title: OGT Orchestrates Intestinal Epithelial Homeostasis and Repair through Coordinated mTORC1 Activity

status: Public on Jul 28 2026

city: Xin Xiang

first: xiwen

last: xiong

address: 602 Jinsui Road

department: School of Forensic Medicine

institute: Xinxiang Medical University

summary: O‑GlcNAc transferase (OGT) mediates O‑GlcNAcylation, a nutrient‑sensitive post‑translational modification that integrates metabolic and signaling cues in diverse biological contexts. However, its role in intestinal stem cell (ISC) homeostasis and epithelial regeneration remains poorly understood. Here, we show that OGT is essential for maintaining intestinal epithelial integrity and regenerative capacity. Inducible deletion of Ogt in Lgr5⁺ crypt base columnar ISCs using Olfm4‑CreER led to crypt hyperplasia, expansion of transit‑amplifying cells, and depletion of the Lgr5⁺ ISC pool, accompanied by Paneth cell dysfunction and impaired epithelial regeneration following X‑ray irradiation. Mechanistically, OGT loss elevated proteasome activity, resulting in increased intracellular free amino acids and subsequent mTORC1 hyperactivation. Conversely, low‑dose rapamycin treatment in OGT‑deficient mice markedly attenuated mTORC1 hyperactivation and substantially improved epithelial regeneration after irradiation. Consistently, OGT‑deficient organoids exhibited heightened sensitivity to irradiation, which was alleviated by rapamycin. Furthermore, pharmacological elevation of O‑GlcNAcylation using the OGA inhibitor Thiamet‑G protected high‑fat diet‑fed mice from irradiation‑induced intestinal damage and promoted epithelial repair. Collectively, our findings establish OGT‑mediated O‑GlcNAcylation as a critical regulator of ISC function and mucosal repair through metabolic control of mTORC1 activity, and suggest that enhancing O‑GlcNAc signaling may represent a therapeutic strategy for radiation‑induced intestinal injury.

overall_design: RNA-seq profiling of ileal IECs from Olfm4∆Ogt and Olfm4Ctrl mice

first: Xiwen

last: Xiong

first: Huimin

last: Zhang


title: Transcriptomic profiling of the main olfactory epithelium of the perinatal mouse

city: Bethesda

first: Whitney

last: Heavner

state: MD

address: 35 Convent Drive

department: NINDS

country: USA

institute: National Institutes of Health

type: Expression profiling by high throughput sequencing

summary: RNA from single cells of the main olfactory epithelium of wild-type C57Bl/6 mice was sequenced over a perinatal developmental timecourse, from birth/postnatal day 1 to weaning/postnatal day 22, to establish developmental lineages, identify changes in gene expression along specific lineages, and predict signaling pathways involved in establishing and maintaining this stem cell niche.

overall_design: Individual live cells were collected from dissociated nasal sesnory epithelium microdissected from wild-type (C57BL/6) mice at postnatal day (P) 1, 3, 5, 8, 15, and 22 using fluorescence activated cell sorting (FACS). 2-4 biological replicates per age were collected. One mouse was used per biological replicate, except for P5, in which two mice were used for each biological replicate. Equal numbers of female and male mice were used for each age, except for P5 (only male).

first: Dana

last: Bakalar

first: John

last: Ngai


title: Loss of wbp11 Causes Multi-System Developmental Defects: A Zebrafish Model of VACTERL Association

city: changsha

first: Haochen

last: Wang

address: 183 Lushan Road, Yuelu District, Changsha City, Hunan Province

country: China

institute: hunan normal university

summary: VACTERL association is a congenital disorder characterized by multi-system malformations, primarily affecting the vertebrae, heart, kidneys, trachea and esophagus, as well as the limbs. Although WBP11 has been identified as a candidate causative gene, existing mouse models fail to fully recapitulate the multi-system phenotypes observed in patients, thereby limiting a comprehensive understanding of the pathogenic mechanisms underlying this gene. In this study, we established and systematically characterized a wbp11 knockdown zebrafish model to investigate the role of wbp11 in early development and its relevance to VACTERL association. Bioinformatics analysis revealed that zebrafish wbp11 shares high amino acid sequence identity with human WBP11, is broadly expressed during early embryogenesis, peaks at the gastrula stage, and displays relatively higher signal intensity in the head, skeletal muscle, and heart. Western blot analysis confirmed that injection of wbp11 morpholino (MO) markedly reduced Wbp11 protein levels, resulted in significantly increased morphological abnormalities, and caused a general delay in embryonic development. Phenotypic characterization demonstrated that wbp11 knockdown leads to multi-system developmental defects, including cardiac malformations, pericardial edema and impaired heart looping; vascular defects, underdeveloped mesenteric vessels and reduced cranial vasculature; spinal curvature and aberrant notochord structure; various fin hypoplasia phenotypes with reduced fin sizes; and transcriptional dysregulation of kidney developmental marker genes. These phenotypes closely resemble the core clinical features of VACTERL association, demonstrating that loss of Wbp11 can induce multi-system congenital anomalies in a vertebrate model. Transcriptomic and differential alternative splicing analyses, together with molecular biological assessments, further revealed significant dysregulation of genes associated with cardiac function, angiogenesis, skeletal patterning, fin development, and kidney development, thereby providing molecular insights into the observed morphological defects. Collectively, this study establishes a wbp11-MO mediated knockdown zebrafish model, demonstrates its capacity to partially recapitulate key features of VACTERL association, and provides a powerful platform for dissecting the underlying molecular mechanisms and exploring potential therapeutic interventions for this disorder.

overall_design: Zebrafish embryos at 72 hpf from the Control-MO and wbp11-MO groups


title: Spatial analysis reveals the evolving organization of IDH-mutant glioma

city: Rehovot

first: Itay

last: Tirosh

address: 234 Herzl St.

country: Israel

institute: Weizmann Institute of Science

summary: Adult diffuse gliomas comprise malignant cell states interwoven with the non-malignant brain microenvironment. Here, we combine spatial transcriptomics and spatial proteomics of IDH-mutant gliomas to define organizational principles across histological grades. In low-grade tumors, spatial organization is shaped by underlying brain anatomy. We identify a functional white–grey matter junction that restricts cortical invasion and is associated with marked changes in tumor composition and cellular phenotypes. This boundary is preferentially traversed by oligodendrocyte progenitor (OPC)-like malignant cells, suggesting a role in tumor expansion. In contrast, intermediate-grade tumors are largely disorganized, with few recurring interactions between cancer cell states and microenvironmental cell types. In high-grade tumors, hypoxia-associated structure emerges, resembling IDH-wildtype glioblastoma. Together, these findings reveal two independent axes of spatial organization—from anatomy-driven structure in low-grade tumors to hypoxia-driven organization in high-grade tumors—and establish a framework linking tumor grade to recurrent spatial interactions.

overall_design: 13 IDH-WT human glioblastoma samples spatially annotated by the surgeon during navigation-guided tumor resection and 24 IDH-mutant glioma samples profiled by 10X Visium spatial transcriptomics

first: Rouven

last: Hoefflin

first: Alissa

middle: C

last: Greenwald

first: Noam

middle: G

last: Darnell

first: Christopher

middle: W

last: Mount

first: Mario

middle: L

last: Suva


title: Hepatocyte RIPK1 scaffolding function protects against alcohol-induced liver injury by restraining ER stress-driven apoptosis and inflammation

city: Nanjing

first: Dan

last: Weng

address: 200 Xiaolingwei Street

institute: Nanjing University of Science and Technology

summary: Alcoholic liver disease (ALD) is a global health burden with limited therapeutic options. The pathogenesis of ALD involves hepatocyte death and inflammation, but the key regulatory mechanisms remain incompletely defined. Receptor-interacting protein kinase 1 (RIPK1) is a critical signaling molecule with distinct kinase-dependent and kinase-independent, scaffold-dependent functions. While RIPK1 kinase activity has been implicated in various pathologies, the role of its scaffolding function in the liver, particularly in ALD, is unknown. Here, using hepatocyte-specific RIPK1 knockout (Ripk1-hepKO) mice, we demonstrate that loss of RIPK1 markedly aggravates ethanol-induced liver injury. In both chronic and acute-binge ethanol feeding models, Ripk1-hepKO mice exhibited significantly elevated serum transaminases, enhanced hepatocyte apoptosis, and amplified hepatic inflammation with increased macrophage infiltration, without a change in steatosis. Transcriptomic analysis revealed enrichment of inflammatory pathways in Ripk1-hepKO livers. Mechanistically, we identified endoplasmic reticulum (ER) stress as a critical contributor to this phenotype. RIPK1 deficiency was associated with attenuated NF-κB/p65 signaling, preferential amplification of eIF2α-ATF4-CHOP-associated stress responses, and enhanced CHOP accumulation, while pharmacological modulation of ER stress-associated pathways using 4-phenylbutyrate (4-PBA) or ISRIB ameliorated hepatocyte apoptosis, liver injury, and inflammation in ethanol-fed Ripk1-hepKO mice. Translating these findings to human disease, liver specimens from ALD patients showed elevated hepatocyte apoptosis, CD68+ macrophage infiltration, and induction of ER stress markers. Our study unveils a previously unrecognized protective role for the scaffold function of hepatocyte RIPK1 in ALD, positioning RIPK1 scaffolding and ER stress-associated signaling as promising therapeutic targets for ALD.

overall_design: Bulk RNA sequencing was performed on liver tissues from eight female mice subjected to the National Institute on Alcohol Abuse and Alcoholism (NIAAA) chronic-plus-binge ethanol feeding model. Four independent EtOH-fed Ripk1-Con control mice (S29, S32, S40, and S41) and four independent EtOH-fed hepatocyte-specific Ripk1 knockout mice (Ripk1-hepKO; S28, S34, S37, and S39) were profiled as biological replicates. Genotype was the comparison variable, while tissue, sex, and ethanol-feeding condition were held constant.

first: Weigao

first: Hu

last: Liu

first: Yunfeng

last: Zhu

first: Yuxin

last: Chen

last: Fu


title: ERK signaling integrates multiple mechanisms to drive cortical evolutionary expansion

city: Shanghai

first: TongYe

address: 138 Yi Xue Yuan Road

institute: Fudan University

summary: A critical first step in human evolutionary divergence from chimpanzees and other primates is the production of greatly increased numbers of cortical pyramidal neurons during development and over evolutionary time. This expansion underpins the enlarged human cerebral cortex and, consequently, higher-order cognition and consciousness. However, the cellular and molecular mechanisms driving this progressive increase in cortical neuron number remain incompletely understood. Here we show that elevated ERK signaling in human cortical radial glia (RGs), relative to mouse RGs, arises from evolutionary changes in the developmental expression of existing shared genes. Using the Emx1-Cre line to overexpress MEK1DD, a constitutively active mutant of rat MAP2K1, we found that enhanced ERK signaling in mouse cortical RGs upregulates cAMP–PKA signaling, along with promoting self-renewal, expanding the RG pool, and accelerating cell cycle progression. Conversely, overexpression of PKA signaling in mouse cortical RGs via in utero electroporation of constitutively active PRKACA mutants (L205R or W196G) reduces ERK activity, prolongs the cell cycle, suppresses SHH–SMO and YAP/TAZ pathway activity, and blocks ependymal gliogenesis. Together, our results demonstrate that ERK and PKA signaling in cortical RGs engage a dynamic balance of synergistic and antagonistic interactions. This interplay couples evolutionarily enhanced ERK and PKA activities to increased cortical RG numbers, prolonged cell cycle progression, and an extended neurogenic period, which collectively culminate in a marked increase in neuronal production. We conclude that heightened ERK pathway activity in cortical RGs serves as a central driver of progressive neocortical expansion across mammalian evolution.

overall_design:
The whole mouse cortex was dissected under a microscope for single-cell RNA sequencing (scRNA-seq) analysis. Briefly, mouse embryos and postnatal brains were collected and immediately submerged in fresh ice-cold Hanks' Balanced Salt Solution (Gibco 12175-095). The cortex was then finely dissected, cut into small pieces, and dissociated into a single-cell suspension using a Papain Cell Dissociation Kit (Miltenyi Biotec, catalog no. 130-092-628) according to the manufacturer’s instructions.
Single-cell RNA-seq libraries were generated using the Chromium droplet-based sequencing platform (10X Genomics) following the manufacturer’s protocol (manual document part number: CG00052 Rev C). After cellular quality filtering, the number of cells included in the dataset were as follows:
E12 MEK1DD mice cortex (7931 cells, 3773 genes/cell), E12 control mice cortex (7563 cells, 3562 genes/cell), E17 PKA mice cortex (6523 cells, 3284 genes/cell), E17 control mice cortex (11091 cells, 2650 genes/cell), P0 control mice cortex (13894 cells, 2891 genes/cell), P2 PKA mice cortex (8211 cells, 3006 genes/cell), P2 control mice cortex (10920 cells, 2871 genes/cell).

first: Tongye

first: Zhuangzhi

first: Wenhui

last: Zheng

first: Zhengang

last: Yang


title: Ancient Somatosensory Circuit Architectures Employ Flexible Molecular Strategies

city: New York

first: Jeremy

last: Dasen

state: New York

address: 435 East 30th St NSB 1104

department: Neuroscience

institute: NYU School of Medicine

summary: The extent to which conserved neural circuit architectures depend on shared molecular specification programs remains unclear. We address this question by examining the somatosensory system of the little skate, Leucoraja erinacea, an early-diverging vertebrate that retains ancestral features of both finned and limb-based body plans. These data were generated to investigate the molecular organization and development of somatosensory neurons and spinal circuits in an early-diverging vertebrate.

overall_design: Spatial transcriptomic profiling was performed using the 10x Genomics Xenium In Situ platform with a custom 300-gene probe panel. Eight transverse embryonic sections containing rostral pectoral, caudal pectoral, and pelvic spinal cord and dorsal root ganglia from stages 31+ and 32 embryos, including unilateral fin-ablated embryos, were analyzed.

first: Hyemin

last: Lee

first: Paul

last: Frazel

first: Elena

last: Singer-Freeman

middle: S


title: PIWIL4 knockdown alters gene expression in RSV-infected immortalized small airway epithelial cells

city: Galveston

first: Tiziana

last: Corsello

address: 301 University Blvd

institute: UTMB

summary:
Respiratory syncytial virus (RSV) is a leading cause of acute lower respiratory tract infection in young children, the elderly, and immunocompromised hosts, and no effective vaccine or therapy exists for infants. PIWIL4, a member of the PIWI protein family known to interact with PIWI-interacting RNAs (piRNAs), was found to be induced by RSV infection in airway epithelial cells. To investigate the role of PIWIL4 in the transcriptional response to RSV, immortalized small airway epithelial (iSAE) cells were transfected with either a non-targeting or a PIWIL4-targeting siRNA and then left uninfected or infected with RSV for 15 hours. Gene expression was profiled using the Agilent Whole Human Genome Oligo Microarray (4x44K) to identify genes differentially expressed upon PIWIL4 knockdown under basal and RSV-infected conditions.
4 samples, one array per condition (no biological replicate arrays; RNA from three pooled technical replicate wells per condition was hybridized to a single array). 2x2 factorial design: siRNA treatment (non-targeting control vs. PIWIL4-targeting) x infection status (uninfected control vs. RSV Long strain infection, MOI 5, 15 hours post-infection) in immortalized human small airway epithelial (iSAE) cells.

overall_design: 4 samples, one array per condition. RNA pooled from a single experiment performed in triplicate wells was hybridized to one array per condition (no biological-replicate arrays). 2x2 factorial design: siRNA treatment (non-targeting control vs. PIWIL4-targeting siRNA, 300 nM) x infection status (uninfected control vs. RSV Long strain, MOI 5, 15 hours post-infection) in immortalized human small airway epithelial (iSAE) cells.

first: Tianshuang

first: Andrzej

last: Kudlicki

first: Yuanyi

last: Zhang

first: Nicholas

last: Dillman

first: Sehar

last: Fazal

first: Roberto

middle: P

last: Garofalo

first: Antonella

last: Casola


title: 7-hydroxycoumarin-β-D-glucuronide protects against cisplatin-induced acute kidney injury via inhibiting p38 MAPK-mediated apoptosis in mice

city: Beijing

first: sijia

last: liu

address: Xiannongtan Street, Xicheng District

institute: Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College

summary: Cisplatin is a common chemotherapeutic agent limited by severe nephrotoxicity, which easily induces acute kidney injury (AKI) in tumor patients. 7-hydroxycoumarin-β-D-glucuronide (7-HCG), a major kidney-enriched metabolite of coumarins from Hydrangea paniculata, was previously found to accumulate specifically in renal tissue with long elimination half-life. In this study, male C57BL/6 mice were pretreated with 7-HCG at three doses, followed by intraperitoneal cisplatin injection to establish AKI model. Renal tissue mRNA sequencing was performed on control, cisplatin model, 15 mg/kg and 30 mg/kg 7-HCG groups to explore transcriptomic changes. Transcriptome analysis revealed that 7-HCG reversed dysregulated MAPK signaling and apoptosis pathways triggered by cisplatin. Further validation confirmed that 7-HCG reduced renal ROS production, suppressed phosphorylation of p38/ERK/JNK, and downregulated pro-apoptotic proteins Bax and cleaved-caspase3. This dataset provides transcriptomic evidence illustrating the protective mechanism of 7-HCG against cisplatin nephrotoxicity through p38 MAPK/apoptosis axis inhibition. All raw RNA-seq reads and processed gene expression matrices are deposited here for public reuse.

overall_design: Male C57BL/6 J wild-type mice (18–22 g) were randomly divided into four groups for transcriptome sequencing: sham control group (PBS pretreatment + saline injection), cisplatin model group (PBS pretreatment + 10 mg/kg cisplatin i.p.), 7-HCG 15 mg/kg treatment group, and 7-HCG 30 mg/kg treatment group. Mice received daily oral 7-HCG/PBS for 5 days, cisplatin was administered on Day 3, and all animals were sacrificed 72 h post cisplatin injection. Whole kidney tissues were harvested for total RNA extraction. PolyA mRNA libraries were constructed and sequenced on Illumina NovaSeq 6000 platform with paired-end 150 bp reads. Differential expression analysis (|log2FC|>1, q<0.05), GO and KEGG enrichment were conducted to identify altered biological pathways. 5 biological replicates were included per group for RNA-seq.

first: Haijie

last: Wu

first: Xiaohu

last: Shi

first: Yingda

last: Zang

first: Xiaodi

last: Zhao

first: Xikun

last: Liu

first: Weida

last: Wang

first: Wenying

first: Clarence T.T.

last: Wong


title: Mitophagy-Replenishment Strategy Targeting the Aberrant Endogenous dsDNA to Enhance Bone Healing Quality in the Elderly

city: Suzhou

first: zhengxia

last: Ni

state: Jiangsu

address: 188 Shizi Road

department: Department of Orthopedics

institute: The First Affiliated Hospital of Soochow University

summary: The increased incidence of delayed bone healing in elderly patients is primarily driven by the senescence of bone marrow mesenchymal stem cells (BMSCs), yet the upstream molecular triggers remain incompletely defined. This study elucidates a novel senescence-driving mechanism: impaired mitophagy and BAX oligomerization-mediated minority mitochondrial outer membrane permeabilization (miMOMP) trigger endogenous dsDNA leakage. This leakage activates the cGAS–STING signaling axis, establishing a vicious cycle that accelerates BMSC senescence and impairs osteogenesis. To precisely intervene, we developed a targeted composite delivery system (GM-UMPA) comprising AE105-functionalized hollow mesoporous polydopamine (HMPDA) nanoparticles loaded with the mitophagy inducer urolithin A (UA), encapsulated within injectable gelatin methacryloyl (GelMA) microspheres. The hollow mesoporous architecture provides a distinct structural advantage by significantly amplifying drug-loading capacity compared to conventional materials, while surface AE105 peptides enable highly specific uPAR-mediated endocytosis into senescent cells. Crucially, the weakly basic HMPDA framework exhibits pH-responsive drug release characteristics, triggering rapid intracellular UA liberation specifically within the acidic microenvironment of senescent BMSCs. Validated using an in vitro BMSC replicative senescence model and an in vivo critical-sized femoral condyle defect model in aged rats, this hierarchical platform successfully cleared damaged mitochondria, suppressed senescence-associated secretory phenotypes (SASP), and substantially accelerated high-quality bone regeneration. Ultimately, this mitophagy-replenishment strategy offers a structurally innovative, responsive nanomedicine paradigm for treating age-related bone healing disorders.

overall_design: RNA-Seq Analysis of Bone Marrow Mesenchymal Stem Cells from Young and Aged Rattus norvegicus


title: Ribosome profiling reveals a high ribosomal occupancy and 5′ bias on mRNAs coding for aggregating proteins in HEK293 cells

city: San Diego

first: Khalyd

last: Clay

state: CA

address: 10550 N. Torry Pines. Rd.

institute: Scripps Research

summary: Ribosome profiling of HEK293 control libraries used for the manuscript C1/C2 Ribo-seq GEO upload set. Files are staged in the dedicated GEO FTP subfolder RiboSeq.

overall_design: Two paired-end control Ribo-seq libraries: C1_RS and C2_RS. The processed matrix contains gene-level 27-29 nt RPF counts for these two uploaded libraries only.

first: Michael

last: Petrascheck


title: Polysome profiling analysis in HEK293 cells of fractionated ribosomal species

summary: RNA-seq profiling of HEK293 cells treated with vehicle control or minocycline for 12 h. Files are staged in the dedicated GEO FTP subfolder RNAseq.

overall_design: Six paired-end RNA-seq libraries: three vehicle/control biological replicates and three minocycline-treated biological replicates.


title: Endometriosis Pain: Genes linked to Inflammation Distinguish Symptomatic from Asymptomatic Disease

city: New Haven

first: Ramanaiah

last: Mamillapalli

state: CT

address: 310 Cedar Street

department: OBGYN

institute: Yale University

summary: Endometriosis is a multifaceted disease, causing debilitating pelvic pain in some patients, while being completely asymptomatic in others. The pathophysiology of endometriosis pain is not well understood and poorly correlated to stage. We hypothesized that this clinical heterogeneity may be explained by examining differences in gene expression. We performed RNA sequencing of 27 formalin-fixed, paraffin-embedded peritoneal biopsies from 9 symptomatic (Sx) and 10 asymptomatic (ASx) subjects. 890 genes were differentially expressed between Sx and ASx samples. Of these, the most significant including genes involved inflammatory signaling (IL16, IL17RA, JAK3, SMPD3, RELT), cell adhesion (OLFML1, CDON, VCAN), and neuromodulation (SEMA6D, ADRA2C, SLC7A5). Gene Set Enrichment Analysis identified functional enrichment in 22 gene ontology (GO) pathways, of which 7 represented immunologic pathways. Weighted Gene Correlation Network Analysis (WGCNA) identified 11 co-expression modules significantly correlated with symptomaticity, including one module strongly enriched for immunologic/inflammatory functions. Of all molecules identified as associated with pain, IL16 expression also correlated with symptom severity when cases were stratified into mild vs. severe pain based on clinical criteria. These findings suggest that endometriotic lesions of symptomatic subjects are characterized by distinct molecular signatures, including altered expression of inflammatory pathways, highlighting potential mechanisms underlying symptom variability and identifying candidate pathways for future therapeutic interventions.

overall_design: Medical charts and surgical records were reviewed for patients receiving a histological diagnosis of endometriosis after undergoing laparoscopy at Yale-New Haven Hospital (New Haven, CT), 2017-2019. Symptomatic patients had undergone laparoscopy for chronic pelvic pain with biopsies confirming endometriosis. Symptoms included both dysmenorrhea and non-menstrual pelvic pain.  A pain score using a numeric rating scale was available for all subjects.  Asymptomatic patients had incidentally diagnosed endometriosis after biopsies were taken during laparoscopy for other gynecologic indications (abnormal uterine bleeding, benign adnexal mass). Medical records were reviewed by at least two independent clinicians to confirm no complaint of chronic pelvic pain preceding surgery. All patients provided written informed consent for the use of deidentified biological samples in research purposes. Tissue blocks corresponding to endometriosis lesions were obtained from the Yale Pathology Tissue Services.

first: Howard

middle: J

last: Li

first: Shant

last: Apelian

first: Monish

last: Kumar

first: Sarah

middle: F

first: Nishita

last: Pondugula

first: Gabriela

last: de Queiroz Campos

first: Sumaiya

last: Sayeed

first: Yonghee

last: Cho

first: Hugh

last: Taylor


title: Peptide-targeted lipid nanoparticles orchestrating IFN-γ and cisplatin crosstalk eliminate ovarian cancer [RNA-seq]

city: shenzhen

first: yongfei

last: Zhou

address: Yutang Subdistrict, Guangming District

institute: Shenzhen Bay Laboratory

summary: Ovarian cancer remains refractory to current immunotherapies, largely due to poor tumor targeting, immunosuppressive feedback, and the absence of durable memory responses. Here, we develop a peptide-targeted lipid nanoparticle (ptLNP) platform modified with an FSHR-affinity peptide (Pep LLV) that enables ovarian-directed co-delivery of interferon-gamma (IFN‑γ) mRNA and cisplatin (CDDP). In an orthotopic mouse model, ptLNP-mediated IFN‑γ delivery suppresses tumor progression but upregulates intraovarian PD‑1 expression, creating an adaptive resistance loop that is relieved by co-delivered anti‑PD‑1 antibody. Single-cell RNA sequencing reveals that CDDP eliminates divergent tumor differentiation trajectories and enforces G2/M arrest, which prevents mitotic dilution of the IFN‑γ effector IRF1 and sustains pro-apoptotic signaling. This mechanism is validated by IRF1 gain- and loss-of-function experiments, demonstrating that IRF1 is both sufficient and necessary for the synergistic effect. In T-cell-deficient xenograft models, the IFN‑γ–CDDP combination achieves complete tumor regression, indicating direct cytostatic activity independent of adaptive immunity. Post-treatment IL‑12 boosting further establishes long-term CD4⁺ and CD8⁺ memory T cell responses, conferring protection against tumor re-challenge. Collectively, this study presents a modular platform that orchestrates cytokine therapy, checkpoint blockade, chemotherapy, and memory immunity, providing a mechanistic framework for combinatorial immunotherapy against refractory ovarian cancer.

overall_design: This study aims to elucidate the mechanistic basis and therapeutic efficacy of a novel combinatorial immunotherapy regimen for refractory ovarian cancer, comprising peptide-targeted lipid nanoparticles (ptLNPs) delivering IFN‑γ mRNA, anti‑PD‑1 antibody, and a cisplatin (CDDP) conjugate. An orthotopic ovarian cancer model was established in C57BL/6 mice by surgical injection of ID8Luci cells into the ovarian bursa following ptLNPFSHα&β-mediated bursa expansion. After 60 days of tumor development, tumor-bearing mice were randomized into five groups (n=10 each): sham control, model control, ptLNPIFN-γ monotherapy, ptLNPIFN-γ&anti-PD-1 dual therapy, and ptLNPIFN-γ&anti-PD-1@CDDP triple therapy, with intraperitoneal injections administered every three days from day 62 to day 95 post-bursa expansion. At the experimental endpoint (day 97 or upon humane endpoint), fresh ovarian tumor samples were harvested and processed for single‑cell RNA sequencing to profile tumor cell heterogeneity, immune microenvironment remodeling, cell‑cycle perturbations, and pseudotime differentiation trajectories across treatment groups. Additional validation experiments included IRF1 gain‑ and loss‑of‑function assays in A2780 and SKOV3 cell lines, T‑cell‑independent efficacy evaluation in nude mouse xenografts, and post‑treatment IL‑12 boosting for memory immunity assessment. The generated transcriptomic data, together with accompanying flow cytometry, immunofluorescence, and survival analyses, are intended to delineate the synergistic mechanisms by which CDDP enforces G2/M arrest to sustain IFN‑γ–IRF1 pro‑apoptotic signaling while anti‑PD‑1 relieves IFN‑γ‑induced immunosuppression, ultimately achieving potent antitumor activity and durable memory responses against ovarian cancer.

first: Yongfei

first: Jiaojiao

last: Nie

first: Wanbo

last: Tai


title: Single cell sequencing of APECED patient and Healthy control peripheral blood cells

city: Tarrytown

first: William

last: Galbavy

state: NY

address: 777 Old Saw Mill River Road

institute: Regeneron

summary: 10 APECED and 10 Healthy control patients peripheral blood cells isolated for single cell sequencing. scRNA-seq and BCRseq analysis illustrate changes to the composition of the B cell compartment in APECED compared to Healthy control such as a reduction in Naïve B cells and increases to IgM CD27+ CXCR3+ and Class switched atypical B cell subsets with alternative activation (TBX21+ ZEB2+).

overall_design: 10 APECED and 10 Healthy control patients whole blood was collected in K2EDTA tubes and shipped refrigerated on ice packs via FedEx Priority Overnight. They were processed immediately upon arrival. Peripheral blood cells were isolated and prepared for flow cytometry and multiomics sequencing. Peripheral blood cell composition, overall B cell composition, isotype specific IgM+ B cells and Class switched B cells compositions were analyzed along with BCR features.

first: Hyunjin

last: Kim

first: Brian

last: Klotz

first: Marine

last: Malbec

first: Carley

last: Tasker

first: Joseph

last: Devlin

first: Benjamin

last: Daniel

first: Christina

last: Adler

first: Wei Keat

last: Lim

first: Asiel

middle: A

last: Benitez

first: Sokol

last: Haxhinasto


title: Social isolation upregulates takeout expression in female Drosophila melanogaster to promote sucrose preference

city: Princeton

first: Elisabeth

last: Tawa

state: NJ

address: Lewis Thomas Lab, Washington Road

institute: Princeton University

summary: Previous research suggests that social isolation induces changes in gene expression that encode a starvation-like brain state and reduce sleep. However, the extent to which social isolation alters behaviors via sex-specific brain changes is unclear. Here, we use Drosophila melanogaster to explore sex differences in isolation-induced behavioral and transcriptomic changes. Male and female adult flies were isolated for seven days, and multiple behavioral sex-based differences were identified through tests of activity, motivation, aggression, and sugar preference. RNA-seq analysis also identified several candidate genes that were associated with sex differences in isolation-induced behavioral changes. Takeout (to) expression and sucrose selection were upregulated exclusively in females following social isolation. Following to knockdown in to-expressing cells, sucrose preference decreased in socially isolated females but increased in males. Overall, our results suggest that manipulating to expression influences sucrose choice in opposite directions between females and males following social isolation. It is possible that isolation-induced to overexpression in non-neuronal cells in the female head could contribute to sex differences in this behavior.

overall_design: RNA-seq profiling of male and female ORE-R adult fly whole heads after seven days of social isolation or group housing.

first: Daniel

last: Notterman


title: Spatial Transcriptomic Activity Atlas of Spinal Sympathetic Neurons Delineates Neural Control of Lipolysis

city: Kobe

first: Haruaki

last: Sato

state: Hyogo

address: BldgC #504, 2-2-3, Minatojimaminamimachi, Chuo Ward

department: Biodynamics Research

country: Japan

institute: RIKEN

summary: The sympathetic nervous system coordinates the functions of diverse organs to maintain homeostasis and mounts adaptive responses to stressors. Although recent molecular and genetic studies have advanced our understanding of peripheral sympathetic neurons, the spatial and functional organization of spinal sympathetic preganglionic neurons (SPNs) during stress responses remains poorly understood. Here we establish a spatial transcriptomics (STx)-based activity atlas of mouse SPNs under distinct stress conditions. This atlas reveals the spinal segment- and sex-biased organization of SPN transcriptomic subtypes. Using immediate early gene (IEG) induction as a readout of neuronal activation, we found that different stressors, such as cold exposure and glucose deprivation, recruit different SPN transcriptomic subtypes.

overall_design: 6 slides containing 18 samples (three from RT/saline, Cold, and 2-DG group, for both sexes) were analyzed with Xenium to capture RNA.

first: Serika

last: Yamada

first: Shuntaro

last: Uchida

first: Masafumi

last: Tsurutani

first: Dooseon

last: Cho

first: Mitsutaka

last: Kadotaka

first: Takefumi

last: Kondo

first: Kazunari

last: Miyamichi


title: Smarcc1 drives optic stalk patterning and optic nerve head astrocyte differentiation

city: Guangzhou

first: Guizhong

last: Cui

state: Guangdong

address: 188 KaiYuan Road, Huangpu District

institute: Guangzhou Lab

summary: The optic nerve develops from the neuroectodermal optic stalk, which undergoes coordinated morphogenesis and gives rise to optic nerve astrocytes that support retinal ganglion cell (RGC) axons. Here, we define the progression of astrocyte formation from the optic stalk and identify stage‑specific functions of the SWI/SNF scaffolding subunits Smarcc1 (Baf155) and Smarcc2 (Baf170). Both factors are co‑expressed in retinal pigment epithelium (RPE) and optic stalk progenitors, with Smarcc2 persisting in differentiated RPE and astrocytes. Conditional deletion using Dct‑Cre revealed compensatory activity in pigmented lineages, whereas Smarcc1 loss uniquely disrupted optic nerve head (ONH) morphogenesis, resulting in glial lamina collapse, RGC degeneration, and progressive visual decline. Spatial transcriptomics and functional assays show that Smarcc1 enables dorsal optic stalk progenitors to transition from a pigmented, RPE‑like state to astrocyte progenitors by repressing pigment gene programs and permitting Pax2/Sox2 activity. After specification, Smarcc1 is also required for glial lamina assembly and astrocyte migration into the inner retina. These findings demonstrate that Smarcc1‑dependent chromatin remodeling coordinates astrocyte specification with ONH morphogenesis to maintain long‑term retinal function.

overall_design: The spatial transcriptome of the developing RPE and OS was obtained according to the Geo-seq (Chen et al. 2017) protocol with minor modifications. Briefly, E12 and E14 mouse embryonic heads were fresh frozen embedded in OCT and cryosectioned at a thickness of 12 μm. Sections were transferred onto LCM PEN membrane slides, immediately fixed in ethanol, and stained with 1% (v/v) Cresyl Violet acetate in 75% ethanol solution. From the selected sections, using LCM, we isolated four RPE sections and six OS sections of the E12 embryos (four controls), or three sections of the transverse OS from the E14 embryos (four controls and five Smarcc1-DCT-cKO ).

first: Nitay

last: Zuk-Bar

first: Shai

last: Ovadia

first: Naihe

last: Jing

first: Ruth

last: Ashery-Padan


title: Codon-Optimized Npc1 mRNA corrects Niemann-Pick Type C1 disease phenotypes in vitro and in vivo [snRNA-Seq]

city: Oak Ridge

first: Alice

last: Townsend

state: TN

address: 1 Bethel Valley Rd

institute: ORNL

summary: Niemann-Pick type C1 disease is a lysosomal storage disorder caused by mutations in the NPC1 gene, resulting in the accumulation of unesterified cholesterol in multiple tissues. Despite its severity, therapeutic options remain limited. . Using codon-optimized Npc1 mRNA delivered by lipid nanoparticles (Co-Npc1:LNP), we achieved enhanced NPC1 protein expression and prolonged therapeutic activity in vitro, correcting both primary and secondary disease defects. In an Npc1-/- mouse model, a single intravenous injection of Co-Npc1:LNP restored hepatic NPC1 protein levels, normalized autophagic flux, improved lipid abnormalities, and altered markers of liver injury. To interpret transcriptional changes post-Co-Npc1:LNP administration, we performed bulk RNA sequencing and applied MENTOR, a network-based clustering algorithm, and MENTOR-IA, an unbiased functional annotation tool, and identified restored pathways including cholesterol metabolism, lysosomal and mitochondrial function, and liver homeostasis. Overall, Co-Npc1:LNP in the Npc1-/- mouse liver showed a transcriptional shift towards a more Npc1+/+ state. Integration of single-nucleus RNA sequencing with our bulk transcriptomics further revealed cell-type-specific correction of disease-associated gene expression across hepatic cell types. Together, we report the development and in vivo validation of the first mRNA-based therapeutic for Niemann-Pick type C1.

overall_design: We performed single-nucleus RNA sequencing (snRNA-seq) on livers of Npc1-/- mice and littermate controls at 7 weeks of age using three biological replicates for each genotype.

first: Ellen

middle: R

last: Koufer

first: Youngseo

first: Adele

middle: B

last: Correia

first: Noah

middle: K

last: Latham

first: Koralege

last: Pathmasiri

first: Kyle

last: Sullivan

first: Troy

last: Halseth

first: Elizabeth

last: Phillippi

first: Matthew

last: Lieberman

first: Stephanie

middle: M

last: Cologna

first: Andrew

last: Jacobson

first: Anna

last: Schwendeman

first: Mark

last: Schultz


title: AKAP6 Kinase binding domain (KBD) peptide improves cardiac function in HFpEF pigs [scRNA-seq]

city: Palo Alto

first: Michael

middle: Seth

last: Kapiloff

state: California

address: 1651 Page Mill Road, Room 2112

institute: Stanford University

summary: The purpose of this RNA-seq analysis is to investigate the effects of KBD expression on gene expression profiles in HFpEF pig hearts.

overall_design: Nuclei were isolated from control and HFpEF Ossabaw swine left ventricular tissue 6 months after induction of heart failure by obesity due to high-fat diet and aortic banding and treatment with saline or AAV9 for cardiomyocyte-selecitive expression of the KBD peptide. Additional control swine were fed a standard chow and not subjected to aortic banding or AAV treatment.  Nuclear RNAs were barcoded individually, then sequenced for gene expression analysis. Experiments were performed using 3-4 hearts per cohort.

first: Jinliang

last: Li

first: Ying

last: Zhu


title: AKAP6 Kinase binding domain (KBD) peptide improves cardiac function in HFpEF pigs

overall_design: Total RNA were extracted from control and HFpEF Ossabaw swine left ventricular tissue 6 months after induction of heart failure by obesity due to high-fat diet and aortic banding and treatment with saline or AAV9 for cardiomyocyte-selecitive expression of the KBD peptide. Additional control swine were fed a standard chow and not subjected to aortic banding or AAV treatment. Total RNA samples were sequenced for gene expression analysis. Experiments were performed using 4 hearts per cohort.


title: Intracellular complement factor H protects neurons during CNS inflammation [bulkRNA-seq]

city: Hamburg

first: Christina

last: Mayer

address: Falkenried 94

country: Germany

institute: University Medical Center Hamburg-Eppendorf

summary: Complement factor H (CFH) has been implicated in neuroprotection during inflammatory neurodegeneration, but its neuron-intrinsic functions remain poorly understood. Here, we performed bulk RNA sequencing of primary neuronal cultures from Cfh conditional knockout (Cfh-cKO) and control mice under basal conditions or following glutamate-induced oxidative stress. This dataset was generated to characterize transcriptional changes associated with neuronal Cfh deficiency and to identify pathways regulated by intracellular CFH during neuronal stress responses.

overall_design: Primary neuronal cultures were prepared from Cfh-flox mice and transduced at 4 days in vitro (DIV4) with an AAV-PhP.eB vector expressing Cre recombinase under the hSyn1 promoter to generate neuronal Cfh-cKO cultures or with a control virus. RNA was isolated from Cfh-cKO and control neurons under unstimulated conditions or after glutamate stimulation, followed by bulk RNA sequencing.

first: Manuel

last: Friese


title: Mechanoimmunological Control of Metastatic Site Selection

first: Morgan

last: Huse

address: 417 E 68th St

institute: Sloan Kettering Institute

summary: To explore the molecular mechanisms underlying stiffness modulation in vivo, GFP+ B16F10 MTCs from the lungs of wild type mice and from the lungs and bones of Prf1-/- mice were subjected to single cell RNA-sequencing (scRNA-seq). Uniform manifold approximation and projection (UMAP) analysis of the resulting data revealed 9 distinguishable populations of cancer cells. Lung metastases from wild type and Prf1-/- animals contained all 9 populations, implying that cellular cytotoxicity does not drastically alter tumor composition in this organ. Nevertheless, subtle shifts in the size and make-up of certain clusters were apparent, consistent with some degree of immune pressure. B16F10 composition differed dramatically in Prf1-/- bone, with several clusters shifting substantially in the UMAP plot or disappearing altogether.

overall_design: B16F10 MTCs extracted from wild type lung, Prf1-/- lung, and Prf1-/- bone were hashed using oligonucleotide-conjugated antibodies (TotalSeq B, hashes 1, 2, and 3) to uniquely label individual samples, which were then pooled together in equal proportions to enable multiplexed scRNA-seq.

first: Yassmin A

last: Elbanna


title: Bulk RNA sequencing of control (NT) and Spp1 knockout mouse samples

summary: Bulk RNA sequencing was performed to assess transcriptional differences between control (NT) and Spp1 knockout (KO) samples. RNA libraries were sequenced using paired-end Illumina sequencing. Reads were trimmed, aligned to the mouse genome (mm10), and quantified to generate gene-level count matrices. Differential expression analysis was performed to identify transcriptional changes associated with gene knockout.

overall_design: Three biological replicates of control (NT) and knockout (KO) samples were analyzed using bulk RNA sequencing. Reads were processed through a standardized pipeline. Normalization and differential expression analysis were performed using DESeq.


title: Interferon regulatory factor 5 in myeloid cells promotes obstructive nephropathy-induced renal fibrosis in vivo

city: Hangzhou

first: Jia

last: Wei

state: Zhejiang

address: Binsheng Road 3333

institute: Zhejiang University School of medicine Children's hospital

summary: Obstructive nephropathy is a significant and preventable contributor to chronic kidney disease, yet no disease-modifying anti-fibrotic agents are currently available.We hypothesized that interferon regulatory factor 5 (IRF5) functions as a macrophage transcriptional regulator that directly transactivates matrix metalloproteinase 9 (MMP9) to initiate early extracellular matrix (ECM) remodeling. Analysis of 30 human obstructive nephropathy biopsy specimens demonstrated that IRF5+CD68+ macrophage density increased progressively with fibrosis severity and correlated significantly with α-smooth muscle actin (α-SMA) positive areas. In the murine unilateral ureteral obstruction (UUO) model, both global and myeloid-specific Irf5 deletion significantly attenuated collagen deposition, immune cell infiltration, and fibrotic gene expression compared with wild-type controls. Cleavage under targets and tagmentation (CUT&Tag) analysis demonstrated that IRF5 directly binds the Mmp9 enhancer region and increases chromatin accessibility. Consequently, myeloid-specific Irf5 knockout significantly reduced Mmp9 mRNA and MMP9 protein levels. Pharmacological inhibition using the first-in-class IRF5 inhibitor N5-1 mitigated established fibrosis, down-regulated α-SMA and MMP9 expression, and reduced CD68+ macrophage infiltration. These findings identify the IRF5-MMP9 axis as a therapeutically targetable pathway driving macrophage-mediated ECM expansion and provide pre-clinical evidence supporting IRF5 inhibition as a potential treatment strategy for patients with obstructive nephropathy.

overall_design: This study was performed in the mouse UUO model, involving wild‑type mice, global IRF5 knockout (KO) mice, and myeloid‑specific IRF5 conditional knockout (IRF5 MKO) mice. Subsequently, RNA sequencing was performed on kidney samples collected from these mice.

first: Gengyu

last: Du

first: Zixia

first: Min

last: Yang

first: Ting

last: Chen

first: Zihao

last: Xu

first: Zhen

last: Yuan

first: Yidan

last: Zheng

first: Xiang

last: Yan


title: Large transgene arrays modulate a phenotype of myrf-1 in C. elegans

city: Basel

first: Panagiotis

last: Papasaikas

address: Fabrikstrasse 24

country: Switzerland

institute: Friedrich Miescher Institute

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

overall_design: Refer to individual Series


title: Large transgene arrays modulate a phenotype of myrf-1 in C. elegans [DNA-Seq]

summary: Multicopy transgene arrays have enabled crucial advances in C. elegans research. Many have been in use for decades, as they are convenient tools for assaying gene expression and as cell fate reporters. Here, we show a synthetic phenotype of a multicopy molt reporter array and a missense allele, myrf-1(mg412), which was previously reported to cause a heterochronic phenotype, an additional molt in adulthood. This synthetic phenotype is due to the size or composition of the transgene. We demonstrate that additional multicopy arrays also cause synthetic phenotypes with myrf-1(mg412). Finally, using Nanopore long read sequencing, we show that additional integrated arrays all exceed the size of 6 Mb, comprising a large fraction of the nematode genome. We recommend replacing multicopy transgene reporters, whenever possible, with single- or low-copy alternatives with known insertion loci.

overall_design: Oxford Nanopore Long Read DNA sequencing of seven distinct strains of C. elegans. Each strain has a different initegrated array.

first: Iskra

last: Katic

first: Dimosthenis

last: Gaidatzis

first: Milou

last: Meeuse

first: Helge

last: Großhans


title: Large transgene arrays modulate a phenotype of myrf-1 in C. elegans [RNA-Seq]

overall_design: RNA-seq profiling of wild-type N2, VT1367 (HW3826) and GR1395 L1 C. elegans cultured for 4 hours


title: Low-dose allergen targeting to cDC2 induces long-term protection associated with IL-10+ Foxp3- CD8+ regulatory T cells in mice

city: Würzburg

first: Manfred

last: Lutz

address: Versbacher Straße 7

department: Institut für Virologie und Immunbiologie

institute: Julius-Maximilians-Universität Würzburg

summary: The prevalence of allergic diseases is rising worldwide. Desensitizing immunotherapy is currently the only available treatment, but it is often ineffective for certain allergies, underscoring the need for new treatments. This study tested whether direct allergen targeting to DC subsets can improve desensitization. An Ovalbumin (OVA)-mediated allergy mouse model was used to compare a Standard desensitization protocol, which is also used in humans, with a novel antibody-OVA fusion protein targeting the conventional cDC1 and cDC2 subsets via their respective receptors CD205 (CD205-Fp) or DCIR2 (DCIR2-Fp). OVA allergy treatment by cDC2 targeting provided long-lasting protection for up to 56 days after desensitization with only nanogram doses of allergen, whereas the Standard therapy protected for only 20 days, requiring microgram doses and repeated injections with Alum adjuvant. CD205-Fp showed no protective effect. Blocking IL-10 either before administering DCIR2-Fp or before allergen challenge completely abolished protection. Standard therapy had moderate effects on CD4+ T cells, with early expansion of IL-10⁺ Foxp3⁻ T regulatory type-1 cells (Tr1), followed by an increase in both IL-10⁺ and IL-10⁻ Foxp3⁺ regulatory T cells (Treg). DCIR2-Fp therapy initially expanded IL-10⁺ and IL-10⁻ Foxp3⁺ Treg, but these levels returned to baseline by day 80. Notably, we identified Foxp3- CD44high CD8⁺ memory Treg as the primary source of IL-10 at day 80. Overall, our data suggest that cDC2 allergen targeting in allergic mice offers a potent, long-lasting IL-10-dependent protective effect.

overall_design: Single-cell RNA-sequencing (scRNA-seq) was performed to characterize spleen cells of mice sensitized at days 0 and 10 to develop allergy against ovalbumin (OVA) and then groups of mice were 1) left untreated, 2) treated with a standard desensitization at days 20, 22 and 24 with OVA in PBS and again with OVA in Alum at days 40 and 60, or 3) treated at days 20, 22, and 24 with a DCIR-2-Fusion protein connected to OVA. At day 80 the spleen cells of all mice were restimulated for 3h with PMA/Ionomycin. Thereafter cells were sorted into CD45+ CD11b- and CD45+ and CD11b+ fractions, which were then pooled at a 1:1 ratio to enrich for myeloid cells and then used for scRNA-seq.

first: Arpa

last: Aintablian

first: Laura

last: Cyran

first: Helal

last: Moutaz

first: Lehmann

last: Christian H.K.

first: Imdahl

last: Fabian

first: Tom

last: Gräfenhan

first: Riedel

last: Angela

first: Dudziak

last: Diana

first: Kerstan

last: Andreas


title: Nuclear receptor Nur77 resolves the inflammatory response of macrophages primarily by regulating expression of AP-1 transcription factors and their target genes [ChIP-seq]

city: Amsterdam

first: Claudia

last: van Tiel

address: Meibergdreef 15

department: Medical Biochemistry

country: Netherlands

institute: Amsterdam UMC

type: Genome binding/occupancy profiling by high throughput sequencing

summary:
The nuclear receptor Nur77 plays a crucial, protective role in chronic inflammatory diseases and deficiency of Nur77 in macrophages results in excessive pro-inflammatory cytokine secretion. Previous research suggested that Nur77's regulatory function in inflammation is due to repression of the pro-inflammatory transcription factor NF-ĸB, but the underlying mechanism remains unclear. To address this, we applied a genome-wide, multi-omics approach in LPS-stimulated RAW264.7 macrophages with inducible Nur77 expression. Key findings were validated in wild-type and Nur77-deficient bone marrow-derived macrophages. We show that Nur77 suppresses the expression of inflammatory genes through a dual mechanism wherein Nur77 acts as a repressor of AP-1 targets at two levels: First, Nur77 occupies regulatory elements proximal to AP-1 target genes through AP-1 motifs and second, Nur77 regulates the expression of AP-1 family members themselves. These repressive activities of Nur77 result in diminished RNA Pol II on AP-1 genes and their targets. The first zinc finger of the Nur77 DNA-binding domain is required to reduce AP-1 activity.
In summary, Nur77 represses macrophage inflammation through regulation of both immediate-early AP-1 expression, as well as inhibition of AP-1-driven gene programs.

overall_design: ChIP-seq for RNA polymerase II and H3K27ac in murine macrophages, derived from Nur77-deficient mice and wild-type mice, stimulated with 100 ng/ml LPS for 0, 1, and 18 hours. (n=3 per group )

first: Sanne

last: Lith

first: Sebastian

last: Gregoricchio

first: Beatriz

last: Freire

first: Simon

last: Linder

first: Onno

last: Bleijerveld

first: Liesbeth

last: Hoekman

first: Guglielmo

last: Alonzo

first: Wilbert

last: Zwart

first: Marten

last: Hoeksema

first: Carlie

last: de Vries


title: Transcriptomic profiling of AML cell lines MV4-11 and Kasumi-1 treated with CK1α degrader PinA1

city: Seongnam-si

first: Kyeongmi

last: Kim

state: Gyeonggi-do

address: 4th floor, 46, Wiryeseoil-ro, Sujeong-gu

country: South Korea

institute: Pin Therapeutics

summary: Acute myeloid leukemia (AML) is characterized by dysregulated transcriptional programs that support malignant proliferation and survival. Casein kinase 1 alpha (CK1α) has been implicated in the regulation of p53 signaling and represents a potential therapeutic target. In this study, we aimed to investigate whether CK1α degradation induces broad transcriptomic changes in a p53-dependent manner. To address this, we performed RNA sequencing (RNA-seq) in two human AML cell lines with distinct TP53 status: MV4-11 (TP53 wild-type) and Kasumi-1 (TP53 mutant). Cells were treated with a CK1α degrader (PinA1) or vehicle control, followed by transcriptomic profiling. Comparative analysis was conducted to assess the extent and nature of gene expression changes induced by CK1α degradation. Notably, this study was designed to evaluate whether CK1α targeting leads to more pronounced transcriptional alterations in TP53 wild-type cells compared to TP53-mutant contexts. Our data provide insights into the p53-dependent transcriptional consequences of CK1α degradation and support its potential as a therapeutic strategy in AML.

overall_design: RNA-seq profiling of MV4-11 (TP53 wild-type) and Kasumi-1 (TP53 mutant) AML cell lines treated with CK1α degrader (PinA1) or vehicle control for 24 hours, with three biological replicates per condition.

first: Hyunsun

last: Jo

first: Hoon

last: Choi

first: Hyemin


title: Nuclear receptor Nur77 resolves the inflammatory response of macrophages primarily by regulating expression of AP-1 transcription factors and their target genes [ATAC-seq]

overall_design: Comparison of chromatin acessibilitiy in murine macrophages, derived from Nur77-deficient mice and wild-type mice, stimulated with 100 ng/ml LPS for 0, 1, and 18 hours. (n=3 per group )

first: Ingeborg

last: van der Made

last: Jacobs


title: Nuclear receptor Nur77 resolves the inflammatory response of macrophages primarily by regulating expression of AP-1 transcription factors and their target genes [RNA-seq]

overall_design: Comparison of gene expression in murine macrophages, derived from Nur77-deficient mice and wild-type mice, stimulated with 100 ng/ml LPS for 0, 1, 5 and 18 hours. (n=4 per group )


title: α1-adrenergic signaling regulates fibroblast activation in human pulmonary fibrosis

first: Genta

last: Ishikawa

state: Connecticut

address: 300 Cedar Street

department: Pulmonary, Critical Care, and Sleep Medicine

summary: Idiopathic pulmonary fibrosis (IPF) and systemic sclerosis–associated interstitial lung disease (SSc-ILD) are progressive fibrotic disorders characterized by aberrant activation of lung fibroblasts. Emerging evidence suggests that adrenergic signaling regulates fibroblast function and contributes to fibrogenesis. To define the transcriptional programs governed by α1-adrenergic signaling in human lung fibroblasts, we performed bulk RNA sequencing on primary lung fibroblasts derived from patients with IPF and SSc-ILD. Primary human lung fibroblasts were treated with the α1-adrenergic receptor antagonist terazosin or vehicle control, and Poly(A) RNA was subjected to high-throughput sequencing. Comparative transcriptomic analyses were conducted to identify differentially expressed genes and pathways associated with α1-adrenergic blockade. We generated paired-end RNA sequencing data from 16 samples, including fibroblasts from IPF (biological n=4) and SSc-ILD (biological n=4) under two conditions (with or without terazosin treatment), enabling systematic characterization of both shared and disease-specific transcriptional responses. These data provide a resource for elucidating the molecular mechanisms linking adrenergic signaling to fibroblast activation and fibrosis, and may inform the development of targeted therapeutic strategies for fibrotic lung diseases.

overall_design: Bulk RNA sequencing of primary human lung fibroblasts derived from patients with IPF and SSc-ILD treated with the α1-adrenergic receptor antagonist terazosin or vehicle control for 24 hours.

first: Shuai

last: Shao


title: Hepatocytes promote liver metastasis of pancreatic cancer by providing exogenous serine, 2.

city: New York

first: Jason

middle: Rodencal

last: Terrell

address: 530 1st Avenue

institute: NYU Langone Health

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

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

first: Koelina

last: Ganguly

first: Keisuke

last: Yamamoto

last: Rodencal

first: Alec

last: Kimmelman


title: Identification of species differences in structure and function of COMMD3-BMI1 loci in neural stem cells III

city: Higashi-Hiroshima

first: boyang

last: An

state: Hirohsima

address: Kagamiyama 1-3-1

institute: Hiroshima University

summary: Human cerebral development is supported by the continuous proliferation of neural stem cells (NSCs), a process that morphologically and functionally distinguishes humans from other mammals. Several human brain-specific genes are known to contribute to the formation of such species differences. We hypothesize that differences at the epigenomic level also play a role in shaping species-dependent NSC behaviors. In this study, we examined structural interspecies differences in the components of protein regulator of cytokinesis 1 (PRC1), an important transcriptional repressor complex that functions in cortical development. We found that, for BMI1, diversity emerged in the fusion with COMMD3, generating three COMMD3-BMI1 transcripts (COMMD3-BMI1_1-3). We performed a series of knockdown experiments using AF22 cells, a human iPS cell-derived neural stem cell line, and found that the human-specific isoform, COMMD3-BMI1_3, showed the highest NSC proliferative activity, that was comparable to BMI1. These results suggest that the evolutionary acquisition of the human-specific COMMD3-BMI1 isoform has constituted species differences in cerebral development through the enhancement of NSC proliferative activity.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: COMMD3-BMI1 fusion transcripts analysis of RNA-seq data for AF22 NSCs and E11 mouse NSCs.

first: Arisa

last: Makimura

first: Boyang

first: Sota

last: Nishida

first: Tomonori

last: Kameda

first: Fumihiro

last: Morishita

first: Mizuki

last: Honda

first: Takuya

last: Imamura


title: Identification of species differences in structure and function of COMMD3-BMI1 loci in neural stem cells II

overall_design: Comparative gene expression profiling analysis of RNA-seq data for AF22 NSCs and COMMD3/COMMD3-BMI1 KD derivative.


title: Prefrontal cortex bulk RNA-seq analysis of drug-treated Tbr1+/K228E heterozygous mice at P40

city: Daejeon

first: Eunjoon

last: Kim

address: Kuseong-dong

department: Center for Synaptic Brain Dysfunctions/Department of Biological Sciences

institute: IBS/KAIST

summary: Autism spectrum disorder (ASD) affects approximately 2.8% of the population and is characterized by substantial genetic heterogeneity. Bulk RNA sequencing was performed on prefrontal cortex tissue from Tbr1+/K228E heterozygous (HT) and wild-type (WT) mice. Animals were analyzed at postnatal day 40 (P40) following three weeks of treatment with fluoxetine or lithium. Both male and female mice were included. Dissected prefrontal cortex tissue was used for RNA extraction and sequencing.

overall_design: Tbr1+/K228E HT and WT mice of both sexes were treated with fluoxetine or lithium. At postnatal day 40 (P40), prefrontal cortex tissue was collected and subjected to bulk RNA sequencing to compare genotype- and treatment-associated transcriptomic changes.

first: Junyeop Daniel

last: Roh

first: Yukyung

last: Jun

first: Mihyun

last: Bae

first: Hyojin

last: Kang


title: Prefrontal cortex bulk RNA-seq analysis of drug-treated Dyrk1a+/I48X heterozygous mice at P40

summary: Autism spectrum disorder (ASD) affects approximately 2.8% of the population and is characterized by substantial genetic heterogeneity. Bulk RNA sequencing was performed on prefrontal cortex tissue from Dyrk1a+/I48X heterozygous (HT) and wild-type (WT) mice. Animals were analyzed at postnatal day 40 (P40) following three weeks of treatment with fluoxetine or lithium. Both male and female mice were included. Dissected prefrontal cortex tissue was used for RNA extraction and sequencing.

overall_design: Dyrk1a+/I48X and WT mice of both sexes were treated with fluoxetine or lithium. At postnatal day 40 (P40), prefrontal cortex tissue was collected and subjected to bulk RNA sequencing to compare genotype- and treatment-associated transcriptomic changes.


title: Prefrontal cortex bulk RNA-seq analysis of drug-treated PTEN KI heterozygous mice at P40

summary: Autism spectrum disorder (ASD) affects approximately 2.8% of the population and is characterized by substantial genetic heterogeneity. Bulk RNA sequencing was performed on prefrontal cortex tissue from PTEN KI heterozygous (HT) and wild-type (WT) mice. Animals were analyzed at postnatal day 40 (P40) following three weeks of treatment with fluoxetine or lithium. Both male and female mice were included. Dissected prefrontal cortex tissue was used for RNA extraction and sequencing.

overall_design: PTEN KI HT and WT mice of both sexes were treated with fluoxetine or lithium. At postnatal day 40 (P40), prefrontal cortex tissue was collected and subjected to bulk RNA sequencing to compare genotype- and treatment-associated transcriptomic changes.


title: Prefrontal cortex bulk RNA-seq analysis of drug-treated Adnp heterozygous mice at P40

summary: Autism spectrum disorder (ASD) affects approximately 2.8% of the population and is characterized by substantial genetic heterogeneity. Bulk RNA sequencing was performed on prefrontal cortex tissue from Adnp heterozygous (HT) and wild-type (WT) mice. Animals were analyzed at postnatal day 40 (P40) following three weeks of treatment with fluoxetine or lithium. Both male and female mice were included. Dissected prefrontal cortex tissue was used for RNA extraction and sequencing.

overall_design: Adnp heterozygous (HT) and wild-type (WT) mice of both sexes were treated with fluoxetine or lithium. At postnatal day 40 (P40), prefrontal cortex tissue was collected and subjected to bulk RNA sequencing to compare genotype- and treatment-associated transcriptomic changes.


title: Bulk RNA-seq transcriptome profiling of hippocampus across 17 autism spectrum disorder mouse models

summary: Bulk RNA sequencing was performed on hippocampal tissue from 17 autism spectrum disorder (ASD) mouse models, including both male and female mice. The dataset comprises 269 animals and enables cross-model comparison of transcriptomic alterations associated with ASD-related genetic backgrounds.

overall_design: Mutant and wild-type (WT) mice were analyzed at postnatal day 25 (P25). Both male and female animals were included. Hippocampal tissue was dissected and subjected to bulk RNA sequencing.


title: Differential sex-dependent responses of circulating steroid hormones and cortical gene expression in a preclinical traumatic brain injury model

city: Tempe

first: Christopher

last: Plaisier

state: Arizona

department: SBHSE

institute: Arizona State University

summary: Accumulating evidence supports sex differences in traumatic brain injury (TBI) outcomes, however the underlying processes that lead to sex differences are not well understood. TBI results in the initiation of molecular and cellular responses that facilitate the progression of neurodegeneration. Importantly, little is known about how the circulating hormone profile is altered in response to TBI, and whether sex differences in endocrine responses might shape secondary injury pathologies. Using intact male and female mice in a preclinical TBI model, we assessed changes in plasma hormone concentrations and cortical gene expression at 24 and 72 hours after TBI. We demonstrate that males and females exhibit sex-specific alterations in circulating levels of progesterone, testosterone, androstenedione, estradiol and dehydroepiandrosterone (DHEA) in response to TBI. We also identified sex differences in the expression of genes that are involved in immune responses and tissue remodeling after injury. Moreover, we report divergent circulating hormone and gene expression correlations between sexes.

overall_design: To directly evaluate sex-based responses to TBI, our experimental cohorts consisted of naïve intact male and female mice to capture baseline and male and female mice at 24 or 72 hours (hrs) post-TBI (unilateral controlled cortical impact model, CCI). At each timepoint, mice were sacrificed, and blood plasma was analyzed via mass spectrometry to quantify steroid hormone levels for five analytes (progesterone, testosterone, androstenedione, estradiol, and DHEA). Transcriptomic analysis (RNA-seq) on cortical punches from the injured ipsilateral and the uninjured contralateral sides of the cortex was conducted on statistically representative groups for each cohort. We then performed a correlation analysis between the transcriptomic and hormone profiling data sets to gain insight into potential drivers of sex-based TBI pathology. Finally, we used immunohistochemistry to assess the protein expression of key BBB proteins that were significantly upregulated in transcriptomic analysis. Collectively, the experimental design captured snapshots of multiple physiological systems at different points after TBI to assess the holistic response to TBI.

first: Amberlyn

last: Simmons

first: Sierra

last: Wilferd

first: Sofia

last: Campagnuolo

first: Veronica

last: Pena

first: Heather

last: Bimonte-Nelson

first: Jason

last: Newbern

first: Rachael

last: Sirianni

first: Sarah

middle: E

last: Stabenfeldt


title: WDR82 Code Coordinates Transcription and pre-mRNA 3’-End Processing Through Regulated Phosphorylation

city: Oxford

first: Abigail

last: Southers

address: South Parks Road

department: Biochemistry

country: United Kingdom

institute: University of Oxford

summary: Phosphorylation plays a central role in coordinating transcription with pre-mRNA maturation, yet the mechanistic understanding of how transcription is regulated by phosphorylation remains limited. The PP1 phosphatase removes CDK9-dependent phosphorylation of Pol II and Spt5, triggering transcription termination. Here, we demonstrate that PNUTS enhances PP1 activity, whereas WDR82 mediates an interaction between PP1 and the pre-mRNA 3’-end processing machinery subunit Symplekin. We present the structure of a PNUTS-WDR82-Symplekin-Ssu72 complex, revealing that PNUTS and Symplekin bind WDR82 through distinct interfaces using conserved short linear motifs. Mutations that inactivate PP1's catalytic activity or disrupt its interaction with either PNUTS or the 3’-end processing machinery led to impaired transcription elongation, inefficient cleavage of nascent transcripts, altered poly(A) site selection, and widespread transcription termination defects. Our findings demonstrate that the PP1 complex is essential for coupling transcription to pre-mRNA 3’-end maturation, ensuring production of functional mRNA.

overall_design:
We used TT-seq to measure nascent transcription in Schizosaccharomyces pombe strains carrying deletions or catalytic/interaction mutants of the trimeric PP1 phosphatase complex — PP1/Dis2, PNUTS/Ppn1, and WDR82/Swd2.2 — and of the cleavage-and-polyadenylation scaffold Symplekin/Pta1.
Two sets of strains were profiled. In the first set, endogenous genes were deleted or replaced with point mutants: pp1/dis2Δ, pp1/dis2^R245Q^ (catalytically inactive), wdr82/swd2.2Δ, pnuts/ppn1Δ, and pnuts/ppn1^W510A^ (PP1-interaction mutant). The pnuts/ppn1^W510A^ strain was generated by deleting the endogenous ppn1 copy and integrating the W510A-mutant allele at an ectopic locus (leu1), under the native promoter. A wild-type strain was profiled as the common reference/control.
In the second set, endogenous Symplekin/Pta1 — an essential gene — was fused to an auxin-inducible degron at its native locus and depleted with auxin for 24 h. Two degron strains were compared: one carrying a wild-type Pta1 rescue allele and one carrying a DPR→AAA (triple-alanine) mutant rescue allele, each expressed from the native promoter at the ura4 locus. Because both strains were auxin-treated in parallel and depend on the rescue allele for viability, the wild-type-rescue strain serves as the direct control for the mutant-rescue strain; no untreated condition was required.
TT-seq was performed in biological duplicate (n = 2) for all conditions, with the single exception of the Symplekin/Pta1 wild-type-rescue strain at 24 h auxin, which was performed once (n = 1).
Cultures were grown to OD₆₀₀ ≈ 0.5 in YES medium (uracil 10 mg/L) at 25 °C for degron-depletion experiments or 30 °C otherwise. Cells were pulse-labelled with 5 mM 4-thiouracil (4-tU) for 6 min, harvested, and snap-frozen. Before RNA extraction, samples were normalised by OD₆₀₀ and supplemented with a 4-tU-labelled S. cerevisiae spike-in at a ratio of 100:1 (S. pombe : S. cerevisiae, by OD). RNA was isolated by the hot-phenol method, DNase-treated, fragmented with NaOH, and conjugated to an MTSEA-biotin-XX linker. Biotinylated (labelled) RNA was purified with the µMACS Streptavidin Kit, and fragment sizes were assessed on a Bioanalyzer. Strand-specific libraries were prepared with the NEBNext Ultra II Directional RNA Library Prep Kit and sequenced on an Illumina NextSeq 500.

first: Alex

last: Au

first: Krzysztof

last: Kuś

first: Niek

last: Schoemaker

first: Esra

last: Balikci-Akil

first: Charles

last: Hewes

first: Marjorie

last: Fournier

first: Ebru

last: Aydin

last: Sayed Hassanein

first: Luke

last: Slade

first: Cornelia

last: Kilchert

first: Jonathan M.

last: Grimes

first: Lidia

last: Vasiljeva


title: CpG content determines tissue-resident macrophage enhancer selection

city: Debrecen

first: Laszlo

last: Nagy

address: Egyetem ter 1.

country: Hungary

institute: University of Debrecen

summary: Tissue-resident macrophages (TRMs) acquire specialized identities through transcription factor (TF) networks operating in distinct chromatin environments. Early growth response 2 (EGR2) contributes both to alveolar macrophage (AM) identity and to interleukin (IL)-4-driven polarization of bone marrow-derived macrophages (BMDMs), yet the regulatory principles enabling its function across these contexts remain unclear. By integrating RNA-seq and ATAC-seq data from wild-type and Egr2-deficient macrophages, we show that macrophage identity is constrained by DNA methylation-dependent cis-regulatory landscapes. AM-specific enhancers are predominantly CpG-rich and hypomethylated, a feature shared with additional TRM populations, whereas BMDM-accessible regulatory regions are largely CpG-poor. Although IL-4 induces EGR2 together with KLF4 and DEC1 in BMDMs, this TF module fails to engage CpG-rich enhancers, indicating that the BMDM regulatory network lacks additional AM-specific components required for their activation. These findings identify CpG content as a determinant of enhancer competence and provide a mechanistic explanation for the context-dependent activity of EGR2 in macrophages, placing macrophage plasticity under the control of sequence-encoded epigenetic constraints.

overall_design: Transcriptomic and epigenomic comparison of mouse alveolar macrophages (AMs) and bone marrow-derived macrophages (BMDMs) using high trouhgput RNA-seq and ATAC-seq data generated from wild-type (WT) and myeloid-specific conditional Egr2 exon 2 knock-out (KO) cells.

first: Dora

last: Bojcsuk

first: Gergely


title: VHL Loss Orchestrates Pro-Tumor Microenvironment Through BMP10-Induced CXCL13 Signaling in Renal Lymphatics [RNA-Seq]

city: Taichung

first: Hieu-Huy

last: Nguyen-Tran

state: Taichung

address: Xueshi

department: Graduate Institute of Biomedical Sciences

country: Taiwan

institute: China Medical University

summary: Clear-cell renal cell carcinoma (ccRCC) is frequently associated with loss of the tumor suppressor gene VHL. To investigate the early events of ccRCC pathogenesis, we generated a conditional mouse model with Vhlh deletion in renal tubular epithelial cells. The model exhibited key histopathological features reminiscent of human ccRCC, including epithelial disorganization, immune infiltration, and vascular remodeling. VhlhloxP/loxP mice were crossed with Hoxb7-Cre-GFP mice to induce kidney tubule-specific Vhlh deletion. Kidney tissue was analyzed using histology, immunofluorescence, immunohistochemistry, and flow cytometry. Proliferation, immune infiltration, vascular and lymphatic architecture, as well as functional drainage assays and gene expression profiling, were conducted to characterize phenotypic changes. Vhlh-deficient kidneys exhibited clear-cell morphology, tubular hypertrophy, and a ~ 4-fold increase in Ki67⁺ epithelial proliferation compared to wild-type controls. Immune cell (CD45⁺) infiltration and endothelial cell (CD31⁺) expansion were significantly elevated. Lymphatic architecture was disrupted, with increased numbers of  Pdpn⁺ cells, and impaired lymphatic drainage was observed by Evans Blue Dye retention. Pdpn⁺ lymphatic cells expressed high levels of CXCL13, which was validated in both mouse and human ccRCC tissues. BMP10, produced by Vhlh-deficient epithelium, appeared to act through Alk1 signaling to induce CXCL13 expression. CXCL13 in turn promoted proliferation, migration, EMT activation in VHL-deficient epithelial cells via CXCR5. Genetic deletion of CXCL13 or pharmacologic inhibition of Alk1 reduced lymphatic remodeling, inflammation, and epithelial proliferation.

overall_design:
Animals and Tissue Preparation
Male mice (C57BL/6J, 10 -12 weeks old) were used in this study, including Hoxb7-Cre-GFP/+ [Control (Ctrl)] and Hoxb7-Cre-GFP/+; VhlhloxP/loxP (Mut) genotypes (n = 6 per group). All animal procedures were approved by the Institutional Animal Care and Use Committee and conducted in accordance with institutional guidelines.
Tissue Dissociation and Single-Cell Preparation
Male mice (C57BL/6J, 10 -12 weeks old) were used in this study, including Ctrl and VhlhKO (Mut) genotypes (n = 6 per group). Kidneys were harvested from mice and immediately placed in ice-cold phosphate-buffered saline (PBS). Tissues were finely minced into ~1 - 2 mm fragments using sterile scissors and transferred into digestion buffer containing collagenase II (Sigma-Aldrich, Cat. No. 6885), dispase (Sigma-Aldrich, Cat. No. D4693), and DNase I (Roche/Merck, Cat. No. 10104159001) prepared in serum-free medium. Tissue fragments were incubated at 37°C for 15 - 25 min with gentle agitation. During digestion, samples were gently pipetted every 5 min to facilitate tissue dissociation. The enzymatic reaction was terminated by adding an equal volume of cold PBS supplemented with 2% fetal bovine serum (FBS).
The cell suspension was then passed sequentially through 70 µm and 40 µm cell strainers (Corning) to remove undigested tissue fragments and large aggregates. The filtrate was centrifuged at 300 xg for 5 min at 4°C, and the cell pellet was resuspended in PBS containing 2% FBS. The red blood cells were removed using ammonium-chloride-potassium (ACK) lysis buffer for 1 - 2 min at room temperature, followed by immediate washing with PBS containing 2% FBS.
EpCAM-Based Cell Depletion and Antibody Staining for Cell Sorting
To enrich non-epithelial cell populations, EpCAM-positive epithelial cells were depleted by magnetic-activated cell sorting (MACS) using anti-EpCAM microbeads (Miltenyi Biotec, Cat. No. 130-061-101) according to the manufacturer’s instructions. Briefly, single-cell suspensions were resuspended in sorting buffer (PBS supplemented with 2% bovine serum albumin (BSA), 2 mM EDTA, and 0.02% sodium azide (NaN₃)) at a density of up to 1 × 10⁷ cells per 80 µL buffer. Cells were incubated with 20 µL anti-EpCAM microbeads per 1 × 10⁷ cells for 15 min at 4°C with gentle mixing. Following incubation, cells were washed with sorting buffer and centrifuged at 300 xg for 5 min at 4°C to remove unbound beads. The cell pellet was then resuspended and applied onto LS columns (Miltenyi Biotec, Cat. # 130-042-401) pre-equilibrated with sorting buffer and placed in a magnetic separator (Miltenyi Biotec, Cat. # 130-092-168). During separation, EpCAM-positive cells labeled with magnetic beads were retained within the column, whereas unlabeled EpCAM-negative cells passed through and were collected as the flow-through fraction. The column was subsequently washed 3 times with sorting buffer to maximize recovery of EpCAM-negative cells. All procedures were performed on ice or at 4°C to preserve cell viability and maintain surface antigen integrity for downstream staining and cell sorting.
For antibody staining, EpCAM-negative cells were resuspended in staining buffer consisting of PBS supplemented with 2% fetal bovine serum (FBS). Cells were incubated for 30 min at 4°C in the dark with PerCP-conjugated anti-mouse CD45 antibody (BioLegend, Cat. # 103132; 1:50), rabbit anti-Nephrin antibody (Abcam, Cat. # ab136894; 1:100), and APC-conjugated anti-mouse podoplanin (Pdpn) antibody (BioLegend, Cat. # 127410; 1:50). After primary antibody incubation, cells were washed and incubated with Alexa Fluor 488-conjugated goat anti-rabbit IgG secondary antibody (Thermo Fisher Scientific, Cat. # A32731; 1:200) for 30 min at 4°C in the dark. Cells were then washed twice with staining buffer prior to sorting. To define gating thresholds and control for nonspecific binding, isotype-matched IgG control antibodies were included in parallel staining conditions (Supplementary Table S2). All antibodies were titrated before use to determine optimal staining concentrations.
Cell Sorting and Gating Strategy
Podoplanin-positive (Pdpn⁺) cells were isolated using a BD FACSAria III (BD Biosciences) equipped with 488 nm (blue), 561 nm (yellow-green), and 640 nm (red) lasers. Fluorescence signals were detected using the following bandpass filters: FITC/Alexa Fluor 488 (530/30 nm), PE (575/26 nm), PerCP (695/40 nm), and APC (660/20 nm).
A sequential gating strategy was applied to identify the target population:
First, cellular events were selected based on forward scatter area (FSC-A) versus side scatter area (SSC-A) to exclude debris and non-cellular particles. This gate was defined using unstained controls to ensure inclusion of intact cells while excluding low-scatter events. Second, doublets and cell aggregates were excluded by gating on forward scatter height (FSC-H) versus FSC-A, ensuring that only singlet cells were retained for downstream analysis. Third, within the singlet population, hematopoietic cells were excluded based on CD45 expression, detected in the PerCP channel (488 nm excitation/695/40 nm emission) depending on antibody configuration. Fourth, podocyte populations were excluded by removing Nephrin-positive (Nephrin⁺) cells, detected in the FITC/Alexa Fluor 488 channel (488 nm excitation/530/30 nm emission). Finally, within the CD45⁻/Nephrin⁻ singlet population, Pdpn-positive (Pdpn⁺) cells were identified in the APC channel (640 nm excitation/660/20 nm emission) and defined as the target lymphatic-like endothelial population.
Cell Culture and RNA Sequencing
Kidneys from 6 Following isolation, Pdpn⁺ cells were resuspended and cultured in Endothelial Cell Medium (ECM; ScienCell, Cat. No. 1001) supplemented with 5% FBS, 1% endothelial cell growth supplement (ECGS), and 1% penicillin-streptomycin. Cells were maintained at 37°C in a humidified incubator with 5% CO₂ for recovery overnight. The culture medium was replaced every 2 days to remove non-adherent cells and maintain optimal growth conditions.
Cells were cultured for 9 days to allow expansion and stabilization of the Pdpn⁺ population prior to downstream analyses. At the end of the culture period, cells were harvested by gentle dissociation, pelleted by centrifugation at 300 xg for 5 min at 4°C, and processed for RNA extraction.
Total RNA was extracted from Pdpn⁺ cell pellets using standard RNA isolation protocols, followed by DNase treatment to remove residual genomic DNA contamination. RNA quantity and integrity were assessed using a Bioanalyzer system (Agilent Technologies), and only samples with a RNA integrity number (RIN) ≥ 7.5 were used for downstream applications. Each biological replicate corresponded to cells isolated from an individual mouse. Poly(A)-selected RNA was used to generate strand-specific sequencing libraries using Illumina-compatible library preparation kits according to the manufacturer’s instructions. Libraries were quantified and assessed for quality prior to sequencing. Paired-end sequencing (2 × 150 bp) was performed on a NovaSeq 6000 platform (Illumina). To minimize batch effects, libraries were randomized across sequencing lanes.

first: Tien

last: Hsu

first: Tuong-Vi

last: Nguyen

first: Thi-Ngoc


title: Activating RARβ to overcome immunomodulatory drug resistance in t(4;14) human myeloma [ChIP-seq]

city: Chengdu

first: Ling

last: Zhong

state: Please Select

address: No. 32, Section 2, West First Ring Road, Qingyang District

institute: Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital

summary: The t(4;14) translocation is a high-risk cytogenetic abnormality in multiple myeloma (MM) that results in overexpression of fibroblast growth factor receptor 3 (FGFR3) and enhanced MM proliferation, leading to poor prognosis. Herein, we carried out a high-throughput screen on 1855 Food and Drug Administration (FDA)-approved pharmaceuticals and identified all-trans retinoic acid (ATRA), which alone has no anti-MM effect, as a potent drug that enhances the cytotoxic effects of immunomodulatory drugs (IMiDs) in t(4;14) MM cells. Mechanistically, ATRA activates retinoic acid receptor β (RARβ), which then binds to retinoic acid response elements in the FGFR3 promoter. IMiDs enhanced nuclear translocation of histone deacetylase (HDAC)-5 and 3 by reducing HDAC5 Ser498 phosphorylation levels. RARβ, HDAC5 and HDAC3 formed a co-repressor complex that reduced chromatin accessibility and H3K27 acetylation in FGFR3 promoter, FGFR3 expression, and suppressed phosphoinositide 3-kinase/AKT signaling pathways, leading to more MM cell death. Similarly, CD2314, a selective RARβ agonist, sensitized and resensitized t(4;14) MM cells to IMiDs in vitro and in vivo. Thus, these findings underscore the therapeutic potential of ATRA and RARβ agonists in enhancing the efficacy of IMiD-based treatments for t(4;14) MM and offer a promising strategy to overcome IMiD resistance and improve outcomes in this high-risk subgroup.

overall_design: ChIP-seq analysis identified pathway enrichment patterns associated with differential transcription factor binding peaks in OPM-2 cells after 72 hours of exposure to either vehicle control (DMSO), 1 μM all-trans retinoic acid (ATRA), 1 μM pomalidomide (POM), or the dual combination (1 μM ATRA + 1 μM POM).

first: Qiang

last: Wang

first: Qing

last: Yi

first: Xian

last: Miao


title: Activating RARβ to overcome immunomodulatory drug resistance in t(4;14) human myeloma

overall_design: Chromatin accessibility landscapes were assessed by ATAC-seq in OPM-2 cells after 72 hours of exposure to either vehicle control (DMSO), 1 μM all-trans retinoic acid (ATRA), 1 μM pomalidomide (POM), or the dual combination (1 μM ATRA + 1 μM POM).


overall_design: Bulk RNA-seq of NCI-H929 and OPM-2 cells after 72 hours of exposure to either vehicle control (DMSO), 1 μM all-trans retinoic acid (ATRA), 1 μM pomalidomide (POM), or the dual combination (1 μM ATRA + 1 μM POM).


title: Extra-S-phase DNA damage in MSI cells evades cell cycle arrest and leads to lethality upon inhibition of WRN

city: Geneva

first: Sotirios

middle: G.

last: Ntallis

address: 30 quai Ernest-Ansermet

department: Department of Molecular and Cellular Biology

institute: University of Geneva

summary: WRN helicase plays an instrumental role in DNA repair, replication fork stability and genome maintenance. Recently, WRN has emerged as a synthetic lethal target in microsatellite instability (MSI) cancers, which exhibit deficiencies in the DNA mismatch repair pathway. While WRN’s helicase activity is critical for MSI cell survival, the underlying mechanism remains only partially understood. Previous studies suggest that WRN resolves cruciform DNA structures that otherwise induce replication stress. Here, we examine the cell cycle-resolved kinetics of DNA damage following WRN inhibition in MSI cells. We show that inhibition of WRN leads to the accumulation of DNA double-strand breaks throughout the S- and G2-phases, supporting and expanding on the cruciform-resolution model. We further show that the resulting G2 arrest is ATM-dependent and mechanistically distinct from canonical DSB-induced arrest, sharing features with the DNA decatenation checkpoint triggered by topoisomerase II (TOPOII) inhibition. Comparative analysis of MSI cell lines with varying sensitivity to WRN inhibition reveals differences in DNA damage kinetics and response to combined WRN and TOPOII inhibition. Our findings suggest that the dependency of MSI cells to WRN involves multiple DNA damage pathways and provide mechanistic insight that could guide future therapeutic strategies exploiting WRN-MSI synthetic lethality.

overall_design: EdUseq data of HCT116 cells addressing fork progression under DMSO or HRO761 (WRN inhibitor) treatment.

first: Thanos

middle: D

last: Halazonetis


title: The regulatory effect of EA on IgSF-CAMs expression mediated by PR8 infection in BEAS-2B cells

city: Guangzhou

first: liu

last: lifu

address: Panyu xinzao NO.1 Road

institute: Guangzhou Medical University

summary: IgSF-CAMs play a key role in secondarly bacterial infection post-influenza. In this data, we reported the VCAM-1 and CEACAM-1, as the members of IgSF-CAMs, were upregulated by PR8 infection in BEAS-2B cells and inhibited by erucic acid treatment. Our data illustrated the effect of erucic acid on inhibiting IgSF-CAMs expression to prevent secondary bacterial infection post-influenza.

overall_design: BEAS-2B cells were infected with PR8 virus. Following removal of the inoculum, the erucic acid treated groups received DMEM/F12 with erucic acid, while control group and virus group were replaced with fresh DMEM/F12. The total RNA was isolated from cells for RNA-seq.


title: Genome-wide identification of DOT1L-regulated targets via H3K79me2 modification in SW1990 pancreatic cancer cells

city: Changchun

first: Ziyu

last: Liu

address: 1 Xinmin Street

institute: Jilin University

summary: Disruption of epigenetic regulation plays a pivotal role in pancreatic cancer progression, yet the genome-wide targets of DOT1L-mediated histone H3 lysine 79 dimethylation (H3K79me2) remain poorly defined. In this study, we investigated the epigenetic landscape regulated by DOT1L in SW1990 pancreatic ductal adenocarcinoma cells. Cells were treated with EPZ-5676, a selective DOT1L inhibitor, or vehicle control, followed by chromatin immunoprecipitation sequencing (ChIP-seq) using an H3K79me2-specific antibody. We identified differentially enriched regions between EPZ-5676-treated and untreated cells, reflecting global loss of H3K79me2 upon DOT1L inhibition. Integration with gene annotation data revealed putative DOT1L-regulated genes involved in transcriptional regulation, cell proliferation, and cancer signaling pathways. These findings provide insight into the role of DOT1L in maintaining the active chromatin state and transcriptional programs in pancreatic cancer cells and highlight potential therapeutic targets in epigenetic intervention.

overall_design: ChIP-seq analysis of H3K79me2 modification in SW1990 pancreatic cancer cells treated with EPZ-5676 or DMSO as control. Chromatin was extracted and immunoprecipitated using an anti-H3K79me2 antibody, followed by high-throughput sequencing.

first: Feng

last: Wei


title: Transcrpitomic analysis of Oral lichen planus and oral lichenoid lesions

city: Shanghai

first: Xiaojie

last: Yang

address: No. 639 Zaozhiju Rd., Huangpu District

department: Department of Oral Medicine

institute: Shanghai Ninth People's Hospital

summary: This dataset contains bulk RNA sequencing profiles of human buccal mucosal tissues collected from 42 individuals, including 10 healthy controls, 16 patients with oral lichen planus (OLP), and 16 patients with oral lichenoid lesions (OLL). The objective of this study was to investigate the immune heterogeneity underlying OLP and OLL by comparing transcriptomic differences among the three groups. All tissue samples were obtained from the buccal mucosa, and RNA-seq was performed to identify immune-related gene expression patterns and molecular signatures. This dataset provides a valuable resource for exploring the immunopathogenesis of OLP and OLL.

overall_design: bulk RNA-seq of human buccal mucosal tissues collected from 42 individuals, including 10 healthy controls, 16 patients with oral lichen planus (OLP), and 16 patients with oral lichenoid lesions (OLL)

first: Yufeng


title: AoHal4b Interacts with AoAdv-1 Governs Hyphal Fusion, Nematode Predation Ability, and Secondary Metabolism in Arthrobotrys oligospora

city: Kunming

first: Xuewei

state: Yunnan

address: Chenggong District

institute: Yunnan University

summary: Serine/threonine kinases (STKs) are crucial for contribute to the virulence, pathogenicity, and potassium homeostasis in filamentous fungal pathogens. However, STK functions in hyphal fusion, trap morphogenesis, and lifestyle transitions of nematode-trapping (NT) fungi remain unclear.

overall_design: RNA-seq analysis between six wild-type samples and six mutant samples, with three biological replicates per sample, and prediction of multiple cytological processes that may affect trap formation in Arthrobotrys oligospora.

first: Jinkui

first: Meichen

last: Zhu

first: Lirong


title: Targeting Ccr1, Ccr3, Ccr2 and Ccr5 in H3.1K27 Mutant Diffuse Midline Gliomas (DMGs).

city: NEW YORK

first: Alexander

last: Tsankov

state: New York

address: 1425 Madison Ave

department: Genetics and Genomic Sciences

institute: Icahn School of Medicine at Mount Sinai

summary: Novel mouse was generate delta 1235 that allowed to abolish CCR2 positive monocytes and CCR1 positive neutrophils and evelate the effect on survival and immune composition of H3.1K27M mutant DMG

overall_design:
We have generated H3WT and H3.1K27M mutant DMG using RCAS-PDGFB, RCAS-shP53, RCAS-H3.1K27M and RCAS-ACVR Mut and compared their tumor and immune landscape.
The raw files for GSM9075664, GSM9075665, and GSM9075666 were submitted to SRA previously (PRJNA1029612).

first: Dolores

last: Hambardzumyan

first: Puigdelloses Vallcorba

last: Montserrat

first: Nishant

last: Soni


title: Chromatin conformation capture (4C-seq) of lncRNAs CTD-2566J3.1

city: CDMX

first: Stephanie Iraiz

last: Nuñez Olvera

address: Circuito, Mario de La Cueva s/n

country: Mexico

institute: Universidad Nacional Autónoma de México

summary: In cancer, lncRNAs have emerged as crucial regulators of tumor development and progression by serving as scaffolds for chromatin-modifying complexes and facilitating long-range chromatin interactions that influence 3D genome organization and gene regulation. This study focused on the antisense lncRNA CTD-2566J3.1, located at the RAD51B locus, which shows enhancer-associated epigenetic marks such as H3K27ac and H3K4me1. Using 4C-seq on BT-474 and T47D luminal breast cancer cells cultured under both 2D and 3D conditions, we identified frequent physical interactions between CTD-2566J3.1 enhancer regions and three target genes: RAD51B, MAP3K9, and ACTN1 in 3D cultures. These regions were also enriched with estrogen-related transcription factors ESR1 and FOXA1, suggesting hormonal regulation. These findings indicate that CTD-2566J3.1 acts as a multifunctional lncRNA regulating key oncogenic pathways in breast cancer through chromatin interactions and gene expression control, emphasizing the importance of 3D culture models to uncover context-dependent regulatory mechanisms.

first: S

middle: I

last: Nuñez-Olvera

first: L

last: Aguilar-Arnal


title: TRPA1 inhibition in high-temperature incubated chickens: dorsal root ganglia snRNA-seq

city: Beijing

first: Tian-Yu

last: Feng

address: 1 Beichen West Road, Chaoyang District

department: Institute of Zoology

institute: Chinese Academy of Sciences

summary: We performed single-nucleus RNA sequencing (snRNA-seq) on dorsal root ganglia (DRG) and attached nerves from chickens. This study aims to investigate the effect of inhibition of TRPA1 heat activation on the DRG of chickens incubated at high temperature.

overall_design: Chicken eggs were incubated under intermittent high temperatures, with or without injection of the TRPA1 inhibitor. After hatching, DRG and attached nerves were collected for snRNA-seq.

first: Shilong

first: Wei-Guo

last: Du


title: Effect of Ptpn1/2 knockout on the transcriptome of unstimulated or IFN-beta stimulated B16-OVA cells

city: Montreal

first: Michel

last: Tremblay

state: Quebec

address: 1160 Pine Avenue West

country: Canada

institute: Goodman Cancer Research Centre

summary: Immune evasion by cancer cells remains a major barrier to the success of immune checkpoint blockade (ICB). Here, we identify the phosphatases PTPN1 and PTPN2 as cooperative regulators of tumor immune resistance. Dual genetic ablation or pharmacologic inhibition of PTPN1/2 enhances Type I and II interferon signaling, MHC-I and CXCL9 expression, and sensitizes tumor cells to cytotoxic T lymphocyte–mediated killing. The small-molecule inhibitor KQ791 phenocopies these effects and synergizes with anti-PD1 therapy to suppress tumor growth in murine models, including immunotherapy-refractory cancers. Mechanistically, PTPN1/2 loss augments STAT1/3/5 signaling and primes cancer cells for immunogenic cell death via IFNγ/TNFα-induced pathways. Moreover, PTPN1/2 inhibition enhances antigen release and cross-presentation, promoting robust antigen-specific CD8⁺ T cell responses. These findings highlight PTPN1&2 as essential mediators of cancer immune evasion and support their inhibition as a strategy to broaden the effectiveness of immune checkpoint blockade in solid tumors.

overall_design: RNAseq of sgCTL, sgPtpn1, sgPtpn2, sgDKO or sgCTL with KQ791 treatment, either with or without stimulation with IFN-beta for 6 hours. n=3 replicates/condition. N=30 samples.

first: Alexandre

last: Poirier


title: Transcriptome analysis in the prefrontal cortex of Ank2 heterozygous mice treated with drug

first: Eunjoon

last: Kim

summary: Autism spectrum disorders (ASD) affect ~2.8% of the population, but the underlying biological mechanisms remain poorly understood, largely due to significant genetic heterogeneity. Mouse models have identified numerous candidate mechanisms; however, whether these can be grouped into functionally coherent subtypes remains unclear, limiting targeted, mechanism-based treatments. We analyzed prefrontal cortex transcriptomes from 17 distinct ASD mouse models, encompassing both sexes, under baseline and two separate drug-treatment conditions, totaling 1,008 mice across 204 groups.

overall_design: Ank2-HT and WT mice were analyzed on postnatal day 25 (P25), immediately following 3 weeks of drug treatment (P3-24) administered via maternal milk before weaning. Male and female mice were administered two different drugs (fluoxetine and lithium), and prefrontal cortex regions of the mice were dissected to perform RNA-seq.

first: Junyeop Daniel

last: Roh

first: Yukyung

last: Jun

first: Mihyun

last: Bae

first: Hyojin

last: Kang