title: Neuropilin-1 is a novel host factor facilitating the entry of hepatitis B virus

city: Chongqing

first: Juan

last: Chen

address: 1 Yixueyuan Road, Yuzhong District

institute: Chongqing Medical University

summary: Sodium taurocholate cotransporting polypeptide (NTCP) has been identified as the cellular receptor for HBV. However, hepatocytes expressing NTCP exhibit diversely susceptibilities to HBV infection. In this study, we identified multiple membrame proteins played a critical role in facilitating HBV infection in liver biopsy obtained from children with chronic hepatitis B by using singlecell RNA sequencing (scRNA-seq).

overall_design: Liver biopsy samples from five hepatitis B virus-infected children who had not received antiviral therapy, and two groups of primary human hepatocytes cells infected with HBV.


title: Reduced levels of BMI1 inhibit trophoblast proliferation and migration via the epigenetic enhancement of CSTA and TGFB2 in spontaneous abortion

status: Public on May 31 2026

city: Suzhou

first: huimin

last: Li

state: Jiangsu

address: No.26.Daoqian Street

department: Center for Human Reproduction and Genetics

country: China

institute: Suzhou Municipal Hospital

type: Genome binding/occupancy profiling by high throughput sequencing

summary: BMI1, a polycomb transcriptional repressor, regulates the cell cycle, stem cells, proliferation, invasion, and apoptosis. However, the specific role of BMI1 in spontaneous abortion (SA) remains unclear. BMI1 expression levels were detected in control and SA tissues by qRT-PCR and immunofluorescence. HTR-8/SVneo cells were subjected to interference, PTC-209 treatment, or overexpression experiments to evaluate the impact of BMI1 on the biology of trophoblasts and reactive oxygen species (ROS) production in vitro. RNA-seq, ChIP-seq, ChIP-qPCR, and cell salvage assays, identified CSTA and TGFB2 as target molecules associated with the epigenetic regulation of BMI1. Individuals with SA exhibited a reduced levels of BMI1 in villous tissues, as confirmed by qRT-PCR and immunofluorescence. In vitro interference with BMI1, or the application of PTC-209, a BMI1-specific inhibitor, inhibited the proliferation, clonogenicity, and migration of trophoblast cells but enhanced apoptosis. BMI1 overexpression induced the opposite effects. Moreover, we observed enhanced proliferation, migration, and colony formation in cells that had been treated with PTC-209 and a diverse range of NAC concentrations when compared to cells treated with PTC-209. Despite the reduction of ROS, full restoration was not achieved. CSTA and TGFB2 were identified as novel target molecules that participate in the epigenetic regulation of BMI1. Specifically, the overexpression of CSTA did not exert influence on total AKT protein expression but significantly reduced the levels of phosphorylated AKT. The overexpression of TGFB2 did not influence the levels of SMAD2/3 but induced a notable increase in phosphorylated SMAD2/3 proteins. Finally, the suppression of CSTA and TGFB2 counteracted the effects of BMI1 deficiency in trophoblasts. The regulation of trophoblast function by BMI1, including the production of ROS in the cytoplasm and the epigenetic modifications of CSTA and TGFB2 in nuclei, could facilitate the identification of mechanisms underlying SA.


title: H3K9 di-methylation dynamics underlies mouse minor zygotic genome activation [spike-in ChIP-seq of mESC]

status: Public on Apr 19 2026

city: Suita-shi, Osaka

first: Ryo

last: Maeda

address: Yamadaoka 1-3

country: Japan

institute: The University of Osaka

summary: Minor zygotic genome activation (ZGA) is crucial for early development and totipotency acquisition, yet the regulatory mechanisms driving minor ZGA genes remain elusive. Here we show that dynamic regulation of H3K9me2 is essential for minor ZGA. H3K9me2 levels at minor ZGA gene loci are reduced at early 2-cell and are re-established by morula. Maternal depletion of the H3K9 demethylases KDM3A and KDM3B leads to increased H3K9me2 and impaired minor ZGA in early 2-cell, followed by developmental arrest at 2- to 4-cell. In mESCs, H3K9 at minor ZGA loci is highly di-methylated; combined loss of the H3K9 methyltransferases G9a and SETDB1 leads to synergistic de-repression of minor ZGA genes. Mechanistically, SETDB1 specifically targets Dux, while G9a broadly represses minor ZGA genes through H3K9 di-methylation linked to lamina-associated heterochromatin formation. These findings establish H3K9me2 dynamics as a key regulator for minor ZGA, highlighting the indispensable role of epigenetic control in early embryogenesis.

overall_design: Epigenome profiling by high throughput sequencing

first: Makoto

last: Tachibana


title: H3K9 di-methylation dynamics underlies mouse minor zygotic genome activation [RNA-seq of mESC]

type: Expression profiling by high throughput sequencing

overall_design: RNA-seq of mESC


title: H3K9 di-methylation dynamics underlies mouse minor zygotic genome activation

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

overall_design: Refer to individual Series


title: H3K9 di-methylation dynamics underlies mouse minor zygotic genome activation [RNA-seq of early embryo]

overall_design: Expression profiling by high throughput sequencing

first: Shunsuke

last: Kuroki

first: Azusa

last: Inoue


title: EBNA1 inhibitors reveal CDC7 and POU2F1 as direct functional targets in EBV epithelial cancers [ChIP-Seq]

status: Public on Apr 17 2026

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

country: USA

institute: The Wistar Institute

summary: Epstein-Barr virus (EBV) latent infection is ubiquitously associated with nasopharyngeal carcinoma and gastric cancer, expressing very few viral protein components (EBNA1 and LMP1/2A). We previously showed that EBNA1 inhibitor VK1727 blocked cell cycle progression and growth of EBV+ tumors in vivo. However, the underlying molecular mechanism requires more evidence. In this study, we employed VK1727 to remove EBNA1 binding to viral and cellular genomes in three EBV+ epithelial tumors (PDX C15, C666-1 and SNU719). Then we integrated EBNA1 ChIP-seq and transcriptomic analysis to identify direct gene targets of VK1727, which involve in cell cycle progression and cell proliferation. Our analysis characterized a cell cycle dependent kinase CDC7 and a stem cell transcription factor POU2F1. Further analysis illustrated that EBNA1 binding to CDC7 promoter and POU2F1 intron promotes RNA Pol II-pS5 to initiate transcription of these two genes. Moreover, our results revealed CDC7 inhibitor Simurosertib is epistatic with VK1727 in reduction of EBV copy number, induction of cell cycle arrest, and inhibition of cell proliferation in EBV+ epithelial cancer. While POU2F1 knockdown reduced copy number of EBV, decreased expression of viral genes and inhibited proliferation of SNU719 cells. Our study revealed two functional gene targets of VK1727 in EBV+ epithelial cancers, which provides two potential biomarkers for following therapeutical research.

overall_design: 20 million C666-1 cells were collected for  chromatin precipitation sequencing to characterize EBNA1-bound gene targets in EBV+ epithelial cancers, which were performed using antibody against EBNA1

first: Songtao

last: HE

first: Niseno

last: Terhuja

first: Bhanu Chandra

last: Karisetty

first: Paul

last: Lieberman


title: Transcriptomic profiling of the intra-amygdala kainate mouse model across the stages of epileptogenesis

status: Public on Apr 16 2026

city: Seoul

first: Sangwoo

last: Kim

state: State...

address: 50-1 Yonsei-ro, Seodaemun-gu

department: Dept. of Biomedical Systems Informatics

country: South Korea

institute: Yonsei University College of Medicine

summary: Mesial temporal lobe epilepsy (MTLE) is a prevalent form of drug-resistant epilepsy often associated with hippocampal sclerosis (HS). While various rodent models exist to study this condition, their molecular fidelity to human MTLE requires detailed evaluation. As part of a larger cross-species transcriptomic meta-analysis, we generated this dataset to characterize the intra-amygdala kainate mouse model, which provides a unique framework for studying status epilepticus-induced epileptogenesis. We performed bulk RNA-sequencing on hippocampal tissues to capture the evolving molecular landscape during the acute, intermediate, and chronic phases following seizure induction. This dataset allows for the investigation of key epileptogenic processes, including neuroinflammation, neuronal death, and reactive gliosis, and serves as a critical component in comparing chemical induction models against human MTLE pathophysiology.

overall_design: Adult male C57BL/6 mice (8–10 weeks old) were used to induce a model of temporal lobe epilepsy. Status epilepticus was triggered via a unilateral stereotaxic microinjection of kainic acid into the basolateral amygdala. Control animals received an equivalent volume of vehicle (PBS). To ensure survival and standardize seizure duration, diazepam was administered intraperitoneally 40 minutes after the injection. Ipsilateral hippocampal tissues were harvested at three distinct time points post-injection: 3 days (Acute), 7 days (Intermediate), and 14 days (Chronic). Total RNA was extracted (RIN values 8.0–9.5) and libraries were prepared using the TruSeq Stranded mRNA Sample Preparation Kit. High-throughput sequencing was performed on the Illumina NovaSeq X Plus platform, generating 100 bp paired-end reads.

first: Joonho

first: Bora

first: Won-Joo


title: Association of serum uric acid with cardiovascular risk and exploratory profiling of circulating tsRNAs in gout patients

status: Public on Apr 14 2026

city: Guangzhou

first: Huan

last: Dong

state: Guangdong

address: No. 58, Zhongshan Road, Yuexiu District, Guangzhou

institute: Sun Yat-sen University First Affiliated Hospital

type: Non-coding RNA profiling by high throughput sequencing

summary: Sreum from gout patients and healthy controls underwent high-throughput small-RNA sequencing to profile tRNA-derived small RNAs(tsRNAs) in gout.

overall_design: High-throughput sequencing was conducted on serum samples from 10 gout patients and 10 matched healthy controls to identify differentially expressed tsRNAs.

first: Shaofan

last: Zhang

first: Ting

last: Liu

first: Youjun

last: Xiao

first: Hanshi

last: Xu

first: Hao

first: Liuqin

last: Liang

first: Qian

last: Qiu


title: Reprogramming Dedifferentiation Regulatory Networks Preserves Human Chondrocyte Phenotypes (RNA-Seq)

first: Ellen

address: 36th Street and Hamilton Walk

department: Orthopaedic Surgery

institute: University of Pennsylvania

summary: Chondrocyte-based cartilage repair strategies such as autologous chondrocyte implantation (ACI) require extensive in vitro expansion to obtain clinically relevant cell numbers. However, monolayer expansion drives chondrocyte dedifferentiation, reducing matrix-forming capacity and contributing to variable repair outcomes, a long-standing problem in cell-based cartilage repair.

overall_design: RNA-seq was performed on primary human articular chondrocytes from 4 independent donors (D1-D4) at three in vitro passage numbers (P0, P3, P6), yielding 12 samples total (4 donors x 3 passages). Paired-end 2×150bp sequencing was performed on an Illumina HiSeq X.

first: Su Chin

last: Heo


title: The transcriptomic profile of the naïve or CpG-stimulated Rfx7-deficient mouse Follicular B cells and RFX7-transfected lymphoma human cell line U-2932

status: Public on Apr 15 2026

city: Bellinzona

first: Greta

last: Guarda

address: Via Francesco Chiesa 5

country: Switzerland

institute: Institute for Research in Biomedicine (IRB)

summary: PART 1) Alterations of the transcription factor RFX7 have been reported in different B-cell malignancies. We therefore set out to study the role of RFX7 in B cell activation. So we performed bulk RNA-seq on sorted wild-type or Rfx7-deficient follicular B cells, either naive or activated with CpG. PART 2) RFX7 frameshift and non-sense mutations have been reported in different B-cell malignancies. We therefore set out to study the role of selected truncations in a human lymphoma cell line. We performed bulk RNA-seq on sorted U-2932 cells transfected with different RFX7 encoding constructs.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: PART 1) FO B cells were FACS-sorted as B220+/CD19+/CD23+ and either directly processed or activated with CpG (2 μg/ml) for 18h in vitro. PART 2) U-2932 cells were transfected with different eGFP- or mCherry-RFX7 encoding plasmids for 24h and sorted for eGFP and/or mCherry positivity.


title: Targeting the ADAR1 p150 isoform triggers tumor growth inhibition and antitumor immunity to overcome immunotherapy resistance

status: Public on Apr 12 2026

city: Shanghai

first: Zhichao

last: Ai

state: Shanghai

address: 371 Lishizhen Road

department: Oncology

institute: China Innovation Center of Roche (CICoR)

summary: Cancer immunotherapy efficacy is often limited by primary and acquired resistance. The RNA- editing enzyme ADAR1 has emerged as a key regulator of tumor immune evasion, yet therapeutic targeting is challenged by the essential physiological roles of its constitutively expressed p110 isoform. Here, we identify the interferon-inducible p150 isoform and its Zα domain as a critical therapeutic vulnerability. We demonstrate that ADAR1 p150 is frequently overexpressed in human cancers and correlates with an immunosuppressive tumor microenvironment. Genetic ablation of ADAR1 p150 intrinsically inhibits tumor proliferation and extrinsically triggers a robust type I interferon response and profound remodeling of the tumor immune landscape, converting immunologically "cold" tumors to "hot." Furthermore, we establish that myeloid-specific ADAR1 deletion synergizes with anti-PD-1 therapy by enhancing antigen presentation and fostering a pro-inflammatory microenvironment. Crucially, we delineate the Zα domain as the essential structural determinant for dsRNA editing selectivity. Targeted disruption of this domain alone, without affecting the catalytic deaminase domain, is sufficient to recapitulate the potent antitumor effects of complete ADAR1 ablation, leading to accumulation of immunogenic dsRNA, activation of cytosolic sensors (MDA5/PKR), and potent anti-tumor immunity. Our work provides a compelling rationale for selectively targeting the ADAR1 p150-Zα axis to reverse malignant RNA editing and overcome resistance to immunotherapy, offering a refined strategy with a potentially superior therapeutic index.

overall_design: We performed 150bp paired-end RNA-seq on 2 biological replicates of WT vs KO cells_x000D_

first: Yuying

last: Bian

first: Gang

last: Li


title: Targeting the ADAR1 p150 isoform to overcome immunotherapy resistance

summary: Cancer immunotherapy efficacy is often limited by primary and acquired resistance. The RNA-editing enzyme ADAR1 has emerged as a key regulator of tumor immune evasion, yet therapeutic targeting is challenged by the essential physiological roles of its constitutively expressed p110 isoform. Here, we identify the interferon-inducible p150 isoform and its Zα domain as a precise therapeutic vulnerability. We demonstrate that ADAR1 p150 is frequently overexpressed in human cancers and correlates with an immunosuppressive tumor microenvironment. Genetic ablation of ADAR1 p150 intrinsically inhibits tumor proliferation and extrinsically triggers a robust type I interferon response and profound remodeling of the tumor immune landscape, converting immunologically "cold" tumors to "hot." Furthermore, we establish that myeloid-specific ADAR1 deletion synergizes with anti-PD-1 therapy by enhancing antigen presentation and fostering a pro-inflammatory microenvironment. Crucially, we delineate the Zα domain as the essential structural determinant for dsRNA editing fidelity. Targeted disruption of this domain alone, without affecting the catalytic deaminase domain, is sufficient to recapitulate the potent antitumor effects of complete ADAR1 ablation, leading to accumulation of immunogenic dsRNA, activation of cytosolic sensors (MDA5/PKR), and potent anti-tumor immunity. Our work provides a compelling preclinical rationale for selectively targeting the ADAR1 p150-Zα axis to reverse malignant RNA editing and overcome resistance to immunotherapy, offering a refined strategy with a potentially superior therapeutic index.

overall_design: There are 4 mouse samples, consisting of tumour samples collected from mouse beared with WT or Za mutant MC38 colon adenocarcinoma treated with anti-PD1 therapy, with whole tissue single cell sequencing.


title: H3K9 di-methylation dynamics underlies mouse minor zygotic genome activation [CATCH-seq of early embryo]

first: Ryo

last: Maeda

overall_design: ChIP-seq of early embryo

first: Shunsuke

last: Kuroki

first: Masahiro

last: Matsuwaka

first: Azusa

last: Inoue

first: Makoto

last: Tachibana


title: Integrated stress response couples mitochondrial fitness with lineage reprogramming to drive cancer evolution. [RNA-Seq]

city: Montréal

first: Antonis

last: Koromilas

state: QC

address: 3755 Chem. de la Côte-Sainte-Catherine

country: Canada

institute: Lady Davis Institute - McGill University

summary: Tumour progression towards dedifferentiated cell clusters plays a critical role in intratumour heterogeneity and therapy resistance. While tumour microenvironmental stress has been implicated, the underlying mechanisms remain poorly defined. Using mouse models of lung adenocarcinoma, we demonstrate that activation of the integrated stress response (ISR)—marked by phosphorylation of eIF2 (p-eIF2) and ATF4 induction—drives tumour heterogeneity. ISR activation facilitates the emergence of high-plasticity, undifferentiated and pre-epithelial-to-mesenchymal transition clusters characterized by elevated ATF4 and MYC activity. This process is MYC dependent and involves ISR-mediated repression of NKX2-1, a key determinant of alveolar identity, and induction of CHCHD10, a regulator of mitochondrial integrity and metabolic fitness. Disruption of the p-eIF2–ATF4 axis induces mitochondrial dysfunction, limits dedifferentiation and suppresses tumour growth. In human lung adenocarcinoma, ISR-driven dedifferentiation correlates with advanced disease and poor prognosis, identifying the ISR as a central driver of lineage reprogramming and metabolic fitness in tumour progression.

overall_design: To investigate the role of integrated stress response, specifically p-eIF2, in LUAD evolution, we conducted scRNA-seq on GFP+/CD45- lung tumor cells isolated by Fluorescence-Activated Cell Sorting (FACS). The isolated tumor cells were treated with siCHCHD10 or shATF4 and then subjected to RNA-seq.

first: Shiqi

last: Diao

first: Jia

last: Zou

middle: E


title: Spatial transcriptomics analysis of dual-pathway spots

status: Public on Apr 10 2026

city: Bronx

first: Jeffrey

last: Pessin

state: NY

address: 1301 Morris Park Avenue

department: Medicine and Molecular Pharmacology

institute: Albert Einstein College of Medicine

summary: It is generally accepted that hepatic gluconeogenesis is active in the fasted state and inactive in the fed state. In contrast, de novo lipogenesis is active in the fed state and is inactive in the fasted state. We report a subset of periportal spots (hepatocytes) in spatial transcriptomics that are positive of both transcriptionally gluconeogenic and de novo lipogenic.

overall_design: We performed spatial transcriptomics on a) normal chow diet fed C57Bl/6J mouse (fast12h and refed4h), b) 3-month high-fat diet fed C57Bl/6J mouse (fast12h and refed4h), and c) humanized liver mouse (refed4h).

first: Junichi

last: Okada

first: Li

last: Liu

first: Kosaku

last: Shinoda

first: Takeshi

last: Saito


title: Dehydration promotes intracellular lipid synthesis and lipid accumulation

city: Durham

first: Integrative

last: Bioinformatics

state: NC

address: 111 TW Alexander Drive

department: BCBB

institute: NIEHS

summary: NFAT5 is transcription factor that regulates gene expression in response to hypertonic stress. Here we profile NFAT5 occupancy before and hour following hypertonic stress in mouse inner medulla collecting duct cells, as resource to localize sites with tonicity depend chromatin occupancy.  In addition, we test the occupancy of the active histone mark H3K27ac and the repressive mark H3K27me3.

overall_design: Occupancy of NFAT5 and H3K27 histone marks in mouse IMCD cells under isotonic and hypertonic conditions

first: Jason

last: Watts

first: Juan

last: Arroyo Ornelas

first: Ma

last: Wan

first: Don

last: Delker


title: Pathogen-specific immune responses might underlie divergent outcomes of coronavirus and influenza infection in the natural porcine host

city: Pirbrigh

first: liu

last: yang

address: Ash Rd

country: United Kingdom

institute: The Pirbright Institute

summary: Coronaviruses and influenza A viruses are major respiratory pathogens with pandemic potential. Using pigs as a translational large-animal model, we compared the virulence, pathogenesis, and immune responses to porcine respiratory coronavirus (PRCV) and pandemic H1N1 2009 influenza virus (pH1N1). PRCV infection resulted in prolonged viral shedding, more severe lung pathology, and higher viral loads in lung tissue and bronchoalveolar lavage fluid, accompanied by pronounced epithelial necrosis and inflammation. Single-cell RNA sequencing at 12 days post-infection revealed distinct transcriptional signatures and immune activation patterns. PRCV induced stronger mucosal and systemic immunity, with elevated IFN-γ, TNF, and IL-2-secreting T cells, and greater numbers of antigen-specific B cells in blood and airways. Nasal microbiome profiling identified both shared and virus-specific alterations. Together, these findings highlight fundamental differences in coronavirus and influenza virus–host interactions and establish the pig as a powerful comparative model for studying respiratory virus pathogenesis and immunity.

overall_design: We generated single-cell suspensions from lung tissue of control (n = 4), PRCV-infected (n = 4 at 1 DPI and n = 4 at 12 DPI), and pH1N1-inoculated (n = 3 at 1 DPI and n = 5 at 12 DPI) pigs, a total of 20 samples.

first: Ehsan Sedaghat

last: Rostami

first: Liu

last: Yang

first: Ashutosh

last: Vats

first: Basudev

last: Paudyal

first: Emily

last: Briggs

first: Brigid Veronica

last: Carr

first: Graham

last: Freimanis

first: Ines

last: Ruedas-Torres

first: Tim

last: Downing

first: Christine

last: Rollier

first: Katherine

last: Marougka

first: Cornelis A.M.

last: de Haan

first: Jai

last: Mehat

first: Roberto

last: La Ragione

first: Andrew

last: Muir

first: Arianne C

last: Richard

first: Kristien

last: van Reeth

first: Francisco

last: Salguero

first: Wilhelm

last: Gerner

first: Elma

last: Tchilian


title: Menstrual Fluid-Derived Small Extracellular Vesicles: A Novel Reservoir with Distinct Molecular Signatures and Implications for Endometriosis Etiopathology

status: Public on Apr 08 2026

city: Santiago

first: Gino

last: Nardocci

address: Av. Mons. Álvaro del Portillo 12.455

country: Chile

institute: Universidad de los Andes

summary:
STUDY QUESTION: Can the transcriptomic profile of small extracellular vesicles (sEV) derived from menstrual fluid (MF) provide insight into their potential roles as biomarkers and mediators in endometriosis (EM) development?
SUMMARY ANSWER: MF-derived sEV from EM patients display altered molecular signatures reflective of EM pathophysiology and exhibit enhanced proangiogenic activity in vitro.
WHAT IS KNOWN ALREADY: EM is a chronic gynecological disorder affecting approximately 10% of reproductive-age women, associated with pain, infertility, and delayed diagnosis. Small extracellular vesicles carry cargo that resembles their cellular origin, making them promising biomarkers for various diseases. While sEV have previously been isolated from MF and their protein content analyzed, their transcriptomic profile and angiogenic potential remain unexplored.
STUDY DESIGN, SIZE, DURATION: The two cross-sectional study involved cohorts of nulliparous (n = 10) and multiparous (n = 12) women, EM (n = 10) and control (n = 11) patients, recruited at the Obstetrics and Gynecology Unit of Clínica Universidad de los Andes, Santiago, Chile. Peripheral blood was collected by a trained midwife and MF was self-collected using a menstrual cup on the second day of menses.
PARTICIPANTS/MATERIALS, SETTING, METHODS: sEV were isolated from the plasma fraction of MF and from peripheral blood plasma. Nanoparticle tracking analysis, transmission electron microscopy, and FACS were used to assess sEV concentration, size, morphology, and tetraspanin expression. Next-generation sequencing was performed to analyze sEV transcriptomic profiles, and proangiogenic function was assessed through endothelial tubule formation assays using human umbilical vein endothelial cells (HUVECs).
MAIN RESULTS AND THE ROLE OF CHANCE: MF-sEV exhibited canonical sEV characteristics and were significantly more abundant than those isolated from peripheral blood (P = 0.008). Neither parity nor disease affected MF-sEV concentration or size; however, CD63 expression was significantly reduced in sEV from nulliparous women and EM patients (P =0.02). Transcriptomic analysis revealed unique mRNAs and long noncoding RNAs (lncRNAs) signatures that reflect their contribution to disease etiopathology. Functionally, EM-derived sEV, significantly enhanced tubule formation in vitro (P < 0.05), supporting their proangiogenic role in EM. LARGE SCALE DATA: Raw sequencing data has been submitted to GEO.
LIMITATIONS, REASONS FOR CAUTION: While sample size was sufficient for initial characterization and the in vitro validation, larger cohorts and in vivo studies are necessary to confirm these findings and clarify the molecular mechanisms underlying sEV proangiogenic effects.
WIDER IMPLICATIONS OF THE FINDINGS: The non-invasive isolation and disease-associated transcriptomic signatures of MF-sEV highlights their potential as biomarkers for EM. The current gold-standard for EM diagnosis is invasive laparoscopic surgery, resulting in delayed identification and staging of the disease. The proangiogenic effect of MF-sEV observed in vitro suggest that their cargo may offer relevant insights into disease progression and response to treatment. These findings are in line with a recent report that explored the proteome of MF-sEV from EM patients, demonstrating their involvement in mesothelial barrier disruption, which reinforces the role of MF-sEV in EM progression.

overall_design:
RNA was isolated from menstrual fluid plasma-derived sEV using TRIzol LS (Invitrogen, USA) on a 60 uL sEV sample volume. RNA concentration was assessed with a NanoDrop One (Thermo Fisher Scientific, USA). A minimum of 250 ng RNA was used for RNA sequencing (RNA-Seq). RNA-Seq was performed by Azenta Life Sciences (South Plainfield, NJ, USA). Briefly, library preparation was performed without rRNA depletion, and sequencing was carried out on an Illumina next generation sequencing platform with paired-end 150 bp reads. DESeq2 (Love et al. 2014) normalized counts were used for downstream analyses. Genes with a log2(Fold Change) ≥ 0.5 and a -log10(p value) ≥ 1.301 were considered differentially enriched (DE) in sEV. Data analysis was conducted using R (v4.2.3) (Team 2023), and graphs and heatmaps were generated using ggplot2 (v3.4.4) (Wickham 2016) package. Gene Ontology (GO) enrichment analysis was performed using the clusterProfiler (v4.6.2) (Yu et al. 2012) package.

UPDATES:
[Jun-03-2026] The GSE310627_normalized_counts.txt.gz file was replaced.
[Jun-04-2026] The raw data fastq files have been replaced.

first: Vicente

last: Peragallo-Papic

first: Paz

last: Cerda-Castro

first: Aliosha

last: I Figueroa-Valdés

first: Hugo

last: E Tobar

first: Patricia

last: Valdebenito

first: Manuel

last: B Donoso

first: Benjamín

last: Bustos

first: Javiera

last: Yakcich

first: Reyna

last: Peñailillo

first: Stephanie

last: Acuña-Gallardo

first: Sebastián

last: E Illanes

first: Francisca

last: Alcayaga-Miranda

first: Lara

last: J Monteiro


title: Aldosterone-induced gene expression changes in the brain [scRNA-Seq]

status: Public on Apr 03 2026

city: Iowa City

first: Jon

last: Resch

state: Iowa

address: 51 Newton Rd

institute: University of Iowa

summary: To uncover how aldosterone regulates gene expression in HSD2 neurons, we performed single-nucleus RNA sequencing on HSD2 neuron-enriched dorsal vagal complex samples from mice treated with vehicle or aldosterone for 24 hours. We then performed differential gene expression analysis on HSD2 neurons, comparing the vehicle and aldosterone-treated conditions.

overall_design: Male and female Hsd11b2-IRES-Cre mice were injected with AAV-DIO-H2b-mCherry to label HSD2 neurons. 10-14 days later, mice were then treated with vehicle or aldosterone (250 ng/hr) for 24 hours via mini osmotic pumps before brain harvesting. Single nuclei were isolated from the dorsal vagal complex of 1mm-thick coronal brainstem slices and samples were enriched for HSD2 neurons via fluorescence-activated nuclei sorting (FANS). Then, RNA profiling was performed on single nuclei from the dorsal vagal complex.

first: Miriam

middle: C

last: McDonough

first: Ahmet

last: Kuralay

first: Trevor

last: Butler

first: Silvia

last: Gasparini

first: Madelin

middle: R

last: Schwager

first: Christopher

middle: L

last: Jacobs

first: Anton

last: Gulko

first: Alysia

middle: B

last: Meyers

first: Linus

middle: T

last: Tsai

first: Joel

last: Geerling

middle: M


title: Aldosterone-induced gene expression changes in the brain [Multiomic]


title: Purine bias in bacterial genes is driven by runaway transcription

city: Cambridge

first: K Julia

last: Dierksheide

state: MA

address: 31 Ames St.

department: Biology

institute: Massachusetts Institute of Technology

summary: Genes in many bacteria are rich in purine nucleotides and poor in pyrimidines. We show that this purine preference is critical for gene expression because it prevents premature transcription termination in species that exhibit runaway transcription. In contrast to coupled transcription-translation, runaway RNA polymerases that outpace trailing ribosomes have exposed nascent RNA and are vulnerable to the termination factor Rho. Using a massively parallel reporter assay in Bacillus subtilis, we found that Rho-dependent termination requires a high C-to-G skew and high T content. Consequently, purine-rich coding (sense) sequences escape premature termination, whereas the correspondingly pyrimidine-rich antisense sequences are targeted by Rho and transcriptionally silenced. This purine requirement drives biased codon usage in most bacterial species with runaway transcription, except in lineages that have lost Rho. Our results suggest that the avoidance of premature transcription termination imposes major constraints on nucleotide content during genome evolution and adaptation of foreign genes.

sample_organism: Bacillus subtilis subsp. subtilis str. 168

overall_design: Antibiotic selection-based reporter assay was applied to assay for transcription termination sites encoded in gDNA fragments. Assay was performed in B. subtilis, on fragments of the B. subtilis 168 and E. coli MG1655 genomes. Antibiotic selection assay was performed in the presence and absence of the Rho inhibitor bicyclomycin-benzoate (BCM) to separate Rho-dependent termination events. Sequencing data was collected by gDNA sequencing of the B. subtilis library before (preselection) and after (postselection) selection at the site of the fragment integration to measure the representation of each genomic fragment in the library before and after antibiotic selection. Transcription termination drives antibiotic resistance, increasing representation in post-selection sample.

first: James

last: Taggart

first: Grace

last: Johnson

first: Gene-Wei

last: Li


title: Cancer associated fibroblasts promote epithelial to mesenchymal transition and classical to basal change in pancreatic cancer cells in association with loss of IL-8 expression

status: Public on Apr 01 2026

city: Baltimore

first: Jacquelyn

middle: W

last: Zimmerman

state: Maryland

address: 1650 Orleans St, Room 186

institute: Johns Hopkins Sidney Kimmel Comp. Cancer Center

summary: Pancreatic ductal adenocarcinoma (PDAC) carries an extremely poor prognosis, in part resulting from cellular heterogeneity that supports overall tumorigenicity. Cancer associated fibroblasts (CAF) are key determinants of PDAC biology and response to systemic therapy. While CAF subtypes have been defined, the effects of patient-specific CAF heterogeneity and plasticity on tumor cell behavior remain unclear. Here, multi-omics was used to characterize the tumor microenvironment (TME) in tumors from patients undergoing curative-intent surgery for PDAC. In these same patients, matched tumor organoid and CAF lines were established to functionally validate the impact of CAFs on the tumor cells. CAFs were found to drive epithelial-mesenchymal transition (EMT) and a switch in tumor cell classification from classical to basal subtype. Furthermore, we identified CAF-specific interleukin 8 (IL-8) as a contributing modulator of tumor cell subtype. Finally, we defined neighborhood relationships between tumor cell and T cell subsets.

overall_design:
Patient matched organoids and cancer associated fibroblasts were generated from PDAC surgical speciments gathered at JHU. Samples were cultured in either monoculture or coculture conditions using a matrigel substrate. For bulk-RNA sequencing, samples were FACS sorted based on EPCAM (for organoids) and FAP (for CAFs) expression prior to RNA isolation.

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


title: Nuclei Isolation from Rat and Bovine White Adipose Tissue for Single-Nuclei RNA Sequencing

city: East Lansing

first: Leah

last: Terrian

state: MI

address: 775 Woodlot Dr.

institute: Michigan State University

summary: Perivascular adipose tissue (PVAT) is a complex tissue that is increasingly recognized for its roles in vascular health and disease. The form and function of PVAT is different depending on species and anatomical location and understanding its cellular and molecular characteristics gives greater insights. We had previously successfully performed single nucleus RNA-sequencing (snRNAseq) on brown fat depots, the thoracic aortic PVAT (taPVAT) and subscapular brown adipose tissue (BAT), from Dahl SS rats.  However, application of the same nuclei isolation method to white adipose tissue (WAT) depots (perivascular and non-perivascular) from the same rat strain resulted in insufficient nuclei capture and low transcript numbers. These challenges were also encountered when processing WAT from cattle. While nuclei isolation methods have been developed and optimized for human and mouse WAT depots, they have not been evaluated across WAT depots from other species such as the cow and rat. Because these latter species are important models for cardiovascular and metabolic diseases, this study aimed to validate and optimize a nuclei isolation protocol for use with WAT from them. Protocols were evaluated based on (a) the quantity of nuclei isolated, (b) the quality of nuclei determined by microscopic visualization, and (c) the total number of detected transcripts and genes following snRNAseq. A modified protocol developed for human WAT, incorporating liquid nitrogen pulverization and Dounce homogenization of flash-frozen tissue was tested. This protocol, with key modifications for optimization, proved translatable to rat and cow WAT depots to improve nuclei yield (rat retroperitoneal fat: 3100 nuclei/mg tissue; rat mesenteric perivascular adipose tissue: 2200 nuclei/mg tissue; cow white fat 2050 nuclei/mg). Further analysis by snRNAseq, however, identified limitations. While cow WAT expressed nearly 1,720 median genes/cell, both rat white depots were significantly lower (mesPVAT: 189, RP fat: 294 median genes/cell), hindering downstream analyses in the rat tissue. These findings suggest that biological differences in adipose depots within and between species pose important challenges for the application of snRNAseq on rat WAT.

sample_organism:
Bos taurus
Rattus norvegicus

platform_organism:
Bos taurus
Rattus norvegicus

overall_design: Single-nucleus RNA-sequencing of adipose tissues from Dahl SS rat and Holstein dairy cow. Cow subcutaneuos white adipose tissue samples were taken from the right paralumbar fossa cranial to the tensor fascia latae muscle on the right flank. Rat adipose tissues were the thoracic aorta perivascular adipose tissue (PVAT), subscapular brown adipose tissue, mesenteric PVAT, and retroperitoneal adipose tissue. 5 samples were processed using Parse Biosciences WT Evercode v3 kit and 1 mesenteric PVAT sample was processed using 10x Genomics Chromium Next Gem 3' v3 kit. Sequencing was done by Novogene on an Illumina NovaSeq 6000.

first: Miguel

last: Chirivi

first: Janice

last: Thompson

first: Andres

last: Contreras

first: Stephanie

last: Watts

first: Rance

last: Nault


title: Single-cell multi-omic analysis of post-transplant mesenchymal cells reveals molecular signatures and regulators of lung fibrosis (single-cell multiome sequencing)

city: Ann Arbor

first: Lu

last: Lu

address: 100 Washtenaw Ave.

department: Department of Computational Medicine and Bioinformatics

institute: University of Michigan, Ann Arbor

summary: Chronic lung allograft dysfunction (CLAD) is a critical challenge in lung transplantation. Dysregulated gene expression and epigenomic states in lung mesenchymal cells (MCs) play a key role in these conditions. We performed single-cell multi-omic profiling on MCs isolated from human bronchoalveolar lavage samples of lung transplant recipients with CLAD, compared with time-matched controls. Our results provide deeper insights into the transcriptomic and epigenomic changes in post-transplant MCs, nominating biomarkers and disease-associated factors with implications for future therapeutic efforts.

overall_design: MCs from patients who had a diagnosis of CLAD at the time of BAL (CLAD-MCs) were compared to the MCs obtained from control CLAD-free patients (non-CLAD MCs). The incidence of CLAD increases with time post-transplant, and CLAD diagnosis is generally made after the first year of lung transplantation. To investigate if transcriptional and epigenomic changes are inherent or acquired, MCs were also studied from BAL samples obtained early in the course (<6 weeks post-transplant). These patients were later clinically classified as having developed CLAD or remained CLAD-free.

first: Aidan

middle: P

last: McLinden

first: Natalie

last: Walker

first: Ragini

last: Vittal

first: Michael

last: Combs

first: Joshua

middle: D

last: Welch

first: Vibha

middle: N

last: Lama


title: DOT1L enhances BLM-induced pulmonary fibrosis by inducing endothelial-to-mesenchymal transition via H3K79me2 [ChIP-seq]

first: Shu

last: Meng

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

department: Department of Basic Science Research

institute: Guangzhou National Laboratory

summary: Endothelial-to-mesenchymal transition (EndoMT) have been reported to contribute to pulmonary fibrosis. Here, we showed that induction of EndoMT activated DOT1L expression and enhanced H3K79me2 level by TGFβ2 in human umbilical vein endothelial cells (HUVECs) in vitro. Using a bleomycin (BLM)-induced idiopathic pulmonary fibrosis (IPF) model, endothelial-lineage tracing reporter mice, and endothelial-specific Dot1L knockout mice, we confirmed that DOT1L mediates EndoMT and drives pulmonary fibrosis in vivo through H3K79 methylation. ChIP-seq revealed direct binding of SMAD2/3 to the DOT1L promoter and increased H3K79me2 deposition at fibrosis-related genes following TGFβ2 stimulation.

overall_design: HUVECs were collected at 24 h with TGFβ2 treatment or not, and histone mark H3K79me2 was profiled using ChIP-seq.

first: Yaofeng

last: Wang

first: Xing

last: Peng


overall_design: HUVECs were collected at 24 h with TGFβ2 treatment or not, and ChIP-seq for SMAD2/3 was performed.


title: H2AK119ub1-MLL2 counteraction underlies heritable H3K27me3 formation in oocytes

city: Yokohama

first: Azusa

last: Inoue

state: Kanagawa

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

department: Center for Integrative Medical Sciences

institute: RIKEN

summary: Polycomb group (PcG) and Trithorax group (TrxG) proteins establish bivalent chromatin marked by H3K27me3, H2AK119ub1, and H3K4me3. However, how bivalent chromatin is formed in vivo in mammals is poorly understood. In mouse oocytes, it arises at thousands of promoters, including noncanonical imprinted loci whose H3K27me3 is intergenerationally inherited by early embryos. Here, we show that H3K27me3 is deposited at H3K4me3-premarked promoters in an H2AK119ub1-dependent manner during oogenesis. We find that H2AK119ub1 deficiency causes transcriptional derepression and loss of H3K27me3 proportional to preexisting H3K4me3 levels in oocytes. Importantly, concomitant deficiency of H2AK119ub1 and MLL2-mediated H3K4me3 substantially restores transcriptional silencing and H3K27me3 deposition, leading to partial restoration of noncanonical imprinting in offspring. Taken together, we propose that H2AK119ub1 antagonizes MLL2 function to repress bivalent genes during oogenesis, thereby conferring heritable H3K27me3. This study reveals how PcG and TrxG counteraction shapes the maternal epigenome for the next generation’s development.

overall_design: RNA-seq were performed in wild type (WT) and PRC1 catalytic dead (PRC1-CD) oocytes, in WT, Pcgf1/6 DKO, Pcgf1/6/Mll2 TKO oocytes, and in WT, Pcgf1/6 maternal DKO, Pcgf1/6/Mll2 maternal TKO morula embryos. Then comparative analysis was done between the WT and mutants.

first: Hailiang

last: Mei

first: Chisayo

last: Kozuka

first: Mami

last: Kumon

first: Haruhiko

last: Koseki


title: Gene expression profiling of mouse lung tissue in a bleomycin-induced pulmonary fibrosis model

summary: This study investigates the gene expression changes in mouse lung tissue over time in a bleomycin-induced pulmonary fibrosis model. Lung tissues were collected at day 0 (baseline), day 7, day 14, and day 21 post-bleomycin treatment to analyze the progression of fibrosis. Total RNA of whole lung tissues was extracted, and transcriptomic profiling was performed to identify key genes and pathways involved in the pulmonary fibrosis development. Our study provides insights into the temporal dynamics of gene expression during the fibrotic process.

overall_design: Mouse lung tissues were collected at day 0, day 7, day 14, and day 21 after bleomycin treatment. We got three replicates for each time point. Total RNA were extracted and subjected to RNA-seq profiling.

first: Zhimin

last: Song


title: Morphological, Behavioral, and Transcriptomic Profiling Reveals Developmental Toxicity of PCB Metabolites in Zebrafish

status: Public on Mar 31 2026

city: Corvallis

first: Robyn

last: Tanguay

state: OR

institute: Oregon State University

summary: Polychlorinated biphenyls (PCBs) persist in the environment as complex mixtures and undergo extensive biotransformation, yet the developmental toxicity of PCB metabolites remains poorly defined. We evaluated developmental, neurobehavioral, and molecular effects of parent PCBs, hydroxylated, methoxylated, and sulfated metabolites, and environmentally relevant mixtures using embryonic zebrafish. Morphological abnormalities and photomotor behavior were assessed across early development, followed by targeted cyp1a reporter analysis and transcriptomic profiling for a subset of potent exposures. Most chemicals induced morphological effects, with hydroxylated and sulfated metabolites producing effects more frequently and at lower benchmark concentrations than parent congeners. Behavioral alterations were more prevalent in embryonic photomotor response than larval photomotor response and generally co-occurred with morphological effects. Environmental mixtures elicited broad phenotypic profiles comparable to highly active individual compounds. Despite pronounced developmental toxicity, cyp1a induction was limited to PCB126, indicating that aryl hydrocarbon receptor activation was not a dominant mechanism for most exposures. Transcriptomic analyses revealed minimal responses for parent PCBs but robust, exposure-specific gene expression changes for select metabolites, particularly 5-OH-PCB11, and mixtures. Differentially expressed genes were enriched for xenobiotic metabolism, immune signaling, and neuroactive pathways, alongside consistent downregulation of circadian regulators. Together these results demonstrate contributions of PCB metabolites and mixtures to toxicity.

overall_design: At 6 – 7 hpf, static chemical exposures were initiated. Twenty-eight PCBs, including individual congeners, metabolites, and mixtures, were dispensed into individual wells, normalized to 1% DMSO, using a Hewlett-PackardHP D300 Digital Dispenser. Final nominal concentrations reflected the direct addition of each chemical to the 100 μL exposure volume in the wells. Embryos were exposed to 7 concentrations (0-100 μM) with one row per concentration (n = 12) and a single chemical per plate. After dosing chemical addition, all 96-well plates were sealed with ThermalSeal RTS (Excel Scientific) to minimize evaporation and placed on an orbital shaker at 225–235 rpm for 18 h at 28 °C in the dark to ensure homogenous mixing. At 24 hpf, embryos were evaluated for embryonic photomotor response, then transferred to a static 28 °C incubator and kept in the dark for the remainder of the exposure period until 120 hpf when larval photomotor response and morphology screening were conducted.

first: Nicole M

last: Breese

first: Lisa

last: Truong

first: Xueshu

last: Li

first: Robyn L

first: Hans-Joachim

last: Lehmler


title: Spatiotemporal transcriptome atlas of human embryos after gastrulation

city: shenzhen

first: CNSA

last: CNGB

address: BGI

institute: BGI

summary: The comprehensive spatiotemporal atlas of gene expression during early human embryonic development is critical for insights into embryogenesis, organogenesis, and disease origins. Leveraging Stereo-seq technology, we generated spatial transcriptomic profiles across 77 sagittal sections of 13 whole human embryos ranging from Carnegie stage 12 to 23, integrated with single-nucleus RNA-seq to elucidate gene expression patterns within defined cellular contexts, revealing the cellular heterogeneity that drives organ-specific differentiation. Our study has established a regulatory profile for the development of 50 organs and 198 substructures, and identified potential tissue-identity regulators. Notably, it uncovered previously uncharacterized gene functions in cardiac and brain development. The atlas not only substantiates and refines current understanding of human organ development but also highlights key organs susceptible to viral infections and genetic disorders. Furthermore, we characterized the allelic gene expression within specific organs at different developmental stages. This work presents a groundbreaking compilation of genome-wide gene expression profiles for each spatially defined cell population, which can be visualized as a spatial display of the embryonic transcriptional landscape. These results offer the most thorough delineation to data of the spatiotemporal transcriptomic dynamics of human organogenesis.

overall_design:
Spatial transcriptomic profiles across 77 sagittal sections of 13 whole human embryos ranging from Carnegie stage 12 to 23.

***************************************************************
Raw data are missing due to patient privacy concerns.
***************************************************************

first: Jiexue

last: Pan

first: Yuejiao

first: Zhongliang

last: Lin

first: Qing

last: Lan

first: Ying

last: Zhang

first: Huixi

last: Chen

first: Shengwei

last: Sui

first: Man

last: Zhai

first: Lijian

last: Zhao

first: Hongbo

last: Yang

first: Ya

last: Gao

first: Guolian

last: Ding

first: Xun

last: Xu

first: Hefeng

last: Huang


title: The chromatin remodeling complex PRC2 safeguards cell fate in alveolar epithelial type 2 cells

city: CINCINNATI

first: William

last: Zacharias

state: OH

address: 3333 BURNET AVE

institute: Cincinnati Children's Hospital Medical Center

summary: Maintenance of the gas exchange surface throughout life and regeneration of the lung after injury requires tight regulation of epithelial cell fate and function. Alveolar epithelial type 2 (AT2) cells serve as the progenitors of the distal epithelium, differentiating into alveolar epithelial type 1 (AT1) cells or proliferating to maintain the quorum of AT2 cells. Here we describe the role of the chromatin regulator polycomb repressive complex 2 (PRC2) in the maintenance of AT2 cell fate in the adult alveolus. Cross-species single-cell transcriptomic analyses identified PRC2 activation in proliferative AT2 populations. PRC2 loss of function in human iPSC-derived AT2 (iAT2) cells and primary murine AT2 cells in vitro resulted in loss of AT2 cell state and emergence of programs reminiscent of alveolar-basal intermediate (ABI) cell states, while overexpression of the PRC2 enzymatic component EZH2 in human iAT2 cells augmented the AT2 cell program. Genetic loss of PRC2 function in the AT2 lineage in adult mice in vivo led to emphysematous remodeling of the lung and induced a time-dependent series of transitions of AT2 cells through an ABI state into Krt5+ basal-like cells. Comparison of murine ABI cells to human ABI cells demonstrates de-repression of canonical PRC2 targets during transition to ABI and basal-like states in humans, implicating PRC2 as a conserved regulator of AT2 cell fate. Together, these findings define PRC2 complex function during AT2 cell self-renewal as a critical guardrail for maintaining epithelial cell fate in the adult lung.

overall_design: scRNAseq of Sftpc-CreERT2 x EEDf/f x R26R-EFYP with associated Sftpc-CreERT2 x R26R-EFYP postiive controls at 2mo, 4mo, and 9mo following tamoxifen treatment to induce recombination. EYFP+ EPCAM+ epithelial cells were isolated by FACS. Cells isolated from N=3-4 animals per genotype were combined and then loaded for 10x Genomics 3v4 sequencing

first: Helen

last: Warheit-Niemi


title: DOT1L enhances BLM-induced pulmonary fibrosis by inducing endothelial-to-mesenchymal transition via H3K79me2 [RNA-seq]

city: Guangzhou

first: Shu

last: Meng

overall_design: HUVECs were collected at 24 h with TGFβ2 treatment or not (three replicates for each group). Total RNA were extracted and subjected to RNA-seq profiling.

first: Yaofeng

last: Wang

first: Xing

last: Peng


title: Olfr2-positive macrophages originating from monocytes proliferate in situ and present a pro-inflammatory foamy-like phenotype

city: La Jolla

first: Sujit Silas

last: Armstrong Suthahar

state: California

address: 9420 Athena Cir

institute: La Jolla Institute for Immunology

summary: Olfactory receptor 2 (Olfr2) has been identified in a minimum of 30% of vascular macrophages, and its depletion was shown to reduce atherosclerosis progression. Mononuclear phagocytes, including monocytes and macrophages within the vessel wall, are major players in atherosclerosis. Single-cell RNA sequencing studies revealed that atherosclerotic artery walls encompass several monocytes and vascular macrophages, defining at least nine distinct subsets potentially serving diverse functions in disease progression. This study investigates the functional phenotype and ontogeny of Olfr2-expressing vascular macrophages in atherosclerosis.

overall_design: Olfr2+ macrophages rapidly increase in Apoe−/− mice’s aorta when fed a Western diet (WD). Mass cytometry showed that Olfr2+ cells are clustered within the CD64 high population and enriched for CD11c and Ccr2 markers. Olfr2+ macrophages express many pro-inflammatory cytokines, including Il1b, Il6, Il12, and Il23, and chemokines, including Ccl5, Cx3cl1, Cxcl9, and Ccl22. By extracting differentially expressed genes from bulk RNA sequencing (RNA-seq) of Olfr2+ vs. Olfr2− macrophages, we defined a signature that significantly mapped to single-cell data of plaque myeloid cells, including monocytes, subendothelial MacAir, and Trem2Gpnmb foamy macrophages. By adoptive transfer experiments, we identified that Olfr2 competent monocytes from CD45.1Apoe−/−Olfr2+/+ mice transferred into CD45.2Apoe−/−Olfr2−/− recipient mice fed WD for 12 weeks, accumulate in the atherosclerotic aorta wall already at 72 h, and differentiate in macrophages. Olfr2+ macrophages showed significantly increased BrdU incorporation compared to Olfr2− macrophages. Flow cytometry confirmed that at least 50% of aortic Olfr2+ macrophages are positive for BODIPY staining and have increased expression of both tumour necrosis factor and interleukin 6 compared to Olfr2− macrophages. Gene set enrichment analysis of the Olfr2+ macrophage signature revealed a similar enrichment pattern in human atherosclerotic plaques, particularly within foamy/TREM2hi-Mφ and monocytes.

first: Klaus

last: Ley

first: Marco

last: Orecchioni


title: Novel Roles of Sonic Hedgehog Signaling in Retinal Patterning and Neurogenesis During Mammalian Eye Development

city: Davis

first: Sergi

last: Simo

state: CA

address: One Shields Avenue, 3402 Tupper Hall

department: Cell Biology and Human Anatomy

institute: University of California Davis

summary: The Sonic Hedgehog (Shh) signaling pathway is essential for the patterning, growth, and morphogenesis of many tissues. During early eye development, Shh is critical for the formation of the two optic vesicles, which give rise to the retina, retinal pigment epithelium (RPE), and optic stalk. It also regulates the balance between cell proliferation and differentiation during retinal histogenesis, a key process in shaping the cellular architecture of the mature retina. Despite these well-established roles, the temporal dynamics, region-specific functions, and downstream consequences of Shh signaling during retinal development remain poorly understood. Here, we present a comprehensive analysis of Shh signaling across multiple stages of retinal development using temporally and spatially controlled deletion of Smoothened (Smo), an essential transducer of the pathway. This approach uncovers context-dependent requirements for Shh signaling in eye patterning. We also show that Shh signaling coordinates neurogenesis by sustaining the retinal progenitor pool while also regulating progenitor competence, ensuring appropriate proportions of retinal cell types. Our data indicate that both proliferative capacity and the timing of cell fate specification are shaped by Shh pathway activity. Together, these findings establish new mechanistic links between Shh signaling, regional patterning, and temporal regulation of neurogenesis, providing novel insights into how morphogen signaling is repurposed across developmental time to orchestrate complex tissue architecture.

overall_design: RNA seq profiling of embryonic day 13 retinas from control (n=4) and retina-specific smoothen knock-out (n=4) mice

first: Miranda

last: Krueger

first: Simranjeet

middle: K

last: Cheema

last: Simó

first: Nadean

last: Brown

first: Anna

last: La Torre


title: Molecular Basis for Methylation-sensitive Editing by Cas9

city: Grand Rapids

first: Renee

last: Hoffman

state: Michigan

address: 333 Bostwick Ave NE

institute: Van Andel Research Institute

type: Methylation profiling by genome tiling array

summary: The bacterial CRISPR-Cas9 (Cas9) nuclease has become a powerful genome manipulation tool for a wide range of organisms 1-3. However, it has yet to fully leverage the pervasive presence of DNA methylation in genomes4-10. To fill this gap, we report biochemical, structural, and human genome editing characterizations of a methylation-sensitive Cas9 (ThermoCas9). ThermoCas9 efficiently binds and cleaves DNA upstream of its protospacer adjacent motif (PAM) 5´-NNNNCGA-3´ or 5´-NNNNCCA-3´ in vitro. Methylation of the fifth cytosine in either PAM sequence (5mCpG or 5mCpC), however, significantly inhibits ThermoCas9 activity. Cryogenic electron microscopy structures of ThermoCas9 in pre- and post-cleavage states at 2.8 Å and 2.2 Å resolution, respectively, reveal the molecular basis for the stringent requirement of the unmethylated cytosine in PAM binding and provides guidance for further enzyme engineering. We demonstrated methylation-sensitive editing by ThermoCas9 in human cell lines with distinct DNA methylation landscapes. Moreover, we demonstrated that a catalytically enhanced ThermoCas9 efficiently targets luminal expression signature genes that are consistently hypomethylated in breast cancer patients. Due to its sensitivity to DNA methylation, ThermoCas9 can target cells specifically with disease-related hypomethylation which adds another layer of precision to genome editing technologies.

overall_design: MCF-7 and MCF10-A cells were cultured as recommended on the ATCC website. Genomic DNA was extracted from these cultured cell lines, bisulfite converted, and profiled using Infinium methylation EPIC array v2.

first: Mitchell

last: Roth

first: Yuerong

last: Shu

first: Yu

last: Zhao

first: Despoina

last: Trasanidou

first: Christian

last: Sudfeld

first: Eugenios

last: Bouzetos

first: Nikoloas

last: Trasanidis

first: Michael

last: Zawrotny

first: Mary

last: Gelasco

first: Megan

last: Medina

first: Anuska

last: Das

first: Jay

last: Rai

first: Hemant

last: Goswami

first: Bing

first: John

last: van der Oost

first: Hong

last: Li


title: Pathogenesis of Diffuse Large B-cell Lymphoma Proteogenotypes

city: Frankfurt

first: Julius

last: Enssle

address: Theodor-Stern-Kai 7

country: Germany

institute: University Hospital Frankfurt

summary: The clinical and molecular heterogeneity of diffuse large B-cell lymphoma (DLBCL) is incompletely understood. By integrating proteomic, transcriptomic and genomic data from 478 DLBCL tumors, we identify seven DLBCL proteogenotypes (PGs) reflecting specific pathophysiological features and spanning cell-of-origin (COO) as well as genetic subtypes. PG4 is associated with poor outcome, independent of known risk factors including COO, genetic features or the international prognostic index. PG4 is enriched for subsets of activated B-cell-like DLBCL, germinal-center-B-cell-like tumors and genetically unclassified cases. It shares a dark-zone related B-cell phenotype and an enrichment of BTG1 and TBL1XR1 mutations. Single-cell sequencing and spatial transcriptomics further reveals enhanced MYC and TCF3/4 transcriptional activity while MYC translocations were absent, as well as exhausted CD8 T cells as common driver mechanisms in PG4. Our proteogenomic framework identifies heretofore unknown biological heterogeneity among DLBCL tumors, including high-risk proteogenomic features that provide a basis for innovative diagnostic and therapeutic approaches.

overall_design: Cell lines were cultured using RPMI with 10% fetal bovine serum (FBS), 1% L-Glutamin and 1% Penicillin-Streptomcin. 1x10e6 cells per sample were harvested for RNA extraction. Total RNA was extracted from cells using the MagNA Pure System (Roche, Basel, Switzerland) according to the manufacturer’s instructions. Library preparation for whole transcriptome sequencing (WTS) was performed using the NEBNext Ultra II RNA Kit (New England Biolabs, Ipswich, MA, USA). For each sample, 250 ng of RNA with a RIN value >5 was used as input. Sequencing was carried out on a NovaSeq 6000 system (Illumina, San Diego, CA, USA) aiming for approximately 50 million clusters per library and using 2 × 100 cycles.

first: Thomas

last: Oellerich


title: The effects of oleic acid diet on ovarian cancer tumor growth in murine xenograft model

city: Chicago

first: Didi

last: Zha

state: IL

address: 303 E SUPERIOR ST

institute: Northwestern University

summary: Oleic acid is an unsatuarated fatty acid that is converted by SCD1 (Stearoyl-CoA Desaturase 1), which is highly expressed in in ovarian cancer and has protective effect on cancer cell survival. We here report oleic acid high diet has upregulated serveral cell cycle related pathways such as E2F targets, mitotic spindle and G2M targets to promote cell proliferation in murine xenograft model.

overall_design: RNA-seq profiling of murine xenograft from OVCAR5 cisplatin-resistant cells through intraperitoneal injection to nude mice fed with control and oleic acid diet.

first: Isac

last: Ana

first: Matei

last: Daniela

first: Yinu

last: Wang

first: Zha

last: Didi


title: Autism-like phenotypes and increased NMDAR2D expression in mice with KDM5B histone lysine demethylase deficiency [CUT&Tag]

city: Exeter

first: Michiel

middle: Albert

last: Basson

address: Hatherly Labs, Prince of Wales Road

institute: University of Exeter

summary: Loss-of-function mutations in genes encoding lysine methyltransferases (KMTs) and demethylases (KDMs) specific for trimethylated of lysine 4 of histone 3 (H3K4me3) are associated with neurodevelopmental conditions, including autism spectrum disorder and intellectual disability. To study the role of KDM5B (Lysine DeMethylase-5B)-mediated H3K4me3 demethylation, we investigated neurodevelopmental phenotypes in mice without KDM5B demethylase activity. These mice exhibited autism-like behaviours and increased brain size. H3K4me3 levels and the expression of neurodevelopmental genes were increased in the developing Kdm5b mutant neocortex. These included elevated expression of Grin2d. The Grin2d gene product NMDAR2D was increased in synaptosomes isolated from the Kdm5b-deficient neocortex and treating mice with the NMDAR antagonist memantine rescued deficits in ultrasonic vocalisations and reduced repetitive digging behaviours. These findings suggest that increased H3K4me3 levels and associated Grin2d gene upregulation disrupt brain development and function, leading to socio-communication deficits and repetitive behaviours, and identify a potential therapeutic target for neurodevelopmental disorders associated with KDM5B deficiency.

overall_design: CUT&Tag for H3K4me3 was performed on neocortices from wild-type and Kdm5b deltaARID/deltaARID mice at postnatal day 5. Nuclei were isolated and samples were processed with CUTANA CUT&Tag kit (Epicypher Primer Set 1).

first: Leticia

last: Pérez-Sisqués

first: Shail

middle: U

last: Bhatt

first: Angela

last: Caruso

first: Josephine

last: Robb

first: Alex

last: Donovan

first: Rosemary

middle: A

last: Bamford

first: Alejo

last: Torres-Cano

first: Shoshana

last: Spring

first: Eleanor

last: Hendy

first: Talia

last: Gileadi

first: Martyna

last: Panasiuk

first: Jed

last: Trengove

first: Neeru

last: Jindal

first: Mohi

last: Ahmed

first: Joyce

last: Taylor-Papadimitriou

first: Diana

last: Cash

first: Nicholas

last: Clifton

first: Jacob

last: Ellegood

first: Laura

last: Andreae

first: Jason

last: Lerch

first: Maria Luisa

last: Scattoni

first: K

last: Giese

first: Cathy

last: Fernandes

first: M


title: RNASeq profiliting of spermatogonia from Wt and Sirt7-/- mice

city: Badalona

first: Irene

last: Fernández Duran

state: State...

address: Josep Carreras Building, Ctra de Can Ruti, Camí de les Escoles, s/n,

country: Spain

institute: Josep Carreras Leukaemia Research Institute

summary: Sirtuin 7 is a stress response enzyme involved in chromatin regulation. Sirt7-/- mice exhibit a premature ageing phenotype which includes dysfunctional reproductive traits. To understand better this phenomenon, in this study we investigated the transcriptional changes that occur in spermatogonia from 5 day post-natal Wt and Sirt7-/- mice.

overall_design: RNASeq profiling of mouse spermatogonia from 5 days post-natal Wt and Sirt7-/- mice.


title: SIRT7 links H3K36ac epigenetic regulation with genome maintenance in the aging mouse testis

summary: Reproductive aging is an increasing health concern affecting family planning and overall well-being. While extensively studied in females, the mechanisms driving male reproductive aging remain largely unexamined.  Here we found that mammalian Sirtuin 7 (SIRT7) sustains spermatogenesis in an age-dependent manner through the control of histone 3 lysine 36 acetylation (H3K36ac). SIRT7 deficiency in mice resulted in increased levels of H3K36ac in spermatogonia and spermatocytes, a pattern also observed during natural testicular aging.  SIRT7 deficiency altered chromatin accessibility, which was directly linked to H3K36ac activity in a germ cell line, and increased vulnerability to genotoxic stress. Importantly, undifferentiated spermatogonia, which are required for continuous sperm production, decreased prematurely in Sirt7-/- mice and showed enhanced genome damage accumulation during aging or under acute environmental stress. These changes were concurrent with age-dependent defects in double strand break (DBS) repair and partial meiotic arrest. Taken together, our results indicate that SIRT7 connects H3K36ac epigenetic regulation to long-term genome stability in male germ cells, ensuring steady-state spermatogenesis during the lengthy male reproductive lifespan.

overall_design: 50,000 spermatogonia from Pnd 5 mouse testes where isolated and subjected to anti-H3K36ac ChIP-Seq

first: A

last: Guitart-Solanes

last: Romero

first: I

last: Fernandez-Duran

last: Gamez-Garcia

first: B

last: Niedenberger

first: C

last: Madrid-Sandín

first: N

last: Spears

last: Roig

last: Geyer

last: Vaquero

last: Schindler

last: Vazquez


title: SIRT7 links H3K36ac epigenetic regulation with genome maintenance in the aging mouse testis [ATAC-Seq]

overall_design: 50,000 spermatogonia from Pnd 5 mouse testes where isolated and subjected to ATAC-Seq


title: Ambient temperature regulates CD4⁺ T cell tonic T cell receptor signaling and responsiveness

city: Cincinnati

first: Senad

last: Divanovic

state: Ohio

address: 3333 Burnet Avenue

summary: Mice (Mus musculus) used in biomedical research are commonly housed at 19-23 °C, below their thermoneutral zone (29-34 °C), where metabolic homeostasis occurs. Although traditional housing exposes mice to chronic cold stress and modulates their immune response, cellular mechanisms by which thermoneutrality shapes immune responses remain underdefined. CD4+ T cells are major contributors to host immunity through T cell receptor (TCR) signaling activated via recognition of peptide-major histocompatibility complex class II (pMHCII). We demonstrate that thermoneutral housing, compared to traditional housing, enhances tonic TCR signaling, upregulates genes associated with endogenous TCR stimulation, and increases TCR-driven TNF expression in CD4⁺ T cells. Mechanistically, these effects are in part dependent on tonic TCR engagement with self-pMHCII. In inflammatory disease models, thermoneutrality-driven increased CD4⁺ T cell TNF production correlates with amplified tissue inflammation. Together, these findings reveal how housing temperature may shape inflammatory responses through self-pMHCII-dependent TCR signaling in CD4⁺ T cells.

overall_design: Bulk RNA-Seq on splenic CD4+ T cells from Nur77-GFP transgenic mice

first: Keisuke

last: Sawada

first: John

last: Eom

first: Bree

last: Mahoney-Sutherland

first: Traci

last: Stankiewicz

first: Jarren

last: Oates

first: Daniel

last: Giles

first: Pablo

last: Alarcon

first: Michelle

last: Damen

first: Angela

last: Cannata

first: Julie

last: Hargis

first: Jaclyn

last: McAlees

first: Cassidy

last: Ulanowicz

first: Jennifer

last: Wayland

first: David

last: Hildeman

first: Ian

last: Lewkowich

first: Simon

last: Hogan

first: Nathan

last: Salomonis

first: Maria

last: Moreno-Fernandez


title: Identification of a set of transcriptional regulators involved in the temporal regulation of neuron subtype differentiation

city: Shinjuku-ku

first: Takuya

last: Shimazaki

state: Tokyo

address: 35 Shinanomachi

department: Physiology

institute: Keio University School of Medicine

summary: The sequential generation of various types of neurons and glia from neural stem /progenitor cells (NSPCs) during development is a major part to build complex central nervous system. COUP-TFI/II (NR2F1/2) are critical factors for the temporal specification of NSPCs including neurogenesis-to-gliogenesis switch. MicroRNA miR-17 has also been shown to regulate acquisition of gliogenic competence by NSPCs downstream of COUP-TFs. We tried to identify candidate genes that are involved in the temporal change of the potency of NSPCs for the sequential generation of different neuron subtypes but not acquisition of gliogenic competence downstream of COUP-TFs.

overall_design: Gene expression profiling of shRNA control, Nr2f1/2- knockdown, miRNA control and miR-17 overexpression cultures of primary (P0) and tertiary (P2) neurospheres (NSPCs) derived from mouse embryonic stem cells.

first: Hayato

last: Naka-Kaneda

first: Hideyuki

last: Okano


title: Identification of a set of transcriptional regulators involved in the temporal regulation of neuron subtype differentiation [RNA-Seq]

summary: The sequential generation of various types of neurons and glia from neural stem /progenitor cells (NSPCs) during development is a major part to build complex central nervous system. Here, we identify PHF21b, ZFP7 and ZFP57 as crucial factors that regulate the transition from early-born neuron to late-born neuron generation by NSPCs in the developing mouse cortex and ganglionic eminence. Combinatorial overexpression of these three factors in the stage progressed NSPCs generating late-born neurons resulted in prolonged generation of early-born neurons. Conversely, simultaneous knockdown of these genes suppressed generation of early-born neurons.

overall_design: RNAseq profiling of wildtype mouse NSPCs grown as neurospheres derived from E12.5 cerebral cortex (CTX) or E13.5 ganglionic eminence (GE) and their combinatorial overexpression derivatives (PHF21b, ZFP7, and ZFP57) at Day5 of growth, and of wildtype mouse primary cultures from E11.5 CTX or GE and their simultaneous knockdown derivatives (shPhf21b, shZfp7, and Zfp57) at Day5 of differentiation.

first: Daisuke

last: Hisamatsu


title: A Unique Pediatric Activated T-cell Acute Liver Failure Endotype Characterized by Perforin and Interferon Gamma Expressing Circulating CD8 Tissue Resident Memory T-cells.

city: Philadelphia

first: david

last: smith

state: Pennsylvania

address: 3501 Civic Center Blvd

institute: CHOP

summary: Activated T-cell Pediatric Acute Liver Failure (TC-PALF) is the most common cause of non-acetaminophen PALF with poor transplant-free survival. Livers in TC-PALF are infiltrated by effector cytotoxic T lymphocytes with markers of tissue-resident memory function (CD8 Trm) and an interferon gamma (IFNg) transcriptional signature. The PALF-Immune Response Network (PALF-IRN) and the prospective TReatment for ImmUne Mediated PathopHysiology (TRIUMPH) clinical trial (NCT04862221) aim to characterize the TC-PALF immune pathology and utility of T-cell directed therapy to improve transplant free survival.

overall_design: TRIUMPH patients with TC-PALF were compared to healthy children and disease controls utilizing multiparameter flow cytometry and 3’ single cell RNA sequencing from peripheral blood mononuclear cells. TC-PALF patient serum was compared to healthy children and those with PALF from other causes utilizing the Olink Inflammation I 384 protein assay. Two distinct endotypes of TC-PALF were identified which differed in flow cytometry CD8+ Perforin1 (Prf) expression and liver biopsy staining of Prf. TC-PALF patients with high CD8+ Prf (TC-PALF High Prf) had monocytosis, with a unique circulating CD8 IFNg+ Trm and IFNg-responsive CD14/CD16 monocyte ligand-receptor interaction. TC-PALF patients with normal CD8+ Prf expression had hypergammaglobulinemia, increase in class switched B-cells, and decrease in serum inflammatory proteins associated with myeloid activation

first: Tamir

last: Diamond

first: Catherine

last: Chapin

first: Caroline

last: Diorio

first: Sarah

last: McCuaig

last: Lau

first: Niansheng

last: Chu

first: Nora

last: Gibson

first: Portia

last: Kreiger

first: Kathleen

last: Loomes

first: Estella

last: Alonso

first: Edward

last: Behrens


title: Casein kinase 1δ/ε inhibition suppresses CLL through cell-intrinsic and microenvironmental mechanisms [RNA-Seq]

city: Brno

first: Vitezslav

last: Bryja

address: Kamenice 5

department: Department of Experimental Biology

country: Czech Republic

institute: Masaryk University

summary: Chronic lymphocytic leukemia (CLL) is a consequence of pathological B cell accumulation in blood and lymphoid organs. Due to high refractoriness, CLL is considered incurable which calls for novel therapeutic options. Previously, we showed casein kinase 1δ/ε (CK1δ/ε) inhibition prolonged survival of Eµ-TCL1 mice with CLL-like disease. Herein, we elucidate mechanisms mediating CK1δ/ε inhibition efficacy in CLL suppression. Using in vivo Eµ-TCL1 adoptive transfer (AT) model, we showed CK1δ/ε inhibition mediated cell cycle  slowdown and CLL cell accumulation at S/G2 interface. This observation was validated using multiple CLL cell lines and EdU/Click-iT reaction applied in vivo. Furthermore, we showed CK1δ/ε inhibition led to T cell decrease in lymph nodes (LN). Using system mimicking LN microenvironment in vitro, we observed CK1δ/ε inhibition triggered downregulation of nuclear factor κ B (NFκB) pathway that acts downstream of T-cell-mediated CD40L:CD40 stimulus, inducing CLL cell proliferation. Finally, we showed CK1δ/ε inhibition counteracted proliferation of CLL cells from wide range of patients, with lower efficacy only in patients bearing TP53 defects.

overall_design: RNA-seq profiling of CLL cells cultured in presence/absence of M2-10B4 cells and CK1 inhibitor PF-670462 (10 uM) for 6 hours.

first: Antonia

last: Mikulova

first: Hana

last: Plesingerova

first: Michaela

last: Chorvatova

first: Pavlina

last: Kebkova

first: Jana

last: Bartosikova

first: Petra

last: Prochazkova

first: Jan

last: Verner

first: Dominik

last: Mulidran

first: Stepan

last: Cada

first: Olga

last: Vondalova-Blanarova

first: Nela

last: Kolcakova

first: Tomas

last: Loja

first: Terezia

last: Kurucova

first: Eva

last: Hoferkova

first: Boris

last: Tichy

last: Kotaskova

first: Marek

last: Mraz

first: Lukas

last: Kubala

last: Janovska


title: Casein kinase 1δ/ε inhibition suppresses CLL through cell-intrinsic and microenvironmental mechanisms

first: Vitezslav

last: Bryja

overall_design: RNAseq profiling of sorted splenic CLL cells from Eµ-TCL1 adoptive transfer experiment combined with daily peroral treatment with 10% kolliphor/PBS (CTRL) or with CK1 inhibitor, 50 mg/kg PF-670462, dilluted in 10% kolliphor/PBS (CK1i) that the mice underwent for in total 8 weeks

first: Antonia

last: Mikulova

last: Plesingerova

last: Chorvatova


title: A tissue-intrinsic mechanism sensitizes HIV-1 particles for TLR-triggered innate immune responses

city: Heidelberg

first: Oliver

middle: Till

last: Fackler

address: Im Neuenheimer Feld 344

department: CIID

institute: Universityhospital Heidelberg

summary: In vivo, HIV-1 replicates within tissues, yet the impact of three-dimensional (3D) environments on viral spread remains poorly understood. We previously showed that collagen-rich 3D extracellular matrix (ECM) imposes an Environmental Restriction to cell-free Virus Infectivity (ERVI). Here, we demonstrate that ERVI is mediated by adhesive ECM components assembled into tissue-like scaffolds. Transient interactions with collagen fibers rapidly diminish virion infectivity across diverse primary strains by impairing virus fusogenicity. Notably, collagen-experienced particles also induce a distinct antiviral transcriptional program and strong pro-inflammatory cytokine secretion in monocyte-derived macrophages. Mechanistically, collagen contact induces conformational changes in the viral glycoprotein Env, enhances its interaction with toll-like receptor 2 (TLR2), and promotes trafficking into TLR8-positive endosomes, thereby amplifying innate immune sensing. Thus, ERVI acts through a dual mechanism: reducing virion fusogenicity while increasing innate immune detection. These findings identify the biophysical properties of the ECM as a tissue-intrinsic arm of antiviral innate immunity.

overall_design: RNAseq profiling of human monocyte derived macrophages (MDMs) from 3 healthy donors after challenge with HIV-1 virions derived from suspension or collagen cultures, for 6 or 24h. Mock and LPS treated MDMs were harvested at t=24h.

first: Samy

last: Sid Ahmed


title: Foxp3 and BATF cooperatively direct cis-regulatory programs and gene expression for effector Treg cell differentiation [CUT&Tag]

city: Hongo, Bunkyo-ku

first: Ryuichi

last: Murakami

department: Graduate School of Pharmaceutical Sciences

institute: The University of Tokyo

summary: Mechanisms by which diverse transcription factors (TFs), particularly the master regulator Foxp3, shape the heterogeneous transcriptional and epigenetic landscape of regulatory T (Treg) cells remain poorly understood. Here, we discovered that Foxp3 cooperates with BATF to direct cis-regulatory programs and gene expression essential for differentiation of immunosuppressive effector Treg (eTreg) cells. Simultaneous single-cell chromatin accessibility and transcriptome profiling, combined with topic modeling, identified cis-regulatory elements and associated programs jointly regulated by these TFs in eTreg cells. Genome-wide mapping of Treg cell-specific BATF and eTreg cell-specific Foxp3 binding sites revealed their co-binding at some of these cis-elements, synergistically enhancing accessibility and transcription. Furthermore, we provide evidence that Foxp3 interacts with specific TFs to orchestrate diverse cis-regulatory programs among Treg cell differentiation states. Thus, Foxp3 serves as a master, but context-dependent regulator, cooperating with other TFs, including BATF, to shape the heterogeneous cis-regulatory and transcriptional landscape critical for functional Treg cell differentiation.

overall_design: Genome binding/occupancy profiling by high throughput sequencing

first: Suzu

last: Kawagoe

first: Shohei

last: Hori


title: Single cell landscape of MBL/CLL transition [MBL_CLL_GEO_DataSet3]

city: Berlin

first: Livius

last: Penter

address: Augustenburger Platz

institute: Charité - Universitätsmedizin Berlin

summary: The transition of monoclonal B cell lymphocytosis (MBL) to chronic lymphocytic leukemia (CLL) remains ill-defined at the epigenetic and transcriptional level. Here, we performed single cell RNA and ATAC sequencing of low-count (LC) and high-count (HC) MBL and CLL blood samples to track the continuum from physiologic B cells to CLL.

overall_design: Single cell RNA and ATAC sequencing was performed on single cell suspensions after ficoll density centrifugation using 5' RNA and v2 ATAC chemistry (10x Genomics). Total-seq A staining was performed to capture surface marker expression in select cases. BCR sequencing was performed using the V(D)J kit.

first: Catherine

middle: J

last: Wu


title: H3K9me3 controls epidermis development by repressing RNA Pol II activity on key promoters and enhancers

city: Ithaca

first: Chris

middle: Ke

last: Bai

state: NY

address: 526 Campus Rd

department: MBG

institute: Cornell University

summary: Histone H3K9me3 silences repetitive elements and represses non-lineage genes during early development, but its role in organogenesis is understudied. Here, we show that H3K9me3 deposition is dynamic during epidermis morphogenesis and essential for lineage diversification. We ablate Suv39h1, Suv39h2, and Setdb1 histone methyltransferases, in the embryonic mouse epidermis, to induce H3K9me3 loss. This causes complete failure of keratinocyte differentiation, skin barrier formation, hair follicle development, and Merkel cell specification. Single-cell transcriptomics reveals aberrant cell fates with mixed epidermal subtype identities and dysregulated non-lineage and lineage-specific transcription programs. Affected pathways include differentiation, metabolism, cell cycle, cytoskeletal organization, and extracellular matrix. H3K9me3 primarily restricts RNA Pol II transcription initiation at key developmental promoters and enhancers and has minimal direct effect on promoter-proximal pause release. We uncover a cooperative and indispensable role for Suv39h1, Suv39h2, and Setdb1 in gene expression control of epidermal morphogenesis, establishing H3K9me3 as a critical developmental determinant of skin organogenesis.

overall_design: Refer to individual Series


title: Transcription factor codes patterning neuronal groundplans of the cerebrum

city: Ann Arbor

first: Eleanor

middle: Josephine

last: Clowney

address: 1105 N University Ave

department: MCDB

institute: University of Michigan

summary: Brain regions that regulate motivated behaviors, including the vertebrate hypothalamus and arthropod cerebrum, house bespoke neural circuits dedicated to perceptual and internal regulation of many behavioral states. These circuits are built to purpose from complex sets of cell types whose patterning has been challenging to elucidate. Here, we developed methods in Drosophila melanogaster to embed well-studied neurons that regulate mating in the transcriptional contexts of the neuronal lineages that generate them. By comparing transcription within and between lineages, we identified a large set of transcription factors expressed in complex combinations that delineate cerebral hemilineages – classes of postmitotic neurons born from the same stem cell and sharing Notch status. Hemilineages comprise the major anatomic classes in the cerebrum and these transcription factors are required to generate their gross features. We show that subtypes of the same hemilineage can provide a common computational module to circuits regulating different drives, and identify an orthogonal set of transcription factors that stratify hemilineage subtypes of differing birth order. Our findings suggest that distinct sets of transcription factors operate in a hierarchical system to build, diversify, and sexually differentiate lineally-related neurons that compose motivated behaviors circuits. By linking developmental patterning to separable transcriptional axes that produce gross versus fine aspects of information flow, we provide a logical framework for cerebral control of diverse drives.

overall_design: Drosophila melanogaster neuronal lineages were isolated using fluorescence-activated cell sorting (FACS) and analyzed by scRNA-seq at two distinct developmental time points with and without an apoptotic block.

first: Najia

last: Elkahlah


title: Single cell landscape of MBL/CLL transition [MBL_CLL_GEO_DataSet2]


title: Functional interaction of Epidermal growth factor and Angiotensin II in female human primary vascular smooth muscle cells

city: Halle (Saale)

first: Virginie

last: Dubourg

address: Magdeburger Str. 6

department: Julius Bernstein Institute for Physiology

institute: Martin Luther University - Halle-Wittenberg

summary: RNAsequencing was performed for human primary aortic (HAoSMC) and cornary artery (HCASMC) smooth muscle cells from female donors after incubation with Epidermal Growth Factor and/or Angiotensin II, in order to investigate the functional interaction of these two pathways

overall_design: HAoSMC and HCASMC were incubated for 48h with 10 µg/L EGF or/and 10 nM Angiotensin II (N=11)

first: Michael

last: Gekle

last: Kopf

first: Sigrid

last: Mildenberger


title: SNP-array analysis in pediatric and adult T-cell lymphoblastic neoplasia

city: Muenster

first: Birgit

last: Burkhardt

address: Albert-Schweitzer-Campus 1

department: Pediatric Hematology and Oncology and NHL-BFM study center

institute: University Hospital Muenster

summary: Illumina Infinium whole genome genotyping (WGG) arrays are increasingly being applied in cancer genomics to study gene copy number alterations and allele-specific aberrations such as loss-of-heterozygosity (LOH). Methods developed for normalization of WGG arrays have mostly focused on diploid, normal samples. However, for cancer samples genomic aberrations may confound normalization and data interpretation. Therefore, we examined the effects of the conventionally used normalization method for Illumina Infinium arrays when applied to cancer samples.

overall_design: To investigate the effects of a quantile normalization of Illumina Infinium data, compared to conventional normalization using BeadStudio (www.illumina.com), we renormalized 535 individual hybridizations conducted on Illumina 300K, 370K and 550K BeadChips. Sample types included breast cancer, colon cancer, urothelial carcinoma, leukemia as well as normal blood and HapMap samples. This series includes the 6 breast cancers hybridized on Illumina HumanHap 550K BeadChips.

first: Sarah

last: Sandmann

first: Marcel

last: te Vrugt


title: ZNF274 constrains lineage plasticity and drives intrinsic resistance to CDK7 inhibitors in pancreatic cancer

city: Seattle

first: Sita

last: Kugel

state: WA

address: 1100 Fairview Ave N

department: Human Biology

institute: Fred Hutch Cancer Center

summary: Pancreatic Ductal Adenocarcinoma (PDAC) is characterized by two distinct transcriptional subtypes: classical and basal, which may interconvert. We show the KRAB-ZNF protein, ZNF274, correlates with PDAC subtype and regulates sensitivity to CDK7 inhibition by facilitating heterochromatin maintenance and gene suppression. We find ZNF274 loss drives a classical to basal transition, induces invasive protrusions and facilitates invasion capacity. We define two mechanistic arms to this regulation.  ZNF274 directly suppresses ZEB1 expression. When ZNF274 is lost, ZEB1 facilitates acquisition of mesenchymal features, keratin gene expression, and susceptibility to CDK7 inhibition. Second, ZNF274 dampens expression of repetitive elements including human endogenous retroviruses (HERVs). HERV expression following ZNF274 loss induces a double stranded RNA response that reinforces the classical to basal subtype transition. Here, we show ZNF274 is an important epigenetic regulator of cellular plasticity and sensitivity to CDK7 inhibition, presenting a therapeutic liability of PDAC subtype transition that is actionable in the clinic.

overall_design: This dataset comprises RNA-seq and CUT&RUN experiments investigating the transcriptional and epigenomic role of ZNF274 in pancreatic cancer cell lines. RNA-seq was performed following transient siRNA-mediated knockdown of ZNF274 in ASPC1 and CFPAC1 cells, alongside 5 µM AZA or DMSO treatment. Additionally, ZNF274 overexpression was performed in Panc3.27 cells, which express low endogenous ZNF274. CUT&RUN profiling of ZNF274 and H3K9me3 was performed in ASPC1 cells following stable shRNA-mediated knockdown of ZNF274, with IgG as a negative control. All conditions were performed in biological triplicate.

first: Jessica

middle: E

last: Gianopulos

first: Aidan

last: Schutter

first: Stephanie

last: Dobersch

first: Adrianne

last: Wallace-Povirk

first: Sophie

last: Kogut

first: Andrea

last: Doak

first: Pritha

last: Chanana

first: Sabrina

last: Ge

first: Luke

last: Mangino

first: Naomi

last: Yamamoto

first: Liberalis

last: Boila

first: Monica

last: Padilla-Galvez

first: Justin

last: Hui

first: Nicole

last: Rhoads

first: Robert

last: Gifford

first: Kevin

last: Cheung

first: Daniel

last: Blanco Melo

first: Faiyaz

last: Notta


title: Plasma proteomics and single cell RNAseq identify cellular and soluble mechanisms of graft rejection after HSCT

first: Stella

last: Davies

address: 3333 Burnet Ave

department: Cancer & Blood Disease Institute

institute: Cincinnati Children's Hospital

summary: Interferon, TNF and ferroptosis pathway activation occurs in graft rejection and merit further study as biomarkers/therapeutic targets. Recipient NK cells and T-cells increase during graft rejection, suggesting these recipient cells are the primary drivers of rejection.

overall_design: Human patient peripheral blood mononuclear cells (PBMCs) from a graft rejection patient were previously isolated using a ficoll gradient and then cryopreserved at -150C. Cells were then thawed rapidly at 37C, washed with PBS and single cell RNAseq was performed comparing the PBMCs at the time of rejection to a prior timepoint after initial engraftment.


title: Single cell landscape of MBL/CLL transition [MBL_CLL_GEO_DataSet1]

first: Livius

last: Penter

first: Catherine

last: Wu


title: Foxp3 and BATF cooperatively direct cis-regulatory programs and gene expression for effector Treg cell differentiation [scMultiome]

first: Ryuichi

last: Murakami

overall_design: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

first: Shohei

last: Hori


title: Cancer agnostic potential of CAR T cells targeting the urokinase plasminogen activator receptor

city: New York

first: Yu-Jui

last: Ho

address: 1275 York Avenue

institute: Memorial Sloan Kettering Cancer Center

summary: Chimeric Antigen Receptor (CAR) T cells have demonstrated transformative efficacy in hematologic malignancies and have shown promise in non-cancer contexts such as autoimmune diseases. We previously identified the urokinase plasminogen activator receptor (uPAR) as a cell-surface protein expressed on subsets of myeloid cells and broadly upregulated in senescent states. Murine uPAR-targeting CAR T cells can ameliorate fibrosis and prophylactically prevent metabolic syndrome in aged mice, paving the way for their use in senescence-driven pathologies. uPAR can also be expressed at high levels in cancer and, by performing a pan-cancer analysis, we now show that subsets of most tumor types display strong uPAR expression, which correlates with an epithelial-mesenchymal transition (EMT)-like state, increased fibrosis, metastasis, and poor patient outcomes. Single-cell and spatial analyses revealed that tumors with high uPAR expression in tumor cells often harbor senescent-like, uPAR-positive stromal cells, typically subsets of fibroblasts and macrophages. In mouse models, CAR T cells with uPAR-targeting single-chain variable fragments (scFvs) showed potent and persistent efficacy against multiple tumor types. In the context of high-grade serous ovarian cancer, adjuvant CAR T cell treatment following primary tumor debulking surgery cured mice by eliminating distal organ metastases. uPAR CAR T cells were well-tolerated, demonstrating efficacy in syngeneic and humanized immune system models without significant disruption of the myeloid compartment. Beyond direct tumor targeting, uPAR facilitated non-invasive cancer monitoring via soluble uPAR and PET imaging. Senescence-inducing therapies further enhanced uPAR expression and showed combinatorial activity with uPAR CAR T cells. These findings establish uPAR CAR T cells as a cancer-agnostic therapeutic strategy with a favorable safety profile and clear clinical potential in oncology, including solid tumors harboring a fibrotic tumor microenvironment linked to accumulation of senescent stromal cells.

overall_design: Spatial transcriptomic using Xenium (10X) of treatment naïve human PDAC (n=1)

first: Zeda

last: Zhang

first: Elif

last: Ozcelik

first: Yu-jui

first: Jose

last: Reyes

first: Aveline

last: Filliol

first: Scott

last: Lowe


title: Autism-like phenotypes and increased NMDAR2D expression in mice with KDM5B histone lysine demethylase deficiency

city: London

first: Leticia

last: Perez Sisques

address: Great Maze Pond

department: Centre for Craniofacial and Regenerative Biology

institute: King's College London

summary: Loss-of-function mutations in genes encoding lysine demethylases specific for trimethylated lysine 4 of histone 3 (H3K4me3) are associated with neurodevelopmental conditions, including autism spectrum disorder (ASD) and intellectual disability. To study the role of KDM5B (Lysine DeMethylase-5B)-mediated H3K4me3 demethylation, we investigated neurodevelopmental phenotypes in mice without KDM5B demethylase activity. These mice exhibited autism-like behaviours and increased brain size. H3K4me3 levels and the expression of neurodevelopmental genes were increased in the developing Kdm5b mutant neocortex. Increased H3K4me3 levels at the promoter and associated expression of the Grin2d gene was associated with increased levels of NMDAR2D protein in synaptosomes isolated from the early postnatal Kdm5b-deficient neocortex. Treating mice with the NMDAR antagonist memantine rescued deficits in ultrasonic vocalizations. These findings suggest that increased H3K4me3 levels and associated Grin2d gene upregulation disrupt brain development and function, leading to socio-communication deficits and identify a potential therapeutic target for neurodevelopmental disorders associated with KDM5B deficiency.

overall_design: Total RNA was extracted using Trizol Reagent. RNA was next purified with the Monarch total RNA miniprep kit (New England Biolabs) following manufacturer’s instructions, including the DNAse step. Cortical mRNA profiles of WT and Kdm5b ΔARID/ΔARID mice at postnatal day 5 were generated by sequencing on the Illumina Hiseq 6000.

last: Perez-Sisques

first: Shail

last: Bhatt

first: Angela

last: Caruso

first: Josephine

middle: L

last: Robb

first: Alex

last: A Donovan

first: Rosemary

last: Bamford

first: Alejo

last: Torres-Cano

first: Soshana

last: Spring

first: Eleanor

last: Hendy

first: Talia

last: Gileadi

first: Martyna

last: Panasiuk

first: Jed

last: Trengove

first: Neeru

last: Jindal

first: Mohi

last: Ahmed

first: Mara

last: Sabbioni

first: Joyce

last: Taylor-Papadimitriou

first: Diana

last: Cash

first: Nicholas

last: Clifton

first: Jacob

last: Ellegood

first: Laura

middle: C

last: Andreae

first: Jason

last: Lerch

first: Maria Luisa

last: Scattoni

first: K Peter

last: Giese

first: Cathy

last: Fernandes

first: M Albert

last: Basson


title: Foxp3 and BATF cooperatively direct cis-regulatory programs and gene expression for effector Treg cell differentiation [ATAC-Seq]

first: Ryuichi

last: Murakami

first: Norihito

last: Hayatsu

first: Suzu

last: Kawagoe

first: Shohei

last: Hori


title: Spatial Transcriptomics of  human hepatocellular cancer

city: Birmingham

first: Shishir

last: Shetty

state: West Midlands

address: 5th Floor IBR, Medical School, University of Birmingham

institute: University of Birmingham

summary:
Background: Immune checkpoint inhibition is now standard of care for patients with advanced hepatocellular cancer (HCC) and yet many patients remain resistant to this therapy. The presence of innate immune populations in the tumour microenvironment (TME) have been implicated in regulating the efficacy of these agents. CLEC14A has previously been shown to be upregulated on tumour endothelial cells and we found endothelial upregulation of CLEC14A in a subset of HCC tumours as well as acute liver injuries.  This led us to explore the role of CLEC14A in neutrophil recruitment, critical populations in both liver pathologies.
Methods:Immunohistochemical analysis was undertaken of CLEC14A in human liver tissue across a range of liver diseases and HCC. CLEC14A regulation and function was then explored in primary human liver endothelial cells including responses to shear stress and flow based adhesion assays. Liver injury models were undertaken CLEC14A knockout mice followed by intravital microscopy. Finally, CLEC14A expression was studied in both publically available HCC data sets and through spatial transcriptomics of HCC tissue.
Findings:We found that CLEC14A mediates neutrophil recruitment across liver endothelium in both in vitro and in vivo settings. This process appears to be independent of its interaction with its known ligand Multimerin-2. Additionally, we demonstrated a correlation of CLEC14A expression in human HCC with a neutrophil transcriptional signature.
Interpretation:This study unveils a new link between a tumour angiogenic receptor and neutrophil infiltration to the liver and highlights the potential of combining current immunotherapy in HCC with agents targeting the CLEC14A pathway.

overall_design: A cohort of surgically resected hepatocellular cancers paraffin embedded samples were analyzed for CLEC14A expression by immunohistochemistry,  six cases were selected with strong vascular staining of CLEC14A and six cases were selected with low vascular staining of CLEC14A.  Further sections were taken from these samples and underwent digital spatial profilng by Nanostring GeoMx.

first: Joanne

last: O'Rourke

first: Daniel

last: Patten

first: Dean

last: Kavanagh

first: Catherine

last: Willoughby

first: Josep

last: Llovet

first: Helen

last: Reeves

first: Peter

last: Hewett

first: Neena

last: Kalia

first: Tahir

last: Shah

first: Yuk

middle: T

last: Ma

first: Kelly

last: Hunter

first: Jack

last: McMurray

first: Joe

last: Flint

first: Owen

last: Cain

first: Derek

last: Mann

first: Amy

last: Naylor

first: Victoria

last: Heath

first: Roy

last: Bicknell

first: Fabian

last: Spill

first: Kylie

last: Savoye

first: Kaiyi

last: Yang


title: Foxp3 and BATF cooperatively direct cis-regulatory programs and gene expression for effector Treg cell differentiation [ChIP-Seq]

first: Ryuichi

last: Murakami

first: Norihito

last: Hayatsu

first: Shohei

last: Hori


title: Mitochondrial remodeling in skeletal muscle underlies exercise-induced reversal of age-associated functional decline in mice and humans

status: Public on Mar 30 2026

city: Madrid

first: Jose

middle: Luis

last: Cabrera

state: Madrid

address: Melchor Fernández Almagro, 3

institute: CNIC

summary: RNA-seq experiment to investigate the effect of training on muscle tissue in WT C57BL/6J and G6PD-tg mice. The goal of the study is to assess differential gene expression related to genotype and training status.

overall_design: A total of 40 samples were collected under trained or non-trained conditions. RNA-seq libraries were prepared from 50 ng total RNA using the NEBNext Ultra II Directional kit, including poly(A)+ selection, fragmentation, cDNA synthesis, adaptor ligation, and PCR amplification.  Sequencing was performed on a NextSeq 2000 (Illumina) platform.

first: Esther

last: García-Domínguez

first: José

last: Enríquez

first: María

last: Gómez-Cabrera