao


title: Illumina short-read and PacBio long-reads of rRNA-depleted RNA from WT S. mediterranea across multiple regeneration time points

city: Poznań

first: Paulina

last: Jackowiak

address: Zygmunta Noskowskiego str. 12/14

country: Poland

institute: Institute of Bioorganic Chemistry

summary:
Illumina short-read sequencing of rRNA-depleted RNA composite sample: A single composite sample generated from a mixture of 8 time points (0, 1, 3, 6, 9, 12, 24, 48 hours post-amputation) plus one non-regenerating sample, representing WT specimens.
PacBio Iso-Seq long-read sequencing of rRNA-depleted RNA from amputated WT S. mediterranea at 0 hpa. A single sample from WT worms at 0 hours post-amputation with rRNA depletion applied prior to library preparation.

overall_design:
Illumina short-reads: Wild-type non-regenerating and regenerating (8 time-points) S. mediterranea worms were collected. Total RNA was ribodepleted and used for library preparation, followed by sequencing using NovaSeq 6000.
PacBio Iso-Seq long-reads: Wild-type S. mediterranea worms were amputated and collected immediately. Total RNA was ribodepleted and used for library preparation using Iso-Seq express 2.0 kit and Iso-Seq SMRTbell prep kit 3.0. The library was sequenced using Sequel IIe.

first: Annasha

last: Dutta

first: Anastasiia

last: Zaremba

last: Samelak-Czajka

first: Małgorzata

last: Marszałek-Zeńczak


title: Single-Cell Exon Deletion Profiling Reveals Splicing Events That Shape Gene Expression and Cell State Dynamics [RNA-seq_BaseEditor]

status: Public on Jan 08 2026

city: Frederick

first: Thomas

last: Gonatopoulos-Pournatzis

state: MD

address: Building 560

institute: National Cancer Institute

summary: Alternative splicing is a pervasive gene regulatory mechanism critical for diversifying the human proteome. To systematically investigate its role in cell fate determination, we developed scCHyMErA-Seq, a scalable CRISPR-based exon deletion screening platform integrated with 10x Genomics single-cell transcriptomic readouts. This tool enables efficient exon deletion while simultaneously capturing Cas9/Cas12a guides and polyadenylated transcripts at single-cell resolution. Applying scCHyMErA-Seq to high-throughput profiling of alternative cassette exons, we identified numerous exons with strong regulatory effects on gene expression. Analysis of NRF1 alternative exon-7 revealed that this exon modulates NRF1 transcriptional activity by regulating its recruitment to the promoters of target genes. Importantly, gene expression profiles generated using scCHyMErA-Seq accurately recapitulate findings from traditional, labor-intensive orthogonal methods, while offering enhanced scalability and efficiency. Overall, scCHyMErA-Seq represents a robust and versatile platform for systematically unraveling the functional impact of alternative splicing by directly linking specific splicing variants to transcriptional phenotypes.

overall_design: RNA sequencing was performed in HEK293T cells transfected with base-editing vectors designed to introduce mutations at the splice sites of endogenous NRF1 exon 7, effectively promoting exon skipping.

first: Bandana

last: Kumari

first: Arun

middle: P

last: Damodaran

first: Wilfried

last: Guiblet

first: Mei-Sheng

last: Xiao

first: Amit

middle: K

last: Behera

first: Tyler

last: On

first: Carl

last: Mcintosh

first: Maxwell

last: Teszler

first: Chelsee

last: Holloway

first: Sandra

last: Le

first: Nikhil

last: Parab

first: Yongmei

last: Zhao

first: Michael

last: Aregger


first: Shivani

last: Srivastava

overall_design: Bulk RNA-seq profiling of ROR1 CAR-T, cJun.ROR1 CAR-T, and BATF.ROR1 CAR-T cells pre-infusion or sorted 8 days post-infusion from KP-ROR1 tumors

first: Andrew

last: Snyder


title: Astrocytic Sox9 preserves cognitive function in models of Alsheimer's Disease

city: Houston

first: Brittney

last: Lozzi

state: TX

address: 1 Baylor Plaza

department: Cell & Gene Therapy

institute: Baylor College of Medicine

summary: Astrocytes play essential roles in the brain and their dysfunction is associated with nearly every form of neurological disease. Despite their ubiquity, our knowledge of how astrocytes contribute to disease pathogenesis is incomplete, accordingly harnessing their biology towards therapeutics remains a major challenge. Here we show that the transcription factor Sox9 plays a context specific role in maintaining astrocyte function and circuit activity in the aging hippocampus and Alzheimer’s Disease (AD) models. We found that Sox9 overexpression in astrocytes in AD models clears existing amyloid beta (Aβ) plaques and preserves cognitive function. Mechanistically, Sox9 promotes the phagocytosis of Aβ plaques by astrocytes through the regulation of the phagocytic receptor MEGF10, which is sufficient to preserve cognitive function in AD models. Collectively, these studies highlight new roles for astrocytic Sox9 during aging and AD, while identifying Sox9-MEGF10 signaling as a prospective astrocyte-based therapeutic approach to ameliorate cognitive decline in neurodegenerative disease.

overall_design: ChIP-Seq of the transcription factor Sox9 in the hippocampus of WT mice, AD mice, and aged (18month) mice.

first: Dongjoo

last: Choi

first: Eun-Ah Christine

last: Song

first: Benjamin

last: Deneen


title: Cartography and mechanism of enhanced transcriptome plasticity by transposable elements

city: Irvine

first: Ivan

last: Marazzi

state: CA

address: 839 Health Sciences Road

department: Department of Biological Chemistry

institute: University of California

summary: Transposable elements (TEs) in our genome are the heritage of ancient parasitic infections. While most of human DNA is comprised of TEs and TE-derived elements, their repetitive nature poses technical challenges and thus little is known about their positional identity and regulatory roles. Here, by integrating long-read and multidimensional transcriptional analyses, we investigated when, where and how TEs become part of a gene. We characterized how TE-derived isoform and new genes change across mouse-human variation and are linked to gene regulatory networks controlling cell states during differentiation, organogenesis and health (aging and pathological states). Mechanistically, we identified an RNA degradation-dependent and a splicing-dependent quality control mechanism that operate independently of conventional mechanisms of TE suppression (DNA methylation and heterochromatinization) and prevents TE-exonization and TE-induced cell differentiation. Overall, our findings reveal new mechanisms by which viral-derived elements enhance transcriptome plasticity.

overall_design: RNA-seq profiling of WT and Exosc3 cKO mESCs treated with major and minor splicing inhibitors (U1 and U6atac AMO) and MERVL ASO.

first: Youngseo

last: Cheon

first: Erik

last: Alvstad


title: Cerebrospinal fluid-driven ependymal motile cilia defects are implicated in multiple sclerosis pathophysiology

city: Montreal

first: Jo Anne

last: Stratton

address: 3801 Rue University

institute: McGill University

summary: Background: Multiple sclerosis is a neurodegenerative autoimmune disorder of the central nervous system (CNS) in which autoreactive immune cells migrate through a damaged blood brain barrier, resulting in focal demyelinating lesions of both the white and grey matter. Of increasing interest is the repeated observation that beyond focal lesions, there are also diffuse, surface-in gradients of pathology in MS, wherein damage is most severe directly adjacent to cerebrospinal fluid (CSF)-contacting surfaces, such as the subpial and periventricular areas. This observation suggests that toxic factors within MS CSF may be contributing to the emer-gence and/or evolution of surface-in gradients. Directly separating the CSF from the periventricular parenchyma are ependymal cells – a glial epithelium that expresses tufts of motile cilia which are critical for circulating CSF solutes and regulating local fluid flow. While damage to ependymal cilia has the potential to drastically modify CSF homeostasis and thus contribute to the damage of CSF exposed regions, these motile cellular structures have yet to be investigated in the context of MS. Methods: We first conducted single cell RNA sequencing of fresh human periventricular brain tissue containing ependymal cells from MS patients and non-MS disease controls. We subse-quently collected CSF from MS patients and exposed cultured rodent ependymal cells to this CSF in order to evaluate impact on ependymal ciliary function. To complement our direct eval-uation of cilia in the context of MS, we also confirmed whether cilia were altered in a classic animal model of MS, experimental autoimmune encephalomyelitis (EAE), and also designed a novel transgenic animal model to evaluate the cellular and behavioural effect(s) of adult ep-endymal ciliary disruption. Results: Single cell RNA sequencing analysis of human ependymal cells in MS demonstrated largescale dysregulation of ciliary genes; in situ stains of MS brain tissue confirmed a loss of ependymal cilia in MS compared to control. Exposure of ependymal cells to MS CSF led to transcriptional modification of ciliary gene expression and reduced ciliary beating frequency. Likewise, analysis of ependymal cells in EAE also demonstrated altered cilia gene expression. Conditional knockout of the critical cilia-associated gene Ccdc39 in ependymal cells led to transient ventricular enlargement, increased periventricular microglial density, and alterations in nesting behaviour. Conclusion: These data suggest that cilia are dysregulated in CNS autoimmunity. More im-portantly, however, they provide evidence to suggest that ependymal cilia disruption could play an active role in the development of periventricular pathology in MS, and can lead to behav-ioural deficits that may underlie aspects non-motor MS symptomatology.

overall_design: Primary rat ependymal cell cultures were exposed to MS patient CSF samples for 48 hours (controls were left untreated), then bulk RNA sequencing was conducted to assess the resulting transcriptomic effects.

first: Maxime

last: Bigotte

first: Adam

last: M.R. Groh

first: Elia

last: Afanisiev

first: Vincent

last: Wong

first: Kevin

last: Lancon

first: Moein

last: Yaqubi

first: Finn

last: Creeggan

first: Craig

last: S. Moore

first: Adil

last: Harroud

first: Raphael

last: Schneider

first: Philippe

last: Séguéla

first: Alexandre

last: Prat

first: Simon

last: Thebault

first: Stephanie

last: Zandee

first: Jo

last: Anne Stratton


title: Astrocytic Sox9 preserves cognitive function in models of Alsheimer's Disease [RNA-Seq]

first: Brittney

last: Lozzi

overall_design: RNA-Seq profiling of young (4months) and aged (18months) astrocytes sorted from the hippocampus using GFP expression in Aldh1l1-GFP mice. RNA-Seq profiling of wildtype and their Sox9 knockout  age matched counterparts in young (4months) and aged (18months) astrocytes sorted from the hippocampus using GFP expression in Aldh1l1-GFP;Sox9fl/fl mice. RNA-Seq profiling of astrocytes sorted from the hippocampus in mice modeling alzheimer's disease (AD) with and without overexpression of Sox9.

first: Dongjoo

last: Choi

first: Yi-Ting

last: Chen

first: Teng-Wei

last: Huang

first: Benjamin

last: Deneen


title: Remodeling of self-assembled microvascular networks under long term flow

city: Cambridge

first: Charles

middle: Ara

last: Demurjian

state: MA

address: 31 Ames Street

institute: BioMicro Center at MIT

summary: The incorporation of a functional perfusable microvascular network (MVN) is a common requirement for most organ on-chip-models. Long-term perfusion of MVNs is often required for the maturation of organ phenotypes and disease pathologies and to model the transport of cells and drugs entering organs. In our microphysiological system, we observe that flow can recover perfusion in regressed MVNs and maintain perfusable MVNs for at least 51 days. Throughout the 51 days, however, the MVNs are continuously remodeling to align with the direction of bulk flow and only appear to attain morphological homeostasis with the use of maintenance medium without growth factors. We observed that the flow resistance of the MVNs decreases over time, and using a computational model, we show that stable vessels have higher flow rates and velocities compared to regressing vessels. Cytokine analysis suggests that static conditions generate an inflammatory state, and that continuous flow reduces inflammation over an extended period. Finally, through bulk RNA sequencing we identify that both the endothelial and fibroblast cells are actively engaged in vascular and matrix remodeling due to flow and that these effects persist for at least 2 weeks. This MPS can be applied to study hemodynamically driven processes, such as metastatic dissemination or drug distribution, or to model long-term diseases previously not captured by MPS, such as chronic inflammation or aging-associated diseases.

overall_design: bulkRNA seq of endothelial and fibroblast cells, extracted from MVNs at varying days following flow (or static conditions)

first: Floryan

last: Marie

first: Kamm

last: Roger

first: Demurjian

last: Charles


title: Dps binds and protects DNA in starved Escherichia coli with minimal effect on chromosome accessibility, dynamics and organization

city: Bloomington

first: Xindan

last: Wang

state: IN

address: 1001 E 3rd St

department: Biology

institute: Indiana University at Bloomington

summary: Dps is the most abundant nucleoid-associated protein in starved Escherichia coli with ∼180000 copies per cell. Dps binds DNA and oxidizes iron, facilitating survival in harsh environments. Dps–DNA complexes can form crystalline structures, leading to the proposed model that Dps reorganizes the starved E. coli nucleoid into a compact liquid crystal, slowing chromosome dynamics, and limiting access of other proteins to DNA. In this work, we directly tested this model using live-cell super-resolution microscopy and Hi-C analysis. We found that after 96 h of starvation, Dps compacts the nucleoid, and increases short-range DNA–DNA interactions but does not affect chromosome accessibility to large protein nanocages or small restriction enzymes. We also report that chromosome dynamics and organization are primarily impacted by the bacterial growth phase; the effect of Dps is relatively minor. Our work clarifies the role of Dps in modulating nucleoid properties, and we propose an updated model for Dps–DNA interactions in which Dps binds, protects, and compacts DNA largely without influencing chromosome access, dynamics, and organization. Additionally, this work provides a general framework for assessing the impact of nucleoid-associated proteins on key aspects of chromosome function in live cells.

sample_organism: Escherichia coli str. K-12 substr. W3110

overall_design: Hi-C, ChIP-seq, and whole genome sequencing experiments were performed on wild-type and mutant Escherichia coli W3110 growing in High-Def Azure medium supplemented with 0.2% glucose.


title: Disrupted Energy Metabolism is Associated with Retinal Ganglion Cell Degeneration in Autosomal Dominant Optic Atrophy

city: New York

first: Eugene Yu-Chuan

last: Kang

address: 701 W. 168 St, HHSC 2nd floor, 210

institute: Columbia University Irving Medical Center

summary: This study investigated the impact of an Opa1 variant on mitochondrial function and retinal metabolism using a novel knock-in mouse model (Opa1V291D/+) that mirrored autosomal dominant optic atrophy (ADOA). The model recapitulated RGC-specific structural and functional deficits, highlighting mitochondrial dysfunction characterized by reduced Complex I activity, increased oxidative stress, and diminished ATP production. Spatial metabolomics revealed metabolic imbalances, with heightened glycolysis in the outer retina but an energy deficit in the inner retina, particularly affecting RGCs. Single-nucleus RNA sequencing (snRNA-seq) confirmed a selective downregulation of energy-production genes in RGCs, underscoring their susceptibility to energy deficits. These findings established a mechanistic link between disrupted energy metabolism and RGC degeneration in ADOA and provided a valuable platform for exploring therapeutic strategies targeting energy pathways to prevent vision loss.

overall_design: To investigate transcriptomic changes underlying RGC degeneration in ADOA, we performed single-nucleus RNA sequencing (snRNA-seq) on retinal tissues from Opa1V291D/+ and WT mice at 360 days, enabling the identification of cell-type-specific gene expression alterations, particularly in energy metabolism pathways across different retinal cell populations.

first: Yun-Ju

last: Tseng

first: Nan-Kai

first: Chyuan-Sheng

last: Lin


title: Bombali virus infection of cynomolgus macaques as a survival model of Ebola virus disease

city: Galveston

first: Jacquelyn

last: Turcinovic

address: Galveston National Laboratory, 301 University Blvd.

department: Microbiology and Immunology

institute: University of Texas Medical Branch

summary: Ebolaviruses are a genus of emerging RNA viruses of which multiple species are known to cause severe disease and multiple outbreaks in humans. The most recently discovered ebolavirus species, Bombali virus (BOMV), was detected via metagenomic surveillance of bats in Sierra Leone. Additional surveillance detected BOMV in bats from Kenya, Guinea, Mozambique, and Tanzania. Infectious BOMV isolation from field samples has been unsuccessful; however, a recombinant BOMV (rBOMV) has been recovered via reverse genetics. While rBOMV has been used to challenge IFNAR-/- and humanized mice, it has yet to be characterized in a nonhuman primate (NHP) model, which is the gold-standard model for Ebola virus disease (EVD). We challenged eight macaques were challenged intramuscularly with 1000 PFU of rBOMV. Four macaques survived to the predetermined natural history study endpoint (28 DPI), and four were sacrificed at 7 DPI to characterize the disease pathology. NHPs sacrificed at 7 DPI had clear involvement in target organs of ebolavirus replication. Antigen-positive mononuclear cells were present in multiple tissues including the liver (Kupffer cells), lymph nodes, and adrenal gland. NHPs in the natural history study developed classic signs of EVD including coagulopathy with thrombocytopenia, lymphopenia, neutrophilia, and elevated inflammation markers. Disease signs correlated with viremia with onset at ~7 DPI and resolution by 15-21 DPI. BOMV-challenged NHPs developed a robust adaptive immune response, with strong BOMV-specific IgG and neutralizing titers by study endpoint at 28 DPI. This combination of Ebola-like yet nonlethal disease makes rBOMV challenge of cynomolgus macaques an attractive survival model of EVD.

overall_design: RNA-seq of whole blood longitudinally samples from cynomolgus macaques challenged with recombinant Bombali virus

first: John

middle: H

last: Connor

first: Robert

last: Cross

first: Thomas

last: Geisbert


title: Cocultures of anaerobic fungi and chain-elongating bacteria stably convert lignocellulose to butyrate and hexanoate

city: Santa Barbara

first: Elaina

last: Blair

address: 3357 Engineering II Building, UCSB

institute: University of California, Santa Barbara

summary: This study looks at the gene expression of two chain-elongating bacteria, Pseudoramibacter alactolyticus and Megasphaera elsdenii, in monoculture and in coculture with anaerobic gut fungi (Neocallimastix lanati). P. alactolyticus in particular has appeared stable in synthetic cocultures with anaerobic fungi based on metabolic output, and this RNA-seq study was designed to further assess that stability. Additionally, chain-elongating bacteria can use fungal fermentation products to generate short- and medium-chain fatty acids, and this study was employed to see how genes involved in this process (reverse beta oxidation) were regulated in coculture compared to monoculture.

sample_organism:
Megasphaera elsdenii
Pseudoramibacter alactolyticus
Neocallimastix lanati (nom. inval.)

overall_design: RNA-seq of chain-elongating bacteria (P. alactolyticus or M. elsdenii) in monoculture with lactate added and in coculture with Neocallimastix lanati.


title: BRD2 bridging TFIID and histone acetylation in transcriptional initiation [PRO-Seq]

city: Chicago

first: Ali

last: Shilatifard

state: IL

address: 320 E Superior St

department: Department of Biochemistry and Molecular Genetics

institute: Northwestern University Feinberg School of Medicine

summary: Members of the bromodomain and extraterminal domain (BET) transcription factor family play a central role in the regulation of gene expression. BET domain factors have also been proposed as major targets for multiple diseases, with inhibitors designed to block the binding of BET bromodomains to acetylated histones. However, recent studies demonstrated that the BETdomain of BRD4 is not involved in its transcriptional function and the specific mechanisms by which other individual BET-domain containing proteins distinctly regulate transcription remain poorly understood. Here, we demonstrate that BRD2 promotes transcriptional initiation by RNA Polymerase II (Pol II) at gene promoters and enhancers, predominantly in a bromodomaindependent manner. Our biochemical studies demonstrated that histone H4K16 acetylated histone-bound BET domain of BRD2 facilitates the recruitment of the transcription preinitiation complex TBP/TFIID to chromatin. Loss or inhibition of BRD2 bromodomains prompts the formation of BRD2-specific nuclear foci that sequester TFIID away from chromatin, leading to a genome-wide defect in transcriptional initiation. Our molecular studies demonstrated that the BET domains of BRD2 and BRD4 are not functionally exchangeable, highlighting distinct but cooperative roles for BET-domain family members in transcriptional initiation and elongation control to promote proper regulation of gene expression

overall_design: Precision Run-On Sequencing (PRO-seq) of DLD-1 and DLD-1 BRD4-AID cells

first: Bin

last: Zheng

first: Ruxuan

last: Qiu

first: Yuki

last: Aoi

first: Marta

last: Iwanaszko


title: Mechanistic basis of gene regulation by SRCAP and H2A.Z (CUT&RUN)

city: Lausanne

first: David

middle: Michael

last: Suter

address: EPFL SV-IN Station 19

department: Institute of Bioengineering

institute: École polytechnique fédérale de Lausanne

summary: A central problem in gene regulation is to discriminate gene regulatory functions of chromatin composition from the one of chromatin-modifying complexes. This question has been virtually unexplored in the context of the H2A.Z histone variant and its incorporation into nucleosomes by the Snf2 Related CREBBP Activator Protein (SRCAP) complex. Here we combine rapid SRCAP depletion, a SRCAP mutant lacking H2A.Z deposition activity, and quantitative genome-wide approaches to dissect how SRCAP and H2A.Z regulate transcription in pluripotent stem cells. We find that SRCAP exhibits essential H2A.Z-independent functions in preventing DNA binding of lineage-specific transcription factors at enhancers and stimulating transcription factor binding at promoters. In contrast, H2A.Z acts mainly as a transcriptional repressor that requires dynamic reloading by SRCAP throughout the cell cycle. Our study clarifies how the SRCAP-H2A.Z axis broadly orchestrates transcription to promote self-renewal, inhibit differentiation, and maintain plasticity of pluripotent stem cells.

overall_design: Chromatin immunoprecipitation on H2A.Z, histone PTM and several TF in mESC depleted or not for SRCAP

first: Armelle

last: Tollenaere

first: Enes

last: Ugur

first: Cedric

last: Deluz

first: Heinrich

last: Leonhardt


title: Oncostatin M drives multifaceted immune pathogenesis in atopic dermatitis-like inflammation via neutrophil-dependent mechanisms

city: Inchon

first: YunJae

last: Jung

address: 155 Gaetbeol-ro, Yeonsu-gu

department: Microbiology

country: South Korea

institute: College of Medicine, Gachon University

summary: Atopic dermatitis (AD) is a chronic inflammatory skin disease characterized by T helper 2 cell dysregulation and accumulation of innate immune cells. While recent studies have highlighted a role for neutrophils in the onset and progression of AD, their precise contributions remain incompletely defined. In a mouse model of AD-like inflammation induced by calcipotriol and ovalbumin, neutrophils were identified as a major source of the cytokine oncostatin M (OSM). Neutrophil-derived OSM promoted broad immune cell recruitment, exacerbated skin inflammation, and enhanced the expression of neuronal markers associated with pruritus. Knockdown of OSM and neutrophil depletion both attenuated inflammatory responses and neuronal activation. Publicly available single-cell RNA-sequencing datasets further confirmed increased OSM expression in neutrophils from lesional AD skin, underscoring the translational relevance of our findings. These results reveal a previously unrecognized intercellular communication axis in which neutrophil-derived OSM orchestrates multifaceted immune and neuroinflammatory responses in AD. Targeting this signaling pathway may offer a novel therapeutic avenue for AD and related inflammatory disorders.

overall_design: Mice ears were treated with calcipotriol and ovalbumin to induce AD-like inflammation. Immune responses were assessed through histological examination and quantitative PCR. RNA sequencing was conducted for unbiased transcriptomic analysis of skin lesions. To investigate the role of selected inflammatory mediators, small interfering RNA (siRNA) and neutralizing antibodies were employed in cell lines and mouse models, respectively.

first: Minji

last: Park

first: Jin-Ok

last: Baek


title: BRD2 bridging TFIID and histone acetylation in transcriptional initiation [ChIP-Seq]

overall_design:
ChIP-seq of Pol2, BRD4, BRD2, TBP,TAF1, GFP in the DLD-1, DLD-1 BRD2-AID, and DLD-1 BRD4-AID cells
ChIP-seq of H3K27ac, H4K5ac, H4K12ac, H4,K16ac in DLD-1 BRD2-AID cells


city: Shanghai

first: wenjie

last: liang

address: Guoquan North Road

institute: Fudan university

type: Methylation profiling by high throughput sequencing

summary: In mammals, it has long been hypothesized that DNA damage could induce DNA hypermethylation and contribute to carcinogenesis. However, the evidence that DNA damage is a cause of genome hypermethylation is still insufficient. Here, we demonstrated that, in plant, DNA damage can induce DNA hypermethylation in the context of symmetric CG, CHG as well as asymmetric CHH. Mechanically, DNA damage regulates the DREAM complex, to induce CG and CHG methylation. Moreover, DNA damage also utilizes the RdDM pathway to induce CHH hypermethylation. The hypermethylation sites of CG and CHG resulting from DNA damage tend to localize to gene body, and a large proportion of them are de nove generated. In contrast, the hypermethylation sites of CHH induced by DNA damage were mainly concentrated in the centromere and pre-centromere regions, and most of them are amplification of existing CHH methylation. Importantly, withdrawing the DNA damage or blocking the DNA damage response signal could fully abolish the CHH hypermethylation, partially rescue the CHG hypermethylation, but rarely recover the CG hypermethylation, indicating that DNA damage leaves symmetric DNA methylation as genetic imprinting. Collectively, our results suggest that DNA damage drives DNA methylation generation and evolution in plants.

overall_design: whole genome bisulfite sequencing of seedlings total DNA from different arabidopsis thaliana samples cultured for 14 days

first: Jinchao

last: Li

first: Wenjie

last: Liang

first: Weiqiang

last: Qian


title: BRD2 bridging TFIID and histone acetylation in transcriptional initiation [RNA-Seq]

first: Ali

last: Shilatifard

overall_design: RNA-seq profiling of wild type DLD-1 cells