title: Divergent proteome tolerance against gain and loss of chromosome arms

city: West Haven

first: Wenxue

last: Li

state: CT     Connecticut

address: 300 Heffernernan Dr Bldg A42,, Bldg 840, Room ABC 367

summary: How aneuploid cells tolerate chromosome arm gains or losses remains an open question. Using an isogenic human lung cell model with either 3p loss or 3q gain, combined with quantitative mass spectrometry and isotopic labeling, we reveal distinct proteostasis mechanisms for gain- and loss-type aneuploidy. Surprisingly, while compensation for 3q gain is primarily driven by increased degradation of excess protein complex subunits, 3p loss is neither counteracted by global protein degradation nor selectively reduced degradation, but rather by relatively upregulated protein synthesis to maintain protein complex stoichiometry. Additionally, proteins encoded on 3p exhibit increased thermal stability in loss-type aneuploidy, potentially via their interactions with other proteins from euploid chromosomes. Together, our findings uncover distinct proteomic buffering strategies that enable cells to tolerate either excessive or deficient single-arm aneuploidy.

overall_design: mRNA expression was quantified in chromosome 3 WT, 3q gain, and 3p loss cells, with three biological replicates for each genotype. Additionally, ribosome-protected fragments were quantified in chromosome 3 WT and 3p loss cells, also with three biological replicates. Furthermore, mRNA expression was measured in chromosome 8 WT and 8p loss cells with three biological replicates.

last: Di

first: Joan

last: Castellano

first: Wenjie

last: Jin

first: Wei

last: Hu

first: Alison

middle: M

last: Taylor

first: Yansheng

last: Liu


title: Hijacking innate immunity to enhance mRNA therapeutics

status: Public on Mar 25 2026

city: Guangzhou

first: Shu

last: Meng

state: Guangdong

address: No.9, XingDaoHuanBei Road, Guangzhou International Bio-island, Haizhu District

department: Department of Basic Research

country: China

institute: Guangzhou National Laboratory

type: Expression profiling by high throughput sequencing

summary: The therapeutic success of in vitro-transcribed (IVT) mRNA depends on its stability and efficient translation. However, IVT mRNA is highly susceptible to immune-mediated degradation, limiting its efficacy. Here, we co-transfected IVT mCherry mRNA with immune suppressor M or SOCS1 mRNA in human umbilical vein endothelial cells (HUVECs) for 6h and 24h to explore whether hijacking innate immunity could enhance expression and half-life of IVT mRNA. Subsequently, RNA-seq was performed to investigate the transcriptomic changes in HUVECs after transfecting IVT mRNA. We sought to clarify the potential mechanism underlying degradation of IVT mRNA.

overall_design: HUVECs were transfected with IVT mCherry mRNA, IVT mCherry mRNA + Luc, IVT mCherry mRNA + M, and IVT mCherry mRNA + SOCS1, respectively. Then, HUVECS were collected at 6h and 24h after transfection. Control group was also included. We got three replicates for each time point and each group. Total RNA were extracted and subjected to rRNA depletion-based RNA-seq profiling.

first: Tinghong

last: Zhang

first: Jinling

last: Qin

first: Xing

last: Peng


title: Genome-wide association mapping for cardiomyocyte ploidy identifies Shroom3 as responsible for hyperpolyploidy and ventricular dilation [bulkRNA-Seq]

city: Milwaukee

first: Anooj

last: Arkatkar

state: WI

address: 8701 W Watertown Plank Rd.

department: Cell Biology, Neurobiology, and Anatomy

country: USA

institute: Medical College of Wisconsin

summary: Cardiomyocyte (CM) polyploidy is widely observed across the animal kingdom and various ploidy states are associated with cardiac injury responses, including regeneration and heart failure. However, our understanding of the comprehensive mechanisms governing CM ploidy and its relationship with heart physiology has been hindered by a lack of experimental tools. To address this issue and uncover novel genetic regulators, we surveyed CM ploidy across a new genetic resource known as the Hybrid Rat Diversity Panel and founnd significant variation in ploidy phenotypes across the panel. Using select rat strains with divergent displays of CM ploidy, we found that hyperpolyploidization (≥8N) positively correlates with various physiological parameters namely left ventricular dilation and reduced ejection fraction. Genome-wide association mapping identified several loci significantly associated with frequency of hyperpolyploid CMs. Investigation of genes harboring damaging protein coding variants within these loci identified enrichment of cytoarchitectural genes, of which the ACTIN-binding protein, Shroom3, was found to be strongly and specifically expressed in CMs and harbors 7 damaging protein coding variants. CM-specific deletion of Shroom3 resulted in increased hyperpolyploidization and promoted left ventricular dilation and reduced ejection fraction. Furthermore, functional characterization of single nucleotide variants resulting in amino acid changes within SHROOM3 confirmed two protein coding variants that disrupted SHROOM3-ACTIN interaction and led to altered expression of cell cycle genes. This study elucidates the genetic determinants of CM ploidy phenotypes and solidifies a correlative relationship between CM ploidy and left ventricular function. Importantly, CM intrinsic expression of at least one gene mapped in this study, Shroom3, is confirmed to regulate CM hyperpolyploidization and cardiac function.

overall_design: RNA-seq profiling of neonatal rat ventricular cardiomyocytes (NRVCMs) transduced with GFP, Shroom3 1073S, or Shroom3 1073G adenovirus vectors

first: Alexandra

middle: L

last: Purdy

first: Amirala

middle: B

last: Nik

middle: A

first: Prottoy

last: Hasan

first: Michael

last: Flinn

first: Priyanka

last: Choudhury

first: Cheyret

last: Wood

first: Akiko

last: Takizawa

first: Lynn

last: Malloy

first: Monika

last: Tutaj

first: Brian

last: Link

first: Timothy

middle: F

last: Plageman Jr

first: Anne

middle: E

last: Kwitek

first: Melinda

middle: R

last: Dwinell

first: Laura

last: Saba

first: Caitlin

middle: C

last: O'Meara

first: Michaela

last: Patterson


title: Immune response to adeno-associated viral vectors in a human iPSC-derived microglia chimeric mouse model

city: Braine L'Alleud

first: Jan

last: Detrez

address: Chemin du Foriest 1

country: Belgium

institute: UCB

summary: Adeno-associated virus (AAV)-based gene therapy for severe neurological diseases is challenged by immune responses, which are difficult to study accurately in genetically divergent rodent models or in in vitro human iPSC-derived microglia (iMGL) that acquire activated phenotypes lacking complex brain environment cues. To address this, we generated human microglia chimeric mice. We developed a high-yield iMGL differentiation protocol incorporating a cryopreservation stopping point at the induced hematopoietic precursor cell (iHPC) stage, which increased flexibility and enabled high level of chimerism. Engrafted iMGL transcriptionally and phenotypically resembled primary human microglia and were functionally active, displaying phagocytosis and immune response to inflammatory stimuli. Assessment of AAV serotypes revealed that murine microglia induced a larger immune response compared to human iMGL, cautioning against overinterpreting inflammatory responses in rodent models. This model provides a critical tool to define the human immune response to AAVs early in vector discovery.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: iHPCs were thawed, cultured 3 days in iMGL differentiation medium to generate iMGL progenitors, then harvested and resuspended at 250,000 cells/µl in PBS for P3–4 pup engraftment. Mice were perfused and samples were processed with transcriptional inhibitors (actinomycin D, triptolide, anisomycin), plus RNase inhibitor and DTT. Samples were dissociated using a papain kit at 37°C for 30 minutes with periodic gentle trituration. Papain was quenched with albumin-ovomucoid plus DNase. Single cells were filtered (40 µm), myelin was removed with Myelin Removal Beads II and magnets, and loaded onto the Chromium system.


title: Spatial transcriptomic profiling identifies lacrimal gland epithelial cell-driven mechanisms underlying autoimmunity in Sjögren’s disease

city: Boston

first: Sharmila

last: Masli

address: 72 E. Concord St Instructional (L)

institute: Boston University

summary: Sjögren’s disease (SjD) is a second most prevalent rheumatic disease involving autoimmune pathology of tear-producing lacrimal glands that leads to a common clinical manifestation of chronic ocular surface disease. Despite advances in understanding of SjD, lacrimal gland pathology remains incompletely understood limiting diagnosis and treatment. Here we analyze spatial transcriptomic profile of lacrimal glands from wild-type (C57Bl/6) mice and Thrombospondin (TSP)-1-/- mice, a spontaneous mouse model of SjD. We uncover molecular mechanisms underlying functional loss of major epithelial cell subtypes – acinar, duct and myoepithelial cells. We identify potential early mechanisms and markers of glandular damage. By integrating spatial and cellular profiles, we uncover the presence of antigen presenting cells in the proximity of duct epithelial cells that were not described previously in lacrimal glands. We further identify role of epithelial cells as active participants in promoting or sustaining inflammation. Our findings help reveal potential molecular and cellular cues that drive periductal infiltrates containing B cells and Tfh cells that form germinal centers to facilitate local autoantibody production. Overall, our study can provide a framework for therapeutic targeting of epithelial cell types and multicellular interactions underlying autoimmune pathology.

overall_design: Nanostring GeoMx

first: Shivali

last: Gupta

first: Nikolaos

last: Kalavros

first: Athanasios

last: Ploumakis


title: Filifactor alocis FtxA-dependent suppression of inflammation and apoptosis

city: Umeå

first: abdelbasset

last: yabrag

address: Tråggränd 41 LGH 1003

department: Molecular biology

country: Sweden

institute: Umeå University

summary: Filifactor alocis is regarded as an emerging oral pathogen with roles in the etiology of periodontal, peri-implantitis, and endodontic infections. It was recently discovered that approximately 50% of known strains of this organism encode and express a Repeats-in-Toxin (RTX) protein, FtxA. This potential toxin appears to be associated with both progress and severity of periodontal disease. Mechanism(s) how FtxA may promote periodontitis are not yet known but could be linked to an enhanced proliferation of F. alocis in ftxA-positive strains. In the present work, we have investigated possible mechanistic correlations based on the activity of FtxA, as present in bacterial whole cells, in association with extracellular vesicles, and as a recombinant protein, exploiting macrophage-like THP-1 cells as a model. For this, we have used the ftxA-expressing strain, ATCC 35896, and F. alocis 148B-17U, which naturally lacks the gene encoding FtxA. Using RNA-Seq and cytokine array analysis we have pinpointed a role of FtxA in shifting the host response towards immunosuppression, also inhibiting apoptosis, immune cell recruitment, and with a potential role as well in downregulating mitochondrial and oxidative phosphorylation pathways in the THP-1 cells. Such role(s) in immune suppression could provide a plausible explanation why FtxA is associated with the progress and severity of periodontal disease, and further studies on mechanistic interactions between FtxA and host cells might therefore reveal novel potential therapeutic targets.

overall_design: THP-1 cells were cultivated and stimulated as described above, following their exposure to EVs isolated from F. alocis strains ATCC 35896 (ftxA+) and 148B-17U (ftxA-), or purified FtxA toxin for 4 hours. The total RNA was extracted using an RNeasy Mini Kit (Qiagen). Library preparation and sequencing was completed by BMKGene, with a paired-end protocol and read length of 150 nt (PE150), resulting in a total output of 20 million reads per sample. All reads outputs were checked for compliance with Illumina quality standards (Ewels et al. 2016; Wingett and Andrews 2018). Raw data were cleaned up with Trimmomatic 0.36 (Bolger et al. 2014) to remove sequences originating from Illumina adaptors and low quality reads. Files were aligned with the human reference genome hg38 (Rhead et al. 2010) using TopHat/2.1.1 (Trapnell et al. 2009) with the default options. Once the alignment was completed, Samtools 1.8 (Li et al. 2009) was used to select and sort the reads that were aligned in proper pair. The reads counting per gene was performed with HTSeq 0.9.1 (Anders et al. 2015), using stranded mode and exon as a feature. Differential expression analysis was performed using DESeq2 (Love et al. 2014). Genes with adjusted P<0.05 and log2 fold changes more than two were considered differentially expressed and were functionally characterized using the Metascape tools (Zhou et al. 2019) and Gene set enrichment analysis (GSEA) (Subramanian et al. 2005).

first: Zeinab

last: Razooqi

first: Kai

last: Bao

first: Abdelbasset

last: Yabrag

first: Raviprakash

middle: T

last: Sitaram

first: Mark

last: Lindholm

first: Mattias

last: Pettersson

first: Anders

last: Johansson

first: Georgios

middle: N

last: Belibasakis

first: Rasmus

last: Sten

first: Aftab

last: Nadeem

last: Oscarsson


title: Histone 3 lysine 36 trimethylation by SETD2 shapes an epigenetic landscape in intestinal stem cells to orchestrate lipid metabolism and prevent cell senescence [ATAC-seq I]

city: Shanghai

first: Yue

last: Xu

address: 上海市徐汇区华山路

institute: 上海交通大学

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The self-renewal capacity of intestinal stem cells (ISCs) declines with aging, leading to a loss of homeostasis and an increased susceptibility to intestinal diseases. Despite the established significance of lipid metabolism and epigenetic regulation in ISC function, the molecular mechanisms that connect these processes to aging-related ISC dysfunction remain elusive. Here, we demonstrate that Histone 3 lysine 36 trimethylation (H3K36me3) caused by SETD2 is critical for ISC stemness. We found that H3K36me3 deficiency results in reduced ISC proliferation and differentiation, disrupts fatty acid oxidation (FAO) metabolism, and induces ISC senescence. Mechanistically, the loss of H3K36me3 triggers the activity of the SWI/SNF chromatin remodeling complex and leads to increased chromatin accessibility and enhancer activation, which alters FAO- and senescence-related gene expression. Importantly, we discover that metabolic intervention can prevent the senescence of ISC due to H3K36me3 deficiency. Our findings reveal a crucial role for H3K36me3 in maintaining the epigenetic landscape that orchestrates FAO metabolism and determines intestinal stem cell functions, emphasizing the role of FAO as a key modulator between H3K36me3 and ISC aging, suggesting that metabolic intervention may help mitigate age-related ISC dysfunction.

overall_design: adult  Lgr5-EGFP-CreERT2; Setd2f/f  mice were intraperitoneal (i.p.) injected with tamoxifen daily for five days. Control mice were intraperitoneal (i.p.) injected with corn oil. The crypts single cells isolated from Lgr5-EGFP mice. We subsequently overlapped the differentially expressed genes and those located near differentially accessible regions.

first: Ziyi

last: Wang


title: The Deubiquitinating Enzyme Otub2 Modulates Pancreatic Beta-Cells Function and Survival

city: Rehovot

first: Sima

last: Lev

address: 234 Herzl St.

department: Molecular Cell Biology

country: Israel

institute: Weizmann Institute of Science

summary: We have previously shown that otubain 2 (OTUB2), a deubiquitinating enzyme, inhibits caspase-3/7 activity in primary human islets; promotes insulin secretion and inhibits cytokine-induced nuclear factor-κB (NFκB) activity. In the present work we show that overexpression of Otub2 in MIN6 cells inhibits NFκB activity and the expression of its target genes MCP-1 and iNOS. Consequently, both the basal and the cytokine-induced apoptosis of cultured MIN6 cells and dispersed human islets were inhibited. Overexpression of Otub2 in MIN6 cells increase the mRNA levels of NKx6.1 and Glut2 and concomitantly increased glucose-stimulated insulin secretion (GSIS) (by 2-3-fold). The beneficial effects of Otub2 on β-cell function was demonstrated by the phenotype of   Otub2-/+ and Otub2-/- mice, which manifested impaired glucose tolerance and increased expression of NFkB target genes (e.g. IP-10, MCP-1 and IL-1b).  RNAseq analysis of pancreata derived from OTUB2 KO mice revealed reduced expression of genes that down regulate K+ transporters (e.g. Ank2, Cacna1a and Kcnab1) combined with an increase in oxidative phosphorylation related genes. Given that closure of K+ channels is crucial for insulin secretion, these results could account, at least in part, for the impaired GSIS in the OTUB2 KO mice. Indeed, mass-spectrometry analysis of proteins co-immunoprecipitated with Otub2 revealed the voltage-gated potassium channel subunit Kv9.3 as a major Otub2 binding-partner. Additional binding partners included the Peg3 and Camk2d proteins, which promote NFκB signaling and β-cell death. Hence, by deubiquitinating proteins in complexes that contain Peg3 and Camk2d, Otub2 might inhibit propagation of NFκB signaling and β-cell apoptosis. Collectively our findings implicate Otub2 as a key regulator of b cell function, mainly affecting NFkB signaling and the K+ channels that regulate insulin secretion.

overall_design: RNA sequencing was perfomed on RNA extracted from pancreas and liver of OTUB2 knock-out mice (homozygote, heterozygotes) and WT mice.

first: Yehiel

last: Zick

first: Michal

last: Oshri

first: Yaron

last: Vinik


title: Androgen activity in the male embryonic hindbrain drives lethal PFA ependymoma [mm_FCG_scRNA_batch2]

city: Toronto

first: Michael

middle: D.

last: Taylor

state: Ontario

address: 555 University Ave

department: DSCB

country: Canada

institute: The Hospital for Sick Children

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

overall_design: Four Core Genotype mouse cerebellum from 2 developmental stages were processed for single-cell RNA sequencing.

middle: D


title: FABP4 Contributes to Preeclampsia Through Dysregulating Lipid Metabolism and Inducing Mitochondrial Oxidative Stress in Trophoblasts

city: Dongtai

first: Hui

last: Sun

state: Jiangsu

address: No. 2 Kangfu West Road

department: Medical Laboratory Department

institute: Affiliated Dongtai Hospital of Nantong University

summary: Preeclampsia (PE) is a pregnancy-specific hypertensive disorder characterized by abnormal placental development and systemic endothelial dysfunction. Previous studies have suggested that fatty acid binding protein 4 (FABP4) is involved in lipid metabolism and oxidative stress regulation in various metabolic and cardiovascular diseases. However, its specific role and underlying mechanisms in PE, particularly in trophoblast function and mitochondrial homeostasis, remain unclear. This study aims to investigate the role of FABP4 in the pathogenesis of PE by exploring its effects on trophoblast cell function and mitochondrial oxidative stress through regulating lipid metabolism.

overall_design: Placental tissues were collected from 25 PE patients and 21 healthy pregnant women to detect FABP4 expression using qRT-PCR. In vitro experiments were conducted on HTR-8/SVneo trophoblast cells. FABP4 was silenced by siRNA (si267) or inhibited by BMS309403. Cell proliferation was assessed via CCK-8 and EdU assays. RNA sequencing was performed to analyze related pathways. Free fatty acid (FFA) levels, reactive oxygen species (ROS) production, mitochondrial membrane potential, and ATP content were measured to evaluate lipid metabolism, oxidative stress, and mitochondrial function. Statistical analyses were done using t-test and one-way ANOVA.


title: Maintenance of β-cell identity through the transcription co-factors TBL1X and TBL1XR1

city: Neuherberg

first: Peter

last: Weber

address: Ingolstädter Landstraße 1

country: Germany

institute: Helmholtz Zentrum München

summary: Loss of β-cell identity is a main mechanism of β-cell dysfunction in diabetes, controlled by transcription factors that induce β-cell identity gene expression and “disallowed” gene repression. How transcription factors facilitate simultaneous expression and repression is not fully understood, representing a serious knowledge gap in diabetes research. We identified the transcriptional co-factors transducin β-like 1 x-linked (TBL1X) and its homolog TBL1X-related (TBL1XR1) (short: TBL/R1) as crucial regulators of β-cell identity and function, as β-cell specific knockout in mice leads to progressive hypoinsulinemia and hyperglycemia. Single-cell RNA sequencing revealed loss of β-cells, the emergence of polyhormonal cells, and reduced β-cell maturity upon TBL/R1 knockout, indicating dedifferentiation. Interactome screens and chromatin immunoprecipitation showed TBL/R1 directly regulate insulin gene expression by forming a gene regulatory network with PAX6 and HDAC3, which was also evident in human models. Our study uncovers a new regulatory layer maintaining β-cell identity, crucial for diabetes development and progression.

overall_design: To investigate the transcriptomic changes in pancreatic beta-cells upon TBL1X and TBL1XR1, pancreatic islets from mice with a beta-cell specific TBL1X and TBL1XR1 kockout (n=4) and control littermates (n=4) were isolated, pooled (150 islets/group), and subjected to scRNA-Seq

first: A

last: Walth-Hummel

first: M

last: Rohm

last: Sterr


title: Dendritic cells accelerate CAR T cells in irradiated tumors through chimeric synapses [RNA-seq]

city: New York

first: Laszlo

last: Halasz

state: NY

address: 1470 Madison Avenue

department: Department of Oncological Sciences

institute: Mount Sinai Icahn School of Medicine

summary: Sustaining Chimeric Antigen Receptor (CAR) T cell activity in the tumor microenvironment (TME) is a major challenge that continues to hinder the advancement of this therapy for solid tumors. Here we report dramatically enhanced longevity of CAR T cells targeted to irradiated orthotopic lung tumors, leading to durable control in a syngeneic mouse model. CAR T cells robustly infiltrated into irradiated tumors where they maintained elevated expression of cytotoxic effector genes and demonstrated enhanced cytotoxicity. Remarkably, enhanced CAR T cell persistence in irradiated tumors was critically dependent on dendritic cells through a surprising mechanism. Dendritic cells that underwent “antigen-dressing” of tumor-derived target antigens could activate CAR T cells through the chimeric receptor, while resident and infiltrating myeloid subsets that also underwent antigen-dressing did not, suggesting that DCs were unique amongst myeloid cells in the capacity to maintain CAR T cells. Furthermore, tumor irradiation did not enhance CAR T cell activity through depletion of tumor associated macrophages alone, as targeted depletion of CSF1R-dependent myeloid cells had no measurable impact on CAR T cell persistence or tumor control. Rather, these data indicate that tumor irradiation generates conditions conducive for CAR T cells and antigen-dressed dendritic cells to engage effectively. The discovery that a well-tolerated dose of radiation bolsters CAR T cell persistence in solid tumors marks a pivotal advance with significant translational potential, and demonstrates for the first time the indispensable role dendritic cells have in sustaining CAR T cell activity against solid tumors.

overall_design:
To investigate the transcriptomic profiles of CAR T cells from irradiated tumors versus unirradiated tumors, we sorted CAR T cells from mice with established lung tumors, half that were irradiated before adpotive transfer and half that were unirradiated. The CAR T cells were further sorted into CD4+ CAR T cells and CD8+ CAR T cells. CD4+ CAR T cells sorted from the irradiated and unirradiated mice were pooled by treatment conditions due to lower cell count. CD8+ CAR T cells were left separated by mice, for a total of five samples from the irradiated group and five samples from the unirradiated group.
We then performed RNA-seq gene expression profiling analysis using data from five samples of CD8+ CAR T cells from the irradiated mice, five samples of CD8+ CAR T cells from the unirradiated mice, pooled CD4+ CAR T cells from five irradiated mice, and pooled CD4+ CAR T cells from the five unirradiated mice.
We then performed comparative gene profiling RNA-seq analysis was performed between CD8+ CAR T cell samples from five mice with irradiated tumors and CD8+ CAR T cell samples from five mice with unirradiated tumors; similarly, comparative analysis was performed between CD4+ CAR T cells from irradiated tumors and CD4+ CAR T cells from unirradiated tumors.

first: Ishibashi

last: Maki

first: Ahmed

last: Jalal

first: Sophia

last: Navarre


title: Prolonged KRAS-MAPK Inhibition Induces Interferon-mediated Epithelial-to-Mesenchymal Transition and Reveals Therapeutic Opportunities [RNA-Seq]

first: Ashenafi

last: Bulle

state: Missouri

address: 660 S Euclid Ave

department: Molecular Oncology

institute: Washington University School of Medicine

summary: Direct targeting of KRAS to inhibit the MAPK cascade is poised to transform the therapeutic landscape of pancreatic ductal adenocarcinoma (PDAC). However, analyses of PDAC samples from patients treated with KRASG12C inhibitors have revealed secondary mutations restoring MAPK signaling and promoting epithelial-to-mesenchymal transition (EMT) as key mechanisms of acquired resistance. Here, we show that human PDAC specimens and patient-derived cell lines treated with the ERK inhibitor ulixertinib display upregulation of EMT-associated and inflammatory gene programs, particularly those linked to the interferon response. Using the GeneRep-nSCORE computational framework to reconstruct and rank regulatory networks enriched in ERKi and KRASi-resistant PDAC cells, we identified TRIM22, an interferon-inducible E3 ubiquitin ligase, as a critical mediator of EMT and treatment resistance. Mechanistically, TRIM22 promotes proteasomal degradation of IκBα, leading to activation of NF-κB signaling, a known driver of EMT. Notably, we identify TACSTD2, encoding Trophoblast Cell Surface Antigen 2 (TROP2), as an NF-κB target gene upregulated following EMT. Functionally, combining ulixertinib or the KRAS inhibitor MRTX1133 with the TROP2-directed antibody-drug conjugate sacituzumab govitecan significantly suppressed the growth of PDAC patient-derived xenografts. Together, our work identifies TRIM22 as a molecular link between interferon signaling and EMT and reveals TROP2 as a druggable vulnerability to sustain the therapeutic efficacy of KRAS-MAPK pathway inhibitors.

overall_design: Bulk RNAseq analysis of Capan-1 cell over expressing TRIM22  in comparison to Vector group

first: Kian-Huat

last: Lim

first: Yali

last: Chen


title: Prolonged KRAS-MAPK Inhibition Induces Interferon-mediated Epithelial-to-Mesenchymal Transition and Reveals Therapeutic Opportunities

overall_design: Bulk RNAseq analysis of Pa01C, Pa02C, Pa03C and Pa14C cells following ulixertinib treatment in comparison to DMSO treatment group


title: Histone Variant H2A.J is a Key Epigenetic Regulator in Human Trophoblast Development [polyA primed transdifferential]

city: New Haven

first: Tyler

middle: Barry

last: Jensen

state: CT

address: 10 Amistad Street 214A

department: Genetics

institute: Yale University

summary: The preimplantation development in eutherian mammals is diverse. However, ethical and technical constraints significantly limit our understanding of the molecular and biochemical pathways governing human development. In this study, we discovered an unexpected, species-specific epigenetic pathway regulated by H2A.J, a largely uncharacterized histone variant in preimplantation development using human Blastoid models, IVF bovine embryos, and in vitro human stem cell models. We discovered that H2A.J is expressed in human and bovine placentas, contrasting with its absence in mice, and that H2A.J is essential for trophoblast expansion and viability in human and bovine. Our findings also revealed that H2A.J is enriched at promoters and introns of genes and interacts with RNA Polymerase I and II and pro-elongation factors, thereby regulating RNA Polymerase elongation and trophoblast maintenance in human embryo development. This study sheds light on a novel chromatin factor crucial for proper development in humans and large mammals, offering insights into the evolution of preimplantation development in eutherians. Our research provides valuable insights into evolutionarily divergent epigenetic mechanisms and biological functions in trophoblast lineage maintenance and transcriptional regulation, laying the groundwork for future investigations into the essential but understudied process of human placentation.

overall_design: Using various trophoblast and ESC models, we knocked down H2AJ and performed ribodepleted RNAseq.

first: Liangwen

last: Zhong

first: Andrew

last: Xiao

first: Berna

last: Sozen

first: Zongliang

last: Jiang


title: Prolonged KRAS-MAPK Inhibition Induces Interferon-mediated Epithelial-to-Mesenchymal Transition and Reveals Therapeutic Opportunities [scRNAseq-RMC-6236]

overall_design: scRNAseq analysis of KPPC mice treated with RMC-6236  in comparison to DMSO treatment group


title: Conflict resolution between the replisome and Pol II

city: Montreal

first: Yajie

last: Huang

state: Quebec

address: 900 saint-Denis

institute: CRCHUM

summary: The replisome and RNA polymerase II (Pol II) use the sample DNA template during the S phase. Inevitably, there is a conflict between these two machineries when they try to pass each other to accomplish their respective tasks. How such a conflict is resolved, especially in mammalian cells, is a quintessential biological question of which we only have a limited understanding. Using several recently developed techniques, we determined in vivo the replication fork speed, direction, and interruption when the replisome met Pol II. Based on nsRNA-seq of the mouse embryonic fibroblasts (MEFs), we revealed that a tiny fraction of all the genes, i.e., about 1.5 %, downregulated their transcription during the S-phase compared to the G1 phase. A moderate 20% reduction of II density in the S-phase-enriched  MEFs compared to asynchronous MEFs was observed. These two means represent the means of temporal segregation from replication. A moderate and significant bias (about 17% difference) was found favoring the co-directional forks over head-on forks. The encounter between the replisome and Pol II was quite eventful. About 21% of the forks were aborted in the Pol II-dense TSS region. Although the majority of the forks could still pass the TSS region, they hesitated and slowed down when the tips of the forks approached the Pol II dense region. Paradoxically, the forks traveled faster in genome regions dotted with more Pol IIs as long as their tips were not near the latter, probably due to a higher degree of chromatin negative supercoiling near Pol IIs. Our study demonstrated that the mammalian cells relied on multiple measures, such as temporal segregation, co-direction preference, and fork abortion, to mitigate the danger of replication-transcription conflict, but all these measures operated only as auxiliaries. The majority of the forks could pass Pol IIs unscathed, indicating the existence of a so-far unidentified, very efficient conflict resolution mechanism.

overall_design: ChIP-seq of asynchronous or S-phase-enriched (synchronized) mouse embryonic fibroblasts from E13.5 wild type mice.

first: Hongyu

last: Luo

first: Jiangping

last: Wu


title: Integrated Perturb-seq and Computational Modeling Identifies KAT6A-Menin-DOT1L Synergy and Associated Gene Program as Therapeutic Targets in Acute Myeloid Leukemia [RNA-Seq]

city: Birmingham

first: Changde

last: Cheng

state: Alabama

address: 1824 6th Ave S, WTI 510G

department: Department of Medicine - Hematology & Oncology

institute: The University of Alabama at Birmingham

summary:
Background:
Acute myeloid leukemia (AML) is a heterogeneous malignancy characterized by genetic and epigenetic dysregulation. Despite advances in targeted therapies against individual epigenetic regulators, clinical responses are often transient due to complex compensatory mechanisms. Identifying functional interactions between chromatin regulators and their associated transcriptional programs represents a promising strategy to overcome resistance and enhance therapeutic efficacy.

Results:
Using Perturb-seq combined with computational modeling and machine learning approaches, we systematically investigated 16 key epigenetic regulators across the Menin-MLL, Polycomb, and histone acetyltransferase complexes in MOLM-13 cells. Single-cell transcriptomic analysis of 31,015 cells revealed 17 distinct gene programs with differential impacts on AML pathogenesis. We identified strong synergy between KAT6A and the Menin-DOT1L axis in regulating oncogenic pathways, particularly gene program P-15 (Pro-Differentiation Program), which significantly correlates with favorable clinical outcomes in both TCGA and Beat-AML cohorts. Notably, P-15 showed high expression in NPM1-mutated AML and remission-stage patients but was suppressed in TP53-mutated cases with poor prognosis. Validating our computational predictions, dual inhibition of Menin (VTP-50469) and KAT6A (WM119, a preclinical compound) demonstrated significant therapeutic synergy in MOLM-13 cells, reducing the IC50 from 35nM to 12nM. Conversely, PCGF1 disruption conferred resistance to DOT1L inhibition, revealing a novel mechanism of therapeutic resistance. Bulk RNA-seq analysis of combination treatments confirmed that dual KAT6A-Menin inhibition uniquely modulates specific gene modules associated with myeloid differentiation.

Conclusions:
Our integrated experimental-computational approach, distinct from prior studies examining individual epigenetic regulators in isolation, identifies the KAT6A-Menin-DOT1L axis as a critical regulator of AML transcriptional programs in MLL-rearranged leukemia and reveals gene program P-15 as both a favorable prognostic biomarker and potential therapeutic target. These findings provide mechanistic insights into epigenetic regulation in AML and establish a framework for developing rational combination therapies targeting cooperative epigenetic dependencies while preventing compensatory resistance mechanisms.

overall_design: mRNA profiles in MOLM-13 cells with DMSO, VTP50469 , WM119 and Combination treatment.

first: Sajesan

last: Aryal

first: Rui

last: Lu


title: MicroRNA expression profiling of synovial fluid in early and late Osteoarthritis and comparison with Rheumatoid Arthritis

city: Chandigarh

first: Jyotdeep

last: Kaur

state: Chandigarh

address: PGIMER, Sector 12

department: Department of Biochemistry

country: India

institute: Postgraduate Institute of Medical Education and Research (PGIMER)

summary: This study employed miRNA microarray profiling to characterize differential expression patterns in synovial fluid samples (n=14) obtained from patients with osteoarthritis across different disease stages, as well as from patients with rheumatoid arthritis. Comparative analyses were performed to explore variations in miRNA expression associated with disease progression and across related arthritic conditions. Selected miRNAs were further evaluated using quantitative real-time PCR (qRT-PCR) in an independent validation cohort comprising early-stage osteoarthritis, late-stage osteoarthritis, and rheumatoid arthritis patients.

overall_design:
Osteoarthritis (OA) cases were classified into early-stage (Kellgren–Lawrence [KL] grade II) and late-stage (KL grades III–IV) based on radiographic evaluation. Patients with inflammatory joint diseases, infective arthritis, bone tumors, bone tuberculosis, prior knee replacement surgery, or recent viscosupplementation (within 6 months) were excluded. Rheumatoid arthritis (RA) patients without radiographic evidence of degenerative knee changes were included as disease controls.
In the discovery phase, miRNA microarray profiling was performed on synovial fluid samples from OA (early n=4; late n=6) and RA (n=4) patients. RNA quality was assessed using the Agilent 2100 Bioanalyzer. miRNA expression profiling was carried out using the Agilent Human miRNA Microarray (8×60K). Data were extracted using Feature Extraction software and analyzed in GeneSpring GX (v14.8). Quantile normalization and baseline transformation were applied. Comparative analyses were performed across groups.
In the validation phase, miRNA expression in an independent cohort of OA patients (early n=17; late n=20) was analyzed using qRT-PCR.

first: Diksha

last: Rana


title: Features of Group 3-like medulloblastoma mouse model [scRNA-Seq]

city: Pittsburgh

first: Baoli

last: Hu

state: PA

address: 4401 Penn Ave

department: Neurological Surgery

institute: University of Pittsburgh School of Medicine

summary: Group 3 medulloblastoma is the most aggressive among the four medulloblastoma subgroups, with poor prognosis and early metastasis making treatment particularly challenging. The lack of an immune-competent mouse model has hindered effective in vivo testing of potential drugs and mechanisms. Given the prevalent MYC overexpression in Group 3 medulloblastoma, we developed a Group 3-like medulloblastoma mouse model in C57BL/6J mice by overexpressing MYC in the cerebellum of newborn pups. This model provides a valuable tool for studying Group 3 medulloblastoma more effectively.

overall_design: scRNA-seq for postnatal day 60 mouse induced Group 3 medulloblastoma on postnatal day 2 by overexpressing MYC or EGFP control vector.

first: Han

last: Zou


title: Conflict resolution between the replisome and Pol II [RNA-seq]

overall_design: Nascent RNA-seq of asynchronous or S-phase-enriched (synchronized) mouse embryonic fibroblasts from E13.5 wild type mice.


title: Features of Group 3-like medulloblastoma mouse model [RNA-Seq]

overall_design: RNA-seq for mouse induced Group 3 medulloblastoma on postnatal day 2 or 5 by overexpressing MYC with or without SMARCD3.


title: Histone Variant H2A.J is a Key Epigenetic Regulator in Human Trophoblast Development

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

overall_design: Refer to individual Series


title: Histone 3 lysine 36 trimethylation by SETD2 shapes an epigenetic landscape in intestinal stem cells to orchestrate lipid metabolism and prevent cell senescence.

first: Yue

last: Xu

overall_design: adult  Lgr5-EGFP-CreERT2; Setd2f/f  mice were intraperitoneal (i.p.) injected with tamoxifen daily for five days. Control mice were intraperitoneal (i.p.) injected with corn oil. The crypts single cells isolated from Lgr5-EGFP mice.  Total RNA from sorted-ISCs was isolated and sequenced.

first: Ziyi

last: Wang


title: Histone 3 lysine 36 trimethylation by SETD2 shapes an epigenetic landscape in intestinal stem cells to orchestrate lipid metabolism and prevent cell senescence [ATAC-seq II]

overall_design: adult  Lgr5-EGFP-CreERT2; Setd2f/f mice were intraperitoneal (i.p.) injected with tamoxifen daily for five days. Control mice were intraperitoneal (i.p.) injected with corn oil. The crypts single cells isolated from Lgr5-EGFP mice. We subsequently examined correlation was observed between changes in ATAC-seq and alterations in histone markers.


title: MOS4-Associated Complex subunits 3A and 3B modulate FLM splicing to repress floral transition in short day

city: Taipei city

first: Chin-Mei

last: Lee

address: No. 1, Sec. 4, Roosevelt Rd.

department: Institute of Plant Biology

country: Taiwan

institute: National Taiwan University

summary: Flowering initiation is a crucial and complex process tightly regulated at the molecular level. Alternative splicing introduces transcript variability under different environments. MAC3A and MAC3B, components of the MOS4-associated Complex (MAC) in Arabidopsis, play pivotal roles in this process. This study investigates the intricate role of MAC3A and MAC3B in shaping the flowering cascade via alternative splicing. Previous observations on the flowering phenotype of mac3a/mac3b knockdown mutants highlight the negative role of MAC3A and MAC3B on flowering initiation specifically under short-day conditions, but the mechanism remains unknown. To explore the underlying reason, We perform RNA-seq analysis, which reveals extensive splicing defects in flowering initiation pathways, indicating the broad influence of MAC3A and MAC3B on flowering induction. Moreover, mac3a/mac3b mutants exhibit the early flowering trait, most possibly because of the deficient FLOWERING LOCUS C (FLC) expression and the abnormal splicing patterns FLOWERING LOCUS M (FLM), namely the lower ratio between cool-temperature-induced FLM-𝜷 to warm-temperature-induced FLM-𝜹, under short days.

overall_design: To investigate the underlying mechanisms of the early flowering trait of mac3amac3b double mutants, we performed RNA sequencing with 40dayold leaves of mac3amac3b mutants and Col-0, which were still in the vegetative phase under short days.The aim is to explore the effect of insufficient mac3amac3b by compare wildtype and mac3amac3b mutants.

first: Yu-Wen

first: Chih-Yen

last: Tseng

first: Yi-Tsung

last: Tu

first: Yu-Sen

first: Hsin-Yu

last: Hsieh

first: Yun-Tung

last: Ly

first: Yu-Zhen

last: Chen

first: Shih-Long


title: RRM1 inhibition sensitizes lung adenocarcinoma to decitabine treatment

city: Hangzhou

last: Jiang

state: Zhejiang

address: Yuhangtang Road No.866

institute: Zhejiang university

summary: Aberrant DNA methylation has been implicated in tumorigenesis and development of lung cancer. However, Nucleoside analog DNA methyltransferase inhibitors have demonstrated clini-cal utility in treatment of myelodysplastic syndrome and acute myeloid leukemia, the drugs have not shown commensurate clinical efficacy in solid tumors. Mechanisms mediating the primary resistance to DNA hypomethylating agents in solid tumors are not fully understood. Here, we hy-pothesized that factors that limit incorporation of nucleoside analog DNA methyltransferase in-hibitors in genomic DNA may underlie the tumor cell intrinsic primary resistance to decitabine in lung cancer. We found that RRM1 expression levels were inversely correlated with decitabine incorporation rates detected by LC-MS/MS. RNA interference mediated depletion of RRM1, the catalytic subunit of ribonucleotide reductase (RNR), or pharmacological inhibition of RNR signifi-cantly potentiated inhibition of lung cancer cell clonogenic survival in vitro and xenograft growth in vivo by decitabine treatment. Additionally, RRM1 knockdown or pharmacological inhibition of RNR enhanced decitabine mediated upregulation of tumor suppressor genes and STING-related im-mune response. RNR inhibition led to increased incorporation of decitabine into genomic DNA by reducing the availability of dCTP. These findings nominate the promising combination therapy of decitabine and RNR inhibitors as being ripe for further clinical translation.

overall_design: To systematically investigate the transcriptomic response to RRM1 knockdown and DAC treatment in LUAD A549 cells, we collected 4 groups of A549 cells for RNA-seq: control group (Ctrl), DAC treatment group (DAC), RRM1 knockdown group (RRM1 KD) and combination group (Comb, DAC treatment plus RRM1 knockdown).

first: Jianyong

last: Liu

first: Vaghasia

last: Ajay

first: Anders

last: Nicole

first: Rudek

last: Michelle

first: G. Nelson

last: William

first: Wanqiang

last: Sheng

first: Yegnasubramanian

last: Srinivasan

first: Jianya

last: Zhou


title: Effect of PTPMT1 deficiency on regulatory T cells

city: Cologne

first: Mauro

last: Corrado

address: Joseph-Stelzmann-Str. 26

institute: University of Cologne

summary: CD4 T cells were isolated from Wt and PTPMT1 DT mice. Cells were activated in vitro and differentiated into regulatory T cells for 4 days. At this time point WT and KO cells were harvested and analysed by proteomics.

overall_design: Two gorups of samples: 4 Wt treg samples and 4 KO Treg samples


title: Histone Variant H2A.J is a Key Epigenetic Regulator in Human Trophoblast Development [CUT&RUN]

first: Tyler

last: Jensen

overall_design: Deposition of Flag tagged H2AJ in human syncytiatrophoblasts derived from hESCs and RNAPII S2 and S5 in shControl and shH2AJ human hESC derived STBs

first: Liangwen

last: Zhong

first: Andrew

last: Xiao

first: Berna

last: Sozen

first: Zongliang


title: Recovery from Heart Failure: Microvascular Mechanisms

first: Krishan

last: Gupta

state: MASSACHUSETTS

address: 300 Longwood Avenu, Boston children's Hospital

institute: Boston Children's Hospital/Harvard Medical School

summary:
Background: Heart failure (HF) is a significant global health problem. Left-ventricular assist device (LVAD) implantation serves as a bridge for patients awaiting heart transplantation. Intriguingly, LVAD support often improves cardiac histology and function, sometimes enough to avoid transplantation after LVAD removal. However, the cellular programs underlying this recovery remain unclear.
Methods: Myocardial tissues were obtained from patients with HF at the time of LVAD implantation (pre-LVAD) and explantation (post-LVAD) for histological analysis and single-nucleus RNA sequencing (snRNA-seq). A murine model of HF recovery, combined with lineage tracing studies, was employed to define cellular sources of vascular repair. Cardiac function, fibrosis, and vascular density were assessed using echocardiography, histology, and fluorescent microsphere perfusion. A patient-derived cardiac non-myocyte culture system was established to interrogate mechanisms of cell-fate regulation.
Results: Post-LVAD myocardial tissues exhibited reduced fibrosis and increased capillary density compared to pre-LVAD samples. Across samples, fibroblast abundance inversely correlated with endothelial cell abundance, consistent with enhanced angiogenesis during recovery. SnRNA-seq identified a fibroblast subset predisposed to undergo mesenchymal-to-endothelial transition, acquiring an endothelial cell identity. Additionally, non-myocytes from pre-LVAD hearts proliferated poorly and failed to form vascular structures, whereas non-myocytes from post-LVAD hearts displayed greater proliferative and angiogenic capacity, forming vessel-like structures, reinforcing the association of HF recovery with angiogenic reprogramming. Mechanistically, knockdown of c-Myc by siRNA shifted post-LVAD non-myocytes to a pre-LVAD-like state, while c-Myc overexpression by mRNA in pre-LVAD cells induced a post-LVAD-like phenotype, implicating c-Myc as one contributor to this fate switch. A model of heart failure recovery in mice mimicked the histological and functional changes in patients, with physiological evidence of increased microvascular perfusion, associated with a fibroblast-to-endothelial transition documented by lineage tracing.
Conclusions: HF recovery involves reduced fibrosis and enhanced microvascularization, partly driven by fibroblast-to-endothelial cell fate transition. c-Myc functions as one regulator of this transition, offering a mechanistic entry point to develop regenerative therapies in HF.

overall_design: We isolated nuclei from frozen human heart tissue samples and constructed 3’ single cell gene expression libraries (Next GEM v3.1) using the 10x Genomics Chromium system. The libraries were sequenced with ~200 million PE150 reads per sample on Illumina NovaSeq. After sequencing, clean reads were analyzed with human reference genome GRCh38 using Cell Ranger v6.1.2. Introns were included in the analysis.

first: Rajul

middle: K

last: Ranka

first: Shuang

last: Li

first: Alexander

last: Lu

first: Keith

last: Youker

first: Kaifu

first: John

middle: P

last: Cooke


title: High levels of interferon-gamma-inducible protein 30 blocks PD-L1-mediated lysosomal degradation and increase CD8+ immune cells infiltration to improve response to immunotherapy

city: Santa Monica

first: Dave

last: Hoon

state: CA

address: 2200 Santa Monica Boulevard

department: Translational Molecular Medicine

institute: Saint John's Cancer Institute

summary: A total of 25 human melanoma lymph node metastasis (MLNM) formalin-fixed paraffin-embedded (FFPE) sections were analyzed using HTG AutoImmune (AI) assay. The FFPE tissues were obtained from patients who underwent surgery and were pathological diagnosed with MLNM.

overall_design: Formalin-fixed paraffin-embedded (FFPE) from melanoma lymph node metastasis (MLNM) were collected from 25 patients who underwent surgery and were pathological diagnosed with MLNM. FFPE 5 µm sections were analyzed using HTG AutoImmune (AI) assay to profile the 2,002 genes. The 25 MLNMs were divided into two groups: a control group having lymph node pathologically diagnosed as negative (LNM (-) and experimental groups with 17 patients diagnosed positive (LNM (+).

first: Shodai

last: Mizuno

first: Yuka

first: Kelly

last: Chong

first: Yuta

last: Kobayashi

last: S Hoon

first: Matias

last: Bustos


title: Histone 3 lysine 36 trimethylation by SETD2 shapes an epigenetic landscape in intestinal stem cells to orchestrate lipid metabolism and prevent cell senescence [CUT&Tag]

first: Yue

last: Xu

address: 上海市徐汇区华山路

institute: 上海交通大学

summary: The self-renewal capacity of intestinal stem cells (ISCs) declines with aging, leading to a loss of homeostasis and an increased susceptibility to intestinal diseases. Despite the established significance of lipid metabolism and epigenetic regulation in ISC function, the molecular mechanisms that connect these processes to aging-related ISC dysfunction remain elusive. Here, we demonstrate that Histone 3 lysine 36 trimethylation (H3K36me3) caused by SETD2 is critical for ISC stemness. We found that H3K36me3 deficiency results in reduced ISC proliferation and differentiation, disrupts fatty acid oxidation (FAO) metabolism, and induces ISC senescence. Mechanistically, the loss of H3K36me3 triggers the activity of the SWI/SNF chromatin remodeling complex and leads to increased chromatin accessibility and enhancer activation, which alters FAO- and senescence-related gene expression. Importantly, we discover that metabolic intervention can prevent the senescence of ISC due to H3K36me3 deficiency. Our findings reveal a crucial role for H3K36me3 in maintaining the epigenetic landscape that orchestrates FAO metabolism and determines intestinal stem cell functions, emphasizing the role of FAO as a key modulator between H3K36me3 and ISC aging, suggesting that metabolic intervention may help mitigate age-related ISC dysfunction.

overall_design: adult  Lgr5-EGFP-CreERT2; Setd2f/f mice were intraperitoneal (i.p.) injected with tamoxifen daily for five days. Control mice were intraperitoneal (i.p.) injected with corn oil. The crypts single cells isolated from Lgr5-EGFP mice. CUT&Tag was performed according to the instruction of the Vazyme Hyperactive Universal CUT&Tag Assay Kit for Illumina(TD903-01).We subsequently examined correlation was observed between changes in ATAC-seq and alterations in histone markers.

first: Ziyi

last: Wang


title: The myth of postnatal lung maturation dominated by increased pulmonary blood flow and its clinical implications

first: zheng

last: sixie

address: 1678 Dongfang Road

institute: Shanghai Children's Medical Center Affiliated to Shanghai Jiaotong Univerisity School of Medicine

summary: We reported the RNAseq analyses of lung in two groups of mice (5 in each group) at postnatal day 30 (P30). The mice in increased pulmonary blood flow (IPF) group underwent an abdominal surgery by puncture from aorta to inferior vena cava at P7, mice in Sham group underwent the same surgery except for the puncture. The results revealed that there were differentially expressed genes between IPF and sham group at P30.

overall_design: RNAseq analyses of lung in volume overload.

first: Sixie

last: Zheng

first: Lincai

last: Ye


title: Enterococcus faecalis-Induced Bystander Effect Drives Histone Acetylation Leading to Epithelial-Mesenchymal Transition via TGF-β Signaling

city: Nantong

first: Xingmin

address: 399 Century Ave.

department: Institute of Genetics and Reproductive Medicine

institute: Nantong Maternity and Child Healthcare Hospital

summary: Objective: Enterococcus faecalis has been implicated in the development of colorectal cancer (CRC) in murine models through the microbiota-induced bystander effect (MIBE). This study aimed to investigate whether this commensal bacterium induces epigenetic alterations via MIBE. Methods: Murine macrophage RAW264.7 cells were treated with either superoxide-producing E. faecalis OG1RF or superoxide-deficient WY84. Conditioned medium (CM) was then collected and used to treat IEC-6 rat intestinal epithelial cells. Histone acetylation states and related signaling pathways were analyzed using immunoblotting, immunofluorescent staining, and chromatin immunoprecipitation sequencing (ChIP-seq). Results: CM derived from E. faecalis-infected macrophages significantly induced histone H3 acetylation at lysine 27 and 9 (H3K27ac/H3K9ac) in IEC-6 cells compared to controls. Furthermore, this CM inhibited histone deacetylases, which contributed to the increased in H3 acetylation. ChIP-seq analysis revealed widespread alterations in H3K27ac across the genome in cells treated with E. faecalis-infected macrophage-derived CM. Additionally, these changes were associated with aberrantly activated TGF-β signaling, leading to epithelial-mesenchymal transition (EMT). Targeted metabolomic analysis indicated that E. faecalis activated arachidonate lipoxygenase-12 (Alox12) in macrophages, resulting in the production of 12-hydroxyeicosatetraenoic acid (12-HETE), which induces H3 acetylation via the bystander effect (BSE). Conclusion: Infection with E. faecalis activates Alox12 in macrophages, leading to the production of 12-HETE that subsequently induces H3 acetylation through the BSE. This aberrant H3 acetylation alters gene expression associated with TGF-β signaling, promoting EMT. These findings elucidate the mechanisms by which commensal bacteria may initiate and promote CRC, potentially providing insights for the development of novel strategies for CRC prevention and treatment.

first: Lili


title: Conjugation to a transferrin receptor 1-binding Bicycle peptide enhances ASO and siRNA potency in skeletal and cardiac muscles

city: Carlsbad

first: Juliana

middle: S

last: Capitanio

address: 2855 Gazelle Court

institute: Ionis Pharmaceuticals

summary: Improving the delivery of antisense oligonucleotides (ASOs) and small interfering RNAs (siRNAs) to skeletal and cardiac muscles remains a pivotal task toward the broader application of oligonucleotide therapeutics. The targeting of myofibers and cardiomyocytes via conjugation of ASOs and siRNAs to ligands that bind the human transferrin receptor 1 (TfR1) has gathered significant interest in recent years. However, the selection of ligands with low molecular weight and optimal biophysical and binding properties is crucial to maximize the potential of the TfR1 ligand-conjugated antisense (LICA) technology. Here, through effective combination of phage display and peptide medicinal chemistry, we identified and characterized a bicyclic peptide (Bicycle® molecule BCY17901), with a molecular weight of ∼2 kDa, that binds human TfR1 with high affinity and specificity. Conjugation to BCY17901 improved ASO and siRNA potency in skeletal and cardiac muscles of human TfR1 knock-in mice, after either intravenous or subcutaneous administration. Furthermore, single-nucleus RNA sequencing showed that conjugation to BCY17901 enhanced ASO activity in myonuclei of different muscle fiber types. Importantly, we demonstrated good translatability of our TfR1-targeting platform in skeletal and cardiac muscles of nonhuman primates. Our results offer great promise toward potential future applications of low-molecular-weight Bicycle LICA therapeutics for the treatment of diseases affecting skeletal muscle and heart.

overall_design: Gastrocnemius muscle samples from a total of eight mice were processed for single nuclei RNA sequencing. Two mice had been dosed with PBS (vehicle control), three with unconjugated Malat1 ASO at 3 mg/kg, and three with BCY17901-Malat1 ASO at 3 mg/kg (ASO equivalents).

first: Michael

last: Østergaard

first: Michele

last: Carrer

first: Brooke

last: Anderson

first: Megan

last: Afetian

first: Mohsen

last: Bakooshli

first: Jinro

last: Santos

first: Stephanie

last: Klein

first: Graeme

last: Freestone

last: Tanowitz

first: Rodrigo

last: Galindo-Murillo

first: Hans

middle: J

last: Gaus

first: Chrissa

last: Dwyer

first: Michaela

last: Jackson

first: Paymaan

last: Jafar-nejad

first: Frank

last: Rigo

first: Punit

last: Seth

first: Katherine

middle: U

last: Gaynor

first: Steven

last: Stanway

first: Liudvikas

last: Urbonas

last: St. Denis

first: Simone

last: Pellegrino

first: Gustavo

last: Bezerra

last: Rigby

first: Ellen

last: Gowans

first: Katerine

last: Van Rietschoten

first: Paul

last: Beswick

first: Liuhong

last: Chen

last: Skynner

first: Eric

last: Swayze


title: Elevation of caldesmon-1 is essential for the differentiation of aortic valve interstitial cells into osteoblasts.

city: Toon

first: Tomohisa

last: Sakaue

address: Shitsukawa

department: Cardiovascular and Thoracic Surgery

country: Japan

institute: Ehime University

summary: The molecular mechanisms underlying calcification and fibrosis in aortic valve leaflets remain unclear. This study highlights the functional roles of Caldesmon1 (CALD1), a cytoskeletal regulatory protein, in the progression of calcific aortic valve disease (CAVD), with a focus on its effect on valvular interstitial cell (VIC) behavior and osteoblast differentiation. RNA-seq analysis combined with ingenuity pathway analysis was performed to clarify the functional roles of CALD1 in aortic valve calcification.

overall_design: Control VICs and CALD1-knockdown VICs were cultured in Osteogenesis Differentiation Medium or MesenPRO RS™ Medium .

first: Munenori

last: Komoda

first: Hironori

last: Izutani


title: Single cell multiome  atlas of pediatric ependymoma

city: Memphis

first: Stephen

middle: C.

last: Mack

state: Tennessee

address: 262 Danny Thomas Place

institute: St. Jude Children’s Research Hospital

summary: ZFTA-RELA is the most recurrent genetic alteration seen in ependymoma, and sufficient to initiate tumors when expressed during mouse brain development. Despite ZFTA-RELA’s potent oncogenic potential, ZFTA-RELA gene fusions are observed exclusively in ependymoma and have never been documented in any other adult or pediatric malignancy. We hypothesized that specific chromatin modules accessible during brain development would render specific cells-of-origin at increased risk of transformation by ZFTA fusion proteins. To this end we performed integrated single cell ATAC and RNA-seq analysis (referred to as scMultimome) in mouse and human ependymoma tumors driven by the ZFTA-RELA fusion. We demonstrate that specific epi-developmental programs present in radial glia and regulated by Plagl1 are at direct risk of transformation. Oncoprotein engagement of this chromatin module leads to persistent oncogene expression, a failure to halt cellular proliferation, and initiate terminal cellular differentiation. Surprisingly, ependymomas exhibit significant heterogeneity across lineage differentiation programs, and continued activation of Plagl1 networks in differentiated cell types such as tumor neuronal-like cells contribute to tumor progression. These findings implicate specific chromatin modules in cells of origin as critical mediators of ependymoma initiation. Persistent activation and erosion of developmetn lineage programs serve as drivers of tumor development and contribute to the cellular heterogeneity of the tumor microenvironment.

overall_design: The forebrains from a healthy mouse at E14.5, a GBM mouse IUE model, and three ZFTA-RELA ependymomas mouse IUE models were processed for 10xMultiome (snATAC + snRNA) sequencing.

first: Hua

last: Sun

first: Alisha

last: Kardian


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

city: St Louis

first: Tiandao

last: Li

state: MO

address: 4444 Forest Park Ave

institute: Washington University

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

overall_design: mRNA profiles of Murine articular chondrocyte treated with TGFb1 and BMP2

first: Regis

last: O'Keefe


title: BRD4-mediated ER membrane contact creates functionally distinct mitochondrial subtypes

city: Ann Arbor

first: Abhijit

last: Parolia

state: MI

address: 1500 E Medical Center Dr

institute: Michigan Medicine

summary: Inter-organellar communication is critical for cellular metabolism. One of the most abundant inter-organellar interactions occurs at the endoplasmic reticulum and mitochondria contact sites (ERMCSs). However, an understanding of the mechanisms governing ERMCS regulation and their roles in cellular metabolism is limited by a lack of tools that permit temporal induction and reversal. Through screening approaches, we identified fedratinib, an FDA-approved drug that dramatically increases ERMCS abundance by inhibiting the epigenetic modifier BRD4. Fedratinib rapidly and reversibly modulates mitochondrial and ER morphology, induces a distinct ER-mitochondria envelopment structure, and alters metabolic homeostasis. Moreover, ERMCS modulation depends on mitochondrial electron transport chain complex III function. Comparison of fedratinib activity to other reported inducers of ERMCSs revealed common mechanisms of induction and function, providing clarity to a growing body of experimental observations. In total, our results uncovered a novel epigenetic signaling pathway and an endogenous metabolic regulator that connects ERMCSs and cellular metabolism.

overall_design: SW480 cell were culture in regular media and treated with DMSO (control), Fedratinib, (1 uM for 4 hr), or Thapsigargin (50 nM for 4 hr)

first: Branden

first: Eleanor

last: Young

first: Costas

last: Lyssiotis

first: Yatrik

last: Shah


title: INHBA activated PI3K/AKT pathway in gastric cancer cell line MKN45

city: Ji'nan

first: Shi

last: Duanbo

state: Shandong

address: wenhua xi road 44#

institute: Shandong University

summary: The gastric cancer cell' migration ability, invasion ability and the tumor growth could be promoted by INHBA. To investigate the mechanism underlying the regulation of INHBA  in promoting gastric cancer progression, high-throughput sequencing was carried in gastric cancer cell line MKN45.The results showed that PI3K/AKT pathway was activated by INHBA. Which indicated that INHBA regulated gastric cancer progression by activating  PI3K/AKT pathway.

overall_design: INHBA was overexpressed in gastric cancer cell MKN45, then high-throughput sequencing was carried out. The differentially expressed genes and pathways were investigated between  INHBA overexpressing cells and negative  control cells subseqently.

first: Duanbo

last: Shi

first: Peng

last: Gao


title: Selective Translation of ZNF281 as Part of the Integrated Stress Response System has Therapeutic Relevance for Cardio-Oncology

status: Public on Mar 24 2026

city: Edmonton

first: Maria Areli

last: Lorenzana Carillo

state: Alberta

institute: University of Alberta

summary: This study aims to investigate the role of ZNF281 in cardiomyocyte function and tumor biology by integrating RNA-seq and ChIP-seq datasets. Using a C57BL/6 mouse model, we isolated cardiomyocytes from ZNF281 overexpression (OE) and knockdown (Kd) mice, along with their respective controls, to analyze transcriptomic changes and ZNF281 genome-wide binding patterns. Additionally, we included tumor samples from nude mice, specifically A549 ZNF281 knockout (KO) tumors and parental A549 tumors, to explore the differential regulation and binding patterns of ZNF281 between cardiac tissue and tumors. RNA-seq was performed to identify differentially expressed genes regulated by ZNF281 in both contexts, while ChIP-seq was conducted to map ZNF281 DNA-binding sites and its role in transcriptional regulation. This study will provide insights into the context-dependent functions of ZNF281 in the heart and tumors, enhancing our understanding of its role in cardiac biology and cancer progression.

overall_design: Bulk RNA-seq and ChIP-seq were performed in human A549 tumor cells and mouse cardiomyocytes under multiple experimental conditions (n = 3 biological replicates per group). In A549 cells, parental, ZNF281 knockout (KO), and ZNF281 overexpression (OE) conditions were analyzed. In cardiomyocytes, control and experimental conditions were examined. RNA-seq was used to assess differential gene expression, and ChIP-seq was performed to identify genome-wide binding profiles. Sequencing reads were aligned to the hg38 (human) or mm10 (mouse) reference genomes. RNA-seq data were processed using STAR and HTSeq-count, followed by TMM normalization and differential expression analysis using limma–voom. ChIP-seq reads were aligned using Bowtie2, and peaks were identified using MACS2 and annotated to the nearest transcription start site using BEDtools.

first: Lorenzana-Carrillo

last: Maria Areli


title: AMPK-p38 axis converts human pluripotent stem cells to naïve state [scRNA-seq]

city: Bunkyo

first: Zhennan

last: Yang

state: Tokyo

department: Graduate School of Medicine, Department of Cellular and Tissue Communications

institute: The University of Tokyo

summary: Pluripotent stem cells (PSCs) have been reported to exhibit two stages of pluripotency, ‘primed’ and ‘naïve’ states. Typical human PSCs (hPSCs) are in the primed state. Though several methods for conversion from primed to naive state have been reported, the mechanism of the process is not fully understood. Here, we report that 5' adenosine monophosphate-activated protein kinase (AMPK) and its downstream p38 is a signaling axis that can induce the naïve conversion of hPSCs with single pathway activation. The simple addition of an AMPK activator, 5-aminoimidazole-4-carboxamide-1-β-D-ribofuranoside (AICAR), or overexpression of a constitutive active form of p38 (CA-p38) alone in primed hPSCs induced naïve hPSCs that satisfied naïve state criteria: differentiation ability to three germ layers and naïve state-specific transcriptional expression, epigenomic resetting, and mitochondrial activity. RNA-seq analysis demonstrated that our AICAR- or CA-p38-induced naive hPSCs show closely similar gene expression patterns to naive state human embryonic stem cells (HNES1) derived from human inner cell mass (ICM). This novel and simple naïve conversion method provides new avenues for understanding and elucidating the fundamental mechanism of naive conversion.

overall_design:
We analyzed single-cell RNA-seq profiles of naïve hESCs (700 cells), primed hESCs (700 cells), PXGL+AICAR d14 (4011 cells) and PXGL+AICAR d28 (902 cells).  The MEF (Mouse Embryonic Fibroblast) feeder cells used in PXGL+AICAR d14 and d28 were depleted by using anti-mouse (MHC) H-2 clone M1/42. Naïve hESCs tagged with human HT10,  primed hESCs tagged with human HT7, PXGL+AICAR d14 tagged with human HT8 and PXGL+AICAR d28 tagged with human HT9.
contributor ImmunoGeneTeqs company

first: Junko

last: Yamane

first: Wataru

last: Fujibuchi

first: Shigeyuki

last: Shichino


title: The microbiome protects against septic hyperinflammation and bacterial proliferation in a zebrafish model of blood infection with E.coli and mycobacteria

city: LEIDEN

first: Li

last: Liu

address: Verbeekstraat 29D

country: Netherlands

institute: Leiden University

summary: The microbiome is an important immune regulator, but the mechanisms by which commensal microbes shape systemic host defense during bloodstream infection remain poorly defined and commonly used pre-clinical models have practical, ethical and scientific limitations. Here, we establish a gnotobiotic zebrafish larval model to investigate microbiome-dependent protection against systemic blood infection by E. coli bacteria, an important cause of early onset neonatal sepsis and  nontuberculous mycobacteria to investigate the contribution of Toll-like receptor 2 (TLR2) in the defense responses. Germ-free (GF) and conventionalized (CONVD) larvae derived from the same clutches were systemically infected with E. coli, revealing that microbiome colonization significantly reduces early mortality. RNA-seq revealed a conserved core immune activation program in both GF and CONVD larvae, but the absence of a microbiome was associated with a broader transcriptional response and stronger repression of metabolic pathways, suggesting that commensal microbes buffer infection-induced metabolic suppression. Extending this framework to nontuberculous mycobacteria, we performed systemic infections with fluorescent Mycobacterium marinum and M. avium in tlr2 wild-type and mutant larvae under GF and CONVD conditions. While survival was largely unchanged, imaging-based quantification demonstrated increased bacterial proliferation in tlr2 mutants and in GF larvae, with microbiome-mediated restriction of bacterial burden evident in wild-type but not tlr2-deficient hosts. Together, these data show that microbiome colonization buffers septic outcomes by reshaping systemic inflammatory and metabolic programs, and identify TLR2 as a key node linking microbial colonization to effective host defense during nontuberculous mycobacterial infection

overall_design: We establish a gnotobiotic zebrafish larval model to investigate microbiome-dependent protection against systemic E. coli bacterial infection by using RNAseq. 5 dpf larvae were collect for the sequencing of E.coli-injected or PBS-injected zebrafish larvae in germ free condition or in microbiome colonized condition.

first: Herman

last: Spaink

first: Bjørn

last: Koch

first: Elke

middle: H

last: Krekels


title: Histone Variant H2A.J is a Key Epigenetic Regulator in Human Trophoblast Development [scRNA-seq]

city: New Haven

first: Tyler

last: Jensen

address: 10 Amistad Street 214A

institute: Yale University

summary: The preimplantation development in eutherian mammals is diverse. However, ethical and technical constraints significantly limit our understanding of the molecular and biochemical pathways governing human development. In this study, we discovered an unexpected, species-specific epigenetic pathway regulated by H2A.J, a largely uncharacterized histone variant in preimplantation development using human Blastoid models, IVF bovine embryos, and in vitro human stem cell models. We discovered that H2A.J is expressed in human and bovine placentas, contrasting with its absence in mice, and that H2A.J is essential for trophoblast expansion and viability in human and bovine. Our findings also revealed that H2A.J is enriched at promoters and introns of genes and interacts with RNA Polymerase I and II and pro-elongation factors, thereby regulating RNA Polymerase elongation and trophoblast maintenance in human embryo development. This study sheds light on a novel chromatin factor crucial for proper development in humans and large mammals, offering insights into the evolution of preimplantation development in eutherians. Our research provides valuable insights into evolutionarily divergent epigenetic mechanisms and biological functions in trophoblast lineage maintenance and transcriptional regulation, laying the groundwork for future investigations into the essential but understudied process of human placentation.

overall_design: scRNAseq of WT and H2AJ KD hBlastoids

first: Liangwen

last: Zhong

first: Andrew

last: Xiao

first: Berna

last: Sozen

first: Zongliang

last: Jiang


title: Genetic variation in a plant-parasitic nematode is associated with host gene expression signals conserved across evolutionarily distant host plants

city: Raleigh

first: Dahlia

middle: M

last: Nielsen

state: NC

address: Campus Box 7566

department: Biological Sciences

institute: North Carolina State University

summary: A hallmark of the interactions between endoparasites (parasites that live within plant tissue) and their hosts, is the parasites' ability to hijack host gene expression to support their own existence. While a number of studies have been performed to identify plant genes that are recruited in this manner, there is much that remains unknown. One mechanism by which this behavior can be explored is by using a traditional genetics approach: identifying connections between genetic variation and phenotype variation. To that end, we leverage experiments examining tissue from three host plant species, each infected with one of two genetically distinct strains of the endoparasite Meloidogyne hapla. Using RNA-Seq data, we identify plant gene expression patterns that differ according to the genetic background of the parasite they are infected with. We also show that parasite genotype-host expression phenotype associations are consistent across plant species. These results indicate that the plant genes recruited by the parasite are influenced by the parasite's genetic background, and that these differential choices are conserved across evolutionarily distant hosts. We also leverage public data to identify conserved host expression differences when comparing M. hapla-infected plants to uninfected plants. Finally, we demonstrate that parasite gene expression varies according to the parasites' genetic background, and show that these signals are also conserved under different host species.

sample_organism:
Glycine max
Medicago truncatula
Meloidogyne hapla

overall_design: Genetically homogeneous plants were inoculated with one of two strains of Meloidogyne hapla root knot nematodes (half the plants received one strain and half received the other strain). RNA from infected roots was collected, so that read counts for both plants and parasites could be calculated.


title: PAX3-SIX2 muscle stem cell heterogeneity drives muscle-specific repair dynamics diversification

city: Hong Kong

first: Dawon

last: Choi

address: Clear Water Bay, Kowloon

department: Division of Life Science

country: Hong Kong

institute: Hong Kong University of Science and Technology

summary: Skeletal muscle regeneration relies on muscle-specific stem cells (MuSCs) expressing PAX7. Its paralog, PAX3, a key regulator of embryonic myogenesis, is selectively expressed in a subset of adult MuSCs, with variable proportions across muscles. Here, using lineage tracing and muscle injury models, we show that PAX3-driven MuSC diversity underlies muscle-specific regeneration rates. PAX3⁺ MuSCs exhibit enhanced proliferation and differentiation, supporting rapid repair, while PAX3 loss leads to proliferation arrest and cell death. Single-cell RNA-sequencing revealed that PAX3 regulates SIX2 expression, and that SIX2 modulates MuSC proliferation, with its loss impairing, and ectopic expression promoting, repair dynamics. PAX3/SIX2 expression correlates with distinct proliferative and differentiation behaviors, influencing regeneration in a muscle-type-dependent manner. Our findings uncover an unrecognized layer of muscle-specific regulation in MuSCs-mediated repair and suggest that PAX3-SIX2 heterogeneity could be leveraged for targeted therapies in muscle-wasting diseases.

overall_design: PAX3⁺(GFP⁺) and PAX3⁻(GFP⁻) muscle stem cells with overexpressed SIX2 through plasmid transfection were sequenced using DNBSEQ-T7

first: Virginia

last: Zoglio

first: Sarah

last: Chebouti

first: Fayez

last: Issa

first: Théo

last: Massard

first: Benjamin

last: Polin

first: Sylvie

last: Manin

first: Pascal

last: Maire

first: Indigo T.C.

last: Chan

first: Tom

last: Cheung

first: Joana

last: Esteves de Lima

first: Frederic

last: Relaix


title: ATAC Sequencing of Murine Articular Chondrocytes Treated with TGFb1 and BMP2

first: Tiandao

last: Li

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

overall_design: ATAC profiles of Murine articular chondrocyte treated with TGFb1 and BMP2

first: Jie

last: Shen


title: Androgen activity in the male embryonic hindbrain drives lethal PFA ependymoma [mm_FCG_scRNA_batch1]

city: Toronto

first: Michael

last: Taylor

state: Ontario

address: 555 University Ave

institute: The Hospital for Sick Children

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

overall_design: Four Core Genotype mouse cerebellum from 2 developmental stages were processed for single-cell RNA sequencing.


title: Histone Variant H2A.J is a Key Epigenetic Regulator in Human Trophoblast Development [Ribodepleted HS MM]

first: Tyler

last: Jensen

overall_design: We compared counts of H2AJ between human and mouse term placenta tissue by bulk ribodepleted RNAseq

first: Liangwen

last: Zhong

first: Andrew

last: Xiao

first: Berna

last: Sozen

first: Zongliang

last: Jiang


title: Histone Variant H2A.J is a Key Epigenetic Regulator in Human Trophoblast Development [Ribodepleted H2AJ KD]

overall_design: Using various trophoblast and ESC models, we knocked down H2AJ and performed ribodepleted RNAseq.


title: AMPK-p38 axis converts human pluripotent stem cells to naïve state [RNA-Seq]

first: Zhennan

last: Yang

overall_design:
We analyzed gene expression profile of primed hESCs and induced naive hESCs by VPA, AICAR and CA-p38

This series includes re-analyzed samples from GSE60955, GSE69692, GSE80732, and  ERR1924222, ERR1924223, ERR1924224, ERR1924243, ERR1924244, ERR1924245, ERR590400, ERR590398, ERR590399, ERR590408,  ERR590410, ERR590401.

first: Junko

last: Yamane

first: Wataru

last: Fujibuchi


title: The MEK/MYC/p21 Axis Drives Senescence Bypass and BCL-xL Dependence in Vincristine-Resistant Rhabdomyosarcoma

city: Seattle

first: Eleanor

last: Chen

state: WA

address: 1959 NE Pacific St

department: Laboratory Medicine and Pathology

institute: University of Washington

summary: Rhabdomyosarcoma (RMS) is the most common pediatric soft tissue sarcoma, with outcomes for relapsed or metastatic disease remaining poor, with 3-year survival rates below 30%. Despite aggressive multimodal therapy, no new effective treatments have been introduced for relapsed RMS in more than three decades, underscoring the urgent need to elucidate mechanisms of therapy resistance. We generated vincristine-resistant fusion-negative (FN) RMS cell lines through long-term dose escalation and identified enhanced MAPK pathway activation, evidenced by increased ERK phosphorylation in vitro and a major subset of post-chemotherapy patient tumor specimens. Pharmacologic MEK inhibition with trametinib or genetic suppression of MEK1 significantly impaired the growth of resistant cells and enhanced vincristine efficacy in a KRAS(G12D)-induced zebrafish FN RMS model, leading to reduced tumor burden and delayed relapse. Mechanistically, trametinib induced a senescence-associated cell-cycle arrest in resistant cells through a MYC–p21 regulatory axis, wherein MYC directly represses CDKN1A (p21) expression by binding to its promoter, and MYC depletion or trametinib-mediated MYC suppression result in p21 upregulation and senescence induction. Importantly, MYC overexpression rescued cells from trametinib-induced senescence, confirming its role in senescence bypass. Vincristine-resistant cells also exhibited increased dependence on the anti-apoptotic protein BCL-xL for survival, demonstrating heightened sensitivity to the selective BCL-xL inhibitor A-1155463. Accordingly, combined inhibition of MEK and BCL-xL using trametinib and A-1155463 significantly suppressed tumor growth and induced apoptosis in vincristine-resistant cells, producing significant antitumor activity in both cell line and zebrafish xenograft models of vincristine-resistant tumors. Collectively, these findings identify enhanced MAPK signaling and MEK/MYC/p21-mediated senescence bypass as key drivers of vincristine-resistant FN RMS and reveal a therapeutic vulnerability to combined MAPK and BCL-XL targeting, providing a rational therapeutic strategy and preclinical rationale for combination therapy in treatment-refractory RMS.

overall_design: RNA-seq profiling of wild-type RD cells and their vincristine-resistant derivatives created through gradual vincristine dose escalation over 9-12 months

first: Yadong

last: Wang

first: Andrea

last: Largent

first: Dorothy

last: Lee

first: Paulomi

last: Modi

first: Long

first: Anshu

last: Bandhlish

first: Myron

last: Ignatius

middle: Y


title: Accelerated cerebromicrovascular senescence contributes to cognitive decline in a mouse model of paclitaxel (Taxol)-induced chemobrain

city: Oklahoma City

first: Roland

last: Patai

state: Oklahoma

address: 975 NE 10th street

department: Department of Neurosurgery

institute: University of Oklahoma Health Campus

summary: Chemotherapy-induced cognitive impairment ("chemobrain") is a frequent side-effect in cancer survivors treated with paclitaxel (PTX). The mechanisms responsible for PTX-induced cognitive impairment remain obscure, and there are no effective treatments or prevention strategies. Here, we test the hypothesis that PTX induces endothelial senescence, which impairs microvascular function and contributes to the genesis of cognitive decline. We treated transgenic p16-3MR mice, which allows the detection and selective elimination of senescent cells, with PTX (5 mg/kg/day, 2 cycles; 5 days/cycle). PTX-treated and control mice were tested for spatial memory performance, neurovascular coupling (NVC) responses (whisker-stimulation-induced increases in cerebral blood flow), microvascular density, blood-brain barrier (BBB) permeability and the presence of senescent endothelial cells (by flow cytometry and single-cell transcriptomics) at 6 months post-treatment. PTX induced senescence in endothelial cells, which associated with microvascular rarefaction, NVC dysfunction, BBB disruption, neuroinflammation, and impaired performance on cognitive tasks. To establish a causal relationship between PTX-induced senescence and impaired microvascular functions, senescent cells were depleted from PTX-treated animals (at 3 months post-treatment) by genetic (ganciclovir) or pharmacological (treatment with the senolytic drug ABT263/Navitoclax) means. In PTX treated mice, both treatments effectively eliminated senescent endothelial cells, rescued endothelium-mediated NVC responses and BBB integrity, increased capillarization and improved cognitive performance. Our findings suggest that senolytic treatments can be a promising strategy for preventing chemotherapy-induced cognitive impairment.

overall_design: The authors used single-cell RNA sequencing to identify senescent cell populations in the brains of paclitaxel (PTX)-treated p16-3MR mice. Whole brains were collected after perfusion, dissociated into single-cell suspensions, and processed for high-throughput droplet-based sequencing using a gel bead-in-emulsion platform. Single-cell libraries were generated through barcoded cDNA synthesis and amplification, followed by next-generation sequencing. Data were analyzed using unsupervised clustering to identify major brain cell types based on canonical marker genes, and a senescence gene set enrichment approach was applied to detect senescent cells, revealing a prominent accumulation of senescent capillary endothelial cells.

first: Anna

last: Csiszar

first: Zoltan

last: Ungvari

first: Tripti

last: Gautam

first: Tamas

last: Kiss


title: Rejuvenation of the Aged Cerebrovascular System via Protein Corona–Guided Fusogenic Liposome Delivery

summary: Brain vascular aging is increasingly recognized as a critical therapeutic target for age-related cognitive decline. Oxidative stress, bioenergetic dysfunction, and molecular damage play central roles in the progression of vascular aging, contributing to cerebrovascular dysfunction and impaired cognitive function. While naturally occurring polyphenols such as resveratrol (RSV) have demonstrated potential in mitigating aging-related pathologies, their poor bioavailability and limited brain targeting efficiency significantly constrain their therapeutic impact. As a result, high doses or advanced drug delivery strategies are necessary to achieve meaningful physiological effects. We introduce a novel nanocarrier system designed to enhance RSV delivery to the cerebral endothelium by leveraging the natural formation of an apolipoprotein E (ApoE)-enriched protein corona around fusogenic liposomes (FL) in vivo. These nanoparticles directly fuse with cytoplasmic cell membranes and thus evade endocytosis. We found that once in the circulation FL spontaneously acquire a protein corona, which is highly enriched in ApoE, a key ligand for brain endothelial low-density lipoprotein receptors (LDLR). Based on this observation, we engineered an ApoE-functionalized protein corona around FL (ApoE-FL) to systematically evaluate whether this mechanism could be exploited for targeted brain delivery. Following optimization and physicochemical characterization, the RSV-loaded liposomes were evaluated in vitro using human cerebral microvascular endothelial cells and in vivo C57BL/6 aged mice to assess their therapeutic potential. Both FL and engineered ApoE-FL liposomal delivery systems exhibited a strong affinity for endothelial cell membranes in vitro. The knockdown of the ApoE receptor, low-density lipoprotein receptor-related protein 1 (LRP1), significantly reduced liposomal docking. Microscopy analysis revealed that both ApoE-FL and non-functionalized FL directly fused with endothelial plasma membranes, thus bypassing intracellular organelles and minimizing lysosomal degradation. This suggests that the naturally formed ApoE corona in vivo may contribute to efficient cerebrovascular targeting, a property successfully replicated by the engineered ApoE corona strategy. In vivo biodistribution and kinetic studies demonstrated that especially ApoE-FL achieved enhanced brain-targeting efficiency, prolonged cerebrovascular retention, and extended targeting distance along the arteriovenous axis. This emphasizes that fusogenic liposomes effectively engage almost the entire microvascular network, including capillaries and post-capillary venules. Functionally, fusogenic liposome-delivered RSV improved blood-brain barrier (BBB) integrity, enhanced neurovascular coupling (NVC) responses, and promoted brain vascularization in aged mice. Single-cell RNA sequencing (scRNA-seq) revealed enhanced endothelial angiogenesis and barrier protective transcriptional profiles in cerebrovascular cells treated with ApoE-FL/RSV, suggesting a molecular basis for the observed vascular benefits. Liposomal RSV delivery achieved near-complete cerebrovascular and cognitive rejuvenation in aged mice applying a 2000-fold lower RSV dose than oral administration used as control sample. Thus, ApoE-FL liposomes exhibited exceptionally high delivery efficiency in deeper brain regions, further expanding their therapeutic potential. These findings underscore the importance of targeted drug delivery in optimizing therapeutic outcomes and establish ApoE-functionalized fusogenic liposomes as a promising strategy for mitigating brain vascular aging and cognitive decline.

overall_design: The authors used single-cell RNA sequencing to characterize cerebrovascular cell populations and transcriptional changes associated with aging and treatment. Brains were collected after PBS perfusion from young and aged mice (n =4-5 per group), dissociated into single-cell suspensions, cleared of debris, and enriched for viable cells using low-pressure FACS following SYTOX Green live/dead staining. The resulting cells were processed using the 10x Genomics Chromium Single Cell 3′ platform, with libraries prepared using the Next GEM 3′ Gene Expression v3 kit and sequenced on an Illumina NovaSeq 6000. Downstream analysis included clustering to identify major cell types such as endothelial cells, pericytes, and glial populations, followed by comparative analyses across experimental groups (young, aged, and liposome-treated conditions). The design incorporated differential cell abundance, gene ontology enrichment, and cell–cell interaction/network analyses to evaluate pathways related to angiogenesis, blood–brain barrier integrity, inflammation, and cellular senescence, thereby linking transcriptional changes, particularly in endothelial cells, to functional vascular outcomes.

first: Agnes

first: Tae-Gyu

last: Oh

first: Jenny

last: Gipson

first: Makayla

middle: L

last: Foster


title: Synovial Th17 transdifferentiation into exTh17 sustains chronic IL-17-independent  inflammatory arthritis [Visium]

city: los angeles

first: yizhou

last: wang

address: 8700 beverly blvd

institute: cedars-sinai medical center

summary: Rheumatoid arthritis (RA) is the most common systemic autoimmune disease. T helper 17 (Th17) cells  are found in the inflamed synovium in RA and believed to play a pathogenic role. However, IL-17  targeted interventions have shown limited efficacy in established RA. Inflammation can induce Th17  transdifferentiation into IL-17 negative Th1 or Tr1 like exTh17. To assess the potential phenotype and  role of exTh17 in inflammatory arthritis, we performed Th17 fate mapping studies in the SKG mouse  model of RA. We generated triTh17-SKG (IL-17Cre.IfngYFP.Il10eGFP.R26tdTomfl.Zap70SKG) mice and  leveraged them to show that in arthritic mice synovial Th17 transdifferentiate into IFNγ- and IL-10-  exTh17 which become the most prominent CD4 population in chronic arthritis. These exTh17 cells are  more arthritogenic than Th17, and able to sustain arthritis that is IL-17 independent but enriched with  IL-6 and TNF, two known RA-promoting cytokines. Synovial exTh17 present a unique gene signature  including upregulation of CD44 and S1PR4 that has correlates in the profile of CD4 T cells found in  human RA synovium. We further demonstrate that a crosstalk with synoviocytes and S1P signaling  promote Th17-exTh17 conversion and that CD44 – another known target for RA- is necessary for the  arthritogenic effect of exTh17. Our study suggests that the synoviocyte expansion which occurs during  RA progression can drive progressive conversion of Th17 into exTh17, which in turn sustain  inflammation that has hallmarks of human established RA.

overall_design: Spatial Transcriptomic (Visium 10X) on Rheumatoid Arthritis (RA) Human Synovium from ACPA and RF positive RA patients with active disease

first: Martina

last: Zoccheddu

first: Mattias

last: Svensson

first: Paramita

last: Dutta

first: Myungja

last: Ro

first: Yizhou

first: Hyobin

last: Kim

first: Zbigniew

last: Mikulski

first: Katarzyna

last: Dobaczewska

first: Francesca

last: Ingegnoli

first: Angela

last: Denn

first: Roberto

last: Caporali

first: Pietro

last: Randelli

first: David

middle: A

last: McBride

first: Nisarg

last: Shah

first: Wang

last: Zhipin

first: Jason

last: Moore

first: Kyoung

last: Won

first: Ferhat

last: Ay

first: Nunzio

last: Bottini


title: Vib1  regulates the development of Penicillium oxalicum fungi and the expression of cellulolytic genes

city: Qingdao

first: Panpan

last: Zhang

address: No. 72, Coastal Road, Aoshanwei Sub-district, Jimo District, Qingdao City, Shandong Province

institute: ShanDong University

summary: The goals of this study are to compare different gene expressions for Penicillium oxalicum wild type strain (WT) and vib1 deletion strain (Dvib1) under conditions of  2% glucose,2% N-GlcNAc  and 1% bran + 1% microcrystalline cellulose as carbon source.

overall_design: Examination of differential gene expressions by digital gene expression tag profiling in Penicillium oxalicum wild type strain and vib1 deletion mutant strains in 24h in modifeid Mendal’s medium with  2% glucose,2% N-GlcNAc  or 1% bran + 1% microcrystalline cellulose as carbon source. Three replicates were included for each samples.

first: Yuqi

last: Qin


title: Effect of JV001 genetic therapy on gene expression during transverse aortic constriction (TAC) and angiotensin II (Ang II) induced heart failure.

city: shanghai

first: yinlong

last: zhao

address: Shanghai 200125, China A419, Bldg #2, 115 Jinzun Road,

institute: Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine

summary: Telomeric ends are capped to prevent activation of DNA damage response by the shelterin complex. To design a gene therapy that recap telomeric ends, engineering of the telomerase protein was considered given its preference to bind 3’ overhang terminally. We designed a pan-HF gene therapy (the modified TERT, JV001) – that acts through telomeric reprotection and restore myocardial mitochondrial biogenesis – and validate safety and efficacy in heart failure murine models. Heart failure were induced with the TAC surgery and the use of Ang II, and the study about either of the two models of heart failure consisted of three groups: control group, heart failure group, heart failure with JV001 treatment group. The control group standed for mice receiving sham surgery in the TAC study, and mice receiving saline infusion in the Ang II study. The heart failure group induced with either TAC or Ang II were injected with empty vector, for the comparison with the JV001 group. After the experiment, we employed RNA-sequencing to analyze the cardiomyocytes from the mouse models.

overall_design: In the TAC study, we performed cardiac pressure overload by TAC surgery on wild type (8-week-old) mice to induce heart failure, and the control group received sham surgery. At 15 days after TAC surgery, mice were injected with JV001 to monitor cardiac function and structure at multiple time points over 56 days. In the Ang II study, heart failure in wild type mice was induced by subcutaneously infusing angiotensin II (Ang II, 1000ng/kg/min) into the mice for 28 days, and the control group took subcutaneous saline infusion instead. JV001 or Vector were manufactured and administered to mice via tail vein injection 10 days after Ang II administration. Finally, cardiomyocytes were isolated from mice and performed RNA-sequencing.

first: Alex

middle: C

last: Chang

first: Yinlong

last: Zhao

first: Xiaolu

last: Bao

first: Weiyao

last: Xiong


title: AMPK-p38 axis converts human pluripotent stem cells to naïve state

first: Zhennan

last: Yang

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

overall_design: Refer to individual Series

first: Junko

last: Yamane

first: Wataru

last: Fujibuchi

first: Shigeyuki

last: Shichino

first: Jun

last: Yamashita


title: microRNA expression in patients with pulmonary hypertension due to valve heart disease

city: Madrid

first: Ana I

last: Fernandez-Avila

state: Madrid

address: C/ Doctor Esquerdo, 46

department: Cardiology

country: Spain

institute: Hospital GU Gregorio Marañon

type: Non-coding RNA profiling by high throughput sequencing

summary: To delve deeper into the molecular mechanisms underlying pulmonary hypertension secondary to left heart disease (PH-LHD). In this study, we analyzed microRNA of a unique cohort of patients with persistent PH due to valvular heart disease (PH-VHD) to identify biological pathways associated with disease prognosis. The analysis was performed using the well-characterized SIOVAC (Sildenafil for Improving Outcomes after Valvular Correction) clinical trial cohort. We included 113 patients with demonstrated PH-LHD after valvular correction, and 30 VHD patients with no or mild PH (Control).

overall_design: smallRNA sequencing in 112 PH-VHD and 30 Control samples to compare patient clustering according to mRNA analysis

first: Jorge

last: Martinez-Solano

first: Javier

last: Bermejo