title: In vivo engineering tumor cells to a universal ‘all-in-one’ cancer vaccine with full antigen spectrum [scRNA-Seq]

city: Shanghai

first: wang

last: wanting

address: 800 Dongchuan Road

institute: Shanghai Jiao Tong University

summary: Cancer vaccines offer a promising strategy to initiate de novo T cell responses or enhance existing ones, either functioning independently or synergizing with T cell-modulating therapeutics to reduce tumor burden. The clinical development of cancer vaccines faces challenges such as limited antigen coverage, insufficient antigen presentation, immune suppressive microenvironment, and the availability of personalized vaccines. In this study, we developed a Universal ‘all-in-one’ Cancer cell-derived Vaccine (UniCVac) with comprehensive antigen spectrum coverage by programming tumor cells into antigen-presenting cells (APCs) through the co-delivery of CIITA, NLRC5, CD80, and IL-2. This reprogramming mimics the professional APC phenotype, providing simultaneous HLA-I and HLA-II antigen presentation, co-stimulation, and T cell proliferation signals. These tumor-derived UniCVac can directly activate both CD4+ and CD8+ T cells in vitro, independent of APCs. Additionally, their co-stimulation and T cell growth-stimulating capabilities result in superior CD4+ and CD8+ T cell activation and proliferation comparable to traditional APCs, with enhanced PI3K-AKT   pathways activation. Single cell transcriptome analysis confirmed the similarity in cellular subtypes between UniCVac and traditional APCs activated T cells. In mouse models, the UniCVac vaccination reprogramed the tumor microenvironment from immunosuppressive to immune-permissive, induced robust CD4+ and CD8+ T cell expansion in both preventive and therapeutic tumor models and achieved complete tumor regression in vivo. Our approach provides a platform for the development of universal cancer vaccines with full antigen spectrum coverage and the ability to directly activate both CD4+ and CD8+ T cells, offering potential combinatorial opportunities with existing T cell-based immunotherapies against cancer.

overall_design: Single-cell RNA sequencing of tumor microenvironment in vehicle- and UniCVac-treated mice to evaluate immune cell remodeling.Additionally, scRNA-seq was performed on human T cells to validate the translational potential of the UniCVac-induced immune response.


title: In vivo engineering tumor cells to a universal ‘all-in-one’ cancer vaccine with full antigen spectrum

status: Public on Jul 15 2026

country: China

type: Expression profiling by high throughput sequencing

overall_design: TCR- T cells were harvested after co-culture with different stimulation conditions, including control, BAPC and the engineered vaccine UniCVac. The experiment included 3 biological replicates per group for bulk RNA sequencing to evaluate the direct transcriptomic alterations induced by the vaccine.


title: Frequency and prognostic significance of genetic abnormalities in a subgroup of intermediate risk neuroblastoma patients: A SIOPEN study

city: Newcastle upon Tyne

first: Graham

last: Smith

address: Framlington Place

department: Bioinformatics Support Unit

country: United Kingdom

institute: Newcastle University

summary:
PURPOSE:
Intermediate-risk neuroblastoma patients >18 months of age, with non-MYCN amplified, International Neuroblastoma Risk Group Staging System (INRGSS) localised, unresectable or International Neuroblastoma Staging System (INSS) stage 3 tumors, and unfavourable histology have inferior outcomes compared to other intermediate-risk patients. This study aimed to identify genetic prognostic biomarkers within this rare subgroup.
PATIENTS AND METHODS:
We conducted a large, international study including chromosomal copy number in all cases, next-generation DNA sequencing in most, and telomere maintenance mechanisms (TMM) and gene expression in a subset, and correlated results with patient survival.
RESULTS:
Among 98 tumors, 9/98 (9.2%) had oncogene amplifications (CDK4/MDM2/TERT co-amplification (n=1), CDK4/MDM2 co-amplification (n=4), CDK4 (n=2), TERT (n=1), and MYC (n=1)), while 63/98 (64.3%) had typical segmental chromosomal aberrations (tSCAs). Patients with tumors with oncogene amplification had the worst 5-year event-free survival (EFS) [0%] (p<0.0001 log rank test) and 5-year overall survival (OS) [44.4% (95% CI: 21.4-92.3%)] (p <0.01 log rank test). Patients with tumors harbouring tSCAs had inferior EFS compared to those with numerical chromosomal aberrations only [51.7% (95% CI: 40.6-65.8%) vs. 93.3% (95% CI: 81.5-100%)] (p <0.01). Patients with p53 pathway tumor alterations (n=10) had worse EFS than those without [0% vs. 61.1% (95% CI: 50.3-74.3%)] (p <0.0001, log-rank test) and worse OS [26.7% (95% CI: 8.9-80.3%) vs. 80.9% (95% CI: 71.8-91.3%)] (p<0.001 log rank test). Multi-variable analysis identified tSCAs as an independent prognostic variable for EFS and oncogene amplification or p53 pathway abnormalities as independent prognostic variables for EFS and OS.
CONCLUSION:
Oncogene amplification and/or p53 pathway abnormalities and/or typical SCAs identify patients with intermediate-risk neuroblastoma with inferior outcome for whom intensified or alternative treatments should be considered.

overall_design: Transcriptomic profiling of 18 intermediate-risk neuroblastoma tumors samples at diagnosis. Correlating gene expression with genomic alterations, as well as classifying tumors by adrenergic or mesenchymal signatures and other risk stratification signatures, correlating signatures with patient event-free and overall survival.

first: Hannah

middle: E

last: Hartley

first: Fang Chyi

last: Fong

first: Alem

middle: S

last: Gabriel

first: Louise

middle: K

last: Stevenson

first: Emily

last: Beckett

first: Lisa

middle: M

last: Allinson

first: Angharad

last: Goodman

first: Aaron

last: Potts

last: Whittle

first: Ruby

last: Barford

first: Alice

last: Lamparelli

first: Fiona

last: Herd

first: Katia

last: Mazzocco

first: Annalisa

last: Pezzolo

first: Martina

last: Morini

last: Ardito

first: Alessandra

last: Eva

first: Marzia

last: Ognibene

first: Matthias

last: Fischer

first: Sandra

last: Ackermann

first: Carolina

last: Rosswog

first: Barbara

last: Hero

middle: R

first: Adrienne

middle: A

last: Unsworth

first: Michael

last: McCorkindale

first: Sally

middle: L

last: George

first: Jennifer

last: Tall

first: Jan

middle: J

last: Molenaar

first: Yvette

last: Matser

first: Karin

last: Langenberg

first: Godelieve

last: Tytgat

first: Rosa

last: Noguera

first: Ana

middle: P

last: Berbegall

first: Jaime

last: Font de Mora

first: Valérie

last: Combaret

first: Gaelle

last: Pierron

first: Annick

last: Mühlethaler-Mottet

first: Jacqueline

last: Schoumans

first: Joëlle

last: Tchinda

first: Irina

last: Banzola

first: Marta

last: Jeison

first: Michal


title: CDO1 is a new biomarker to discriminate aggressive forms of prostate cancer

city: Créteil

first: Virginie

last: Firlej

address: Ur Trepca

country: France

institute: UPEC TrePca

summary: Worldwide, prostate cancer (PCa) ranks second in terms of incidence and eighth in terms of mortality. While most cancers remain silent after initial treatment, some tumors recur. At present, we are unable to predict which patients are at risk of recurrence. In order to determine this risk of recurrence as early as at the biopsy stage, and to enable better therapeutic management of patients, it is essential to identify new biomarkers.  In this study, we have demonstrated that Cysteine Dioxygenase CDO1 could be a predictive marker in PCa progression. In PCa, CDO1 expression could be regulated by methylation and androgen signaling pathway. Furthermore, inhibition of CDO1 expression in VCaP prostate cancer cells led to increased cell migration and non-adherent growth. Finally, transcriptomic analysis of these cells with inhibited CDO1 expression demonstrates the complex role of CDO1 and its involvement in the mechanisms regulating endoplasmic reticulum stress and protein unfolding. Altogether, these results describe the loss of CDO1 as a marker of aggressiveness in PCa. Furthermore, the loss of CDO1 is thought to be responsible for tumor progression in vitro by acting on multiple signaling pathways.

overall_design: RNA seq of VCaP cells transfected by siRNA directed against CDO1 or control

first: Jeanne

last: Gaspar Lopes


title: Slc44a2 deficiency unveils an IFN-I–dependent feedback control of pDC egress II

city: Beijing

first: Ruiqun

last: Chen

address: Tsinghua University,Hai Dian, Beijing

institute: Tsinghua University

summary: Plasmacytoid dendritic cells (pDCs) are a specialized subset of innate immune cells capable of sensing viral nucleic acids and rapidly producing large amounts of type I interferons (IFN-I). However, excessive IFN-I production can cause various immunopathogenic conditions. The capacity for IFN-I production by pDCs is tightly regulated, yet the underlying mechanisms remain incompletely understood. Here, we describe two levels of negative regulatory mechanisms controlling IFN-I production by pDCs. First, we identified SLC44A2 as a negative regulator of IFN-I production. SLC44A2 was highly expressed in resting pDCs but significantly downregulated upon activation. Deficiency of SLC44A2 led to excessive IFN-I production. Mechanistically, SLC44A2 may restrict IFN-I production by exporting threonine, asparagine, and glutamine, amino acids that we found to be essential for IFN-I production in pDCs. Second, we uncovered an IFN-I-dependent negative feedback mechanism controlling pDC egress. Excessive IFN-I restrained pDC migration by downregulating CCR2 and CCR5. This feedback was generally observed during viral infections, autoimmune diseases, and in Slc44a2-deficient mice. Taken together, these two regulatory mechanisms are essential for maintaining pDC homeostasis and preventing systemic overactivation of IFN-I responses.

overall_design: RNA-seq profiling of BM pDC from WT and Slc44a2 cKO mice

first: Tao

last: Wu

first: Li

first: Ligong


title: Genome-wide analysis of histone H3K18 lactylation in a kainic acid-induced epilepsy model

city: chongqing

first: yuan

last: meng

address: No. 1 Youyi Road, Yuzhong District

department: Department of Neurology

institute: The First Affiliated Hospital  of Chongqing Medical University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Metabolic reprogramming has been increasingly linked to epilepsy, but the epigenetic mechanisms connecting altered glucose metabolism to seizure susceptibility remain incompletely understood. In this study, we aimed to investigate whether lactate-associated histone modification contributes to epileptogenesis and to define its downstream transcriptional targets. Using a kainic acid (KA)-induced temporal lobe epilepsy model, we examined genome-wide chromatin occupancy of histone H3 lysine 18 lactylation (H3K18la) in control and epileptic mouse hippocampal tissues by ChIP-seq. The objective of this study was to characterize H3K18la-associated epigenetic changes during epileptogenesis and to identify candidate genes and pathways regulated by this histone mark. These data provide a genome-wide resource for understanding how glycolysis-related histone lactylation is involved in transcriptional regulation during seizure development.

overall_design: Chromatin immunoprecipitation sequencing(ChIP-seq) for histone H3 lysine 18 lactylation (H3K18la) was performed in hippocampal tissues from control mice and kainic acid-induced temporal lobe epilepsy model mice to characterize genome-wide H3K18la changes during epileptogenesis.

first: Fei

last: Xiao

first: Yuan

last: Meng

first: Yanlin

last: Guo

first: Liumi

last: Jiang

first: Jing

last: Luo

first: Yan

last: Liu

first: Ziwei

last: Yuan


title: Slc44a2 deficiency unveils an IFN-I–dependent feedback control of pDC egress


title: Glo1 promotes glioma progression by modulating Sox2 transcriptional networks in glioma stem-like cells

city: Houston

first: Dongjoo

last: Choi

state: TX

address: 1 baylor plaza

country: USA

institute: BCM

summary: Single cell RNA sequencing was performed to investigate transcriptional programs associated with Glyoxalase 1 (Glo1) perturbation in glioma stem-like cells. Three experimental conditions were analyzed including control glioma stem-like cells, Glo1 knockdown, and Glo1 overexpression.

overall_design: Three experimental conditions were analyzed: control glioma stem-like cells (conGBM), Glo1 knockdown (Glo1KD), and Glo1 overexpression (Glo1OV). Single cell RNA sequencing libraries were generated using the 10x Genomics Chromium platform and sequenced on an Illumina platform. Gene expression matrices were generated using Cell Ranger and downstream analyses were performed in Seurat.

first: Dong-Joo

first: Yeunjung

last: Ko

first: Benjamin

last: Deneen


title: Integrative single-nucleus multiomic, CUT&Tag, and bulk RNA-seq profiling of human and mouse prefrontal cortex reveals gene regulatory mechanisms of cortical development and Meis2 function

city: New Haven

first: Saejeong

last: Park

state: Connecticut

address: 100 College St

institute: Yale University

summary: The development of the prefrontal cortex (PFC) is governed by coordinated transcriptional and epigenomic regulatory programs. To comprehensively characterize these processes, we generated an integrative multi-modal dataset combining single-nucleus multiomic (snRNA-seq and snATAC-seq), CUT&Tag, and bulk RNA-seq data from human and mouse PFC. Single-nucleus multiomic data from human mid-fetal dorsolateral prefrontal cortex (dlPFC) samples and mouse postnatal day 1 (P1) medial prefrontal cortex (mPFC) and motor cortex (MC) and provide matched gene expression and chromatin accessibility profiles across diverse cell types. Complementary CUT&Tag experiments profiling key transcription factors (RARA, RARB, RXRG, MEIS2) and histone modifications (H3K27ac, H3K4me3) further define regulatory elements and transcriptional control landscapes. To investigate the functional role of Meis2, bulk RNA-seq was performed on mouse P0 medial prefrontal cortex (mPFC) from control and Meis2 conditional knockout (cKO) samples. These data enable the identification of gene expression changes associated with Meis2 perturbation. Together, this integrated dataset provides a resource for studying gene regulatory networks underlying cortical development and for linking transcription factor activity to downstream gene expression programs across species.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Single-nucleus multiomic profiling (snRNA-seq and snATAC-seq) and CUT&Tag were performed on human mid-fetal (PCW18-19) dorsolateral prefrontal cortex (dlPFC) samples. Single-nucleus multiomic profiling was performed on medial prefrontal cortex (mPFC) and motor cortex (MC) from wild-type mice at postnatal day 1 (P1). Bulk RNA-seq was performed on mPFC from control and Meis2 conditional knockout (cKO) mice at P0.


title: A viscous DES-AAV-Foxo1 delivery system with high transfection efficiency for the treatment of corneal endothelial dysfunction by restoring mitochondria-ER contacts

city: Qingdao

first: Hongran

last: Zhao

state: Shandong

address: ShiNanQu

institute: Shandong Eye Institute

summary: Corneal endothelial dysfunction is a major cause of global blindness, with an estimated 12.7 million patients awaiting corneal transplantation, and the severe shortage of donor grafts underscores the urgent need for non-surgical therapies. Gene therapy offers a promising alternative, but is hindered by the limitations in existing delivery systems and the scarcity of validated molecular targets capable of reversing core pathophysiology. To address this, we first employed multi-omics analysis and identified FOXO1 as a central and under-explored therapeutic target for corneal endothelial dysfunction. In vivo FOXO1 overexpression effectively improved corneal endothelial function by preserving mitochondria-associated endoplasmic reticulum membrane integrity and mitochondrial Ca²⁺ homeostasis, yet its therapeutic potential was limited by low transfection efficiency. To overcome this, we engineered an AAV-Foxo1 delivery system using a viscous choline chloride-fructose-based deep eutectic solvent (DES) as the carrier. The DES-AAV-Foxo1 delivery system exhibited good biocompatibility, significantly prolonged anterior chamber retention, and enhanced transfection efficiency in corneal endothelial cells compared to conventional AAV delivery. Animal experiments confirmed that it effectively improved corneal endothelial pump activity and mitigates endothelial dysfunction in type 1 diabetes mellitus and Fuchs endothelial corneal dystrophy mouse models. Our findings demonstrated the therapeutic potential of DES-AAV-Foxo1 delivery system for corneal endothelial disorders.

overall_design: Our study aims to observe the effect of overexpressing FOXO1 on the transcription of corneal endothelial cells under high glucose conditions.


title: Transcriptomic profiling of thalamic tissue from APOE4-carrying 5xFAD mice with or without Lilrb4a deficiency

city: Chongqing

first: Hongsheng

last: Zhang

address: 1 Youyi Road, Yuzhong District

institute: Chongqing Medical University

summary: The microglial immune receptor Lilrb4a is strongly induced in Alzheimer’s disease (AD) mouse models and has been proposed to function as a receptor for APOE4. To define the molecular programs associated with Lilrb4a deficiency in an APOE4-dependent AD context, we conducted bulk RNA-seq on thalamic tissue from 5xFAD mice carrying human APOE4 (5EL) and Lilrb4a-deficient 5EL mice (5ELKO). Transcriptomic analysis identified significant changes in inflammatory and metabolic pathways, with prominent enrichment of PPAR signaling and broader lipid/energy metabolic programs in Lilrb4a-deficient mice. This dataset provides a transcriptomic resource for investigating Lilrb4a-dependent molecular pathways in APOE4-associated AD-like pathology.

overall_design: The sequencing samples were randomly selected from 5 ELKO and 5 EL mice, with all tissues taken from the thalamus.Gene expression profiles were compared between genotypes to identify differentially expressed genes and pathways associated with loss of Lilrb4a in the APOE4 background.

first: Chao

last: Wang

first: Changxu

last: Nie

first: Ruixi

last: Yang


title: NSCLC KRAS G12C MUTANT CELLS ARE DEPENDENT ON MUC1-C FOR RESISTANCE TO RAS(ON) INHIBITORS

city: Boston

first: Shinkichi

last: Takamori

state: MA

address: 450 Brookline Avenue

institute: Dana-Farber Cancer Institute

summary: Treatment of NSCLC KRAS G12C mutant tumors with targeted KRAS inhibitors, such as sotorasib and adagrasib, is invariably associated with the emergence of acquired resistance. The mechanisms responsible for resistance to these agents have largely remained unclear. We report that patients with NSCLC KRAS G12C tumors expressing increased levels of the MUC1 gene exhibit decreases in overall survival in response to sotorasib and adagrasib. In investigating the basis for this finding, we found that exposure of NSCLC KRAS G12C mutant cells to these agents induces expression of the oncogenic MUC1-C/M1C protein. Studies of RAS(ON)-resistant (RMC-R) cells further reveal upregulation of M1C chromatin levels in association with activation of the epithelial-mesenchymal transition (EMT). Mechanistically, M1C drives NF-kB p65-mediated induction of the ZEB1 EMT-TF. Furthermore, targeting M1C NF-kB ZEB1 signaling suppresses EMT and sotorasib resistance. Having identified this M1C dependence, we demonstrate that targeting M1C with an antibody-drug conjugate (ADC) is effective against sotorasib-resistant cells growing in vitro and as tumor xenografts. These findings identify M1C as a major effector of sotorasib resistance and as a target for ADC treatment of patients with refractory NSCLC KRAS G12C mutant tumors.

overall_design: RNA Seq in RAS(ON)-resistant (RMC-R) Cell line with MUC1-C shRNA silencing. We conpared DMSO and DOX treatment cells for differential gene expression analysis. MUC1shRNA (MISSION shRNA TRCN0000122938; Sigma, St. Louis, MO, USA)  was inserted into the pLKO-tet-puro vector (Plasmid #21915; Addgene, Cambridge, MA, USA) . Vector-transduced cells were selected for growth in 1–2 μg/ml puromycin. Cells were treated with 0.1% DMSO as the vehicle control or 500 ng/ml doxycycline (DOX; Millipore Sigma).


title: Vascular endothelial growth factor receptors 1 and 3 mediate placental trophoblast leptin production in preeclampsia, inducing vascular dysfunction

city: Augusta

first: Jessica

last: Faulkner

state: Georgia

address: 1120 15th Street

department: Physiology

institute: Augusta Univeristy

summary: Heightened soluble FMS-like tyrosine kinase-1 (sFlt-1) level is a hallmark of preeclampsia patients and induces a state of angiogenic imbalance by sequestering free vascular endothelial growth factor (VEGF) and placental growth factor (PlGF). The receptors for VEGF and PlGF, membrane-bound VEGFR, are expressed in placental trophoblast cells, but their functions in this cell type are largely unknown. Placenta production of leptin significantly increases in preeclampsia, and we recently showed leptin induces placental and vascular endothelial dysfunction in pregnancy. We hypothesized that inappropriately high sFlt-1 in preeclampsia leads to an increase in trophoblast leptin production. We treated human placental explants, trophoblast and adipose cells with sFlt-1 and show an increase in leptin peptide production, which is ablated by coadministration with either VEGF or placental growth factor (PlGF). We further demonstrate that VEGFR1 and 3, not R2, expressions are predominant in human trophoblasts and that reducing activation of these receptors mediates trophoblast leptin production. In pregnant mice, we show that sFlt-1 infusion induces vascular endothelial dysfunction in association with significantly elevated plasma leptin levels. In pregnant sFlt-1-infused mice, treatment with leptin receptor antagonist significantly ablated vascular endothelial dysfunction. Collectively, these data indicate that angiogenic imbalance in preeclampsia impacts placental trophoblast endocrine function by suppressing VEGFR1 and 3 activation, resulting in leptin overproduction. Furthermore, sFlt-1 induces vascular endothelial dysfunction in mice dependent on leptin receptor activation.

overall_design: BeWo cells were treated with sFlt-1 or vehicle as above and harvested and RNA isolated as described above. Raw sequencing reads in FASTQ format were obtained from the sequencing provider (Novogene©, Sacramento, CA), where adapter trimming was performed. Transcriptome alignment was conducted using STAR (v2.7) with the GRCh38 human reference genome for both mapping and annotation. Default parameters were applied. Feature counting was performed using subread (v2.0.3) to generate gene-level count matrices based on the aligned reads. Differential expression analysis was conducted using DESeq2 in R, following standard normalization and statistical modeling procedures. Genes with a p-value < 0.05 were considered significantly differentially expressed.  All computational analyses were performed in an R-based environment, and statistical significance was determined using appropriate multiple-testing corrections where applicable.

first: Mona

last: Elgazzaz

first: Safia

last: Ogbi

first: Desmond

last: Moronge

first: Elisabeth

last: Mellott

first: Kristin

last: Backer

first: Amalia

last: Brawley

first: Gabrielle

last: Hernendez

first: Joanna

last: Hitchings

first: Luis

last: Valesquez Zarate

first: Sravankumar

last: Kavuri

first: Tae Jin

last: Lee

first: Daria

last: Ilatovskaya

first: Padmashree

middle: C

last: Woodham

first: James

last: Maher

first: Brian

middle: H

last: Annex


title: Inhibition of SIRT7 Overcomes Radioresistance in Pancreatic Neuroendocrine Tumors by Reactivating MEN1 Expression

city: shanghai

first: jianyun

last: jiang

address: dong'an road 270

institute: fudan university shanghai cancer center

summary: Pancreatic neuroendocrine tumors (PanNETs) frequently exhibit loss or reduced expression of the tumor suppressor MEN1, a key regulator of tumor progression and DNA damage response (DDR). However, the upstream mechanisms driving MEN1 silencing remain unclear. Here, a pooled epigenetic CRISPR–Cas9 screen identified the NAD⁺-dependent deacetylase SIRT7 as a critical suppressor of MEN1 expression. Mechanistically, SIRT7 interacts with DNMT1 and promotes catalytic activity–dependent recruitment of DNMT1 to the MEN1 promoter, leading to promoter hypermethylation and transcriptional repression. Clinically, SIRT7 is overexpressed in PanNET tissues and inversely correlates with MEN1 levels and patient prognosis. Genetic or pharmacologic inhibition of SIRT7 restored MEN1 expression, reduced MRN complex abundance, and impaired double-strand break repair. Graded MEN1 re-expression demonstrated a quantitative relationship between MEN1 levels, DNA repair efficiency, and radiosensitivity. Functionally, SIRT7 inhibition enhanced radiation-induced DNA damage and apoptosis in a partially MEN1-dependent manner and significantly suppressed tumor growth in patient-derived organoids and multiple independent xenograft models. Collectively, these findings define a catalytic activity–dependent SIRT7–DNMT1–MEN1 epigenetic axis that modulates DDR and radiosensitivity, supporting SIRT7 targeting as a strategy to improve radiotherapy efficacy in PanNETs.

overall_design: Two independent RNA-seq experiments were performed in human pancreatic neuroendocrine tumor (PanNET) cells, with 3 biological replicates per group for all samples: To determine the impact of SIRT7 depletion on global gene expression, RNA-seq was performed in SIRT7-knockdown QGP-1 cells (PanNET cell line) and matched control QGP-1 cells, focusing on DNA damage response (DDR) and DNA repair–related gene expression changes. A total of 1,960 genes were significantly altered, with DDR components prominently downregulated. To dissect the transcriptional mechanisms driving acquired radioresistance, RNA-seq was conducted in parental BON-1 PanNET cells and the stably radioresistant BON-1/RR subline (established by stepwise fractionated irradiation), aiming to identify differentially expressed genes and enriched DDR pathways associated with radioresistance.


title: Single-bacterium RNA-seq protocol to uncover heterogeneous expression of coding and noncoding genes in Bacteroides thetaiotaomicron

city: Wurzburg

first: Elise

last: Bornet

address: Josef-Schneider Strasse 2

country: Germany

institute: Helmholtz Insitute

summary: Single-cell RNA sequencing is increasingly applied to bacterial model species, but a protocol for obligate anaerobic gut commensals belonging to the Bacteroidota phylum has not previously been established. Here, we present a technique to profile global gene expression of individual Bacteroides thetaiotaomicron cells. We describe steps for transcriptome stabilization and FACS-based collection and lysis of single Bacteroides cells. We then detail procedures for reverse transcription, sensitive depletion of ribosomal sequences, and cDNA library generation. This experimental pipeline has potential to uncover cell-to-cell variability in predominant bacterial members of the healthy human gut microbiota.

overall_design: Single-bacterium RNA-seq protocol performed using the MATQ-seq protocol. Here the protocol is described for Bacteroides thetaiotaomicron. Bacteria were harvested at mid-expotential phase (OD600=2).

first: Alexander

last: J Westermann


title: Immune checkpoint LAG-3 governs stage-dependent and disease-associated microglial modules in ALS model mice

city: Minato-ku

first: Yuta

last: Morisaki

state: Tokyo

address: 1-5-30, Shibakoen

department: Faculty of Pharmacy

country: Japan

institute: Keio University

summary: Immune checkpoint molecules, inhibitory receptors originally characterized in T cell biology, have recently emerged as regulators of microglial function in neurodegeneration, yet their roles in amyotrophic lateral sclerosis (ALS) remain unexplored. Here, we investigated LAG-3, an inhibitory immune checkpoint receptor, in microglial regulation during ALS pathogenesis using SOD1G93A mice. LAG-3 expression was progressively upregulated in spinal cord microglia during disease progression, and LAG-3-high microglia exhibited a disease-associated microglia (DAM) transcriptional signature. Genetic deletion of LAG-3 produced a biphasic phenotype, with accelerated disease onset but significantly prolonged disease duration. LAG-3 deficiency enhanced inflammatory microglial responses at the early disease stage, whereas at the late stage it suppressed inflammatory signaling while selectively preserving phagocytic effector gene expression, demonstrating that LAG-3 dissociates the inflammatory and phagocytic modules within the DAM program in a stage-dependent manner. These transcriptional changes translated into enhanced phagocytic capacity in primary microglia and were accompanied by amelioration of the spinal cord environment, reflected by suppression of inflammatory pathways and restoration of oxidative phosphorylation. Our findings identify LAG-3 as a stage-dependent regulator of microglial functional states in ALS and support the concept that immune checkpoint molecules constitute a class of module-level regulators of microglial function in neurodegeneration.

overall_design: Microglia from the lumbar spinal cord of SOD1G93A mice were sorted as CD45int/CD11b+ populations and further separated into LAG-3-high and LAG-3-low subpopulations by FACS, with wild-type microglia as controls, for transcriptional characterization of LAG-3-expressing microglia. Additionally, microglia from SOD1G93A/LAG-3+/+ and SOD1G93A/LAG-3−/− mice were sorted at two disease stages (P120 and P140). Total RNA was also extracted from lumbar spinal cord tissue of P140 SOD1G93A/LAG-3+/+ and SOD1G93A/LAG-3−/− mice for bulk RNA-seq analysis.

first: Motoki

last: Ohshima

first: Nanaka

last: Nomura

first: Miruto

last: Matsuda

first: Hidemi

last: Misawa


title: NCOR2 represses MHC class I molecule expression to drive metastatic progression of breast cancer

city: San Francisco

first: Valerie

last: Weaver

state: CA

address: 513 Parnassus Avenue, HSE 560, Box 0456

department: Department of Surgery and Center for Bioengineering and Tissue Regeneration

institute: Johns Hopkins Univeristy

summary: Metastatic progression depends upon the ability of disseminated tumor cells to evade immune surveillance. MHC-mediated antigen presentation facilitates T cell-dependent eradication of metastatic tumor cells. We identified nuclear corepressor 2 (NCOR2) as an epigenetic regulator of MHC class I molecule presentation on breast tumor cells. Patients with triple negative breast cancers (TNBC) that expressed high levels of NCOR2 also exhibited reduced metastasis-free survival and decreased MHC class I expression, and metastatic lesions in patients with TNBC had high nuclear NCOR2 and reduced CD8+ T cells. Reducing NCOR2 expression or preventing its interaction with HDAC3 enhanced innate immune cell recruitment and activity, and elevated MHC class I levels on disseminated cancer cells to potentiate CD8+ T cell activity and apoptosis induction that prevented metastatic progression. The studies provide evidence to support NCOR2 as a targetable epigenetic regulator of metastasis towards which therapies could be developed to reduce patient mortality.

overall_design: NCOR2 binding sites in 4T07 cells were profiled using CUT&Tag. EGFP knockdown 4T07 cell lines were used as negative controls.

first: Pavla

last: Ticha

first: Jason

last: Northey

first: Radhika

last: Narain

first: Shivang

last: Sharma

first: Jonathan

middle: N

last: Lakins

first: Hugo

middle: G

last: Velozo

first: Kelly

last: Kersten

first: Alastair

last: Ironside

first: Allison

last: Drain

first: Martin

last: Zidek

first: Kelvin

middle: T

last: Tsai

first: Yunn-Yi

last: Chen

first: Eugene

last: Shenderov


title: Influenza-induced tuft cell expansion alters ILC-mediated inflammation [nonimmune]

city: Philadelphia

first: Andrew

last: Vaughan

state: PA

address: 3800 Spruce Street

institute: University of Pennsylvania

summary: Tuft cells act as sentinels that amplify type 2 inflammation primarily by activating type 2 innate lymphoid cells (ILC2s). Although normally absent from the distal lung, ectopic tuft cells form after severe lung injury including influenza infection in mice. Here, we investigated the function of these ectopic tuft cells in shaping innate immunity following influenza injury. We observed that IFNγ restrains tuft cell differentiation, whereas ILC2s drive tuft cell expansion, establishing a reciprocal regulatory axis. Tuft cell–deficient mice exhibited reduced eosinophilic inflammation and expansion of ILC1s and ILC3s after influenza injury resolution. Single-cell RNA-seq of influenza infected whole lung revealed transcriptional signatures consistent with type 1 pathway activation, type 2 suppression and oxidative stress. Following influenza injury and subsequent Alternaria alternata challenge, tuft cell–deficient mice also showed neutrophilic and ILC3 expansion. Together, these data identify a distal-airway tuft-cell–ILC2 circuit that helps maintain a balanced inflammatory environment in response to viral injury and aeroallergens.

overall_design: RNA-seq profiling of uninfected and infected Pou2F3+/- and Pou2F3-/-  mice at Day 22 following infection: non-immune cells (CD45⁺) only.

first: Maria

last: Gentile

first: Michael

last: Maiden

first: Evelyn

last: Martinez

first: Madeline

last: Singh

first: Harshini

last: Kelam

first: Nicholas

last: Holcomb

first: Joanna

last: Wong

first: Diana

last: Abraham

first: Alena

last: Klochkova

first: Sara

last: Kass-Gergi

last: Avughan


title: Influenza-induced tuft cell expansion alters ILC-mediated inflammation [immune]

overall_design: RNA-seq profiling of uninfected and infected Pou2F3+/- and Pou2F3-/-  mice at Day 22 following infection: immune cells (CD45⁺) only.


title: Hierarchical Chromatin Rewiring Orchestrates Early Transcriptional Regulation in Mouse Cerebral Cortex Following Focal Ischemia

city: MADISON

first: Hadjer

last: Namous

state: WI

address: 600 highland ave

department: Neurological Surgery

institute: University of Wisconsin Madison

summary: Focal cerebral ischemia induces rapid and extensive transcriptional changes in the brain, yet how higher-order chromatin architecture contributes to this response remains poorly defined. In this study, we profile genome-wide chromatin organization and transcriptional activity in the mouse cerebral cortex following transient middle cerebral artery occlusion (tMCAO). Using  Hi-C alongside prior transcriptomic data and cis-regulatory annotations at early reperfusion time points, we show that ischemic injury triggers hierarchical reorganization of chromatin structure, including alterations in compartmentalization, topologically associating domains, and enhancer–promoter interactions. These structural changes are temporally coordinated with early gene expression programs involved in inflammation, stress response, and neuronal remodeling. Our data reveal that transcriptional activation following ischemia is constrained and guided by multi-scale chromatin architecture, providing a systems-level framework for understanding genome regulation during acute brain injury.

overall_design: Peri-infarct cerebral cortex tissue was collected from adult male mice at 6 h and 24 h following transient middle cerebral artery occlusion (tMCAO). Sham cortical tissue was collected from animals that did not undergo tMCAO. In total, 36 mice were used in the study, including sham controls. Tissue from three animals was pooled to generate each biological sample, yielding four pooled samples in total across all experimental conditions. Genome-wide chromatin architecture was profiled using Arima genomics Hi-C

first: Raghu

last: Vemuganti


title: YTHDF1 functions as a non-canonical nuclear checkpoint that couples R-loop homeostasis to innate immune restraint and adaptive immune resistance in cancer（CUT&Tag）

city: Nanjing

first: Shan

last: Gao

address: No. 2 Sipailou, Xuanwu District

institute: Southeast University

summary: Innate immune signaling within cancer cells plays an important role in shaping antitumor immunity, yet the nuclear mechanisms that restrain inappropriate immune activation remain incompletely defined. YTHDF1 is an mRNA-binding protein previously characterized as a cytoplasmic m⁶A reader. Emerging evidence indicates that YTHDF1 also functions in the nucleus, where it associates with chromatin and contributes to the regulation of R-loop homeostasis. Loss of YTHDF1 results in R-loop accumulation, genomic instability, cytosolic DNA release, and activation of the cGAS–STING–type I interferon pathway. Mechanistically, YTHDF1 interacts with the chromatin remodeler ARID1A at immune-associated genomic regions, suggesting a cooperative role in maintaining genome stability and regulating immune-related transcriptional programs. To investigate the transcriptomic and chromatin-level consequences of YTHDF1 and ARID1A perturbation, we generated RNA sequencing (RNA-seq) and R-loop CUT&Tag datasets in A549 human lung cancer cells. RNA-seq was performed in two experimental settings: (1) wild-type (WT) and YTHDF1 knockout (YTHDF1-KO) cells; and (2) WT, YTHDF1-KO, ARID1A knockdown (siARID1A), and combined YTHDF1-KO with ARID1A knockdown cells. In parallel, R-loop CUT&Tag profiling was conducted under the same respective conditions to assess genome-wide R-loop distribution. These datasets provide integrated transcriptomic and chromatin profiling resources for studying the roles of YTHDF1 and ARID1A in regulating R-loop dynamics and tumor-intrinsic innate immune signaling

overall_design: CUT&Tag assays were performed in A549 cells under four experimental conditions: wild-type (WT), YTHDF1 knockout (YTHDF1-KO), ARID1A knockdown (siARID1A), and combined YTHDF1-KO with ARID1A knockdown.  Chromatin profiling was conducted using antibodies against YTHDF1 and ARID1A to assess their genome-wide occupancy across the four conditions. Normal IgG was included as a negative control to evaluate background signal. Following antibody binding, pA-Tn5–mediated tagmentation was performed, and sequencing libraries were generated for high-throughput sequencing analysi

first: Xiaofeng

last: Zhu


title: YTHDF1 functions as a non-canonical nuclear checkpoint that couples R-loop homeostasis to innate immune restraint and adaptive immune resistance in cancer（R-loop CUT&Tag）

overall_design: R-loop CUT&Tag was performed to profile genome-wide R-loop distribution in A549 cells. R-loops were detected using the S9.6 antibody, which specifically recognizes RNA–DNA hybrids.


title: YTHDF1 functions as a non-canonical nuclear checkpoint that couples R-loop homeostasis to innate immune restraint and adaptive immune resistance in cancer（RNA-seq II）

overall_design: RNA-seq was performed to compare transcriptomic profiles among four experimental groups: wild-type (WT), YTHDF1 knockout (YTHDF1-KO), ARID1A knockdown (siARID1A), and combined YTHDF1 knockout with ARID1A knockdown A549 cells.


title: Obesity-associated meta-inflammation alters influenza A antiviral responses in Göttingen minipigs

city: Kongens Lyngby

first: Betina Lyngfeldt

last: Henriksen

address: Anker Engelunds Vej 101

country: Denmark

institute: Technical University of Denmark

summary: Obesity is a well-recognized risk factor for increased severity following influenza A virus (IAV) infection, likely by promoting meta-inflammation and immune dysregulation, but its effects on antiviral and inflammatory responses  remain poorly understood. Using a Göttingen minipig model of diet-induced obesity, we compared antiviral and inflammatory responses before and after IAV infection. Respiratory tract transcriptomics and histopathology revealed no clear obesity-associated immune or inflammatory changes in uninfected minipigs. In contrast, obese pigs showed reduced viral clearance in nasal mucosal tissue accompanied by altered antiviral gene expression pattern four days post infection. Furthermore, cellular infiltration of the respiratory tract was observed in obese pigs after infection. Finally, C-reactive protein concentrations increased significantly in obese pigs, indicating enhanced systemic inflammation in response to respiratory infection. These findings demonstrate that diet-induced obesity in Göttingen minipigs is associated with altered antiviral and inflammatory responses following IAV infection and support the translational value the obese minipig model.

overall_design: Castrated nine weeks old Göttingen Minipigs (n=26) were randomized into two diet groups and fed a diet high in fat, fructose, and cholesterol (n=13) (Ossabaw pig diet – 5B4L, TestDiet) or standard minipig chow (SD, n=13) (Mini-pig, Special Diets Services) and described previously. Ninety-nine days after initiation of the feeding (henceforth termed 0 dpi), pigs from both the obese (n=9) and lean (n=9) groups (designated obese-IAV and lean-IAV, respectively) were inoculated with 2 ml/nostril of 1.6x108 TCID50/ml A/swine/Denmark/12687/2008 (H1N2) IAV using a nebulization device (Mad Nasal Intranasal Mucosal Atomization Devices (Teleflex)). Groups of obese (n=4) and lean (n=4) pigs (designated obese-mock and lean-mock, respectively) were inoculated with 2 ml/nostril virus-free growth medium. Blood and nasopharyngeal swab samples were collected daily from 0 to 4 dpi. At 4 dpi, all 26 pigs were euthanized, and lower trachea samples were collected. Total RNA was extracted using a gentleMACS Dissociator (Miltenyi Biotec) for homogenization and miRNeasy Kit (Qiagen) for extraction. Due to low RNA quality one samples was exclude from RNA-seq.

first: Sofie M. R.

last: Starbæk

first: Louise

last: Brogaard

first: Charlotte

last: Kristensen

first: Siri

last: Wolthoorn

last: Lohse

first: Anders

last: Stockmarr

first: Henrik Elvang

last: Jensen

first: Lars E.

last: Larsen

first: Peter M. H.

last: Heegaard

first: Kerstin

last: Skovgaard


title: YTHDF1 functions as a non-canonical nuclear checkpoint that couples R-loop homeostasis to innate immune restraint and adaptive immune resistance in cancer（RNA-seq i）

overall_design: RNA-seq was performed to compare transcriptomic profiles between WT and YTHDF1 knockout A549 cells.


title: Endothelial TGFβ signaling regulates choroidal neovascularization severity via myeloid–endothelial interaction

city: Hamburg

first: Andreas

last: Neueder

address: Falkenried 94

department: Center for Molecular Neurobiology (ZMNH)

institute: University Medical Center Hamburg-Eppendorf

summary: The blood-retinal barrier (BRB) is essential for maintaining retinal homeostasis, yet its disruption contributes to pathological angiogenesis in diseases such as neovascular age-related macular degeneration (nAMD). Here, we investigated how endothelial TGF-β signaling interacts with microglia to regulate choroidal neovascularization (CNV). Using a laser-induced CNV model in mice with endothelial-specific Tgfbr2 deletion (Tgfbr2∆EC) and concomitant microglia depletion via PLX5622, we demonstrate that loss of endothelial TGF-β signaling significantly exacerbates CNV, an effect fully rescued by microglia depletion. Bulk RNA sequencing and RNAscope analyses of CNV lesions identified fibrinogen alpha chain (Fga) as a microglia-derived factor upregulated exclusively in Tgfbr2∆EC mice. These findings suggest a TGF-β-dependent interaction between endothelial cells and microglia that promotes angiogenesis through microglia derived Fga expression.

overall_design: RNAseq of retinal and choroidal tissue from wildtype and TGFBR2-/- mice, with and without PLX5622 treatment

first: Anja

last: Schlecht

first: Lisa

last: Müllerbauer

first: Katja

last: Fitz

first: Nico

last: Hofmann

first: Jost

last: Hillenkamp

first: Süleyman

last: Ergün

first: Barbara

last: Braunger


title: Gut mycobiota-associated tryptophan catabolites protect against metabolic dysfunction-associated steatotic liver disease

first: Shuangya

last: Fan

address: 22 Hankou Road, Gulou District, Nanjing, Jiangsu Province, China

department: Medical school

institute: Nanjing University

summary: Accumulating evidence suggests that the intestinal microbiota participates in the development of metabolic dysfunction-associated steatotic liver disease (MASLD) through metabolite-host interaction. However, the beneficial role of commensal mycobiota in MASLD progression remains poorly understood. Comparing the gut microbiome differences, we demonstrated that the deficiency of Caspase Recruitment Domain-containing protein 9 (CARD9), an adaptor protein for a microbiota recognition receptor, exacerbated HFD-induced MASLD in a gut fungi-dependent manner. CARD9 deficiency reduced the abundance of Saccharomyces cerevisiae (S. cerevisiae), which was a probiotic alleviating MASLD progression. S.cerevisiae promoted a significantly greater abundance of 5-hydroxyindoleacetic acid (5-HIAA) in intestine through TLR1, which then alleviated MASLD phenotypes via “gut-liver” axis. Particularly, 5-HIAA directly bond to aryl-hydrocarbon receptor (AhR) and stimulated its nuclear translocation, subsequently inducing fatty acid oxidation via carnitine palmitoyl transferase 1A (CPT1A) and acyl-CoA oxidase 1 (ACOX1) transactivation. MASLD patients exhibited decreased levels of S. cerevisiae and 5-HIAA, and S.cerevisiae effectively ameliorated hepatic steatosis and improved glucose homeostasis in patients with MASLD. In summary, our findings identified a novel pathway of fungi-S. cerevisiae stimulating intestinal 5-HIAA production and indicated that S. cerevisiae and 5-HIAA might alleviate MASLD progression, highlighting that mycobiota-dependent gut-liver axis was a promising target for the prevention of MASLD.

overall_design: RNA-seq analysis of liver tissues from high-fat diet (HFD)-fed wildtype (WT) mice and HFD-fed Card9-deficient (Card9-/-) mice, to explore the molecular basis of Card9 deficiency-associated liver steatosis.

first: Tingting

last: Wang

first: Shuping

last: Qiao

first: Juan

last: Xu

first: Zhen

first: Chen

last: Peng

first: Junxing

last: Qu


title: Pharmacological inhibition of FKBP51 mitigates early life adversity-induced social deficits

city: Solna

first: Juan Pablo

last: Lopez

address: Solnavagen 9

department: Neuroscience

country: Sweden

institute: Karolinska Institutet

summary: Early life adversity (ELA) is a major risk factor for psychiatric disorders, but targeted preventative strategies are lacking due to poor mechanistic insight. The FKBP51 protein, a co-chaperone of the glucocorticoid receptor, is a key mediator of stress vulnerability. We tested if pharmacological inhibition of FKBP51 with the selective inhibitor SAFit2 prevents the long-term consequences of ELA. Mice exposed to ELA exhibited persistent deficits in social behavior, manifesting as social subordination in adolescence and adulthood. Early-life SAFit2 treatment fully rescued these ELA-induced behavioral impairments. Transcriptional profiling across six stress-relevant brain regions revealed that SAFit2 normalized ELA-driven gene expression changes, particularly in the medial prefrontal cortex and nucleus accumbens. Functional analysis showed the rescue converged on immunoregulatory and neuroactive ligand-receptor signaling pathways. Our findings establish FKBP51 as a critical pharmacological target for reversing the lasting impact of early life adversity on brain function, offering a path toward preventative treatment for ELA-related psychopathology.

overall_design: RNA-seq profiling of six stress-relevant brain regions of adult male mice from early life adversity (ELA) and control (Ctrl) backgrounds that received either treatment with vehicle control (Vehicle) or SAFit2 (SAFit2). The brains were collected after exposure to a novel conspecific for 10 minutes (SocialInteraction) or without the exposure (NoInteraction). The samples include the following coditions: Ctrl_Vehicle_NoInteraction, ELA_Vehicle_NoInteraction, ELA_SAFit2_NoInteraction, Ctrl_Vehicle_SocialInteraction, ELA_Vehicle_SocialInteraction, ELA_SAFit2_SocialInteraction, from six brain regions: medial prefrontal cortex, infralimbic and prelimbic (PFC), anterior cingulate cortex (ACC), nucleus accumbens shell (Nacc), basolateral amygdala (BLA), dorsomedial thalamus (DMT), and ventral hippocampus (HC).

first: Xiuqi

last: Ji

first: Serena

last: Gasperoni

first: Joeri

last: Bordes

first: Mathias

middle: V

last: Schmidt


title: Mitochondrial DNA Mutations Drive Tumor Heterogeneity in Papillary Thyroid Carcinoma

city: Seoul

first: HAN SAI

last: LEE

address: 1, Gwanak-ro, Gwanak-gu, Seoul, Republic of Korea

country: South Korea

institute: Seoul National University Seoul Metropolitan Government Boramae Medical Center

summary: Tumor heterogeneity presents a major challenge to understanding cancer evolution and therapeutic resistance in thyroid cancer. While previous studies have focused on nuclear driver mutations, the role of mitochondrial DNA (mtDNA) alterations in this heterogeneity remains elusive. Through multi-regional whole-genome and transcriptome sequencing of aggressive papillary thyroid carcinoma (PTC), we reveal that mtDNA mutations exhibit significant spatial and evolutionary heterogeneity, contrasting with conserved nuclear drivers. High mtDNA mutation burden correlated with increased mitochondrial gene expression, tumor dedifferentiation, and immune pathway activation via damage-associated molecular pattern signaling. This burden further remodeled the tumor microenvironment, favoring pro-inflammatory epithelial states over normal stromal populations. Clinically, these features were associated with reduced disease-free survival. Our findings identify mtDNA mutations as key drivers of heterogeneity and immune remodeling in PTC, suggesting mitochondrial mutational burden as a potential prognostic biomarker and therapeutic target.

overall_design:
Nine PTC patients were recruited for this study, from whom multiple spatially distinct tumor regions (3-6 regions per patient) were obtained, including primary tumor sites and matched lymph node metastases where available. Please see the 'Anonymized_Metadata_2026-01-16.csv' for de-identified clinical data of samples .
Sumitters' statement:
Local laws may prohibit the sharing of raw human sequencing data, identifiable human genetic data, or patient data. Cell Press will make reasonable compromises to general policy in these cases.

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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: Han Sai

last: Lee

first: Jinsun

last: Lim

first: Jin-Hyung

last: Heo

first: Hak Hoon

last: Jun

first: Young Shin

last: Song


title: Effects of PAX8 rescue following PAX8 loss on gene expression in proximal tubule epithelial cells.

city: Ann Arbor

first: Jeffrey

last: Beamish

state: MI

address: 1500 E. Medical Center Drive, SPC 5364

department: Department of Internal Medicine, Division of Nephrology

institute: University of Michigan

summary: PAX2 and PAX8 are homologous DNA-binding proteins that orchestrate kidney development, regulate urine concentration in the kidney medulla, and contribute to sensitivity to and recovery from acute kidney injury. In some contexts, Pax proteins can recruit KMT2C/D histone methyl-transferase complexes that deposit histone H3K4 methylation marks to promote transcription or recruit the Polycomb Repressor Complex to silence gene expression. However, the spectrum of targets and functions of Pax proteins in kidney physiology remains poorly defined. This project aimed to identify genes regulated by PAX proteins in the proximal tubule. Proximal tubule epithelial cells were derived from mice with floxed Pax2 and Pax8 alleles and expressing a constitutive tamoxifen-response CreERT2 (mice described in PMID: 32381599). During propagation, Pax2 was spontaneously recombined, yielding a Pax2-null, Pax8-conditional cell line which was named PT-22. In this submission, the PT-22 line was transduced with a Tet-on expression system linked to a hemagglutinin (HA)-tagged Pax8a transgene and a mixed population of successfully transduced cells selected. PAX8 was depleted from these modified PT-22 cells with tamoxifen, then rescued by inducing re-expression of Pax8a transgene with doxycycline. Gene expression was measured to determine gene targets altered by PAX8 re-expression.

overall_design: Modified PT-22 cells were cultured to confluence and treated with 4-hydroxytamoxifen (1 uM) to deplete PAX8 for 6 d. Then cells were treated with doxycycline (1 ug/ml) every 2 d for additional 6 d. Bulk RNA samples were collected at baseline, 6 d, and 12 d and were submitted for RNA-seq.

first: Gregory

last: Dressler

first: Jason

last: Watts


title: Effects of PAX8 depletion on gene expression in proximal tubule epithelial cells.

summary: PAX2 and PAX8 are homologous DNA-binding proteins that orchestrate kidney development, regulate urine concentration in the kidney medulla, and contribute to sensitivity to and recovery from acute kidney injury. In some contexts, Pax proteins can recruit KMT2C/D histone methyl-transferase complexes that deposit histone H3K4 methylation marks to promote transcription or recruit the Polycomb Repressor Complex to silence gene expression. However, the spectrum of targets and functions of Pax proteins in kidney physiology remains poorly defined. This project aimed to identify genes regulated by PAX proteins in the proximal tubule. Proximal tubule epithelial cells were derived from mice with floxed Pax2 and Pax8 alleles and expressing a constitutive tamoxifen-response CreERT2 (mice described in PMID: 32381599). During propagation, Pax2 was spontaneously recombined, yielding a Pax2-null, Pax8-conditional cell line which was named PT-22. In the experiments in this submission, PAX8 was depleted from PT-22 cells with tamoxifen and gene expression was measured over time to identify likely activating and repressive targets of PAX8.

overall_design: PT-22 cells were cultured to confluence and treated with 4-hydroxytamoxifen (1 uM) to deplete PAX8. Bulk RNA samples were collected at baseline and 2, 6, and 12 d following treatment and were submitted for RNA-seq.


title: Effects of PAX8 loss on chromatin modifications [ChIP-Seq]

summary: PAX2 and PAX8 are homologous DNA-binding proteins that orchestrate kidney development, regulate urine concentration in the kidney medulla, and contribute to sensitivity to and recovery from acute kidney injury. In some contexts, Pax proteins can recruit KMT2C/D histone methyl-transferase complexes that deposit histone H3K4 methylation marks to promote transcription or recruit the Polycomb Repressor Complex to silence gene expression. However, the spectrum of targets and functions of Pax proteins in kidney physiology remains poorly defined. This project aimed to identify genes regulated by PAX proteins in the proximal tubule. Proximal tubule epithelial cells were derived from mice with floxed Pax2 and Pax8 alleles and expressing a constitutive tamoxifen-response CreERT2 (mice described in PMID: 32381599). During propagation, Pax2 was spontaneously recombined, yielding a Pax2-null, Pax8-conditional cell line which was named PT-22. In the experiments in this submission, PAX8 was depleted from PT-22 cells with tamoxifen and Pax8 chromatin occupancy and histone marks (H3K4me3 and H3K27me3) were measured after 6 d using chromatin immunoprecipitation followed by sequencing (ChIP-seq).

overall_design: PT-22 cells were cultured to confluence and treated with 4-hydroxytamoxifen (1 uM) to deplete PAX8 or vehicle. Chromatin was collected at 6 d following treatment.


title: Effects of PAX8 loss on chromatin modifications [ATAC-seq]

summary: PAX2 and PAX8 are homologous DNA-binding proteins that orchestrate kidney development, regulate urine concentration in the kidney medulla, and contribute to sensitivity to and recovery from acute kidney injury. In some contexts, Pax proteins can recruit KMT2C/D histone methyl-transferase complexes that deposit histone H3K4 methylation marks to promote transcription or recruit the Polycomb Repressor Complex to silence gene expression. However, the spectrum of targets and functions of Pax proteins in kidney physiology remains poorly defined. This project aimed to identify genes regulated by PAX proteins in the proximal tubule. Proximal tubule epithelial cells were derived from mice with floxed Pax2 and Pax8 alleles and expressing a constitutive tamoxifen-response CreERT2 (mice described in PMID: 32381599). During propagation, Pax2 was spontaneously recombined, yielding a Pax2-null, Pax8-conditional cell line which was named PT-22. In the experiments in this submission, PAX8 was depleted from PT-22 cells with tamoxifen and chromatin accessibility was measured after 0, 3, and 24 d using Assay for Transposase-Accessible Chromatin sequencing (ATAC-seq).

overall_design: PT-22 cells were cultured to confluence and treated with 4-hydroxytamoxifen (1 uM) to deplete PAX8. Samples were prepared at 0, 3, and 24 d following PAX8 depletion.


title: Chromatin accessibility and gene expression profiling of primary and metastatic ER+ breast cancer [RNA-seq]

city: San Juan

first: Hector

last: Franco

state: Puerto Rico

address: 2nd Floor Centro Medico- Office #275

institute: University of Puerto Rico Comprehensive Cancer Center

summary: In this project, we generated a resource dataset that includes ATAC-seq and RNA-seq data from ER positive primary breast tumors and matched liver and lung metastases. We collected samples from four patients at diagnosis in addition to samples from eight patients at autopsy following cancer-related death, allowing us to gain insights into the molecular mechanisms driving metastasis. Our research centered on the hypothesis that breast cancer metastasis is driven by tissue-specific enhancer programs, where differential transcription factor motif activity orchestrates distinct gene regulatory networks in metastatic sites. Peaks with divergent TF motif activity between tissues may define key regulatory nodes that control metastatic colonization and tissue adaptation. For ATAC-seq, reads were processed using the PEPATAC pipeline, and DiffBind was applied to identify differentially accessible regions, with ChIPseeker used to annotate metastatic-specific peaks. RNA-seq reads were aligned with STAR and quantified using HTSeq, and DESeq2 was employed to identify differentially expressed genes while controlling for batch effects. We established peak-to-gene correlations within a 0.5 Mbp window between chromatin accessibility and gene expression, assessing significance using a conservative null model. To investigate transcription factor (TF) activity, we applied TOBIAS footprinting, which infers TF occupancy by integrating chromatin accessibility with motif information. Leveraging footprinting scores together with RNA-seq expression, we computed a Total Functional Score of Enhancer Elements to identify the most relevant TFs per tissue. Using this approach, we linked TF motif activity at each peak with gene expression correlations, revealing peaks with tissue-specific TF activity and contrasting motif patterns between Liver and Breast.  By connecting ATAC-seq peaks to RNA-seq expression, we identified putative metastasis driver genes, including 99 genes in Liver and 9 in Lung, as well as 23 genes shared across both metastatic sites, such as CCNF, SPINT1, and SLC2A1, which may play critical roles in metastatic progression. Notably, we discovered that the majority of these genes are correlated 3 or more enhancers in the metastatic tissue but not in the primary tissue.

overall_design: RNA-seq profiling of  primary Breast tumors and liver and lung matched metastasis at autopsy

first: Heredia

last: Frances

first: Maldonado

last: Natalia

first: Fogle

last: Homer

first: Kelly

last: Michael R

first: Wisniewsk

last: Kamila

first: Care

last: Lisa A.

first: Franco

last: Hector L.


title: Chromatin accessibility and gene expression profiling of primary and metastatic ER+ breast cancer [ATAC-seq]

overall_design: ATAC-seq profiling of  primary Breast tumors and liver and lung matched metastasis at autopsy


title: Reconstituting central nervous system niche cues partially restores homeostatic identity in cultured murine primary microglia

city: Halle

first: Martin

middle: Sebastian

last: Staege

address: Ernst-Grube-Str. 40

department: Paediatrics I

institute: Martin Luther University Halle-Wittenberg

summary:
Microglia rapidly lose their characteristic homeostatic phenotype after isolation and plastic adherence, undermining the interpretability of in vitro studies.
We systematically evaluated culture conditions that reconstitute central nervous system (CNS) niche inputs to stabilize microglial identity.

overall_design: Primary mouse microglia were isolated by fluorescence-activated cell sorting (FACS). In addition, neonatal microglia were isolatedby a shaking protocoll and cultured in the presence (stimulated microglia) or absence (control microglia) of cytokines

first: Victoria

last: Ilse

first: Susan

last: Barendrecht

first: Julia

last: Hahndorf

first: Stefanie

last: Geissler

first: Benjamin

last: Hietel

first: Daniel-Christoph

last: Wagner

first: Holger

last: Cynis


title: Reconstituting central nervous system niche cues partially restores homeostatic identity in cultured murine primary microglia.

summary: Microglia rapidly lose their characteristic homeostatic phenotype after isolation and plastic adherence, undermining the interpretability of in vitro studies.

overall_design: We systematically evaluated culture conditions that reconstitute central nervous system (CNS) niche inputs to stabilize microglial identity.


title: A multi-omics approach to maize (Zea mays) tassel development

city: Davis

first: Blake

last: Meyers

address: 451 Health Sciences Drive

department: Department of Plant Sciences

institute: UC  Davis Genome Center

type: Non-coding RNA profiling by high throughput sequencing

summary: The development of the male inflorescence in maize (Zea mays L.) is a complex and highly regulated process that is essential for reproductive success and yield. To gain a comprehensive understanding of the regulatory programs involved in tassel formation, including the initial specification of anther cell types, the transcriptomes, small RNAs (sRNAs), and proteomes were profiled at four developmental stages (0.5–2.0 cm). The RNAseq analysis indicates dynamic shifts in gene expression underlying the transition from indeterminate meristems to organ initiation and germinal cell determination by 2.0 cm. Complementing these data, sRNA sequencing uncovered 182 microRNAs (miRNAs) with distinct temporal patterns. A core set of 126 miRNAs was expressed throughout tassel development, while others displayed strong stage-specific enrichment. Notably, families of miRNAs that target auxin signaling were dynamically regulated, suggesting fine-tuning of hormone signaling in relation to meristem activity. Later stages were enriched for miR2275 and miR11969, which previously have both been associated with meiocytes, indicating the onset of reproductive sRNA pathways during the early stages of anther differentiation. Together, these datasets provide a broad overview of tassel development and form a backbone to enrich existing RNAseq and single cell RNAseq data sets of specific steps in tassel and initial anther development, while also adding new data on sRNA expression.

overall_design: Samples from four tassel developmental stages (0.5–2.0 cm) of maize cultivar W23 were analysed by small RNA sequencing. Each sample contained two tassels and each stage was analysed in two biological replicates (i.e. two individual samples).

first: Finn

last: Hartmann

first: Sandra

last: Mathioni

first: Atul

last: Kakrana

first: Virginia

last: Walbot

first: Karina

last: Linde


title: Single-Cell Multi-omics Profiling of Mouse Hepatic Immune Microenvironment Reveals Neutrophil-Kupffer Cell Crosstalk via Thrombospondin-1/CD36 after Surgical Stress

city: Manhasset

first: Hai

last: Huang

state: NY

address: 350 community drive

department: Institute of Molecular Medicine

institute: Feinstein Institutes for Medical Research

summary: The hepatic immune microenvironment comprises both innate and adaptive immune responses, to surgical stress during liver surgeries, leading to ischemia/reperfusion (I/R) injury. Traditional approaches to treat I/R injury have predominantly targeted single, known injury mechanisms, often overlooking the complexity of the hepatic immune microenvironment. Consequently, pharmaceutical interventions focusing on isolated pathways have yielded minimal therapeutic success, underscoring an urgent need for a more comprehensive understanding of the underlying cellular and molecular dynamics. By leveraging single-cell multi-omics technologies, we dissected the multifaceted cellular interactions and molecular alterations within the hepatic immune microenvironment post-surgery. Importantly, we demonstrate that targeting the interaction between infiltrating neutrophils and hepatic resident macrophages, Kupffer cells, through the thrombospondin-1/CD36 pathway during liver I/R. Together, these findings unveil extensive reprogramming of immune cell populations and activation of multiple signaling pathways in response to surgical stress, emphasizing the significance of myeloid cell interactions. This research opens avenues for investigating interactions among different hepatic immune cell types in response to liver damage.

overall_design: This study aims to investigate the transcriptional landscape and spatial organization of mouse liver following ischemia-reperfusion (IR) injury. We employed a multi-omics approach combining single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics (ST). A total of 12 samples were analyzed: scRNA-seq: 4 biological replicates for the IR group and 4 for the Sham group to identify cell-type-specific responses. Spatial Transcriptomics: 2 tissue sections for the IR group and 2 for the Sham group were processed to map gene expression changes within the anatomical context of the injury site. Comparison between IR and Sham groups was performed to identify differentially expressed genes, altered cellular communication, and localized molecular signatures associated with IR-induced damage and repair.

first: Hongji

last: Zhang

first: Xingping

first: Preethi

last: Jayakumar

first: Yunwei

first: Ti

last: Yang

first: Meihong

last: Deng


title: RNA-seq of WT and Rbm25-deficient peritoneal macrophages infected with vesicular stomatitis virus (VSV)

city: Shanghai

first: Xingguang

last: Liu

address: Xiangyin road 800

department: National Key Laboratory of Immunity & Inflammation

institute: Naval medical university

summary: The purpose of this study is to detect differentially expressed genes in wild type (WT) and Rbm25-deficient peritoneal macrophages (PMs) infected with vesicular stomatitis virus for 4 hours. Gene expression differences between two samples could be found using transcriptome profiling (RNA-seq) analysis. Mouse PMs from WT and Rbm25-deficient mice were cultured in DMEM medium. PMs were stained to confirm the surface expression of CD11b and F4/80. Cells with purity >97.5% were used for subsequent experiments. WT and Rbm25-deficient PMs were infected with vesicular stomatitis virus for 4 hours, of which RNA profiles were generated by deep sequencing, using Illumina. We identified several differently expressed genes in the two groups of cells.

overall_design: RNA-Seq profiling of WT and Rbm25-deficient peritoneal macrophages infected with vesicular stomatitis virus.

first: Yinhying

last: Ding

first: Huiying

last: Chen

first: Yunkai


title: NSCLC KRAS G12C MUTANT CELLS ARE DEPENDENT ON MUC1-C FOR RESISTANCE TO KRAS INHIBITORS

city: Boston

first: Shinkichi

last: Takamori

address: 450 Brookline Avenue

institute: Dana-Farber Cancer Institute

summary: Treatment of NSCLC KRAS G12C mutant tumors with targeted KRAS inhibitors, such as sotorasib and adagrasib, is invariably associated with the emergence of acquired resistance. The mechanisms responsible for resistance to these agents have largely remained unclear. We report that patients with NSCLC KRAS G12C tumors expressing increased levels of the MUC1 gene exhibit decreases in overall survival in response to sotorasib and adagrasib. In investigating the basis for this finding, we found that exposure of NSCLC KRAS G12C mutant cells to these agents induces expression of the oncogenic MUC1-C/M1C protein. We show that M1C induction is STAT1 dependent and that targeting M1C increases sensitivity to sotorasib. Studies of sotorasib-resistant cells further reveal upregulation of M1C chromatin levels in association with activation of the epithelial-mesenchymal transition (EMT). Mechanistically, M1C drives NF-kB p65-mediated induction of the ZEB1 EMT-TF. Furthermore, targeting M1C NF-kB ZEB1 signaling suppresses EMT and sotorasib resistance. Having identified this M1C dependence, we demonstrate that targeting M1C with an antibody-drug conjugate (ADC) is effective against sotorasib-resistant cells growing in vitro and as tumor xenografts. These findings identify M1C as a major effector of sotorasib resistance and as a target for ADC treatment of patients with refractory NSCLC KRAS G12C mutant tumors.

overall_design: RNA Seq in H358 Cell line with MUC1-C shRNA silencing. We conpared DMSO and DOX treatment cells for differential gene expression analysis. MUC1shRNA (MISSION shRNA TRCN0000122938; Sigma, St. Louis, MO, USA)  was inserted into the pLKO-tet-puro vector (Plasmid #21915; Addgene, Cambridge, MA, USA) . Vector-transduced cells were selected for growth in 1–2 μg/ml puromycin. Cells were treated with 0.1% DMSO as the vehicle control or 500 ng/ml doxycycline (DOX; Millipore Sigma).


title: Postnatal day 3 (P3) mouse cortical projection neurons: Ctrl versus Cdk7 KO

city: Liège

first: Arnaud

last: Lavergne

state: Liège

address: Avenue de l'hôpital 11

department: GIGA

country: Belgium

institute: University of Liège

summary: Transcriptional profiling of primary Cdk7 KO mouse cortical projection neurons compared to Ctrl neurons. Samples were obtained by FACS sorting EYFP+ cells from postnatal day 3 (P3) NexCre/+;Cdk7lox/lox, R26EYFP/+ (Cdk7 KO) and NexCre/+;Cdk7+/+, R26EYFP/+ (Ctrl) mouse cortices. Goal was to determine the effects of Cdk7 elimination on gene transcription in developing cortical projection neurons.

overall_design: Two-condition experiment, NexCre/+;Cdk7lox/lox, R26EYFP/+ (Cdk7 KO ) vs NexCre/+;Cdk7+/+, R26EYFP/+ (Ctrl) neurons. Biological replicates: 5 mice per genotype (one preparation of FACS-sorted P3 neurons per mouse)

first: Sébastien

last: Verteneuil

first: Laura

last: Van Hees

first: Jean-Marc

last: Lassance

first: Camille

last: Lejon

first: Tine

last: d'Aes

first: Quentin

last: Marlier

first: Pascale

last: Quatresooz

first: Laurence

last: Delacroix

first: Laurent

last: Nguyen

first: Renaud

last: Vandenbosch

first: Brigitte

last: Malgrange


title: Leukemia stem cells defend ferroptosis by controlling cystine uptake via PIEZO1-HIF1A-SLC7A11 axis

city: Wuhan

first: Haojian

last: Zhang

address: Donghu Rd.

institute: Wuhan University

summary: Metabolism reprogramming is intimately accompanied with mitochondrial oxidative stress in driving many human diseases including cancers. Excessive oxidative stress frequently induces cell death including ferroptosis, which needs to be tightly balanced for maintaining cellular homeostasis. However, the precise mechanisms for balancing metabolic reprogramming and oxidative stress under different contexts remain elusive. Here, by studying acute myeloid leukemia stem cells (LSCs) that are largely fueled by OXPHOS, we reveal a defense system of LSCs against oxidative stress-induced ferroptosis. We find that the mechano-sensor PIEZO1 plays key role in promoting acute myeloid leukemia development and maintaining LSCs stemness. PIEZO1 deletion impairs cystine uptake and induces ROS and lipid peroxidation, causing ferroptosis of leukemia cells. Mechanistically, HIF1A mediates the function of PIEZO1 by transcriptionally regulating the expression of SLC7A11 and SLC3A2. Further, inhibition of PIEZO1 and SLC7A11 suppresses LSC function and contributes to AML treatment. In summary, our findings reveal that LSCs control cystine uptake through PIEZO1-HIF1A-SLC7A11 axis to defend ferroptosis, representing a unique vulnerability of LSCs.

overall_design: RNAseq of mice LSCs sorted from WT and Piezo1cko BM leukemia cells

first: Tiantian

first: Ziyan

last: Cao

first: Kexin

last: Gao

first: Shuxin

last: Yao

first: Yanbing

last: Zheng

first: Manman

last: Cui


title: PARN-Driven Alternative Polyadenylation Regulates Immunoglobulin Homeostasis in Antibody-Secreting Cells [PARN ISO-seq]

city: Beijing

first: NAIJING

last: HU

address: No.11 Xizhimen South Street, Xicheng District

institute: Peking University People's Hospital

summary: Class switch recombination (CSR) is a programmed DNA recombination process that enables B cells to switch the isotype of antibodies they produce, thereby generating high-affinity immunoglobulins essential for adaptive immunity. Of note, systemic lupus erythematosus (SLE) frequently arises in the context of hypersensitivity; however, the precise mechanisms underlying its pathogenesis remain incompletely understood. Here, we demonstrate that poly(A)-specific ribonuclease (PARN), an RNA-binding protein, acts as a critical regulator of CSR. In antibody-secreting cells, loss of PARN impairs CSR, resulting in a reduced proportion of cells producing post-switched immunoglobulin isotypes. Mechanistically, PARN specifically binds to the enhancer motif UGUA and the polyadenylation signal AAUAAA. PARN subsequently promotes transcript 3’ UTR shortening through alternative polyadenylation to regulate RNA stability. Depletion of PARN contributes to widespread 3’ UTR lengthening across the transcriptome, significantly affecting the Foxp1 transcript, and consequently impedes CSR efficiency. We further identified PTBP1 and PABP1 as cofactors that functionally cooperate with PARN to suppress CSR. Analysis of human datasets further reveals that Parn expression is elevated in patients with SLE. In an SLE mouse model, targeted Parn knockout in B lymphocytes undergoing CSR alleviates disease severity. This study unveils PARN as a key modulator of CSR in B cells, highlighting its therapeutic potential in SLE.

overall_design: PARN ISO-seq was performed with LPS-stimulated B cells, and two biological replications were labeled as rep1 and rep2 respectively.

first: Siyuan

last: Sun

first: Naijing

last: Hu

first: Shengyao

first: Juan

last: Chen


title: PARN-Driven Alternative Polyadenylation Regulates Immunoglobulin Homeostasis in Antibody-Secreting Cells [CRIC-seq]

overall_design: PARN CRIC-seq was performed with LPS-stimulated B cells, and two biological replications were labeled as rep1 and rep2 respectively. Two biological repeats of mouse IgG CRIC-seq in LPS-activated B cells were labeled as rep1 and rep2.


title: PARN-Driven Alternative Polyadenylation Regulates Immunoglobulin Homeostasis in Antibody-Secreting Cells [CLIP-seq]

overall_design: PARN CLIP-seq was performed with naïve spenic B cells and LPS-stimulated B cells, and two biological replications were labeled as rep1 and rep2 respectively. Two biological repeats of mouse IgG CLIP-seq in LPS-activated B cells were labeled as rep1 and rep2.

first: Changchang


title: PARN-Driven Alternative Polyadenylation Regulates Immunoglobulin Homeostasis in Antibody-Secreting Cells [2P-seq]

overall_design: PARN 2P-seq was performed with LPS-stimulated B cells, and two biological replications were labeled as rep1 and rep2 respectively.


title: Inhibiting primary cilia formation attenuates gingival fibroblast senescence and gingival aging via the PI3K-AKT pathway

first: wenjun

last: shao

address: 237 Luoyu Road, Wuchang District

department: Hubei Key Laboratory of Stomatology

institute: School & Hospital of Stomatology, Wuhan University

summary: Aging, as an intrinsic risk factor, accelerates gingival inflammation and periodontal diseases. However, the cellular and molecular mechanisms driving gingival aging remain unclear, hindering the development of targeted therapies.

overall_design: In this study, we performed the first single-cell transcriptomic analysis of aging human gingiva, identifying primary cilia as pivotal regulators of gingival fibroblast senescence. We demonstrated that aged gingival tissues exhibit increased fibroblast senescence and enhanced cilia formation compared to young tissues. Genetic knockdown of ciliogenesis-associated genes (IFT88 and KIF3A) significantly reduced senescence markers and alleviated DNA damage in aged fibroblasts through activation of the PI3K-AKT signaling pathway. Functionally, adeno-associated virus-mediated inhibition of ciliogenesis in aged mice mitigated gingival fibroblast senescence, reduced inflammation, and diminished tissue fibrosis. These findings highlight primary cilia and the PI3K-AKT pathway as novel therapeutic targets for managing aging-related gingival diseases, providing a potential strategy to improve periodontal health in the elderly.

first: Wenjun

last: Shao


title: PARN-Driven Alternative Polyadenylation Regulates Immunoglobulin Homeostasis in Antibody-Secreting Cells

summary: Class switch recombination (CSR) is a programmed DNA recombination process that enables B cells to switch the isotype of antibodies they produce, thereby generating high-affinity immunoglobulins essential for adaptive immunity. Notably, systemic lupus erythematosus (SLE) frequently arises in the context of hypersensitivity; however, the precise mechanisms underlying its pathogenesis remain incompletely understood. Here, we demonstrate that poly(A)-specific ribonuclease (PARN), an RNA-binding protein, acts as a critical regulator of CSR. In antibody-secreting cells, loss of PARN impairs CSR, resulting in a reduced proportion of cells producing post-switched immunoglobulin isotypes. Mechanistically, PARN specifically binds to the enhancer motif UGUA and the polyadenylation signal AAUAAA. PARN subsequently promotes transcript 3’ UTR shortening through alternative polyadenylation to regulate RNA stability. Depletion of PARN contributes to widespread 3’ UTR lengthening across the transcriptome, notably affecting the Foxp1 transcript, and consequently impedes CSR efficiency. We further identified PTBP1 and PABP as cofactors that functionally cooperate with PARN to suppress CSR. Analysis of human datasets further reveals that Parn expression is elevated in patients with SLE. In an SLE mouse model, targeted Parn knockout in B lymphocytes undergoing CSR alleviates disease severity. This study unveils PARN as a key modulator of CSR in B cells, highlighting its therapeutic potential in SLE.

overall_design: PARN RNA-seq was performed with or without the depletion of PARN in activated B cells. Two biological replications were labeled as Rep1 and Rep2 respectively.


title: EV Modulates Osteogenic differentiation in hPDL-MSCs

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

summary: Periodontal homeostasis is maintained by a delicate balance between tissue regeneration and degradation, orchestrated through complex regulatory networks of cellular and molecular signaling. The delivery of microRNAs (miRNAs) by EVs serves as a crucial post-transcriptional regulatory mechanism, fine-tuning these signaling cascades. In this study, we identified significant candidates contained in the EVs secreted by human periodontal ligament mesenchymal stem cells (hPDL-MSCs) that contribute to PDL-MSC homeostasis and osteogenic differentiation.

overall_design: Culture media devoid of FBS were collected and processed for EV collection. microRNAs from EVs was purifeid and analyzed by microarray.

first: Ye Yint Kaung

last: Myint

first: Jingyi

first: Kazuki

last: Morita

first: Masahiro

last: Hatasa

first: Anhao

last: Liu

first: Supreda Suphanantachat

last: Srithanyarat

first: Takanori

last: Iwata


title: hPDL-MSC Extracellular Vesicles-delivered miRNAs Regulates Osteogenesis via miRISC-mediated Targetome Silencing

city: Tokyo

first: ANHAO

last: LIU

address: 1-5-45 Yushima, Bunkyo-ku

department: Department of Periodontology

institute: Tokyo Medical and Dental University

summary: Periodontal homeostasis is maintained by a delicate balance between tissue regeneration and degradation, orchestrated through complex regulatory networks of cellular and molecular signaling. miRNAs act as pivotal post-transcriptional regulators that fine-tune these signaling cascades. Despite increasing recognition of their regulatory potential, the specific miRNAs governing stem cell maintenance and differentiation in the periodontium remain insufficiently defined. In this study, we identified hsa-181c-5p and hsa-let-7c-3p within the extracellular vesicles secreted from human periodontal ligament mesenchymal stem cells (hPDL-MSCs) as a candidate regulator contributing to PDL-MSC homeostasis. hsa-let-7c-3p promotes the proliferation and migration while suppressing osteogenic differentiation of hPDL-MSCs. In the meanwhile, miR-181c-5p was consistently upregulated in hMSCs during osteogenesis, and its gain- and loss-of-function produced concordant effects. Integrative analyses combining AGO2-based immunoprecipitation sequencing (RIP-Seq), RNA-Seq, dual-luciferase reporter, and western blot identified miRISC-mediated targetome of miRNAs. Collectively, our study unveiled novel miRNA-mRNA networks through which hPDL-MSC–derived EVs affecting osteogenic differentiation and proliferation, providing new mechanistic insight into miRNA-mediated stem cell regulation and periodontal regeneration.

overall_design: RNA-immunoprecipitation sequencing (RIP-seq) and bulk RNA-seq were performed to screen the potential target genes of hsa-let-7c-3p, and hsa-miR-181c-5p.

last: Gao


title: RNA sequencing analysis of transcriptomic changes in human umbilical vein endothelial cells co-cultured with exosomes derived from GLS1-knockdown head and neck cancer cells

city: ATLANTA

first: Yong

last: Teng

state: GA

address: Bench 31 C4038, Winship Cancer Inst

institute: emory university

summary: The aim of this study is to investigate the influence of exosomes derived from GLS1-knockdown head and neck cancer cells on the transcriptomic profile of human umbilical vein endothelial cells

overall_design: Investigation of mRNA profiles in human umbilical vein endothelial cells co-cultured with exosomes derived from GLS1-knockdown head and neck cancer cells

first: Jianqiang

last: Yang

first: Fan


title: RNAseq for cultured ctrl and TgAPPsweOCN-Cre osteoblasts from skull bone

city: Cleveland

first: Wen-Cheng

last: Xiong

state: Ohio

address: 2210 circle drive

institute: Case western reserve university

summary: Purpose: To investigate how APPswe+ osteoblasts affect skull bone and skull bone marrow remodeling, we isolated tdTomato⁺ calvarial osteoblasts from the skulls of TgAPPswemOCN-Cre;Ai9 mice and control (mOCN-Cre;Ai9) mice at 6-MO using fluorescence-activated cell sorting (FACS) and subjected them to bulk RNA sequencing. Methods: (1) Calvariae from TgAPPswemOCN-Cre;Ai9 mice and control (mOCN-Cre;Ai9) mice were transferred to a dish containing PBS, and the soft tissues were carefully removed using tweezers. The cleaned bones were then cut into small fragments of approximately 1–2 mm² and sequentially digested with collagenase solution (37 °C, 30 min, twice) and trypsin solution (37 °C, 30 min) to remove residual soft tissue and adherent cells. After an additional collagenase digestion, the bone fragments were washed three times with culture medium and transferred to 60 mm culture dishes containing DMEM supplemented with 10% FBS, 1% penicillin/streptomycin, 10 mmol/L β-glycerophosphate, and 50 μmol/L L-ascorbic acid-2-phosphate. The culture medium was replaced three times per week. Osteoblasts began to migrate from the bone chips after 3–5 days. After two weeks, the monolayer cells were detached by incubation with trypsin solution and replated onto 100 mm tissue culture dishes in α-MEM supplemented with 10% FBS and 1% penicillin/streptomycin. (2) Total RNA was extracted from purified Td⁺ osteoblasts isolated by flow cytometry from mOCN-Cre; Ai9 and TgAPPswemOCN-Cre; Ai9 mice. RNA integrity was assessed for each sample, and only samples with a RNA Integrity Number (RIN) > 2 were included for further analysis. RNA-seq was performed by BGI America (Cambridge, MA) using the DNBseq platform. Gene expression levels were normalized as fragments per kilobase of transcript per million mapped reads (FPKM). Differentially expressed genes (DEGs) were identified using DESeq2 and PoissonDis algorithms, with P-values adjusted by the Benjamini–Hochberg (BH) method. Genes with adjusted P ≤ 0.05 and log₂ fold change ≥ 1 were considered significantly differentially expressed. Results: Transcriptomic profiling revealed 425 upregulated and 478 downregulated genes in APPswe-expressing osteoblasts compared to controls. Gene ontology (GO) pathway analysis showed that the upregulated genes were primarily enriched in pathways related to positive regulation of cell migration, cytokine production, Wnt/β-catenin signaling, angiogenesis, cell-cell adhesion, and negative regulation of cell proliferation, while downregulated genes were associated with cell-cell signaling, cell proliferation, and osteoclast differentiation. Conclusions: Early thinning of the skull in TgAPPswemOCN-Cre mice may result from reduced osteoblast proliferation.

overall_design: Cultured skull bone osteoblasts mRNA profiles of 6-month-old mOcn-Cre;Ai9 and TgAPPswemOCN-Cre;Ai9 mice.

first: Lei

first: Dong

first: Hao-Han

last: Guo

first: Daehoon

last: Lee

first: Zhipeng

first: Lin

last: Mei


title: Targeting Ewing sarcoma by ex vivo expanded IL1RAP CAR modified TGFbeta imprinted NK cells in combination with IL-15 agonist and anti-GD2 antibody

city: Valhalla

first: Wen

last: Luo

state: New York

address: 15 Dana Road

institute: New York Medical College

summary: The prognosis of patients with metastatic Ewing sarcoma (ES) is dismal, largely due to therapy resistance within the tumor microenvironment (TME). Here, we aim to overcome ES TME resistance to natural killer (NK) cells by a combinatorial immunotherapy approach that enables NK tumor-specific-targeting via chimeric antigen receptor (CAR) against interleukin-1 receptor accessory protein (IL1RAP), circumvents transforming growth factor beta (TGFβ)-mediated immunosuppression by TGFβ-imprinting of NK cells, increases NK cell antibody dependent cellular cytotoxicity (ADCC) via an anti-GD2 antibody dinutuximab, and improves NK cell persistence and ADCC by an IL-15 agonist NKTR-255. Single-cell-RNAseq analyses of cells from xenograft tumors were performed to identify mechanisms of response/resistance to this combinatorial immunotherapy.

overall_design: Tumors were dissociated using the human Tumor Dissociation Kit (130-095-929, Miltenyi Biotec) with the gentleMACS Octo Dissociator with heater according to the manufacturer’s instructions. Cell suspension was passed through a 70 mm Cell Strainer (431751, Corning, Corning, NY) and red blood cells were removed from the cell suspension using RBC Lysis Buffer (420301, BioLegend, San Diego, CA, USA). Dead cells were removed using the Dead Cell Removal Kit (130-090-101, Miltenyi Biotec) according to the manufacturer’s instructions. The viability of the cells was evaluated by Trypan blue staining. Viable cell suspensions were loaded into the Chromium Controller (10xGenomics, Pleasanton, CA, USA) to generate gel beads-in-emulsion (GEM) with each GEM containing a single cell as well as barcoded oligonucleotides. Next, the GEMs were placed in the SimpliAmp 96-well Thermal Cycler (Thermo Fisher Scientific, Wilmington, DE, USA), and reverse transcription was performed in each GEM (GEMRT). After the reaction, the complementary cDNA was amplified and cleaned using Silane DynaBeads (10X Genomics, Pleasanton, CA, USA) and the SPRIselect Reagent kit (Beckman Coulter, Indianapolis, IN, USA). Amplified full-length cDNAs from polyadenylated mRNA were then used to generate 3′ Gene Expression library (Chromium GEM-X Single Cell 3′ Reagent Kits v4) following the manufacturer’s instructions (10x Genomics, Pleasanton, CA, USA). Amplified cDNAs and the libraries were measured by the Qubit dsDNA HS assay (Thermo Fisher Scientific, Wilmington, DE, USA), and quality was assessed by the BioAnalyzer (Agilent Technologies, Santa Clara, CA, USA). Libraries were sequenced on Illumina NextSeq 2000 system (Illumina, San Diego, CA, USA).

first: Changxin

last: Xu


title: Sustained A2AR expression and loss paradoxically promote CD8+ T cell exhaustion

city: CHICAGO

first: Bin

last: Zhang

state: IL

address: 300 E Superior st., Tarry 4-725

department: Department of Medicine; Hematology/Oncology Division

institute: NORTHWESTERN UNIVERSITY (Feinberg school of medicine)

summary: Although A2AR is a key immunoregulatory receptor that suppresses CD8⁺ T-cell activation in response to elevated extracellular adenosine in inflamed or hypoxic microenvironments, its role in CD8⁺ T cell differentiation and cell-fate decisions during chronic viral infection and cancer remains poorly understood. Using A2AR-eGFP reporter mice, we show that A2AR expression is rapidly induced by TCR stimulation and persists under chronic antigen exposure and hypoxia, with sustained expression strongly associated with terminal exhaustion via the canonical Gαs–cAMP–PKA pathway. Paradoxically, A2AR loss does not alleviate exhaustion but instead accelerates differentiation toward the terminally exhausted state. Single-cell multiomics profiling revealed that A2AR deficiency activates CD122 (IL-2Rβ)–dependent signaling, driving T-cell exhaustion. Genetic deletion of CD122 in A2AR-deficient CD8⁺ T cells reduced terminal exhaustion, identifying CD122 signaling as a key mediator of A2AR loss–driven exhaustion. Intriguingly, both sustained A2AR expression and A2AR loss converge to promote T cell exhaustion differentiation through distinct mechanisms. These findings uncover a paradoxical role of A2AR in shaping CD8⁺ T cell fate choices during chronic infection and cancer.

overall_design: scMultiomics (scRNA + scATAC): Adora2afl/fl P14 CD45.1+ and Adora2afl/fl LckCreP14 CD45.1+ cells from spleens on day 30 after LCMV Cl13 infection, A2AR-eGFP P14 CD45.1+ from the spleens of mice on day 8 and day 30 after LCMV Cl13 infection were FACS-sorted. Nuclei were isolated and processed using the Chromium Single Cell Multiome ATAC + Gene Expression Reagent Kit (10x Genomics) according to the manufacturer’s instructions.

first: Longzhen

last: Song

first: Arjun

last: Kharel

first: Ping

last: Xie

first: Jie

last: Fan

first: Abu

last: Baker

first: Yuqi

first: Yi

first: Weiguo

last: Cui


title: Kaempferol Attenuates Spaceflight-associated Knee Cartilage Degeneration by Targeting NOX4-Mediated Mitochondrial Dysfunction

city: Pittsburgh

first: Shuchang

last: Liu

address: 203 Lothrop Street

institute: University of Pittsburgh

summary: Microgravity and space radiation experienced during spaceflight have negative effects on musculoskeletal health, yet their impact on articular cartilage remains poorly understood. In this study, we demonstrated that simulated spaceflight on Earth leads to cartilage degeneration in the knees of mice. Similar changes were also observed in mice exposed to actual space flight. To investigate the mechanisms behind spaceflight-associated cartilage loss, human chondrocytes were encapsulated within a hydrogel scaffold and then subjected to rotary culture to mimic the alterations caused by microgravity. Simulated microgravity increased the expression of biomarkers related to inflammation and cellular senescence. Additionally, rotary culture decreased mitochondrial respiration and increased the production of reactive oxygen species. Through RNA sequencing and bioenergetic profiling, we identified NADPH oxidase 4 (NOX4) as a crucial factor driving these changes. Additionally, kaempferol, a naturally occurring flavonoid that directly binds to NOX4, was found to partially reverse the harmful effects of microgravity on chondrocytes. Finally, systemic administration of kaempferol reduced cartilage degradation in mice subjected to simulated spaceflight on the ground. These findings establish that NOX4-mediated mitochondrial dysfunction is a key mechanism underlying spaceflight-induced cartilage degeneration and highlight kaempferol as a potential protective measure for joint health in space.

overall_design: Chondrocytes from static, rotary, or rotary + Kaempferol (KMP) hydrogels were measured. Chondrocyte-laden hydrogels were cultured in a Rotary Cell Culture System (RCCS; Synthecon Inc., Houston, TX, USA) to simulate a microgravity environment. Each bioreactor vessel was filled with chondrogenic medium to eliminate air bubbles and minimize shear stress. The system was operated at a rotation speed of 32.5 revolutions per minute (RPM) inside a standard humidified cell culture incubator (37 °C, 5% CO₂). Under these conditions, the constructs remained in continuous free fall, providing a dynamic, low-shear environment that promotes nutrient exchange and three-dimensional tissue formation. Gels were maintained in chondrogenic differentiation medium consisting of high-glucose DMEM supplemented with 1× ITS, 0.5 ng/mL TGF-β3, 50 µg/mL ascorbic acid, and 1% penicillin–streptomycin. Medium was refreshed every two to three days. Samples were harvested on days 3, 7, and 14 for subsequent analyses.

first: Yuesong

last: Yin

first: Ruiling

first: Meagan

last: Makarczyk

first: Silvia

first: Matthew

last: Shi

first: Roberta

last: Di Carlo

first: Michael

last: Almeida

first: Alex

last: Garris

first: Sarah

last: Day

first: Rebekah

last: Sanchez-Hodge

first: Jonathan

last: Schisler

first: Aleeza

last: Zilberman

first: Noah

last: Allen

first: Angela

last: Kubik

first: Elizabeth

last: Blaber

first: Arnold

middle: Z

last: Olali

first: Wanqing

first: Douglas

last: Wallace

first: Jia-Jun

first: Christopher

last: Mason

first: Peter

last: Alexander

first: Giuseppe

last: Intini

first: Afshin

last: Beheshti

first: Hang

last: Lin


title: Opposing functions of AEBP2 isoforms fine-tune PRC2 catalytic activity

city: Seoul

first: Yingying

last: Li

state: Seoul

address: 103 Daehak-ro

department: Department of Biomedical Sciences

institute: Seoul National University

summary: Polycomb Repressive Complex 2 (PRC2) represses genes through catalyzing H3K27me3, a histone modification essential for maintenance of cellular identity. The complex’s catalytic activity, chromatin localization, and propagation along chromatin are modulated by accessory proteins such as AEBP2, MTF2, JARID2 and PALI, which is specifically required for mouse embryogenesis. AEBP2 exists in distinct isoforms: a short isoform that enhances PRC2 catalytic activity and promotes H3K27me3 spreading, facilitating robust gene repression, and a long isoform whose function has remained unclear. Here, we report that the N-terminal region of the long isoform contains a conserved DE-motif that inhibits PRC2 activity, both EZH2 automethylation and H3K27 methylation. Notably, re-expression of the long isoform in Mtf2/Jarid2/Aebp2 triple-knockout mouse embryonic stem cells failed to restore H3K27me3 and caused defective differentiation, unlike the short isoform. These findings uncover an isoform-specific regulatory mechanism by which AEBP2 controls PRC2 activity and contribute to a broader understanding of PRC2’s dynamic regulation during development

overall_design: CUT&Tag for H3K27me3 and RNA-seq were performed at both Day 0 (ESC state) and Day 4 (differentiated state). CUT&Tag for H3K4me3 and ChIP-seq for AEBP2 and SUZ12 were performed in the ESC state (Day 0) only. All experiments were conducted in E14 WT, TKO, TKO AEBP2 long rescue, and TKO AEBP2 short rescue cells. Day 4 samples were collected following differentiation to assess secondary transcriptional changes.

first: Chul-Hwan

last: Lee


title: Single-nucleus RNA-seq of gonadotropin-releasing hormone 3 (GnRH3) neurons in 7 day-post-fertilization (dpf) Tg(gnrh3:EGFP) zebrafish

city: Baltimore

first: Yalong

last: Sun

state: MD

address: 701 E Pratt Street

institute: IMET, UMBC

summary: We applied a single-nucleus RNA sequencing approach using 10x Genomics snRNA-seq to examine the developmental heterogeneity of GnRH3 neurons in 7 dpf zebrafish. GnRH3 serves as the key hypophysiotropic regulator of reproduction, yet the heterogeneity within its migratory neuronal population has remained unclear in 7 dpf zebrafish. By profiling nuclei from 7 dpf Tg(gnrh3:EGFP) larvae, this study provides the first single-cell-transcriptomic characterization of migrating GnRH3 neurons in 7 dpf zebrafish and offers new insights into their developmental organization and functional specialization.

overall_design: GnRH3 neurons were isolated by Fluorescence-activated cell sorting (FACS) from 7 dpf Tg(gnrh3:EGFP) zebrafish and analyzed using snRNA-seq.

first: Nilli

last: Zmora

first: Yonathan

last: Zohar

first: Matan

last: Golan