title: SOWAHA as a cancer suppressor gene Influence Metabolic Reprogramming

city: Chengdu

first: Xiaohong

middle: Huang

last: Yi

state: Sichuan

address: 1166 Liutai Avenue, Wenjiang District, Chengdu City

department: School of Basic Medical Science

institute: CDUTCM

summary: Background: SOWAHA, also known as ANKRD43, is a member of the ankyrin repeat domain family. Studies have indicated that SOWAHA is associated with the microsatellite instability (MSI) status in colorectal cancer patients and could serve as a prognostic biomarker in pancreatic cancer. However, there are rarely reports about SOWAHA in other types of cancer and the specific mechanism of SOWAHA in cancer is also unclear. Methods: Based on National Center for Biotechnology Information (NCBI), The Cancer Genome Atlas (TCGA), Genotype-Tissue Expression Project (GTEx), cBioPortal, Human Protein Atlas (HPA), Integrative Onco Genomics (IntOGen), and other database, we uncovered the potential tumor genomic features of SOWAHA, including the correlation with prognosis, mutation, immune cell infiltration, and DNA methylation, and evaluated the association with tumor heterogeneity and stemness, chemokines chemokine receptors, and immunomodulators in pan-cancer. Besides, we knocked down SOWAHA in SW620 cells and performed RNA-seq analysis, then we conducted functional enrichment to uncover the biological significance of SOWAHA. Results: SOWAHA is a suppressor gene in colorectal carcinoma (COAD), and has early diagnostic potential, with low expression levels linked to poor prognosis in Glioblastoma and Lower Grade Glioma (GBMLGG), Pancreatic adenocarcinoma (PAAD), and other cancers. It is associated with immune cell infiltration, DNA methylation, tumor heterogeneity, and stemness in several epithelial cancers. Furthermore, our experiments revealed that SOWAHA is significantly enriched in the metabolic related pathways in cancer, such as 'P53 signaling pathway', 'PI3K-AKT signaling pathway', and 'pathways in cancer', 'Ubiquitin-Mediated Proteolysis', 'RNA Degradation', etc. We also identified two potential transcription factors regulating SOWAHA, TBX4, and FOXP2, which are misregulated in SW620 cells. Conclusion: SOWAHA, identified as a suppressor gene, may also serve as a valuable biomarker for diagnosis, prognosis, and immunotherapy in some carcinomas, particularly colorectal carcinoma. Its role in the progression of colorectal cancer is primarily mediated through metabolic reprogramming mechanisms.

overall_design: RNA-seq

first: Xianwen

last: Zhang

first: Claire

last: H. Zhao

first: Yumei


title: JNKinhibitors for the treatment of inflammation and endometriosis [epithelial cells]

status: Public on Jul 31 2026

city: Houston

first: FEI

last: YUAN

state: TX

address: 1 Baylor Plaza

department: Pathology & Immunology

country: USA

institute: Baylor College of Medicine

type: Expression profiling by high throughput sequencing

summary: Endometriosis is a prevalent gynecological disease that impact ~10% of women of reproductive age. In addition to causing chronic pain, and inflammation, women with endometriosis experience high rates of infertility, migraine, inflammatory bowel disease and autoimmune conditions. In this study, the efficacy of newly developed inhibitors of the c-Jun N-terminal kinases (JNK) were tested as therapeutics for endometriosis. Using state-of-the-art DNA encoded library screens, JNK inhibitors CDD-2728 and CDD-3013, with high specificity and efficacy were identified and tested in in vitro models of endometriosis. The ability of the inhibitors to decrease inflammation-related gene expression were evaluated in immortalized cell models of endometriosis, 12Z cells, and in primary derived endometriotic stromal cells from patients with the disease. Transcriptomic profiling was performed, as well as endpoints related to cell viability, cytotoxicity, and apoptosis. These studies identified that CDD-2728 and CDD-3013 were potent suppressors of IL1beta-induced inflammation, decreasing the expression of classical markers of inflammation, such as IL6, IL8, IL18, and PTGS2.

overall_design: RNAseq analysis of 12Z peritoneal epithelial cells from endometriosis lesions treated with IL1beta (10ng/ml) in the presence or absence of JNK inhibitor CDD-2728 (1µM and 10µM) and CDD-3013 (1µM) for 6 hours.

first: Diana

last: Monsivais

first: Stephen

last: Palmer


title: Hidden outcomes of CRISPR/Cas9 genome editing revealed by targeted sequencing in isogenic human iPSC clones

status: Public on Jul 30 2026

city: Novisibirsk

first: Veniamin

last: Fishman

address: Prospekt Lavrentyeva 10

country: Russia

institute: Institute of Cytology and Genetics The Siberian Branch of the Russian Academy of Sciences

summary: CRISPR/Cas9 editing can create complex on-target alterations that escape conventional PCR genotyping. We characterized ten edited human induced pluripotent stem cell clones derived from four related parental lines carrying a tandem Xq25 duplication encompassing STAG2. Targeted genomic sequencing revealed inversions, plasmid integration, and complex rearrangements and resolved discrepancies between genotyping and transcriptomic observations. This GEO submission provides quantitative genome-browser coverage tracks supporting the transcriptomic and whole-genome analyses. BioProject: PRJNA1499378.

overall_design:
Low-coverage whole-genome sequencing of the human iPSC line iP149-1 was used to characterize the Xq25 tandem duplication encompassing STAG2. This submission provides the quantitative genome-wide coverage bigWig track and is linked to BioProject PRJNA1499378. Per depositor instruction, the WGS raw reads are not included.

***************************************************************
Raw files for human/patient samples were not submitted to GEO due to concerns about submitting personally identifiable sequence data for open access.
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first: Tubalova

last: Maria

first: Koksharova

last: Galina

first: Costa

last: Silvia

first: Krepischi

last: Ana

first: Fishman

last: Veniamin

first: Gridina


title: Impact of phosphomimetic Raptor S791D mutation on gene expression in brown adipocyte

city: Nashville

first: Shristi

last: Shrestha

address: 2213 Garland Ave

institute: Vanderbilt University

summary: To determine the impact of Raptor S791 phosprylation on borwn adipocyte function and metabolism, we previously established HIB-1B brown adipocyte models that stably expresses a wide-type (WT) RAPTOR or a Ser to Asp (S791D) phosphorylation-mimetic RAPTOR mutation (Liu et al., JCI, 2016). In this study we performed RNA-seq experiment to determine the trasncriptomic changes between the WT and S791D brown adipocytes.

overall_design: HIB-1B brown adipocyte stably expressing WT or S791D Raptor were differentiated as described (Liu et al. JCI 2016). RNA was extracted and subjected to RNA-seq analysis.

first: Fubiao

last: Shi

first: Dianxin

last: Liu

first: Jean-Philippe

last: Cartailler

first: Sheila

last: Collins


title: Hidden outcomes of CRISPR/Cas9 genome editing revealed by targeted sequencing in isogenic human iPSC clones [RNA-seq]

overall_design:
Ten CRISPR/Cas9-edited human iPSC clones were derived from parental lines iP146-1, iP146-7, iP149-1, and iP149-4. Total RNA from each clone was analyzed by stranded oligo-dT RNA sequencing. This submission contains one CPM-normalized, 1-bp-resolution bigWig coverage track per clone. Per depositor instruction, RNA-seq raw reads are not included. Targeted NGS and PCR-genotyping raw reads are deposited separately in SRA under BioProject PRJNA1499378.

***************************************************************
Raw files for human/patient samples were not submitted to GEO due to concerns about submitting personally identifiable sequence data for open access.
***************************************************************


title: Cholesterol maintains the degradative capacity of lysosomes during clearance and recycling of dysfunctional mitochondria

city: Singapore

first: Yasunori

last: Saheki

address: 11 Mandalay Road

country: Singapore

institute: Lee Kong Chian School of Medicine, NTU

summary: Efficient clearance and recycling of dysfunctional mitochondria through the robust catabolic activity of lysosomes is essential for cellular health. However, how membrane lipids contribute to maintaining the degradative capacity of lysosomes remains poorly understood. Here, we show that cholesterol plays a critical role in preserving the functional integrity of degradative lysosomes. Clearance of damaged mitochondria by degradative lysosomes is tightly coupled with the acute accumulation of phosphatidylinositol 4-phosphate (PI4P) on the lysosomal surface via PI4KIIα activity. This PI4P accumulation activates oxysterol-binding protein (OSBP)-mediated cholesterol transport from the endoplasmic reticulum (ER) to lysosomal membranes. The resulting efflux of cholesterol from the ER activates sterol regulatory element-binding protein 2 (SREBP-2), enhancing cholesterol production. Sustained cholesterol accumulation on lysosomal membranes maintains lysosomal acidity and membrane integrity for efficient mitochondrial degradation. This degradation process then leads to the release of free fatty acids and their recycling and storage through the formation of DGAT1-dependent lipid droplets. These findings uncover a key phosphoinositide-regulated cholesterol transport pathway that promotes the clearance and recycling of dysfunctional mitochondria, a process whose impairment is closely linked to neurodegeneration.

overall_design: RNA-seq profiling of wildtype N/TERT-1 cells treated with ethanol (Control) or Oligomycin and Antimycin A (O/A).

first: Haoning

last: Yang

first: Koji

last: Matsuhisa

first: Meng

last: Wei

first: Wataru

last: Nishi

first: Dylan Hong Zheng

last: Koh

first: Aik Yong

last: Sim

first: Isabelle

last: Bonne


title: Truncating RELA variants drive autoinflammation and autoimmunity by impairing the negative feedback control of NF-k

city: Munich

first: Johanna

last: Klughammer

address: Feodor Lynen Str 25

country: Germany

institute: Gene Center LMU

summary: The NF-κB signaling pathway coordinates inflammation, cell survival, and proliferation, while restraining excessive cell death to maintain immune homeostasis. Truncating mutations in RELA, encoding the NF-κB subunit p65, have been linked to autoinflammation and autoimmunity, but the underlying mechanisms remain incompletely defined. We investigated six patients from five unrelated families carrying novel heterozygous truncating RELA variants. Despite reduced p65 expression, patients exhibited a broad spectrum of inflammatory manifestations alongside elevated baseline and stimulus-induced pro-inflammatory cytokines. Functional analyses in patient-derived cells and mutant RELA knock-in models showed that upstream NF-κB signaling was intact, but induction of inhibitory regulators such as IκBα and A20 was impaired. This defective feedback control shifted immune homeostasis toward amplified inflammatory responses that depended on the residual activity of the remaining functional RELA allele. Single-cell transcriptomics revealed distinct cell type-specific consequences: monocytes displayed constitutive type I interferon and NF-κB activation, B cells retained partial compensatory signaling, whereas T and NK cells exhibited transcriptional signatures of cell death pathways. Patient fibroblasts and mutant RELA knock-in cells further confirmed enhanced TNF-induced inflammatory gene expression and hypersensitivity to apoptosis and necroptosis. These findings establish RELA haploinsufficiency as a cause of systemic immune dysregulation, and link defective NF-κB feedback control to unchecked inflammation and inflammatory cell death.

overall_design:
PBMCs of patients with mutations in the RELA gene as well as healthy controls were analyzed using 10x Chromium singel-cell RNA sequencing.

***************************************************************
Raw files for human/patient samples were not submitted to GEO due to concerns about submitting personally identifiable sequence data for open access.
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first: Min

middle: A

last: Lee-Kirsch


title: Brachyury expression levels predict lineage potential and axis-forming ability of in vitro derived neuromesodermal progenitors

city: Edinburgh

first: Anahi

last: Binagui-Casas

address: 5 Little France Drive

department: Institute for Regeneration and Repair

country: United Kingdom

institute: The University of Edinburgh

summary: Neuromesodermal progenitors (NMPs) produce the spinal cord and musculoskeleton in the elongating anterior-posterior axis. In vivo, NMPs possess dual potency, coinciding with regions coexpressing SOX2 and Brachyury (TBXT). In vitro, SOX2/TBXT co-expressing cells can be produced from pluripotent cells and, like their in vivo counterparts, can produce neural tube and somitic mesoderm. However, the functional characteristics of in vitro SOX2/TBXT co-expressing cells remain unclear, confounding comparisons with in vivo data. To address this, we developed a dual Sox2/Tbxt reporter mouse ESC line. SOX2/TBXT reporter-positive cells emerge in vitro from pluripotent populations with dynamics that mirror their appearance in the embryo. Purified SOX2/TBXT co-expressing populations can differentiate towards neurectoderm or mesoderm, including lateral mesoderm upon BMP stimulation. In gastruloids, quantitative live imaging shows that WNT or NOTCH inhibition rapidly leads to downregulation of TBXT expression and diminished axial extension. We show that clonally plated SOX2/TBXT co-expressing cells are bipotent NMPs that can also self-propagate.  By combining clonal analysis with mathematical inference, we identify two thresholds of TBXT and/or SOX2 expression, switching clonal output from neural- to mesoderm- biased, and from mesoderm-biased to mesoderm-specified.  Image analysis of embryonic NMPs supports a model whereby SOX2 and TBXT independently influence neuromesodermal differentiation. Thus, this Sox2/Tbxt double reporter cell line highlights unsuspected heterogeneity in NMPs, and together with image analysis of embryonic SOX2/TBXT levels, challenges an assumption that neuromesodermal fate choice is primarily governed by mutual antagonism between SOX2/TBXT.

overall_design: Bulk RNAseq profiling of sorted populations along a mouse neuromesodermal progenitor extended culture period (+7d post NMP induction). Starting from a pure Sox2/Tbxt co-expressing population (NMP), to a 48h single Sox2 or Tbxt population, to their +7d derivatives.

first: A


title: The role of GLS1 and MPC2 in germinal center B cell regulation

city: Atlanta

first: Chris

last: Scharer

state: GA

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

institute: Emory University

summary: The efficiencies with which activated B lymphocytes proliferate and develop into antibody (Ab)-secreting plasma cells are critical determinants of adaptive humoral immunity and central to sustaining certain autoimmune diseases. Increasing evidence indicates that specific pathways in intermediary metabolism, or their substrate supply, influence lymphocyte differentiation and function. To investigate the role of glutaminolysis by GLS1 and mitochondrial pyruvate import via MPC2 on germinal center B cell differentiaiton and function flow-purified we immunized wild-type, GLS1-KO, MPC2-KO, or double KO mice with SRBC and FACS isolated germinal center B cells after 7 days for transcriptional profiling.

overall_design: RNA-seq profiling of germinal center B cells in triplicate from Wild-type, GLS1-KO, MPC2-KO, and double KO mice.  For controls, naïve B cells were also profiled in triplicate.

first: Christopher

middle: D

first: Mark

last: Boothby


title: Bulk RNAseq of sorted Treg cells from a single ascending dose clinical trial in healthy adults of IL-2 mutein MK-6194 (formerly known as PT-101)

city: Seattle

first: Laura

last: Cooeny

state: WA

address: 1201 9th Ave

department: University of Michigan

institute: Immune Tolerance Network

summary: The objectives are to use cryopreserved PBMC samples from the Phase 1a single ascending dose trial of IL-2 mutein (MK-6194/PT-101) in healthy adults to define the transcriptional responses of regulatory CD4+ T cells (CD25hiCD127lo Treg), and determine how this varies with both dose and time after treatment.

overall_design: The clinical trial was a randomized double-blind, placebo-controlled, single-dose escalation trial. Participants per cohort received a single administration of MK-6194/PT-101 or placebo subcutaneously on day one. PBMCs were collected and cryopreserved on day -10, day 1 (prior to IL-2 mutein administration), and days 8, 15, and 29. Dosing cohorts included placebo, 1mg, 3.5mg, 5mg, and 10mg, with RNAseq conducted on 5-7 participants per dosing cohort. PBMCs were thawed after study completion for batched analysis and Tregs (CD4+CD127-CD25+) were sorted using flow cytometry. Purified Tregs were then analyzed by bulk RNAseq to determine the effects of IL-2 mutein treatment on Treg gene expression. Sample sorting, sequencing, and data analysis were all performed at the Benaroya Research Institute.

first: Harris

last: Kristina

first: Campbell

last: Dan

first: Cooney

last: Laura

first: Long

last: Alice

first: Fanning

last: Mitch


title: ADAT2/3-mediated tRNA editing promotes cancer cell growth and tumorigenicity

city: Boston

first: Qi

last: Liu

state: MA

address: 1 Blackfan Circle

institute: Boston Children's Hospital

summary: Transfer RNAs (tRNAs) are subject to various chemical modifications that influence their stability or function. Adenosine to Inosine (A-to-I) editing in the tRNA anticodon at position A34 is an important modification that expands anticodon-codon recognition at the wobble position and is required for normal mRNA translation. The relevance of tRNA editing in cancer remains unexplored. Here we find that decreased tRNA editing upon ADAT2 depletion leads to defective translation of a subset of mRNAs. Thus, ADATmediated tRNA modification promotes oncogenesis by enhancing the translation of growth promoting mRNAs that are enriched in NNC codons that lack cognate tRNAs and therefore depend on A-I tRNA editing for decoding and mRNA translation.

overall_design: Ribo-seq of ADAT2/3 knockdown and control samples

first: Julia

middle: R

last: Moya

first: Richard

middle: I

last: Gregory


title: Faf2 is required for neural differentiation in embryonic neural progenitor cells

city: Boulder

first: Anneke

middle: Dixie

last: Kakebeen

state: Colorado

address: A1B43 MCDB Main Office, 1945 Colorado Ave

department: Molecular Cellular and Developmental Biology

institute: university of colorado boulder

summary: Neural progenitor cell differentiation is a complex process requiring the proper integration of instructive and permissive factors. Instructive cues including signaling molecules and transcription factor networks have been well studied in this context, but permissive factors such as cell homeostasis have not. Cell homeostasis is critical to support the health and stability of a cell and enable the cell to act on instructive differentiation cues. Our study investigates a homeostasis protein, FAF2, and its function in neural progenitor cells. FAF2 is an adaptor protein involved in endoplasmic reticulum (ER) associated degradation to remove misfolded proteins and restore ER homeostasis. Here we show that knocking out FAF2 in neural progenitor cells results in increased ER stress signature at the protein and transcription level, indicating a conserved functional role in neural progenitor cells. Induced neural differentiation of FAF2 deletion cells shows a failure of neurite development but RNA-seq indicates genes that support neural differentiation are induced. Reducing ER stress in FAF2 knockout cells with a small molecule inhibitor can rescue neural differentiation, providing evidence that excess ER stress contributes to the inhibited differentiation. Taken together, these results reveal that FAF2 is a critical protein in neural progenitor cells for the maintenance of ER homeostasis and execution of neural differentiation.

overall_design: RNA-Seq profiling of WT NE-4C cells and their Faf2 knockout derivatives that have been treated with and without all-trans retinoic acid. Retinoic acid treated cells were treated for 24 hours with retinoic acid before being moved to basal media until collection at 3 days post induction.

first: Leon

last: Dunphy

first: Heather

middle: K

last: Hazen

first: Lee

last: Niswander


title: Single-cell analysis identifies monocyte signatures of disease activity and clinical subtypes in Behçet’s disease

city: Pittsburgh

first: Amr

middle: H

last: Sawalha

state: PA

address: 530 45th Street

department: Department of Pediatrics

institute: University of Pittsburgh

summary: This study used single-cell RNA sequencing of PBMCs from 34 Behçet’s disease patients and 12 healthy controls to characterize immune dysregulation across disease activity states and clinical phenotypes. BD was marked by expansion and activation of monocyte subsets, with strong IFN-γ, heat-shock, and antigen-presentation signatures, particularly during active disease. These inflammatory programs decreased in remission, which showed restoration of regulatory and metabolic pathways and increased type I interferon-related gene expression, suggesting a potentially protective role. Distinct monocyte signatures were also associated with vascular, ocular, and non-organ-involved BD. Overall, the study identifies monocyte-driven inflammation as a central feature of BD and highlights activity- and phenotype-specific pathways that may guide targeted therapies.

overall_design:
The submission includes peripheral blood mononuclear cell samples from patients with Behçet’s disease and healthy control donors. The main experimental variables are disease status and clinical phenotype. Samples include Behçet’s disease patients with active disease, patients in remission, and sex-matched healthy controls without autoimmune or inflammatory disease. Active Behçet’s disease was defined by the presence of recent clinical manifestations, whereas remission samples were collected after clinical improvement following systemic therapy. The study includes biological replicates from 34 Behçet’s disease patients and 12 healthy controls, with an additional subset of 4 patients sampled longitudinally before and after treatment, allowing paired active versus remission comparisons. Clinical phenotype groups include vascular, ocular, and mucocutaneous Behçet’s disease, as well as patients without major organ involvement.Healthy control samples serve as the reference/control group. The experimental design supports comparisons between Behçet’s disease and healthy controls, active disease and remission, paired pre-treatment and post-treatment samples, and phenotype-stratified Behçet’s disease subgroups.
The clinical_dataBD.csv includes additional sample-level information relevant to the experimental design, including disease status, clinical phenotype, and treatment/remission-related information among others.
The All.merged6_SCT_FLT_clean.rds contains the processed single-cell Seurat object to facilitate interpretation of the dataset together with the previously submitted raw FASTQ files and demultiplexed data.

first: Carmona

last: Elio

first: Deniz

last: Rabia

first: Cemal

last: Bes

first: Direskeneli

last: Haner

first: Gül

last: Ahmet

first: Sawalha

last: Amr


title: Adipocyte ILF3 Deficiency Improves Diet-induced Obesity and Metabolic Disorders through PUFA Synthesis

city: Jinan

first: Fei

last: Xie

address: 107 Wenhua West Road, Lixia District, Jinan City, Shandong Province

country: China

institute: Qilu Hospital of Shandong University

summary: A moderate long-chain polyunsaturated fatty acids (LC-PUFAs) intake may improve obesity and metabolic disorders. However, regulating endogenous LC-PUFAs and their function is unclear. Here, adipocyte ILF3 expression promotes high-fat diet (HFD)–induced obesity and metabolic disorders by inhibiting endogenous omega-3 LC-PUFAs (n-3-LC-PUFA) biosynthesis. In patients with obesity, serum ILF3 levels are elevated and positively correlate with high triglyceride levels. The expression of ILF3 in adipose tissue from patients with obesity and HFD-induced obese mouse models is positively correlated with adipocyte size. Adipose tissue ILF3 expression in patients with obesity and HFD–induced obese mice positively correlates with adipocyte size. Adipocyte ILF3 deficiency significantly increases white adipose tissue browning, promotes brown adipose tissue thermogenesis, and improves HFD–induced obesity and metabolic disorders. ILF3 recruits DNMT1, which reduces FADS2 transcription and inhibits n-3-LC-PUFA biosynthesis. Similarly, sc26196, a FADS2-specific inhibitor, exacerbates obesity and metabolic disorders. Fenofibrate, an anti-triglyceride drug, improves obesity and metabolic disorders by inhibiting ILF3 expression and increasing endogenous n-3-LC-PUFA biosynthesis. Collectively, inhibiting adipocyte ILF3 expression may be an effective alternative treatment for these conditions.

overall_design: RNA-seq profiling of epididymal white adipose tissue of obese ILF3flox/flox and ILF3AKO mice

first: Hong-rui

last: Yang

first: Ya-min

last: Hou


title: Assembly Factors and snoRNAs Manage Programmable RNA Folding and Misfolding to Support Growth in Stationary Phase

first: zahrat el oula

last: hassoun

state: TN

address: 200 Robinson research

department: Biochemistry

summary: This research demonstrates how ribosomal RNA folding is actively controlled during 40S ribosome assembly to prevent a misfolding intermediate where helix h24 becomes mispositioned when bound by the protein Rrp5. We show that assembly factors Rrp36 and snoRNAs (snR31, snR54) cooperatively prevent this misfolding by tethering Rrp5 away from the platform and delaying h24 formation, respectively. Disrupting these interactions leads to widespread structural alterations that persist into mature ribosomes. Interestingly, we reveal that this misfolding pathway is not an evolutionary mistake but rather serves a physiological function. This work reframes assembly factors and snoRNAs as molecular chaperones that actively reshape the RNA folding landscape, with broader implications for understanding ribosome heterogeneity and conditional ribosome specialization.

overall_design: Two independent DMS_MaPseq experiments were performed. In the first experiment, pre_40S ribosomes were purified via Utp9_TAP from cells expressing either wild_type Rrp5 with H375A or Rrp5_mL with H375A. For each condition, DMS_treated samples and untreated controls were prepared. Three biological replicates were analyzed for each condition. In the second experiment, mature ribosomes were isolated from BY4741 and BY4741_Δsnr31,Δsnr54 cells. For each condition, DMS_treated samples and untreated controls were prepared. Three biological replicates were analyzed for each condition.

first: Hassoun

last: Zahrat El Oula

first: Katrin

last: Karbstein


title: snRNA-seq dataset for "A conserved population of genetically defined striatal neurons gates opioid reward"

city: Birmingham

first: Jeremy

last: Day

state: Alabama

address: 1825 University Blvd SHEL 910

department: Neurobiology

institute: University of Alabama at Birmingham

summary: This dataset contains single-nucleus RNA-seq results from rat nucleus accumbens brain tissue.

overall_design: This experiment contains 12 biological samples (nucleus accumbens tissue from 6 male and 6 female adult rats), which are combined into 6 sequenceing replicates. Tissue was obtianed from from flash frozen brains that were stored at -80°C prior to tissue punch collection, nuclei isolation, and single nucleus RNA-seq on the 10X Genomics Chromium GEM-X platform. Libraries were sequenced on an Illumina NovaSeq 6000 to an average read depth of ~23,000 read pairs per nuclei. Forward and reverse paired-end reads are denoted as "R1" or "R2" in raw file names. Samples are from 2 experimental groups, all of which underwent heroin self-administration prior to administration of either saline or naloxone 1 hour prior to brain extraction.

first: Olivia

last: Drake

first: Caroline

middle: M

last: Fiore

first: Emily

middle: T

last: Jorgensen

first: Catherine

middle: E

last: Newman

first: Luke

last: Potter

first: Austyn

last: Trull

first: Lara

last: Ianov

first: Jamie

last: Peters

first: Jasper

last: Heinsbroek

middle: J


title: Ureterovesical junction: a stem cell niche for ureteral urothelial renewal and bladder urothelial injury repair

city: New York

first: Yi

last: Liao

state: New York

address: 423 23rd Avenue

department: Urology

institute: NYU Grossman School of Medicine

summary: Epithelial stem cells are essential for lineage specification, tissue renewal, and regeneration. Here we show that ureterovesical junction (UVJ) of urinary tract harbors a major cluster of label-retaining urothelial cells that exhibit organoid-forming activities. During lineage-tracing, these Foxa2-expressing UVJ urothelial cells renew ureteral urothelium, but do not migrate into the bladder during homeostasis or mild bladder injury. Upon mechanical and chemical denudation of bladder urothelium, UVJ cells migrate rapidly into the bladder to replace bladder urothelium. This reepithelization also occurs during combination chemotherapies and severe bladder infection. Common to these injury repair processes is the early-phase and selective phosphorylation of TRKA and AKT which drives urothelial proliferation and differentiation. Nascent bladder urothelial cells derived from UVJ express both UVJ and bladder urothelial markers, signifying active remodeling influenced by intrinsic and extrinsic factors. Modulating the activities of UVJ cells may enhance bladder urothelial regeneration and combat challenging bladder diseases.

overall_design: The epithelia of urinary bladder and ureter are derived from endoderm and mesoderm respectively, therefore RNAs from rat urinary bladder and ureteral urothelial cells were extracted for RNA-seq profilling. Four of 6 week old female Fisher CDF rats from same litter were used for variation.

first: Fenglin

last: Zhang

first: Yan

last: Liu

first: Xiaohong

last: Li

first: Fiona

last: Kuo

first: Teng

first: Yuan

last: Wei

first: Takwah

last: Wong

first: Herbert

last: Lepor

first: Ellen

last: Shapiro

first: Fangming

last: Deng

first: Cathy

last: Mendelsohn

first: Xueru

last: Wu


title: Murine pancreatic tumors induce pathological remodeling of muscles critical to chewing and swallowing [RNA-seq]

city: Gainesville

first: Andrew

last: Judge

state: FL

address: 1275 Center Drive, Biomedical Sciences Building RM J303

institute: University of Florida

summary: Cancer cachexia is a debilitating syndrome defined by involuntary weight loss due to loss of muscle mass, with or without loss of fat mass. Cachexia is particularly prevalent in pancreatic cancer, affecting up to 70% of patients at diagnosis, and is associated with reduced physical function, impaired treatment tolerance, and worsened survival. Skeletal muscle, including muscles involved in respiration and locomotion, exhibit extensive pathological remodeling in cachexia, including myofiber atrophy and transcriptional reprogramming. Whether muscles that are critical to chewing and swallowing respond similarly remains unknown. To address this gap, we collected masseter (chewing) and digastric (swallowing) muscles from cachectic mice bearing orthotopic KPC pancreatic tumors (n=8) and cancer-free Sham controls (n=8). Hematoxylin and eosin staining revealed increased mononuclear cell content, centralized nuclei, and expanded interstitial spaces in both muscles of KPC mice. Myofiber cross-sectional area was reduced by 42% in the masseter and 23% in the digastric. RNA sequencing revealed distinct transcriptional responses between these muscles. The masseter muscle showed enrichment of catabolic signaling pathways, including proteolytic and stress-response programs, alongside downregulation of extracellular matrix and growth-related programs. In contrast, the digastric muscle exhibited robust upregulation of immune and inflammatory pathways, including innate and adaptive immune signaling, with minimal overlap between muscles. Collectively, these findings demonstrate that pancreatic cancer drives pathological remodeling and atrophy in muscles central to chewing and swallowing while eliciting distinct, muscle-specific transcriptional responses, changes that could negatively affect food and nutrient intake and thereby contribute to cachexia progression.

overall_design: RNA-seq profiling of digastric and masseter muscles from cancer-free control Sham mice and mice with KPC pancreatic tumors.

first: Jeremy

last: Ducharme


title: Role of Snord116 in pituitary growth hormone deficiency of Prader-Willi Syndrome

first: YIYING

last: ZHANG

address: 1150 St. Nicholas Ave

department: Pediatrics

institute: Columbia University

summary: Prader-Willi Syndrome (PWS) is a complex genetic disorder resulting from the deficiency of several maternally imprinted genes, including SNORD116, in the 15q11-q13 region. Loss of Snord116 in mice recapitulates some of the most salient clinical features of PWS, including growth hormone (GH) deficiency and hypogonadism. This study explored the impact of Snord116 deficiency on early postnatal pituitary development and growth in Snord116 KO mice.  Snord116 was found to be expressed in both anterior and posterior pituitary. Pituitary transcriptomes of Snord116 KO and wild-type (WT) mice at two developmental stages, postnatal day 0 (P0) and 4 weeks of age, were interrogated and related to ex vivo analyses of GH secretion in the pituitaries of 5-week-old mice. Significant differences in pituitary transcriptomes were detected between Snord116 KO and WT mice at 4 weeks of age but not at P0. The differentially expressed genes and affected molecular pathways play important roles in regulating embryonic and postnatal pituitary development. Our results suggested that PWS GH deficiency was mainly due to pituitary hypoplasia and decreased GH production but not to reduced GH secretory function per se, implicating Snord116 in the specific molecular/cellular pathways that account for impaired postnatal pituitary development and GH deficiency in PWS.

overall_design: RNASeq profiling mouse pituitaries from Snord116 knockout mice and wild-type controls at P0 and 4 weeks of age

first: Gabriel

middle: F

last: Batzli

first: Kaiying

last: Guo

first: Fahrünisa

middle: B

last: Erol

first: Charles

last: LeDuc

first: Lisa

middle: C

last: Burnett

first: Rudolph

middle: L

last: Leibel

first: Yiying


title: Transient CB2R Modulation Promotes Luminal-like Differentiation and Restricts Breast Cancer Plasticity

city: Madrid

first: Leonardo

last: Beccari

address: Nicolas Cabrera 1

country: Spain

institute: Centro de Biología Molecular Severo Ochoa (CSIC)

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Cancer cell plasticity enables therapy resistance and metastasis by allowing transitions between stem-like and differentiated states. Differentiation-based strategies aim to stabilize tumor cell identity, yet pharmacological approaches that induce durable lineage restriction remain limited. Here, we show that transient modulation of cannabinoid receptor 2 (CB2R) promotes persistent luminal-like stabilization in breast cancer models. Using patient-derived and murine tumor organoids, we demonstrate that brief, low-dose CB2R modulation reduces self-renewal, invasiveness and tumor-initiating capacity, while enhancing tamoxifen sensitivity and limiting the emergence of resistant phenotypes. These effects persist under pro-dedifferentiation conditions, including TGFb exposure, stromal co-culture, immune signaling and mechanical stress, and are long-term maintained in vivo following orthotopic transplantation. RNAseq analyses reveal a trajectory from an early plastic state toward a stabilized luminal-like identity, supported by CUT&Tag profiling that uncovers chromatin remodeling in this transition. Together, our findings redefine CB2R as a regulator of tumor cell state rather than solely a mediator of cytotoxic responses and establish transient CB2R modulation as a strategy to durably constrain breast cancer plasticity through differentiation-based therapy.

overall_design: CUT&Tag was performed using the Active Motif protocol (Active Motif #53160) following the manufacturer’s instructions. Briefly, organoids were enzymatically dissociated into single cells using collagenase P (3 µM; Thermo Fisher Scientific, Cat. No. 11249002001) for 10 min at 37 °C, followed by incubation with TrypLE Express (Thermo Fisher Scientific) for an additional 10 min at 37 °C. Enzymatic digestion was monitored while preserving cell viability. Approximately 500,000 cells per sample were immobilized on concanavalin A-coated magnetic beads. Cells were incubated overnight at 4°C with primary antibodies against H3K4me3 (Sigma, 17-614) or H3K27me3 (Abcam, ab6002), followed by incubation with species-specific secondary antibodies (anti-rabbit for H3K4me3 and anti-mouse for H3K27me3) to enhance signal detection. Bead-bound cells were then incubated with protein A–Tn5 transposase preloaded with sequencing adapters, and tagmentation was carried out for 60 min at 37°C. DNA fragments were released by proteinase K digestion and purified using column-based cleanup. Libraries were generated using KAPA polymerase (Roche, KK2612) and single-index barcoded primers. The number of PCR cycles was determined by qPCR (Ct + 2 cycles). Libraries were purified using SPRI beads (CleNA, #CNGS-0050), and quality was assessed by fluorometric quantification and fragment size analysis. Sequencing was performed on an Illumina NovaSeq X platform using 150 bp paired-end reads.

first: Jorge

last: Mañes-García

first: Camila

last: Quezada- Gutiérrez

first: María

last: Salazar-Roa


title: Longitudinal CITE-seq analysis in juvenile-onset systemic sclerosis monocytes following autologous stem cell transplant

first: Kathryn

last: Torok

email: TRH107@pitt.edu, kst7@pitt.edu

address: 4401  Penn Ave

summary: Juvenile systemic sclerosis (jSSc) is a rare and severe autoimmune disease marked by skin fibrosis and damage to multiple organ systems. This study implements autologous stem cell transplantation (ASCT), a newly available treatment protocol which aims to restore immune homeostasis, in this case amongst jSSc patients. Here, we analyze peripheral blood mononuclear cells (PBMCs) from 3 jSSc patients prior to ASCT and 6, 12, and 24 months post treatment. These samples were then sequenced and tagged with antibodies using cellular indexing of transcriptomes and epitopes (CITE-seq). To analyze these samples and how they change over time, this study implements a newly designed generalized linear model. It was adopted from an established method with a coefficient for time since ASCT to identify numerous genes and pathways with downward longitudinal trends, many of which have previously been implicated in SSc development, and may help further understand disease pathogenesis.  Our longitudinal differential gene expression analysis focused mainly on monocytes, which demonstrated strong downwards trends in multiple pathogenic genes/pathways. Specifically, nuclear factor-B (NFB)-driven inflammatory signaling was increased in jSSc monocytes at baseline compared to healthy controls, but decreased to match healthy monocyte levels over time following ASCT. We also note a sharp longitudinal reduction in jSSc monocyte expression of SERPINE1, a gene which has previously been implicated in SSc pathogenesis.This workflow describes immune reprogramming in three jSSc patients who underwent ASCT and introduces a statistically-justified framework for longitudinal single-cell modeling.

overall_design: CITE-seq was performed on three sets of blood samples from the patients undergoing ASCT and age- and sex- matched controls. 1.5 million cells from each patient sample (baseline before ASCT, 6 months post ASCT, 12 months post ASCT, 24 months post ASCT) with a 95% viability were first diluted and subjected to Fc receptor blocking by adding Human TruStain FcX to cells suspended in Cell Staining Buffer according to the manufacturer’s protocol. All four samples from each subject were stained with TotalSeq™-C Human Universal Cocktail, V1.0 (BioLegend, Cat No. 399905) and four individual hashtags (TotalSeq-C0251 antihuman hashtag 1: Cat # 394661, TotalSeq-C0252 antihuman hashtag 2: Cat # 394663, TotalSeq-C0253 antihuman hashtag 3: Cat # 394665, and TotalSeq-C0254 antihuman hashtag 4: Cat # 394667) in a single step. Stained samples were then washed three times to remove unbound antibodies, and then pooled together to load onto one single-cell sequencing reaction per subject. In other words, for each subject, all four timepoints were run on the same single-cell reaction. The entire process was carried out using the manufacturer’s protocol. The cDNA amplification step was carried out first, followed by SPRI selection to separate mRNA-derived and antibody-oligo-derived cDNAs. The mRNA-derived cDNA was then subjected to standard 10x genomics protocol for cDNA sequencing and library preparation all according to 10x Chromium Next GEM Single Cell 3' Kit v3.1, 4 rxns protocol (product number 1000269). These premade 10x 5-prime single-cell transcriptome libraries were then shipped off to Novogene (U.S., Sacramento Sequencing Center ,CA), where they were sequenced. FASTQ files were downloaded from their portal.

first: Julia

last: Elrod

first: Theresa

last: Hutchins

first: Anwesha

last: Sanyal

first: William

last: Townes


title: RhoA wild-type allele loss unleashes the cancer driver function of RhoA E40Q

city: Copenhagen

first: Jesper

middle: Bøje

last: Andersen

address: Ole Maaloes Vej 5

department: BRIC

country: Denmark

institute: University of Copenhagen

summary: Cancer hotspot mutations of unknown function often obscure the functional understanding of the molecular pathways underlying cancer formation and limit precision medicine progress. Here, we investigated unresolved driver functions of RhoA in Head and neck squamous cell carcinoma (HNSCC). Our investigation reveals that RhoA E40Q is a partial loss-of-function allele which paradoxically promotes tumorigenesis only in the absence of wild-type RhoA. Therefore, mice expressing RhoA E40Q specifically in keratinocytes lacking wild-type RhoA spontaneously developed squamous cell carcinoma and showed defective hair shafts formation. Mechanistically, RhoA E40Q expression in RhoA-deficient cells impaired genome maintenance as shown by increased nuclear foci of gh2AX, a marker for DNA double-strand breaks. This genomic instability was mirrored by reduced cellular fitness upon RhoA E40Q knock-in in MCF10A cells, a phenotype also observed in BRCA2 loss. These convergent data establish RhoA E40Q as an unusual, context-dependent oncogenic driver: a seemingly inactive variant that unleashes its tumor-promoting potential only when the wild-type allele is absent.

overall_design: The experiments include RNA-seq data from primary mouse keratinocytes of three genotypes: wild type, RhoA E40Q heterozygous, and RhoA E40Q homozygous, each with three biological replicates.

first: Qiuyue

last: Wang

first: Yuewan

last: Luo

first: Cord

last: Brakebusch


title: Single-cell profiling identifies rare normal mesenchymal-like urothelial cells associated with sarcomatoid urothelial carcinoma

city: Buffalo

first: Qiang

last: Li

state: NY

address: Elm and Carlton Streets

institute: Roswell Park Comprehensive Cancer Center

summary: The bladder urothelium is a stratified epithelium, categorized as basal, intermediate, and umbrella cells. While epithelial–mesenchymal transition is known to occur during bladder injury, regeneration, and sarcomatoid tumor formation, it remains unclear whether normal urothelial cells intrinsically possess a mesenchymal-like epithelial state. We analyzed scRNA-seq data of EPCAM+ urothelial cells from both mouse and human urothelium. Vimentin-positive cells were evaluated by immunostaining to determine their distribution in normal urothelial layers and sarcomatoid tumors. Here, we identified and characterized a rare population of mesenchymal-like urothelial cells, termed M-cells, representing ~1–3% of urothelial cells. M-cells co-express epithelial markers with mesenchymal and stemness genes and engage stem-associated transcriptional regulators. Lineage tracing with the Upk2-Cre mT/mG reporter mice confirmed their urothelial origin, excluding a fibroblast lineage. M-cells are enriched within the basal layer but present across all urothelial compartments. M-cells exhibit high transcriptional plasticity between basal cells and intermediate cells. In addition, we identified a 16-gene transcriptional signature uniquely expressed in M-cells but absent in fibroblasts. RNA deconvolution of MB49 tumors demonstrated strong enrichment of this signature, suggesting that MB49 tumors are more likely to represent sarcomatoid urothelial carcinoma rather than fibroblast-derived sarcoma. The clinical relevance of M-cells and the M-cell state was validated in primary human sarcomatoid tumors and their corresponding patient-derived xenografts. Together, these findings establish transcriptionally unique and rare mesenchymal-like cells within the normal urothelium as a novel highly plastic population with translational implications for both mouse and human sarcomatoid urothelial carcinoma.

overall_design: scRNA-seq profiling of normal bladder tissue from mouse models (male bladder fundus tissues collected from Upk2-Cre;mT/mG mice). Cells from 4 individual mice were pooled into a single library.

first: Justine

last: Jacobi

first: Dongbo

last: Xu


title: A non-canonical function of the tyrosine degradation enzyme FAH drives CDK4/6 inhibitor resistance in breast cancer II

first: Jonathan

middle: David

last: Lee

address: 3 Blackfan Circle, Rm. 424

institute: BIDMC

summary: Resistance to standard-of-care therapies remains a major clinical challenge in the treatment of the most common breast cancer, the hormone receptor–positive (HR+) subtype. Cyclin-dependent kinase 4/6 (CDK4/6) inhibitors improve outcomes in early-stage HR+ disease, yet many patients relapse. Resistance mechanisms of relapsed tumors include genetic alterations, but in many cases no genetic drivers are identified. Here, we investigated mechanisms underlying resistance to CDK4/6 inhibitors using breast cancer patient-derived models and tumors. We identified an unexpected, non-catalytic nuclear function of fumarylacetoacetate hydrolase (FAH), an enzyme in the tyrosine catabolism pathway, as a driver of resistance. FAH translocated to the nucleus upon CDK4/6 inhibition, where it interacted with cyclin-dependent kinase 9 (CDK9), and promoted resistance. Nuclear FAH was enriched in tumors from relapsed patients, and inhibition of CDK9 reversed FAH-mediated resistance. These findings establish nuclear FAH as a biomarker of resistance and revealed CDK9 as a therapeutic vulnerability in CDK4/6 inhibitor-resistant HR+ breast cancer.

overall_design: RNA-seq profiling of MCF7 control cells and FAH WT cells at day 3 of Abemaciclib treatment

first: Jenny

last: Hogstrom

first: Taru

last: Muranen


title: Lenvatinib-treated Tregs exhibit superior anti-inflammation effect in autoimmune diseases [skin]

city: Hangzhou

first: Zeyu

last: Ma

address: No. 3 Qingchun East Road

department: Department of Gastroenterology

institute: Sir Run Run Shaw Hospital, Medical School of Zhejiang University

summary: Adoptive transfer of regulatory T cells (Tregs) holds promise for treating autoimmune diseases (AIDs) such as inflammatory bowel disease (IBD), psoriasis, and rosacea, but its clinical application is hampered by the difficulty of generating sufficient stable and functional Tregs. Here, we identified a novel immunomodulatory function of the multi-kinase inhibitor lenvatinib (Lenv) in specifically promoting Treg differentiation without affecting other T helper cell subsets. Mechanistically, Lenv inhibited VEGFR/AKT signaling and activated Foxo1, thereby enhancing Foxp3 expression. Adoptive transfer of Lenv-treated Tregs (Lenv-Tregs) in murine models of IBD, psoriasis, and rosacea achieved superior alleviation of clinical symptoms and inflammation compared with vehicle-treated Tregs (Ctrl-Tregs). Our findings uncover a novel role for Lenv in Treg differentiation and provide a robust strategy to generate a considerable number of highly potent immunosuppressive Tregs for cell-based therapy against AIDs.

overall_design: skin lesions from psoriasis mice transferred with Ctrl-Tregs or Lenv-Tregs were collected for RNA-seq


title: Lenvatinib-treated Tregs exhibit superior anti-inflammation effect in autoimmune diseases

overall_design: LI samples from IBD mice transferred with Ctrl-Tregs or Lenv-Tregs were collected for RNA-seq


title: Nuclear transcriptome analysis-based verification of sample purity for Purkinje cell nuclei isolated by fluorescence-activated nuclear sorting (FANS).

city: Tallinn

first: Kert

last: Mätlik

address: Akadeemia tee 15

department: Department of Chemistry and Biotechnology

country: Estonia

institute: Tallinn University of Technology

summary: We employed fluorescence-activated nuclear sorting (FANS) or Purkinje cells from post-mortem brain tissue of individuals carrying an expanded CAG repeat in ATXN3 gene, a mutation causing spinocerebellar ataxia type 3 (SCA3). Purity of sorted samples was verified by comparing the nuclear transcriptome of Purkinje cell nuclei to the transcriptome of cerebellar granule cell nuclei and glial cell nuclei isolated from unaffected control individuals. The goal was to assess the stability of ATXN3 CAG repeat in pure Purkinje cell samples.

overall_design: Nuclei of Purkinje cells, cerebellar granule cells, astrocytes, oligodendrocytes and microglia, isolated from post-mortem human cerebellum, were labeled with cell type-specific probes and separated by Fluorescence-activated cell sorting. Genomic DNA and RNA were extracted from these isolated populations of cell nuclei and nuclear transcript levels were quantified using RNA-seq analysis. The resulting gene expression profiles were used to assess the purity of collected populations, analyzing cell type-driven clustering of RNA-seq datasets in principal component analyses, enriched expression of cell type-specific marker genes in the labeled population, as well as depletion of transcripts specific for other cell types.

first: Nathaniel

last: Heintz


title: Placental DNA methylation gene networks correlate with  wildfire-informed particulate matter exposure and child neurodevelopment outcomes.

city: Davis

first: Logan

middle: Allan

last: Williams

state: CA

address: 1275 Med Sci Dr

department: Medical Microbiology and Immunology

institute: University of California, Davis

type: Methylation profiling by high throughput sequencing

summary: Background: Particulate air pollution represents an increasingly prominent prenatal exposure in the western United States, particularly in regions afflicted with heightened wildfire severity. However, the epigenetic impact of these exposures on the placenta remains poorly characterized.  Objectives: We investigated whether prenatal exposure to particulate air pollution, from both ambient sources and wildfires, associate with coordinated alterations in placental DNA methylation networks.  Methods: We performed whole-genome bisulfite sequencing (WGBS) on 221 placentae from the MARBLES and B-SAFE, then performed comethylation network analysis to identify modules of correlated  DNA methylation associated with wilfire-informed particulate exposures  and neurodevelopmental outcomes.  Results: We identified 85 placental comethylation modules, 22 of which were significantly associated with prenatal air pollution exposures. Preconception and pregnancy exposures associated with distinct module sets. Pregnancy air pollution preferentially correlated with modules annotated to semaphorin signaling and cytoskeletal remodeling pathways, including SEMA3A and RND3. In contrast, preconception exposures were enriched for modules proximal to transcriptional regulators. Ten exposure-associated modules also correlated with child neurodevelopmental measures, including ASD diagnosis. These modules contained neurodevelopmentally relevant genes, including NHIP, AUTS2, EBF3, PLCB1, and SLIT2, and were enriched for synaptic and cell-cell signaling pathways. Conclusions: Prenatal air pollution exposure associates with temporally and source-specific placental methylation networks enriched for signaling pathways relevant to placental function and neurodevelopment. These findings support the placenta as an epigenetic interface linking air pollution exposure to altered developmental trajectories.

overall_design: Placenta DNA from 221 participants (85 reported here) from a prospective ASD cohort (MARBLES) and a wildfire exposure cohort (BSAFE) was isolated and subjected to whole-genome bisulfite sequencing. Variable maternal air pollution exposures (as estimated by geocoding) allowed for identification of a comehtylation network and differentially methylated regions associated wiht air pollution metrics. Remaining samples used in this study not described here can be found at GSE178206.

middle: A

first: Matthew

last: Kramer

first: Amanda

last: Goodrich

first: Sean

last: Raffuse

first: Elizabeth

last: Angel

first: Janine

last: LaSalle

first: Rebecca

last: Schmidt


title: Sexually Dimorphic Transdifferentiation of Endothelial Cells in Atherosclerosis

city: Chongqing

first: Qing

middle: Rex

last: Lyu

state: Chongqing

address: #118 Xingguang Avenue

department: Affiliated Chongqing General Hospital

institute: Chongqing University

summary: Aims: Sex differences in atherosclerosis are well recognized clinically, yet the underlying mechanisms remain incompletely understood. Given the pivotal role of endothelial cell (EC) dysfunction in atherogenesis, this study aimed to delineate and compare EC fate trajectories and uncover transcriptional networks driving atherosclerosis progression in males and females. Methods and results: EC-specific lineage-tracing mice (Apoe−/−/Cdh5-CreERT2/Rosa26-mTmG) of both sexes were generated. Following tamoxifen-induced Cre recombination, mice were fed a high-fat diet (HFD) to induce hypercholesterolemia and atherosclerosis. Single-nucleus RNA sequencing (snRNA-seq) of plaque-bearing aortae identified and validated nine distinct EC subpopulations. Differential abundance analysis using miloR revealed that female aortae were enriched for capillary and lymphatic ECs expressing Sox17, Myh11, Mki67, or Ly6a, whereas male aortae were enriched for ECs expressing Col8a1 and Fmo2. Fate inference by GeneTrajectory and single-cell lineage tracing demonstrated that approximately a quarter of GFP⁺ ECs transdifferentiated into adipocyte-like cells, smooth muscle cell (SMC)-like cells, and fibroblast-like cells. Female ECs exhibited a greater propensity for EC-to-SMC-like conversion, whereas male ECs showed a stronger inclination toward EC-to-adipocyte-like transition. Regulatory network analysis using pySCENIC identified Klf2 and Creb5 as key transcription factors governing EC fate decisions in atherosclerosis. Conclusions: Endothelial cells exhibit sex-specific transdifferentiation trajectories during atherosclerosis progression, contributing to distinct vascular phenotypes in male and female plaques and revealing potential targets for precision therapeutics.

overall_design: TeloHAEC is an immortalized endothelial cell line generated based on human aortic endothelial cells. This experiment aims to investigate the role of female hormone, estradiol (E2), in TeloHAEC. Since we are mimic the enviroment of in vivo atherosclerotic-prone environment, palmitric acids (PA) was supplied in the culture media.

first: Yuyan

first: Songmao

last: Wang

first: Cheng

last: Luo


title: A high-resolution RNA interaction atlas of Arabidopsis thaliana TUDOR STAPHYLOCOCCAL NUCLEASE 1 captured by in vivo iCLIP

city: Ciudad Autonoma de Buenos Aires

first: Maria

middle: Clara

last: Fontana

state: Buenos Aires

address: INTENDENTE GUIRALDES 2160, IFIBYNE

country: Argentina

institute: Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE)

summary: RNA-binding proteins (RBPs) are key regulators of the RNA life cycle, exerting broad effects on plant physiology and development. Their function relies on direct RNA interactions, making the identification of in vivo targets and binding patterns critical for understanding their regulatory roles. Here, we characterize the RNA-binding landscape of the Arabidopsis thaliana RBP TUDOR STAPHYLOCOCCAL NUCLEASE 1 (TSN1), previously implicated in stress responses in plants. Using an adapted individual-nucleotide resolution crosslinking and immunoprecipitation (iCLIP2) approach, we mapped TSN1 binding sites across the transcriptome and identified 1,504 direct RNA targets, predominantly protein-coding transcripts. Motif analysis revealed three enriched consensus sequences: a U-rich motif, an A-rich motif and a G/U-rich motif. Functional enrichment analysis of TSN1 targets showed significant associations with core metabolic processes, including photosynthesis, as well as hormonal pathways involved in plant immunity responses. Together, these data provide a high-resolution map of TSN1–RNA interactions that serves as a resource to explore TSN1-dependent role in gene expression regulation in plants.

overall_design: iCLIP2-seq profiling of the RNA interactome of GFP-tagged Tudor-SN1 (TSN1, AT5G07350) in an Arabidopsis thaliana wild-type (Columbia-0 / Col-0) background.

first: María

first: Martin

last: Lewinski

last: Iglesias

first: Dorothee

last: Staiger

first: Julieta

last: Mateos


title: Xenium dataset for "A conserved population of genetically defined striatal neurons gates opioid reward"

first: Jeremy

last: Day

summary: This dataset contains Xenium results for coronal mouse brain sections through the anterior/posterior extent of the nucleus accumbens.

overall_design: High throughput in situ RNA hybridization was performed with the 10X Genomics Xenium Analyzer using brain tissue from experimentally naïve mice, and includes sections from 2 male brains and 2 female brains (4 sections per brain).

first: Olivia

middle: R

last: Drake

first: Caroline

last: Fiore

first: Emily

last: Jorgensen

first: Catherine

last: Newman

first: Luke

last: Potter

first: Austyn

last: Trull

first: Lara

last: Ianov

first: Jamie

last: Peters

first: Jasper

last: Heinsbroek


title: DGCR8 promotes RNA polymerase II pause release independently of DROSHA [ChIP-seq]

city: Shanghai

first: ying

last: cai

address: Fudan University, 131 Dong'an Road, Shanghai

institute: Fudan University

summary: DiGeorge syndrome critical region gene 8 (DGCR8) is best known as the RNA binding subunit of the microprocessor complex required for canonical microRNA (miRNA) biogenesis. Whether DGCR8 also exerts a direct, microprocessor independent function in the RNA polymerase II (Pol II) transcription cycle remains unclear. Here, we combined rapid, acute protein depletion with nascent transcription profiling and uncovered a non-canonical role for DGCR8 in transcriptional control in mouse embryonic stem cells (mESCs). We found that DGCR8 broadly occupies promoters and transcription start sites (TSSs) with limited co occupancy by its catalytic microprocessor partner DROSHA. Acute DGCR8 depletion triggers an immediate, genome wide reduction in nascent RNA synthesis that is not phenocopied by acute DROSHA depletion. Mechanistically, DGCR8 loss decreases Pol II engagement at promoters and induces a pervasive blockade in promoter proximal pause release, indicating a direct requirement for DGCR8 in the transition to productive elongation. We further identified physical interactions linking DGCR8 to Enhancer of Rudimentary Homolog (ERH) and the elongation factor SPT5, and showed that acute ERH depletion similarly suppresses nascent transcription. Together, our data implicate a potential model in which promoter bound DGCR8 facilitates Pol II pause release through an ERH–SPT5 linked regulatory network, establishing DGCR8 as a non canonical regulator of the core transcription machinery.

overall_design: Examination of DGCR8 and ERH binding in dTAG-DGCR8 cells treated with DMSO or 100 nM dTAG for 24 hours.Examination of DROSHA binding in dTAG-DROSHA cells treated with DMSO or 100 nM dTAG for 24 hours.

first: Ying

last: Cai


title: Maternal obesity imprints methylation marks in oocytes to drive intergenerational metabolic dysfunction

city: Nanjing

first: YIQIU

last: WU

state: Jiangsu

address: LongMian Road

institute: Nanjing medical university

summary: Maternal obesity predisposes offspring to metabolic disease, yet how oocytes transmit this risk remains unclear. In the present study, genome-wide profiling revealed that maternal obesity induces locus-specific DNA methylation changes in oocytes. Of them, a subset of metabolic genes, particularly Hnf1α, Thra, and Pdk4, exhibited persistent transcriptional dysregulation across two successive generations. Notably, aberrant methylation at these loci was erased during embryogenesis but re-established postnatally in both germline and somatic tissues, supporting the concept of “methylation memory”. At single-CpG resolution, we identified methylation landmarks at three metabolic loci that strongly correlated with gene expression. Furthermore, by employing methylation-edited mouse model, we demonstrated that targeted oocyte hypermethylation at Hnf1α enhanced hepatic gluconeogenesis in the offspring, whereas Pdk4 hypermethylation impaired muscle glucose tolerance, both in a female-specific manner. Similarly, the elevated methylation of HNF1A and THRA was observed in oocytes from obese women. In sum, our findings provide direct causal evidence that germline methylation at defined loci can drive metabolic reprogramming across generations, highlighting the pre-conceptional period as a critical window for potential intervention in humans.

overall_design: Methylation profiling by high throughput sequencing

first: Longsen

last: Han

first: Yiqiu

last: Wu

first: Jiashuo

last: Li


title: Crosstalk Between Acetylation and Ubiquitination Contributes to PRMT1 methyltransferase Homeostasis

city: Philadelphia

first: George

last: Burslem

address: 422 Curie Blvd., 1013 Stellar-Chance Bldg.

institute: University of Pennsylvania

summary: PRMT1 plays pivotal roles in normal and disease biology. Understanding its regulation is crucial for therapeutic targeting. We demonstrate that p300-mediated acetylation of PRMT1 at K228 triggers degradation via FBXL17-dependent ubiquitination at K145. Using mass spectrometry, cellular biochemistry, and genetic code-expansion, we reveal the crosstalk between acetylation and ubiquitination in PRMT1 homeostasis, highlighting mechanisms governing protein stability. This study results in Identification of K228 acetylation and K145 ubiquitination sites on PRMT1, FBXL17 as the E3 ligase mediating PRMT1 ubiquitination and interdependence of p300 acetylation and FBXL17 ubiquitination in PRMT1 degradation. We have used Co-IP MS to look for protein-protein interactions (e.g., PRMT1-FBXL17/p300 complexes), IP-MS to map  Acetylation/ubiquitination sites (PRMT1 post-translational modifications) and genetic code-expansion (site-specific incorporation of acetyl-lysine)

overall_design: RNA-seq profiling was done in HEK293T cells in vector control and PRMT1 overexpressed conditions

first: Mohd

last: Altaf Najar

first: Jenna

last: N. Beyer

first: Callie

last: Crawford

last: M. Burslem


title: DGCR8 promotes RNA polymerase II pause release independently of DROSHA [PRO-seq]

overall_design: dTAG Cells were treated with DMSO or dTAG-13 for 3h.


title: DGCR8 promotes RNA polymerase II pause release independently of DROSHA [TT-seq]

overall_design: dTAG Cells were treated with DMSO or dTAG-13 for 3h. Add 4SU directly to the tissue culture medium to a final concentration of 500 μm. Incubate the cells with 4SU for 15 min.


title: Prenatal Alcohol Exposure Selectively Induces Gut Microbiota Alterations in male adolescent C57Bl/6 Mice

city: Florence

first: Sara

last: Bertorello

address: Viale Gaetano Pieraccini 6

country: Italy

institute: University of Florence

summary: Background: Alcohol consumption during pregnancy may cause a complex syndrome known as Fetal Alcohol Spectrum Disorders (FASD), characterized by lasting physical, cognitive, and behavioral impairments. While several mechanisms and potential treatments have been identified, no cure exists for FASD. Recent studies indicated that gut microbiome (GM) research could lead to promising diagnostic or therapeutic option. However, the GM’s role in FASD is still poor explored. This study aimed to examine how early PAE affects the GM of adolescent offspring to identify potential targets for early diagnosis or treatment. Methods: Female C57Bl/6 mice were exposed to 10% ethanol solution during the first 10 days of pregnancy, and then to water for the rest of gestation (PAE group). Control mice received only water throughout their entire pregnancy (Control group). Fecal and blood samples were collected to analyze GM composition and short-chain fatty acids (SCFAs), using 16S rRNA gene sequencing and gas chromatography-mass spectrometry. Results: PAE mice showed a significant reduction in alpha diversity and notable changes in beta diversity of their GM compared to controls. Gender analysis revealed that PAE males had distinct microbial genera compared to controls, with significant increases in Bacteroides, Bilophila and Clostridioides. Moreover, fecal analysis in males revealed higher levels of isobutyric, isovaleric, and 2-methylbutyric acids—metabolites known for their anti-inflammatory properties. Conclusions: These results suggest that PAE causes sex-specific alterations in the microbiota-gut- brain axis, highlighting the gut microbiota as a promising target for preventive or supportive therapies aimed at reducing the cognitive and behavioral impairments linked to FASD.

first: Simone

last: Baldi

first: Francesco

last: Cei

first: Antonino Iurato

last: La Rocca

first: Valentina

last: Scianaro

first: Gianluca

last: Bartolucci

first: Guido

last: Mannaioni

first: Elisabetta

last: Gerace

first: Amedeo

last: Amedei


title: Premature birth and cesarean section affect neonatal CD4+ T cell gene expression and cellular function

city: Cuernavaca

first: LInda

middle: AImara

last: Kempis

state: Morelos

address: Avenida Universidad 1001

department: CIDC

country: Mexico

institute: UAEM

summary: Premature birth and cesarean section are major perinatal factors influencing immune development and are associated with increased morbidity and inflammatory diseases. However, their impact on neonatal adaptive immunity remains incompletely understood. To determine how gestational age and mode of delivery shape early immune programming, we analyzed CD4⁺ T cells, central regulators of adaptive responses, from preterm neonates (28–36 wga) and full-term neonates delivered by cesarean section or natural birth. We performed transcriptomic profiling by mRNA sequencing, complemented by functional assessment of T cell activation, proliferation, and cytokine production following stimulation. The mode of delivery exerted a dominant effect on the CD4⁺ T cell transcriptome and function. CD4⁺ T cells from full-term neonates delivered by natural birth exhibited an immune activation signature compared with those from cesarean section and produced higher levels of multiple cytokines, but showed reduced proliferative capacity.  In contrast, prematurity induced modest changes in basal gene expression relative to full-term cesarean section neonates. Despite these limited transcriptional differences, CD4⁺ Tcells from preterm neonates displayed enhanced proliferation and increased secretion of inflammatory cytokines IL-13, TNFα, IL-6, and IL-17F, indicating heightened responsiveness. Collectively, our findings suggest that CD4⁺ T cell immune programming begins in utero, as preterm neonates exhibit heightened inflammatory responsiveness. At term, the mode of delivery further refines this developmental trajectory. Cesarean section is associated with a restrained functional profile, whereas natural birth induces an immune activation signature and enhanced cytokine production. These results provide functional evidence that neonatal CD4⁺ T cell trajectories are established during fetal life and subsequently modulated at birth, underscoring the layered influence of perinatal factors on immune development.

overall_design: RNA-seq analysis was performed on 11 biological samples from human neonatal naïve CD4⁺ T cells, comprising three samples from full-term neonates delivered by natural birth, four from full-term neonates delivered by cesarean section, and four from preterm neonates delivered by cesarean section.

first: Carlos Jesús

last: Ventura-Martínez

first: Linda Aimara

last: Kempis-Calanis

first: Sebastian

last: Mijares-Guevara

first: Alejandra

last: Cedillo-Baños

first: Ingrid Yaritzit

last: Carreón-Cortés

first: Darely Yarazeth

last: Gutiérrez-Reyna

first: Stephania

last: Vázquez-Rodríguez

first: Addy Cecilia

last: Helguera-Repetto

first: Claudine

last: Irles

first: Salvatore

last: Spicuglia

first: Otoniel

last: Rodríguez-Jorge

first: María Angélica

last: Santana


title: Mitochondrial DNA mutation triggers early-onset intestinal epithelial cell dysfunction during acute colitis [mtscATAC-seq]

first: Guo-shi

last: Chai

state: --- Select One ---

address: No. 600 Dunyu Road, Sandun Town, Xihu District, Hangzhou, Zhejiang PR China

institute: Westlake University

summary: Mitochondrial DNA (mtDNA) mutations cause multisystem disorders, involving gastrointestinal (GI) dysfunction. However, the mechanism underlying the selection against mutant mtDNA and the impact of pathogenic mtDNA mutations on intestinal epithelial cells (IECs) remain unclear. Here, we employed mitochondrial single-cell assay for transposase-accessible chromatin with sequencing (mtscATAC-seq) to examine the heteroplasmy of IECs in m.G5081A (mt-tRNA) and m.G12918A (mt-mRNA) mutant mouse models over a two-year lifespan. Our findings reveal age-dependent purifying selection against mutant mtDNA across nine IEC subtypes, a process originating in intestinal stem cells (ISCs) that does not strengthen during cellular differentiation. Combining the analysis of single-cell RNA sequencing, we found that young mice with high m.G5081A mutation loads exhibit IEC dysfunction, including impaired enterocyte differentiation and defective Paneth cell granule formation. The m.G5081A mutant mice exhibit increased susceptibility to DSS-induced acute colitis due to compromised intestinal barrier function and impaired wound healing caused by the mtDNA mutation. Collectively, our findings reveal the cellular dynamics of mtDNA selection in IECs and demonstrate the functional consequences of mitochondrial dysfunction on intestinal health, providing insights relevant to mitochondrial disease pathogenesis and management.

overall_design: Single epithelial cells were sorted through FACS and fixed with formaldehyde and lysed, and the library was constructed with 10x Chromium Next GEM Single Cell ATAC Kit v2.

first: Qian

last: Zhang

first: Xiaoling

last: Deng

first: Guoshi

first: Min

last: Jiang


title: An In Vitro Exhaustion Model for Vγ9Vδ2 T Cells: Characterization and Reactivation Strategies for Advancing Immunotherapy Development

city: NANTES

first: Emmanuel

last: SCOTET

state: Loire Atlantique

address: IRS UN, 8 quai Moncousu

country: France

institute: Emmanuel SCOTET

summary: Recent advancements in cancer immunotherapies have highlighted the potential of Vγ9Vδ2 T cells as key players in the immune response against cancer. These cells, initially recognized for their broad activity in combating infections and tumors, are now emerging as promising candidates for targeted immunotherapeutic strategies, including T cell Engagers (TCEs). However, like other immune cells, Vγ9Vδ2 T cells can enter a state of dysfunction and exhaustion within the tumor microenvironment, driven by factors such as TCR overstimulation, immunosuppressive cytokines (e.g., TGF-β), and hypoxia. While the mechanisms of T cell exhaustion have been extensively studied in in vivo CD8+ T cells, the lack of a murine Vγ9Vδ2 subset complicates the investigation and generation of large numbers of exhausted Vγ9Vδ2 T cells. To address this, we present a novel in vitro protocol for rapidly generating exhausted Vγ9Vδ2 T cells through co-culture with Zoledronate activated human tumor cells. We characterized the resulting cells using phenotypic, metabolomic, and transcriptomic analyses, comparing their profiles to published data on in vivo-exhausted cells. Furthermore, we measured the reactivation potential of these exhausted Vγ9Vδ2 T cells using anti-CD3 monoclonal antibodies, demonstrating that CD3 stimulation can partially reverse exhaustion and restore anti-tumor effector functions. Furthermore, exhausted Vγ9Vδ2 T cells retained some cytotoxic activity upon stimulation with T Cell Engagers, underscoring the versatility and applicability of our in vitro exhaustion model. This model offers a robust platform for the evaluation of novel immunotherapies targeting Vγ9Vδ2 T cells, facilitating preclinical assessments before transitioning to in vivo studies.

overall_design: Bulk RNA-seq comparing αβ and expanded Vγ9Vδ2 T Cells after different exhaustion protocols

first: Morgane

last: Chauvet

first: Joseph

last: Léger

first: Mélanie

last: Laurent-Blond

first: Claire

last: Pecqueur

first: Christelle

last: Harly

first: Dorothée

last: Bourges

last: Scotet


title: Mitochondrial DNA mutation triggers early-onset intestinal epithelial cell dysfunction during acute colitis [scMultiome]

overall_design: Single epithelial cells were sorted through FACS and fixed with formaldehyde and lysed, and the library was constructed with 10x Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent.


title: Mitochondrial DNA mutation triggers early-onset intestinal epithelial cell dysfunction during acute colitis [scRNA-Seq]

overall_design: Single cells were sorted through FACS and the library was constructed with 10x Chromium Next GEM Single Cell 3' Reagent Kit.


title: Smoking effect on DNA methylation in human blood cell types (1)

city: Research Triangle Park

first: Xuting

last: Wang

state: NC

address: 111 TW Alexander Dr

institute: NIEHS/NIH

summary: Tobacco smoking alters DNA methylation profiles of immune cells which may underpin some of the pathogenesis of smoking-associated diseases. However, approaches linking smoking-driven epigenetic effects in specific immune cell types with disease risk are limited. We isolated six leukocyte subtypes, CD14+ monocytes, CD15+ granulocytes, CD19+ B cells, CD4+ T cells, CD8+ T cells, and CD56+ natural killer cells, from whole blood of healthy adult smokers and nonsmokers for epigenome-wide association study (EWAS).

overall_design:
As part of the Epigenetic Biomarkers of Tobacco Smoke Exposure project, a group of healthy volunteers (69 smokers and 74 nonsmokers) was recruited at the NIEHS Clinical Research Unit (protocol 10-E-0063) between March 2013 and January 2018 from the Raleigh, Durham and Chapel Hill, NC area. All nonsmokers were self-reported as not having smoked >100 cigarettes in their lifetime. Smokers reported their average daily cigarette consumption for the past 3 months [Su D et al. 2016].   For each individual, granulocytes were isolated directly from whole blood using CD15 Dynabeads (Invitrogen, Waltham, MA), magnetic beads covalently coupled with an anti-human CD15 antibody, according to the manufacturer’s protocol. Additionally, whole blood was layered on Histopaque-1077 Ficoll medium in Accuspin™ Tubes (Sigma-Aldrich, St. Louis, MO) and density gradient centrifugation was performed to isolate the mononuclear layer.  Peripheral blood mononuclear cells (PBMCs) were then counted for viability and incubated with CD34 MicroBeads magnetic beads (Miltenyi Biotec, San Jose, CA).  CD34 negative cells were collected in the flowthrough, recounted on a Cellometer Auto T4 Bright Field Cell Counter (Nexcelom, St. Lawrence, MA), and incubated with CD14 Dynabeads to isolate CD14+ monocytes according to the manufacturer’s protocol.  Flowthrough (CD14-) cells were again counted and split by volume.  One half of the cells were incubated with CD19 PanB Dynabeads for isolation of CD19+ B cells. The other flowthrough half was split in two, with half incubating with CD4 Dynabeads (for CD4+ T cells) and half incubating in CD8 Dynabeads (for CD8+ T cells).  All flowthrough (CD19-, CD4-, or CD8- cells) was then combined and incubated with CD56 MicroBeads (Miltenyi Biotec) according to the manufacturer’s protocol to isolate CD56+ NK cells.
This submission has new data in addition to our previous dataset (GSE224807)

first: Michelle

last: Campbell

first: Douglas

last: Bell


title: Transcriptional changes and epigenetic landscapes in fetal hematopoietic stem and progenitor cells with DDX21 knockout [ATAC-seq]

city: Shatin

first: Hoi-Hung

middle: Hoi Hung

last: Cheung

state: NT

address: Rm.707, School of Biomedical Sciences, Area 39, The Chinese University of Hong Kong

department: School of Biomedical Sciences

country: Hong Kong

institute: The Chinese University of Hong Kong

summary: Fetal hematopoietic stem cells and their committed progenitors (HSPCs) are highly proliferative cells that rely on active ribosome biogenesis to support their rapid expansion during fetal hematopoiesis. Insufficient ribosome biogenesis, a pathological condition known as ribosomopathy, activates the p53 pathway and induces cell cycle arrest in immature progenitor cells, leading to disrupted hematopoiesis and erythroid aplasia (anemia). DDX21 is an RNA helicase that regulates ribosome biogenesis by modulating rRNA splicing, processing, and ribosomal protein transcription. To elucidate the role of DDX21 in hematopoiesis, we generated Ddx21 conditional knockout (Ddx21cKO) in hematopoietic cells by crossing Ddx21f/f with Vav1-Cre mice. The Ddx21cKO embryos showed defective hematopoiesis and decreased HSPC numbers and their committed progenitors (CMP, GMP, and MEP). In this study, transcriptional changes in E13.5 HSPCs were analyzed by RNA-seq. Epigenetic marks associated active chromatin (H3K4me3, H3K27ac) and repressive chromatin (H3K27me3, H4K4me1) were analyzed by CUT&Tag. Chromatin accessibility was analyzed by ATAC-seq, whereas chromatin occupancies by Ddx21 and Kdm5a were analyzed by CUT&Tag.

overall_design: ATAC-seq of E13.5 fetal liver LK cells (Lineage- Kit+) of WT (Ddx21f/f) and Ddx21 cKO (Vav1-Cre, Ddx21f/f) embryros. Live LK cells were FACS-sorted from fetal liver suspension.

first: Adrian On-Wah

last: Leung

first: Chang

last: Li

first: Albert


title: Single-cell profiling identifies rare normal mesenchymal-like urothelial cells associated with sarcomatoid urothelial carcinoma [bulk RNA-seq]

first: Qiang

summary: The bladder urothelium is a stratified epithelium, categorized as basal, intermediate, and umbrella cells. While epithelial–mesenchymal transition is known to occur during bladder injury, regeneration, and sarcomatoid tumor formation, it remains unclear whether normal urothelial cells intrinsically possess a mesenchymal-like epithelial state. We analyzed scRNA-seq data of EPCAM+ urothelial cells from both mouse and human urothelium. Vimentin-positive cells were evaluated by immunostaining to determine their distribution in normal urothelial layers and sarcomatoid tumors. Here, we identified and characterized a rare population of mesenchymal-like urothelial cells, termed M-cells, representing ~1–3% of urothelial cells. M-cells co-express epithelial markers with mesenchymal and stemness genes and engage stem-associated transcriptional regulators. Lineage tracing with the Upk2-Cre mT/mG reporter mice confirmed their urothelial origin, excluding a fibroblast lineage. M-cells are enriched within the basal layer but present across all urothelial compartments. M-cells exhibit high transcriptional plasticity between basal cells and intermediate cells. In addition, we identified a 16-gene transcriptional signature uniquely expressed in M-cells but absent in fibroblasts. RNA deconvolution of MB49 tumors demonstrated strong enrichment of this signature, suggesting that MB49 tumors are more likely to represent sarcomatoid urothelial carcinoma rather than fibroblast-derived sarcoma. The clinical relevance of M-cells and the M-cell state was validated in primary human sarcomatoid tumors and their corresponding patient-derived xenografts. Together, these findings establish transcriptionally unique and rare mesenchymal-like cells within the normal urothelium as a novel highly plastic population with translational implications for both mouse and human sarcomatoid urothelial carcinoma.

overall_design: Bulk RNA-seq profiling of normal  and SARC intravesical bladder tumor tissue from mouse models (MB49)

first: Justine

last: Jacobi

first: Dongbo

last: Xu


title: Plasma microRNA profile in infertile patients with adenomyosis, infertile control and fertile control

city: Valencia

first: Ana

last: Corachán

state: València

address: Avenida Fernando Abril Martorell, 106, torreA, Planta 7

institute: IVIRMA Global Research Alliance, IVI Foundation, IIS La Fe

type: Non-coding RNA profiling by high throughput sequencing

summary: Background: Despite advancements in imaging techniques, the non-invasive diagnosis of adenomyosis remains particularly challenging due to the overlap of imaging features with other uterine diseases, and the lack of consistent correlation with clinical presentation limits its diagnostic value, being histological confirmation after hysterectomy still necessary. In this context, circulating miRNAs emerge as promising candidates for accurate non-invasive diagnosis. The study aims to determine, using miRNA sequencing, whether patients with adenomyosis exhibit a differential circulating miRNA plasma profile that can be used as a diagnostic marker.

overall_design: Plasma samples were collected in the secretory phase from patients undergoing hormone replacement therapy, and processed to obtain plasma. Total RNA was extracted, libraries were prepared using NEXTFLEX® Small RNA-Seq Kit v4, and miRNAseq was performed on the NextSeq 550 NGS platform.

first: Mar

last: Pérez-Ferrer

first: Amparo

last: Faus

first: Pilar

last: Alamá

first: Camen

last: Vidal

first: Juan

last: Giles

first: Antonio

last: Pellcer

first: Juan Antonio

last: García Velas

first: Hortensia

last: Ferrero


title: Whole-genome microarray profiling of nutrient-deprived medium (NDM) in human PANC-1 pancreatic cancer cells

city: Numazu

first: Takefumi

last: Onodera

address: 18-24 Miyamoto

department: Numazu

country: Japan

institute: Institute of microbial chemistry

summary: Pancreatic ductal adenocarcinoma cells often encounter nutrient deprivation in the tumor microenvironment and are thought to adapt by altering the expression of multiple genes. However, comprehensive time-resolved profiling of transcriptional responses under nutrient-deprived conditions remains limited. Here, we performed whole-genome microarray expression profiling to characterize gene expression changes in the human pancreatic cancer cell line PANC-1 cultured in nutrient-deprived medium. The dataset captures dynamic nutrient stress–associated gene sets and metabolic remodeling, including induction of genes linked to pentose phosphate pathway–related adaptation (e.g., TKTL1). This dataset provides a resource for studying transcriptional dynamics underlying pancreatic cancer cell survival under nutrient deprivation.

overall_design: PANC-1 cells were cultured under standard conditions and then switched to nutrient-deprived medium. Total RNA was harvested at 0, 3, 6, 12, 24 and 48 hours after the medium change, and gene expression was measured using Agilent Whole Human Genome 4×44K v2 microarrays (one-color). The study includes 14 arrays in total (0 h, n=4; 3, 6, 12, 24, 48 h, n=2 each). For the differential expression analysis reported in the associated manuscript, late time points (12, 24, and 48 h) were combined and compared against 0 h. Supplementary processed files include a DEG list generated in GeneSpring GX after re-normalization within the subset of samples used for this comparison (0 h plus 12, 24, 48 h; n=10).

first: Onodera

last: Takefumi

first: Momose

last: Isao


title: Targeting mutation-agnostic disease pathways ameliorates ciliopathy-related mesenchymal drift in RPE

city: Bethesda

first: David

last: McGaughey

state: MD

address: 10 Center Dr

department: NEI

institute: NIH

summary: Ciliopathies  are a family of disorders involving mutations in over 150 genes affecting the primary cilium, with retinal degeneration as a prominent feature driven by concomitant developmental and maturation defects in photoreceptors and the retinal pigment epithelium (RPE). Current single-gene-targeted therapeutic approaches are expensive with limited scalability. We hypothesized that downstream of primary cilium dysfunction, mutation-agnostic shared pathways initiate tissue defects. To test this hypothesis, we developed induced pluripotent stem cell-derived RPE models (iRPE) from multiple (BBS1, BBS10, BBS16, CEP290, LCA5, MYO7A, PRPF31) ciliopathy patients with severe retinal degeneration. Despite varying in severity, consistent with the structural ciliary defects, all ciliopathy iRPE displayed abnormal epithelial polarization and mitochondrial health initiated by dysregulated TGF-B signaling driven mesenchymal drift. Addressing these gene-agnostic disease phenotypes, our study identifies two drugs, Pioglitazone, a mitochondrial metabolic modulator, and Galunisertib, a TGFBR1 inhibitor, as potential therapeutic candidates for multiple ciliopathy subtypes.

overall_design: RNA Sequencing of ciliopathy iPSC-derived RPE. Lines included: CTRL,  BBS1, BBS10, CEP290, MYO7A, BBS16, LCA5 and PRPF31 patient derived lines. Cells after 5 weeks of maturation. And the data of CTRL, BBS10, LCA5 and CEP290 lines trated with and without Pioglitazone and Galunisertib for 4 weeks.

first: Dominik

last: Reichert

first: Kapil

last: Bharti


title: CD73 inhibition overcomes adaptive immune resistance to PARP inhibition in models of prostate cancer

city: Chicago

first: ping

last: xie

state: IL

address: 300 E Superior St, Tarry 4-726

institute: Northwestern University Feinberg School of Medicine, Chicago , Illinois, US

summary: Metastatic castration-resistant prostate cancer (mCRPC) remains a major cause of cancer-related mortality in the male population. While poly(ADP-ribose) polymeraseinhibitors (PARPi) are approved for selected mCRPC patients with homologous recombination repair (HRR) deficiencies, combinations with PD-1/PD-L1 inhibitors immunotherapy have demonstrated limited efficacy in unselected populations. To investigate the immunomodulatory effects of PARPi in an unbiased manner, we performed bulk RNA sequencing on HRR-proficient MyC-CaP cells treated with PARPi Olaparib or control vehicle. Pathway enrichment analysis revealed a marked upregulation of CD73 (NT5E), an emerging immune checkpoint ectoenzyme that generates extracellular adenosine, suggesting an adaptive mechanism that undermines PARPi efficacy and enables unwanted immunosuppression. CD73 induction by PARPi was confirmed in both human and mouse prostate cancer cell lines, with more pronounced effects in the HRR-compromised PTEN knock-out (KO) cells. Mechanistically, Olaparib-driven CD73 expression was mediated through the DNA damage-activated ATR-CHEK1-IRF1 and TGF-β1-ΑΚΤ signaling pathways. Concurrently, PARPi enhanced tumor cell immunogenicity by activating the type I interferon pathway and antigen presentation machinery. In vivo, combining Olaparib with CD73 blockade therapy delayed tumor growth, improved T-cell infiltration, and augmented antigen-specific CD8⁺ T-cell effector function across HRR-proficient and PTEN KO prostate cancer models. These findings highlight PARPi-induced CD73 upregulation as a novel resistance mechanism and support PARPi plus CD73 blockade as a promising therapeutic strategy for mCRPC, irrespective of HRR status.

first: Ping

last: Xie

first: Renqiang

last: Ma

first: Minghui

last: Zhang

first: Jie

last: Fan

first: Longzhen

last: Song

first: Yong

last: Wan

first: Bin


title: MEX3B leads to aberrant expression of VCAN aggravating the thoracic aortic dissection by contributing to the phenotype transformation of VSMCs

city: Hangzhou

first: Fan

last: He

address: No.50 Majiaqiao Street

institute: Zhejiang University

summary: To investigate the differentially expressed genes of mice with TAD, we collected aortic tissues for sequencing.

overall_design: Three-week-old mice were fed a normal diet and exposed to water containing 1g/kg/d β-aminopropionitrile monofumarate for 4 wk. At 7-week-old, osmotic mini pumps administering 1 μg/kg per min angiotensin II were implanted subcutaneouslly.  Mice were euthanized 24 h after implantation. RNA-seq profiling analysis of aortic tissues in TAD and control groups were further perfomed.


title: in vivo proximity-based mapping of subcellular proteomes, transcriptomes, and RNA structuromes

first: Jiapeng

last: Liu

address: Yueyang Road 320

department: SIBCB

institute: CEMCS, CAS

summary: Understanding the spatial organization of biomolecules in living organisms is a central but challenging goal in biology. Here we introduce Peroxidase Reactions Activated by D-amino Acids (PRADA), which uses an engineered oxidase to convert non-proteinogenic D-amino acid into H2O2 for in situ activation of a genetically fused peroxidase. PRADA enables versatile proximity-based chemistries, including protein labeling, RNA labeling, and functional polymer assembly, with minimal toxicity and background. We demonstrate that PRADA is broadly applicable inside living organisms, including flies, worms, fish, and mice. By further leveraging a unique RNA reactivity of PRADA, we develop a mutational profiling sequencing strategy for spatiotemporally-resolved mapping of RNA secondary structure. Application of this multifaceted PRADA platform in a mouse tumor model offered insights into its mitochondrial proteome, transcriptome, and RNA structurome, revealing distinct RNA folding pattern as a critical layer of mitochondrial gene expression regulation. Collectively, the application of PRADA in diverse systems holds promise to uncover the intricate organization of biomolecules in vivo.

overall_design: Labeled and enriched MITO-PRADA cell lines cultured in vitro and xenograft tumors in vivo, followed by library preparation.

first: Shuo

last: Han


title: A non-canonical function of the tyrosine degradation enzyme FAH drives CDK4/6 inhibitor resistance in breast cancer I

city: Boston

first: Jonathan

last: Lee

state: MA

address: 3 Blackfan Circle, Rm. 424

institute: BIDMC

summary: Resistance to standard-of-care therapies remains a major clinical challenge in the treatment of the most common breast cancer, the hormone receptor–positive (HR+) subtype. Cyclin-dependent kinase 4/6 (CDK4/6) inhibitors improve outcomes in early-stage HR+ disease, yet many patients relapse. Resistance mechanisms of relapsed tumors include genetic alterations, but in many cases no genetic drivers are identified. Here, we investigated mechanisms underlying resistance to CDK4/6 inhibitors using breast cancer patient-derived models and tumors. We identified an unexpected, non-catalytic nuclear function of fumarylacetoacetate hydrolase (FAH), an enzyme in the tyrosine catabolism pathway, as a driver of resistance. FAH translocated to the nucleus upon CDK4/6 inhibition, where it interacted with cyclin-dependent kinase 9 (CDK9), and promoted resistance. Nuclear FAH was enriched in tumors from relapsed patients, and inhibition of CDK9 reversed FAH-mediated resistance. These findings establish nuclear FAH as a biomarker of resistance and revealed CDK9 as a therapeutic vulnerability in CDK4/6 inhibitor-resistant HR+ breast cancer.

overall_design: RNA-seq profiling of T47D control cells and FAH knockout cells at day 3 of Abemaciclib treatment

first: Jenny

last: Hogstrom

first: Taru

last: Muranen


title: RACK1 maintains mouse hematopoietic stem cells by directly binding to and stabilizing LDB1

city: beijing

first: lijiao

last: deng

state: beijing

address: taipingroad

institute: beijing Institute of Basic Medical Sciences

summary: Hematopoietic stem cells (HSCs), with the capability of self-renewal and all blood lineages reconstruction, serve a crucial role in maintaining steady-state hematopoiesis within bone marrow during adulthood. The adaptor protein receptor for activated C kinase 1 (RACK1) has been implicated in the regulation of various transcription factors and signaling pathways by modulating their activation and/or stability. However, the specific role of RACK1 in the transcriptional control of HSC fates has not been previously elucidated. Here, we reported that RACK1 is enriched in adult mouse hematopoietic progenitors. Adulthood Rack1 deletion in IFN-I-responsive cells leads to rapid and profound hematopoietic failure and HSC loss. Furthermore, prenatal deletion of Rack1 in hematopoietic cells results in reduced and defective HSCs in the fetal liver. Such phenotypes result from cell-intrinsic defects with enhanced apoptosis of HSCs. Single-cell RNA sequencing indicates that adulthood Rack1 deletion in IFN-I-responsive cells leads to aberrant lineage-geneset-scores of transcriptional HSCs and the emergence of HSC-like cells. Mechanistically, RACK1 prevents HSC loss through maintaining the protein level of LDB1. The direct interaction between RACK1 and LDB1 stabilizes LDB1 through suppressing its ubiquitination and subsequent degradation.

overall_design: Bone marrow mononuclear cells of adult Rack1(F/F) and Rack1(F/F;Mx1-Cre) mice were subjected to MACS enrichment of c-Kit+ cells 12 days after poly(I:C) injection, followed by FACS sorting of live Lin−/lowc-Kit+ singlets. Live Lin−/lowc-Kit+ singlets from same genotype mice (n = 4 mice/sample) were spooled together and subjected to scRNA-seq

first: Lijiao

last: Deng

first: Junjie

last: Du

first: Jiyan


title: RACK1 maintains mouse hematopoietic stem cells by directly binding to and stabilizing LDB1 [scRNA-Seq]

overall_design: Bone marrow mononuclear cells of adult Rack1(F/F) and Rack1(F/F;Mx1-Cre) mice were subjected to MACS enrichment of c-Kit+ cells 6 weeks after poly(I:C) injection, followed by FACS sorting of live Lin−/lowc-Kit+ singlets. Live Lin−/lowc-Kit+ singlets from same genotype mice (n = 4 mice/sample) were spooled together and subjected to scRNA-seq


title: RNA-seq of PAPRi-resistant BRCA2-deficient cancer cells

city: North Chicago

first: Weihang

last: Chai

state: Illinois

address: 3333 N Green Bay Rd, IRP 257

department: Center for Genetic Diseases

institute: Rosalind Franklin University of Medicine and Sciences, Chicago Medical School

summary: Bulk RNA-seq of PARPi-resistant cells derived from ovarian cancer cell line PEO1, its parental cell PEO1, and PEO4 cells

overall_design: RNA-Seq Profiling of PEO1, PEO1-R (Olaparib resistant) and PEO4 cells without any treatment (Constitutive mRNA levels)

first: Qi-En

last: Wang

last: Li


title: Synovial transcriptomic response to intra-articular 2.5% polyacrylamide hydrogel in equine experimental osteoarthritis [RNAseq_SF]

city: Fort Collins

first: Steven

last: Dow

state: CO

address: 300 W Drake Rd

department: Clinical Sciences

institute: Colorado State University

summary: Background - Osteoarthritis (OA) represents one of the most common conditions treated by equine practitioners. Despite this high prevalence, no approved pharmacological intervention, biological therapy, or procedure prevents or reverses progressive destruction of degenerative joints. Intra-articular injectable polyacrylamide hydrogels (iPAAG), which consist of biocompatible non-degradable synthetic polymers, have been introduced with reported clinical efficacy. However, their potential mechanisms of action have not been fully investigated. Objectives – To determine differential gene expression in synovial tissues following intra-articular injection of 2.5% iPAAG in experimentally induced equine OA. Study Design – Prospective randomized placebo-controlled longitudinal cohort study.

overall_design: Methods - Osteoarthritis was induced in one middle carpal joint of 16 2 to 5-year-old horses (7 mares, 9 geldings) via surgical osteochondral fragment (OCF) induction; contralateral limb underwent sham operation. Horses were exercised 5 days/week, weeks 2-10 post-operatively. The OCF joint was injected with 2 mL 2.5% iPAAG or saline at 2 weeks (n=8 horses/group). Synovial biopsies (week 0,10) and synovial fluid (SF) were obtained (week 0,2,4,6,8,10). RNA was extracted from synovium and SF cells and subjected to transcriptomic sequencing to determine differentially expressed genes (DEG) and enriched pathways.

first: Lynn

last: Pezzanite

first: Lyndah

last: Chow