title: FBXL6 promotes bladder cancer progression by stabilizing ENO1 through K63-linked ubiquitination

city: Wuhan

last: Xiao

address: Donghu Road 169

department: Department of Urology

institute: Zhongnan Hospital of Wuhan University

summary: Ubiquitin-mediated post-translational modifications play critical roles in tumor progression, yet their regulatory mechanisms in bladder cancer (BLCA) remain incompletely understood. Here, we identified FBXL6, belonging to the F-box protein family, as a potential oncogenic driver in BLCA through integrative bioinformatic analysis of multiple public datasets and validation in clinical specimens. Functional analyses demonstrated that FBXL6 accelerates both the in vitro proliferation and migration of BLCA cells and the in vivo progression of tumors and metastatic spread. Mechanistically, transcriptomic profiling and metabolic analyses suggested that FBXL6 regulates glycolysis, with particular involvement of the glycolytic enzyme ENO1. While ENO1 mRNA remained largely unchanged upon FBXL6 knockdown, Western blot analysis revealed corresponding changes in ENO1 protein levels, indicating post-transcriptional regulation. Co-immunoprecipitation assays confirmed a physical interaction between FBXL6 and ENO1, and domain-mapping analysis revealed that the leucine-rich repeat (LRR) region of FBXL6 mediates ENO1 binding. Moreover, ubiquitination assays demonstrated that FBXL6 enhances K63-linked polyubiquitination of ENO1, leading to its stabilization. Restoration of ENO1 expression partially rescued the suppressed proliferation and migration induced by FBXL6 knockdown, as demonstrated by rescue assays. Overall, our data support a novel model in which FBXL6 facilitates BLCA progression through K63-linked stabilization of ENO1, highlighting its potential value in targeted therapy for bladder cancer.

overall_design: To uncover the underlying mechanism by which FBXL6 promotes BLCA tumor growth and metastasis, RNA-seq analysis was performed on T24 cells transfected with siNC or siFBXL6.

first: Ruoyu

last: Huang

first: Xinghuan

last: Wang


title: The KMT2F histone methyltransferase interacts with the RNA polymerase I machinery to promote ribosomal RNA transcription.

status: Public on Apr 24 2026

city: Hyderabad

first: Shweta

last: Tyagi

state: Telangana

address: Opp. to Metro Rail Pillar No.NUP-9, Inner Ring Road, Uppal

country: India

institute: Centre for DNA Fingerprinting and Diagnostics (CDFD)

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Trimethylation of histone 3 lysine 4 (H3K4me3) is a mark of active transcription, and its regulatory role in RNA polymerase II-mediated transcription has been well-studied. However, if and how this mark regulates RNA polymerase I (RNA Pol I) is not known. Here, we used customized genome assemblies for rDNA to demonstrate that KMT2A and KMT2F bind to entire rDNA loci. The binding of these enzymes was mirrored by the binding of H3K4me2 and H3K4me3 marks. Using biochemical assays, we demonstrate the interaction of KMT2- specific subunits with RNA Pol I transcriptional machinery. Our findings reveal KMT2F as the primary KMT depositing the H3K4me3 on rDNA. Loss of H3K4me3 adversely affects the epigenetic landscape and leads to repression of the rDNA locus. Mechanistically, using mammalian cells as a model system, we demonstrate that KMT2F promotes the formation of the pre-initiation complex by RNA Pol I. Our findings highlight the thus far undiscovered role of H3K4me3 in the transcriptional initiation of rDNA genes.

overall_design: Chromatin immunoprecepitation DNA-sequencing (ChIP-seq) for KMT2A and KMT2F reported in this study as well as ChIP seq data analysed for RNA Pol I,UBF,H3k4ME2 and H3K4me3 reported from other studies in HEK293T cells

first: Kaisar

middle: A

last: Lone

first: Amit

middle: M

last: Karole

first: Geethanjali

last: Ravindran


title: Ductal Epithelial MXD3 Promotes Disease Progression in Acute Pancreatitis through Wnt/b-catenin-Mediated Inflammation and Injury

status: Public on Apr 23 2026

city: Zhoukou

first: Xuejin

last: Liu

state: Henan

address: No. 26 East Renmin Road

department: Department of Gastroenterology

country: China

institute: Zhoukou Central Hospital Affiliated to Henan Medical University

type: Expression profiling by high throughput sequencing

summary: Acute pancreatitis (AP) is a severe inflammatory disease where epithelial injury and dysregulated repair are central to pathogenesis, yet the underlying transcriptional mechanisms remain poorly understood. This study employed an integrated approach to identify and characterize the transcription factor MXD3 as a master regulator of AP progression. Using single-cell RNA sequencing in a cerulein-induced rat AP model, we delineated a pathogenic epithelial trajectory from ciliated through non-ciliated to a proliferative state, with MXD3 emerging as the most significantly upregulated transcription factor in the proliferative cluster. Subsequent validation in pancreatic ductal epithelial-specific MXD3 knockout rats revealed profound protection against AP, manifesting as reduced histological damage, diminished fibrosis, attenuated neutrophil infiltration (MPO+ cells), and decreased expression of pro-inflammatory cytokines (IL-6, TNF-a, IL-1b). Mechanistically, we demonstrated that MXD3 directly activates the Wnt/b-catenin pathway, as evidenced by increased non-phospho b-catenin, its nuclear accumulation, and transcriptional upregulation of canonical targets (c-Myc, Cyclin D1, Axin2). Furthermore, functional rescue experiments confirmed the pathway's necessity, wherein the b-catenin inhibitor ICG-001 substantially reversed MXD3-driven apoptosis, necrosis, and pro-inflammatory cytokine secretion (IL-1b, IL-6, MCP-1) in vitro. Our findings establish a novel MXD3-Wnt/b-catenin axis as a crucial mechanism governing epithelial pathology in AP, revealing MXD3 as a promising therapeutic target for this debilitating condition.

relation:
Reanalysis of: GSM9464502
Reanalysis of: GSM9464503
Reanalysis of: GSM9464504
Reanalysis of: GSM9464505
Reanalysis of: GSM9464506
Reanalysis of: GSM9464507

overall_design:
We constructed a cerulein-induced acute pancreatitis (AP) model using wild-type mice, with 3 biological replicates in both the AP group and the saline-treated control group (n=3 per group).

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

last: Jia

first: Bingbing

last: Cui


title: Acquired genetic and cell state changes in IDH-mutant glioma progression [snATAC]

city: New Haven

first: Kevin

middle: C

last: Johnson

state: CT

address: 333 Cedar Street

department: Neurosurgery

country: USA

institute: Yale University

summary: Isocitrate dehydrogenase (IDH)-mutant gliomas are malignant brain tumors that typically arise in early- to mid-adulthood and nearly always recur following treatment. However, the genetic and cellular state changes that drive IDH-mutant glioma progression under treatment remain incompletely understood. Here, we integrated single-nucleus transcriptomic profiles, chromatin accessibility profiles and bulk DNA/RNA sequencing from 75 temporally separated gliomas across 35 patients comprising both the oligodendroglioma and astrocytoma IDH-mutant glioma tumor types. We show that malignant cell states transcriptionally resemble stages of normal glial-neuronal lineage development or a reactive mesenchymal-like state, mirroring states previously described in IDH-wildtype glioblastoma. Malignant cell states displayed distinct chromatin accessibility profiles that were comparable between both IDH-mutant glioma types. The abundance of less differentiated malignant cells increased with grade and with genetic alterations such as PDGFRA amplification. Longitudinal analysis highlighted two major malignant cell state transition patterns. First, reduced lineage differentiation and increased proliferative malignant cells at recurrence were pronounced in gliomas that acquired recurrence-associated genetic events, including treatment-associated hypermutation, increased copy number changes, and cell cycle alterations. Second, increased mesenchymal-like state abundance occurred independently of acquired genetic alterations and instead coincided with heightened macrophage expression. Overall, our findings provide an integrative model that traces the cell-intrinsic and extrinsic factors that shape cellular states during IDH-mutant glioma disease progression.

overall_design:
Nuclei from frozen IDH-mutant glioma tissues were isolated and profiled by 10x Genomics Multiome ATAC and Gene Expression. ATAC fragments are provided here.

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

last: Spitzer

first: Frederick

middle: S

last: Varn

first: Masashi

last: Nomura

first: Luciano

last: Garofano

first: Anna

last: Lasorella

first: Mario

middle: L

last: Suvà

first: Antonio

last: Iavarone

first: Itay

last: Tirosh

first: Roel

middle: G

last: Verhaak


title: Effects of GOLPH3 knock-out on the mouse liver transcriptomic profile

city: Lausanne

first: Giovanni

last: D'Angelo

address: Station 19

department: SV-IBI

country: Switzerland

institute: EPFL

summary: The Golgi complex serves as the central hub of the biosynthetic pathway, where anterograde and retrograde trafficking converge. How cargo and Golgi-resident proteins traverse this organelle has long been debated. Recent studies have identified a molecular machinery that sorts resident proteins into retrograde-directed COPI vesicles during cisternal maturation. Golgi phosphoprotein 3 (GOLPH3) is a key component of this system; however, its physiological relevance and regulatory mechanisms remain poorly defined. Here, we show that GOLPH3 depletion in mice alters both protein and lipid glycosylation, causes partially penetrant embryonic lethality and severely impairs growth and bone mineralization. At the molecular level, we find that GOLPH3 is regulated by functionally antagonistic S-acylation events that control the topology of its membrane association. To mediate retrograde trafficking of Golgi-resident glycosyltransferases, GOLPH3 must bind their cytosolic tails. This occurs via a negatively charged surface region, which is correctly oriented only in one of the S-acylated GOLPH3 conformations. Together, these findings reveal a lipid-mediated regulatory mechanism for intra-Golgi trafficking and establish the critical role of GOLPH3 in vertebrate development.

overall_design: Bulk RNA-seq profiling of  WT or GOLPH3-knockout mice liver samples obtained from both female and male cohorts.

first: Anastasia

last: Theodoropoulou

first: Anita

last: Nasrallah

first: Luciano A.

last: Abriata

first: Laurence

last: Abrami

first: Juliane

last: Da Graca

first: Irmak

last: Kaysudu

first: Francesco

last: Talotta

first: Maria J.

last: Marcaida

first: Muhammad U.

last: Anwar

first: Ondrej

last: Kovac

first: Sergey Y.

last: Vakhrushev

first: Alejandro

last: Calleja

first: Sylvia

last: Ho

first: Antonino

last: Asaro

first: Francisco S.

last: Mesquita

first: Leila

last: Alieh

first: Charlotte

last: Gehin

first: Lucie

last: Bracq

first: Nika

last: Gorsek

first: Sarah

last: Vacle

first: Arthur

last: Samurkas

first: Alessio

last: Prunotto

first: Miroslav

last: Machala

first: Olaia

last: Naveiras

first: Katrine T.

last: Schjoldager

first: F. Gisou

last: Van der Goot

first: Matteo

last: Dal Peraro


title: Acquired genetic and cell state changes in IDH-mutant glioma progression [snRNA-seq]

first: Kevin

last: Johnson

overall_design:
Nuclei from frozen IDH-mutant glioma tissues were isolated and submitted to a 10x Genomics workflow for profiling by single-nucleus RNA-sequencing.

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

first: Avishay

last: Spitzer

first: Frederick

last: Varn

first: Masashi

last: Nomura

first: Luciano

last: Garofano

first: Anna

last: Lasorella

first: Mario

last: Suvà

first: Antonio

last: Iavarone

first: Itay

last: Tirosh

first: Roel

last: Verhaak


title: Complement-regulated Homeostatic Proliferation Controls Memory B Cell Longevity and Repertoire Composition

city: New York

first: David

last: Dominguez-Sola

state: NY

address: One Gustave L. Levy Place, Box 1044A

department: Oncological Sciences

institute: Icahn School of Medicine at Mount Sinai

summary: Memory B cell (Bmem) survival is essential for guarding against reinfection, yet processes ensuring their longevity remain unclear. As decay-accelerating factor (DAF, CD55), a negative regulator of complement activation, is requisitely downregulated on germinal center B cells and is re-expressed on Bmem, we investigated the effects of deleting DAF on murine (B1-8hi) Bmem in competitive settings. Kinetic analysis showed a progressive reduction in DAF-/- Bmem numbers over six weeks, without affecting Bmem production, pool size, or their ability to respond to rechallenge. Following transfer into unimmunized hosts, wild-type Bmem proliferated to maintain stable Bmem pool sizes, outcompeting DAF-/- Bmem, reflecting homeostatic proliferation. Reduced proliferation and increased cell death in DAF-/- Bmem associated with transcriptional differences in metabolism and migration pathways. Wild type Bmem proliferation increased in C3-/- hosts, and vaccination with a heterologous antigen, which induces local complement activation, locally inhibited bystander B1-8hi Bmem proliferation. Thus, complement-dependent regulation of Bmem homeostatic proliferation influences Bmem longevity and repertoire composition in mice.

overall_design: RNA-Seq profiling of flow-sorted wildtype and DAF/CD55-null memory B cells (B220+ IgD- CD38+ GL7- Igλ+ NP+), sorted using congenic markers (CD45.2 for wildtype, CD45.2 for DAF KO). Each replicate is a pool of 2-3 mice. Cells isolated 4 weeks after immunization.

first: Evan

last: Cody

first: Peter

last: Heeger


title: Interleukin-34 induced Arg1+ macrophages play a key role in breast cancer brain metastasis.

city: Durham

first: Vaibhav

last: Jain

state: North Carolina

address: 300 N Duke St

department: Duke Molecular Physiology Institute

institute: Duke University

summary: We use 10x Genomics to perform the Single cell RNA sequencing result shows cell type clusters and percentage of the corresponding cell types in the HP organoids that we used for our model.

overall_design: To further define the cell types present in these organoids, we performed single cell RNA-Seq (scRNA-Seq) on the HP organoids.

first: Xiaoqing

last: Cheng

first: Khooshbu Kantibhai

last: Patel

first: Maureen

last: Highkin

first: Simon

last: Gregory


title: Interleukin-34 induced Arg1+ macrophages play a key role in breast cancer brain metastasis

summary: We use 10x Genomics to perform the visium RNA sequencing on two tumor tissue, which showed cell type clusters and whole genome profiling in each cell clusters. Visium CytAssist Spatial Gene Expression kit was used for FFPE (Mouse Transcriptome, 6.5 mm, 4 rxns, PN-1000521,10x Genomics).

overall_design: To study the tumorenvironment and  the cell types present in those breast cancer brain metastases, we generated spatial transcriptomics data from two biological replicates of the cerebellar BCBM generated from HP organoids.


title: Acquired genetic and cell state changes in IDH-mutant glioma progression [organoids]

first: Kevin

last: Johnson

overall_design:
Freshly resected glioma samples were used to produce IDH-mutant glioma organoids as described by Jacob et al Cell 2020 (PMID: 31883794). Tumor tissue diagnosis was performed by pathological assessment and confirmed with molecular information provided by clinical whole exome sequencing. All three organoid models were confirmed to be IDH1-mutant astrocytomas with immunohistochemistry confirming that the organoids maintained the IDH1 R132H mutation. For each patient-derived glioma organoid model (GBO), samples were either treated with a single 10Gy dose of irradiation or were not exposed to irradiation (control) followed by recovery for 7 days before single-cell RNA sequencing.

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

first: Tanyeri

last: Barak

first: A. Gulhan

last: Ercan-Sencicek

first: Ayse Buket

last: Peksen

first: Linbin

last: Zhang

first: Jennifer

last: Moliterno


title: Distinct activity in prefrontal projections promotes temporal control of action

city: Iowa

first: Nandakumar

last: Narayanan

state: IA

address: 169 Newton Road

department: Neurology

institute: University of Iowa

summary: Prefrontal neurons can have diverse activity during cognitive functions such as working memory, attention, and timing; however, the importance of this heterogeneity is unclear. Our goal was to better understand the diversity of prefrontal activity through anatomical connectivity. We harnessed circuit-specific tools in mice to capture activity within prefrontal projections during interval timing, a highly translational cognitive process that requires working memory for temporal rules and attention to the passage of time to estimate a temporal interval of several seconds. We used neuronal recordings to capture prefrontal activity during interval timing, with major patterns characterized by monotonic time-dependent ramping over a temporal interval. We then leveraged retrograde viruses to interrogate prefrontal cortex (PFC) projections to the mediodorsal thalamus (PFC-MD) and to the dorsomedial striatum (PFC-DMS). We report three novel results. First, circuit-specific calcium fiber photometry revealed that PFC-MD and PFC-DMS activity encoded distinct temporal signals, with PFC-MD projections ramping down and PFC-DMS ramping up to interval timing response times. Second, circuit-specific inactivation revealed that PFC-DMS inactivation disrupted animals’ internal estimates of time. Third, circuit-specific single-nucleus RNA sequencing of prefrontal projections revealed distinct transcriptomic profiles between PFC-MD and PFC-DMS projections, with enriched genes for cortical layers as well as genes such as Cux2, Camk2n1, Htr4, and Foxp2. These data suggest differences in gene expression and connectivity distinguish prefrontal activity during interval timing. These findings advance our fundamental understanding of prefrontal function and dysfunction in human disease.

overall_design: To label PFC projection neurons, male and female H2B-TRAP mice received bilateral stereotaxic injections of retrograde AAV-Cre into either the mediodorsal thalamus (MD) or dorsomedial striatum (DMS). After a 2-week recovery period, mice were sacrificed, and dorsal and ventral PFC tissues were microdissected based on mCherry fluorescence. mCherry-positive nuclei were isolated and collected by fluorescence-activated nuclei sorting for downstream single-nucleus analyses.

first: Xin

last: Ding

first: Trevor

last: Butler

first: Jon

last: Resch

first: Matthew

last: Weber

first: Alexandra

last: Bova

first: Stephanie

last: Guerrero

first: Rachel

last: Cole

first: Christopher

last: Hunter

first: Hannah

middle: R

last: Stutt

first: Madison

last: McMurrin

first: Mackenzie

last: Spicer

last: Conlon

first: Shane

last: Heiney

first: Youngcho

last: Kim


title: Runx3 instructs Aire+ mTEC development, TSA gene expression, and central tolerance

city: San Francisco

first: Jun Hyung

last: Sin

state: CA

address: 513 Parnassus Ave S-1076

department: Pediatrics

institute: University of California, San Francisco

summary: The transcription factor Runx3 modulates key gene expression programs important for the development of multiple tissues. Here, we uncover new functions for Runx3 in thymic epithelial lineage development and show Runx3 expression in medullary thymic epithelial cells (mTECs) is required for both Autoimmune Regulator + (Aire+) mTEC development and tissue-specific antigen (TSA) gene expression. Consequently, TEC-specific deletion of Runx3 in mice results in a profound decrease in Aire+ mTECs, a global loss of TSA gene expression, and the development of autoimmunity. Moreover, loss of Runx3 in TECs results in an expansion of immature CCL21+ mTECs and a loss of Aire-dependent mimetic cells. Single-cell analysis reveals Runx3 modulates core transcriptional programs in TECs that correlate with the observed cellular changes. Our findings highlight a previously undescribed role for Runx3 in mTEC development and thymic central tolerance.

overall_design: scRNA-sequencing EpCAM+ mTECs from Runx3 cKO mice and Runx3 WT mice

first: Sloan

middle: H

last: Phillips

first: Michael

last: Waterfield


title: PROX1 loss in adult mouse Schlemm’s canal causes permanent ocular hypertension

city: Chicago

first: Benjamin

last: Thomson

state: IL

address: 303 E Superior St. SQ8-500

department: Feinberg Cardiovascular and Renal Research Institute

institute: Northwestern University Feinberg School of Medicine

summary: Glaucoma is associated with ocular hypertension and lowering intraocular pressure is a key objective of glaucoma therapies. Recent studies have established a role for the Schlemm’s canal endothelium in this pressure increase and have shown it to have a unique, lymphatic-like, hybrid phenotype. However, the role of these lymphatic phenotypes in the adult canal remains uncertain. Long-term functional studies have been limited by systemic importance of lymphatic genes and lack of Schlemm’s canal–specific animal models. Here, we designed and validated a strategy using 4OH-tamoxifen-loaded nanocarriers to generate targeted, Schlemm’s canal specific knockout mice lacking lymphatic phenotypes. Using this system, we selectively deleted Prox1, the master transcription factor governing lymphatic fate. Within four weeks, intraocular pressure significantly increased, and ocular hypertension was maintained for at least 24 weeks. Unlike lymphatic vessels, which degenerate following Prox1 deletion, Schlemm’s canal reverted to a less functional vein-like phenotype with no change in size or morphology.  These results highlight the utility of nanocarriers for tissue-specific genetic recombination and demonstrate that changes in lymphatic phenotypes alter intraocular pressure, providing new targets for glaucoma therapy. Moreover, as we found that PROX1 was downregulated with age in human Schlemm’s canal, these canal-specific conditional Prox1 knockout mice are a valuable new adult-onset model of ocular hypertension that captures key features of age-related human disease.

overall_design: Bulk RNA sequencing of total RNA isolated from primary human Schlemm's canal endothelial cells treated with either scrambled control siRNA or PROX1-specific siRNA

first: Sofia

last: Ochoa

first: Hoi Lam

last: Li

first: Hyeohn

first: Zihang

last: Yan

first: Natalia

last: Mendonca

first: Pan

last: Liu

first: Hyunjoo

middle: J

last: Lee

middle: P

last: Vincent

first: Hao

middle: F

last: Zhang

first: Haiyan

last: Gong

first: Evan

last: Scott

first: Mark

last: Johnson


title: Transcriptomic profile of the hippocampus of rat strains with contrasting nervous system excitability

status: Public on Apr 25 2026

city: Калининград

first: Irina

last: Shalaginova

state: Калининградская область

address: Черняховского 36-11

country: Russia

institute: Pavlov Institute of Physiology

summary: Bulk RNA sequencing of the hippocampus in male rats from two selectively bred strains differing in nervous system excitability: LT (low threshold, high-excitability) and HT (high threshold, low-excitability). The aim was to characterize baseline interstrain transcriptomic divergence in intact animals and identify major functional themes associated with inherited differences in excitability.

overall_design: Hippocampal tissue was collected from intact 5-month-old male rats of two selectively bred strains, LT and HT, with 5 biological replicates per group. Total RNA was extracted from the whole hippocampus, poly(A)+ RNA libraries were prepared, and single-end 50-bp sequencing was performed on the Illumina HiSeq1500 platform. Differential expression was assessed between LT and HT samples.


title: ATF7ip inhibits the tumor immune response by promoting terminal CD8+ T cell Exhaustion III

summary: CD8+ T cell exhaustion limits the immune response to tumors because of ineffective T cell effector functions. Thus, therapies that inhibit T-cell exhaustion are critical for optimizing cancer treatment. Recent studies have implicated epigenetic proteins in T-cell exhaustion. Here, we identified activating transcription factor 7 interacting protein (ATF7ip) as an epigenetic protein critical for inducing T cell exhaustion. Loss of Atf7ip in CD8+ T cells results in decreased terminal exhaustion and increased numbers of progenitor-exhausted cells in both chronic viral infections and cancer. Owing to decreased exhaustion, Atf7ip-deficiency in CD8+ T cells leads to an enhanced immune response to tumors. Mechanistically, ATF7ip functions to stimulate the deposition of repressive H3K9me3 at critical immune-effector gene loci, such as Il7r and Il2 leading to enhanced exhaustion. Our data suggest that ATF7ip may be a rational target for deletion in adoptive T-cell therapies to reduce CD8+ T-cell exhaustion.

overall_design: Approximately 500 intratumoral P14+/Atf7ip-sufficient or 500 intratumoral P14+/Atf7ip-deficient CD8+ T cells per sample were sorted directly into lysis buffer from the SMART-seq v4 [Takara Bio] kit. Lysed cells were given to the UCSF Genomics COLAB for Library Preparation. Libraries prepared by the core were submitted to the UCSF Center for Advanced Technology for single-end sequencing.

first: Sujit

last: Kashyap


title: ATF7ip inhibits the tumor immune response by promoting terminal CD8+ T cell Exhaustion II

first: Jun Hyung

last: Sin

overall_design: p14+Cd8+ T cells from tumors of 3-4 Atf7ip-sufficient and Atf7ip-deficient mice were pooled and FACS sorted into 1.5 ml tubes containing DMEM with 2 FBS. About 20,000 cells per 100 ul were sent out for 10X sequencing. Single cells were captured using the 10X chromium microfluidics system and barcoded and sequenced on the Illumina NovaSeq.


title: MECP2 Mutations Rewire Human ESC Fate and Bias Cortical Lineage Commitment II

city: Montreal

first: Anthony

last: Flamier

state: QC

address: 3175 chemin de la Côte-Sainte-Catherine

department: Neurosciences

country: Canada

institute: Université de Montreal

summary: Rett syndrome arises from loss-of-function mutations in the X-linked chromatin regulator MECP2, yet the earliest molecular derailments in human development remain poorly defined. Using isogenic hESC models carrying three patient-derived MECP2 mutations, we followed the transcriptome from pluripotency through neuro-ectoderm, neural stem, and neural progenitor stages and into four-month cerebral organoids. Stage dominated transcriptional variance, but mutants shared a secondary program enriched for synaptic-membrane and extracellular-matrix genes. Single-cell profiling revealed a naïve-like, hyper-proliferative state marked by up-regulation of ZFP42 at ESC stage. Strikingly, EMX1, a cortical radial-glia determinant, was consistently suppressed from the earliest stage onward, and cerebral organoids subsequently generated fewer excitatory neurons in favour of inhibitory and glial lineages. These data chart a continuous developmental trajectory for MECP2-mutant human cells and nominate ZFP42 and EMX1 dysregulation as tractable entry points for dissecting Rett pathogenesis.

overall_design: Single-nucleus RNA sequencing on MECP2-WT, MECP2-R133C, MECP2-R168X and MECP2-R270X cerebral organoids (3 months old).

first: Marion

last: Guillon

first: Margaux

last: Brin


title: MECP2 Mutations Rewire Human ESC Fate and Bias Cortical Lineage Commitment [RNA-Seq]

overall_design: Bulk RNA sequencing on MECP2-WT, MECP2-R133C, MECP2-R168X and MECP2-R270X hESC lines differentiated for 0 (hESC), 3 (Neuroectoderm), 7 (Neural progenitor) and 21 (Neural stem) days.


title: MECP2 Mutations Rewire Human ESC Fate and Bias Cortical Lineage Commitment

overall_design: Single-cell RNA sequencing on MECP2-WT, MECP2-R133C, MECP2-R168X and MECP2-R270X hESC lines.


title: A time-resolved atlas of histone modifications during mitotic entry

city: Edinburgh

first: Shaun

middle: Michael

last: Webb

address: 2.21 Swann Building, Kings Buildings

department: Wellcome Trust Centre for Cell Biology

country: United Kingdom

institute: University of Edinburgh

summary: Mitotic chromosome formation is essential for faithful chromosome segregation in metazoans. While condensin complexes are critical for the formation of rod-shaped mitotic chromosomes, additional mechanisms—particularly those involving phosphorylation and deacetylation of specific histone residues—have been proposed to contribute a further 2- to 4-fold reduction in mitotic chromatin volume. In this study, we employ high-resolution mass spectrometry to determine the kinetics of histone modifications in cell cultures undergoing a highly synchronous mitotic entry at 2.5-minute resolution. Our analysis reveals three different programmes of histone H3 phosphorylation on T3, S10 and S28. These modifications are consistent with methyl-phos switches regulating the association of readers with chromatin other than at promoters. Mass spectrometry and quantitative ChIP-Seq reveal that H3 T3 phosphorylation is a general marker of heterochromatin and not specifically centromeres as previously suggested. Finally, we show that histone acetylation undergoes only modest changes as rod-shaped chromosomes form during unperturbed mitotic entry. Thus, previously reported reductions in acetylation associated with chromosome formation were apparently attributable to delays in mitotic exit used as part of mitotic synchronisation protocols. The mechanism of condensin-independent chromatin compaction in mitosis remains unexplained.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for H3K4me1, H3K4me2, H3K4me3, H3K9me3 and Caliburated ChIP-seq for H3T3ph and CENP-H in G2, prophase, and prometaphase.

first: Moonmoon

last: Deb

middle: Y

last: Kochanova

first: Axel

last: Imhof

first: William

last: Earnshaw


title: First-in-Class CAR T Cell Therapy Selectively Eliminates Mutant Calreticulin-Driven Malignancies in a Fibrotic Niche

city: Oxford

first: Bethan

last: Psaila

state: Oxfordshire

address: John Radcliffe Hospital MRC Weatherall Institute – Molecular Medicine

department: MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine

institute: University of Oxford

summary: Pathogenic mutations in calreticulin (mutCALR) are found in one third of patients with myeloproliferative neoplasms. All mutCALR variants yield the same protein neoepitope that forms an aberrant complex with the thrombopoietin receptor, driving oncogenic stem cell expansion, megakaryocyte hyperplasia and fibrosis. We developed a novel, first-in-class chimeric antigen receptor (CAR) T-cell therapy targeting mutCALR and evaluated efficacy in a bespoke human chimeroid model of the bone marrow. We used 10x single-cell RNA sequencing (scRNA-seq) to analyze cell composition, transcriptional differences, and cell-cell interactions.

overall_design: Human iPSC-derived bone marrow organoids were engrafted with either mutCALR+ CD34+ stem/progenitor myelofibrosis cells, mutCALR-targeting CAR T cells, none, or both. These 'chimeroids' were pooled together (n=12 per condition) and dissociated after 72 hours in culture. scRNA-seq libraries were prepared with live, FACS-isolated cells.

first: Zoë

last: Wong

first: Charlotte

middle: K

last: Brierley


title: Hypoxia shapes both therapeutic response and resistance in metastatic clear cell renal cell carcinoma [Spatial Transcriptomics]

first: Fengshen

last: Kuo

state: New York

address: 1275 York Ave

institute: Memorial Sloan Kettering Cancer Center

summary: Vascular endothelial growth factor receptor-targeting tyrosine kinase inhibitors (VEGFR-TKIs) and aPD1 combinations are effective in multiple solid tumors, particularly in clear cell renal cell carcinoma (ccRCC), due it’s characteristic pseudo-hypoxic, hyper-angiogenic state driven by biallelic VHL-loss. However, long-term durability is inferior to dual aPD1/aCTLA4 regimens, yet the mechanisms underlying these differences remain unclear. Since tumor-associated macrophages (TAMs) are implicated in therapeutic resistance, we used scRNAseq to investigate TAM evolution following VEGFR-TKI, aPD1 and combined VEGFR-TKI/aPD1 treatment in a transgenic ccRCC mouse model. We identify hypoxia-responsive SPP1+ TAMs that are absent in baseline pseudo-hypoxic tumors. This proxy of true hypoxia tracks with successful response to VEGFR-TKI/aPD1 in mouse and human on-treatment samples, reflecting treatment-induced hypoxic necrosis. Paradoxically, pretreatment hypoxia predicted worse outcomes across multiple VEGFR-TKI/aPD1 trial and real-world cohorts and extended exposure to hypoxia-inducing VEGFR-TKIs and aPD1 exacerbated metastasis in mice, highlighting the dual implications of hypoxia in ccRCC disease trajectory.

overall_design: FFPE sections from advanced ccRCC tumors surgically resected following various tyrosine kinase inhibitor (TKI) or immune checkpoint blockade (ICB) therapy combinations, were analysed by Visium (v1) spatial transcriptomics.

first: Lynda

last: Vuong

first: Abraham

last: Hakimi


title: Hypoxia shapes both therapeutic response and resistance in metastatic clear cell renal cell carcinoma [scRNAseq]

overall_design: Advanced ccRCC tumors surgically resected following various tyrosine kinase inhibitor (TKI) or immune checkpoint blockade (ICB) therapy combinations, were minced, digested, flow sorted for live cells, and analysed by scRNAseq.


title: Hypoxia shapes both therapeutic response and resistance in metastatic clear cell renal cell carcinoma [bulk RNA-seq]

overall_design: Bulk RNAseq analysis of flash frozen or FFPE pre-treatment surgically resected tumors from ccRCC patients who later received various tyrosine kinase inhibitor (TKI) or immune checkpoint blockade (ICB) therapy combinations.


title: Detachment-induced gene expression changes in lung adenocarcinoma cell lines, A549 and H441.

city: Shimotsuke

first: Toshiro

last: Niki

state: Tochigi

department: Department of Pathology

country: Japan

institute: Jichi Medical University

summary: The aims of the study was to analyze gene expression changes induced by detachment from culture plate.

overall_design:
Lung adenocarcinoma cell line, A549 and H441, were plated onto ultra-low attachment culture plate and RNA was extracted at day 1 and day 7 using the RNeasy Mini Kit. A549 and H441 cells that were cultured and maintained on ultra-low attachment culture plate for more than 2 months were designated A549-FL and H441-FL, respectively. RNA was extracted from A549-FL and H441-FL cells, both in standard culture and in ultra-low attachment culture. The RNA samples were then subjected to Agilent microarray analysis. There were no replicates for each sample (n=1).

In the normalized expression data, ID_REF represents the Agilent FeatureNum. Annotation information linking FeatureNum to probes and genes is provided in the supplementary file GSE319366_RAW.tar.

first: Daisuke

last: Komura


title: Hypoxia shapes both therapeutic response and resistance in metastatic clear cell renal cell carcinoma

overall_design: Individual tumors from KVpR mice treated with Lenvatinib, aPD-1, CSF1Ri or combinations were dissected, digested, flow sorted for live cells, and analysed by scRNAseq.


title: Thymic alveolar type II epithelial mimetic cells revealed by Runx1-deficiency [CUT&Run]

last: Sin

summary: The mechanisms used to prevent autoimmune lung disease are incompletely understood. Recent studies in the thymus have identified unique populations of medullary thymic epithelial cells (mTECs) called mimetic cells that transcriptionally mimic peripheral epithelial populations. These mimetic cells have been found to have important functions in the thymus in immune tolerance and the diversity and cell types represented in this pool of cells represents an active area of investigation. Here, we utilized a mouse line with thymic specific deletion of the Runt related transcription factor 1 (Runx1) to identify a novel mimetic cell type that transcriptionally mimic alveolar type II (AT2) lung epithelial cells. Runx1 binds to genomic regions associated with epidermal growth factor receptor (EGFR) signaling suggesting a function for EGFR in regulating AT2 mTEC development.

overall_design:
CUT & RUN of Runx1, IgG, and H3K27ac in EpCAM+ mTECs from B6 control mice:
WT1 = CUT&Run of IgG
WT3 = CUT&Run of Runx1
WT5 = CUT&Run of H3K27ac

first: Michael

last: Waterfield


title: Transcriptome of Ag-specific B cells upon stimulation with soluble or particulate Ag

first: Julie

last: Zikherman

address: 513 Parnassus Ave

department: Medicine, Rheumatology

summary: Primary B cells from MD4 mice have transgenic B cell receptors that recognize hen egg lysozyme (HEL).  Previous studies have shown that antigens presented in different formats induce qualitatively different signaling responses in B cells.  Here, we compare the transcriptomes induced by the following stimuli: LPS (10 mg/mL), particulate HEL (1pM liposomes with reduced affinity HEL-3X protein conjugated to surface at epitope density 243), soluble HEL (1mg/mL), and co-stimulation with soluble HEL and anti-CD40 (100 ng/mL).

overall_design: Lymph nodes were harvested from MD4 mice and B cells were purified by benchtop negative selection. 10^6 B cell / well were plated into 96 well plates with aforementioned stimuli in abstract in total of 200uL media. Following overnight in vitro stimulation in culture at 37C, B cell pellets were snap frozen for RNA-sequencing. Three biological replicates were prepared for each condition. Unstimulated samples were harvested after 2 hr 27C culture.

first: Julianne

last: Riggs

first: Alexander

last: Ritter


title: Thymic alveolar type II epithelial mimetic cells revealed by Runx1-deficiency [scRNA-seq]

first: Jun Hyung

overall_design: scRNA-sequencing EpCAM+ mTECs from Runx1 cKO mice and Runx1 WT mice


title: Flavonoid and isoflavonoid biosynthetic gene expression is affected by MYB36 transcription factor deficiency in Lotus japonicus

city: Sevilla

first: MARCO

last: BETTI

state: Sevilla

address: C. Prof. García González 1

department: Bioquímica Vegetal y Biología Molecular

country: Spain

institute: Universidad de Sevilla

summary: MYB36 was recently identified as a transcription factor (TF) that may be involved in isoflavonoid metabolism and stress responses in the model legume Lotus japonicus. To further explore its role, we performed a comparative transcriptomic and (iso)flavonoid profiling analysis of wild-type (WT) plants and two independents homozygous Ljmyb36 mutant lines under two abiotic stress conditions: UV-B irradiation and salinity. The results obtained showed a markedly distinct and almost reciprocal global transcriptomic response of WT plants under both types of stress conditions. Under UV-B irradiation, genes related to isoflavonoid biosynthesis were induced, accompanied by increased isoflavonoid accumulation. In contrast, under salt stress, most of the genes modulated in the mutants corresponded to genes specifically involved in isoflavonoid, but not flavonol biosynthesis, highlighting candidate genes potentially regulated by MYB36. Metabolite profiling also indicated opposite changes in flavonoid and isoflavonoid metabolite in response to salt and UV-B treatments, reflecting the reciprocal patterns of gene expression found in salt and UV-B treatment conditions. These results suggest a role, for the first time, of MYB36 as a specific transcription factor in the regulation of (iso)flavonoid biosynthesis. In addition, the results obtained support the role of MYB36 as a crucial TF in the response to salt stress in legume plants.

overall_design: Lotus japonicus WT and two independent LORE1-insertion mutants MYB36 lines were used. RNAseq analysis was carried out in the shoots of plants under control conditions (no abiotic stress) and after UV-B treatment or salt stress treatment. Three independent biological replicates were used for each genotype/condition, with each biological replicate consisting of 5 plants pooled together for RNA extraction.

first: María

middle: D

last: Monje-Rueda

first: Margarita

last: García-Calderón


title: Single cell RNA-sequencing of the preoptic area of hypothalamus from sleep deprivation and rebound sleep mice

city: Shanghai

first: Huateng

last: Cao

address: 320 Yue Yang Road

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

summary: Using single-cell transcriptomics to search for hypothalamic neurons representing and controllling sleep pressure, we identified a group of neurons expressing Gpr139  in the preoptic area (POA) selectively activated during rebound sleep (RS) after sleep deprivation (SD).

overall_design: Wildtype mice underwent 6 hours SD or SD followed 2 hours RS, brain tissues of the POA region were dissected and applied to scRNA-seq. Single-cell transcriptomic analyses of cluster markers and immediate early genes were performed to identify neuron population in the POA activated during rebound sleep.

first: Zhe

last: Zhang


title: DNA methylation modulation by Azacytidine can restore T cell function and exhaustion in AML.

status: Public on Apr 22 2026

city: Portland

first: Brett

last: Davis

state: Oregon

address: 3181 SW Sam Jackson Park Rd

institute: Oregon Health and Science University

type: Methylation profiling by high throughput sequencing

summary: AML is an aggressive malignancy of the blood and bone marrow associated with poor clinical outcome. Chemotherapy remains the standard of treatment, yet relapse is common, highlighting the need to find alternative therapies. T cell dysfunction and exhaustion are prominent in AML and represent a key barrier to effective immunotherapy. DNA methylation is a major driver of T cell exhaustion and inhibition of de novo methylation can restore T cell function in other disease contexts. Here we investigated the impact of Azacytidine (Aza), an FDA approved hypomethylating agent, on T cell exhaustion in AML. Using a spontaneous AML mouse model and AML patient samples, we find that Aza treatment modulates T cell function. In vivo Aza treatment decreased tumor burden and reshaped CD8+ T cells states, increasing memory subsets and decreasing regulatory T cells (Tregs) frequency in mice. Functionally, Aza treatment overcomes the impaired proliferation in both CD4 and CD8+ T cells in our model.  DNA methylation sequencing reveled hypomethylation and increased expression of stem like precursor gene TCF7 and E2F2, a regulator of cell cycle progression and proliferation. Similar changes in phenotypes are observed in cultures of AML patient samples with Aza. Collectively, we show that Aza remodels epigenetic and functional states in AML and has the potential to reverse T cell exhaustion, with enhanced memory and proliferation capacity. Our work provides a mechanistic framework supporting the rationale of combining hypomethylating agents with T cell based immunotherapies for this lethal disease.

overall_design: After treatment with Aza or PBS for three weeks, CD4 and CD8+ T cells were isolated from spleens of these mice and reduced representation bisulphite sequencing was performed

first: Ravina

last: Pandita

first: Yoko

last: Kosaka

first: Jessica

last: Mulkey

first: Lucia

last: Carbone

first: Evan

last: Lind


title: Hepatocyte-specific PPARγ Deletion Uncovers Role of an Antagonistic PPARγ–HNF4α Transcriptional Axis in MASLD Progression

city: Pittsburgh

first: Shuchang

last: Liu

state: PA

address: 203 Lothrop Street

institute: University of Pittsburgh

summary: Systemic PPARγ agonist therapies have been investigated for clinical use in MASLD. Previous studies, however, have shown that PPARγ activation in hepatocytes worsens MASLD. Overall, the precise molecular mechanisms regulated by PPARγ in hepatocyte during MASLD remain incompletely defined. Hepatocyte-specific PPARγ knockout mice were fed a clinically-relevant fast-food diet (FFD) for 2 or 5-months to characterize the role of PPARγ in MASLD progression. PPARγ expression and activity were increased in murine FFD-model and in hepatocytes of human MASLD/MASH patients, based on single-nucleus RNA-sequencing analysis. PPARγ-deletion conferred protection against diet-induced steatosis, fibrosis, and liver injury by suppressing lipogenic, inflammatory, and fibrogenic signaling. Although de-novo fatty-acid synthesis was only modestly affected and compensated with disease progression, enhancement of lipolysis and suppression of lipid droplet stabilization machinery was persistent. PPARγ-deletion robustly inhibited expression and signaling-activity of TGFβ1, a master regulator of hepatic ¬fibrosis, throughout the progression of MASLD. Importantly, a novel PPARγ-HNF4α regulatory axis in MASLD was identified, with increased HNF4α mRNA/protein expression and activation of its downstream metabolic networks in PPARγ-deficient livers. Further, integration of ChIP-seq and transcriptomic analysis revealed that HNF4α might be co-regulating a major fraction (>70%) of genes under direct control of PPARγ during MASLD. This study provides a comprehensive temporal framework for hepatocyte PPARγ function in MASLD, revealing an antagonistic PPARγ-HNF4α transcriptional network that governs hepatic metabolic fate.

overall_design: Male PPARγflox/flox mice (Jackson Laboratory, stock #004584) at 8 weeks of age received a single intraperitoneal injection of adeno-associated virus AAV8.TBG.PI.Cre.rBG (2.5 × 1011 viral particles/mouse) to generate hepatocyte-specific PPARγ knockout (KO) mice. This vector expresses Cre recombinase under the control of the hepatocyte-specific thyroxine-binding globulin (TBG) promoter. Control littermates received the same dose of AAV8.TBG.PI.eGFP.WPRE.bGH (2.5 × 1011 viral particles/mouse). Both viral preparations were obtained from Addgene (Cre vector: #107787-AAV8; eGFP vector: #105535-AAV8). Following AAV8 injections, both KO and control groups were placed on a “fast-food” diet (FFD; ENVIGO #TD.88137), consisting of high saturated fat (21% by weight; 42% kcal from fat), cholesterol (0.2%), and sucrose (34% by weight), accompanied by fructose-glucose–enriched drinking water (18.9 g/L d-glucose and 23.1 g/L d-fructose) as previously described. Mice were maintained on this regimen for either 2 or 5 months.

first: Shehnaz

last: Bano

first: Matthew

last: Copeland

first: Jia-Jun

first: Anne

last: Orr

first: John

middle: W

last: Stoops

first: Wendy

last: Mars

first: Silvia

first: Joseph

last: Locker

first: George

last: Michalopoulos

first: Bharat

last: Bhushan


title: Osteopontin mediates acquired resistance to hypoxia-inducing antiangiogenics and promotes anti-PD-L1 refractoriness in breast cancer models

city: Madrid

first: Leonardo

middle: Daniel

last: Garma

state: Madrid

address: Melchor Fernández Almagro 3

institute: Spanish National Cancer Research Center

summary: Resistance to antiangiogenics is a major challenge in cancer therapy. These agents can either normalize or exacerbate tumor vascular abnormality and hypoxia. The mechanisms of resistance remain unclear in the latter setting. By integrating data from mouse models and clinical trials, we showed that hypoxia-inducing anti-VEGF therapy upregulated programmed cell death ligand 1 (PD-L1), yet failed to sensitize tumors to PD-L1 blockade. Mechanistically, early hypoxic stress triggered epithelial osteopontin (SPP1) production, which recruited monocytes and skewed macrophages toward M2 states, suppressing T cell cytotoxicity. Pharmacological SPP1 depletion impeded the development of hypoxia, reduced M2 infiltration, restored T cell activity, and enabled synergy between antiangiogenics and anti-PD-L1. Genetic dissection - tumor-epithelial Spp1-KO grafts and bone marrow chimeras generated by lethal irradiation and reconstitution with Spp1-/- or WT hematopoietic donors - showed that myeloid SPP1 contributed only marginally compared with epithelial SPP1. These findings identified SPP1 as a central mediator of resistance to hypoxia-inducing antiangiogenics, contributed to a comprehensive model of antiangiogenic resistance, and supported SPP1-targeted strategies to personalize immunotherapy and antiangiogenic therapy according to tumor hypoxia.

overall_design: Splenocyte-derived cells from wild-type FVB mice were co-cultured with RAW 264.7 cells that were exposed to different experimental conditions: normoxia +/-Spp1 and hypoxia +/-Spp1 for 72h. First, Raw 264.7 cells were seeded in a 24-well plate (40,000 cells/well) and placed in a humidified 5% CO2 incubator at 37 °C. After 24h, fresh media with/without Spp1 (Biotechne, #441-OP-050/CF) at 1 g/mL were added to the corresponding wells, and cultures were maintained under normoxic (21%O2 and 5%CO2) or hypoxic (1%O2, 5%CO2 and 94%N2) incubator conditions. After 72h, primary splenocytes were obtained from wild-type FVB mice. Briefly, WT mice were sacrificed in a  CO2 chamber, and their spleens were harvested in cold PBS immediately after sacrifice. Splenocytes were mechanically dissociated using a syringe plunger. The cell suspension was filtered thought a 40µM strainer and centrifuged at 300g for 5 min at room temperature (RT). Red blood cells were lysed using RBC lysis buffer (Invitrogen, #00-4333-57). After  centrifugation, 300× g for 5 min, the cell pellet was resuspended in DMEM supplemented with 10% fetal bovine serum for counting. 1.5x106 splenocytes per well were co-cultured with RAW 264.7 cells exposed to different conditions. Cultures were maintained at 37ºC in a 5% CO2 atmosphere for 48 h. After 48h, 1x Brefeldin A (BioLegend, #420601) was added. Splenocytes were collected for FACS analysis and RNAseq analysis. Experiments were independently replicated at least three times. RNA was extracted using RNAeasy Mini Plus Kit (Qiagen, #74134) and quantified in LabChip GX Touch Nucleic Acid Analyzer (PerkinElmer). RNA quality was determined by Agilent's 2100 Bioanalyzer Lab-Chip technology. Only samples with RNA Integrity Number (RIN)>7 was used for sequencing. Sequencing libraries were prepared with the “QuantSeq 3′ mRNA-Seq Library Prep Kit” (Lexogen, #015). Libraries were sequenced in single-read format in a NovaSeq X instrument (Illumina). Raw RNA-seq reads were trimmed using bbduk to remove adapter sequences and polyA tails. The trimmed reads were aligned to the GRCh38 genome assembly using STAR 2.7.10b. The results from the alignment were quantified using the featureCounts tool from the Rsubread 2.0.3 package. Gene counts were normalized to counts per million reads (CPM) using the rnanorm Python library.

first: José Luis

last: Ruiz-Sepúlveda

first: Verónica

last: Jiménez-Renard

first: Rebeca

last: Jimeno

first: Miguel

last: Quintela-Fandino


title: Laminaria japonica Polysaccharide Mitigates Acute Neuroinflammation in Cerebral Ischemia-Reperfusion Injury

city: zhanjiang

first: tangming

last: guan

address: No. 57, South Renmin Avenue, Xiashan District

institute: Affiliated Hospital of Guangdong Medical University

summary: Cerebral ischemia-reperfusion (I/R) injury triggers acute neuroinflammation, which exacerbates neuronal damage and functional deficits. Laminaria japonica polysaccharide (LJP) has been reported to exert anti-inflammatory and neuroprotective effects, but its molecular mechanisms in I/R injury remain unclear. In this study, we performed transcriptome sequencing on ischemic brain tissues from Sham, Vehicle, and LJP-treated mice to elucidate the molecular mechanisms underlying LJP’s anti-inflammatory actions. Our results show that LJP treatment significantly modulated the expression of key genes involved in inflammatory responses, particularly through the regulation of Csf3-mediated pathways. These findings provide novel insights into the therapeutic potential of LJP for ischemic stroke and identify potential targets for future interventions.

overall_design: RNA sequencing (RNA-seq) was performed on ischemic brain tissues collected from three groups of mice: (1) Sham-operated control group; (2) Vehicle-treated I/R injury group; and (3) LJP-treated I/R injury group. Total RNA was extracted from the tissues, libraries were constructed, and sequencing was conducted to profile gene expression changes. The aim was to identify differentially expressed genes and signaling pathways associated with LJP’s anti-inflammatory and neuroprotective effects.

first: Tangming

last: Guan

first: Siyu

last: Chen

first: Dongbo

last: Jiang

first: Weiming

last: Cai

first: Huayan

first: Yan

last: Wang

first: Kefeng

last: Wu

first: Xin

last: Zhou


title: CB2R Agonism Protects Intestinal Epithelium through β-Catenin/HoxA10 Loop in Radiation Injury

city: 重庆

first: Qianyi

last: Yao

address: 重庆市渝中区医学院路1号

institute: 重庆医科大学

summary: Background: Radiation-induced intestinal injury (RIII) represents a significant dose-limiting complication of radiotherapy, characterized by substantial loss of intestinal epithelial cells (IECs). While the activation of cannabinoid receptor 2 (CB2R) is protective in immune‑mediated colitis, the intrinsic role of CB2R in IECs and its potential therapeutic relevance in RIII have not been defined. Methods: An RIII mouse model was established in wild-type and CB2R-/- mice. Small-molecule CB2R agonists were screened for radioprotective efficacy, followed by pharmacological and siRNA-based interrogation of CB2R signaling in intestinal epithelial cell lines and primary mouse intestinal epithelial cells. RNA sequencing and bioinformatics were combined with permeability assays, immunofluorescence, electron microscopy, and molecular analyses of oxidative stress and ferroptosis to elucidate underlying mechanisms. Results: Irradiation induced CB2R expression in the intestinal epithelium, and genetic ablation of CB2R markedly aggravated RIII. A focused pharmacological screen identified a recently synthesized dual‑target compound, CB2R/FAAH modulator‑2 (CF‑2), which combines CB2R agonistic activity with fatty acid amide hydrolase (FAAH) inhibition and significantly mitigated radiation‑induced colonic injury while exerting protective effects on the small intestine and spleen. Mechanistically, CB2R activation attenuated irradiation‑induced ferroptosis and preserved intestinal epithelial integrity. Integrative transcriptomic analyses identified Homeobox A10 (HoxA10) as a critical epithelial‑enriched transcriptional amplifier that reinforced CB2R/β‑catenin signaling through a positive‑feedback loop, thereby enhancing CB2R‑mediated epithelial protection. Conclusions: This study defines an epithelial‑intrinsic CB2R signaling axis in RIII, linking ferroptosis suppression to preservation of intestinal barrier integrity. CF‑2 is positioned as a promising mechanism‑based candidate for radioprotection.

overall_design: Colon tissue samples were collected from 8-week-old male C57BL/6 mice. Animals were randomly assigned to three groups (n=3 per group): Control group (Con): untreated control mice, administered with sterile saline; IR group (IR): mice subjected to 13 Gy abdominal irradiation; IR+CF-2 group (IR+CF-2): mice subjected to the same irradiation and treated with CF-2 at a dose of 7.5 mg/kg via intraperitoneal injection. CF-2 was administered four times: 1 hour before irradiation, and at 24, 48, and 72 hours post-irradiation. All animals were euthanized at 84 hours post-irradiation.

first: Ying

last: Tian

first: Yi

last: Yuan

first: Yongqing

first: Qunfang

last: Yang

first: Lanfang

last: Zhang

first: Yunong

last: Li

first: Tanjun

last: Wei

first: Qin

last: Ouyang

first: Haigang

first: Xiaoli

first: Tao

last: Liu


title: Adipose tissue inflammation mediated by CCL19 overexpression exacerbates experimental periodontitis via elevated circulating saturated fatty acids and osteopontin in Western-diet-fed mice

city: Fukuoka

first: Takanori

last: Shinjo

state: fukuoka

address: Maidashi 3-1-1

department: Section of Periodontology

institute: Kyushu University

summary: Introduction: Individuals with obesity may be at a higher risk of developing severe periodontitis. We previously reported that C-C motif ligand 19 (CCL19) plays a pivotal role in adipose inflammation in obesity and that adipocyte-specific Ccl19 knock-in (CCL19-KI) mice exhibited greater inflammatory cell infiltration in visceral fat, increased weight gain, and abnormal glucose metabolism than wild-type (WT) mice under a 40% high-fat diet (HFD). In this study, we examined the susceptibility of mice fed diets with different fat contents to the severity of experimental periodontitis. Methods: Six-week-old male WT and CCL19-KI mice were fed either a normal diet (ND), 40% HFD, or 60% HFD for 8 weeks, after which ligature-induced periodontitis (LIP) was established. Two weeks after ligation, alveolar bone resorption, gingival inflammatory and osteoclastogenic gene expression, and serum free fatty acid (FFA) levels were compared among the groups. Additionally, RNA-sequencing (RNA-seq) was performed on epididymal white adipose tissue (eWAT) of each ligatured mouse to explore potential factors mediating periodontitis aggravation. Furthermore, in vitro studies using macrophages were conducted to investigate a possible mechanism in the progression of periodontitis. Results: Alveolar bone resorption, gingival inflammatory and osteoclastogenic gene expression, and serum FFA levels were significantly higher in ligated CCL19-KI mice than those in ligated WT mice under a 40% HFD. RNA-seq revealed that the OPN gene (Spp1) expression in eWAT was significantly upregulated in CCL19-KI mice fed an ND or 40% HFD compared with that in WT mice, which was consistent with serum OPN levels. Peritoneal macrophages from 40% HFD-fed CCL19-KI mice secreted significantly higher amounts of TNF-a than those from WT mice fed the same diet under Escherichia coli lipopolysaccharide (LPS) stimulation. Both palmitic acid priming and OPN significantly promoted osteoclastogenesis in RANKL-treated BMMs, and their combination further enhanced this effect. Conclusions: CCL19-modified adipose tissue inflammation may contribute to the severity of periodontitis via the upregulation of circulating saturated fatty acids and Spp1, resulting in enhanced TNF-a production in macrophages and increased osteoclastogenesis in BMMs under mild to moderate obesity.

overall_design: Normal diet or 40% HFD-fed or 60% HFD-fed WT and Adipoq-CCL19-KI mice (14 weeks old, feeding for 8 weeks) were induced ligature-induced experimental periodontitis for 2 weeks. Epididymal adipose tissue (eWAT) were collected and RNA was extracted from each mouse eWAT. RNA-seq was performed using eWAT RNA (n=3/group).

first: Naoaki

last: Ryo

first: Miyu

last: Shida

first: Kohei

last: Sato

first: Tatsuro

last: Zeze

first: Honoka

last: Otsuka

first: Yuki

last: Nishimura

first: Mio

last: Imagawa

first: Al-kafee

last: Ahmed

first: Gulinigeer

last: Dilimulati

first: Chikako

last: Hayashi

first: Akiko

last: Yamashita

first: Takao

last: Fukuda

first: Terukazu

last: Sanui

first: Misaki

last: Iwashita

first: Fusanori


title: Transneuronal cytokine delivery promotes functional recovery across spinal cord contusion severities via descending circuit plasticity

city: Cologne

first: Dietmar

last: Fischer

address: Paul-Schallück-Straße 8

department: Pharmacology

country: Germany

institute: University Hospital of Cologne

summary: Spinal cord injury (SCI) frequently leads to permanent motor and sensory deficits, with complete injuries causing total loss of function below the lesion and incomplete injuries preserving only partial connectivity. Intracortical delivery of an AAV2 vector encoding the designer cytokine hyper-interleukin-6 (AAV2-hIL-6) enhances recovery after complete SCI by transneuronally stimulating raphe nuclei. Here, we verified that AAV2-hIL-6 transneuronally activates subcortical neurons in the medulla and evaluated that this strategy enables recovery in clinically more relevant mouse models of mild, moderate, and severe contusion injury. Across all severities, AAV2-hIL-6 treatment significantly improved locomotor function compared to AAV2-GFP-treated controls. Although lesion size and neuronal loss correlated with contusion severity and were unaffected by the AAV2-hIL-6 treatment, it robustly increased the number and length of descending serotonergic axons in the lumbar cord. Selective ablation of serotonergic neurons abolished these gains, confirming their essential role in functional sensorimotor recovery. However, while AAV2-hIL-6 also reduced corticospinal tract (CST) axon retraction, it did not induce axon regeneration beyond the lesion, suggesting that CST regeneration was not required for recovery. Thus, intracortical AAV2-hIL-6 delivery drives circuit remodeling and functional restoration across contusion severities, highlighting its promise as a regenerative therapy for SCI with spared pathways.

overall_design: RNA-seq analysis of the medullary brainstem, including the raphe nuclei three weeks after intracortical stereotactic AAV2-GFP or AAV2-hIL-6 injections

first: Leibinger

last: Marco

first: Moskaliov

last: Igor

first: Ani

last: Chinonso-John

first: Halawani

last: Dalia

first: Fischer

last: Dietmar


title: PTPRN2 hypomethylation and PHB2-modulated miR-153-3p maturation reveal dual epigenetic mechanisms linked to symptom variability in Myalgic Encephalomyelitis

first: Alain

last: Moreau

address: 3175 Côte-Ste-Catherine

institute: Azrieli Research Center of CHU Sainte-Justine

type: Methylation profiling by genome tiling array

summary:
Background: Myalgic encephalomyelitis (ME) is a chronic, debilitating condition increasingly linked to epigenetic changes. With its unclear pathophysiology and no validated diagnostic biomarkers, DNA methylation becomes of interest. Specifically, DNA methylation patterns in saliva, to study ME-related epigenetic changes.
Methods: Saliva samples from 54 ME patients and 21 sedentary healthy controls were analyzed by DNA methylation array. Symptom assessment was conducted using validated questionnaires (SF-36, MFI-20, and DSQ).
Results: A significant DNA hypomethylation at the CpG site cg19803194 (Bonferroni-corrected p=3x10-7) within the PTPRN2 gene body was identified. This hypomethylation was associated with cognitive impairments in both sexes, such as difficulties expressing thoughts and comprehension, commonly known as "brain fog," and as well as respiratory issues in male patients. The hypomethylation also corresponded with reduced circulating levels of miR-153-3p, an intronic microRNA of PTPRN2, which was associated with impaired memory recall in both sexes. Interestingly, the mitochondrial protein Prohibitin 2 (PHB2) emerged as a negative regulator of miR-153-3p maturation, likely through its physical interaction with immature forms of miR-153 within cells, which was attenuated in female patients due to increased extracellular export of PHB2.
Conclusions: These findings propose a potential epigenetic mechanism in ME involving PTPRN2 body hypomethylation and PHB2-modulated miR-153-3p maturation. While the directionality between gene-body methylation and expression remains a biological hypothesis, these results shedding light on possible pathways contributing to symptom variability and sex differences in ME severity.

overall_design: This is a prospective pilot study in which 54 consecutive ME patients diagnosed according to the Canadian Consensus Criteria were enrolled. We also recruited 21 sedentary healthy controls free from chronic pain conditions, mental disorders, recent infections (within 3 months). Saliva samples were collected using DNA Genotek Oragene kits according to the manufacturer's instructions. Genomic DNA was extracted from the saliva samples using the PureLink Genomic DNA Mini Kit following the provided protocol. This ensured efficient genomic DNA isolation for subsequent analyses. We employed a robust data processing and quality control pipeline for the Illumina Methylation EPIC microarray dataset (Illumina, San Diego, CA, USA), encompassing 75 saliva samples using the R Package Champ (Version 2.28.0) within R (Version 4.1.2) to ensure accuracy and reliability. First, the raw signal intensity data for each of the 75 samples were imported into Champ. Subsequently, these raw intensities were transformed to generate a beta value matrix. The beta values, which range from 0 to 1, reflect the methylation ratios of individual probes. To ensure data integrity, low-quality probes and samples were filtered out. Probes were removed based on the following criteria, including non-CpG probes, multi-hit probes, probes with Beadcount < 3, low-quality or failed probes with signal-background detection, P values exceeding 0.05 and probes residing on single-nucleotide polymorphism (SNP) sites or chromosomes X and Y. Simultaneously, samples containing more than 10% failed or low-quality probes were excluded from the analysis, in accordance with standard data quality practices.


title: Charachterizing the Discordance Between ARID1A Protein and Genotype in Endometrioid Type Endometrial Tumors

city: Chapel Hill

first: Andrew

middle: B

last: Gladden

state: NC

address: 160 N. Medical Drive

department: Department of Pathology & Laboratory Medicine

institute: The University of North Carolina at Chapel Hill

summary: ARID1A is one of the most frequently mutated genes in endometrial cancer, with approximately 40% of patients harboring an ARID1A mutation. However, relatively little is known about how ARID1A protein loss shapes endometrial cancer pathogenesis. Mounting evidence from other malignancies suggests that ARID1A protein can be regulated post-translationally, independent of genotype. However, most studies in endometrial cancer evaluate genotype alone, overlooking the potential for alternative mechanisms of ARID1A loss. To address this gap, ARID1A protein expression and genotype were examined in endometrioid tumors and associated transcriptional changes were characterized. Evaluation of ARID1A protein in 71 human endometrioid tumors demonstrates that protein loss can occur regardless of ARID1A genotype. Retention or deficiency of ARID1A protein was not significantly related to variant allele frequency or location of mutation in human tumors with mutant ARID1A. A human endometrial cancer cell model suggests that ARID1A protein loss can occur through proteasomal degradation. Furthermore, ARID1A protein expression was found to be a predictor of worse overall survival in a TCGA cohort of ARID1A wild-type endometrioid tumors. Spatial transcriptomics of 16 human endometrioid tumors revealed that both genotype and protein expression of ARID1A play a role in shaping unique transcriptional signatures in endometrial cancer and can be used to predict patient prognosis. Suggesting evaluation of ARID1A should not be done solely by sequencing techniques.

overall_design: Sixteen formalin-fixed paraffin embedded endometrioid tumors with either wild-type(5) or mutant (11) ARID1A were analyzed using whole transcriptome digital spatial analysis. Tumors had varying levels of ARID1A protein expression with some experiencing retention of ARID1A throughout the tumor while others exhibited heterogenous or deficient ARID1A protein expression. Six regions of interest were chosen per tumor based on ARID1A protein expression, resulting in 51 ROIs which retained ARID1A protein expression and 44 which were ARID1A protein deficient.

first: Savannah

middle: E

last: LaBuda

first: Katherine

last: Spence

first: Rahul

last: Niranjan

first: Isurika

last: Weeranshige

first: Macy

last: Osborne-Frazier

first: Russell

last: Broaddus


title: An Engineered Viral RNA Degrader on Mitochondrial Surface that Mitigates RNA Virus Infection [E vs ECD]

city: Taipei

first: Wei-Ting

last: Liao

address: No. 7, Chung-Shan S. Rd., Chung-Cheng District

country: Taiwan

institute: NTU

summary: Infections by RNA viruses cause diseases. Host factor(s) that restrain viral propagation might offer opportunities for designing new anti-virus treatments. We used vesicular stomatitis virus (VSV) as a study model, and observed the synthesis of VSV RNAs at mitochondria /endoplasmic reticulum (mito/ER) spheres accompanied by the leakage of endonuclease G (ENDOG), a mitochondrial nuclease, to the cytosol. We provide evidence that ENDOG released from mitochondria is a host anti-viral factor by eliminating viral RNAs for replication. However, ENDOG outside mitochondria can be translocated to nuclei to cause nuclear DNA damages. We engineered an ENDOG expressed on mitochondrial outer membrane (MOM), namely MOM-ENDOG, to increase the accessibility to viral RNA transcripts synthesized at mitochondrial sites without damaging nuclear DNA (nDNA). Delivery of modified mRNA of wild-type but not catalytic-dead MOM-ENDOG markedly suppressed not only the propagation of VSV, but also Dengue, and Zika virus. Thus, this organelle-specific viral RNA degrader might be developed as a broad-spectrum anti-viral agent.

overall_design: RNA-seq profiling of A549 cells with MOM-ENDOG overexpression vs MOM-ENDOGCD overexpression

first: Zee-Fen

last: Chang

first: Chih-Wei

last: Chen

first: Tung

last: Chao

first: Yi-Han

first: Shih-Che

last: Weng

first: Shin-Hong

last: Shiao

first: Yun-Jung

last: Li

first: Kai-An

last: Cheng


title: Histone H4 acetyl-methyllysine marks accessible chromatin that resists compaction

city: Orange

first: Matthew

last: Simon

address: West Campus, 100 West Campus Drive, Ste MIC312A

department: MBB

institute: Yale University

summary: Regulatory DNA often remains accessible even under conditions of widespread chromatin compaction. Specific factors and histone modifications mark these regions and help maintain local accessibility. Here, we examine the genomic landscape of acetyl-methyllysine (Kacme), a recently discovered histone post-translational modification. Across multiple systems, Kacme is highly enriched at sites of accessible chromatin, including active promoters, enhancers, silencers, and CTCF-binding sites. We find that Kacme is selectively retained at loci that resist condensation during mitosis, marks XIST and escapee regions on the inactive X chromosome in female cells, and demarcates the boundaries of broad heterochromatin domains. Using the KDM6A/6B inhibitor GSK-J4 to elevate H3K27me3 levels, we show that Kacme-marked insulator elements block heterochromatin spreading and protect adjacent genes from transcriptional repression. Taken together, our findings define the chromatin features associated with Kacme and support a model in which Kacme safeguards chromatin accessibility, particularly at loci that remain active despite compaction and silencing pressures.

overall_design: TimeLapse-seq, ATAC-seq, and CUT&RUN with Kacme and H4K5ac antibodies in HEK293T cells at select timepoints during mitosis and early-G1. ChIP-seq with Kacme, H4Kacme, and H4Kac antibodies in THP-1 cells +/- PMA (40 ng/mL, 72 h). CUT&RUN with Kacme in HEK293T cells treated with Triptolide (10 uM, 1h). TimeLapse-seq and CUT&RUN with H3K27me3 antibody in untreated HEK293T cells or HEK293T cells treated with GSK-J4 (5 uM, 6/24 h). CUT&RUN with CTCF antibody and ChIP-seq with H3K27ac antibody in wild-type HEK293T cells. All experiments performed in duplicate or triplicate. Inputs included.

first: Andreas

last: Pintado-Urbanc

first: Charlie

last: Brown

first: Leah

last: Connor

first: Joshua

middle: T

last: Young

first: Yeil

last: Kim

first: Elizabeth

middle: M

last: Black

first: Lilian

last: Kabeche


title: An Engineered Viral RNA Degrader on Mitochondrial Surface that Mitigates RNA Virus Infection

first: Wei-Ting

overall_design: RNA-seq profiling of A549 cells with No Transfect vs MOM-ENDOG overexpression


title: Multi-omic analysis reveals nitric oxide dependent remodeling in classically activated macrophages and identifies negative regulation mediated by AKR1A1

city: Madison

first: Jing

last: Fan

state: WI

address: 330 N. Orchard St.

institute: Morgridge Institute for Research

summary: Nitric oxide (NO•) is an important signaling molecule in many biological processes, including immune response. During response to classical activation stimuli lipopolysaccharide (LPS) and interferon-γ (IFNγ), macrophages generate NO• via inducible nitric oxide synthase (iNOS). To comprehensively define the effects of NO•, we applied a multi-omic strategy integrating proteomics and transcriptomics to profile murine macrophages across conditions with or without LPS/IFNγ-activation, with or without iNOS expression or exogenous NO• donor treatment. The results revealed NO• has broad, yet selected and controlled, regulatory effects, playing a key role in coordinating the systematic remodeling during macrophage classical activation. Among the proteins that are most suppressed in a NO•-dependent manner, electron transport chain (ETC) is the most enriched. NO• drives complex-specific remodeling of ETC, causing selected downregulation of complex I, II, and IV, through a different combination of transcriptional and post-transcriptional mechanisms for each complex. Functionally, we found NO• is required, but not sufficient, for the strong suppression of cellular respiration upon macrophage activation. Among the most consistently upregulated proteins are many enzymes involved in redox defense. AKR1A1 was identified as a top hit. We found Akr1a1 induction requires both NO• and LPS/IFNγ stimulation. The S-nitroso-CoA reductase activity of AKR1A1 mitigates NO•-driven inhibition of pyruvate dehydrogenase complex by limiting the inhibitory modifications targeting its lipoyl cofactor. Knocking out Akr1a1 causes accelerated remodeling of TCA cycle, dysregulated immunoregulatory metabolite level, and altered functional gene expression and cytokine production at later stage of immune response. Thus, the NO•-dependent upregulation of AKR1A1 forms a negative regulatory loop to fine-tune NO•-mediated metabolic and functional remodeling during immune response. Together, this work provided a systems-level map of NO•-dependent regulation, revealed the crosstalk between NO• and immune signaling, and demonstrated mechanisms providing redox adaptation and precise control of NO•’s effects.

overall_design: To investigate how gene expression changes in macrophages with stimulation, wild-type or iNOS KO bone-marrow derived macrophages, or wild-type or Akr1a1 KO RAW264.7 cells were treated with continuous 48-hour LPS+IFNy stimulation. Then the stimulants were washed off and RNA was collected.

first: Nicholas

middle: L

last: Arp

first: Uzziah

middle: S

last: Urquiza

first: Marcel

last: Morgenstern

first: Jonathan

last: Schrope

first: James

middle: A

last: Votava

first: Steven

middle: V

last: John

first: Felicia

last: Deng

first: Jack

last: Stevens

first: Anna

last: Huttenlocher

last: Coon


title: Transcriptomic profiling reveals substrate- and shear stress_x0002_dependent maturation of human small intestinal epithelial cells

city: Berlin

first: Rainer

last: Glauben

address: Hindenburgdamm 30

department: Klinik für Gastroenterologie, Infektiologie und Rheumatologie

institute: Charite CBF

summary: Primary human intestinal epithelial cells (IECs) require microenvironments that reproduce various in vivo cues to maintain survival, differentiation, and function in vitro. In this study, we investigated how intestinal stem cell (ISC)-derived monolayers respond to biomimetic substrates and shear stress using 3D-printed hydrogels based on bioactive decellularized and methacrylated small intestinal submucosa (dSIS-MA) integrated into a custom millifluidic system. Extensive bulk RNA sequencing experiments revealed that, compared with Matrigel-coated tissue culture plastic, dSIS-MA hydrogels supported survival- and differentiation-related signaling, stabilized gene expression over time, and promoted absorptive lineage maturation while reducing crypt-associated signatures. By applying dynamic culture conditions to the hydrogel system, IECs underwent transcriptional remodeling, characterized by activation of metabolic and immune pathways. Longitudinal analysis further indicated that shear stress enhanced metabolic pathway–associated gene expression and promoted differentiation toward absorptive lineages. These findings establish dSIS-MA hydrogels with controlled fluid flow as a biomimetic in vitro model that supports survival, maturation of human IECs and enables transcriptional adaptation to defined biochemical and mechanical cues, supporting future applications in disease modelling, drug testing, and regenerative medicine.

overall_design: RNA-seq profiling of intestinal stem cell/organoid derived monolayers cultured on either Matrigel-coated tissue culture plastic or 3D-printed dSIS-MA hydrogels, under static or dynamic flow in a custom millifluidic system. All experiments were performed using two biological replicates and three to four technical replicates per condition.

first: Nadra

last: Alzain

first: Ahed

last: Almalla

first: Ketaki

last: Sandu

first: Lorenz

last: Gerbeth

first: Jörn

last: Ziegler

first: Catharina

last: Gutwein

first: Patrick

last: Weidner

first: Marie

last: Weinhart

first: Britta

last: Siegmund


title: Editing of SlMYB60 Reveals a Role in Cuticle Formation in Tomato

city: Milano

first: Raul

last: Pirona

address: Via Alfonso Corti 12

country: Italy

institute: IBBA-CNR

summary: The transcriptional regulator, SlMYB60 (Solyc10g081490.1.1) stands out as the tomato ortholog of AtMYB60, a well-characterized guard cell-specific transcription factor in Arabidopsis involved in integrating multiple stress signals in stomata. To investigate the role of SlMYB60, CRISPR-Cas9 editing was applied to two commercial tomato cultivars (Ailsa Craig and Red Setter), generating knockout alleles through multiple sgRNAs. T1 slmyb60-edited plants were assessed for stomatal aperture and drought response. Unexpectedly, mutant lines showed a slight but significative increase in stomatal pore opening in both leaves and cotyledons compared to wild type. Under dry-down conditions, leaf area, fresh weight, and relative water content were significantly affected by both genotype and treatment. RNA-seq analyses confirmed the strong downregulation of SlMYB60 in the edited lines and identified 186 differentially expressed genes (DEGs), many of which involved in cell wall or cuticle biosynthesis. Chlorophyll leaching assays indicated increased permeability in mutant lines, while electron microscopy revealed defects in epidermal cell surface structure and patterning. Notably, slmyb60 mutants exhibited thinner stomatal ledges compared to wild type, suggesting defects in stomatal architecture. Although modulating stomatal activity remains a promising strategy to improve drought resilience in tomato, our findings reveal that SlMYB60, unlike its Arabidopsis homolog, is not confined to guard cells and plays broader roles in epidermal development, indicating divergences in the MYB60 regulatory network between Arabidopsis and tomato.

overall_design: RNA was extracted from leaves of the wild type and the two mutants (Cr1 and Cr2) each with four biological replicates. Libraries were prepared from poly(A)-enriched mRNA fractions and sequecced on a NovaSeq 6000 platform using 150 bp paired-end reads.

first: Sara

last: Colanero

first: Beatrice

last: Landoni

first: Giulia

last: Castorina

first: Diana

last: Gervasoni

first: Manuela

last: Rigano

first: Elena

last: Baldoni

first: Damiano

last: Martignago

first: Lucio

last: Conti

first: Massimo

last: Galbiati


title: miRNA expression profiling of mouse hearts following myocardial infarction

city: Durham

first: Walter

middle: J

last: Koch

address: 487 CARL Building, 213 Research Drive

department: Surgery

institute: Duke University School of Medicine

summary: Background: Pathological upregulation of G protein-coupled receptor kinase 2 (GRK2) is a hallmark of heart failure and contributes to maladaptive signaling, hypertrophic remodeling, and cardiomyocyte death. MicroRNAs (miRNAs) are key post-transcriptional regulators of cardiac stress responses, however whether GRK2 is subject to miRNA targeting has not yet been fully established.    Objective: We investigated potential miR-181a-mediated regulation of GRK2 in cardiomyocytes to better understand its effects on cardiac stress responses.    Methods: miRNA microarray profiling was performed on mouse hearts two weeks after myocardial infarction. Bioinformatic target prediction analysis identified candidate miRNAs that are predicted to bind GRK2 in the 3’ untranslated region (UTR). Direct binding was assessed using luciferase reporter assays, and miR-181a was selected as the miRNA of interest to further pursue mechanistic and functional validation. miR-181a was overexpressed or inhibited in neonatal rat ventricular myocytes (NRVMs) and exposed to several modes of cellular stress to induce hypertrophy, hypoxia, and accumulation of reactive oxygen species. GRK2 expression, hypertrophic remodeling, oxidative stress, cell viability, and cyclic AMP (cAMP) signaling were assessed using quantitative PCR, immunoblotting, fluorescence imaging, and biochemical assays.    Results: miR-181a directly targeted the GRK2 3′UTR and suppressed GRK2 expression at both mRNA and protein levels. miR-181a overexpression attenuated stress-induced hypertrophic gene expression, reduced cardiomyocyte cell size, decreased oxidative stress, improved survival under hypoxia, and enhanced cAMP production under β-AR stimulation. Conversely, inhibition of miR-181a resulted in sustained GRK2 expression, exacerbated hypertrophic signaling, and decreased cAMP production.    Conclusion: These findings identify miR-181a as a functional post-transcriptional regulator of GRK2 that limits maladaptive signaling, hypertrophic remodeling, and cardiomyocyte injury. miR-181a-mediated GRK2 inhibition represents a potential therapeutic strategy for mitigating pathological signaling in heart failure.

overall_design: Male C57BL/6J mice aged 9-12 weeks underwent sham or MI surgery. At 2 weeks post-MI, total RNA was extracted from the left ventricular (LV) tissue of the mouse myocardium.

first: Heidi

last: Cho

first: Melissa

last: Lieu

first: Erhe

last: Gao

first: Samuel

last: Slone


title: Progression of Nipah virus infection in African green monkeys: role of macrophages and dendritic cells in early virus spread

city: Galveston

first: Jacquelyn

last: Turcinovic

state: TX

address: Galveston National Laboratory, 301 University Blvd.

department: Microbiology and Immunology

institute: University of Texas Medical Branch

summary: Nipah virus (NiV) infection causes severe respiratory disease and encephalitis in humans and nonhuman primates with high case fatality rates.  While end-stage disease in primates has been well studied, particularly in African green monkeys (AGM), little is known about the development of NiV disease. Here, 12 AGM were infected with NiV and examined sequentially over 5 days to investigate the pathological and immunological events of NiV infection leading to death. DC-SIGN-positive immature dendritic cells in tonsil and alveolar macrophages were identified at 3 days postinfection (DPI) as early targets of NiV, implicating their important role in the spread of NiV to other tissues.  By 5 DPI, NiV spread to other tissues and cell types, including endothelium of medium caliber vessels and respiratory epithelium. Multifocal regions of fibrin deposition in small and medium caliber vessels and into alveolar spaces were also noted at 5 DPI. NiV antigen was not detected in cells of central nervous system tissues from any AGM at 3-5 DPI, indicating that neuroinvasion is a late event in untreated primates.  NiV infection elicited a biphasic host response characterized by early loss of anticoagulant factors followed by robust induction of interferon-stimulated cytokines, chemokines, and endothelial activation markers, revealing a tightly coupled inflammatory-coagulatory cascade underlying disease progression. RNA-seq analyses of tonsil and lung identified a robust, complement-driven immune response in tonsil but a muted, interferon-driven response in lung. The sequence of pathogenetic events identified here may provide insight into developing new therapeutic interventions and optimizing lead candidate antivirals.

overall_design: Time series NanoString data from African green monkeys challenged Nipah virus

first: Thomas

last: Geisbert


overall_design: Tonsil and lung samples from 0, 3, 4, and 5 days postinfection. Each tissue's postinfection timepoints are compared to health baseline


title: DEVELOPMENTAL LANDMARKS AND CELLULAR TRANSITIONS DURING EXTRAVILLOUS TROPHOBLAST CELL DIFFERENTIATION [scRNA-Seq]

city: Kansas City

first: Michael

last: Soares

state: KS

address: 3901 Rainbow Blvd

department: Pathology

institute: University of Kansas Medical Center

summary: Human trophoblast stem (TS) can be captured, maintained in vitro under specific conditions, and differentiated into extravillous trophoblast (EVT) cells. The regulatory mechanisms that govern the self-renewal and differentiation of human TS cells into EVT cells are largely unknown.  In this study, bulk RNA-sequencing (RNA-seq) and single cell RNA-seq (scRNA-seq) were performed on human TS cells maintained in the stem state and on cells progressing from the stem state into EVT cells (differentiation days 3, 6, and 8). Distinct bulk and single cell transcript profiles were identified for each day of analysis. Day 3 of EVT cell differentiation represented a striking transition point and was readily distinguished from stem state and days 6 and 8 of EVT cell differentiation. Analysis of scRNA-seq led to the identification of several unique cell populations. Trophoblast cell developmental state-specific regulons and trajectories. We elucidated functional roles of key regulators of EVT cell development: cyclin B1, CCAAT/enhancer-binding protein beta, and ADAM metallopeptidase with thrombospondin type 1 motif 20. Collectively, we have defined developmental landmarks and transitional cell populations during EVT cell differentiation. These findings provide a valuable resource and foundation for future investigations into regulatory mechanisms controlling TS cell differentiation into the EVT cell lineage

overall_design: Single-cell RNA sequencing (scRNA-seq) was performed on CT27 trophoblast stem (TS) cells (Okae et al.) maintained in the stem state, as well as on cells differentiating into EVT cells at days 3, 6, and 8. Two biological replicates were collected for each condition (D0, D3, D6, and D8). In addition, day 6 EVT samples were collected from three TS cell lines: CT27, CT29, and CT20.

first: Ayelen

last: Moreno-Irusta

first: Malay

last: Basu

first: Esteban

last: Dominguez

last: Chen

first: Sawyer

middle: H

last: Smith

first: Kaela

last: Varberg

first: Hiroaki

last: Okae

first: Takahiro

last: Arima


title: Wounding activates HSFA1 to  promote cellular reprogramming in Arabidopsis

city: Yokohama

first: Duncan

middle: Peter

last: Coleman

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

department: CSRS

institute: Riken

summary: Mechanical injury is a primary trigger for cellular reprogramming during organ regeneration, yet the transcriptional mechanisms that link wounding to reprogramming remain poorly understood. In this study we identify the HEAT SHOCK FACTOR A1 (HSFA1) class of transcription factors, key regulators of the heat stress response, as a central player in wound-induced callus formation and shoot regeneration in Arabidopsis. Loss of HSFA1 function in the hsfa1abd triple mutants severely impairs cellular reprogramming, reducing callus formation from wounded hypocotyls and shoot regeneration from explants. Conversely, overexpression of a gain-of-function HSFA1d variant markedly enhances regeneration. Time-series RNA-seq and ChIP-seq analyses revealed that HSFA1 directly activates key reprogramming regulators, WOUND-INDUCED DEDIFFERENTIATION 1 (WIND1), PLETHORA 3 (PLT3) and ZINC FINGER OF ARABIDOPSIS THALIANA 6 (ZAT6). Furthermore, we demonstrate that the HSFA1d activity is attenuated by SIZ1-mediated SUMOylation, linking post-translational modification to the regulation of wound responses. Our findings establish HSFA1 as an early transcriptional hub that integrates wound signals to activate a broad gene network that drives cellular reprogramming, thereby providing a mechanistic framework for understanding how stress-responsive transcription factors control regeneration.

overall_design: RNA-seq experiment of WT Col-0 and hsfa1abd-2 mutant hypocotyls explants at T0, 30min, 1h, 3h, and 24 hours after wounding.

first: Coleman

last: Duncan

first: Sugimoto

last: Keiko

first: Kawamura

last: Ayako


title: DEVELOPMENTAL LANDMARKS AND CELLULAR TRANSITIONS DURING EXTRAVILLOUS TROPHOBLAST CELL DIFFERENTIATION

overall_design: Bulk RNA-sequencing (RNA-seq) were performed on CT27 Trophoblast stem cells (TS- Okae et.al.)  maintained in the stem state and on cells progressing  into EVT cells differentiation (differentiation days 3, 6, and 8). 3 biological replicates each conditions (D0, D3,D6 and D8)

last: Basu.


title: Thyroid hormones maintain parvalbumin neuron functions in mouse neocortex

city: Lyon

first: Frédéric

last: Flamant

state: France

address: 46 allée d'Italie

department: IGFL

country: France

institute: ENSL

summary: Parvalbumin-expressing (PV) GABAergic interneurons play a key role in maintaining the excitation-inhibition balance in the mammalian neocortex. Here we investigate the function of thyroid hormones in PV neurons in the mouse neocortex. To this end, Cre/loxP recombination system was used to express a dominant negative mutated receptor of thyroid hormones only in PV neurons. We analyzed the neocortical phenotype of these mice, in which thyroid hormone signaling is selectively disrupted in PV neurons, by combining genomics, histology, electrophysiology, sleep recordings and behavioral analysis. In the mutant mice, gene expression analysis revealed a decreased expression of key perineuronal net components of PV neurons. PV neuron excitability was decreased, leading to behavioral hyperactivity and increased susceptibility to seizures. Additionally, sleep analysis revealed that mutant mice spent more time awake, and a delayed transition to sleep, suggesting impairments in sleep regulation mechanisms. Electrophysiological recordings further demonstrated altered gamma oscillations in the somatosensory cortex. These results highlight that thyroid hormones are not only required for the differentiation of PV interneurons, but also for the maintenance of their inhibitory function after the onset of parvalbumin expression.

overall_design: The Cre/loxP recombination system was used to restrict the expression ofa transgene which drives the expression of a nuclear fluorescent protein.  . A Cre driver additionnal transgene was used to restrict the expression to parvalbumin neurons (Pv-Cre). Four groups of mice were prepared. Group3 mice were treated with PTU for 2 weeks to decrease the circulating levels of thyroid hormones.  Group 1 mice are untreated controls, with wild-type Thra alleles (Ctrl). Group 2 mice are littermates with the ThraAMI floxed allele -(Mut). These mice express the dominant negative thyroid hormone receptor TRalpha1L400R. Group 3  were treated with PTU for 2 weeks to lower the circulating levels of thyroid hormones (PTU). Group4 mice  were treated with PTU for 2 weeks and received an injection of thyroid hormones 24h before cortex dissection (PTU+TH). Fluorescent nuclei were sorted from the cerebral cortex of adult mice. RNA was extracted from the sorted nuclei and libraries were prepared for RNA-seq.

first: Juan

last: Ren

first: Suzy

last: Markossian

first: Romain

last: Guyot

first: Denise

last: Aubert

first: Jiemin

last: Wong

first: Dong Dong

last: Li

first: Fabrice

last: Riet

first: Bruno

last: Cauli

first: Thierry

last: Galopin

first: Sabine

last: Richard


title: DEVELOPMENTAL LANDMARKS AND CELLULAR TRANSITIONS DURING EXTRAVILLOUS TROPHOBLAST CELL DIFFERENTIATION [bulk_rna_seq_kds]

first: Michael

last: Soares

overall_design: CT27 Trophoblast stem (TS- Okae et.al.) cell transduced with control shRNAs (shCTR) were used as a control or  shRNAs targeting CEBPB (shCEBPB), ADAMTS20 (shADAMTS20) or CCNB1 (shCCNB1 )were used as treatment. RNA-seq was performed in control and treatment cells after 8 days of differentiated into extravillous trophoblast (EVT) cells. 3 biological replicates each conditions.

first: Ayelen

last: Moreno-Irusta

first: Malay

last: Basu

first: Esteban

last: Dominguez

first: Thomas

last: Chen

first: Sawyer

last: Smith

first: Kaela

last: Varberg

first: Hiroaki

last: Okae

last: Arima


title: Context-dependent regulation of IgH V(D)J recombination by cohesin-STAG1 and cohesin-STAG2 [HTGTS-V(D)J-Seq]

city: East Lansing

first: Yu

last: Zhang

state: MI

address: 567 Wilson Rd, Biomedical and Physical Sciences Building, Rm 5176

department: Microbiology, Genetics and Immunology

institute: Michigan State University

summary: Cohesin-mediated loop extrusion is central to IgH V(D)J recombination in early developing B cells, driving D-to-JH rearrangements and  VH-to-DJH rearrangements, with the latter step regulated by the cohesin release factor WAPL. Here, we investigate the distinct contributions of two cohesin subunits, STAG1 and STAG2, which are incorporated in the somatic cohesin variants, cohesin-STAG1 and cohesin-STAG2, respectively. Using WAPL-sufficient mouse v-Abl pro-B cells to model the D-to-JH recombination stage, we show that STAG2 promotes balanced D-to-JH joining and restrains STAG1 expression. Loss of STAG2 elevates cohesin-STAG1 occupancy on chromatin, leading to premature long-range loop formation and expanded VH usage at the expense of distal DH usage. This phenotype persists in the absence of the cohesin acetyltransferase ESCO1 but requires the N-terminal YDF motif of CTCF, which protects cohesin from WAPL-mediated chromatin release. In WAPL-depleted cells modeling the VH-to-DJH recombination stage, the CTCF N-terminus is dispensable and both cohesin variants act cooperatively to establish a diverse VH repertoire. Thus, our findings uncover context-dependent and complementary roles of these two cohesin variants in shaping antibody gene diversity, and also highlight a regulatory axis between STAG1, STAG2, and CTCF in controlling long-range chromatin dynamics.

overall_design: We performed HTGTS-V(D)J-Seq in v-Abl transformed pro-B cells and their various mutant derivatives to study the differential potential of cohesin-STAG1 and cohesin-STAG2 in mediating IgH V(D)J recombination.

first: Fujung

last: Chang


title: Context-dependent regulation of IgH V(D)J recombination by cohesin-STAG1 and cohesin-STAG2 [ChIP-seq]

overall_design: We performed cohesin and CTCF ChIP-Seq in WT and mutant v-Abl transformed pro-B cells to study the role of cohesin-STAG1 and cohesin-STAG2 in IgH V(D)J recombination.

first: FuJung


title: Context-dependent regulation of IgH V(D)J recombination by cohesin-STAG1 and cohesin-STAG2 [3C-HTGTS]

overall_design: We performed 3C-HTGTS in v-Abl transformed pro-B cells and their various mutant derivatives to study the roles of cohesin-STAG1 and cohesin-STAG2 in IgH V(D)J recombination.


title: Steatosis shifts the histopathological heterogeneity of liver metastases towards poor prognosis replacement growth in colorectal cancer patients

city: Leuven

first: Juan

last: Fernández-García

address: Campus Gasthuisberg, O&N4, Herestraat 49, box 912

department: VIB-KU Leuven Center for Cancer Biology

country: Belgium

institute: VIB/KU Leuven

summary: Liver metastases are a leading cause of cancer-related deaths, particularly in colorectal cancer. Two distinct histological growth patterns characterize liver metastases: the desmoplastic growth pattern, marked by a stromal encapsulating ring around the metastasis, and the replacement growth pattern, where cancer cells integrate into and replace the native hepatocyte architecture. The replacement pattern is associated with poorer therapeutic responses and worse overall prognosis. Concurrently, obesity, which alters the liver microenvironment, is linked to unfavorable outcomes in colorectal cancer patients. This study explores the interplay between a lipid-rich liver microenvironment and histological growth patterns in metastases. Using resected patient specimens and preclinical mouse models of obesity, we observed a correlation between liver steatosis and a shift toward the more aggressive replacement growth pattern. Mechanistically, lipid-rich environments, both in vitro and in vivo, were found to enhance proline synthesis in colorectal cancer cells, promoting extracellular matrix (ECM) production. This phenotypic switch is driven by fatty acid oxidation, which generates acetyl-coenzyme A, leading to the accumulation of the transcription factor MYC. Inhibiting fatty acid oxidation or silencing MYC reversed the aggressive growth advantage in lipid-rich conditions. Interestingly, cancer cells lose the aggressive phenotype once the lipid abundance is withdrawn. Furthermore, publicly available patient datasets revealed upregulated proline and ECM metabolism in inherent replacement growth patterns. Targeting these pathways significantly reduced liver metastasis outgrowth in preclinical models.

overall_design: RNA-seq profiling of CMT93 spheroids treated with vehicle (ethanol + BSA) or 200 µM palmitate (ethanol + BSA-conjugated sodium palmitate).

first: Yiming

last: Peng-Winkler

first: Sarah-Maria

last: Fendt