title: Impact of PD-L1 overexpression on immune checkpoint inhibitor efficacy in triple-negative breast cancer using a 4T1 murine model.

city: Seoul

first: Ju Hee

last: Kim

address: 71, Daehak-ro

institute: Seoul National University Hospital

summary: Bulk RNA sequencing was performed to investigate transcriptomic changes in 4T1 tumors treated with anti-PD-L1 therapy. Tumors were derived from 4T1 control and PD-L1-overexpressing cells injected into mice, followed by IgG or anti-PD-L1 treatment. Gene expression analysis revealed distinct immune-related pathway alterations, with reduced immune activation in PD-L1-overexpressing tumors. Differentially expressed genes suggested an immunosuppressive tumor microenvironment, potentially contributing to resistance to anti-PD-L1 therapy. These findings provide insights into the molecular mechanisms underlying immune checkpoint inhibitor response in triple-negative breast cancer.

overall_design: Syngeneic mouse models were established by injecting 1 × 10⁵ control 4T1 or PD-L1-overexpressing 4T1 cells into the mammary fat pad of BALB/c mice. Tumor-bearing mice were treated twice weekly with either IgG (150 µg/100 µL) or anti-PD-L1 inhibitor (BP0101; 150 µg/100 µL) via intraperitoneal injection. Tumor growth was monitored using digital calipers, and the study concluded after three treatment sessions (17 days in total). Tumors were harvested post-euthanasia and subjected to bulk RNA sequencing to analyze transcriptional changes associated with PD-L1 overexpression and anti-PD-L1 therapy. This study aimed to identify immune-related gene expression differences contributing to treatment response.

first: A Young

last: Park

first: Sangeun

last: Lee

first: Hong Kyu

first: Han-Byoel

first: Wonshik

last: Han


title: Atlantic salmon scale explants in bacteria-host interaction studies: in vitro challenge model.

status: Public on Mar 30 2025

city: Ås

first: Aleksei

last: Krasnov

state: Viken

address: Øreveien, 47B

country: Norway

institute: Nofima AS

summary: Atlantic salmon scale explants is a promising model for bacterial challenges. Exposure to pathogens (Moritella viscosa and Tenacibaculum finnmarkense) and commensal bacteria consistently upregulated a suite of immune genes in a dose response manner. This panel includes chemokines, cytokines, genes involved in eicosanoid metabolism, and both humoral and cellular effectors. The prevalence of genes related to signaling and communication suggests that salmon scales function as sentinels, mobilizing immune responses upon encountering bacteria. While common immune responses were evident across all trials, scales also revealed differences between bacterial species. Combining commensal bacteria with M. viscosa enhanced responses to pathogens, and differences were observed between M. viscosa and T. finnmarkense. The effects of commensal bacteria varied in magnitude. Exposed cells showed changes in morphology and increased iNOS expression.

overall_design: The data set includes four experiments with similar setup. Cultures of scale explants were exposed to pathogenic or commensal bacteria in marine broth medium (or only medium in controls) for 2h. The cell culture medium was thereafter removed, scale explants were washed twice and replaced with fresh medium including antibiotics. Cells were harvested 24 hours post-exposure.

first: A

last: Johny

first: C

last: Karlsen


title: TDP-43 seeding induces cytoplasmic aggregation heterogeneity and nuclear loss-of-function of TDP-43

status: Public on Mar 28 2025

city: Leuven

first: Kristofer

middle: James

last: Davie

address: Herestraat 49

department: Center for Brain and Disease Research

country: Belgium

institute: Vlaams Instituut voor Biotechnologie

type: Expression profiling by high throughput sequencing

summary: Cytoplasmic aggregation and nuclear depletion of TDP-43 are hallmarks of several age-related neurodegenerative disorders. Yet, recapitulating both features in cellular systems has been a major challenge. Here, we produced amyloid-like fibrils from the recombinant low-complexity-domain of TDP-43, and demonstrate that sonicated fibrils trigger TDP-43 pathology in human cell lines and iPSC-derived neurons. Fibril-induced cytoplasmic TDP-43 inclusions acquire distinct biophysical properties, recapitulate pathological hallmarks such as phosphorylation, ubiquitin- and p62-accumulation, and recruit nuclear endogenous TDP-43 leading to nuclear-loss-of-function-driven disease-specific cryptic splicing defects. Cytoplasmic TDP-43 aggregates exhibit, with time, distinct heterogeneous morphologies as in patients including compacted, filamentous or fragmented, through the activation of cellular protein clearance pathways. Cell-specific progressive toxicity is provoked by seeded TDP-43 pathology in human neurons. These findings identify templated aggregation of TDP-43 as a key mechanism driving both cytoplasmic gain- and nuclear-loss-of-function, offering a valuable approach to identify modifiers of sporadic TDP-43 proteinopathies.

overall_design: TDP-43-mNLS-Clover expressing U2OS cells (doxycycline induced) were transfected with fibril seeds produced from recombinant TDP-43 LCD (50nM) to induce TDP-43 aggregation. In control conditions, TDP-43-mNLS-Clover expressing U2OS cells were mock transfected with protein storage buffer. Each transfection reaction was performed in triplicates, serving as 3 independent biological replicates. 48 hours after fibril (or control) transfection, cells were collected and image-based FACS sorting was performed using FACSDiscover S8 to isolate cells with TDP-43-Clover aggregates (from fibril transfected condition) or cells with diffuse TDP-43-Clover (from mock transfected condition). FACS-purified cell populations (aggregates vs no_aggregates) were subsequently processed for RNA-Seq.

first: Jens

last: Rummens

first: Bilal

last: Khalil

first: Günseli

last: Yıldırım

first: Pedro

last: Silva

first: Valentina

last: Zorzini

first: Nicolas

last: Peredo

first: Marta

last: Wojno

first: Meine

last: Ramakers

first: Ludo

last: Van Den Bosch

first: Philip

last: Van Damme

first: Jelle

last: Hendrix

first: Frederic

last: Rousseau

first: Joost

last: Schymkowitz

first: Sandrine

last: Da Cruz


title: The malignant trajectory from the notochord to chordoma and the role of the TBXT rs2305089 germline single nucleotide polymorphism

city: London

first: Lucia

last: Cottone

address: 72 Huntley Street

country: United Kingdom

institute: UCL Cancer Institute

summary: The rare bone cancer chordoma and its putative precursor the Benign Notochordal Cell Tumor (BNCT) express the notochordal transcription factor, TBXT. The aim of this study was to elucidate the role of rs2305089 germline single nucleotide polymorphism in TBXT in the pathogenesis of chordoma. A radiological and genotyping association study demonstrated that BNCTs are associated with chordomas (P<0.001) and with the rs2305089 polymorphism (P=0.002). We then engineered mesoderm/notochord models which differed only by their rs2305089 genotype. Expression of TBXT was higher and the gene regulatory network activated by TBXT was enriched in heterozygous compared to wild type cell lines. Heterozygous cell lines displayed enrichment of Wnt/beta-catenin and epithelial mesenchymal transition pathways while wild type cell lines were enriched for metabolic pathways and MTORC1 signalling. Moreover, the variant A allele induced faster cell migratory capacity together with changes in the expression of endoplasmic reticulum and intracellular transport mediators, thus suggesting that rs2305089 regulates notochord vacuoles as lysosome-related organelles in the aberrant regression of the notochord. In conclusion, we show for the first time that the rs2305089 variant allele is associated not only with chordoma but also with the BNCT and provide functional evidence that this SNP regulates notochordal cell differentiation in the pathogeneis of BNCTs and chordomas.

overall_design: Six cell lines which differed only by their genotype at the rs2305089 locus were engineered using CRISPR homology directed repair: three heterozygous (labelled 463N1-3) and three wild type/unedited cell lines (labelled 4610N1-3). Induced pluripotent stem cells were differentiated into mesoderm by 48 hours and mesenchymal stem cells (MSC) by 72 hours.

first: Inga

last: Usher

first: Adrienne

middle: M

last: Flanagan


title: T:B cell cooperation in ectopic lymphoid follicles propagates CNS autoimmunity

city: Planegg

first: Anneli

last: Peters

address: Großhaderner Str. 9

country: Germany

institute: Institute for Clinical Neuroimmunology, Biomedical Center, University Hospital of the Ludwig-Maximilians University Munich

summary: Meningeal ectopic lymphoid follicle (eLF)-like structures have been described in multiple sclerosis, but their role in central nervous system (CNS) autoimmunity is unclear. Here, we used a T helper 17 (TH17) adoptive transfer experimental autoimmune encephalomyelitis model featuring formation of eLFs. Single-cell RNA sequencing revealed that clusters of activated B cells and B1/marginal zone-like B cells were overrepresented in the CNS and identified B cells poised for undergoing germinal center reactions and clonal expansion in the CNS. Using intravital imaging to directly visualize TH17-B cell interactions, we demonstrated that T and B cells form long-lasting antigen-specific contacts in meningeal eLFs that result in reactivation of autoreactive T cells. CNS T cells depended on CNS B cells to maintain a proinflammatory cytokine profile. Our study reveals that extensive T-B cell cooperation occurs in meningeal eLFs, promoting both B cell differentiation and T cell reactivation, and may thereby propagate smoldering inflammation in the CNS.

overall_design: For each mouse, B cells from CNS, spleen and cLNs were pooled (90.000 B cells in total), centrifuged and, after a washing step, resuspended in PBS containing 0.04 % BSA at a concentration of 1000 cells/μl. The viability of cells was confirmed by staining with trypan blue solution. Further processing of samples was performed using the 10x Chromium Single Cell 5` Solution (Chromium Next GEM Single Cell V(D)J v1.1 with Feature Barcoding Technology for Cell Surface Protein, 10x Genomics) according to the manufacturer`s instructions. Prior to loading on the chip, 5000 cells of each compartment were labeled with anti-mouse hashtag oligonucleotide (HTO) antibodies (TotalSeq™-C0301/C0302/C0303, Biolegend) and pooled together. cDNA libraries were pooled and send for sequencing. scRNA-seq and scBCR-seq libraries were sequenced on NovaSeq S4 Flowcells using 150-bp paired-end reads and 8 bp for the i7 index, aiming for 50,000 reads per cell for gene expression and 5,000 reads per cell for BCR enrichment. Cell hashing libraries were sequenced on NovaSeq S1 Flowcells using 50-bp paired-end reads and 8 bp for the i7 index, aiming for 10,000 reads per cell.

first: Kolz

last: Anna

first: de la Rosa

last: Clara

first: Kavaka

last: Vladislav

first: Beltran

last: Eduardo

first: Peters

last: Anneli


title: Cardiac sympathetic denervation mitigated ischemic cardiomyopathy progression in a rat model of sleep apnea.

city: Grenoble

first: Florent

last: Chuffart

state: La Tronche

address: Site Santé - Allée des Alpes

country: France

institute: IAB - INSERM (U1209) - CNRS (UMR5309)

summary: Aims Ischemic cardiomyopathy with comorbid sleep apnea syndrome (SAS) is associated with worse long-term outcomes. Intermittent hypoxia (IH), a key feature of SAS, exacerbates sympathetic activity, hastening cardiac dysfunction and remodeling in ischemic cardiomyopathy rat models. This study explores whether targeted cardiac sympathetic denervation (CSD) can limit IH-induced progression of ischemic cardiomyopathy.  Methods and results Male Wistar rats underwent myocardial infarction (MI) via permanent left coronary artery ligation, and CSD was simultaneously achieved through ablation of the left middle cervical and stellate ganglions. Rats were exposed to IH (21–5% fraction of inspired O2, 60 s cycle, 8 h/day) or normoxia (N) for 14 weeks starting 3 days post-surgery. Throughout the intervention period, cardiac sympathetic activity was assessed using spectral analysis of heart rate variability (HRV) from vigil ECG collected with a specialized jacket. Cardiac function and remodeling were monitored via echocardiography. Additionally, isolated cardiomyocytes from rats exposed to IH or N for 6 weeks were assessed for calcium transient, sarcomere shortening and adrenergic reserve using isoproterenol stimulation (100 nM). CSD reduced cardiac sympathetic activity and prevented IH-induced blunting of cardiomyocyte response to isoproterenol challenge. In hypoxic animals, CSD reduced alterations in long-term ejection fraction and mitigated cardiomyocyte hypertrophy. Transcriptomic analysis unveiled that CSD triggered biological processes related to cardiac repair and regeneration. Immunohistochemistry further supported these findings, demonstrating increased cardiomyocyte proliferation in the hypoxic group, as indicated by elevated Ki67 expression colocalized with MF20 markers.  Conclusions Our data demonstrate that cardiac sympathetic denervation prevents IH-induced depletion of cardiac adrenergic reserve and deterioration of cardiac function in a rat model of ischemic cardiomyopathy. This study questions the role of sympathetic activity and hypoxia in cardiac regeneration and on the optimal management of sympathetic hyperactivity in ischemic cardiomyopathy in the specific context of associated SAS.

overall_design: Male Wistar rats were submitted to myocardial infarction (MI) and cardiac sympathetic denervation (CSD) or sham surgery. After 3-day recovery, rats were randomly exposed to intermittent hypoxia (IH) or normoxia (N) for 14 weeks. Randomization was adjusted to form homogeneous groups based on baseline ejection fraction. Animals were exposed daily to 8 consecutive hours of IH or N during their daytime sleep period. The IH stimulus was performed using a specifically designed device (HypE platform Grenoble), with alternating 30 s of hypoxia (5% fraction of inspired O2 (FiO2)) and 30 s of normoxia (21% FiO2). Normoxic rats were exposed to similar air streams to reproduce equivalent levels of noise and turbulence related to gas circulation. Then, we performed a transcriptomic analysis by RNA-seq on left ventricle heart in the remote area of the infarct.  Groups: Two surgical groups (MI CSD and MI Sham CSD) underwent two exposure conditions (N or HI) : - MI_NOC_NO = Myocardial infarction + Sham CSD + Normoxia (n = 5) - MI_NOC_IH =  Myocardial infarction + Sham CSD + Intermittent Hypoxia (n = 5) - MI_CSD_NO = Myocardial infarction + CSD + Normoxia (n = 5) - MI_CSD_IH =  Myocardial infarction + CSD + Intermittent Hypoxia (n = 5)

first: Maximin

last: Détrait

first: Claire

last: Arnaud

first: Jonathan

last: Gaucher


title: Placental Privilege: Evidence of Organ Resilience in severe COVID-19

city: Los Angeles

first: Suhas

middle: G

last: Kallapur

address: 10833 Le Conte Avenue

country: USA

institute: UCLA

summary: The blood of pregnant women affected by severe COVD-19 shows profound changes in immune cells. On the contrary, their placentas are relatively protected from severe perturbations.

overall_design:
We compared transcriptomics of maternal blood and placenta from COVID19+ (with different severity scores) and COVID19- pregnant women.

This study was supported by:

. K12 HD000849 (Yalda Afshar)
. The Burroughs Wellcome Fund (Yalda Afshar)

first: Pietro

last: Presicce

first: Morselli

last: Marco

first: Anhyo

last: Jeong

first: Marie

last: Altendhal

first: Guadalupe

last: Martinez

first: Giorgia

last: Del Vecchio

first: Sherin

last: Devaskar

first: Matteo

last: Pellegrini

first: Yalda

last: Afshar


title: An ER-anchored peptide C4orf3/ALN controls UCP1-independent Ca2+ cycling thermogenesis in adipose tissue

city: Boston

first: Masanori

last: Fujimoto

state: MA

address: Center for Life Sciences 3 Blackfan Circle, Room CLS730

department: Division of Endocrinology

institute: Beth Israel Deaconess Medical Center, Harvard Medical School

summary: Adipose tissue thermogenesis contributes to energy balance via mitochondrial uncoupling protein 1 (UCP1) and UCP1-independent pathways. Among UCP1-independent thermogenic mechanisms, one involves Ca2+ cycling via SERCA2b in subcutaneous adipose tissues; however, the molecular underpinnings of this process remain elusive. Here, we report that an ER-membrane anchored peptide C4orf3 (also known as anotherregulin, ALN) uncouples its Ca2+ transport from ATP-hydrolysis by interacting via the cytoplasmic domain, rendering the SERCA2b-C4orf3/ALN complex exothermic. Loss of C4orf3/ALN improved the energetic efficiency of SERCA2-dependent Ca2+ transport, thereby reducing adipose tissue thermogenesis and increasing the adiposity of mice. In turn, overexpression of C4orf3/ALN promotes Ca2+ cycling thermogenesis in the microsomal compartment. Of note, genetic depletion of C4orf3 led to compensatory activation of mitochondrial thermogenesis via UCP1 following cold challenge. We found that genetic loss of both C4orf3 and Ucp1 additively impaired cold tolerance in vivo. Together, this study uncovers the molecular mechanisms and the physiological role of UCP1-independent Ca2+ cycling thermogenesis in adipose tissue. This RNA-seq data set showed that double knockdown (DKO) of UCP1 and C4orf3/ALN increased lipid catabolism in adipose tissue.

overall_design: Wild type, UCP1 KO, C4orf3/ALN knockdown (ALN KD) and double knockout mouse (DKO) were exposed to cold for 5 h. Then RNA of white inguinal adipose tissue were isolated from each mouse, and subjected to RNA-seq.

first: Christopher

last: Auger

first: Shingo

last: Kajimura


title: Tumor-associated myeloid cells aid GBM infiltration by organizing invasion tracks via guidance receptor Plexin-B2

city: New York

first: Mary

middle: Elizabeth

last: Ughetta

state: NY

address: 1 Gustave L. Levy Pl

institute: Mount Sinai

summary: Glioblastoma (GBM) is highly invasive primary brain tumor. Here, we retraced early steps of GBM invasion and interactions with tumor-associated myeloid cells (TAM) in a highly infiltrative murine GBM model in immunocompetent background. We reveal early mobilization of microglia in a wide onco-field ahead of GBM invasion, forming glial nets encircling tumor micro-infiltrates that are enmeshed with a dense network of extracellular matrix (ECM). Physical contacts with GBM cells initiate an astounding morphological, spatial, and functional transformation of microglia and monocyte-derived macrophages to form collectively organized migration streams with intertwined GBM cells, paralleled by major ECM restructuring along invasion tracks. Mechanistically, this requires upregulation of guidance receptor Plexin-B2 in TAM, which functions to resolve collisions with GBM cells by providing cell contact guidance for cell alignment and ECM restructuring. Together, our results on stage- and niche-specific mobilization of microglia/macrophages, on governing factors, and the molecular insights into pro-invasion signaling open new therapeutic opportunities to curb GBM invasion.

overall_design: Single cell RNA sequencing of mice brain bearing intracranial SD3 GBM transplants. Cells from SD3 GBM bearing brain from ICR-SCID mouse were prepared and ran with 10x genomics pipeline.

first: Sangjo

last: Kang

middle: E

first: Jack

last: Zhang

first: Anirudh

last: Sattiraju

first: Alexander

last: Tsankov

first: Roland

middle: H

last: Friedel

first: Hongyan

last: Zou


title: The three-dimensional genome structure shapes the recombination landscape of chromatin features during female germline stem cell development [RNA-Seq]

city: Shanghai

first: Ji

last: Wu

address: No.800, Dongchuan Road, Minhang District

country: China

institute: Shanghai Jiao Tong University

summary: We use in situ Hi-C to report the most comprehensive survey to date of chromatin organization during FGSC development

overall_design: Integrative analysis of the chromatin architecture during FGSC development

first: Geng

last: Tian


title: Epigenomic Landscapes Define Differential JAK Inhibitor Sensitivity in IFN-γ-Primed Human Macrophages [RNA-seq]

status: Public on Mar 29 2025

city: Cheongju-si

first: Geunho

last: Kwon

state: Chungcheongbuk-do

address: 1, Chungdae-ro, Seowon-gu, 310, S1-5

country: South Korea

institute: Chungbuk National University

summary: We analyzed mRNA sequences to demonstrate selective regulation of genetic programs by JAKi in IFN-γ primed human macrophages.

overall_design: To investigate the suppressive impact of JAK inhibitors (JAKi) on macrophages primed with IFN-γ, THP-1 monocytes were co-treated with PMA for differentiation and IFN-γ for priming, followed by a JAKi (tofacitinib) treatment.

first: Yebin

last: Park

first: Keunsoo

first: Kyung-Hyun

last: Park-Min

first: Kyuho


title: Calcitonin gene-related peptide sustains CD8 T cell inflammatory reactions in drug -induced reactions [CD8 Smart-seq]

status: Public on Mar 31 2025

city: Guangzhou

first: Xiaobao

last: Huang

state: Guangdong

address: No. 58 Zhongshan Second Road, Guangzhou, Guangdong, China

institute: The First Affiliated Hospital, Sun Yat-sen University

summary: We investigated the differentiation pattern induced by CGRP on CD8+ T cells

overall_design: For stimulation experiment, CD8+ T cells were treated with either vehicle  or 10nM α-CGRP for 48 h.

first: Suiting

last: Ao

first: Fang

last: Wang


title: Newborn apical resection preserves the proliferative capacity of cardiomyocytes located throughout the left ventricle

status: Public on Mar 27 2025

city: Birmingham

first: Thanh

middle: Minh

last: Nguyen

state: AL

address: 1670 University Blvd, Volker Hall G094

department: Department of Biomedical Engineering

institute: University of Alabama at Birmingham

summary:
Background: When pigs underwent apical resection (AR) on postnatal day (P) 1 (ARP1) followed by myocardial infarction (MI) on P28, the hearts had little evidence of scarring; meanwhile, hearts underwent MI on P28 without ARP1 showed large infarcts on P56; and the improvement of ARP1 hearts was driven primarily by cardiomyocyte proliferation. AR and MI were performed ~5 mm (AR) and ~20 mm (MI) above the heart apex; thus, we hypothesize that ARP1 preserved the cardiomyocytes cell-cycle throughout the left ventricle, rather than only near the resection site.
Methods: Sections of cardiac tissue were collected from the left ventricle of uninjured pigs and from both the border zone (BZ) of AR and uninjured regions (remote zone, [RZ]) in ARP1 hearts. Cardiomyocyte proliferation was evaluated via immunofluorescence analysis of phosphorylated histone 3 [PH3] and symmetric Aurora B (sAuB). Single nucleus RNA sequencing (snRNAseq) data collected from the hearts of fetal pigs, uninjured pigs, and the BZ and RZ of ARP1 pigs was evaluated via our cell-cycle-specific Autoencoder to identify proliferating cardiomyocytes.
Results: Cardiomyocyte PH3 and sAuB expression, and percentage of proliferating cardiomyocytes in snRNA data was significantly more common in both BZ and RZ of ARP1 than uninjured hearts but did not differ significantly between the ARP1-BZ and ARP1-RZ at any time point. Heat shock protein HSPA5 and HSP90B1 were overexpressed at both ARP1-BZ and ARP1-RZ. In AC16 cell, overexpression (and knockdown) of HSPA5-HSP90B1 increased (and decrease) cell-cycle activity.
Conclusion: ARP1 preserved proliferative capacity of cardiomyocytes located throughout the left ventricle.

overall_design: On neonatal day 1, apical resection was performed by removing 4-5 mm of tissue from the ventricular apex; then, the sternum was re-approximated, the chest was closed in layers, and air was evacuated from the mediastinum. On postnatal day 2, 4, 8, 15, and 28, the hearts were explanted. Tissue from the border zone (next to the resected apex) and remote zone (>2cm above the apex) were collected and being sent for single-nuclei RNA sequencing data.

first: Kaili

last: Hao

first: Yuji

last: Nakada

first: Gregory

last: Walcott

first: Yuhua

last: Wei

first: Yalin

first: Daniel J

last: Garry

first: Peng

last: Yao

first: Jianyi


title: The transcription factor LHX2 mediates and enhances oncogenic BMP signaling in medulloblastoma

city: Uppsala

first: Mohamad

middle: Moustafa

last: Ali

state: Uppsala län

address: husargatan 3, Biomedical Center

department: IMBIM

country: Sweden

institute: Uppsala University

summary: In this study, we investigate the potential role of BMP stimulation on the oncogenic capacity of Medulloblastoma cells. BMP7 stimulation demonstrated pleiotropic effects on the investigated cells, inducing high cancer stem cell capacity or cell death. In addition, we uncovered the role of LHX2 as a prominent target of BMP7 signaling that can alter the stem cell capacity and positively modulate BMP signaling through a forward feedback loop.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Medulloblastoma cells (CHLA01, CHLA01R, MB002 and D425) treated with BMP7 ligand for 72 hours with respective PBS-treated controls. Additional comparison is done for CHLA01R treated with LDN (BMP signaling inhibior) with respect to DMSO-treated cells.

first: Yae

last: Ohata

first: Fredrik

last: Swartling

first: Carl-Henrik

last: Heldin

first: Aristidis

last: Moustakas


title: Epigenomic Landscapes Define Differential JAK Inhibitor Sensitivity in IFN-γ-Primed Human Macrophages [ATAC-seq]

first: Geunho

last: Kwon

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We analyzed ATAC sequences to demonstrate selective regulation of genetic programs by JAKi in IFN-γ primed human macrophages.

first: Yebin

last: Park

first: Keunsoo

last: Kang

first: Kyung-Hyun

first: Kyuho


title: Changes in neurotensin signalling drive hedonic devaluation in obesity

city: Zurich

first: Csaba

last: Földy

state: Zurich

address: Winterthurerstrasse 190

department: Brain Research Institute

country: Switzerland

institute: University of Zurich

summary: Calorie-rich foods, particularly those high in fat and sugar, evoke pleasure in both humans and animals. However, prolonged consumption of such foods may reduce their hedonic value, potentially contributing to obesity. Here, we investigated this phenomenon in mice on a chronic high-fat diet (HFD). While these mice preferred high-fat food over regular chow in their home cages, they showed reduced interest in calorie-rich foods in a no-effort setting. This paradoxical decrease in hedonic feeding has been reported previously, but its neurobiological basis remains unclear. We found that in regular diet mice, neurons in the lateral nucleus accumbens projecting to the ventral tegmental area (NAcLat→VTA) encoded hedonic feeding behaviors. In HFD mice, this behavior was reduced and uncoupled from neural activity. Optogenetic stimulation of the NAcLat→VTA pathway increased hedonic feeding in regular diet mice but not in HFD mice, though this behavior was restored when HFD mice returned to a regular diet. HFD mice exhibited reduced neurotensin expression and release in the NAcLat→VTA pathway. Furthermore, neurotensin knockout in the NAcLat and neurotensin receptor blockade in the VTA each abolished optogenetic-induced hedonic feeding behavior. Enhancing neurotensin signaling via overexpression normalized aspects of diet-induced obesity, including weight gain and hedonic feeding. Altogether, our findings identify a neural circuit mechanism linking the devaluation of hedonic foods with obesity.

overall_design: Neurons from the nucleus accumbens projecting to the VTA were collected from control mice (NORM) and mice on high fat diet (HFD)

first: Neta

last: Gazit Shimoni

first: Amanda

middle: J

last: Tose

first: Charlotte

last: Seng

first: Yihan

last: Jin

first: Tamas

last: Lukacsovich

first: Hongbin

last: Yang

first: Jeroen

last: Verharen

first: Christine

last: Liu

first: Michael

last: Tanios

first: Eric

last: Hu

first: Jonathan

last: Read

first: Lilly

middle: W

last: Tang

first: Byungkook

last: Lim

first: Lin

last: Tian

first: Stephan

last: Lammel


title: glioma-associated mesenchymal stem cell (GA-MSCs) transcriptome chip data

city: WUHAN

first: YIHAO

last: WANG

state: HUBEI

address: No. 1277 JIEFANG AVENUE

department: Department of Neurosurgery

institute: Union Hospital, Tongji Medical College, Huazhong University of Science and Technology

summary: GA-MSCs extracted from glioblastoma specimens classified as WHO grade IV (confirmed by pathological examination) were cultured in T25 culture flasks. Once the cell density reached approximately 70%-80%, the cells were treated with either DMEM (control condition) or GSC-CM (experimental condition). Each condition was tested in triplicate.  After three days of incubation, total RNA was extracted using the TRIzol reagent (TAKARA, Japan). RNA quality was assessed using a Nanodrop 2000 and an Agilent Bioanalyzer 2100, and only samples meeting quality control criteria were included in the microarray analysis. The RNA samples were poly-A-tailed, biotin-labeled, and analyzed using the Affymetrix GN-GeneChip Human Clariom D Array 2.0 (Affymetrix, USA).

overall_design: The experiment analyzed a total of six samples, with three replicates in both the experimental group and the control group.

first: Yihao

last: Wang


title: Regulatory mechanisms of the Hippo/YAP axis by G-protein coupled estrogen receptor in gastric signet-ring cell carcinoma

city: JiNan

first: Dong

last: Sun

address: 440 Jiyan Road, Huaiyin District

institute: Shandong First Medical University Affiliated Cancer Hospital

summary: Although aberrant activation of Hippo/YAP has been demonstrated to contribute to the development of gastric cancer, functional studies of this cascade in the context of gastric signet-ring cell carcinoma (GSRC) remain absent. Our previous single-cell sequencing results showed that G protein-coupled estrogen receptor (GPER) is overexpressed in GSRC, and this overexpression is associated with aberrant activation of the Hippo/YAP axis. Identifying effective treatment targets that modulate the Hippo/YAP axis to suppress development of GSRC is of critical importance.GPER was identified as highly overexpressed in GSRC and correlated with worse prognosis. Its activation facilitated tumor proliferation by YAP nuclear translocation and subsequent transcriptional activation. Mechanistically, GPER disrupted LATS1-mediated YAP phosphorylation by competitively binding to ARRB2, thereby enhancing YAP activity. Moreover, YAP bound to the GPER promoter, forming a positive feedback loop that reinforced oncogenic signaling.These findings revealed the key role of the GPER-YAP positive feedback loop in GSRC progression. Targeting this signaling axis, particularly via dual inhibition of GPER and YAP, offered a promising therapeutic strategy for GSRC.

overall_design: RNA-seq profiling of wildtype SNU668 cells and their knockdown derivative(shGPER).

first: Yufei

first: Jie

last: Chai


title: Transcriptomic characterization of cardiac LECs and macrophages isolated from ACKR3∆Lyve1 and wild type mice with or without LAD ligation

city: Chapel Hill

first: Kathleen

last: Caron

state: NC

address: 111 Mason Farm Rd

institute: University of North Carolina at Chapel Hill

summary:
In our study, we detected activation of ACKR3 signaling in cardiac lymphatics adjacent to the site of ischemic injury of left anterior descending artery (LAD) ligation. Furthermore, we found that Ackr3∆Lyve1 mice exhibited better survival and were protected from the formation of acute tissue edema after ischemic cardiac injury, in addition to a denser cardiac lymphatic network after LAD ligation, especially in the injured tissues.
To characterize the transcriptomic changes in cardiac lymphatic endothelial cell (LEC) and macrophage populations in the heart upon ischemic cardiac injury in Ackr3∆Lyve1 mice, CD68+ macrophages and CD68-/LYVE1+ LECs were immunoprecipitated from the ventricles of Ackr3fl/fl and Ackr3∆Lyve1 mice at baseline or 7 days post LAD ligation. We then performed microarray on the collected lymphatic and macrophage RNA samples.

overall_design: CD68+ macrophages and CD68-/LYVE1+ lymphatic endothelial cells isolated from the hearts of male Ackr3∆Lyve1 and littermate control mice with or without LAD ligation. N=3 mice per group.

first: Laszlo

last: Balint


title: Comparative transcriptomic studies to determine the molecular effects of titin mechanical knock-out in skeletal muscles

city: Madrid

first: Roberto

last: Silva-Rojas

address: Calle de Melchor Fernández Almagro 3

country: Spain

institute: Spanish Nacional Center for Cardiovascular Research

summary: Mechanical knock-out (mKO) is a novel tool to study the role of mechanical proteins in physiology by ceasing their force transmission in vivo. Here, titin protein carriying TEV protease recognition site (TEVs-TTN) is cleaved in vivo by the AAV-driven overexpression of TEV protease (TEVp) in skeletal muscles. An acute form of myopathy appears encompassing myofiber atrophy, myonuclei internalization, mitochondrial mislocalization and aggregation, and intersticial fibrosis. To define the molecular pathways affected when titin mechanics are perturbed, we performed RNA-sequencing with WT and homozygous Tttin mKO at 3 different timempoints and heterozygous Titin mKO muscles including saline-injected (-TEVp) and AAV-injected legs (+TEVp).

overall_design: WT and homozygous titin mKO injected with saline or AAV and dissected at 3 different timepoints post-infection and heterozygous titin mKO muscles injected with saline and AAV and dissected at 7 days-post-infection.

first: Silva-Rojas

last: Roberto

first: Alegre-Cebollada

last: Jorge


title: Chromothripsis-associated chromosome 21 amplification orchestrates transformation to blast phase MPN through targetable overexpression of DYRK1A

city: Oxford

first: Charlotte

last: Brierley

address: University of Oxford, Headley Way

institute: MRC WIMM

summary: To investigate the effect of chr21amp on cell differentiation, we performed droplet-based, high-throughput single-cell RNA-seq on Lin-CD34+ cells and total mononuclear cells.

overall_design: We used the 10x genomics platform to profile single-cell transcriptomes of 9,000 CD34+ lineage negative and 9,000 viable mononuclear cells were sorted into 30uL PBS/0.05% BSA (non-acetylated) in a 1.5ml DNA lo-bind Eppendorf. Samples were processed according to the 10x protocol using the Chromium Single Cell 30 library and Gel Bead Kits v3.0 (10x Genomics). Cells and reagents were prepared and loaded onto the chip and into the Chromium Controller for droplet generation. Reverse transcription was conducted in the droplets and cDNA recovered through demulsification and bead purification. Pre-amplified cDNA was used for library preparation, multiplexed and sequenced on a Novaseq S4, aiming to obtain > 50,000 reads per cell. A preliminary, low-depth run was performed to more accurately estimate the number of cells and total sequencing required. BPMPN samples are denoted 'S' and healthy controls 'HC'. Please refer to the manuscript for downstream processing.

first: Adam

last: Mead

first: Beth

last: Psaila


title: ANP32E drives vulnerabiliy to ATR inhibitors in Triple Negative Breast Cancer by accumulation of R-loops [CUT&RUN II]

city: Trento

first: Sara

last: Lago

address: Via Sommarive 9

department: CIBIO

country: Italy

institute: University od Trento

summary: Triple Negative Breast Cancer (TNBC) is often characterized by MYC oncogene overactivation, causing dysregulation of gene expression and uncontrolled proliferation. We found that the expression of ANP32E chaperone protein is increased in dependency of MYC in human mammary epithelial cells, with associated induction of genome instability. TCGA data confirmed that ANP32E is overexpressed in TNBCs with respect to the other BC subtypes. TNBC patients show higher frequency of genomic mutations, correlating with higher ANP32E expression. Investigation of the DNA damage response (DDR) pathways showed an upregulation of several involved genes in correlation with ANP32E overexpression. We demonstrated that inhibiting the DDR master regulator ATR triggers vulnerability of TNBC overexpressing ANP32E in vivo and leads to Double-Strand Breaks and micronuclei accumulation in vitro. We hypothesized the involvement of R-loops (DNA:RNA hybrids) in DDR sensitization, due to their accumulation after ANP32E overexpression and the generation of R-loop dependent Transcription Replication Conflicts. To clarify the underlying mechanism, we tested several DDR players, showing that ANP32E overexpressing cells have: i) sustained stimulation of DDR measured as phRPA32, phChk1, γH2A.X and 53BP1 activation; ii) enhanced recruitment of DDR players to specific chromatin loci; iii) R-loops accumulation at ANP32E chromatin bound sites; ii) elongating RNApolII stalled at R-loops sites, resulting in reduced nascent RNA. With the advantage of Next Generation Sequencing technologies, we mapped R-loops genome wide and observed an accumulation of longer, thus more stable, R-loops in dependency to ANP32E overexpression. Those sites also showed an increased phosphorylation of RPA32, a surrogate marker for Transcription Replication Conflicts. The consequent dependency of cancers with such biological condition from a constant activation of DDR puts the bases for a successful therapy based on ATR inhibitor drugs, which is also empowered thanks to the synergic effect with anti-proliferative molecules such as Navitoclax. In summary, dissection of the molecular mechanism linking ANP32E overexpression to the dependency on DDR specific players and fragile sites will help to rationally design patient-specific therapies and identify novel biomarkers for TNBC diagnosis.

overall_design: CUT&RUN immunoprecipitation profiling analysis performed on the breast cancer cell lines tIMEC, tIMEC-ANP32E and tIMEC-ANP32E-H1 cells.

first: Veronica

last: De Sanctis

last: Bertorelli

first: Paolo

last: Cavallerio

first: Chiara

last: Valentini

first: Alessio

last: Zippo


title: The interleukin 22–oncostatin M axis promotes intestinal inflammation and tumorigenesis [Colon_Tissue_BulkRNA-seq]

city: Berlin

first: Ahmed

middle: Nabil

last: Hegazy

address: Hindenburgdamm 30

department: Department of Gastroenterology, Infectious Diseases and Rheumatology

institute: Charité - University Medicine Berlin

summary: Multicellular cytokine networks regulate the onset of intestinal inflammation and colitis-associated cancer (CAC). Interleukin 22 (IL-22) promotes epithelial cell recovery but can also drive inflammation and tumorigenesis. We demonstrate that IL-22 from innate lymphoid cells activates STAT3 and increases OSM receptor expression in intestinal epithelial cells. This activation leads to sustained STAT3 activity via OSM, promoting inflammation and tumorigenesis. Deleting the OSM receptor or blocking OSM pharmacologically mitigates colitis and CAC. Our findings highlight the IL-22-OSM axis as a potential therapeutic target for these conditions.

overall_design: In this study, we investigated the role of OSM signaling in various resident colon cell types during intestinal inflammation. We generated cell type-specific OSMR-deficient mice by crossing Osmr^fl/fl with Villin^creERT2, Col1a2^creERT2, or Cdh5^cre to delete OSMR in epithelial, stromal, and endothelial cells, respectively. The resulting lines included Villin^creERT2 Osmr^fl/fl (IECΔOsmr), Col1a2^creERT2 Osmr^fl/fl (StomaΔOsmr), and Cdh5^cre Osmr^fl/fl (EndoΔOsmr). Prior to inducing colitis, these mice and their controls were co-housed for at least four weeks. Col1a2^creERT2 and Villin^creERT2 Osmr^fl/fl mice, as well as Villin^creERT2 Stat3^fl/fl mice, were treated with 75 mg/kg body weight of tamoxifen administered intraperitoneally daily for one week, following the Jackson Laboratory protocol. Control mice, either cre+ Osmr^fl/wt or Osmr^fl/fl without creERT2, also received tamoxifen. Colitis was induced by orally inoculating the mice with 1 × 10^8 CFU of H. hepaticus for two consecutive days, followed by weekly 1 mg injections of anti-IL10R antibody. On day 21 after colitis induction, colonic tissues from the proximal, mid, and distal colon were collected. For bulk RNA sequencing analysis of colonic tissue from IECΔOsmr, StomaΔOsmr, and EndoΔOsmr, as well as their respective controls, tissues were initially preserved in RNA Later (Qiagen). RNA was isolated using the RNeasy Mini Kit (Qiagen), following the manufacturer's protocol. The subsequent procedures were conducted at Novogene, where sequencing was performed on a HiSeq X sequencer to generate 150 bp paired-end reads.

middle: N

first: Roodline

last: Cineus

first: Yanjiang

last: Luo

first: Mariia

last: Saliutina


title: The interleukin 22–oncostatin M axis promotes intestinal inflammation and tumorigenesis [Epithelial_cells_BulkRNA-seq]

overall_design: Col1a2creERT2 and VillincreERT2 Osmr^fl/fl mice were treated with 75 mg/kg body weight of tamoxifen intraperitoneally daily for one week, following the Jackson Laboratory protocol. Control mice, either cre+ Osmr^fl/wt or Osmr^fl/fl without creERT2, also received tamoxifen. Colitis was induced by orally inoculating the mice with 1 × 10^8 CFU of H. hepaticus for two days, followed by weekly 1 mg injections of anti-IL10R antibody.


title: Neutrophil dichotomy drives lymphatic metastasis

city: Essen

first: Bettina

last: Budeus

address: Virchowstrasse 173

department: Institute for Cell Biology

institute: University Hospital Essen

summary: The study provides an alternative scenario in which the response of the tumor cell population itself determines the pro-tumor versus anti-tumor outcome of neutrophil-tumor interaction. Experimentally, we show that neutrophils, which were  sequentially stimulated by bacteria and tumor cell secreted factors, killed a certain proportion of tumor target cells. However, the majority of the tumor cells remained  resistant to this neutrophil-mediated killing and underwent a phenotype switch that was reminiscent of partial epithelial-to-mesenchymal transition. This phenotypic switch was associated with physical escape from NK killing and resulted in enhanced lymphatic metastasis.

overall_design: Two different tumor cell lines: FaDu and H460 were treated with three different types of supernatants for 8h, 37°C, 5%CO2. Types of supernatants included: RPMI 1640 - labelled as control, derivative of neutrophils treated with supernatant from bacteria-tumor co-culture - labeled as responder (Staphylococcus Aureus) or non-responder (Streptococcus Pneumoniae or Klebsiella Pneumoniae). Each sample type comes with 3 biological replicates.

first: Jagoda

middle: A

last: Szlachetko

first: Lara-Jasmin

last: Schröder

first: Francisca

last: Hofmann-Vega

first: Claudia

last: Dumitru

first: Sebastian

last: Vollmer

first: Maike

last: Busch

first: Eva-Maria

last: Hanschmann

first: Jan

last: Kehrmann

first: Stephan

last: Lang

first: Nicole

last: Dünker

first: Sven

last: Brandau


title: Tumor-associated myeloid cells aid GBM infiltration by organizing invasion tracks via guidance receptor Plexin-B2

first: Mary

last: Ughetta

overall_design: Single cell RNA sequencing of mice brain bearing intracranial KR158 GBM transplants. Tamoxifen was injected every other day (i.p., 100 mg kg−1) from 3 days before KR158 transplantation until 8 weeks after. Cells from KR158 GBM bearing brains from Control or Plexin-B2 cKO hosts (C57BL/6 background) were prepared and ran with 10x genomics pipeline.

first: Sangjo

last: Kang

first: Jack

last: Zhang

first: Anirudh

last: Sattiraju

first: Alexander

last: Tsankov

first: Roland

last: Friedel

first: Hongyan

last: Zou


title: Phase Ib/II Study of Azacitidine, Venetoclax and Magrolimab in Adult Patients with Newly Diagnosed and Relapsed Refractory Acute Myeloid Leukemia

city: Houston

first: Hussein

last: Abbas

state: Texas

address: 1515 Holcombe Blvd

institute: The University of Texas at MD Anderson Cancer cent

summary: To better understand the mechanisms of response and resistance to azacitdine, venetoclax, and magrolimab (AVM), we performed single-cell RNA-sequencing (scRNAseq) on 27 samples (11 pre- and 16 post-treatment) from 11 TP53-mutated patients with combined therapy

overall_design: Bone marrow biopsies were routinely collected. Samples were freshly frozen with freezing medium containing 20% fetal calf serum (FCS) and 10% dimethyl sulfoxide (DMSO) in Dulbecco’s modified Eagle medium (DMEM) and stored in liquid nitrogen. All frozen BM samples were retrieved immediately before sample processing. The 5 prime gene expression libraries were prepared using a 10x Genomics Chromium Controller instrument and Chromium Single-Cell 5 V5.1 reagent kits (10x Genomics).

first: Patrick

middle: K

last: Reville

first: Bofei

last: Wang


title: ANP32E drives vulnerabiliy to ATR inhibitors in Triple Negative Breast Cancer by accumulation of R-loops

first: Sara

last: Lago

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

overall_design: Refer to individual Series

first: Veronica

last: De Sanctis

first: Roberto

last: Bertorelli

first: Paolo

last: Cavallerio

first: Chiara

last: Valentini

first: Alessio

last: Zippo


title: Normal keratinocyte cell line and skin cancer cell line RNA-seq data

city: Boston

first: Tomonori

last: Oka

department: CBRC

institute: Massachusetts general hospital

summary: Normal keratinocyte cell line (KERTr, HaCaT) and skin cancer cell line (SCC12, SCC13, UW-BCC1) RNA-seq data.

overall_design: We compared two different normal keratinocyte cell lines (KERTr, HaCaT), two different cutaneous squamous cell carcinoma cell lines (SCC12, SCC13) and one basal cell carcinoma cell line (UW-BCC1).

first: Tatsuya

last: Hasegawa

first: Shadmehr

last: Demehri


title: Associations of epigenetic aging and COVID-19: a 3-year longitudinal study

status: Public on Mar 26 2025

city: Budapest

first: Zsolt

last: Radák

address: Alkotás Street 44, building L3

country: Hungary

institute: Research Center for Molecular Exercise Science, Hungarian University of Sports Science

summary: Aging and COVID-19 are known to influence DNA methylation, potentially affecting the rate of aging and the risk of disease. The physiological functions of 54 volunteers—including maximal oxygen uptake (VO₂ max), grip strength, and vertical jump—were assessed just before the COVID-19 pandemic and again three years later. Of these volunteers, 27 had contracted COVID-19. Eight epigenetic clocks were used to assess the rate of aging during the three-year period: DNAmAge showed accelerated aging and five clocks showed slowed aging (DNAmAgeSkinBlood, DNAmAgeHannum, DNAmFitAge, PhenoAge, and DNAmTL). When we considered only females, we observed a stronger effect in the increase of DNAmAge acceleration, while we observed slowed aging in the case of SkinBloodClock, and DNAmTL.   The methylation of the promoter region of the H1FNT genes, which encodes testis-specific histone H1 family member N (H1fnt) and plays a crucial role in spermatogenesis decreased the most significantly. In contrast, the promoter of CSTL1, which encodes Cystatin-like 1, showed the most significant increase. We found that having COVID-19 during the 3-year study period significantly increased the progress of aging assessed by DNAmGrimAge, DNAmGrimAge2, and DNAmFitAge (p=0.024, 0.047, 0.032, respectively after we adjusted the analysis for baseline variables). The data suggest that COVID-19 may have a mild long-term effect on epigenetic aging.

overall_design:
54 adult volunteers were assessed at two-time points: before the COVID-19 pandemic (2019) and three years later (2022-2023). Among them, 27 individuals contracted COVID-19, while 27 remained uninfected. The dataset includes DNA methylation profiles from blood samples, physiological function measurements (VO₂ max, grip strength, vertical jump), and metadata covering age, sex, COVID-19 status, and baseline health variables. DNA methylation analysis was performed using the Illumina EPIC array.
Due to patient privacy concerns, raw data idat files could not be provided.

first: Gabor

last: Farkas

first: Zahira

last: El Mahdaouy

first: Gergely

last: Babszky

first: Matyas

last: Jokai

first: Ferenc

last: Torma

first: Yaodong

last: Gu

first: Ricardo

last: Pinho

first: Ildiko

last: Miklossy

first: Juozas

last: Gordevicius

first: András

last: Benczúr

first: Csaba

last: Kerepesi


title: DNA methylation epitypes of Burkitt lymphoma with distinct molecular and clinical features

city: Burnaby

first: Ryan

middle: D.

last: Morin

state: BC

address: 8888 University Drive

department: Molecular Biology and Biochemistry

country: Canada

institute: Simon Fraser University

type: Methylation profiling by genome tiling array

summary: The genetic drivers of Burkitt Lymphoma (BL) have been comprehensively explored while the role of epigenetics remains unclear. Using samples from patients across four continents, we searched for sites with consistent DNA methylation changes and associations with clinical and molecular features such as Epstein-Barr virus (EBV) status and driver mutations. We identified robust methylation patterns that were not fully explained by EBV status, implying the existence of robust epitypes: HypoBL and HyperBL. The latter had distinct genomic and clinical features including global hypermethylation, a higher mutation burden, elevated aberrant somatic hypermutation, and inferior outcomes. Methylation, gene expression and mutational differences between the epitypes support a model in which each arises from a distinct cell-of-origin. These results suggest an approach for identifying BL patients with a greater risk of treatment failure and provide a basis for the exploration of new therapeutic strategies that target the unique molecular underpinnings of each group.

overall_design: Cases were accrued within the Burkitt Lymphoma Genome Sequencing Project (BLGSP) from the following sites: Uganda Cancer Institute (UCI, Uganda), Epidemiology of Burkitt’s Lymphoma in East-African Children and Minors (EMBLEM) study, at St. Mary’s Hospital, Lacor, Uganda), Children’s Oncology Group (COG, USA) sites that participated in the AALL1131 clinical trial, St. Jude Children’s Research Hospital (USA), Memorial Sloan Kettering Cancer Center (USA), Massachusetts General Hospital (USA), Belo Horizonte (Brazil), Lyon University Hospital (France), Washington University in St. Louis (USA), National Cancer Institute (USA), BC Cancer (Canada), and Robert-Bosch-Krankenhaus (Germany). Patients at the age of enrollment older than 20 years were considered adults for the purpose of this study. The study data set consisted of pediatric and adult BL patients. A total of 218 BL samples and 6 normal centroblast samples were preserved for further analysis. Additionally, 13 BL cell lines were also profiled.

first: Nicole

last: Thomas

first: Carlos

last: Garcia-Prieto

first: Kostiantyn

last: Dreval

first: Laura

last: Hilton

first: Jeremy

middle: S

last: Abramson

first: Nancy

middle: L

last: Bartlett

first: Jeffrey

last: Bethony

first: Jay

last: Bowen

first: Anthony

middle: C

last: Bryan

first: Corey

last: Casper

first: Maureen

last: Dyer

first: Julie

last: Gastier-Foster

first: Alina

last: Gerrie

first: Timothy

last: Greiner

first: Nicholas

middle: B

last: Griner

first: Thomas

last: Gross

last: Harris

first: John

middle: D

last: Irvin

first: Elaine

last: Jaffe

first: Fabio

last: Leal

first: Sam

last: Mbulaiteye

first: Charles

last: Mullighan

first: Andrew

last: Mungall

first: Karen

first: Constance

last: Namirembe

first: Ariela

last: Noy

first: Martin

last: Ogwang

first: Jackson

last: Orem

first: German

last: Ott

first: Hilary

last: Petrello

first: Steven

last: Reynolds

last: Swerdlow

first: Alexandra

last: Traverse-Glehen

first: Wyndham

last: Wilson

first: Marco


title: Genetic or pharmacological inactivation of CREBBP sensitizes B-cell Acute Lymphoblastic Leukemia to Ferroptotic Cell Death upon BCL2 Inhibition [CUT&RUN]

city: Cambridge

first: Sarah

last: Horton

state: Cambridgeshire

address: Jeffrey Cheah Biomedical Centre, Puddicombe Way

department: Wellcome-MRC Cambridge Stem Cell Institute - Department of Haematology

institute: University of Cambridge

summary: B-cell acute lymphoblasTc leukemia (B-ALL) is a leading cause of death in childhood and outcomes in adults remain dismal. There is therefore an urgent clinical need for therapies that target the highest risk cases. MutaTons in the histone acetyltransferase CREBBP confer high-risk and increased chemoresistance in ALL. Performing a targeted drug-screen in isogenic human cell lines, we idenTfied a number of small molecules that specifically targeted CREBBP-mutated B-ALL, with the most potent the BCL2-inhibitor Venetoclax. Of note, this acted through a non-canonical mechanism resulTng in ferroptoTc rather than apoptoTc cell death. CREBBP-mutated cell lines showed differences in cell- cycle, metabolism, lipid composiTon and response to oxidaTve stress, predisposing them to ferroptosis, which were further dysregulated upon acquisiTon of Venetoclax resistance. Lastly, small- molecule inhibiTon of CREBBP pharmacocopies CREBBP-mutaTon, sensiTzing B-ALL cells, regardless of genotype, to Venetoclax-induced ferroptosis in-vitro and in-vivo, providing a potential novel drug combination for broader clinical translation in B-ALL.

overall_design: CUTnRUN was performed  using  the CUTANA CUT&RUN kit (Epicypher, SKU: 15-1016) according to the manufacturer’s protocol (CUTANA™ CUT&RUN Protocol v2.0) in 0.3 million cells per sample of 697WT and 697KI cell lines.

first: Brian

last: Huntly

first: Simon

last: Richardson

first: Alicia

last: Garcia-Gimenez

first: Jonathan

last: Ditcham

first: Dhoyazan

last: Azazi


title: Genetic or pharmacological inactivation of CREBBP sensitizes B-cell Acute Lymphoblastic Leukemia to Ferroptotic Cell Death upon BCL2 Inhibition [ChIP-seq]

overall_design: ChIP-seq was performed using 2.5μg of anTbody (IgG, Proteintech, 30000-0-AP; H3, Cell Signalling Technology, 14269S and H3K27ac, AcTve moTf, 39133). Immunocomplexes were captured using the protein A (10002D) and protein G (10004D) Dynabeads (Invitrogen). Aäer 4h, the immunocomplexes were magneTzed and repeatedly washed in the following buffers in 7 million 697WT and 697KI


title: The geroprotectors trametinib and rapamycin combine additively to extend mouse healthspan and lifespan

city: Cologne

first: Sebastian

last: Grönke

address: Joseph-Stelzmann Str. 9b

department: Biological Mechanisms of Ageing

institute: Max-Planck Institute for Biology of Ageing

summary: Suppression of the insulin-IGF-mTORC1-Ras network ameliorates aging in animals. Many drugs have targets in the network because of its roles in cancer and metabolic disease and are candidates for repurposing as geroprotectors. Rapamycin, an established geroprotective drug, blocks mTORC1 signaling, and trametinib inhibits the Ras-MEK-ERK pathway. In this study, we assessed survival and health of male and female mice treated with trametinib, rapamycin or their combination. We show here that trametinib treatment extended lifespan in both sexes and that its combination with rapamycin was additive. Combination treatment reduced liver tumors in both sexes and spleen tumors in male mice, blocked the age-related increase in brain glucose uptake and strongly reduced inflammation in brain, kidney, spleen and muscle and circulating levels of pro-inflammatory cytokines. We conclude that trametinib is a geroprotector in mice and that its combination with rapamycin is more effective than either drug alone, making the combination a candidate for repurposing as a gerotherapy in humans.

overall_design: Female and male mice were treated from 6 months of age  with (1) rapamycin (biweekly 42mg/kg), (2) trametinib (continuously 1.44mg/kg diet), (3) rapamycin /trametinib (biweekly 42mg/kg/continuously 1.44mg/kg) and (4) control food.  At 24 months of age, kidney, muscle and spleen tissues were collected and used for RNA seq analysis to measure the influence of the drug treatments on age-related gene expression.

first: Lisonia

last: Gkioni

first: Tobias

last: Nespital

first: Maarouf

last: Baghdadi

first: Carolina

last: Monzó

first: Jitin

last: Bali

first: Taim

last: Nassr

first: Anna Lena

last: Cremer

first: Andreas

last: Beyer

first: Joris

last: Deelen

first: Heiko

last: Backes

first: Linda

last: Partridge


title: Competing dynamic gene regulatory networks involved in fibroblast reprogramming to haematopoietic  progenitor cells [RNA-Seq]

city: Singapore

first: Kiyofumi

last: Hamashima

address: 61 Biopolis Drive

country: Singapore

institute: Institute of Molecular and Cell Biology (IMCB)

summary: Direct reprogramming of somatic cells offers a potentially safer therapeutic approach to generate patient-specific haematopoietic cells. However, this strategy is limited by stochasticity of reprogramming. Investigating the gene-regulatory networks involved during reprogramming would help generate functionally relevant cells in adequate numbers. To address this, we developed an inducible system to reprogram fibroblasts to HSPCs by ectopically expressing the two transcription factors SCL and LMO2. Transcriptome and epigenome analysis at different stages of reprogramming revealed uniform silencing of fibroblast genes and upregulation of the haemogenic endothelial program. Integrated analysis suggested that TFs FLI1, GATA1/2, KLF14 are direct targets of SCL/LMO2, which subsequently induce the haematopoietic programme. Single cell RNA-Seq revealed conflicting and competing fate decisions at intermediate stages of reprogramming. Inhibiting signalling pathways associated with competing neuronal fate significantly enhanced haematopoietic reprogramming efficiency. In conclusion, this study identifies early/intermediate reprogramming events and associated pathways that were targeted to improve reprogramming efficiency.

overall_design: To investigate the mechanisms of reprogramming mouse embryonic fibroblasts (MEFs) to blood progenitors, we have performed transcriptome analysis on reprogramming cells (MEFs treated with doxycycline) harvested on days 2, 4 and 14 of reprogramming, with day 14 cells sorted for c-KIT positive cells. MEFs harvested at day 2 (without doxycycline) were used as controls. MEFs from three different embryos were used as biological replicates.

first: Kiran

last: Batta

first: Samiyah

last: Shafiq


title: Competing dynamic gene regulatory networks involved in fibroblast reprogramming to haematopoietic  progenitor cells


title: Competing dynamic gene regulatory networks involved in fibroblast reprogramming to haematopoietic  progenitor cells [ATAC-Seq]

overall_design: To investigate the mechanisms of reprogramming mouse embryonic fibroblasts (MEFs) to blood progenitors, we have performed ATAC-Seq analysis on reprogramming cells (MEFs treated with doxycycline) harvested on days 2 and 4 of reprogramming. MEFs harvested at day 2 (without doxycycline) were used as controls. MEFs from three different embryos were used as biological replicates.


title: ANP32E drives vulnerabiliy to ATR inhibitors in Triple Negative Breast Cancer by accumulation of R-loops [RNA-Seq]

first: Sara

last: Lago

overall_design: Comparative gene expression profiling analysis of total RNA-seq data for the breast cancer cell lines tIMEC, tIMEC-ANP32E and tIMEC-ANP32E-H1 cells.

first: Lisa

last: Fol

first: Veronica

last: De Sanctis

first: Roberto

last: Bertorelli

first: Paolo

last: Cavallerio

first: Alessio

last: Zippo


title: ANP32E drives vulnerabiliy to ATR inhibitors in Triple Negative Breast Cancer by accumulation of R-loops [ATAC-Seq]

overall_design: Comparative chromatin accessibility profiling analysis by mean of ATAC-seq data for the breast cancer cell lines tIMEC, tIMEC-ANP32E and tIMEC-ANP32E-H1 cells.


title: The interleukin 22–oncostatin M axis promotes intestinal inflammation and tumorigenesis

city: South San Francisco

first: Juliette

last: Roels

state: CA

address: 1 DNA Way

institute: Genentech

summary: Multicellular cytokine networks orchestrate the onset and progression of intestinal inflammation and colitis-associated cancer (CAC). Interleukin 22 (IL-22), a member of the IL-10 superfamily, is known for promoting epithelial cell recovery but can inadvertently fuel inflammation and tumorigenesis. Here, we demonstrate that IL-22, derived from group 3 innate lymphoid cells (ILC3), triggers oncostatin M (OSM) responsiveness in intestinal epithelial cells by activating STAT3 and upregulating OSM receptor (OSMR) expression. OSM, a member of the IL-6 cytokine family implicated in inflammatory bowel disease, collaborates with IL-22 to sustain STAT3 activation, promoting proinflammatory adaptations and immune cell chemotaxis to the intestine. Conditional deletion of OSMR in epithelial cells protects mice from colitis and CAC. Additionally, pharmacological blockade of OSM reduces the progression of established CAC. Our study reveals a novel mechanism by which OSM sustains intestinal inflammation and CAC, identifying the IL-22-OSM axis as a promising therapeutic target.

overall_design: The human HCA7 cell line was stimulated for 24 hours with either PBS or 10 ng/ml human OSM in 3 replicates.

first: Nathaniel

middle: R

last: West

first: Joanna

last: Klementowicz


title: Chronic stress stimulated HIF-AS3/HIF-1α loop in neoplastic cells and promoted lung cancer progression through macrophage inactivation [A549 and H1299]

city: Linz

first: Yong

last: Yu

state: Upper-Austria

address: Altenberger Straße 69

country: Austria

institute: Johannes Keppler University Linz

summary: Chronic psychological stress is closely linked to malignant disorders, with novel modulators potentially mitigating tumor progression by regulating interactions between neoplastic cells and immune cells. This study identified lncRNA HIF1A-AS3 as a key driver of stress-induced lung cancer progression. Chronic stress models in mice with implanted lung cancer cells revealed significant upregulation of HIF1A-AS3 in stressed groups and human lung cancer tissues. Functional studies showed HIF1A-AS3 promotes cancer cell proliferation and invasion by activating HIF-1ɑ translation through interaction with YBX1, forming a positive feedback loop where HIF-1ɑ enhances HIF1A-AS3 transcription. Additionally, HIF1A-AS3 drove macrophage M2 polarization and reduced phagocytosis under hypoxia. Targeting the HIF1A-AS3/HIF-1ɑ loop effectively counteracted stress-induced lung cancer progression in vivo, highlighting its potential as a diagnostic and therapeutic target for stress-exacerbated lung cancer.

overall_design: RNA-seq of lung cancer cell A549 and H1299 cells with or without HIF1A-AS3 ecotopic overexpression

first: Cuilan

last: Liu

first: Jingjing

last: Qi

first: Jing

last: Du


title: The interleukin 22–oncostatin M axis promotes intestinal inflammation and tumorigenesis [scRNA-seq]

first: Ahmed

last: Hegazy

overall_design: In this study, we aim to assess the impact of OSM signaling in different resident cell types in the colon within the context of intestinal inflammation. To explore the transcriptional changes in colitis among various tissue-resident cells, we utilized single-cell sequencing to analyze the expression of OSM and OSMR in epithelial, stromal, and endothelial cells. We compared cells isolated from both steady-state and colitic mice. Colitis was induced by gavage of Helicobacter hepaticus and anti-IL-10R administration.

first: Roodline

last: Cineus

first: Yanjiang

last: Luo

first: Mariia

last: Saliutina

first: Pawel

last: Durek

first: Frederik

last: Heinrich

first: Mir-Farzin

last: Mashreghi


title: Genomics and Transcriptomics of 3ANX (NX-2) and NX (NX-3) producing isolates of Fusarium graminearum

status: Public on Mar 25 2025

city: Winnipeg

first: Philip

last: Walker

state: Manitoba

address: 104 Dunrobin Avenue

institute: Agriculture and AgriFood Canada

summary: In this study, we used an -omics approach coupled with high resolution mass spectrometry to characterize twenty  F. graminearum isolates collected from five distinct regions across Manitoba, containing both 3-acetyl deoxynivalenol (3ADON) and 15-acetyl deoxynivalenol (15ADON) chemotypes. These data identified regional F. graminearum populations within Manitoba that demonstrate distinct genomic variation and patterns of gene expression, particularly within pathogenicity associated processes. Further, we identified genetic variation and differential expression between isolates showing high and low levels of pathogenicity, allowing for the identification of previously characterized and novel putative pathogenicity factors, as well as regions of genetic diversity between these groups. Lastly, we detected production of 3ANX and/or NX mycotoxins within the majority of our twenty characterized F. graminearum isolates, suggesting the 3ANX chemotype may be more prevalent than previously expected in Canada. These findings highlight the diversity of F. graminearum across Manitoba, and more importantly uncover specific genomic regions and candidate pathogenicity factors influenced by this diversity. These data can ultimately help researchers develop improved disease management strategies against FHB and the dynamic populations of F. graminearum.

overall_design: Genomic and transcriptomic analysis of twenty distinct Fusarium graminearum isolates across Manitoba

first: Maria Antonia

last: Henriquez


title: Chronic stress stimulated HIF-AS3/HIF-1α loop in neoplastic cells and promoted lung cancer progression through macrophage inactivation [A549_xenograft]

overall_design: RNA-seq of lung cancer cell A549 xenograft tumors with or without HIF1A-AS3 overexpression in BALB/c nude mice.


title: Transcriptomic Landscape Around Wound Bed Defines Regenerative Versus Non-regenerative Outcomes in Mouse Digit Amputation

city: Cleveland

first: Peng

last: Jiang

state: OH

address: 2121 Euclid Ave

institute: Cleveland State University

summary: In the mouse distal terminal phalanx (P3), it remains mystery why amputation at less than 33% of the digit results in regeneration, while amputation exceeding 67% leads to non-regeneration. Unraveling the molecular mechanisms underlying this disparity could provide crucial insights for regenerative medicine. In this study, we aim to investigate the tissues within the wound bed to understand the tissue microenvironment associated with regenerative versus non-regenerative outcomes. We employed a P3-specific amputation model in mice, integrated with time-series RNA-seq and a macrophage assay challenged with pro- and anti-inflammatory cytokines, to explore these mechanisms. Our findings revealed that non-regenerative digits exhibit a greater intense early transcriptional response in the wound bed compared to regenerative ones. Furthermore, early macrophage phenotypes differ distinctly between regenerative and non-regenerative outcomes. Regenerative digits also display unique co-expression modules related to Bone Morphogenetic Protein 2 (Bmp2). The differentially expressed genes (DEGs) between regenerative and non-regenerative digits are enriched in targets of several transcription factors, such as HOXA11 and HOXD11 from the HOX gene family, showing a time-dependent pattern of enrichment. These transcription factors, known for their roles in bone regeneration, skeletal patterning, osteoblast activity, fracture healing, angiogenesis, and key signaling pathways, may act as master regulators of the regenerative gene signatures. Additionally, we developed a deep learning AI model capable of predicting post-amputation time and level from RNA-seq data, indicating that the regenerative probability may be "encoded" in the transcriptomic response to amputation.

overall_design: (a) Tissues around Mouse wound bed was collected (b) Macrophage (in vitro) was collected. We have submitted mouse digit amputation wound bed RNA-seq data (<33% amputation level) to GEO with accession number: GSE130438 before (regenerative digits). In this study, we submitted mouse digit amputation wound bed RNA-seq data (>34% amputation level) and macrophage in vitro (M0, M1 and M2 phenotypes) RNA-seq data to GEO with accession number: GSE279540

first: Prabahar

last: Archana

first: Chamberlain

last: Connie

first: Badylak

last: Stephen

first: Jiang

last: Peng


title: Transcriptomic implications of low herbicide concentrations in hepatic cells: Insights into the individual and combined effects of 2,4-D, glyphosate, and AMPA

city: Botucatu

first: Guilherme

middle: Ribeiro

last: Romualdo

state: SP

address: Rua Dr José Barbosa de Barros, 1486

country: Brazil

institute: UNESP

summary: Glyphosate and 2,4-D are among the most widely used herbicides globally, leading to environmental presence, food contamination, and human contact. Investigations based on current toxicological limits or populational-based herbicide exposures are warranted, and in vitro bioassays provide useful tools for toxicological screening. Thus, this study evaluated the transcriptomic implications of non-cytotoxic exposures to glyphosate, its metabolite aminomethylphosphonic acid (AMPA), or 2,4-D - or to their mixes - on hepatic cells. The half maximal effective concentration (IC50) of each herbicide was calculated (cell viability) in human hepatic C3A cells and 1000-fold lower concentrations were used for transcriptomic analysis (RNA-Seq) after 48h exposure, resembling current toxicological limits and considering herbicide water levels (glyphosate: 0.95 µg/mL; AMPA: 3.7 µg/mL; 2,4-D: 0.56 µg/mL). Glyphosate exposure enriched MAPK-related biological processes (upregulated TNF, FOS, IGF1, and PDGFB), and downregulated genes associated with lipid metabolism (CD36 and PPARA). Many AMPA exposure-related differentially expressed genes (DEGs, such as PFKFB3, HK2, and ALDOA) were associated with glucose metabolic pathways. Glyphosate and its metabolite yielded a common molecular signature, as illustrated by principal component analysis and the function of 212 shared DEGs. The exposure to 2,4-D was associated with the JNK cascade and the solute carrier family annotations. The herbicide mixtures had a discrete effect on enhancing the impact of individual herbicides, although important epithelial-mesenchymal transition genes were exclusively modified by the mixes (COL11A2, LOXL3, SNAI1). Altogether, our data reveals new perspectives on the short-term molecular effects of herbicide exposure in liver cells, emphasizing potential avenues for further exploration.

overall_design: RNA-Seq profile of unexposed C3A cells (HB-8065, ATCC) or exposed to glyphosate: 0.95 µg/mL; AMPA: 3.7 µg/mL; 2,4-D: 0.56 µg/mL for 48h.

first: Letícia

last: Valente

first: Luana

last: Riechelmann-Casarin


title: ANP32E drives vulnerabiliy to ATR inhibitors in Triple Negative Breast Cancer by accumulation of R-loops [DRIP-seq]

first: Sara

last: Lago

overall_design: Comparative R-loop profiling analysis by mean of DRIP-seq data for the breast cancer cell lines tIMEC, tIMEC-ANP32E and tIMEC-ANP32E-H1 cells.

first: Lisa

last: Fol

first: Veronica

last: De Sanctis

first: Roberto

last: Bertorelli

first: Paolo

last: Cavallerio

first: Alessio

last: Zippo


title: ANP32E drives vulnerabiliy to ATR inhibitors in Triple Negative Breast Cancer by accumulation of R-loops [CUT&RUN]

overall_design: CUT&RUN immunoprecipitation profiling analysis performed on the breast cancer cell lines tIMEC, tIMEC-ANP32E and tIMEC-ANP32E-H1 cells.


title: Prolonged airway explant culture enables study of health, disease, and viral pathogenesis

city: Chapel Hill

first: Hong

last: Dang

state: North Carolina

address: 125 Mason Farm Rd, Cb#7248

department: Marsico Lung Institute

institute: University of North Carolina at Chapel Hill

summary: Purpose: To identify cell types and cellular transcriptional profiles in airway explants and precision cut lung slices obtained from non-disease human lung tissue.

overall_design: Methods: Large airway explants (LAE), small airway explants (SAE), and precision cut lung slides (PCLS) obtained from 3 non-disease donor lungs were cryopreserved after 0 (fresh), 2 and 14 days in culture.  Cryopreserved tissues were thawed, enzymatically digested for cell dissociation, and used for scRNA-seq. Single cells were captured using a 10X Chromium controller (10X Genomics) and libraries were prepared following the Single Cell 3’ Reagent Kits v3.1 (Dual Index) User Guide (10X Genomics).

first: Rhianna

middle: E

last: Lee

first: Kenichi

last: Okuda

first: Jacob

last: Galiger

first: Stephen

last: Schworer

first: Troy

last: Rogers

first: Rodney

last: Gilmore

first: Caitlin

last: Edwards

first: Gillian

last: Crisp

first: Satoko

last: Nakano

first: Anne

middle: M

last: Cawley

first: Raymond

last: Pickles

first: Samuel

last: Gallant

first: Elisa

last: Crisci

first: Lauraine

last: Rivier

first: James

last: Hagood

first: Wanda

last: O'Neal

first: Ralph

last: Baric

first: Barbara

last: Grubb

first: Richard

last: Boucher

first: Scott

middle: H

last: Randell


title: Transcript data from a severe malaria study

city: Baltimore

first: JP

last: Courneya

state: United States of America

address: 685 W Baltimore St., HSF2 Room 480

institute: University of Maryland, Baltimore

summary: Transcript data detailing human transcription in severe malaria cases and uncomplicated malaria controls in a Mali study. Severe malaria cases were either cerebral malaria, severe malarial anemia, or concurrent cerebral malaria and severe malarial anemia disease.

overall_design:
Epidemiological matched case control study comparing severe malaria to uncomplicated malaria.

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

first: Mark

last: Travassos

first: Rafal

last: Sobota

first: Emily

last: Stucke

first: Joana

last: Silva


title: Root transcriptional profile of cucumber seedlings supplied with FePO4 nanoparticles as source of Fe and P.

city: Verona

first: Anita

last: Zamboni

address: Strada Le Grazie, 15

department: Biotechnology

institute: University of Verona

summary: FePO4 nanoparticles (NPs) were used as source of Fe and P for the growth of cucumber seedlings. Through a series of transcriptional profiles comparison of plants treated with FePO4 NPs, bulk FePO4 (non-nanometric ) and Fe-deficient and P-deficient plants, transcripts speciffically modulated by NPs as source of Fe and P were identified.

overall_design: Twenty-one root samples were analyzed: 3 biological relicates for each of the seven treatement (C, -P, PNP, PB, -Fe, FeNP and FeB).

first: Andrea

last: Ciurli

first: Davide

last: Sega

first: Zeno

last: Varanini


title: Chronic Stress Stimulates Protumor Macrophage Polarization to Propel Lung Cancer Progression

first: Yong

last: Yu

overall_design: RNA-seq of lung cancer cell A549 xenograft tumors in BALB/c nude mice upon chronic stress.

first: Cuilan

last: Liu

first: Jingjing

last: Qi

first: Jing

last: Du


title: Deciphering the role of RNA in regulating CTCF’s DNA binding affinity in leukemia cells [RNA-Seq.New]

city: Memphis

first: Beisi

last: Xu

state: Tennessee

address: 262 Danny Thomas Pl

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hosipital

summary: CTCF, a highly studied transcription factor, is essential for chromatin interaction maintenance. Several independent studies have reported that CTCF interacts with RNAs in vitro and in cells. Yet continuous debates about the authenticity of the RNA-binding affinity of CTCF and its biological role remain in large part due to limited research techniques available, such as CLIP-seq. Here, we investigated the role RNA plays on CTCF’s transcription factor function through its chromatin occupancy. To systematically investigate whether RNAs affect CTCF’s ability to bind DNA, we perturbed CTCF-RNA interactions by three independent approaches and examined CTCF genome occupancy by ChIP-seq. Although RNase A and Triptolide treatment each affected a certain number of CTCF-binding peaks, few peaks overlapped between treatment groups indicating the effect of RNA in regulating CTCF’s DNA binding affinity was modest and variable between loci. In addition, limited transcriptional or chromatin accessibility changes were observed between cells expressing wild-type CTCF or CTCF lacking the RNA binding region. Our data provide a complementary approach and in silico evidence to reconsider the significance of RNA affecting CTCF’s DNA-binding affinity in a global manner.

overall_design: RNA-seq samples were collected from CTCF-WT cells and CTCF-dRBR cells.

first: Judith

last: Hyle

first: Wenjie

first: Mohamed Nadhir

last: Djekidel

first: Wojciech

last: Rosikiewicz

first: Beis

first: Chunliang

last: Li


title: Competing dynamic gene regulatory networks involved in fibroblast reprogramming to haematopoietic  progenitor cells [scRNA-Seq]

first: Kiyofumi

last: Hamashima

overall_design: Directly reprogramming cells were harvested at days 2, 4, 8 and 14.  Untreated fibroblasts at day 2 were used as controls. Day 14 reprogrammed cells were sorted based c-KIT expression into c-KIT high and c-KIT low.

first: Kiran

last: Batta

first: Samiyah

last: Shafiq


title: Modulating phosphatase DUSP22 with BML-260 ameliorates skeletal muscle wasting via Akt independent JNK-FOXO3a repression

city: gwangju

first: Darren

middle: Reece

last: Williams

address: school of life science, 123, Cheomdangwagi-ro, Buk-gu, Gwangju, Republic of Korea

institute: Gwangju Institute of Science and Technology

summary: Skeletal muscle wasting results from numerous conditions, such as sarcopenia, glucocorticoid therapy or intensive care. It prevents independent living in the elderly, predisposes to secondary diseases, and ultimately reduces lifespan. There is no approved drug therapy and the major causative mechanisms are not fully understood. Dual specificity phosphatase 22 (DUSP22) is a pleiotropic signaling molecule that plays important roles in immunity and cancer. However, the role of DUSP22 in skeletal muscle wasting is unknown. In this study, DUSP22 was found to be upregulated in sarcopenia patients and models of skeletal muscle wasting. DUSP22 knockdown or pharmacological inhibition with BML-260 prevented multiple forms of muscle wasting. Mechanistically, targeting DUSP22 suppressed FOXO3a, a master regulator of skeletal muscle wasting, via downregulation of the stress-activated kinase JNK, which occurred independently of aberrant Akt activation. DUSP22 targeting was also effective in human skeletal muscle cells undergoing atrophy. In conclusion, phosphatase DUSP22 is a novel target for preventing skeletal muscle wasting and BML-260 is a therapeutically effective small molecule inhibitor. The DUSP22-JNK-FOXO3a axis could be exploited to treat sarcopenia or related aging disorders.

overall_design: RNA-seq profiling of TA isolated from 24-month-old mice after one month of BML-260 (5 mpk) injection.

last: Wiilams

first: Sang Hoon

last: Lee


title: Transfer RNA acetylation regulates in vivo mammalian stress signaling [RiboSeq and DisomeSeq]

city: Frederick

first: Colin

last: Wu

state: MD

department: RNA Biology Laboratory

institute: NCI

summary: Transfer RNA (tRNA) modifications are crucial for protein synthesis, but their physiological roles remain poorly understood. Here we investigate the impact of N4-acetylcytidine (ac4C), a highly conserved tRNA modification, using a Thumpd1 knockout mouse model. We find that loss of Thumpd1-dependent tRNA acetylation leads to reduced levels of tRNALeu, increased ribosome stalling and collisions, and activation of eIF2α phosphorylation. Thumpd1 knockout mice exhibit growth defects and sterility. Remarkably, concurrent knockout of Thumpd1 and the stress-sensing kinase Gcn2 causes penetrant postnatal lethality, revealing a critical genetic interaction. Our findings demonstrate that a modification restricted to a single site within type II cytosolic tRNAs can regulate ribosome-mediated signaling in mammalian organisms. By providing insight into how tRNA modifications shape signaling and cell fate in response to stress, this work opens up novel strategies for therapeutic intervention and translational control.

overall_design: Identify ribosome and disome stalling sites. We employed RiboSeq and DisomeSeq to investigate WT and Thumpd1 KO cells.

first: Roxane

last: Khoogar


title: Siglec-E is a Critical Inhibitory Receptor Controlling APC Activation and T Cell-Mediated Transplant Rejection

city: Boston

first: Leonardo

middle: V.

last: Riella

state: MA

address: 149 13th Street

department: Medicine

institute: Massachusetts General Hospital

summary: Early after transplantation, inflammation and tissue injury release danger signals that activate myeloid innate immune cells like DCs, driving adaptive immune responses and acute rejection. Current immunosuppressive drugs primarily target T cells, leaving innate immunity inadequately controlled. Siglec-E (SigE), an innate inhibitory receptor, binds sialic acid-carrying ligands to suppress inflammatory responses. In mouse heart transplants, SigE is upregulated in graft-infiltrating myeloid cells, including DCs. Human homologs Sig-7 and Sig-9 are also upregulated in rejecting heart and kidney transplant biopsies. Genetic ablation of SigE in recipients accelerates acute rejection of heart, kidney, and skin allografts. SigE-deficient DCs are more susceptible to activation by danger signals and show enhanced NF-kB activation and TNF-a production, increasing alloreactive T-cell responses. Overexpressing SigE on DCs reduces their activation by DAMPs and their T-cell allostimulatory capacity. Thus, SigE is a crucial inhibitory receptor controlling APC activation and T cell-mediated transplant rejection.

overall_design: Total RNA was isolated from flow-sorted splenic DCs

first: Thiago

last: Borges

first: Guilherme

last: Ribas


title: Genetic or pharmacological inactivation of CREBBP sensitizes B-cell Acute Lymphoblastic Leukemia to Ferroptotic Cell Death upon BCL2 Inhibition

first: Sarah

middle: J

last: Horton

summary: We performed a targeted drug screen in isogenic human cell lines, identifying a number of actionable small molecules that specifically target CREBBP-mutated B-ALL. The most potent was the BCL2 inhibitor Venetoclax, which acts through a non-canonical mechanism resulting in ferroptotic cell death. CREBBP-mutated cell lines showed differences in cell-cycle, metabolism and response to oxidative stress. Lastly, we demonstrate that small-molecule inhibition of CREBBP sensitizes B-ALL cells, regardless of genotype, to Venetoclax-induced ferroptosis in-vitro and in-vivo, providing a potential novel drug combination for broader clinical translation in B-ALL.

overall_design: To explore the mechanism of action of Venetoclax in CREBBP-mutated 697 cells, we undertook bulk RNA sequencing (RNAseq) of 697WT and 697KIcells, after 24 hours exposure to either dimethyl sulfoxide (DMSO) vehicle, or low-dose Venetoclax (20nM – the IC50 of 697KI cells).

first: Brian

last: Huntly

first: Simon

last: Richardson

first: Dhoyazan

last: Azazi


title: High-throughput Transcriptomics Screen of ToxCast Chemicals in HepaRG Cells

city: RTP

first: Monique

last: Hazemi

address: 109 T.W. Alexander Dr

institute: US EPA

summary: With thousands of chemicals in commerce and the environment, rapid identification of potential hazards is a critical need. Combining broad molecular profiling with targeted in vitro assays, such as high-throughput transcriptomics (HTTr) and receptor screening assays, could improve identification of chemicals that perturb key molecular targets associated with adverse outcomes. We aimed to link transcriptomic readouts to individual molecular targets and integrate transcriptomic predictions with orthogonal receptor-level assays in a proof-of-concept framework for chemical hazard prioritization. Transcriptomic profiles generated via TempO-Seq in U-2 OS and HepaRG cell lines were used to develop signatures comprised of genes uniquely responsive to reference chemicals for distinct molecular targets. These signatures were applied to 75 reference and 1,126 non-reference chemicals screened via HTTr in both cell lines. Selective bioactivity towards each signature was determined by comparing potency estimates against the bulk of transcriptomic bioactivity for each chemical. Chemicals predicted by transcriptomics were confirmed for target bioactivity and selectivity using available orthogonal assay data from US EPA’s ToxCast program. A subset of 37 selectively acting chemicals from HTTr that did not have sufficient orthogonal data were prospectively tested using one of five receptor-level assays. Of the 1,126 non-reference chemicals screened, 201 demonstrated selective bioactivity in at least one transcriptomic signature, and 57 were confirmed as selective nuclear receptor agonists. Chemicals bioactive for each signature were significantly associated with orthogonal assay bioactivity, and signature-based points-of-departure were equally or more sensitive than biological pathway altering concentrations in 81.2% of signature-prioritized chemicals. Prospective profiling found that 18 of 37 (49%) chemicals without prior orthogonal assay data were bioactive against the predicted receptor. Our work demonstrates that integrating transcriptomics with targeted orthogonal assays in a tiered framework can support Next Generation Risk Assessment by informing putative molecular targets and prioritizing chemicals for further testing. NOTE: this GEO entry only includes the HepaRG cell line data; the U-2 OS cell line data can be located via GEO accession number GSE274318.

overall_design: High-throughput transcriptomics (HTTr) screens of 1,201 chemicals in U-2 OS and HepaRG cell lines were used as source data for all transcriptomic analyses. Both screens utilized the same experimental design and bioinformatics pipeline for initial derivation of transcriptional potency values. In brief, DMSO-solubilized chemical stock solutions were provided frozen from the US EPA ToxCast chemical inventory management contractor (EvoTec, Princeton, NJ), and stored at -80°C prior to dose plate preparation. U-2 OS osteosarcoma and HepaRG hepatocyte cell lines were used for chemical exposure. Chemicals were tested at 8 nominal concentrations ranging from 0.03—100 µM using 0.5-log spacing with a final DMSO concentration of 0.05%. All exposures were conducted in triplicate using independent cell cultures. Transcriptomic profiles generated via TempO-Seq in U-2 OS and HepaRG cell lines were used to develop signatures comprised of genes uniquely responsive to reference chemicals for distinct molecular targets. These signatures were applied to 75 reference and 1,126 non-reference chemicals screened via HTTr in both cell lines. Selective bioactivity towards each signature was determined by comparing potency estimates against the bulk of transcriptomic bioactivity for each chemical. NOTE: this GEO entry only includes the HepaRG cell line data; the U-2 OS cell line data can be located via GEO accession number GSE274318.

first: Jesse

last: Rogers

first: Joseph

last: Bundy

first: Joshua

last: Harrill

first: Richard

last: Judson

first: Katie

last: Paul-Friedman

first: Logan

last: Everett


title: Dissecting the molecular basis of flowering time in Camelina sativa through integration of WGCNA, eQTL analysis and transcriptome-wide association study

city: Saskatoon

first: Isobel

last: Parkin

address: 107 Science Pl

institute: Agriculture and Agri-Food Canada

summary: Camelina sativa is an important polyploid oilseed crop with multiple favorable agronomic traits. Capturing the leaf transcriptome of 48 accessions of C. sativa suggests allelic variation for gene expression levels and notably sub-genome dominance, both of which could provide opportunities for crop improvement.  Flowering time (FT) is a crucial factor affecting the overall yield of crops. However, our understanding of the molecular mechanisms underlying FT regulation in C. sativa are still limited, partly due to its complex allohexaploid genome. In this study, weighted gene co-expression network analysis (WGCNA), expression quantitative trait loci (eQTL) analysis and transcriptome-wide association study (TWAS) were employed to explore the FT diversity among 48 C. sativa accessions and dissect the underlying molecular basis. Our results revealed a FT-related co-expressed gene module highly enriched with SOC1s and SOC1-like genes, and identified 10 significant FT-associated single nucleotide polymorphisms (SNPs), thus providing a molecular basis for future genetic improvements in C. sativa breeding

overall_design: Phenotypes (including flowering time) and RNAseq data were collected from 48 Camelina sativa accessions to analyze the underlying genetic basis of flowering time regulation

first: Liyong

last: Zhang

first: Venkatesh

last: Bollina

first: Peng

last: Gao


title: Gain-of-function RNA Polymerase II partitioning is a shared feature of diverse oncogenic fusions

city: Dallas

first: Benjamin

last: Sabari

state: TX

address: 5323 Harry Hines Blvd

institute: UT Southwestern Medical Center

summary: Condensates regulate transcription by selectively compartmentalizing biomolecules, yet the rules of selectivity and their relationship to function remain enigmatic. To identify rules with links to function, we leverage the genetic/evolutionary selection bias of condensate-promoting oncofusions. Focusing on the three most frequent oncofusions driving translocation renal cell carcinoma, we find that they promote the formation of condensates that activate transcription by gain-of-function RNA Polymerase II partitioning through a shared signature of elevated p and p-interacting residues and depletion of aliphatic residues. This signature is shared among a broad set of oncofusions associated with diverse cancers. We find that this signature is necessary and sufficient for RNA Polymerase II partitioning, gene activation, and cancer cell phenotypes. Our results reveal that dysregulated condensate selectivity is a shared molecular mechanism of diverse oncofusions, highlighting the functional role of condensate composition and the power of genetics in investigating relationships between condensate selectivity rules and function.

overall_design: We performed ChIP-seq for TFE3 (ab93808-1001) or RPB1 (Sigma 05-952-I) in Tet-inducible non-target shRNA engineered XP121 cells (NT) or shRNA targeting PRCC-TFE3 engineered XP121 cells.

first: Heankel

last: Lyons

first: Prashant

last: Pradhan

first: Gopinath

last: Prakasam

first: Shubham

last: Vashishtha

first: Xiang

last: Li

first: Mikayla

last: Eppert

first: Christy

last: Fornero

first: Kathy

last: McGlynn

first: Vanina

middle: T

last: Tcheuyap

first: Ze

last: Yu

first: Dinesh

last: Raju

first: Prasad

last: Koduru

first: Chao

last: Xing

first: Payal

last: Kapur

first: James

last: Brugarolas


title: Deciphering the role of RNA in regulating CTCF’s DNA binding affinity in leukemia cells [ATAC-seq]

first: Beisi

last: Xu

summary: CTCF is the most studied transcription factor, which is essential for chromatin interaction maintenance. Although several independent studies reported that CTCF protein could pull down RNAs in vitro and in cells, there are continuous debates about authenticity of the RNA-binding affinity of CTCF and its biological role, mainly due to the concerns of limited research techniques such as CLIP-seq. To systematically investigate the RNA-interaction with CTCF and the impact on gene regulation, we conducted in vivo CTCF ChIP-seq under three conditions, including RNase A treatment, Triptolide-mediated transcription inhibition and auxin-inducible degron mediated RNA-binding domain mutant swap. Our results consistently suggest that when RNA-interaction with CTCF protein was impaired in vivo, the DNA occupancy of CTCF remains the same at the genome-wide scale. Our data provide a complementary approach and in silico evidence to re-considerate the role of RNA-binding affinity of CTCF.

overall_design: ATAC-seq samples were collected from CTCFAID2+HA-CTCF-WT cells and CTCFAID2+HA-CTCF-dRBR cells. ATAC-seq tracks from CTCF-AID with or without auxin treatment were shown as controls.

first: Judith

last: Hyle

first: Mohamed

last: Nadhir Djekidel

first: Wojciech

last: Rosikiewicz

first: Chunliang


title: Single cell multi-omics reveals re-dosing with CD3 bispecific antibody induces a TCF7 high central memory CD8+ T cell population associated with reduced cytokine production

city: Cambridge

first: Hui

last: Ling

address: 220 Massachusetts Ave

institute: Novartis

summary: Background: T cell engaging therapies are commonly accompanied by excessive cytokine production and risk of cytokine release syndrome (CRS). Intriguingly, CRS risk with CD3-engaging bispecific antibody (BSP) is primarily limited to the first dose, termed the first-dose effect. Mechanisms underlying this effect remain unknown. CD3 bispecific induces cytokine cascade via T cell triggering and bystander cells. We hypothesize that distinct T cell biology between doses drives the first-dose effect.  Methods: We used the Re-directed T Cell Cytotoxicity (RTCC) assay to assess tumor killing and cytokine production by human donor T cells after initial versus subsequent CD3/CD20 BSP treatment. After confirming the first-dose effect in the experimental system containing only T cells and target tumor cells, we employed 10x Genomics single cell multi-omics to study the molecular mechanisms.Results: Compared with initial treatment, subsequent treatment exhibited lower cytokine levels and comparable tumor killing. Single cell multi-omics unveiled distinct T cell biology. In initial treatment, T effector memory (Tem) cells are the primary cells that respond to CD3 bispecific antibody stimulus by producing moderate levels of cytolytic and high levels of cytokine gene transcription. In the subsequent treatment, a new population of high TCF7 expressing central memory CD8+ cells (CD8-Tcm-TCF7), possibly originated from stimulated naive T cells, are the primary responding cells that produce a shifted balance with high level of the cytolytic gene transcription (GZMB) and low level of cytokine gene transcription (TNF-alpha and INF-gamma). Dasatinib co-treatment during initial treatment eliminated cytolytic activity and cytokine production, allowing uncompromised tumor killing and reduced cytokine production upon re-challenge. Conclusions: The distinct T cell populations that respond to first and subsequent CD3 bispecific treatment offer an explanation to the first-dose effect, wherein the risk of CRS associated with CD3 bispecific treatment is mainly limited to the initial dose. Furthermore, our work suggests that tumor killing capacity and cytokine production of T cells could be uncoupled, as demonstrated here by utilizing different T cell populations as effector cells. These findings could be further explored for designing mechanism-based strategies to mitigate the risk of CRS.

overall_design: CITEseq experiment was performed on 8 RTCC samples (4 experimental conditions applied to 2 T cell donors). T cells were put through two rounds of RTCC challenging, the first challenging for 24 h and the second for 3 h prior to being processed for CITEseq. These challenges took place under varying conditions, including the presence/absence of 2.5 nM CD3/CD20 BSP, and presence/absence of Ramos cells. On day 5, post the 3 h incubation, cells were prepared for CITEseq. The procedure involved staining the cells using TotalSeq antibody cocktail, and library construction using the Chromium Next GEM Single Cell 5’ Kit v2 (10x Genomics, Cat#1000263), and subsequent sequencing on llumina NovaSeq6000.

first: Lauren

last: Anderson

first: Katie

last: Kubek-Luck

first: Juliane

last: Perner

first: Tyler

last: Burks

first: Sven

last: Schuierer

first: Vera

last: Ruda

first: Keith

last: Mansfield


title: Interferon gamma suppresses T follicular helper cells and antibody responses upon viral infection

city: Milano

first: Chiara

last: Laura

address: Via Olgettina 58

institute: San Raffaele Scientific Institute

summary: Humoral and cellular immunity upon viral infections usually co-exist; however, sometimes, one of the two responses emerges as dominant and is responsible for most of the antiviral activity. For example, infection with lymphocytic choriomeningitis virus (LCMV) induces very strong cellular responses, but weak and inefficient neutralizing Ab (nAb) responses. Lack of nAb responses is an important issue for complete clearance of LCMV and other similar viruses, which in some instances tend to establish chronic infections. Recent work from our group has shown that this unbalance is observed also at the level of CD4 T cells responses, with subcutaneous LCMV infection leading almost exclusively to TH1 but no TFH differentiation.  Here, we report that LCMV-induced TH1 cells are heterogeneous and comprise a Tcf-1+ subset and a GzmB+ subset. We found that none of the subsets is dependent on the major TH1-polarizing cytokine IL-12. Instead, IFN-gamma (IFN-g) was found to promote the development of GzmB+ cells and to suppress the commitment of the Tcf-1+ population into fully differentiated TFH. As a result, blockade of IFN-g led to a rescue in the TFH population, germinal center B cells and antibody responses. Our results shed light on new mechanisms underlying the inefficient nAbs production in response to non-cytopathic viruses such as LCMV and are promising for the design of new vaccination strategies.

overall_design: scRNA-seq was performed on SMARTA CD4+ T cells which are specific for the MHC-II-restricted GP61-80 epitope of the LCMV glycoprotein. Smarta CD4+ T cells were transferred into WT recipients 1 day before s.c. rLCMV infection. WT recipient mice were also treated with a-IFN-g blocking antibody (or isotype Ctrl) at day 0. dLNs were analyzed 5 days post infection.

first: Eleonora

last: Sala

first: Nelli

last: Maria

first: Matteo

last: Iannacone

first: Mirela

last: Kuka