title: Rapamycin Reverses the Hepatic Response to Diet-Induced Metabolic Stress That Is Amplified by Aging.

city: La Jolla

first: Xue

last: Lei

state: CA

address: 10901 N Torrey Pines Rd

institute: SBP medical discovery institute

summary: Aging is associated with increased susceptibility to metabolic stress and chronic liver disease, yet the interactions between age and metabolic stressors and the potential for ameliorating interventions remain incompletely understood. Here, we examined the hepatic response of young (7-month-old) and old (25-month-old) C57BL/6 male mice to a 9-week high-fat diet (HFD) and assessed whether rapamycin, a well-established pro-longevity intervention, could mitigate age-exacerbated effects. While both age groups developed metabolic-associated steatohepatitis (MASH), older mice displayed more severe hepatic steatosis, inflammation, and transcriptional dysregulation. Transcriptomic profiling of whole livers and purified hepatocytes revealed that aging amplifies HFD-induced inflammatory and metabolic gene expression changes, including activation of immune pathways and suppression of metabolic pathways. Notably, treatment of aging mice with rapamycin reversed the majority of HFD-driven transcriptional alterations, including upregulation of pro-inflammatory regulators such as Stat1, and dysregulation of metabolic gene networks. Rapamycin also reduced hepatosteatosis, total body weight, and a tumorigenic transcriptomic signature associated with hepatocellular carcinoma risk. These findings demonstrate that aging intensifies hepatic sensitivity to dietary metabolic stress and identify rapamycin as a promising therapeutic to counteract age-related liver dysfunction and metabolic dysfunction-associated steatotic liver disease (MASLD) progression.

overall_design: Three cohorts were examined: normal diet (ND) + vehicle, high fat diet (HFD, 60% calories from fat) + vehicle and high fat diet + rapamycin (42ppm). Mice were initiated on either ND + vehicle or ND + rapamycin at 4-months of age. Once mice reached 18-months of age, they were either maintained on ND + vehicle, or HFD + vehicle, HFD + rapamycin for 9-weeks. Mice were maintained until euthanized and heptocytes were isolated using 2-step perfusion protocol.

first: Aaron

last: P. Havas

first: Adarsh

last: Rajesh

first: Peter

last: D. Adams


title: Senolytic approaches enhance chemotherapy immunogenicity in prostate cancer

status: Public on Jan 16 2026

city: Worcester

first: Marcus

last: Ruscetti

state: MA

address: 364 Plantation Street

department: MCCB

country: USA

institute: UMass Chan Medical School

type: Expression profiling by high throughput sequencing

summary: Cellular senescence is a common outcome of many standard-of-care cytostatic and cytotoxic cancer therapies. Whereas is some contexts therapy-induced senescence can drive tumor growth suppression and anti-tumor immune surveillance through the senescence-associated secretory phenotype (SASP), in others it can promote tumor progression, metastatic dissemination, and immune suppression. How the heterogeneous senescent phenotypes induced by different classes of cancer therapies directly impact tumor and immune responses, and whether understanding those mechanisms could be leveraged for effective combination therapies, has yet to be evaluated in a systematic manner. Here we compared the effects of various CDK inhibitor combinations, chemotherapies, and other DNA damaging agents commonly used in the treatment of advanced prostate cancer on senescence phenotypes in human and mouse prostate tumor models. We observed that while CDK inhibitors could induce senescence in MYC-driven prostate tumor cells, DNA-damaging chemotherapies and Aurora kinase inhibitors mediated a more robust senescence-mediated growth arrest and SASP program, which was paradoxically enhanced in the context of p53 and Rb tumor suppressor losses. The SASP produced by chemotherapy-induced senescence, and in particular with docetaxel, contained not only inflammatory factors that could influence innate immune responses, but also ECM remodeling factors that could facilitate tumor cell dissemination. Though docetaxel treatment could induce senescence and reduce tumor growth in syngeneic prostate cancer mouse models, it was not sufficient to activate anti-tumor immune surveillance or prevent metastatic dissemination. Use of senolytic therapies targeting anti-apoptotic BCL2 and IAP pathways upregulated after docetaxel-induced senescence could effectively clear senescent tumor cells. SMAC mimetic LCL-161 also induced immunogenic cell death capable to remodeling the inflammatory SASP to confer CD8+ T cell activation to further reduce tumor growth and even prevent metastasis in vivo. Our results suggest that combining senescence-inducing chemotherapies with senolytic agents can enhance the immunogenicity and anti-metastatic potential of standard-of-care chemotherapy used for treating prostate cancer patients.

overall_design: Myc-CaP murine prostate tumor cells were treated for 6 days continously with different senescence-inducing therapies. Bulk RNA-seq analysis was then performed in triplicate.

first: Lin

last: Zhou

first: Kai

last: Hu

first: Lihua

middle: J

last: Zhu


title: The Landscape of regulatory element evolution in Panicum hallii

city: Austin

first: TASLIMA

middle: E.

last: HAQUE

state: TX

address: J.T. Patterson Laboratories Bldg, 2415 Speedway

department: Department of Integrative Biology

institute: University of Texas at Austin

type: Genome binding/occupancy profiling by high throughput sequencing

summary: In this study, we use comparative genomics and chromatin accessibility profiling to study the molecular evolution of putative functional noncoding regulatory regions in Panicoid grasses.

sample_organism:
Panicum hallii var. filipes
Panicum hallii var. hallii

overall_design: Each experiment (RNASeq or ATACSeq) has three replicates of coastal and inland ecotype of Panicum hallii

first: Taslima

last: Haque

first: Bhaskara

last: Govinal Badiger

first: Robert J.

last: Schmitz

first: Thomas E.

last: Juenger


title: Chromosomal instability shapes the tumor microenvironment of esophageal adenocarcinoma via a cGAS–chemokine–myeloid axis

city: Oxford

first: Eileen

last: Parkes

address: Off Roosevelt Drive

department: Department of Oncology

country: United Kingdom

institute: University of Oxford

summary: Chromosomal instability (CIN), a pervasive feature of esophageal adenocarcinoma (EAC), drives tumor aggressiveness and metastasis. CIN stimulates the cGAS–STING pathway, typically linked to anti-tumor immunity. However, despite the high CIN burden in EAC, the cGAS–STING pathway remains largely intact. To address this paradox, we interrogated multiple esophageal cancer models, discovering myeloid-attracting chemokines – with CXCL8 as a prominent hit – as conserved CIN-driven targets in EAC. Using multiplexed immunofluorescence microscopy, we quantified ongoing CIN in human EAC tumors by measuring cGAS-positive micronuclei, validated by whole-genome sequencing. Coupling in situ CIN detection with single-nucleus RNA sequencing and multiplex immunophenotyping of human EAC, we link CIN to tumor-intrinsic innate immune activation, CXCL8 expression, and myeloid cell-mediated immunosuppression. In EAC patients, CIN-high, myeloid-dominated tumors correlate with poor outcomes and aberrant cGAS–STING signaling. These insights explain the counterintuitive maintenance of cGAS–STING and highlight disruption of the CIN–cGAS–inflammation axis as a potential therapeutic strategy in EAC.

overall_design: RNA-seq was performed on isogenic CP-A cell lines exhibiting distinct inherent levels of chromosomal instability (CIN). CIN was progressively induced through sequential CRISPR–Cas9-mediated depletion of TP53 (p53) and CDKN2A (p16), followed by overexpression of a dominant-negative form of the mitotic kinesin MCAK (dnMCAK). Serial genetic alterations were introduced independently across three clonal lineages. A Cas9-expressing parental CP-A clone was included as a control to account for potential confounding effects of Cas9 overexpression.

first: Bruno

last: Beernaert

middle: E


title: Selective modulation of murine intestinal M1 and M3 muscarinic receptor expression has divergent effects on specialized epithelial cells and body weight

city: baltimore

first: yang

last: song

state: MD

address: 670 W. Baltimore St.

institute: university of maryland in baltimore

summary: M1 and M3 muscarinic receptors encoded by CHRM1 and CHRM3 mediate neuronal and non-neuronal cholinergic signaling. Mice with global M3R deficiency reportedly weigh less than controls, but the cell type(s) involved are unknown. As the intestinal epithelium modulates nutrient absorption, we asked if deleting M1R and M3R only from intestinal epithelial cells would alter the distribution of specialized small intestinal epithelial cells or body weight. We reviewed reports of global M1R and M3R deficiency and body weight, used single cell RNA sequencing (scRNA-Seq) to assess Chrm1 and Chrm3 expression by small intestinal epithelial cells, created mice with conditional intestinal epithelial cell M1R and M3R deletion (CKO mice), and compared the distribution of specialized intestinal epithelial cells and body weights of CKO and control mice, and the development of enteroids. Prior weight comparisons commonly used only male mice, frequently without comparison to littermate controls. scRNA-Seq analysis of tissues from M1R and M3R floxed mice revealed robust Chrm1 and Chrm3 expression by enteric goblet cells. CKO mice with selective mucosal depletion of Chrm1 and Chrm3 RNA were viable, fertile, and had fewer small intestinal goblet cells than controls. M3R CKO mice had more tuft cells than controls. Although female mice weighed ~20% less than males, we detected no weight differences between M1R and M3R CKO and control mice; enteroids derived from these mice developed at the same pace. Intestinal epithelial cell M1R and M3R deficiency impacts the distribution of specialized intestinal epithelial cells but not murine body weight.

overall_design: C57BL/6 mice with selective knockdown of two different muscarinic receptor subtypes were used for the generation of organoids. Control mice were used for the generation of single cell suspensions. Additional analysis methods to validate the models and analyze cell subtype differences included included qPCR, immunohistochemistry, and single cell RNA sequencing

first: Natalia

last: Sampaio Moura

first: Alyssa

last: Schledwitz

first: Kunrong

last: Cheng

first: Yang

last: Song

first: Min

middle: S

last: Kwon

first: Cassandra

middle: A

last: Cairns

first: Lea-Pearl

last: Njei

first: Benjamin

last: Raufman

first: Cinthia

middle: B

last: Drachenberg

first: Jian-Ying

last: Wang

first: Bing

last: Ma

first: Jean-Pierre


title: ADAMTS7 promotes smooth muscle foam cell expansion in atherosclerosis

city: New York

first: Lauren

last: Fries

state: NY

department: Medicine

institute: Columbia University

summary: Human genetic studies have repeatedly associated ADAMTS7 with atherosclerotic cardiovascular disease. Subsequent investigations in mice demonstrated that ADAMTS7 is proatherogenic and induced in response to vascular injury and that the proatherogenicity of ADAMTS7, a secreted protein, is due to its catalytic activity. However, the cell-specific mechanisms governing ADAMTS7 proatherogenicity remain unclear. To determine which vascular cell types express ADAMTS7, we interrogated single-cell RNA sequencing of human carotid atherosclerosis and found ADAMTS7 expression in smooth muscle cells (SMCs), endothelial cells (ECs), and fibroblasts. We subsequently created SMC- and EC-specific Adamts7 conditional knockout and transgenic mice. Conditional knockout of Adamts7 in either cell type is insufficient to reduce atherosclerosis, whereas transgenic induction in either cell type increases atherosclerosis. In SMC transgenic mice, this increase coincides with an expansion of lipid-laden SMC foam cells and decreased fibrous cap formation. RNA-sequencing in SMCs revealed an upregulation of lipid uptake genes typically assigned to macrophages. Subsequent experiments demonstrated that ADAMTS7 increases SMC oxLDL uptake through increased CD36 levels. Furthermore, Cd36 expression is increased due to increased levels of PU.1, a transcription factor typically associated with myeloid fate determination. In summary, Adamts7 expression in either SMCs or ECs promotes SMC foam cell formation and atherosclerosis. In SMCs, ADAMTS7 promotes oxLDL uptake via increased PU.1 and Cd36 expression, thereby increasing SMC foam cell formation and atherosclerosis.

overall_design: Primary vascular smooth muscle cells collected from aorta of 8 week old male mice of either wild type or Myh11-Cre-ERT2 with Adamts7 overexpression

first: Allen

last: Chung

first: Hyun

middle: K

last: Chang

first: Huize

last: Pan

first: Esme

last: Dodge

first: Alexander

middle: C

last: Bashore

first: Karissa

last: Shuck

first: Caio

middle: V

last: Matias

first: Juliana

last: Gomez

first: Hanying

last: Yan

first: Mingyao

last: Li

first: Robert

last: Bauer


title: KMT2D maintains Treg homeostasis and protects against inflammatory diseases by regulating the purinergic channel P2X7

city: Zhengzhou

first: Peng

address: Science Avenue

country: China

institute: Zhengzhou University

summary: Regulatory T (Treg) cells are essential for maintaining immune homeostasis and tolerance through the prevention of inflammatory and autoimmune responses. The histone methyltransferase KMT2D is indispensable for induced Treg (iTreg) cell differentiation, its role in the differentiation and function of Treg cells in vivo has remained largely unknown. Here, we demonstrate that KMT2D is critical for the differentiation and function of effector activated Treg (aTreg) cells. We found that KMT2D deficiency in Treg cells impairs aTreg generation and exacerbates inflammatory conditions, such as allergic airway inflammation and colitis. Mechanistically, KMT2D regulates aTreg differentiation through TCR signaling. Furthermore, KMT2D modulates Ca2+ influx by promoting the expression of purinergic receptor P2X7 through H3K4me3 deposition. Collectively, our fundings highlight a pivotal role for KMT2D in Treg cell homeostasis and function, potentially offering a new therapeutic strategy for treating inflammatory diseases.

overall_design: Sorted Treg cells of the spleen form Foxp3YFP-CreKmt2dfl/fl(cKO) and Foxp3YFP-CreKmt2d+/+ mice to perform RNA-seq assay.


title: Tumor Cell Clustering Enhances Metastatic Competence by Regulating the H3K36 Histone Demethylase KDM2A [ChIP-Seq]

city: New Haven

first: Don

last: Nguyen

state: Connecticut

address: 310 Cedar Street

department: Pathology

institute: Yale University

summary: Disseminated tumor cells can form clusters via cell-cell adhesion, which increases their capacity to initiate metastasis. Metastatic clusters are characterized by distinct changes in transcription, suggesting that epigenetic mechanisms underlie their unique phenotypic state. By performingfunctional epigenomic studies in models of non-small-cell lung cancer, we identified the histone H3 lysine 36 (H3K36) demethylase KDM2A as being differentially required for the fitness of metastatic cell clusters. This contextual dependency on KDM2A is predicated by tumor cell-cell aggregation, which specifically induces KDM2A binding to CpG island enriched promoters. At these defined genomic loci, KDM2A maintains H3K36 monomethylation, which preferentially correlates with transcriptional activation. KDM2A directly targets oxidative phosphorylation genes and KDM2A activity is required for optimal mitochondrial respiration and apical cell junction integrity in cell clusters. Consequently, suppressing KDM2A reduces metastatic seeding and colonization in multiple organs, including in the brain. These findings reveal a chromatin regulatory mechanism by which homotypic cell communication instructs the epigenome of disseminated tumor cells to potentiate their metastatic competence.

overall_design: IP and input files for ChIP-sequencing of H3K27Ac, FLAG-KDM2A,  H3K36me1, H3K36me2, and H3K36me3 in H2030-BrM3 cells. FLAG-KDM2A IP is in cells expressing exogenous FLAG-tagged KDM2A. Methylation marks are done on control and cluster grown (H3K36me) and cluster grown (H3K27Ac) shControl and shKDM2A-1 cells. All cells treated with doxycycline.

first: Carolyn

last: Kravitz

first: Kiran

middle: D

last: Patel

first: Emily

last: Wingrove

first: Dejian

last: Zhao

first: Tang

last: Tang

first: Sampada

last: Chande

first: Yuchen

last: Huo

first: Thomas

middle: F

last: Westbrook

first: Qin

middle: X


title: DNA methylation-based classification of hematolymphoid neoplasms

status: Public on Jan 26 2026

city: Wantirna South

first: Rust

last: Turakulov

state: Victoria

address: u23 105 Mountain Hwy

department: Bioinformatics

country: Australia

institute: AGRF

type: Methylation profiling by genome tiling array

summary: Accurate pathological diagnosis is crucial for optimal management of cancer patients. For a number of hematolymphoid tumor entities, standardization of the diagnostic process has been shown to be particularly challenging - with substantial inter-observer variability in the histopathological diagnosis of many tumor types. Genome-wide DNA methylation profiling has been shown to contribute to accurate and precise tumor classification and diagnosis in several tumor types, including central nervous system neoplasms.  We herein present the development of a comprehensive approach for DNA methylation-based hematolymphoid tumor classification across most entities and age groups and demonstrate its application in a clinical setting, defining 44 methylation classes comprising a good proportion of recognized hematolymphoid tumor types. In several cases, methylation signatures separated recognized tumor types into subclasses that showed statistically significant and distinct patient outcomes.  We validate the classifier in independent samples that were not utilized in classifier development and show that the reliability of this method is highly accurate (concordance 97%) with a substantial impact on diagnostic precision in addition to standard methods.  We show a relationship of methylation class match scores with tumor purity, finding that high-tumor-purity samples are more likely to receive a high-confidence match with our classifier. Finally, we show the impact of the classifier in clinical practice, where classifier results resulted in a change in diagnosis in specific hematolymphoid neoplasms. For broader accessibility, a free and user-friendly online portal for access to the hematolymphoid tumor methylation classifier will be available for external users.

overall_design: The reference set from previously published and inhouse data was used to train classifier. The validation dataset asembled from previously published data and new samples processed inhouse and acquired from collaborators. Classification perfomace estimated on validation dataset.

first: Annapurna

last: Saksena

first: Christin

last: Siewert

first: Omkar

last: Singh

first: Zied

last: Abdullaev

first: Ting

last: Zhou

first: Jeremiah

last: Karrs

first: Drew

last: Pratt

first: Deanna

last: Riley

first: Shannon

last: Skarshaug

first: Valerie

last: Zgonc

first: Lana

last: Sultanaeva

first: Ruifeng

last: Teng

first: Liqiang

last: Xi

first: Andreas

last: von Deimling

first: Martí

last: Duran-Ferrer

first: José

middle: I

last: Martín-Subero

first: Elias

last: Campo

first: Stefania

last: Pittaluga

first: Mark

last: Raffeld

first: David

last: Capper

first: Elaine

last: Jaffe

first: Kenneth

last: Aldape


title: Identification and characterization of functional long noncoding RNAs in human fibroblast aging

status: Public on Jan 17 2026

city: Guangzhou

first: xiaojuan

last: teng

address: 2 Lujing Road, Yuexiu District, Guangzhou City

institute: Dermatology Hospital, Southern Medical University

summary: We sought to validate the function of PURPL using gain of function and loss of function assay during BJ cells senescence.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for C3H10T1/2 cells and its KD derivatives (shKDM4D, shNFIB, and shMLL1)

first: Xiaojuan

first: Jiajian

last: Zhou


title: Chromosomal instability shapes the tumor microenvironment of esophageal adenocarcinoma via a cGAS–chemokine–myeloid axis [RNA-seq]

first: Eileen

last: Parkes

overall_design: RNA-seq of cGAS-proficient (Cas9 expressing) and cGAS-deficient (CRISPR-Cas9-mediated cGAS KO) esophageal adenocarcinoma cell line clones (OE33 and SK-GT-4). Cells were treated with the MPS1 inhibitor reversine (pharmacological induction of chromosomal instability) or diluent (DMSO; control) for 48h.

first: Bruno

last: Beernaert


title: H3K27me3Alpha-Ketoglutarate Drives an Osteogenic and Extracellular Matrix Gene Program in Periodontal Ligament Fibroblasts via Selective Reduction of H3K27me3 [RNA-Seq]

city: Okayama

first: Shigeki

last: Suzuki

state: Okayama

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

department: Department of Operative Dentistry

country: Japan

institute: Okayama University

summary: Periodontal disease is a chronic inflammatory condition that destroys tooth-supporting tissues, particularly alveolar bone and the periodontal ligament, and effective regenerative therapies remain limited. While the role of metabolic-epigenomic crosstalk in determining cell fate is well established, the specific mechanism by which a tricarboxylic acid (TCA) cycle metabolite can modulate chromatin regulation to promote periodontal regeneration remains to be elucidated. The impact of one TCA-cycle metabolite, alpha-ketoglutarate (α-KG), was examined in human periodontal ligament fibroblasts cultured under osteogenic induction and profiled by ALP assays, RT-qPCR, analyses of multiple histone modifications, ATAC-seq, and RNA-seq. α-KG increased ALP activity and up-regulated genes associated with osteogenesis and the extracellular matrix (ECM). ATAC-seq revealed minimal genome-wide accessibility changes, whereas histone analyses showed reduced H3K27me3, consistent with an epigenetic mechanism that does not require extensive chromatin opening. The RNA-seq identified α-KG-induced 14 genes upregulated, including multiple components of the OGN-OMD-PLAP1/ASPN-ECM2 locus, supporting an osteogenic/ECM transcriptional program. In a mouse periodontal regeneration model, oral administration of α-KG enhanced alveolar bone regeneration and reduced H3K27me3 signals and collagen-rich tissue organization within the periodontal ligament space. These findings identify α-KG as a metabolite-driven epigenetic modulator that alleviates H3K27me3-mediated repression and supports periodontal regeneration.

overall_design: Examination of the effects of aKG on gene expression in human periodontal ligament cells

first: Ryu

last: Hasegawa


title: H3K27me3Alpha-Ketoglutarate Drives an Osteogenic and Extracellular Matrix Gene Program in Periodontal Ligament Fibroblasts via Selective Reduction of H3K27me3 [ATAC-Seq]

overall_design: Examination of the effects of aKG  on chromatin accessiblity in PDLF cells.


title: Effect of OGT knockdown on gene expression in KGN ovarian granulosa cells

city: Zhenjiang

first: Caifang

last: Ren

address: Xiangshan Road

institute: Jiangsu University

summary: This study aimed to elucidate the spatiotemporal expression pattern of O-GlcNAc transferase (OGT) and its catalyzed O-GlcNAc modification in ovarian tissues, and to investigate their specific functions in ovarian granulosa cells. To this end, high-throughput RNA sequencing was performed to analyze genome-wide transcriptional changes following OGT knockdown in the human ovarian granulosa cell line KGN. Two specific siRNAs targeting OGT (siOGT1 and siOGT2) and a negative control siRNA (siNC) were designed. Each group included two biological replicates, resulting in a total of six transcriptomic libraries. Sequencing was carried out on the Illumina NovaSeq 6000 platform with paired-end 150-bp reads. By comparing the siOGT-treated groups with the siNC control group, 300 and 487 differentially expressed genes (DEGs) were identified in the siOGT1 and siOGT2 groups, respectively, with 176 DEGs overlapping between the two groups. Pathway enrichment analysis indicated that OGT knockdown may affect pathways related to immune defense response, cellular reaction to external stimuli, and cytokine-mediated signaling. This dataset provides a transcriptomic profile of ovarian granulosa cells under OGT interference and serves as a key resource for further investigation into the regulatory mechanisms of the OGT/O-GlcNAc axis in ovarian physiology and pathology.

overall_design: To investigate the transcriptomic alterations following OGT knockdown, we transfected KGN ovarian granulosa cells with siOGT1 and siOGT2 separately, and harvested the samples for RNA-Seq analysis 48 hours post-transfection.


title: Mutant FGFR3 restricts bone yet expands brain via ERK-mediated self-repression

city: Shanghai

first: TongYe

last: Fu

address: 138 Yi Xue Yuan Road

institute: Fudan University

summary: FGFR3 gain-of-function mutations cause achondroplasia, the most common form of dwarfism, yet trigger paradoxical cerebral overgrowth and skeletal stunting. Here， we demonstrate that mutant FGFR3 drives enhanced ERK activation, which then represses Fgfr3 expression and downregulates ERK signaling. In the developing cortex, this mechanism transiently expands cortical stem cells by activating ERK, then shifts signaling to downregulate Fgfr3/ERK/PKA and enhance YAP/TAZ, promoting premature ependymal maturation and cerebral overgrowth. In growing bones, mutant Fgfr3 first elevates ERK to inhibit chondrocyte hypertrophy, then downregulates Fgfr3/ERK/PKA and upregulates YAP/TAZ to accelerate hypertrophy and ossification. Our findings establish that FGFR3 mutations limit bone yet expand brain size via an ERK negative feedback loop, revealing a unified disease mechanism and novel therapeutic targets.

overall_design: After deep anesthetizing the entire mouse, its brain/forelimb was immediately removed and immersed in ice-cold Hanks balanced salt solution (Gibco 14175-095). The dorsal cortex/humerus was dissected into small pieces and dissociated into single-cell suspensions using a papain cell dissociation kit (Miltenyi Biotec, catalog number 130-092-628) or collagenase type 2 according to the manufacturer's instructions. Single-cell RNA sequencing (scRNA-Seq) libraries were prepared using the Chromium droplet-based sequencing platform (10X Genomics), in accordance with the manufacturer’s guidelines (manual document part number: CG00052 Rev C). The cDNA libraries were purified, quantified using an Agilent 2100 Bioanalyzer, and sequenced on an Illumina HiSeq 6000.

first: Zhuangzhi

last: Zhang

first: Tongye

first: Zhengang

last: Yang


title: Regulatory elements of pancreas development license the initiation of pancreatic ductal adenocarcinoma.

city: Copenhagen

first: Luis

last: Arnes

address: Ole Maaløes Vej 5

country: Denmark

institute: Biotech Research & Innovation Centre

summary: Cellular plasticity and transitional cellular states are crucial for tissue regeneration across multiple organs. In the pancreas, oncogenic Kras hijacks this program, acting on tissue-specific enhancers to prevent the resolution of acinar-to-ductal metaplasia (ADM) and lock regeneration into a pro-inflammatory state that progresses to cancer. Enhancer transcription, an early event during cellular state transitions, can generate stable enhancer-associated long noncoding RNAs (lncRNAs) positioned near key transcription factors and chromatin contact boundaries, often enriched for disease-associated variants. While enhancer-associated lncRNAs have been implicated in transcriptional regulation and genome organization, their role in pancreas regeneration and cancer initiation has remained unexplored. In this study, we identified epithelial long noncoding RNAs (lncRNAs) and their target genes in PDAC precursor lesion formation. We demonstrate that LINC00673, expressed from a Sox9-associated super-enhancer during pancreatic development, is reactivated in PDAC. Conditional deletion of LINC00673 in the murine pancreatic epithelium accelerates resolution of ADM and significantly impairs PDAC initiation. Furthermore, we highlight a previously unrecognized role of transcribed super-enhancers in facilitating long-range gene regulation and genome organization during pancreatic cancer initiation. Our study identifies a critical function of LINC00673 in regulating both cell-autonomous and non-cell-autonomous processes during pancreas regeneration and Kras-driven cancer initiation. These findings reveal a novel regulatory layer linking developmental enhancer activity to pancreatic disease progression and highlight new therapeutic opportunities targeting regenerative programs at the earliest stages of neoplastic transformation.

overall_design: RNA sequencing was performed on pancreas of E15.5 embryos of WT (mLINC00673fl/fl) and conditional deletion (Pdx1Cre, mLINC00673fl/fl) of the mouse ortholog of LINC00673 (2610035D17Rik). Each replicate represents an independent animal.

first: Marta

last: Ballester

first: Anita

last: Kurilla

first: Yifan

last: Dai

first: Leire

last: Bergara-Muguruza

first: Katarzyna

last: Radke

first: Carlo

middle: H

last: Maurer

first: Elisa

last: Espinet

first: Kristina

last: Høj

first: Aida

last: Marisch Delgado

first: Philip

last: Seymour

first: Saynab

last: Omar

first: Charlotte

last: Vestrup Rift

first: Jane

last: Hasselby

first: Pia

last: Klausen

first: Peter

last: Vilmann

first: Ainara

last: Castellanos-Rubio

first: Izortze

last: Santin

first: Albin

last: Sandelin


title: Genome-wide binding sites of transcription factor RGSV P3 by DAP-Seq

city: Fuzhou

first: Baogang

last: Zhang

state: Fujian Province

address: No. 15 Shangxiadian Road, Cangshan District

institute: Fujian Agriculture and Forestry University

summary: This study maps the cistrome of RGSV P3 in Oryza sativa using DAP-Seq. Includes 2 libraries: treatment and input control.

overall_design: DAP-Seq was performed with RGSV P3 protein; Input as control. Peaks were called using MACS2  with default parameters against the input control.


title: Polyphosphate predicts and controls nanoparticle-induced antibiotic persistence

city: Beijing

first: Rui

last: Sun

address: No.19, Xinjiekouwai St

department: School of Environment

institute: Beijing Normal University

summary: Nanoparticles (NPs) have emerged as promising agents against persistent bacterial infections. However, repeated exposure to NPs paradoxically leads to a significant increase in persister populations. This effect is linked to the accumulation of polyphosphate (polyP) granules at the cell poles. These polyP granules act as regulatory factors by binding to the Lon protease, inhibiting protein translation, and serving as metal homeostasis agents that chelate harmful intracellular metals. Our findings reveal a novel polyP-based mechanism underlying NP-induced persistence, suggesting innovative therapeutic targets to counteract bacterial survival and adaptive evolution in clinical settings.

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

overall_design: Escherichia coli was cultured in LB medium at 37°C, 180 rpm, in the dark, until the stationary phase (20 h). A 1 mL cell suspension (108 CFU/mL) was collected and exposed to 30 mg/L AgNPs, 20 mg/L CuNPs, or 10 mg/L ZnO NPs. Another 1 mL cell suspension (107 CFU/mL) was collected and exposed to 100 mg/L Fe3O4 NPs, 100 mg/L CeO2 NPs, or 100 mg/L SiO2 NPs separately. The cells were then incubated in the dark for 4 h. After incubation, 100 μL of the mixture was transferred into 10 mL of fresh LB medium for a subsequent 20-h growth phase, completing one cycle. A total of 14 cycles were conducted. After 14 days of exposure to different NPs, the strains were named EAgNPs, ECuNPs, EZnO NPs, EFe3O4 NPs, ECeO2 NPs, and ESiO2 NPs. The ppk gene was knocked out in the EAgNPs strain, which was subsequently named EAgNPs(△ppk). Ewt represents the untreated control with no NP exposure.


title: Bulk RNA-seq of multi-tissue transcriptomes from control and DHEA-treated mice (ovary, uterus, thymus, brain, heart, intestine, kidney, liver and spleen)

city: haidian district

first: yao

last: feng

state: Beijing

address: No.38 xueyuan road

institute: Peking University

summary: To characterize systemic transcriptional changes induced by DHEA treatment, we performed bulk RNA-seq across a panel of tissues collected from control and DHEA-treated mice. Total RNA was extracted from each tissue using a kit-based workflow following mechanical homogenization in lysis buffer. RNA concentration/quality were assessed prior to library construction and high-throughput sequencing.

overall_design: Control and DHEA-treated mice were included. For each group, tissues were collected for transcriptomic profiling, including ovary, uterus, thymus, brain, heart, intestine, kidney, liver and spleen. Immediately after dissection, tissues were placed into lysis buffer, homogenized using a tissue homogenizer, and total RNA was purified using a commercial RNA extraction kit. Purified RNA was quantified and quality-checked, then submitted for bulk RNA-seq library preparation and sequencing.

first: Yaruo

last: Qiu

first: Yao

last: Feng

first: Dan

last: Lv


title: Multi-ome profiles of KP4 cells, a Pancreatic Ductal adenocarcinoma cell line

first: Lorenzo

last: Tomassoni

address: 1130 St Nicholas Avenue

summary: Cells from the KP4 cell line were subjected to single-cell ATAC-seq and scRNA-seq to question whether the PDA MAPK positive and negative states represent stable and epigenetically distinct cell states.

overall_design: Nuclei from KP4 were isolated and profiled by both gene expression and open chromatin using 10x Genomics Chromium Single Cell ATAC-Seq microfluidic cell processing.

first: Pasquale

last: Laise

first: Mikko

last: Turunen

first: Alvaro

last: Garcia

first: Carlo

last: Maurer

first: Ela

last: Elyada

first: Bernhard

last: Schmierer

first: Jeremy

last: Worley

first: Jordan

last: Kesner

first: Xiangtian

last: Tan

first: Ester

last: Fernandez

first: Xue

last: Yuanqing

first: Chen

last: Yining

first: Kelly

last: Wong

first: Urszula

middle: N

last: Wasko

first: Somnath

last: Tagore

first: Alexander

middle: L

last: Wang

first: Sabrina

last: Ge

first: Alina

last: Iuga

first: Aaron

last: Griffin

first: Winston

first: Gulam

last: Manji

first: Mariano

last: Alvarez

first: Faiyaz

last: Notta

first: David

last: Tuveson

first: Kenneth

middle: P

last: Olive

first: Andrea

last: Califano


title: Adipocyte C/EBPa is selectively required for gonadal white adipose tissue development

first: Lauren

last: Fries

summary: Obesity is associated with multiple metabolic comorbidities and continues to be prevalent in the developed world. It has been repeatedly shown that the distribution, not just amount, of excess white adipose tissue (WAT) in obesity correlates with a person’s risk for coronary artery disease and type 2 diabetes. Thus, understanding depot specific mechanisms of WAT development could shed light on mechanisms of metabolic disease. SNPs near the gene CEBPA, which encodes the transcription factor CCAAT/enhancer binding protein alpha (C/EBPa), have been associated by human genome-wide association studies with waist-to-hip ratio, suggesting CEBPA plays depot-specific roles in WAT. C/EBPa is a master regulator of adipocyte differentiation and metabolism, but its role in the development of specific WAT depots is not well understood. We generated mice with AdipoQ-Cre-driven adipocyte-specific Cebpa knockout (Cebpa_ASKO) and found that these mice have drastically reduced gonadal WAT (gWAT) mass. Meanwhile, inguinal WAT (iWAT) develops and is present in normal amounts. However, there are fewer and larger iWAT adipocytes and evidence of altered lipid metabolism, and Cebpa_ASKO mice fail to expand any of their white adipose depots when challenged with a high fat diet. Cebpa_ASKO mice also have multiple other metabolic phenotypes, including hypertrophic, lipid-laden BAT, increased hepatic triglycerides, and increased plasma cholesterol, and each phenotype worsens with prolonged high fat diet feeding. Taken together, these data point to C/EBPa playing depot-specific roles in adipose tissue development, as well as the importance of C/EBPa and visceral adipose tissue in maintaining metabolic homeostasis.

overall_design: Bulk RNA-seq of whole subcutaneous inguinal white adipose tissues (lymph nodes removed) from 3 female Cebpa_fl/fl; AdipoQ-Cre- and 3 female Cebpa_fl/fl; AdipoQ-Cre+ mice in a random fed state.

first: Krista

middle: Y

last: Hu

first: Esme

last: Dodge

first: Olivia

last: Maguire

first: Yu-Lin

last: Ma

first: Caio

last: Matias

first: Hector

last: Himede

first: Juliana

last: Gomez

first: Miriam

last: Cepeda

first: Robert

last: Bauer


title: A preclinical candidate of cyclophilin D inhibition improves alcohol-associated liver injury

first: Zhaoyi

last: Che

state: Guangdong

address: 601 Huangpu Avenue West

institute: Jinan university

summary: Currently, no therapies are approved for alcohol-associated liver disease (ALD). Here, we identify cyclophilin D (CypD) as a critical mediator in the progression of ALD. We observe elevated expression of CypD in ALD patients and a corresponding mouse model. Hepatocyte-specific knockout of CypD mitigates hepatic mitochondrial dysfunction, steatosis, inflammation, and oxidative stress. Conversely, overexpression of CypD exacerbates hepatic mitochondrial stress. In vivo and in vitro experiments demonstrate that a CypD inhibitor, RN-0001, effectively and safely alleviates hepatic damage induced by ethanol exposure; these protective effects are absent in CypD-deficient mice. Biophysical assays indicate that RN-0001 directly binds to CypD. Additionally, absorption, distribution, metabolism, excretion, and toxicity (ADMET) tests and first-in-human phase I clinical trial identify RN-0001 as a promising translational candidate for ALD therapy. Collectively, our study highlights the pathological role of CypD in ALD and introduces a translational candidate for its management. This study was registered at chictr.org.cn (ChiCTR2500106709).

overall_design: RNA-seq profiling was performed after the NIAAA chronic-plus-binge ethanol model (5+10 days) in Ctrl (CypD^flox/flox, control diet), ALD (CypD^flox/flox, ethanol diet), and Ppif_ALD (hepatocyte-specific CypD/Ppif knockout, ethanol diet) mice.

first: Jia

last: Xiao

first: Zhihui

last: Luo

first: Dong

first: Fashu

first: Haoxiong

last: Zhou

first: Yali

last: Song

first: Shanshan

last: Guo

first: Yuan

last: Yuan

first: Hao

last: Wang

first: Ching-Pong

last: Mak

first: Kwok-Fai

last: So


title: Chronic intermittent hypoxia mimicking sleep apnea reshapes the liver circadian metabolic architecture

city: Irvine

first: Kousha

last: Changizi

address: 4038 Donald Bren Hall

department: Computer Science

institute: University of California, Irvine

summary: Obstructive sleep apnea (OSA), characterized by chronic intermittent hypoxia (IH) during sleep, is increasingly recognized as a driver of metabolic dysfunction. However, its impact on circadian metabolic regulation remains poorly understood. Here, we investigated how chronic IH reshapes 24- hour hepatic and systemic metabolic programs in a mouse model mimicking OSA-associated hypoxia. Through integrated circadian transcriptomic, metabolomic, and physiological profiling, we show that four weeks of rest phase-restricted IH reprogram hepatic metabolism in a time-specific manner. This reorganization involves the coordinated circadian regulation of glucose, lipid, and redox pathways, with a shift away from oxidative metabolism and toward oxygen-sparing processes such as gluconeogenesis, glycogen turnover, and lipid mobilization. These changes align with the hypoxic phase and coincide with altered metabolite oscillations and autonomic rhythms, supporting a functional adaptation to intermittent oxygen availability. Mechanistically, we identify rhythmic activation of the cAMP–CREB1 axis as a key transcriptional driver linking adrenergic signaling to circadian metabolic remodeling under IH. Our findings establish chronic IH as a potent metabolic zeitgeber that entrains hepatic transcriptional and metabolic rhythms, revealing a circadian dimension to the metabolic consequences of sleep-disordered breathing.

overall_design: Male C57BL/6JRj mice were exposed to chronic intermittent hypoxia (60 cycles h-¹, 5 % FiO₂, ZT0 – ZT8) or normoxic air for four weeks. Livers were collected every 4 h over a 24-h cycle (ZT0, 4, 8, 12, 16, 20) and poly-A-selected, strand-specific RNA-seq libraries were prepared and sequenced (2 × 100 bp, Illumina NovaSeq 6000). n = 3 biological replicates per time-point and condition.

first: Emilie

last: Montellier

first: Guillaume

last: Vial

first: Sophie

last: Bouyon

last: Changizi Ashtiani

first: Sherif

last: Abdelkarim

first: Emeline

last: Lemarie

first: Antoine

last: Boutin

first: Kenichiro

last: Kinouchi

first: Pierre

last: Baldi

first: Jean-Louis

last: Pepin

first: Jonathan

last: Gaucher


title: Multi-omics profiling reveals microbiota, metabolite, lipid, and immunological heterogeneity underlying distinct pathophysiological mechanisms of age-related endotypes in type 1 diabetes

city: Hefei

first: Lanxin

last: Pan

state: Anhui

address: 96 Jinzhai Road, Baohe District

institute: The First Affiliated Hospital of University of Science and Technology of China

summary: Type 1 diabetes (T1D) is an autoimmune disease characterized by marked heterogeneity in age at diagnosis, clinical progression, and immune pathology. Increasing evidence suggests that age-related T1D endotypes may reflect distinct underlying molecular mechanisms; however, these mechanisms remain incompletely characterized at the cellular and transcriptional levels. To investigate age-associated immune heterogeneity in T1D, peripheral blood mononuclear cells (PBMCs) were collected from a selected cohort of newly diagnosed pediatric individuals with T1D and healthy controls. Single-cell RNA sequencing was performed on PBMCs from 27 individuals with T1D and 27 age- and sex-matched healthy controls to profile peripheral immune cell populations and characterize transcriptional differences associated with age-related T1D endotypes.

overall_design: PBMCs were isolated from peripheral blood samples collected from 27 individuals with type 1 diabetes and 27 age- and sex-matched healthy controls. Single-cell suspensions were processed using the 10x Genomics Chromium Single Cell 3' Reagent Kits v3.1, and sequencing libraries were generated according to the manufacturer’s instructions. Libraries were sequenced on the Illumina NovaSeq 6000 platform to generate single-cell RNA-seq data.

first: Huiling

last: Tan

first: Tong

last: Yue

first: Xueying

last: Zheng

first: Jianping

last: Weng


title: BRD4 promotes endodermal cell fate during mammalian lung development [bulkRNA-Seq]

city: Philadelphia

first: Sylvia

last: Michki

state: PA

address: 3615 Civic Center Blvd

department: Pulmonary & Sleep Medicine

institute: Children's Hospital of Philadelphia

summary: Lung development relies on diverse cell intrinsic and extrinsic mechanisms to ensure proper cellular differentiation and compartmentalization. In addition, it requires precise integration of multiple signaling pathways to temporally regulate morphogenesis and appropriate cell specification. To accomplish this, organogenesis relies on epigenetic and transcriptional regulators to promote cell fate and inhibit alternative cell fates. Using genetic mouse and human embryonic stem cell (hESC) differentiation models, tissue explants, and single-cell transcriptomic analysis, we demonstrated that Bromodomain Containing Protein 4 (BRD4) is required for mammalian lung morphogenesis and cell fate. Endodermal deletion of BRD4 impaired epithelial-mesenchymal crosstalk, leading to disrupted proximal-distal patterning and branching morphogenesis. Moreover, temporal deletion of BRD4 revealed developmental stage-specific defects in airway and alveolar epithelial cell specification with a predominant role in proximal airway cell fate. Similarly, BRD4 promoted lung endodermal cell differentiation into airway lineages in a hESC-derived lung organoid model. Together, these data demonstrated that BRD4 orchestrates early lung morphogenesis and separately regulates cell specification, indicating a multifunctional and evolutionarily conserved role for BRD4 in mammalian lung development.

overall_design: Epithelial cells were sorted from E12.5 mouse lungs for bulk RNA-seq. Shh-Cre negative (“WT”) mice were compared with Shh-Cre x Brdfl/+ (“HET”) and Shh-Cre x Brd4fl/fl (“KO”) mice to determine the effect of epithelial deletion of Brd4 on gene expression of early lung epithelial cells.

first: Hongbo

last: Wen

first: David

last: Frank


title: Improving the histologic detection of DSA-negative antibody-mediated rejection in kidney transplants

city: Edmonton

first: Jessica

last: Chang

address: 250 Heritage Medical Research Centre

country: Canada

institute: University of Alberta

summary: Emerging treatments for antibody-mediated rejection (ABMR, NEJM391(2):122-132) have increased the importance of ABMR detection when donor-specific antibody (DSA) is negative. Lowering MFI cutoffs for DSA-positivity did not improve detection of DSA-negative ABMR. However, simply calling all DSA positive allowed Banff 2022 guidelines to identify 46% more ABMR cases with no measurable DSA, and per Net Reclassification Improvement increased agreement between histologic diagnoses and both dd-cfDNA (P=7.72E-7) and molecular ABMR (P=7.69E-7). New ABMR cases were as strongly positive for dd-cfDNA and molecular ABMR as those found using the conventional DSA interpretation. A validation set analysis using INTERCOMEX study data (ClinicalTrials.gov NCT#01299168) confirmed these findings, and found that the new DSA-negative ABMR cases identified by calling all DSA positive had the same risk for graft loss as those found with conventional DSA interpretation.

overall_design: We addressed this issue in the Trifecta-Kidney study (ClinicalTrials.gov #NCT04239703) using three centralized tests in 690 kidney transplant biopsies: DSA (One Lambda Inc.), blood donor-derived cell-free DNA (dd-cfDNA, ProsperaTM test, Natera, Inc.), and molecular biopsy assessment (MMDx). We used an “AutoBanff 2022” algorithm to model the impact of alternative DSA interpretations on the histologic diagnosis of “DSA-negative” ABMR following Banff guidelines, including agreement with dd-cfDNA and molecular ABMR.


title: Histopathological characteristics of PDA cells in different malignant states [Xenium]

first: Lorenzo

last: Tomassoni

institute: Columbia University

summary: In order to assess whether cells sharing a common transcription state may form specialized niches within the tumor architecture, we examined the histopathological characteristics of PDA cells in different malignant states via 10x Xenium spatial transcriptomics.

overall_design: A custom panel of 100 genes supporting the identification of PDL and MAPK state Master Regulators was designed and used to profile 8 primary tumor samples from chemonaive PDA patients.

first: Pasquale

last: Laise

first: Mikko

last: Turunen

first: Alvaro

last: Garcia

first: Carlo

last: Maurer

first: Ela

last: Elyada

first: Bernhard

last: Schmierer

first: Jeremy

last: Worley

first: Jordan

last: Kesner

first: Xiangtian

first: Ester

last: Fernandez

first: Xue

last: Yuanqing

first: Chen

last: Yining

first: Kelly

last: Wong

first: Urszula

last: Wasko

first: Somnath

last: Tagore

first: Alexander

last: Wang

first: Sabrina

last: Ge

first: Alina

last: Iuga

first: Aaron

last: Griffin

first: Winston

first: Gulam

last: Manji

first: Mariano

middle: J

last: Alvarez

first: Faiyaz

last: Notta

last: Tuveson

first: Kenneth

last: Olive

first: Andrea

last: Califano


title: Human PDA Cell Lines: single cell RNA-Sequencing after treatment with Trametinib (TRAM) and/or Hydroxychloroquine (HCQ)

first: Lorenzo

last: Tomassoni

summary: Several Human PDA Cell Lines (ASPC1, PANC1, KP4, HPAFII, PATU8988S, PK45H, S2013, CAPAN1, BXPC3, HPAC, SW1990, MIAPACA2) were cultured and treated with DMSO, Trametinib (TRAM), Hydroxychloroquine (HCQ) and the combination of them before being prepared for Single-Cell RNA Sequencing

overall_design:
Cells from the Human PDA cell lines were seeded in a 6-well plate and on next day treated with the drugs. Cells were then processed for single cell RNAseq and for each run, 8 samples were combined using Total Seq B antibodies and the recommended protocol from Biolegend
The file SupplTable_GEO_metadata_TRAM_sc_Cell_Lines.xlsx contains the cell-level metadata.

first: Pasquale

last: Laise

first: Mikko

last: Turunen

first: Alvaro

last: Garcia

first: Carlo

last: Maurer

first: Ela

last: Elyada

first: Bernhard

last: Schmierer

first: Jeremy

last: Worley

first: Jordan

last: Kesner

first: Xiangtian

last: Tan

first: David


title: Multi-tissue DNA methylation analysis to identify an appropriate surrogate tissue for a unique neurological tissue specific to spina bifida

city: Boston

first: Maitreyi

last: Mazumdar

address: Department of Neurology

institute: Boston Children's Hospital & Harvard Medical School

summary:
Background: Animal models suggest a role of epigenetic mechanisms, including DNA methylation, in neural tube closure; however, studies characterizing DNA methylation profiles in nervous system tissue from humans with spina bifida are limited, In this study, we assessed DNA methylation profiles in dural tissue of infants with spina bifida, collected at the time of surgical closure of the defect, and examined whether whole blood or buccal swab are appropriate surrogate tissues, as they are more practical to collect in large-scale epidemiological studies, DNA methylation was measured in dural tissue, buccal swab, and whole blood samples collected from 27 unique infants using the Illumina Infinium MethylationEPIC BeadChip array,
Results: Correlation analysis for each CpG site comparing DNA methylation from all participants in dural tissue to DNA methylation in whole blood DNA or buccal swab DNA yielded 1,555 statistically significant associations for the whole blood analysis and 920 significant associations for the buccal swab analysis at the Bonferroni threshold of significance, We also performed paired analysis, calculating differences between tissues within each individual and then averaging differences across individuals, After accounting for multiple hypothesis testing using the FDR adjustment, 33% of CpG sites assessed were not significantly differentially methylated between dural tissue and whole blood samples, compared to the 27% of sites not differentially methylated between dural tissue and buccal swab samples,
Conclusions: These results suggest that in the absence of dural tissue, both whole blood and buccal swab samples may be considered as surrogates for dural tissue, The study warrants replication in larger groups to validate findings and may assist researchers restricted to more accessible biospecimens (i,e, blood) to further characterize epigenetic contributors to neural tube defect etiology,

overall_design:
This dataset comprises EPIC v1,0 DNAme data for 27 infants with spina bifida, where each participant provided dural tissue, buccal swab, and whole blood samples for DNAme assessment (81 total DNAme samples), DNA was extracted using the QIAsymphony DSP DNA Midi Kit (Qiagen, Valencia, CA), Dural samples were treated with EtOH to remove the OCT gel, and DNA was extracted from dural tissue samples using the DNeasy Blood and Tissue Kit (Qiagen, Valencia, CA), DNA was bisulfite converted (Zymo D5007 Kit, Zymo Research, Irvine, CA), DNA was then ampligied, fragmented, purified, and processed on Illumina Infinium MethylationEPIC BeadChips (Illumina, San Diego, CA) according to the manufacturer's instructions, Quality control of the DNAme data was perfomed with the ewastools and minfi packages in R, all samples passed the default thresholds of the control probes and had a mean detection p-values > 0,05, Data were normalized with preprocessNoob and preprocessQuantile using the minfi package, Probes were then filtered to exclude sites with detection p-values > 0,01 in at least one sample, sites mapping to the X and Y chromosomes, sites with annotated probe SNPs, and cross-reactive probes identified by Chen et al, (2013) and Pidsley et al, (2016), A total of 680,819 CpGs in 81 samples remained for downstream analysis across the tissues,
***************************************************************
The IDAT files have not been provided for participant confidentiality regarding the 56 rs genotyping probes present on the EPIC v1.0 array. These probes have been excluded from the submitted dataset and the raw data have thus been provided as methylated and unmethylated signal intensities with corresponding detection p-values, rather than in IDAT form.  IDAT files will be made available upon reasonable request to MM for research use.
***************************************************************

first: Gwen

last: Tindula

first: Sudipta Kumer

last: Mukherjee

first: Sheikh Muhammad

last: Ekramullah

first: D

middle: M

last: Arman

first: Joynul

last: Islam

first: Subrata Kumar

last: Biswas

first: Md Nafaur

last: Rahman

first: Md

last: Ziauddin

first: Ansar Uddin

last: Ahmed

first: Hafiza Sultana

last: Suchanda

first: Benjamin

last: Warf

last: Christiani

first: Bernardo

last: Lemos

first: Liming

last: Liang

first: Andres

last: Cardenas


title: BRD4 promotes endodermal cell fate during mammalian lung development

first: Sylvia

last: Michki

overall_design: Approximately 16500 EPCAM+ cells were sorted by FACS from the lungs of multiple Shh-Cre/+, Brd4-fl/+ (HET control) or Shh-Cre/+, Brd4-fl/fl (KO) mice sacrificed at E17.5 and loaded into independent lanes of a 10X Chromium GEX 3’ v3 microfluidics chip for 3’-biased scRNA-seq in order to compare Brd4 HET vs. Brd4 KO in the Shh+ lung epithelium.

first: Hongbo

last: Wen

first: Derek

last: Liberti

first: Prashant

last: Chandrasekaran

last: Frank


title: Effect of stem cell-derived exosome treatments on gene expression during corneal cell differentiation

city: Taiyuan

first: yuxing

last: gong

state: Shanxi

address: yingze street

department: Ministry of Education, and the Department of Physiology

institute: Shanxi medical university

summary: To investigate the therapeutic mechanisms of stem cell-derived exosomes in dry eye disease (DED), we conducted a comparative transcriptomic analysis in a murine model. C57BL/6 mice were divided into four experimental groups: (1) Control group (untreated healthy mice); (2) DED model group (induced dry eye disease without treatment); (3) Exosome eye drop group (DED mice treated with topical stem cell-derived exosome eye drops); and (4) Exosome intravenous group (DED mice treated with systemic exosome infusion). After the treatment period, corneal tissues were harvested from each group and subjected to RNA sequencing (RNA-seq) to assess genome-wide gene expression changes. Our analysis revealed distinct transcriptional profiles across groups, highlighting key pathways modulated by exosome administration via both delivery routes. This study provides systematic insights into the molecular responses of corneal cells to exosome-based therapy and offers a basis for optimizing delivery strategies for ocular surface regeneration.

overall_design: RNA-seq profiling of corneal tissue from DED model mice across four treatment groups: untreated control, disease model, exosome eye drop therapy, and exosome intravenous therapy, focusing on pathway-level alterations.


title: Identification RBPMS2 as a key regulator in mouse early oocyte development

city: Xuhui, Shanghai

first: Jie

last: Li

state: Shanghai

address: 320 Yueyang Road, Shanghai

institute: Center for Excellence in Brain Science and Intelligence Technology (Institute of Neuroscience), Chinese Academy of Sciences

summary: In the process of follicle formation, oocyte stably maintain large number of RNAs for development. However, how mammalian oocytes regulate these mRNAs, especially in the early oocyte, is unclear. We focused on RNA-binding proteins and identified RBPMS2 as a key factor in this process. Genetic disruption Rbpms2 causes female mouse infertility due to primordial oocyte defect. Transcriptome and RIP-seq analysis revealed that RBPMS2 binds 3′ UTR region to stabilize mRNAs of known oogenesis regulators, such as Lhx8. RBPMS2 also targets transcripts regulating cytoskeleton and cellular trafficking, such as Clasp1 and Rab27a, which are down-regulated in knock out oocytes. Rbpms2 knock out induces impairments in endocytosis and the accumulation of mitochondria and Golgi bodies in primordial oocyte. In summary, our study reveals RBPMS2 regulates mouse oogenesis through stabilizing mRNAs regulating oocyte development cellular trafficking and organelle enrichment, connecting post-transcriptional regulation to organelles accumulation and early oocyte development.

overall_design: P1 ovaries of wild type or Rbpms2 knock out mice are digested with collagenase (2mg/ml) at 37°C for 5-10 minutes. Remove the collagenase and digest the ovaries with trypsin (0.25%) at 37°C for 5-10 minutes, and then pipette gently to dissociate into single cells. FBS is added to stop the reaction and cells are collected by centrifugation (500g, 5-10 min). Resuspend the cells in PBS. Five to ten putative primordial oocytes per group were collected by a mouth pipette into one tube for mRNA amplification which was performed following the manufacturer’s instructions (Vazyme, N712-03) with 18 amplification cycles. Library preparation followed the methods in (Chen et al., 2023). Briefly, after test the concentration by Qubit Flex Fluorometer (Thermo Fisher Scientific) and fragment size by Agilent Bioanalyzer 2100, TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, TD503) was used to prepare the library.

first: Wenbo

first: Weixiang

last: Song

first: Zhen

last: Liu


title: Targeting HMGB2 acts as dual immunomodulator by bolstering CD8+ T cell function and inhibiting tumor growth in hepatocellular carcinoma [ATAC-seq]

city: SHANGHAI

first: WEIFENG

last: QU

address: No.180 Fenglin Road

institute: Zhongshan Hospital, Fudan university

summary: T cell exhaustion is a critical obstacle for durable treatment response in hepatocellular carcinoma (HCC). Developing drugs that control tumor growth and simultaneously bolster immune function is of great significance. The transcriptional regulator high mobility group box 2 (HMGB2) has emerged as a risk factor in prognosis of HCC. However, the role of HMGB2 in HCC tumor microenvironment (TME) is poorly understood. Here, we discovered HMGB2+ CD8+ T cells as being associated with T cell exhaustion and resistance to anti-PD-1 treatment through single-cell RNA sequencing of human and murine HCC tissues. Mechanistically, HMGB2 impaired the mitochondrial oxidative phosphorylation in CD8+ T cells by increasing the ubiquitination of NRF2, thus reduced the antitumor effector function. In tumor cells, HMGB2 inactivated the interferon-γ (IFN-γ) response through TRIM24/STAT1 pathway, inhibiting susceptibility and recruitment to effector T cells. Tannic acid, a specific inhibitor of HMGB2, synergized with PD-1 antibody to attenuate tumor growth and reverse T cell exhaustion. Collectively, this study revealed that HMGB2, a T cell exhaustion associated molecule, contributed to tumor immune escape by dual action on CD8+ T cells and tumor cells. These data also provided translational insight into synergistic treatment strategies.

overall_design: ATAC-seq of NC versus HMGB2-knockout CD8+ T cells in C57BL/6J mice.

first: Weifeng

last: Qu

first: Guiqi

last: Zhu

first: Yinghong

last: Shi


title: ChIP-sequencing analysis of Notch1 intracellular domain (NICD1)

city: Chongqing

first: Lei

address: 1 Youyi Road, Yuanjiagang, Yuzhong District

department: Department of Breast and Thyroid Surgery

institute: The First Affiliated Hospital of Chongqing Medical University, Chongqing, China

summary: This dataset presents ChIP-sequencing analysis of the O-glycosylated Notch1 intracellular domain (O-Glc NICD1) to investigate how O-GlcNAc–mediated post-translational modification influences NICD1 chromatin binding profiles. Notch1 activation relies on the translocation of NICD1 into the nucleus, where it functions as a transcriptional regulator. Emerging evidence suggests that O-glycosylation may modulate NICD1 stability, transcriptional activity, or interaction with chromatin-associated cofactors. To elucidate these regulatory mechanisms, we performed ChIP-seq using an antibody specific for Notch1 in MUG-Chor1 upon pro-O-GlcNAcylation treatment, followed by genome-wide mapping of enriched loci.

overall_design: Chip-seq of the histone modification  in MUG-Chor1 cells

first: Chengjie

last: Lian


title: Multi-omics profiling reveals microenvironmental remodeling as a key driver of house dust mite-induced lung cancer progression

city: La Jolla

first: Shams

last: Al-Azzam

address: 9500 Gilman Dr

institute: University of California San Diego

summary: Chronic exposure to the common aeroallergen house dust mite (HDM) induces lung inflammation and DNA damage, but its impact on lung cancer development remains largely unexplored. Using whole-genome sequencing, RNA-seq, and DNA methylation profiling, we assessed HDM effects in lung epithelial cell lines and a mouse orthotopic lung cancer model. HDM accelerated tumor growth without altering mutational burden. Transcriptomic and epigenetic analyses revealed tissue-specific effects: in normal lung, HDM enhanced pro-inflammatory and immune activation programs, whereas in tumors it suppressed T cell responses, antigen presentation, and chemokine signaling. Immune deconvolution showed a shift toward myeloid enrichment and lymphoid suppression, with reduced cytotoxic T and NK signatures. Notably, HDM-driven tumor promotion was abolished in Il17a−/− but not Il1b−/− mice, identifying IL-17A as a critical mediator. These findings demonstrate that chronic aeroallergen exposure reshapes the lung microenvironment to promote immune suppression and accelerate lung cancer progression.

overall_design: RNA-seq profiling of mouse lung tumors and matched adjacent normal tissues following chronic HDM exposure

first: Al-Azzam

last: Shams

first: Bertin

last: Samuel


title: A Conserved Salicylic Acid Signaling Pathway Controls Plant Immunity against Pseudomonas thought the unique TGA transcription factor in Marchantia polymorpha

city: Madrid

first: Santiago

last: Michavila Puente-Villegas

state: Madrid

address: c/Darwin 3

department: GMP

country: Spain

institute: CNB-CSIC

summary: Land plants have co-evolved with microorganisms since its transition to a terrestrial habitat around 500 million years ago. In angiosperms, salicylic acid (SA) activates plant immunity against hemibiotrophic pathogens thought TGA transcription factors, which bind to the promoter of SA-responsive loci, such as pathogenesis-related (PR) genes, to enforce plants immunity. While those mechanisms are well-known in flowering plants, our understanding in bryophytes remains limited, as genetic evidences for the role of SA in plant immunity are still largely missing. Here, we explore the interaction between Marchantia polymorpha and the bacterium Pseudomonas syringae to gain insights into the evolutionary immune function of SA during bryophyte-pathogen interactions. We combined transcriptomic profiling of P. syringae-infected M. polymorpha with the generation of SA-deficient plants in this liverwort by overexpressing the bacterial NahG gene, a SA-degrading enzyme. Our results indicate that P. syringae induced transcriptional footprint is enriched in SA-responsive genes and that Marchantia NahG plants are compromised in immune responses against P. syringae. We found that MpTGA is modulated by SA and essential for controlling resistance against Pseudomonas. Further transcriptional analysis to identify the coregulatory network controlled by SA and MpTGA, indicate that a SA/MpTGA module might execute the boost of plants' defence responses thought a variety of MpPRs, highlighting a notable control of class III secretory peroxidases belonging to the MpPR9 subfamily. Altogether, our data demonstrate the functional conservation of SA as an immune hormone and underpin the existence of a SA-controlled MpTGA transcriptional cluster driving resistance against Pseudomonas in M. polymorpha

overall_design: RNA-seq of Marchantia WT Tak-1, Mptga mutant and SA-deficient Marchantia NahG plants infected with Pseudomonas syringae pv. tabaci (Pta) 11528 (performed on 3 weeks old whole plants)

last: Michavila

first: Sophie

last: Kneeshaw

first: Loreto

last: Espinosa-Cores

first: Salvador

last: Torres

first: Marina

last: González-Zuloaga

first: Ángel

last: Zamarreño

first: Jose

last: García-Mina

first: Jitka

last: Siroka

first: Ondrej

last: Novak

first: Roberto

last: Solano

first: Selena

last: Gimenez-Ibanez


title: Mechanism of SETX-BRCA1-BARD1 complex in resolution of R-loops and transcription-replication conflicts

city: San Antonio

first: Hanzhou

last: Wang

address: 8403 Floyd Curl Drive, MSC 7784

institute: UT Health at San Antonio

summary: Senataxin (SETX), a RNA-DNA helicase, is recruited to transcription pause sites via the tumor suppressor BRCA1. Here, we define the mechanism by which SETX-BRCA1 resolves transcription-associated R-loops to prevent deleterious outcomes. Specifically, we show that SETX unwinds R-loops, and that the complex of BRCA1 and its obligatory partner BARD1 binds R-loops and stimulates R-loop unwinding by SETX. Importantly, BRCA1-BARD1 alleviates the inhibitory effect of RAD52 on SETX-mediated R-loop unwinding. We also demonstrate that phosphorylation of Ser642 in SETX promotes its interaction with BRCA1 via the tandem BRCT domain of the latter. Accordingly, mutations in the catalytic domain or Ser642 in SETX lead to R-loop accumulation, transcription-replication conflicts, replication fork stalling, and DNA double strand breaks in human cells. Our results thus establish the molecular basis for functional synergy between SETX and BRCA1-BARD1 in R-loop resolution and the mitigation of transcription-replication conflicts to preserve genome integrity.

overall_design: DRIP-seq (DNA-RNA Immunoprecipitation sequencing) was performed to detect R-loops in HAP1 WT and SETX KO cells. Each condition was analyzed in triplicate. RNase H-treated samples served as negative controls to confirm R-loop specificity.

first: Lai

last: Zhao

first: Chen

last: Yidong


title: RNA Expression Profiles of Primary and Recurrent Human Chordoma Tissues

first: Lei

last: Liu

summary: Transcriptome profiling was performed on partially degraded and fragmented RNA extracted from matched primary and recurrent human chordoma tissues using Affymetrix microarrays.

overall_design: Matched primary and recurrent chordoma tissue samples were collected from six patients, resulting in a total of 12 specimens for downstream analysis. Gene expression profiling of all samples was conducted using the PrimeView Human Gene Expression microarray platform.

first: Chengjie

last: Lian


title: Single-cell RNA transcriptome reveals the underlying mechanisms by which losartan alleviates nitrogen mustard induced corneal injury

city: Chicago

first: Han

last: Peng

state: IL

address: 303 E Chicago Ave, Ward 9-120

institute: Feinberg School of Medicine, Northwestern University

summary: Current therapies used for managing limbal stem cell deficiency (LSCD) fail to fully reverse the damage to limbal epithelial stem cells (LESCs) and are often accompanied by side effects following long-term usage. Thus, more effective and safer therapeutic options are required. Here, in contrast to acute injury in other chemical burn models (e.g., alkali burn), we utilized a nitrogen mustard-induced corneal injury model featuring a chronic inflammation and a prolonged chronic/delayed phase of damage, which leads to LSCD hallmarks (corneal haze, chronic inflammation, neovascularization, conjunctivalization). Previously, we demonstrated that Angiotensin-converting enzyme 2 (ACE2) knockout mouse corneas developed haze and neovascularization due to induction of exaggerated inflammation. Such corneal inflammatory response induced by loss of ACE2 can be reversed by treatment of losartan, a widely used anti-hypertension drug with approved long-term safety. Here, we showed that systemic treatment with losartan markedly decreased corneal haze and inflammation during the acute and delayed phases of NM corneal injury. More importantly, in the delayed phase, losartan treatment also reduced the NM-induced neo-vascularized areas in the cornea by 56%. Goblet cells that were detected within the corneal epithelium during the delayed phase, were significantly reduced (43%) following losartan treatment, suggesting that systemic treatment with losartan significantly resolves classical hallmarks of LSCD. Single cell RNA sequencing (scRNA-seq) provided evidence that NM injury induced a dramatic increase of monocytes/macrophages in the cornea and that such increase was attenuated by losartan treatment. Flow cytometry analysis confirmed that losartan attenuated corneal inflammation via reducing the monocytes/macrophages in the cornea. Our findings strongly support a new therapeutic use for losartan in blunting LSCD, which is a consequence associated with numerous corneal inflammatory conditions (e.g., dry eye, bacterial keratitis, diabetic keratopathy).

overall_design: Methods: We conducted scRNA-seq on ocular anterior segmental tissue from 1 uninjured wild-type， 1 nitrogen mustard (NM) injured + saline treated, and 1 nitrogen mustard (NM) injured + losartan treated mice, using a 10X Gemomics pipeline. Cell populations were distinguished by UMAP embedding. Seurat analysis was conducted to compare gene expression profiles between these groups of mice.

first: Seyedeh

last: Parisa Foroozandehasl

first: Robert

last: Lavker


title: Chromosomal instability shapes the tumor microenvironment of esophageal adenocarcinoma via a cGAS–chemokine–myeloid axis [snRNA-Seq]

city: Oxford

first: Eileen

last: Parkes

address: Off Roosevelt Drive

institute: University of Oxford

summary: Chromosomal instability (CIN), a pervasive feature of esophageal adenocarcinoma (EAC), drives tumor aggressiveness and metastasis. CIN stimulates the cGAS–STING pathway, typically linked to anti-tumor immunity. However, despite the high CIN burden in EAC, the cGAS–STING pathway remains largely intact. To address this paradox, we interrogated multiple esophageal cancer models, discovering myeloid-attracting chemokines – with CXCL8 as a prominent hit – as conserved CIN-driven targets in EAC. Using multiplexed immunofluorescence microscopy, we quantified ongoing CIN in human EAC tumors by measuring cGAS-positive micronuclei, validated by whole-genome sequencing. Coupling in situ CIN detection with single-nucleus RNA sequencing and multiplex immunophenotyping of human EAC, we link CIN to tumor-intrinsic innate immune activation, CXCL8 expression, and myeloid cell-mediated immunosuppression. In EAC patients, CIN-high, myeloid-dominated tumors correlate with poor outcomes and aberrant cGAS–STING signaling. These insights explain the counterintuitive maintenance of cGAS–STING and highlight disruption of the CIN–cGAS–inflammation axis as a potential therapeutic strategy in EAC.

overall_design: Single-nucleus RNA sequencing (snRNA-seq) of 16,127 nuclei derived from 9 fresh-frozen esophageal adenocarcinoma (EAC) samples.

first: Bruno

last: Beernaert

middle: E


title: Single cell genome structures of mouse diploid ES cells [CUT&Run]

city: Cambridge

first: David

last: Lando

address: Department Biochemistry , Sanger Bulding, Tennis Court Road

department: Biochemistry

institute: University of Cambridge

summary: We describe the first integrated 3D structural models of an entire mammalian diploid genome using data derived from both chromosome conformation capture and microscopy imaging. This has allowed us to study the association of open DNA regions imaged by ATAC-see and histone with the folding of chromosomes down to a scale of 100kb.

overall_design: Cut and Run data for various histone modifications was collected in a diploid mouse ES cell line as it exited pluripotency. Using a genome build specific for this diploid mouse ES cell line we analysed the Cut and Run data for these histone modifications across the two parental genomes and in genome structures derived from single cell Hi-C.

first: Xiayan

last: Ma

first: Ernest

last: Laue


title: Dnmt3a-dependent de novo DNA methylation enforces lineage commitment and preserves functionality of memory Th1 and Tfh cells [WGEM-seq]

city: Salt Lake City

first: Jeffrey

middle: Scott

last: Hale

state: Utah

address: 15 North Medical Drive

institute: University of Utah

type: Methylation profiling by high throughput sequencing

summary: Following acute viral infection, naïve CD4+ T cells differentiate into T follicular helper (Tfh) and T helper 1 (Th1) cells that generate long-lived memory cells. However, it is unclear how memory Tfh and Th1 cells maintain their lineage commitment. We demonstrate that Tfh and Th1 lineages acquire distinct Dnmt3a-dependent de novo DNA methylation programs that are preserved into memory.  Dnmt3a deletion impairs lineage commitment and functionality of memory Th1 and Tfh cells, resulting in aberrant Runx1 upregulation that represses germinal center Tfh cell differentiation. In contrast, transient pharmacological DNA methyltransferase inhibition during priming impairs repression of Tfh-associated genes while properly silencing Runx1, and results in enhanced Tfh cell functionality in primary and secondary responses to viral infections. Together, these findings demonstrate that Dnmt3a-mediated epigenetic programing is required to enforce T helper lineage commitment and preserve Tfh and Th1-specific functions during the recall response to infection, and reveal novel strategies to improve long-lived adaptive immunity against infectious diseases.

overall_design: Mouse antigen specific CD4+ T cells (SMARTA TCR Transgenic) were sorted from spleens of non-infected mice (CD4+ T cell naïve samples) and LCMV Armstrong infected mice at 7 days post infection (effector Th1 and effector Tfh samples) for Whole Genome Enzymatic Methyl sequencing

first: Scott

first: Bryant

last: Perkins


title: Epigenetic Silencing of LTR12C family in OCI-AML3

city: London

first: Ozgen

last: Deniz

state: Greater London

address: Charterhouse square

institute: Barts Cancer Institute

summary: Chromatin accessibility at LTR12C family  has been shown to b required  to maintain stemness properties in leukemic stem cells. Here using CRISPRi epigenetic silencing strategy, we targetted LTR12C family in OCI-AML3 cell line. Our ATAC-seq and CUT&RUN data demonstrate efficient targeting and silencing of entire family using only 4 sgRNAs. Epigenetic silencing of this family leads to slower growth in targeted OCI-AML3 cells compared to control cells.

overall_design: ATAC-seq and cut&run (H3K27ac and H3K9me3) in OCI-AML3 cells transduced with dCas9-KRAB and empty sgRNA vector or LTR12C sgRNA vector.

first: Bryce

last: Drylie

first: Özgen


title: Dissecting Agronomically Favorable Genotypes in Temperate Japonica Rice via Haplotype Analysis of a Japan-MAGIC Population

city: Tsukuba

first: Hirofunmi

last: Fukuda

state: Ibaraki

address: 1-31-1 Kannondai

institute: National Agriculture and Food Research Organization (NARO)

summary: Crop breeding assembles genomic variants into cultivars via crossing and selection. Phenotypic selection has improved yield and lodging tolerance but has limited genetic insights. We show how specific genomic variants and their combinations underpin advances in modern rice breeding in Japan. Through genome-wide association study using a multi-parent advanced-generation intercross population derived from four temperate japonica cultivars, we identified 11 quantitative trait loci (QTLs) for key agronomic traits, including days to heading, shoot biomass, panicle length, and culm length under field conditions. GA20ox1, GA20ox2, and Hd1 were among the QTLs, and their natural variants were well conserved in temperate japonica cultivars bred in Japan, underscoring distinct selection pressures at these loci. By integrating genotype data with 5-year yield-performance-evaluation trials of elite cultivars, we found that cultivars carrying multiple-copy GA20ox1 and functional Hd1, together with non-functional ga20ox2, tended to have shorter culms and higher grain yield than cultivars with multiple-copy GA20ox1, functional Hd1, and GA20ox2. This yield advantage was consistent across latitudes in Japan. These results reveal favorable genotype combinations underlying modern japonica improvement and provide a genomic framework for breeding semi-dwarf, high-yielding cultivars adapted to temperate rice-growing regions in Asia.

overall_design: Each of the first fully expanded leaf (from the top) of each JAM2 line was collected at 6 weeks after transplanting (1 July 2022 and 29 June 2023) from 9:00 to 11:00 am.

first: Hirofumi

first: Akari

first: Toshihiro

last: Sakamoto

first: Yoshihiro

last: Kawahara

first: Ken

last: Naito

first: Taiji

last: Kawakatsu

first: Jun-ichi

last: Yonemaru

first: Daisuke

last: Ogawa


title: MicroRNA Profiling of Plasma Exosomes in Heart Failure Characterized by Reduced Ejection Fraction Reveals hsa-miR-339-5p as a Regulator of Ventricular Remodeling via NOD-like Receptor Family CARD Domain-Containing 5

city: HEFEI

first: Dan

last: Cheng

state: Shushan

address: 中国安徽省合肥市蜀山区樊洼路安兴太阳湾小区

institute: The First Affiliated Hospital of Anhui University of Chinese Medicine

type: Non-coding RNA profiling by high throughput sequencing

summary: Background: Heart failure characterized by reduced ejection fraction (HFrEF) is characterized by impaired cardiac function, with myocardial remodeling being a key pathological change in its progression. Plasma exosomal microRNAs(miRNAs) are promising non-invasive biomarkers with potential applications in the early prevention and treatment of HFrEF. Materials and methods: We used high-throughput miRNA sequencing to analyze plasma exosomes from 5 patients with heart failure with reduced ejection fraction (HFrEF) and 5 healthy volunteers to identify differentially expressed miRNAs. The miRanda program, Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and WikiPathways were used for target gene prediction and pathway analysis. Using quantitative reverse transcription polymerase chain reaction (qRT-PCR), the expression of exosomal miRNAs was verified in plasma samples from 40 patients with HFrEF and 40 healthy controls. Differential ventricular remodeling miRNAs and target genes predicted by miRanda were verified by qRT-PCR (n=40). Results: In comparison to healthy controls, high-throughput sequencing of the plasma exosomes of HFrEF patients showed that 10 miRNAs were significantly upregulated and 17 miRNAs were significantly downregulated. qRT-PCR validation confirmed that hsa-miR-22-5p, hsa-miR-181b-5p, and hsa-miR-339-5p were significantly upregulated (P < 0.05), while hsa-miR-192-5p (P < 0.05) and hsa-miR-1469 (P < 0.01) were significantly downregulated. No significant difference was observed for hsa-miR-320a-3p (P > 0.05). According to bioinformatics studies, hsa-miR-339-5p regulates the PI3K/AKT signaling pathway to target NOD-like receptor family CARD domain-containing 5 (NLRC5), impacting myocardial remodeling. The plasma levels of NLRC5 were lower in the HFrEF group than in the control group (P＜0.01), whereas the mRNA levels of PI3K and AKT were higher in the HFrEF group than in the control group (P＜0.01). Conclusion: This study highlights the distinct manifestation of plasma exosomal miRNAs in HFrEF and confirms the function of hsa-miR-339-5p in promoting ventricular remodeling through NLRC5. Potential as a treatment target for HFrEF has been demonstrated by hsa-miR-339-5p, providing new directions for future treatment strategies.

first: Jing

last: Hu

first: Mengyao

last: Zhao

first: Shanshan

last: Cai

first: Yulong

last: Liu

first: Lan

last: Ge

first: Xiaoyu


title: LncRNA P4HA2-AS1 Drives Renal Interstitial Fibrosis via TRIM32-Mediated K63 Ubiquitination of ULK1 and Autophagic Dysregulation

city: Wuhan

first: Kang

last: yang

address: No. 238 Jie-Fang Avenue, Wuhan, Hubei, P.R. China

institute: Renmin Hospital of Wuhan University

summary: Renal interstitial fibrosis (RIF), the central pathological driver of chronic kidney disease (CKD) progression, remains mechanistically incompletely defined. While long non-coding RNAs (lncRNAs) are emerging as critical regulators of CKD, their roles in RIF pathogenesis are poorly understood. Here, we identify the fibrosis-associated lncRNA P4HA2-AS1 as a key modulator of RIF through integrated analyses of unilateral ureteral obstruction (UUO) mice and TGF-β-stimulated human renal tubular epithelial cells (HK-2), combined with RNA sequencing, RNA pull-down, ubiquitination profiling, and autophagic flux assays. P4HA2-AS1 was markedly upregulated in fibrotic kidneys, and its suppression attenuated fibrotic phenotypes in vivo and in vitro while restoring autophagic flux. Mechanistically, P4HA2-AS1 directly binds the E3 ubiquitin ligase TRIM32, impeding its proteasomal degradation. This stabilization enhances TRIM32-mediated K63-linked ubiquitination of ULK1, a master autophagy initiator, leading to aberrant autophagic activation and fibrotic progression. Our study uncovers a previously unrecognized P4HA2-AS1/TRIM32/ULK1 axis that couples dysregulated autophagy to RIF, proposing lncRNA-protein interaction targeting as a therapeutic strategy against renal fibrosis.

overall_design: RNA-seq profiling of  TGF-β (10ng/ml for 24h) treated or untreated HK-2 cells and  their knockdown derivative (shP4HA2-AS1).

first: Zhou

last: Pan

first: Fei

last: Xiao

first: Wei

first: Ting

first: Wenjing

last: Shu

first: Yan

last: Leng

first: Qingqing

last: Yi

last: Zeng

first: Fan

first: Hengcheng

last: Zhu

last: Yang


title: Distinct miRNA319a identified from Persicaria chinensis mediates cross-kingdom suppression of cervical cancer targeting ITGA3

city: Beijing

first: Yueyue

last: Yan

address: No. 1 ShuaiFuyuan Road, Dongcheng District

institute: Chinese Academy of Medical Sciences & Peking Union Medical College

summary: Persicaria chinensis, a well-known traditional Chinese medicinal herb that is both edible and medicinal, has been widely acknowledged for its therapeutic effects, such as anti-inflammatory, antioxidant, and antitumor activities. However, the role of miRNAs from this plant in the cross-kingdom regulation of human diseases has not been investigated. In this study, we analyze the miRNA expression profile of P. chinensis using high-throughput sequencing and identify a total of 673 miRNAs, including 422 novel miRNAs that are unique to this plant and 251 conserved miRNAs. Among the conserved miRNAs, pch-miR319a is found to be the most abundant. Moreover, food-oriented pch-miR319a accumulates in the uterus and tumors and exhibits a rich repertoire of target genes within cancer-related pathways, demonstrating significant cross-kingdom regulatory potential. Utilizing the dual-luciferase reporter gene assay, we demonstrate that pch-miR319a from P. chinensis targets the Itga3 gene, which is associated with cervical cancer progression. Overexpression of pch-miR319a significantly decreases the viability, migration, and induces apoptosis of HeLa cervical cancer cells in vitro. Moreover, in a syngeneic mouse tumor model of cervical cancer, treatment with pch-miR319a effectively inhibits tumor growth and downregulates the expression of ITGA3 and the proliferation marker Ki-67. Our study highlights the potential of pch-miR319a from P. chinensis as a novel therapeutic agent for cervical cancer by targeting ITGA3 and provides new insights into the cross-kingdom regulatory mechanisms of plant miRNAs in human diseases.

sample_organism:
Homo sapiens
Mus musculus
Persicaria chinensis

overall_design: 1. Small RNA-seq of Persicaria chinensis: Persicaria chinensis samples were collected from Guangdong Province, China. Total RNA was first extracted from Persicaria chinensis samples by adding Trizol reagent for lysis, followed by chloroform partitioning, isopropanol precipitation, and ethanol washing. The concentration and purity of the RNA were then assessed using a NanoDrop spectrophotometer (Thermo Fisher Scientific, MA, USA), and RNA integrity was evaluated by electrophoresis. Subsequently, miRNA sequencing libraries were constructed using the QIASeq miRNA Library Kit. A pre-adenylated DNA adapter was ligated to the 3′ end of miRNAs, and unbound adapters were removed. An RNA adapter was then ligated to the 5′ end, followed by reverse transcription using a primer with an integrated unique molecular index to generate cDNA. Impurities were removed by magnetic bead purification, and indexed libraries were created through amplification with sample-specific indices, followed by a final round of magnetic bead purification to obtain the miRNA sequencing libraries. The libraries were typically sequenced on the NextSeq 500 System (Illumina Corp) using a paired-end 150 bp sequencing strategy. After sequencing, bioinformatics analysis was performed on the data. 2. mRNA-seq after pch-miR319a transfection in cervical cancer cells: To further elucidate the regulatory effects of pch-miR319a on its target genes, we conducted a comprehensive RNA-seq analysis to determine the differential expression of target genes in response to pch-miR319a overexpression. Cells were seeded into 24-well plates and transiently transfected of control vector or pch-miR319a plasmid using Lipofectamine 3000 (Invitrogen, CA, USA). After 48 hours of transfection, the transfected cells were selected for RNA-seq analysis.


title: Dynamic Transcriptomic Remodeling in Grafted Human Neural Progenitor Cells Uncovers Mechanisms for Vision Preservation in Retinitis Pigmentosa

city: Los Angeles

first: Shaughn

last: Bell

state: CA

address: 8700 Beverly Blvd

department: Regenerative Medicine Institute

institute: Cedars-Sinai Medical Center

summary: Human neural progenitor cells (hNPCs) show promise in slowing retinal degeneration and are currently being tested in clinical trials for retinitis pigmentosa (RP). However, the long-term fate of grafted hNPCs and their interaction with host retinal cells remains unclear. Here, we used single-cell transcriptomics to investigate temporal gene expression changes in grafted hNPCs and host retinal cells following subretinal injection into a rodent model of RP, revealing dynamic transcriptomic changes in the degenerative retinal environment. Grafted hNPCs primarily differentiate into an astroglial phenotype and mature over time, contributing to photoreceptor protection through trophic factor secretion, metabolic modulation, suppression of apoptosis, oxidative stress, and inflammation, alongside extracellular matrix remodeling. CellChat analysis revealed a decline in intercellular signaling and communication strength over time, correlating with weakened hNPC-host interactions. These findings suggest that enhancing trophic factor support, particularly MANF, and improving the host retinal environment are critical for sustaining long-term vision preservation.

sample_organism:
Homo sapiens
Rattus norvegicus

platform_organism:
Homo sapiens
Rattus norvegicus

overall_design:
Following hNPC treatment, rats were sacrificed and retinas were dissected at postnatal days 60 (P60) and 90 (P90). Grafted hNPCs and host retinal cells were isolated by FACS and analyzed using single-cell RNA sequencing. Pre-grafted hNPCs were also sequenced as a control for the grafted hNPCs. Single-cell RNA sequencing data (samples GSM6403183 & GSM640318) from rat retinas from another study (Series GSE209872) were used as a non-disease controls.

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The table below lists GEO accessions reused/reanalyzed for this study.
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first: Saba

last: Shahin

first: Bin

last: Lu

first: Somanshu

last: Banerjee

first: Vivek

last: Swarup

first: Hui

last: Xu

first: Jason

last: Chetsawang

first: Stephany

last: Ramirez

first: Jorge

middle: S

last: Alfaro

first: Alexander

last: Laperle

first: Soshana

last: Svendsen

first: Clive

first: Shaomei

last: Wang


title: Five Substances Powder with Poria ameliorates lipid metabolic disorders in obese mice by modulating gastric inhibitory polypeptide release via intestinal microbiota regulation

city: Nanjing

first: Yue

address: 1 WenYuan Road

institute: Nanjing Normal University

summary: Obesity is a chronic metabolic disorder that increases the risk of various metabolic diseases, such as type 2 diabetes and metabolic dysfunction-associated steatohepatitis (MASH). While previous studies have shown that Five Substances Powder with Poria can alters gut microbiota to improve glycolipid metabolism and obesity, the underlying mechanisms still need to be clarified. The present study aimed to explore the potential mechanisms of Five Substances Powder with Poria in suppressing obesity more deeply through an integrated research strategy.

overall_design: RNA-seq analysis of the small intestine of mice in the ND, HFD and Five Substances Powder with Poria groups (N, H, H1)

first: Kerui

last: Shen

first: Wenjie

last: Zhao

first: Chenxi

last: Guo

first: Yannan

last: Qi

first: Zhigang

last: Hu

first: HongJie

last: Di


title: Disruption of basal cell identity by Rank signaling drives mammary tumorigenesis

first: Osvaldo

last: Graña

state: Comunidad de Madrid

address: C/ Melchor Fernández Almagro, 3

department: Structural Biology

institute: CNIO

summary: Rank signaling regulates mammary gland development and epithelial cell differentiation. Rank receptor is expressed by mammary basal and luminal populations, but, unlike luminal Rank, the contribution of basal Rank signaling to MG homeostasis remains poorly studied. We have combined timely regulated basal specific Rank expression with lineage tracing models and unveiled that basal Rank signaling controls basal cell identity in postnatal mammary glands. Ectopic basal Rank disrupts basal but also luminal cell identity, resulting in aberrant luminal-like differentiation of basal cells and impaired lactogenesis. Mechanistically, overactivation of basal Rank signaling leads to basal cell lineage infidelity, illustrated by the appearance of premalignant lesions composed by a basal-derived hybrid population with alveolar features which ultimately generates basal and luminal breast adenocarcinomas. Proteomic, transcriptomic and chromatin analyses support that the loss of tumor suppressive epigenetic regulators driven by basal Rank contributes to epithelial cell dedifferentiation and tumorigenesis. The basal Rank signature generated associates to poor prognosis particularly in human adenocarcinomas of the luminal subtype stressing the clinical relevance of our findings. Interestingly, our results reinforce the idea that luminal breast tumors might originate from basal cells that have suffered a luminal-like aberrant dedifferentiation triggered by Rank signaling

overall_design: RNA sequencing (ATAC-seq) of mammary gland luminal and basal epithelial cells from K14-Ctrl and K14-Rank (Rank overexpression in basal cells) and K14-RankD/D (Rank depletion in basal cells) female mice  We induce Rank overexpression by treating 4 week old K14-Rank, K14-RankD/D and K14-Ctrl females with 1 mg/ml doxycycline + 20mg/ml sucrose, ad libitum in the drinking water for 4 weeks Then, we collect MGs from adult females and FACS isolate luminal and basal cells for RNA-seq.

first: Eva

last: González-Suárez

first: Jaime

last: Redondo-Pedraza

first: Patrcia

middle: G

last: Santamaria

first: Gonzalo

last: Soria-Alcaide

first: Fátima

last: Al-Shahrour

last: Graña-Castro


title: Dnmt3a-dependent de novo DNA methylation enforces lineage commitment and preserves functionality of memory Th1 and Tfh cells

first: Jeffrey

last: Hale

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

overall_design: Refer to individual Series


title: Targeted citrullination enables p53 binding to non-canonical sites [166]

city: Philadelphia

first: Priyankara

last: Wickramasinghe

address: 3601 Spruce Street

institute: The Wistar Institute

summary: TP53 encodes for the transcription factor p53, which binds to a diverse set of target genes in response to stress.  Activation of p53 results in highly specific transcriptional responses, but the regulation of promoter selectivity by p53 is poorly understood.  Here we report that sequence-specific binding of p53 is regulated by its target gene and binding partner PADI4.  PADI4 enzymatically converts peptidyl-arginine to peptidyl-citrulline in a process known as citrullination.  We show p53 is citrullinated in vitro at the C-terminus by PADI4, and we confirm two citrullination events in vivo (R306, R363).  ChIP-seq reveals that PADI4 expression causes a redirection of p53 away from canonical binding sites to target genes associated with the ETS transcription factor and the interferon response.  Chromatin profiling using citrullination-specific p53 antibodies supports this conclusion.  These findings link citrullination to p53 function and illustrate how chromatin modifiers like PADI4 can redirect the p53 transcriptional response.

overall_design: Chromatin immunoprecipitation followed by DNA-sequencing (ChIP-seq) of H3K27ac, p53, PADI4, and citH3 (citrullinated histone H3 at R2, R8, and R17), and H3R17me2 in M93-047 cells transfected with a tetracycline-inducible system to induce PADI4-D350A expression. Cells were either treated with vehicle (untreated), nutlin, doxycycline, or the combination of nutlin and doxycyline for 24 hours.

first: Alexandra

last: Indeglia

first: Andrea

last: Valdespino

first: Giulia

last: Pantella

first: Sarah

last: Offley

first: Connor

last: Hill

first: Alessandro

last: Gardini

first: Maureen

last: Murphy


title: Single-Cell Barcoded Lineage Tracing in PATU8988S PDA Cell Line

city: New York

first: Lorenzo

last: Tomassoni

address: 1130 St Nicholas Avenue

institute: Columbia University

summary: The PATU8988S PDA cell line was used to experimentally assess cross-lineage plasticiyty between different states of Pancreatic Malignant Cells

overall_design: Cells were transduced with an average of ~3 million random 27-nucleotide barcodes and were subjcted to single-cell RNA-Seq at two different time points, named as T0 and T1 (10 population doubligins).

first: Pasquale

last: Laise

first: Mikko

last: Turunen

first: Alvaro

middle: C

last: Garcia

first: H

last: Maurer

first: Ela

last: Elyada

first: Bernhard

last: Schmierer

first: Jeremy

last: Worley

first: Jordan

last: Kesner

first: Xiangtian

last: Tan

first: Ester

last: Fernandez

first: Xue

last: Yuanqing

first: Chen

last: Yining

first: Kelly

last: Wong

first: Urszula

last: Wasko

first: Somnath

last: Tagore

first: Alexander

last: Wang

first: Sabrina

last: Ge

first: Alina

last: Iuga

first: Aaron

last: Griffin

first: Winston

first: Gulam

middle: A

last: Manji

first: Mariano

last: Alvarez

first: Faiyaz

last: Notta

first: David

last: Tuveson

first: Kenneth

last: Olive

last: Califano


title: Multiplexed Perturbation Enables Scalable Pooled Screens

city: San Francisco

first: Stefan

last: Oberlin

address: 505 Parnassus Ave

department: Department of Microbiology and Immunology

institute: University of California, San Francisco

summary: CRISPR-based genetic perturbation screens have revolutionized the ability to link genes to cellular phenotypes with unprecedented precision and scale. However, conventional pooled CRISPR screens require large cell numbers to achieve adequate sgRNA representation, posing technical and financial challenges. Here, we investigate the impact of multiplexed sgRNA delivery via high multiplicity of infection (MOI) in pooled CRISPR interference (CRISPRi) screens as a strategy to enhance screening efficiency while reducing cell numbers. We systematically evaluate screen performance across varying MOIs, assessing the effects of multiplexing on knockdown efficiency, sgRNA representation, and collision rates. Our data demonstrate that sgRNA multiplexing (MOI 2.5-10) can maintain screen performance while enabling significant reductions in cell requirements. We further apply these optimized conditions to conduct a genome-wide CRISPR screen for regulators of intracellular adhesion molecule ICAM-1, successfully identifying novel candidates using as few as half a million cells. This study provides a framework for adopting multiplexed sgRNA strategies to streamline CRISPR screening applications in resource-limited settings.

overall_design: K-562 cells where infected with CRISPRi guide RNA libraries at varying multiplicity of infection (MOI) to test the effect of guide RNA multiplexing on CRISPR screen performance. After transduction, cells were grown for 14 days with or without selection by imatinib treatment prior to sequencing the guide RNA abundances. In a second experiment, transduced cells were stained for CD54 (ICAM-1) and sorted into high, low and medium CD54-expressing cell prior to sequencing the guide RNA abundances.

first: Michael

middle: T

last: McManus