title: LsCLE12 peptide delays senescence in lettuce and prolongs postharvest life of roses

city: Singapore

first: Sally

last: Koh

address: 1 Research Link

country: Singapore

institute: Temasek Life Sciences Laboratory

summary: The widespread use of chemical inputs in agriculture has raised concern over their long-term environmental and health impacts, driving demand for sustainable, natural product-based alternatives. Peptide-hormone signaling interactions, particularly those regulating senescence, are promising targets for developing such alternatives to advance postharvest technologies. However, most current insights stem from model species, limiting their translation to crops and ornamental plants. This study identifies the CLAVATA3/EMBRYO-SURROUNDING REGION-related (CLE) family CLE12 peptide (CLE12p) in Lactuca sativa as a peptide that shows potential for postharvest management of crops and ornamental flowers. CLE12p interacts with salt (NaCl), abscisic acid (ABA) and ethylene pathways, influencing lettuce development and morphology. Notably, CLE12p induced stomatal closure in a similar manner to that of ABA, suggesting overlapping signalling pathways. Transcriptomic analyses revealed how CLE12p modulates immune and defence responses, fluid transport, and leaf senescence, indicating a broader role in leaf senescence regulation similar to that of ethylene. Functionally, CLE12p delayed senescence in lettuce by preserving leaf greenness and water content following dark treatment and harvest. Additionally, CLE12p extended the longevity of cut roses by maintaining fresh weight and water content. These findings demonstrate the practical potential of CLE peptides in non-model species and support their application as natural tools for extending postharvest shelf life in crops and ornamental plants, paving the way for further exploration of their role in agricultural biotechnology.

overall_design: L. sativa var. Little Gem were grown on MS basal medium under 24 h continuous light at 22°C. Four-day-old seedlings were transferred to the following treatment for 2 h incubation: control (H2O), ethanol control (0.02% ethanol), 10 µM ABA, 10 µM ACC, 10 µM CLE12p, 10 µM ABA + CLE12p and 10 µM ABA + ACC.

first: Daisuke

last: Urano


title: JNK knockdown enhances CAR-T cell cytotoxicity through NFATc1 in preclinical models of ovarian cancer

status: Public on Nov 18 2025

city: Birmingham

first: Charles

middle: Joseph

last: Kuhlmann

state: AL

address: 845 19th St S

department: Microbiology

country: USA

institute: University of Alabama at Birmingham

type: Expression profiling by high throughput sequencing

summary: Background: Boosting the performance of chimeric antigen receptor T (CAR-T) cell therapy in solid tumors may provide a substantial advantage for cancer patients. Recognizing the vital role of the nuclear factor of activated T cells (NFAT) in T cell function, we hypothesized the strategic regulation of NFAT activity by targeting c-Jun N-terminal Kinases (JNK) can bolster the tumor-eradicating potential of CAR-T cells. Methods: We developed a lentivirally encoded short-hairpin RNA (shRNA) for stable knockdown of JNK in CAR-T cells. CAR-T cells targeting human epidermal growth factor receptor 2 (HER2) were produced from human peripheral blood. Functionality was tested in vitro and in two xenograft models of human ovarian cancer. Results: JNK knockdown in CAR-T cells suppressed antigen-induced stimulation and helper T cell cytokine production, while enhancing anti-tumor cytotoxicity in vitro and in ovarian cancer xenograft experiments. Mechanistically, JNK knockdown altered NFAT signaling to facilitate NFATc1-dependent transcription, leading to elevated levels of granzyme B expression. Conclusions: JNK signaling is a significant regulator of CAR-T cell cytotoxicity, offering a potential strategy to directly enhance CAR-T effectiveness in human cancer therapies.

overall_design: CAR-T cells were manufactured from peripherial blood T cells of healthy human donors. CAR vectors encoded shRNA targeting JNK1/2 or a scrambled sequence. CD8+ CAR-T cells were purified, then stimulated with plate-bound HER2-Fc protein for 16 hours. RNA was isolated using Direct Zol RNA Miniprep Plus kit (Zymogen #R2050). RNA was sequenced after poly-A enrichment on the NovaSeq X plus platform (6 gigabytes per sample, paired end reads) through Novogene corporation (Sacramento, California).

first: Chloe

middle: E

last: Jepson

first: Madison

middle: T

last: Blucas

first: Fatema

last: Suleiman

first: Anusha

last: Manda

first: Yoshiko

middle: N

last: Kamata

first: Masakazu


title: An immunocompetent human iPSC-derived multicellular Alveolus-on-Chip reveals early pathological events of M. tuberculosis infection

status: Public on Nov 19 2025

city: London

first: Maximiliano

last: Gutierrez

state: --- Select One ---

address: 1 Midland Road

country: United Kingdom

institute: Francis Crick Institute

summary: Immunocompetent and experimentally accessible alveolar systems to study human respiratory diseases are lacking. Here, we combined cells derived from a single induced pluripotent stem cell (iPSC) source with microfluidic devices that mimic lung 3D mechanical stretching and air-liquid interface. This single donor iPSC-derived Lung-on-Chip (iLoC) combines four alveolar cell types, including alveolar epithelial cells Type II and I, vascular endothelial cells, and macrophages. A combination of imaging and scRNA-seq analysis revealed that the iLoC recapitulated cellular profiles of distal lung cells present in the human lung including a range of AT2-to-AT1 cellular states and alveolar macrophages. We show that the presence of an endothelial barrier in the iLoC impacted tissue immunity in both the epithelium and macrophages. Different from 2D cellular models, infection of iLoC with the human pathogen Mycobacterium tuberculosis (Mtb) showed that both infected macrophages and epithelial cells were infected but not permissive to bacterial replication. Stochastically, large macrophage clusters containing necrotic core-like structure and Mtb replication were observed. Building a genetically engineered autophagy deficient iLoC (GE-iLoC), we found that after Mtb infection, macrophage cell death was elevated upon ATG14 deficiency with a reduced endothelial barrier integrity. Altogether, we report the first of its kind genetically tractable human alveolar model to study infections in human distal lungs.

overall_design: Human iPSC were differentiated into alveolar epithelial cells, vascular endothelial cells and alveolar macrophages and assemble on a microfluidic device to build a lung on chip. The experiment was design to test the significance of vascular endothelial cells and mechanical stretch, therefore the conditions: alveolar epithelium + alveolar macrophage_static (AM_S); alveolar epithelium + alveolar macrophage_breathing (AM_B);  alveolar epithelium + vascular endothelial cells + alveolar macrophage_static (LOC_S) and alveolar epithelium + vascular endothelial cells + alveolar macrophage_breathing (LOC_B)

first: Chak

middle: H

last: Luk

first: Gabriel

last: Conway

first: Irene

last: Rodriguez-Hernandez

middle: G


title: BAF60A KO ATAC seq (primary cells)-Highly discriminative globin gene activation by the non-canonical BAF chromatin remodeling complex

city: Philadelphia

first: Eugene

last: Khandros

state: PA

address: 3615 Civic Center Blvd.

department: Hematology

institute: The Children's Hospital of Philadelphia

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The regulation of beta-like globin genes, including the switch from fetal (HBG) to adult (HBB and HBD) genes has served as a paradigm of developmental transcriptional control. While HBG repressors such as BCL11A and LRF have been well characterized, recent discoveries of HIF1a and BGLT3 as HBG-specific activators have raised interest in finding new activators as potential therapeutic targets. The ATP-dependent chromosome remodeler BRG1 has previously been demonstrated as necessary for hemoglobin gene transcription. In loss of function studies in adult-like HUDEP2 cells, we found that BRG1 depletion preferentially decreased fetal HBG and the minor adult HBD. BRG1 forms multisubunit complexes with combinations of 27 subunits in 3 families - canonical BAF, polybromo BAF, and non-canonical BAF (ncBAF) - to regulate chromatin accessibility and gene transcription in a cell and condition-specific manner. Using CRISPR loss of function studies in HUDEP2 cells and primary adult erythroid cells, we identified the non-canonical BAF complex as a positive regulator of HBG and HBD. Loss of the non-canonical BAF complex subunits BRD9 and BAF60A/SMARCD1 preferentially decreased HBG and HBD in HUDEP2 cells and primary adult erythroid cultures, while accelerating erythroid differentiation and hemoglobinization. Pharmacological depletion of BRD9 led to acute decreases in chromatin accessibility at HBD and HBG promoters and reduced their primary transcripts, while longer treatment recapitulated  genetic ablation effects. This surprising demonstration of BAF complex selectivity within a multi-gene cluster extends our understanding of globin gene transcriptional regulation and identifies a potential target for therapeutic manipulation of beta-like globins.

overall_design: We performed ATAC seq analysis in 4 HUDEP-2 clonal lines generated using single cell cloning of a pool of HUDEP-2 cells. ATAC-seq was conducted following the Omni-ATAC protocol (https://www.nature.com/articles/nmeth.4396). In brief, 100,000 cells underwent lysis using a buffer containing 0.1% NP-40, 0.1% Tween-20, and 0.01% digitonin, followed by incubation with Tagment DNA Enzyme (Illumina cat # 20034197) at 37°C for 30 minutes. DNA was subsequently purified using the QIAGEN MinElute Reaction Cleanup Kit. For library preparation, fragmented DNA was amplified with Phusion High-Fidelity PCR Master Mix supplemented with HF Buffer (Thermo Fisher Scientific, catalog no. F531S) and indexed primers featuring unique dual barcodes. Libraries were purified with AMPure XP beads (Beckman Coulter, catalog no. A63881) at a 1:1 ratio, adhering to the manufacturer’s guidelines.

first: Abhirup

last: Bagchi

first: Sindhu

last: Billakanti

first: Vanessa

last: Shehu

first: Kathryn

middle: M

last: Farrell

first: Sarah

middle: A

last: Cotteta

first: Bailey

last: Godfrey

first: Micaela

last: Alpert

first: Jacob

middle: F

last: Zeranski

first: Krista

last: Budinich

first: Zhuangzhuang

last: Geng

first: Osheiza

last: Abdulmalik

first: Belinda

last: Giardine

first: Cheryl

last: Keller

first: Ross

middle: C

last: Hardison

first: Junwei

last: Shi


title: Connecting cilium, stress response and proteostasis abnormalities inform variant and therapy assessment in RPGRIP1 retinal organoid [scRNA-seq]

city: Westmead

first: Nader

last: Aryamanesh

state: NSW

address: 214 Hawkesbury Rd

department: Bioinformatics

country: Australia

institute: CMRI

summary: RPGRIP1 encodes a connecting cilium (CC) protein essential for normal photoreceptor cell development and maintenance. Damaging variants in RPGRIP1 cause severe inherited retinal degeneration (IRD) and currently incurable vision loss, with mice studies showing promising preclinical gene augmentation therapy results. Almost one-half of variants in RPGRIP1 in the ClinVar database are variants of uncertain significance (VUS), hindering genetic diagnosis for affected individuals, and hence access to clinical trials of novel therapies and other management options. Here, we use human induced pluripotent stem cell (iPSC)-derived retinal organoids to model RPGRIP1-associated IRD, detecting biomarkers of disease including CC interactome dysfunction, stress response and proteostasis abnormalities. In parallel, utilising these novel disease biomarkers we demonstrate the pathogenicity of a missense VUS, RPGRIP1 c.2108 T>C p.(Ile703Thr). Finally, RPGRIP1 gene augmentation therapy rescued disease phenotypes, further supporting the utility of these biomarkers of RPGRIP1-LCA disease for reclassifying VUS and testing response to therapy.

overall_design: scRNA-seq profiling of wild type (Control-1) and RPGRIP1 variant (LCA-1 and MS-VUS) retinal organoids performed with replicates.

first: To Ha

last: Loi

first: Anson

last: Cheng

first: Hani

last: Kim

first: Milan

last: Fernando

first: Benjamin

last: Nash

first: John

middle: R

last: Grigg

first: Pengyi

last: Yang

first: Anai

last: Gonzalez Cordero

first: Robyn

middle: V

last: Jamieson


title: Dipeptidyl peptidase 4 restoration facilitates anti-tumor immunity in KRAS–LKB1–mutant lung cancer

city: Asahikawa

first: Hiraku

last: Yanada

country: Japan

institute: Asahikawa Medical University

summary: KRAS proto-oncogene, GTPase (KRAS)-liver kinase B1 (LKB1)-mutant (KL) non-small cell lung cancer (NSCLC), characterized by a profoundly immunosuppressive tumor microenvironment (TME), is highly resistant to immune checkpoint inhibitors (ICIs). Despite their high tumor mutation burden, KL tumors exhibit low programmed cell death ligand 1 (PD-L1) expression, reduced immune cell infiltration, and suppressed immune signaling pathways. Through systematic genomic analyses, we found that LKB1 loss suppresses dipeptidyl peptidase 4 (DPP4) expression and activity in KRAS-mutant lung cancer. Therefore, we evaluated the therapeutic potential of restoring DPP4 function to improve the immune response in KL lung cancer using patient-derived tumor samples and syngeneic mouse models. Restoration of DPP4 expression reprogrammed the TME and significantly increased immune-related gene signatures, including those involved in T cell migration and natural killer (NK) cell activation. Indeed, DPP4 restoration in three-dimensional microfluidic models enhanced NK cell chemotaxis and activity in targeting tumor spheroids. Furthermore, DPP4 restoration in syngeneic KL murine models synergized with anti-PD-1 therapy to achieve significant tumor regression. These findings suggest that LKB1 loss suppresses DPP4 expression, contributing to the immunosuppressive characteristics of the TME in KL-NSCLC cells, whereas, restoring DPP4 expression promotes NK cell recruitment, facilitates immune activation, and enhances the effects of anti-PD-1 therapy. These results highlight DPP4 as a key immune modulator and a promising therapeutic target, offering a novel strategy to overcome immune resistance and enhance immunotherapy outcomes in this challenging subset of lung cancer.

overall_design: Examination of gene expression using H2122 cells with two biological replicates. H2122-LUC cells were used as controls, and expression levels were compared with H2122-DPP4 cells.

first: Toshiyuki

last: Tenma

first: Ryohei

last: Yoshida

first: Kiichi

last: Nitanai

first: Toshihiro

last: Nagato

first: Kyohei

last: Oyama

first: Nobunari

last: Sasaki

first: Mizuki

last: Homme

first: Chie

last: Mori

first: Takayuki

last: Ohkuri

first: Yusuke

last: Ono

first: Shoichiro

last: Tange

first: Yoshinori

last: Minami

first: Hiroya

last: Kobayashi

last: Mizukami

first: David

last: Barbie

first: Shunsuke

last: Kitajima

first: Takaaki


title: Control and Tgfbr2 cKO Mouse Endometrial Epithelial Organoids +/- E2/MPA Treatment

city: Houston

first: Peixin

last: Jiang

state: TX

address: 1515 Holcombe Blvd

institute: UT MD Anderson Cancer Center

summary: Evaluate the changes in estrogen and progesterone response within the endometrial epithelium of mice with and without uterine Tgfbr2 expression.

overall_design: Endometrial epithelial organoids from control and Tgfbr2 cKO mice were cultured for two days prior to treatment with either vehicle (6 days) or 10nM E2 (2 days) + 10 nM E2/1 µM MPA (4 days). After six days of treatment, organoids were collected in trizol and RNA was isolated for RNAseq.

first: Sydney

last: Parks

first: Diana

last: Monsivais


title: Early life starvation and Hedgehog-related signaling activate innate immunity downstream of daf-18/PTEN and lin-35/Rb causing developmental pathology in adult C. elegans

city: Durham

first: Ivan

last: Falsztyn

state: NC

address: French Science Center

department: Biology

institute: Duke University

summary: Early life experiences such as malnutrition can affect development and adult disease risk, but the molecular basis of such protracted effects is poorly understood. In the nematode C. elegans, extended starvation during the first larval stage causes the development of germline tumors and other abnormalities in the adult gonad, limiting reproductive success. Insulin/IGF signaling (IIS) acts through WNT signaling and lipid metabolism to promote starvation-induced gonad abnormalities, but IIS-independent modifiers have not been identified. We show that the tumor suppressors daf-18/PTEN and lin-35/Rb act independently of IIS to suppress starvation-induced abnormalities. We found that lin-35/Rb antagonizes activity of the Hedgehog (Hh) signaling homologs ptr-23/PTCH-related, wrt-1/Hh-like, wrt-10/Hh-like, and tra-1/GLI, which promote starvation-induced abnormalities. These Hh-related genes transcriptionally activate several genes associated with innate immunity in adults, which also promote starvation-induced gonad abnormalities. Surprisingly, we found that in addition to causing developmental abnormalities, early-life starvation induces an innate immune response later in life, leading to increased resistance to multiple bacterial pathogens. This work identifies a critical tumor-suppressor function of daf-18/PTEN independent of IIS, and it defines a regulatory network, including lin-35/Rb, Hh-related signaling, and the innate immunity pathway, that affects development of tumors and other developmental abnormalities resulting from early life starvation. By revealing that early-life starvation increases immunity later in life, this work suggests a fitness tradeoff between pathogen resistance and developmental robustness.

overall_design: Bulk RNA-seq profiling of early adult wild type (N2) Caenorhabditis elegans. Individuals experienced 8 days of L1 arrest then were recovered on the indicated food source (RNAi treatment)

middle: B

first: Jingxian

last: Chen

first: Rojin

last: Chitrakar

first: James

middle: L

last: Jordan

first: Ryan

last: Baugh


title: Connecting cilium, stress response and proteostasis abnormalities inform variant and therapy assessment in RPGRIP1 retinal organoids [RNA-Seq]

first: Nader

last: Aryamanesh

overall_design: RNA seq profiling of wild type (Control-1) and RPGRIP1 variant (LCA-1 and MS-VUS)  retinal organoids performed in triplicate.

first: To Ha

last: Loi

first: Anson

last: Cheng

first: Hani

last: Kim

first: Milan

last: Fernando

first: Benjamin

last: Nash

first: John

last: Grigg

first: Pengyi

last: Yang

first: Anai

last: Gonzalez Cordero

first: Robyn

last: Jamieson


title: BLU-222, a Potent CDK2 Inhibitor, Synergizes with CDK4/6 Inhibitors to Overcome Drug Resistance in HR–Positive and Triple-Negative Breast Cancer by Inducing p21 and p27

first: Khandan

last: Keyomarsi

state: Texas

department: Experimental Radiation Onc

institute: University of Texas - MD Anderson Cancer Center

summary: Cyclin-dependent kinase 4/6 inhibitors (CDK4/6is) combined with endocrine therapy are the standard first-line treatment for hormone receptor-positive, HER2−negative (HR+/HER2−) metastatic breast cancer, but resistance develops over time. In triple-negative breast cancer (TNBC), the efficacy of CDK4/6i is unclear. Our study shows that the selective CDK2 inhibitor BLU-222, while effective alone, enhances synergistic activity when combined with CDK4/6i in resistant HR+/HER2− and TNBC models, leading to increased apoptosis and cell cycle arrest. In vivo, combining BLU-222 with palbociclib or ribociclib showed significant antitumor effects across 8 models, resulting in durable tumor regression and extended survival. Mechanistically, BLU-222, alone or with palbociclib, upregulated p21 and p27 expression and enhanced p21 binding to CDK2 as well as p21 and p27 binding to CDK4 complexes. CRISPR knockout of p21 or p27 in palbociclib-resistant cells eliminated this synergy. Further, RNA sequencing showed that the combination treatment upregulated senescence and interferon pathways, offering insights into the observed therapeutic synergy.

overall_design: Once the transplanted tumors reached an average volume of 200 mm³, mice were randomized to the indicated treatment arms and treated with vehicle, palbociclib (50 mg/kg once daily, oral gavage), BLU-222 (60 mg/kg twice daily, oral; 50 mg/kg or 100mg/kg twice daily, oral ), or a combination of palbociclib (50 mg/kg) and BLU-222 (50 or 60 mg/kg) plus fulvestrant (2.5 mg/kg, once weekly, subcutaneous). At the end point, tumors were collected for RNA-seq analysis.

first: Linjie

last: Luo

first: Xiayu

last: Rao

first: Jing

last: Wang


title: Macro-scale, scaffold-assisted model of the human bone marrow endosteal niche using hiPSC-vascularized osteoblastic organoids

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

country: Switzerland

institute: University of Basel

summary: Endosteal bone marrow (BM) niches are crucial to sustain non-steady-state hematopoiesis but are challenging to be modeled in their cellular and molecular complexity in standardized, human settings. We report a developmentally guided approach to generate a macro-scale organotypic model of BM endosteal niches (engineered vascularized osteoblastic niche [eVON]) based on human induced pluripotent stem cells and porous hydroxyapatite scaffolds. The eVON contains long-lasting vascular networks covered by pericytes and neural fibers within an osteogenic matrix. Key niche signals (CXCL12, KITLG, and vascular endothelial growth factor A [VEGFA]) are expressed in human-specific patterns. The system supports hematopoiesis in vitro and preserves hematopoietic stem and progenitor cell (HSPC) multilineage repopulation capacity in vivo. eVON perturbations at cellular (removing vasculature) and molecular (deregulating VEGF-A and CXCL12 signaling) levels enabled the investigation of the contribution of endosteal vasculature to myelopoiesis. The eVON faithfully captures phenotypic, structural, and functional features of human endosteal BM, enabling the study of pathophysiological interactions with hematopoietic cells.

overall_design: Three different hiPSC lines (409B2, Wibj and WTC) are differentiated into osteogenic and vascular cells in porous hydroxyapatite scaffolds to generate a standardized and physiological model of the human bone marrow endosteal niche, termed as engineered vascularized osteoblastic niche (eVON). eVONs generated from 409B2, Wibj and WTC cells were compared at transcriptomic level through scRNA-seq.

first: Qing

last: Li

first: Marina

last: Nikolova

first: Gangyu

last: Zhang

first: Igor

last: Cervenka

first: Dominik

last: Bürri

first: Evelia

last: Plantier

first: Andrea

last: Mazzoleni

first: Anaïs

last: Lamouline

first: Barbara

last: Treutlein

first: Ivan

last: Martin

first: Andrés

last: García-García


title: Direct recruitment of TONSOKU by the N-terminal tails of histone variants H2A.X and  H2A.W coordinates DNA repair

city: hangzhou

first: li

last: qi

address: xihu

country: China

institute: zhejiang university

summary: Histone variants play crucial roles in DNA replication and DNA damage repair. Plant TONSOKU (TSK) specifically recognizes unmethylated histone H3.1 to bind post-replicative chromatin for DNA repair, but the precise mechanisms of TSK recruitment to double-stranded break (DSB) sites remain unclear. Here, we discovered that the leucine-rich repeats (LRR) domain of TSK recognizes the N-terminal tail of the histone variant H2A.X, the phosphorylated form of which (also known as γ-H2A.X) is a critical marker of DSBs at both replication forks and euchromatin. Additionally, the LRR domain of TSK recognizes the N-terminal tail of the plant-specific histone H2A variant H2A.W, which is essential for DSB repair in heterochromatin, but not H2A.Z, which primarily regulates gene expression. A motif containing multiple basic and acidic residues (BAR motif), unique to H2A.Z, prevents TSK from binding. Notably, mutations that abolish TSK-H2A.X/W binding interfere with TSK-mediated DNA repair and root development. Genetic analyses indicate that H2A.X and H2A.W are redundantly required for DNA damage repair in vivo, with the N-terminus of H2A.X being particularly indispensable. This study reveals a novel H2A.X/W-dependent mechanism for recruiting the DNA repair protein TSK, highlighting the critical role of their previously uncharacterized N-terminal tails in plants.

overall_design: RNA-seq profiling of Col, h2a.x-1, h2a.w-2, tsk and h2a.x/w-2 in 7-day-old seedling

first: Qi

first: Jie

last: Dong


title: A functional genomics atlas enhanced by convolutional neural networks facilitates clinical interpretation of disease relevant variants in non-coding regulatory elements [ATAC-seq]

city: Rotterdam

first: Tahsin Stefan

last: Barakat

state: South Holland

address: Dr. Molewaterplein 40

department: Clinical Genetics

country: Netherlands

institute: The Erasmus University Medical Center

summary: We provide a novel functional genomics atlas of non-coding regulatory elements derived from human neural stem cells (NSCs), using the massively parallel reporter assay ChIP-STARR-seq. ChIP-STARR-seq was performed in NSCs using chromatin immunoprecipitation for H3K27ac, H3K4me1, YY1 and SOX2, and the generated STARR-seq plasmid reporter libraries were profiled for their enhancer activity in H9 derived NSCs and human embryonic stem cells. Subsequently a multi-omics data integration was performed, including the development of a convolutional neural network called BRAIN-MAGNET that allows to predict the effect of single nucleotide variants in non-coding regulatory elements on the enhancer activity. The various data sets generated in this study include ChIP-seq experiments in NSCs, DNA sequencing of the generated plasmid libraries, RNA-seq of transfected cells from the ChIP-STARR-seq experiments, generated ATAC-seq data sets used for data integration and the contribution scores from BRAIN-MAGNET for each nucleotide assessed in this ChIP-STARR-seq study.

overall_design: ATAC-seq for human neural stem cells (NSC_ATAC_rep1 and NSC_ATAC_rep2) and human embryonic stem cells  (ESC_ATAC_rep1 and ESC_ATAC_rep2)= 4 datasets

first: Stefan

first: Ruizhi

last: Deng


title: A first-in-class small-molecule inhibitor targeting AVIL exhibits safety and antitumor efficacy in preclinical models of glioblastoma

city: Charlottesville

first: Zhongqiu

last: Xie

state: VA

address: 1574 Broad Crossing Rd, , Charlottesville

institute: university of virginia

summary: Compound A  or DMSO treatment with GBM U87 cell samples

overall_design:
Gene expression of U87 cells treated with DMSO or Compound A.

>>>Submitter states that IDAT files are not available for this study because it was performed a long time ago and the files were not kept <<<

first: Sophia

first: Hui


title: Spatially resolved single-cell analysis uncovers protein kinase Cδ-expressing microglia with anti-tumor activity in glioblastoma [scRNA-seq]

city: Charlestown

first: Reid

last: Mcneil

state: MA

address: 149 13th Street

department: Cancer Research

institute: Mass General Hospital

summary: The glioblastoma (GBM) microenvironment contains resident immune cells with intrinsic anti-tumor potential, particularly microglia. Understanding the single-cell spatial heterogeneity and interactions between immune cells and brain tumor–initiating cells (BTICs) is essential for identifying therapeutic targets to reprogram immune responses and suppress BTIC growth. Using single-cell and spatial transcriptomics, we mapped immune cell populations in the GBM microenvironment and identified signaling networks mediating immune–cancer cell interactions. We discovered a previously unrecognized subset of microglia expressing protein kinase Cδ (PKCδ) with anti-tumor activity against BTICs. The presence of PKCδ-expressing microglia was validated in human GBM specimens. Enhancing PKCδ in microglia via adeno-associated virus or niacin increased phagocytosis of patient-derived BTICs in vitro and improved survival in GBM-bearing mice. Data from The Cancer Genome Atlas (TCGA) revealed that high PKCδ expression correlates with increased apoptosis, phagocytosis, and immune signaling pathways. These findings offer highlight PKCδ+ microglia as a promising therapeutic target in GBM.

overall_design: Using GBM mouse models, mice were either treated with niacin or untreated controls, the tumors were resected from the mice and analyzed using single-cell RNAseq.

first: Reza

last: Mirzaei

last: McNeil

first: Charlotte

last: D’Mello

first: Britney

last: Wong

first: Susobhan

last: Sarkar

first: Frank

last: Visser

first: Candice

last: Poon

first: Pinaki

last: Bose

first: Wee

last: Yong


title: Relative adrenal insufficiency is a risk factor in pediatric sepsis

city: Lexington

first: Xiang-An

last: Li

address: 741 S Limestone

institute: University of Kentucky

summary: Glucocorticoid (GC) therapy had been strongly recommended for pediatric sepsis (grade 1A). However, the recommendation was changed to grade 2C in 2020. Thus, there is an urgent need to determine if GC therapy is beneficial in pediatric sepsis. Relative adrenal insufficiency (RAI) develops in 33.3% of pediatric septic patients. But little is known about the pathogenesis of RAI and whether GC therapy should be based on the status of RAI. In this study, we utilized 21-day-old SF1CreSRBIfl/fl mice as a pediatric RAI mouse model to assess the pathogenesis of RAI and evaluate GC therapy. We found that RAI mice were susceptible to both cecal ligation and puncture (CLP) and cecal slurry induced septic death. SF1CreSRBIfl/fl mice featured persistent inflammatory responses, and they were effectively rescued by GC therapy. RNA-seq analysis revealed that RAI leads to the persistent inflammatory responses mainly due to transcriptional dysregulation of AP-1 and NF-κB. A number of prognostic biomarkers reported in pediatric septic patients were also identified in RAI mice. Our findings support a precision medicine approach to guide GC therapy for pediatric patients - use of GC based on the status of RAI.

overall_design: Bulk RNA sequencing of liver from 21-day-old SRBIfl/fl and SF1CreSRBIfl/fl mice (n=3) at CLP 6h

first: Dan

last: Hao


title: A functional genomics atlas enhanced by convolutional neural networks facilitates clinical interpretation of disease relevant variants in non-coding regulatory elements [STARR-RNA-seq]

first: Tahsin Stefan

overall_design: STARR-RNA-seq datasets after transfection into NSCs or ESC = 16 datasets total


title: Distinct transcription factor interactions drive HOXB13 activity in different stages of prostate cancer [ChIP-seq ]

city: Vancouver

first: Nathan

last: Lack

state: British Columbia

address: 2260 Oak st.

country: Canada

institute: Vancouver Prostate Centre

summary: Homeobox-B13 (HOXB13) is a master transcriptional regulator which is exclusively expressed in the prostate tissue and has been shown to be crucial for its embryonic development. There is extensive clinical and experimental evidence to support the role of HOXB13 in prostate cancer (PCa). Yet, despite this critical role, the function of HOXB13 remains controversial with some studies supporting an oncogenic role and others demonstrating a tumor-suppressive role.  While there is a clear relationship between HOXB13 and AR there are conflicting studies if HOXB13 is itself regulated by AR. Interrogating various AR +ve and AR -ve in-vivo and in-vitro models, in this study, we demonstrate that HOXB13 is crucial for the growth and proliferation of PCa regardless of its androgen dependency. We show that HOXB13 activity in these different models is mediated via interactions with cell-specific transcription factors. Yet despite the diverse transcription factor interactions, HOXB13 activity is commonly modulated by SMARCD2, a member of the mSWI/SNF chromatin remodeling complex. The HOXB13/SMARCD2 interaction is stabilized through interactions with transcription factors. This interaction alters the chromatin accessibility at HOXB13 binding sites which leads to increased proliferation in PCa.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for HOXB13 in LNCaP and PC3 cells, for SMARCD2 in PC3 cells, and SMARCD2 in LNCaP cells.

first: Shreyas

last: Lingadahalli

first: Betul

last: Ersoy

first: Umut

last: Altintas


title: A functional genomics atlas enhanced by convolutional neural networks facilitates clinical interpretation of disease relevant variants in non-coding regulatory elements [plasmid DNA-seq]

last: Barakat

overall_design: DNA-seq of ChIP-STARR-seq plasmid library (HIST: H3K27ac and H3K4me1, TF: SOX2 and YY1) in human neural stem cells = 4 datasets

first: Stefan

first: Ruizhi

last: Deng


title: Distinct transcription factor interactions drive HOXB13 activity in different stages of prostate cancer [ATAC-seq ]

overall_design: Assay for transposase-accessible chromatin with sequencing (ATAC-seq) for HOXB13 over expression in DU145 cells.


title: Intrinsic RB activation induces tumoral and stromal anti-tumor responses that limit triple-negative breast cancer [scRNA-Seq]

status: Public on Nov 17 2025

city: Buffalo

first: Jianxin

last: Wang

state: NY

address: 665 Elm Street

department: Molecular and Cellular Biology

institute: Roswell Park Comprehensive Cancer Center

summary: The RB tumor suppressor is a key regulator of cell cycle progression that is often inactivated in triple-negative breast cancer (TNBC). Recent studies indicate that drugs activating RB have multiple tumor-suppressing effects on the tumor and the tumor microenvironment (TME). Here, we utilize a constitutively active RB protein incapable of being phosphorylated and inactivated by CDKs (RBΔCDK) to assess the intrinsic sufficiency of RB activation on tumor suppression. Expression of RBΔCDK in TNBC cell lines uniformly inhibited proliferation. Transcriptomic analysis revealed suppression of cell cycle genes and the induction of genes associated with interferon response. Similarly, tumor growth and metastasis were suppressed in RBΔCDK expressing human xenograft and mouse syngeneic tumor models. RB activation was sufficient to dramatically alter the TME, wherein tumor growth suppression was mediated by CD8+ T cells. Together, these data indicate that active RB suppresses TNBC progression in cancer cell-autonomous and non-autonomous mechanisms.

overall_design: Patient derived TNBC cell lines (HCC1806 and MDA-MB 231) with RBΔCDK isoform and mouse derived TNBC cell lines (AT-3 and 4T1) with RBΔCDK isoform were seeded in 6 well dish at a denisty of 100,000 cells/well. Following 24 hours, the cells were treated with 0.1% DMSO and Doxycycline (1 μg/mL). The tretments were done in triplicates. The cells were exposed to the Doxycycline for 48 hours and RNA was extracted using Quiagen RNeasy plus kit.

first: Yin

last: Wan

first: Thomas

last: O’Connor

first: Vishnu

last: Kumarasamy

first: Ioannis

last: Sanidas

first: Scott

middle: I

last: Abrams

first: Agnieszka

middle: K

last: Witkiewicz

first: Erik

middle: S

last: Knudsen


title: Antioxidant program of islet-resident macrophages preserves β cell physiology [dataset 3]

city: Paris

first: Nicolas

last: Venteclef

address: 156 rue de Vaugirard

country: France

institute: Institut Necker Enfants Malades, INSERM U1151

summary: Macrophages residing inside mouse pancreatic islets have an activated phenotype at steady-state. We revealed that they also harbor an antioxidant profile driven by the cystine/glutamate antiporter SLC7A11. We thus explored the role of SLC7A11 in islet-resident macrophages under steady-state.

overall_design: Islets were isolated and pooled from 6-8 myeloid Slc7a11-MacWT and MacKO (LysMCre/+Slc7a11fl/fl ) mice and dissociated into single cells to FACS-sort CD45+ immune cells. Cells were used for single cell RNA sequencing using 10X genomics.

first: E

last: Dalmas

first: A

last: Jalon

first: M

last: Diedisheim


title: A functional genomics atlas enhanced by convolutional neural networks facilitates clinical interpretation of disease relevant variants in non-coding regulatory elements [wt RNA-seq]

first: Tahsin Stefan

overall_design: RNA-seq datasets for wildtype NSCs = 2 datasets total


title: Intrinsic RB activation induces tumoral and stromal anti-tumor responses that limit triple-negative breast cancer [RNA-Seq]

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: A disintegrin-like and metalloproteinase with thrombospondin motifs 18 (ADAMTS18) cleaves fibronectin and regulates its fibrillogenesis

city: Kuopio

first: Nihay

last: Laham Karam

address: Neulaniementie 2

department: A.I. Virtanen Institute

country: Finland

institute: University of Eastern Finland

summary: Remodelling of the extracellular matrix plays a crucial role in the development, maintenance and repair of all tissues. Therefore, identifying the regulators of this process is essential. Among these, A disintegrin and metalloproteinase with a thrombospondin motif 18 (ADAMTS18) has been implicated in fibronectin (FN) matrix regulation. Knockout of ADAMTS18, either in mouse models or in vitro, was shown to lead to FN accumulation, mutation in epithelial branching and reduction in endothelial sprouting. However, the mechanisms by which ADAMTS18 influences endothelial specific functions and the extracellular matrix, particularly in the regulation of FN fibrils remains unclear. In this study, using both siRNA-mediated knockdown and overexpression of ADAMTS18 in primary endothelial cells, we delineated some of these mechanisms.  Using global RNA sequencing of endothelial cells we demonstrated differential gene regulation of vessel-development and endothelial adhesion genes with ADAMTS18-siRNA knockdown, whereas cell matrix and cell cycle associated genes were affected by overexpression of ADAMTS18. Consistent with the later, we observed reduced endothelial cell proliferation and altered cell cycle with ADAMTS18 overexpression. Using mass spectrometry, we identified two sites in FN that are proteolytically cleaved by ADAMTS18, including a cleavage site in the linker FN-I5-6. Cleavage at this site generated FN molecules lacking the N-terminal FN-I1-5 (29kDa) fragment that is known to be essential for FN fibrillogenesis. Accordingly, ADAMTS18 overexpression greatly impaired FN fibrillogenesis in endothelial cultures and in co-culture with fibroblasts. Our results implicate ADAMTS18 in FN-associated extracellular matrix remodelling and suggest an important role for ADAMTS18 in endothelium biology.

overall_design: The aim of this study was to study the effects of siRNA knockdown of human ADAMTS18 on gene expression over time. Human umbillical endothelial cells (HUVECs) were transfected with siRNA to knockdown ADAMTS18. For siRNA knockdown, dicer-substrate oligonucleotides hs.Ri.ADAMTS18.13.1, hs.Ri.ADAMTS18.13.2, hs.Ri.ADAMTS18.13.3 and DsiRNA control (TriEFCTA Kit DsiRNA Duples; IDTDNA) were transfected into HUVECs at a concentration of 10nM using Oligofectamine (Thermo Fisher Scientific, #12252011). HUVECs were collected 24 or 96 hours after transfection and RNA isolated. The cDNA library and RNA sequencing were performed at AZENTA.

last: Laham-Karam

first: Maria

last: Barbiera

first: Seppo

last: Ylä-Herttuala

first: Mikko

last: Gynther

first: Tetsuya

last: Terasaki

first: Suvi

middle: P

last: Jauhiainen

first: Johanna

middle: p

last: Laakkonen

first: Michael

last: Jeltsch


title: Dietary sulfur amino acid restriction elicits a cold-like transcriptional response in inguinal but not epididymal white adipose tissue of male mice

city: Ithaca

first: Philip

last: Ruppert

address: 244 Garden Avenue

department: Division of Nutritional Sciences

institute: Cornell University

summary: Introduction: About 1 billion people are living with obesity worldwide. GLP-1-based drugs have massively transformed care, but long-term consequences are unclear in part due to reductions in energy expenditure with ongoing use. Diet-induced thermogenesis (DIT) and cold exposure (CE) raise EE via brown adipose tissue (BAT) activation and beiging of white adipose tissue (WAT). Methionine restriction (MetR) is a candidate DIT stimulus, but its EE effect has not been benchmarked against CE, nor have their tissue-level interactions been defined. Objective & Methods: In a 2×2 design (Control vs. MetR; room temperature, RT: 22 °C vs. CE: 4 °C for 24 h), we used male C57BL/6N mice to benchmark MetR-induced thermogenesis against CE and mapped how diet and temperature interact across tissues. Bulk RNA-seq profiled liver, iBAT, iWAT, and eWAT. Differential expression was modeled with main effects and a diet×temperature interaction. KEGG GSEA was used to assess pathway-level enrichment. Results: MetR increased EE at RT and shifted fuel use towards lipid oxidation, supporting MetR as a bona fide DIT stimulus. CE elevated EE across diets and blunted diet differences. Transcriptomic responses were tissue-specific: in liver, CE dominated gene induction while MetR and CE cooperatively repressed genes. The combination enriched glucagon/AMPK-linked and core metabolic pathways. In iBAT, CE dominated thermogenic and lipid-oxidation programs with minimal MetR contribution. In iWAT, MetR and CE acted largely additively with high concordance, enhancing fatty-acid degradation, PPAR signaling, thermogenesis, and TCA cycle pathways. In eWAT, robust co-dependent and synergistic differential expression emerged only with MetR+CE. Conclusion: MetR is a genuine DIT stimulus that remodels metabolism in a tissue-specific manner. Our study provides a tissue-resolved transcriptomic resource that benchmarks diet-induced (MetR) against cold-induced thermogenesis and maps their interactions across liver, iBAT, iWAT, and eWAT.

overall_design: RNA-seq profiling of Liver, iWAT, iBAT and eWAT from C57BL/6N mice (Taconic) exposed to Sulfur amino acid restriction (0.12% Methionine, 0% Cysteine) or Control diets (0.86% Methionine, 0% Cysteine) (Research diets cat no. A11051301B and A11051302B) for 7 days +/- 24h of Cold exposure (22°C to 4°C).

first: Philip M

first: Aylin

last: Güller

first: Marcus

last: Rosendal

first: Natasa

last: Stanic

first: Jan-Wilhelm

last: Kornfeld


title: Bile acids regulate lipid metabolism through selective actions on fatty acid absorption

city: Los Angeles

first: Thomas

middle: Q

last: de Aguiar Vallim

state: CA

address: MRL 3230/3240 675 Charles E. Young Drive South

department: Cardiology

institute: University of California, Los Angeles

summary: Intestinal lipid absorption, the entry point for fats into the body, requires the coordinated actions of bile acids and lipases. Here, we uncover distinct yet cooperative roles of bile acids in driving the differential uptake of dietary fatty acids. We first decreased the bile acid pool size by disrupting the rate-limiting enzyme in bile acid synthesis, Cyp7a1, using liver-directed gene editing in mice. Compared with lipase inhibition, reduced bile acids prevented diet-induced obesity, increased anorectic hormones, suppressed excessive eating, and improved systemic lipid metabolism. Remarkably, decreasing bile acids selectively reduced the absorption of saturated fatty acids but preserved polyunsaturated fatty acids. By targeting additional bile acid enzymes, we identified specific functions of individual bile acid species. Mechanistically, we show that cholic acid preferentially solubilizes polyunsaturated fatty acids into mixed micelles for intestinal uptake. Our studies demonstrate that bile acids can selectively control fatty acid uptake, revealing insights for future interventions in metabolic diseases.

overall_design: RNA-seq profiling of livers obtained from control CRISPR and Cyp7a1 CRISPR mice fed Western diet for 8 weeks.

first: Alvin

last: Chan

first: Kelsey

middle: E

last: Jarrett

first: Rochelle

middle: W

last: Lai

first: Madelaine

last: Brearley-Sholto

first: Angela

last: Cheng

middle: O

last: Taveras

first: Anne

last: Iwata

first: Michelle

last: Steel

first: Andrew

last: Lau

first: Emily

last: Whang

first: John

last: Kennelly

first: Yajing

last: Gao

first: Gabriella

last: Rubert

first: Heidi

last: Schmidt

last: Smith

first: Baolong

last: Su

first: Kevin

middle: J

last: Williams

first: Elizabeth

last: Tarling


title: A functional genomics atlas enhanced by convolutional neural networks facilitates clinical interpretation of disease relevant variants in non-coding regulatory elements [ChIP-seq]

first: Tahsin Stefan

last: Barakat

overall_design: ChIP-seq for H3K27ac, H3K4me1, SOX2 and YY1 + Input control in human neural stem cells; ChIP-seq for YY1 + Input control, and SOX2 + Input control in human embryonic stem cells = 16 datasets total

first: Stefan

first: Ruizhi

last: Deng


title: Single-nucleus transcriptomic profiling of human lung tissue in chronic obstructive pulmonary disease (COPD) [snRNA-seq]

city: New Haven

first: Maor

last: Sauler

state: CT

address: 300 Cedar Street

department: Section of Pulmonary, Critical Care, and Sleep Medicine

institute: Yale School of Medicine

summary: Chronic obstructive pulmonary disease (COPD) is clinically and molecularly heterogeneous. To investigate COPD heterogeneity, we performed single-nucleus RNA sequencing (snRNA-seq) on lung tissue from individuals with and without COPD spanning the full disease spectrum. We generated 1,516,727 high-quality cell transcriptomes from 146 lung lobes obtained from 141 subjects. The dataset captures broad shifts in cellular composition and disease-associated cell states in epithelial, stromal, and immune populations. These data define the cellular landscape of COPD heterogeneity, revealing molecular drivers and biomarkers that could inform therapeutic strategies.

overall_design: Snap-frozen lung tissues from 146 lobes of 141 subjects were processed for snRNA-seq. Lung tissues were obtained from participants in the Lung Transplant Research Consortium, including never-smokers, smokers without COPD, and individuals with COPD across GOLD stages I-IV. Nuclei were isolated and loaded onto the 10x Genomics Chromium platform for library construction, and sequencing was performed on the Illumina NovaSeq 6000.

first: Yuening

last: Zhang

first: Huanhuan

last: Wei

first: Jessica

last: Nouws


title: Functional Comparison to Ezh2 Reveals PRC2-Independent Functions of Jarid2 in Hematopoietic Stem Cell Lineage Commitment

city: St Louis

first: Grant

middle: A

last: Challen

state: MO

address: 660 Euclid Avenue

department: Medicine

institute: Washington University School of Medicine

summary: Our previous studies showed the Polycomb Repressive Complex 2 (PRC2) co-factor Jarid2 represses self-renewal transcriptional networks in mouse multipotent progenitor cells (MPPs).  But only a fraction of de-repressed HSC-specific genes were associated with loss of H3K27me3, implying Jarid2 may have non-canonical (PRC2-indpendent) in hematopoiesis.  Here we sought to delineate any PRC2-independnent functions by comparing stem and progenitor cells genetically deficient for either Jarid2 or Ezh2.  Loss of Ezh2 leads to increased myeloid differentiation in transplantation assays.  In contrast, loss of Jarid2 enhanced T-cell output.  Single cell transcriptomics showed while loss of Jarid2 had minimal impact across progenitor populations, loss of Ezh2 led to accumulation of lymphoid-biased MPP4 cells and B-cell progenitors in the bone marrow.  Functional assays confirmed a differentiation block at the pre-pro B-cell stage.  The maturational arrest of Ezh2-deficient B-cell progenitors contrasts with increased T-cell output from loss of Jarid2, suggesting Jarid2 has non-canonical functions in hematopoiesis.

overall_design: To explore the potentially divergent roles of the PRC2 co‑factor Jarid2 and its catalytic subunit Ezh2, we generated Mx1‑Cre conditional mouse models with floxed alleles of Jarid2 (Jarid2fl/fl) or Ezh2 (Ezh2fl/fl), enabling the targeted ablation of either gene. We then performed single-cell RNA-seq and single-cell multi-omics sequencing to dissect mechanistic differences between Jarid2 and Ezh2 loss-of-function. For Single Cell RNA-seq studies, primary recipient mice were euthanized 18 weeks post-transplant to collect cells, while two-month-old baseline mice were used for the single-cell multi-omics workflow.To further explore the potentially divergent effects of Jarid2 and Ezh2 loss of function on H3K27me3 repressive mark, we performed Cut and Tag analysis on KSL (c-Kit+, Sca1+, Lineage-) cells sorted from the 3 million WBM secondary transplanted recipients. We then assessed the whole genome and gene specific loci depletion of H3K27me3 repressive marker upon Jarid2 and Ezh2 loss of function.

first: Hassan

last: Bjeije

first: Wentao

last: Han

first: Shu

last: Lin

first: Nancy

last: Issa

first: Aishwarya

last: Krishnan

first: Infencia

last: Xavier Raj

first: Jason

last: Arand

first: Yanan

last: Li

first: Wei

last: Yang

first: Jeffrey

last: Magee


title: Leveraging Two Novel Droplet-Based Single-Cell RNA Sequencing Platforms: a Comparative Study With 10x Genomics

city: Moscow

first: Alesya

last: Maluchenko

address: Kulakova str. 20

country: Russia

institute: Moscow Center for Advanced Studies

summary: Here we performed a comparison of two droplet-based high-throughput single-cell platforms, namely, SeekOne and MobiDrop with a widely-used commercial platform from 10x Genomics. The use of different types of samples allowed us to evaluate the performance of the platforms on cell suspensions of varying complexity and quality. 10x showed generally superior performance, although all platforms compared in this study showed acceptable gene yield and allowed identification of all expected cell types. Taking into account the cost and availability of devices and reagents required for each platform and the flexibility in the number of samples loaded onto the chip, SeekOne and MobiDrop might serve as a good alternative. The results of the current comparison will support the community's efforts to compare different aspects, including sample amount requirements, throughput, cell quality, gene capture efficiency and cell type representativeness.

overall_design:
We analyzed the samples of human peripheral blood mononuclear cells, murine adrenal glands and human tumors to compare performance of the three scRNA-seq platforms (10x, SeekOne, MobiDrop).
To compare 3-primed assays of 10x, SeekOne and MobiDrop pooled PBMC derived from 4 patients and murine adrenal gland samples obtained from two-week-old or three-day-old mice were used. Human tumor tissue samples were obtained from two operated patients with non-functioning pancreatic neuroendocrine tumors to compare 10x and MobiDrop 5-primed assays.

first: Alesia

first: Ekaterina

last: Avsievich

first: Iaroslava

last: Zvorygina

first: Zoia

last: Antysheva

first: Denis

last: Maksimov

first: Margarita

last: Boytsova

first: Dmitry

last: Tabakov

first: Natalia

last: Bodunova

first: Olga

last: Glazova

last: Tychinin

first: Alexander

last: Bolbat

last: Petriaikina

last: Svetlichnyy

first: Sergey

last: Yudin

first: Anton

last: Keskinov

first: Vladimir

first: Mary

last: Woroncow

first: Veronika

last: Skvortsova

first: Julia

last: Krupinova

first: Pavel

last: Volchkov


title: An unbiased whole- genome open -reading frame overexpression screen identifies B3GALT2, a novel inducer of cellular ASO activity

first: Roland

last: Schmucki

address: Grenzacherstrase

institute: F. Hoffmann - La Roche AG

summary: Antisense oligonucleotides (ASOs) are a promising class of therapeutics, made out of chemically modified synthetic single-stranded nucleic acid molecules, yet their clinical translation is often hindered by challenges in cellular uptake and delivery. Identifying cellular factors that modulate ASO activity is crucial for overcoming these limitations. Utilizing a whole-genome open-reading frame (ORF) overexpression screen with a genetic splice reporter system to identify genes that can increase or decrease ASOs activity, we identified B3GALT2 as the most significant hit for increasing ASO activity. Subsequent validation in HEK293 and U2OS cell lines demonstrated that B3GALT2 overexpression consistently and significantly enhances the activity of both splice-switching and mRNA-degrading ASOs across different targets (CD81, MALAT1, CERS2). Transcriptomic analysis of B3GALT2-overexpressing cells showed upregulation of endocytic scavenger receptors CUBN and SCARA5, and gene set enrichment analysis indicated an enrichment of proteins involved in clathrin-dependent endocytosis. Mechanistic investigations revealed that B3GALT2 overexpression leads to a significant increase in ASO uptake. These findings highlight B3GALT2 as a novel modulator of ASO cellular entry and establish a new avenue for potentially improving ASO-based therapeutic strategies.

overall_design: Comparison of transcriptomic profiles of HEK293 cells under three conditions: wild-type, cells with doxycycline-inducible B3GALT overexpression, and control cells carrying an empty vector. Induction with doxycycline (0 ng/mL) was performed for 72 hours, and RNA was extracted for sequencing. The key variable under investigation is the effect of B3GALT2 overexpression on gene expression.

last: Hesselmann

first: Liza

last: Malong

first: Fililp

last: Roudnicky


title: Spatial transcriptomic profiling of FFPE and frozen colorectal cancer tissues

city: Bangkok

first: Thanawat

last: Suwatthanarak

address: 2 Wanglang Road, Bangkok-Noi

country: Thailand

institute: Mahidol University

summary: This dataset contains spatial whole-transcriptome profiles from colorectal cancer (CRC) tissues preserved using formalin-fixed paraffin-embedded (FFPE), fresh frozen (FF), and snap frozen (SF) methods. Samples were obtained from a patient with stage IV CRC during surgical resection at Siriraj Hospital, Mahidol University, Thailand. Each tissue type was sectioned, stained for Pan-cytokeratin (PanCK), CD45, and SYTO13, and analyzed using the NanoString GeoMx Digital Spatial Profiler with the Human Whole Transcriptome Atlas panel. A total of 36 areas of illumination (AOIs) representing epithelial (PanCK⁺), immune (CD45⁺), and stromal (PanCK⁻/CD45⁻) compartments were collected. Sequencing was performed on an Illumina NovaSeq 6000 platform, and raw counts were processed using NanoString DSP Analysis Suite v3.1 and R for normalization and quality control. This dataset provides spatially resolved gene-expression information across different preservation conditions of CRC tissues to support comparative analysis and method evaluation in spatial transcriptomics.

overall_design: This study compares spatial transcriptomic profiles of colorectal cancer (CRC) tissues preserved using three methods: formalin-fixed paraffin-embedded (FFPE), fresh frozen (FF), and snap frozen (SF). All samples were obtained from a patient with stage IV CRC to evaluate how preservation methods affect spatial whole-transcriptome measurements. Spatial gene-expression data were generated using the NanoString GeoMx platform, covering epithelial, immune, and stromal regions within each tissue type. The dataset includes 36 spatially resolved transcriptomic profiles and provides a resource for assessing consistency and data quality across different preservation approaches in CRC research.

first: Kullanist

last: Thanormjit

first: Vitoon

last: Chinswangwatanakul

first: Pariyada

last: Tanjak


title: Inhibition of Acetyl-CoA metabolic enzymes by EVT0185 impairs hepatic stellate cell activation and reverses MASH and fibrosis in mouse models.

city: Hamilton

first: Russta

last: Fayyazi

state: ON

address: 1280 Main St W

institute: McMaster University

summary: Metabolic Dysfunction-Associated Steatohepatitis (MASH) is characterized by liver steatosis and inflammation which lead to fibrosis following hepatic stellate cell (HSC) activation. Acetyl-CoA is fundamental for de novo lipogenesis (DNL) and cholesterol synthesis and can be derived from citrate via ATP citrate lyase (ACLY), or from acetate via acetyl-CoA synthetase (ACSS2). Here, we find that EVT0185, an ACLY and ACSS2 inhibitor, leads to resolution of MASH and fibrosis while lowering insulin and glucose in four distinct mouse models. EVT0185 also reduces fibrosis alone and in combination with semaglutide and more effectively than bempedoic acid in a model not characterized by steatosis or insulin resistance. Spatial transcriptomic and scRNAseq reveal marked downregulation of cholesterol synthesis in HSCs with EVT0185 treatment in vivo and in vitro. These data indicate a critical role for ACLY and ACSS2 in HSCs and suggest further clinical evaluation of EVT0185 for reducing MASH and fibrosis may be warranted.

overall_design: To investigate transcriptomic effects of EVT0185 treatment on activated human hepatic stellate cells (HSCs), bulk RNA-seq data was obtained from LX-2 cells, a human HSC immortalized cell line. Two cell lines were generated from the LX-2 cells: One stably expressing an empty control vector (PRP-empty) or another expressing human SLC27A2 (PRP-SLC27A2). All cells were treated with TGFB1 to induce the activated HSC phenotype, and either DMSO or 30 µM EVT0185 for 24 hours. Overall, 4 experimental conditions of n = 3 replicates were generated: PRP-empty DMSO; PRP-empty EVT0185; PRP-SLC27A2 DMSO; PRP-SLC27A2 EVT0185.

first: Fiorella

last: Di Pastena

first: Jaya

last: Gautam

first: James

last: Lally

first: Estelle

last: Grasset

first: Gregory

last: Steinberg


title: ZFTA–RELA ependymomas make itaconate to epigenetically drive fusion expression [ATAC-Seq]

city: Ann Arbor

first: Arul

last: Chinnaiyan

state: MI

address: 1500 East Medical Center Dr

department: MCTP

institute: University of Michigan

summary: ZFTA-RELA ependymomas are malignant brain tumors that are frequently lethal. They are defined by fusions formed between the putative chromatin remodeler ZFTA and the NFkB-mediator-RELA. We identified that ZFTA-RELA cells produced itaconate, a key macrophage-associated immunomodulator metabolite. However, itaconate production by tumor cells and its tumor-intrinsic role are not well-established. Itaconate is synthesized by the enzyme Aconitate Decarboxylase-1 (ACOD1) and the ZFTA-RELA fusion upregulated ACOD1 in an NFkB-dependent manner. Additionally, itaconate production enabled a feed-forward system that maintained pathogenic ZFTA-RELA fusion expression through epigenetic activation. To supply the metabolic fuel needed to generate itaconate, these tumors epigenetically activated PI3K/mTOR signaling to enhance glutaminolysis, which provided the carbons necessary for itaconate synthesis. Consequently, antagonizing glutamine metabolism lowered pathogenic ZFTA-RELA levels and was potently therapeutic in multiple in vivo models. Finally, combining glutamine antagonism with PI3K/mTOR inhibition abrogated spinal metastasis. Our data demonstrate that ZFTA-RELA ependymomas subvert a macrophage-like itaconate metabolic pathway to maintain expression of the ZFTA-RELA fusion driver, implicating itaconate as an oncometabolite. Taken together, our results position itaconate upregulation as a previously unappreciated driver of ZFTA-RELA ependymomas. This study therefore has implications for future drug development for children with this devastating brain tumor and will further our understanding of oncometabolites as a novel class of therapeutic dependencies in cancers.

overall_design: ZFTA-RELA fusion  mouse neural stem cells (mNSCs) were treated with Citraconate (ACOD1 antagonist) or an EZH2 inhibitor (GSK343)

first: Siva Kumar

last: Natarajan

first: Joanna

last: Lum

last: Haggerty-Skeans

first: Minal

last: Nenwani

first: Sanjana

last: Eyunni

first: Mateus

last: Mota

first: Jill

middle: M

last: Bayliss

first: Akash

last: Deogharkar

first: Erin

middle: T

last: Hamanishi

first: Matthew

last: Pun

first: Stefan

last: Sweha

first: Simon

last: Hoffman

first: Eleanor

last: Young

first: Qiuyang

last: Zhang

first: Rijul

last: Mehta

first: Olamide

last: Animasahun

first: Pranav

last: Narayanan

first: Sushanth

last: Sunil

first: Abhijit

last: Parolia

first: Peter

last: Sajjakulnukit

first: Pooja

last: Panwalkar

first: Robert

last: Doherty

first: Madison

last: Clausen

first: Derek

last: Dang

first: Debra

last: Hawes

first: Fusheng

last: Yang

first: Mariarita

last: Santi

first: Alexander

last: Judkins

first: Yelena

last: Wilson

first: Thomas

last: Vigil

first: Andrea

last: Franson

first: Richard

last: Mortensen

first: Tatsuya

last: Ozawa

last: Griesinger

first: Eric

last: Holland

first: Nicholas

last: Foreman

first: Kulandaimanuvel

last: Antony Michaelraj

first: Sameer

last: Agnihotri

first: Michael

last: Taylor

last: Gilbertson

first: Carl

last: Koschmann

first: Costas


title: Antioxidant program of islet-resident macrophages preserves β cell physiology [dataset 4]

first: Nicolas

last: Venteclef

summary: Macrophages residing inside mouse pancreatic islets have an activated phenotype at steady-state. We revealed that they also harbor an antioxidant profile, expressing CD9. We therefore explored the transcriptomic signature of CD9high versus CD9low macrophages using single cell RNA sequencing.

overall_design: Islets were isolated and pooled from 6-8 myeloid WT mice and dissociated into single cells to FACS-sort CD45+ immune cells. Cells were used for single cell RNA sequencing using a TotalSeq-B0813 anti-mouse CD9 antibody (Biolegend Cat# 124823) and 10X genomics.

first: E

last: Dalmas

first: A

last: Jalon

first: M

last: Diedisheim


title: BPTF regulstes androgen receptor activity by enhancing chromatin accessibility and stabilizing the AR-FOXA1 interaction [ATAC-Seq]

city: Baltimore

first: Jianfei

last: Qi

state: MD

address: 655W baltimore street

department: Biochemistry and Molecular Biology

institute: University of Maryland

summary: BPTF, the scaffolding subunit of the nucleosome remodeling factor (NURF) complex, has been implicated in the progression of various malignancies. However, its role in prostate cancer (PCa) remains poorly understood. Here, we demonstrate that BPTF is upregulated in castration-resistant prostate cancer (CRPC) and promotes disease progression. RNA-seq revealed that BPTF primarily upregulates the expression of androgen receptor (AR) target genes. ChIP-seq showed that BPTF facilitates AR binding to enhancers and super-enhancers, while ATAC-seq demonstrated that BPTF increases chromatin accessibility to facilitate AR binding, partly via SMARCA1, a catalytic subunit of the NURF complex. Notably, BPTF/AR shared ChIP-seq peaks are highly enriched for FOXA1 motifs but only weakly enriched for AR motifs. We find that BPTF interacts with both FOXA1 and AR to form a protein complex in which FOXA1 recruits BPTF-AR to chromatin, while BPTF stabilizes the AR–FOXA1 interaction. Importantly, BPTF interacts with AR through its bromodomain, and a BPTF bromodomain inhibitor disrupts this interaction, leading to impaired AR signaling and suppressed PCa cell growth. In summary, our findings establish BPTF as a critical regulator of AR activity by promoting chromatin accessibility and stabilizing the AR–FOXA1 complex, highlighting BPTF as a potential therapeutic target in prostate cancer.

overall_design: ATAC-seq of Rv1 cells transduced with shControl, shBPTF, or shSMARCA1.

first: Hee-Young

last: Jeon


title: BPTF regulstes androgen receptor activity by enhancing chromatin accessibility and stabilizing the AR-FOXA1 interaction [RNA-Seq]

overall_design: RNA-seq profiling in Rv1 cells with knock down derivatives (shcontrol, shBPTF, shSMARCA1, shSMARCA5, and shFOXA1)


title: BPTF regulstes androgen receptor activity by enhancing chromatin accessibility and stabilizing the AR-FOXA1 interaction [Cut&Run]

overall_design: Cut&Run of BPTF, AR, and FOXA1 in Rv1 cells transduced with shControl, shBPTF, or shFOXA1. Cut&Run of BPTF and AR in Rv1 cells transduced with shControl or shAR. Cut&Run of H3K27ac, H3K4me1, and SMARCA1 in Rv1 cells transduced with shControl.


title: Targeted Antisense Oligonucleotide Treatment Rescues Developmental Alterations in Spinal Muscular Atrophy Organoids [bulk RNA-seq]

city: Rozzano

first: Simona

last: Lodato

address: via Manzoni 56

country: Italy

institute: IRCCS Humanitas Research Hospital

summary: Spinal muscular atrophy (SMA) is a severe neurological disease caused by mutations in the SMN1 gene, characterized by early onset and degeneration of lower motor neurons.Understanding early neurodevelopmental defects in SMA is crucial for optimizing therapeutic interventions. Using spinal cord and cerebral organoids generated from multiple SMA type I donors, we revealed widespread disease mechanisms beyond motor neuron degeneration. Single-cell transcriptomics uncovered pervasive alterations across neural populations, from progenitors to neurons, demonstrating SMN-dependent dysregulation of neuronal differentiation programs. Multi-electrode array analysis identified consistent hyperexcitability in both spinal and brain organoids, establishing altered electrical properties as a central nervous system-wide feature of pathogenesis. Early administration of an optimized antisense oligonucleotide (ASO) that restored SMN levels rescued morphological and functional deficits in spinal cord organoids across different genetic backgrounds. Importantly, this early intervention precisely corrected aberrant splicing in newly identified SMN1 targets enriched at critical nodes of neuronal differentiation. Our findings demonstrate that early developmental defects are core features of SMA pathogenesis that can be prevented by timely therapeutic intervention, providing new insights for optimizing treatment strategies.

overall_design: Spinal cord organoids (SCOs) after 2 months of in vitro differentiation from three wilde-type CTRL lines (n=3 lines, 3 individual replicates), two SMA lines (n=2 lines, 3 individual replicates) and SMA SCOs treated with r6-morpholino (MO) and r6-scrambled-MO, as negative control (n=2 lines, 4 individual replicates per each condition).

first: Irene

last: Faravelli

first: Paola

last: Rinchetti

first: Monica

last: Tambalo

first: Illia

last: Simutin

first: Lisa

last: Mapelli

first: Sara

last: Mancinelli

first: Matteo

last: Miotto

first: Mafalda

last: Rizzuti

last: D’Angelo

first: Chiara

last: Cordiglieri

first: Giulia

last: Forotti

first: Clelia

last: Peano

first: Paolo

last: Kunderfranco

first: Luca

last: Calandriello

first: Giacomo

last: Comi

first: Elvezia

last: Paraboschi

first: Eleonora

last: Pali

first: Francesca

last: Beatrice

first: Egidio

first: Serge

last: Przedborski

last: Nizzardo

first: Stefania

last: Corti


title: ZFTA–RELA ependymomas make itaconate to epigenetically drive fusion expression [ChIP-Seq]

first: Arul

last: Chinnaiyan

overall_design: ZFTA-RELA fusion cells (EPN1425 and mouse neural stem cells (mNSCs)) were treated with Citraconate (ACOD1 antagonist) or an EZH2 inhibitor (GSK343)

first: Siva Kumar

last: Natarajan

first: Joanna

last: Lum

first: James

last: Haggerty-Skeans

first: Minal

last: Nenwani

first: Sanjana

last: Eyunni

first: Mateus

last: Mota

first: Jill

last: Bayliss

first: Akash

last: Deogharkar

first: Erin

last: Hamanishi

first: Matthew

last: Pun

first: Stefan

middle: R

last: Sweha

first: Simon

last: Hoffman

first: Eleanor

last: Young

first: Qiuyang

last: Zhang

first: Rijul

last: Mehta

first: Olamide

last: Animasahun

first: Pranav

last: Narayanan

first: Sushanth

last: Sunil

first: Abhijit

last: Parolia

first: Peter

last: Sajjakulnukit

first: Pooja

last: Panwalkar

first: Robert

last: Doherty

first: Madison

last: Clausen

first: Derek

last: Dang

first: Debra

last: Hawes

first: Fusheng

last: Yang

first: Mariarita

last: Santi

first: Alexander

last: Judkins

first: Yelena

last: Wilson

first: Thomas

last: Vigil

first: Andrea

last: Franson

first: Richard

last: Mortensen

first: Tatsuya

last: Ozawa

last: Griesinger

first: Eric

middle: C

last: Holland

first: Nicholas

last: Foreman

first: Kulandaimanuvel

last: Antony Michaelraj

first: Sameer

last: Agnihotri

first: Michael

last: Taylor

last: Gilbertson

first: Carl


title: Detecting the whole genomic binding of PARP1 in H1975 cells  with CUT&Tag assay.

city: Nanjing

first: Changying

last: Guo

state: Jiangsu

address: Longmian Avenue, No. 639

department: School of Life Science and Technology

institute: China Pharmaceutical university

summary: To elucidate the mechanism of EGFR-AS1 on PARP1-DNA binding at genome level, we examined PARP1 binding in response to etoposide stimulation through CUT&Tag technique in H1975 cells which overexpressing EGFR-AS1.

overall_design: Cleavage under targets and tagmentation (CUT&Tag) for PARP1 in EGFR-AS1 overexpressed H1975 cells with or without etoposide treatment.

first: Kun

last: Gao

first: Liang

last: Jin


title: Targeted Antisense Oligonucleotide Treatment Rescues Developmental Alterations in Spinal Muscular Atrophy Organoids [scRNA-seq]

first: Simona

last: Lodato

overall_design: 2-month-old Spinal Cord Organoids (SCOs) from wilde-type CTRL organoids (n=2 C1, n=2 C3) and SMA organoids (n=2 S1, n=2 S3) were profiled by scRNA-seq.

first: Irene

last: Faravelli

first: Paola

last: Rinchetti

first: Monica

last: Tambalo

first: Illia

last: Simutin

first: Lisa

last: Mapelli

first: Sara

last: Mancinelli

first: Matteo

last: Miotto

first: Mafalda

last: Rizzuti

last: D’Angelo

first: Chiara

last: Cordiglieri

first: Giulia

last: Forotti

first: Clelia

last: Peano

first: Paolo

last: Kunderfranco

first: Luca

last: Calandriello

first: Giacomo

last: Comi

first: Elvezia

last: Paraboschi

first: Eleonora

last: Pali

first: Francesca

last: Beatrice

first: Egidio

first: Serge

last: Przedborski

last: Nizzardo

first: Stefania

last: Corti


title: A giant virus creates a subcellular environment to overcome the codon-tRNA mismatch [tRNA-seq]

city: Wako

first: Shintaro

last: Iwasaki

state: Saitama

address: 2-1, Hirosawa

department: Center for Pioneering Research

institute: RIKEN

type: Non-coding RNA profiling by high throughput sequencing

summary: A codon usage consonant with the cellular tRNA pool is important for efficient translation. However, Mimivirus, a giant DNA virus, relies on the host translation system of amoeba yet exhibits a codon usage distinct from its host. How this virus copes with the mismatch between the demand and supply of tRNAs remains unknown. Here, we found that the virus generates a subcellular compartment to translate virus mRNAs efficiently. The combination of genome-wide Ribo-Seq and RNA-Seq reveals that ribosomes traversed along viral mRNAs without pausing, despite the codon usage incompatibility with the host mRNAs. Although the virus encodes tRNA genes in the genome, mim-tRNA-Seq shows that the expression does not impact the composition of the cellular tRNA pool during infection. Instead, we observed that through in situ labeling of newly synthesized proteins, viral protein synthesis locally occurs around the periphery region of the viral factory, likely creating a unique environment to facilitate viral translation. Our data provide a perspective on how local translation shapes viral replication overcoming the mismatch of tRNA supply and codon demand.

overall_design: To study the changes that occur in viral and host translation over the course of Acanthamoeba polyphaga mimivirus (APMV) infection, we applied ribosome profiling, and RNA-seq to Acanthamoeba castellanii str. Neff cells infected with APMV as well as mock infected cells. The cells were infected with APMV at a multiplicity of infection (MOI) of 10 and harvested at 2, 4, and 8 hours post infection (hpi). For each time point, ribosome-protected footprints as well as total RNA were sequenced. Two biological replicates were prepared for each time point. To characterize the changes in tRNA library composition during the course of APMV infection, we applied mim-tRNA-seq on A. castellanii cells infected with APMV as well as mock infected cells. The cells were infected at a MOI of 10 and harvested at 2, 4, and 8 hpi. Two biological replicates were prepared for each time point.

first: Ruixuan

last: Zhang

first: Hiroyuki

last: Hikida

first: Yuichi

last: Shichino

first: Mari

last: Mito

last: Ogata


title: A disintegrin-like and metalloproteinase with thrombospondin motifs 18 (ADAMTS18) cleaves fibronectin and regulates its fibrillogenesis

first: Nihay

last: Laham Karam

overall_design: To investigate the role of ADAMTS18 in endothelial cells, we over-expressed human ADAMTS18 in human umbilical vein endothelila cells (HUVEC) using a lentiviral vector (LV). In addition, to study the effect of knockdown of ADAMTS18 we reduced ADAMTS18 expression in HUVEC using siRNA. We then performed gene expression profiling based on data derinved from RNA-sequencing from 4 independent HUVEC cultures (pool of 3 donors) for each treatment. and harvested after 2 or 3 days. Comparitive gene expression profiling was performed for the over-expression of ADAMTS18 via comparison to control transduced cells over-expressing a reporter gene (green fluorescent protein; GFP) 3 days after transduction. For the knockdown study siADAMTS18 samples were compared to control siRNA (siCTRL) samples, generated 2 days following transfection.

last: Laham-Karam

first: Maria

last: Barbiera

first: Mikko

last: Gynther

first: Tetsuya

last: Terasaki

first: Suvi

last: Jauhiainen

first: Johanna

last: Laakkonen

first: Michael

last: Jeltsch

first: Seppo

last: Ylä-Herttuala


title: Decoding cnidarian cell type gene regulation

city: Barcelona

first: Arnau

last: Sebe-Pedros

address: Dr. Aiguader 88

department: Systems Biology

country: Spain

institute: Centre for Genomic Regulation

summary: Animal cell types are defined by differential access to genomic information, yet the regulatory programs governing cell identity remain largely unexplored across the animal tree of life. We used scATAC-seq to map chromatin accessibility landscapes in ~60,000 cells from whole adult and gastrula stages of the sea anemone Nematostella vectensis. We quantified cell type-specific activity for ~112,000 cis-regulatory elements (CREs), revealing extensive combinatorial enhancer usage and distinct promoter architectures. To further decode regulatory motif grammars, we trained sequence-based models predicting CRE activity and studied ontogenetic relationships between cell types. Integrating sequence motifs with transcription factor expression and CRE accessibility, we reconstructed gene regulatory networks that define cnidarian cell identities. Our work uncovers the complexity and logic of cell type gene regulation in early-branching animals.

overall_design: Nuclei suspensions were obtained from whole adult and gastrula-stage Nematostella vectensis wild-type animals, or Fluorescent-activated cell sorting (FACS) isolated elav+ neurons from NvElav1::mOrange transgenic polyps. Single cell ATACseq (scATACseq) libraries were prepared using 10x Genomics platform

first: Elek

last: Anamaria

first: Iglesias

last: Marta

first: Sebé-Pedrós

last: Arnau


title: A giant virus creates a subcellular environment to overcome the codon-tRNA mismatch [RNA-seq]

first: Shintaro

last: Iwasaki

last: Zhang

last: Hikida


title: Generation and transcriptome profiling of bonobo induced pluripotent stem cells using stealth RNA vectors: a tripartite comparative study with humans and chimpanzees

city: Inuyama

first: Yusuke

last: Hamazaki

state: Aichi

institute: Center for the Evolutionary Origins of Human Behavior, Kyoto University

summary: Bonobos (Pan paniscus), which share a close evolutionary lineage with chimpanzees (Pan troglodytes) and humans, offer vital insights into the genetic and developmental propensities underlying human evolution. In this study, we established nine integration-free bonobo induced pluripotent stem cell (iPSC) lines from cryopreserved peripheral blood mononuclear cells using Sendai virus-derived RNA vectors. These iPSCs exhibited key pluripotency gene expression, normal karyotypes, and the capacity for differentiation into neural, mesodermal, and endodermal lineages, including the first successful induction of limb bud mesoderm cells from great ape iPSCs. Comprehensive transcriptome comparisons among bonobo, chimpanzee, and human iPSCs uncovered significant gene expression and retrotransposon divergence between Homo and Pan species, while highlighting minimal differences between bonobos and chimpanzees. Nevertheless, variation in the expression of mitochondrial metabolism-related genes was observed between the Pan species, suggesting potential interspecies differences in metabolic activity. This work provides a valuable platform for investigating the molecular and cellular mechanisms underlying species-specific developmental traits in closely related hominids and sheds light on the evolutionary origins of human characteristics.

sample_organism:
Pan paniscus
Pan troglodytes

platform_organism:
Pan paniscus
Pan troglodytes

overall_design: transcriptome profiles of bonobo and chimpanzee iPSCs

first: Hiroto

last: Akuta

first: Hikaru

last: Suzuki

first: Kenji

last: Ichiyanagi

first: Takuya

last: Imamura

first: Masanori


title: A giant virus creates a subcellular environment to overcome the codon-tRNA mismatch [Ribo-seq]

first: Ruixuan

first: Hiroyuki

first: Yuichi

last: Shichino

first: Mari

last: Mito

last: Ogata


title: p53 mediates phospholipid headgroup scavenging [ChIP-seq]

city: New York

first: Lydia

last: Finley

address: 430 E 67th St

department: Cell Biology Program

institute: Memorial Sloan Kettering Cancer Center

summary: A growing number of studies have shown that p53 modulates metabolic pathways to support diverse biological functions. Given that p53 is most widely known to act as a transcriptional activator, this raises the possibility that p53 transcriptional activity governs metabolic reprogramming. Here, we performed targeted metabolomics and lipidomic analysis which revealed an increase in the de novo biosynthesis of phosphatidylethanolamine (PE) upon p53 activation. Elevated levels of phosphoethanolamine (PEtn), the PE headgroup, in p53 active cells are sustained through PE headgroup recycling, which is partially mediated through the transcriptional activation of autophagy by p53. Disruption of phospholipid headgroup recycling through genetic perturbation of the CDP-ethanolamine pathway results in defects in cell-state specific perturbations in growth and gene expression. Notably, we observe restructuring of endoplasmic reticulum (ER)-mitochondria contacts in cells where headgroup recycling was abrogated, likely an attempt to maintain lipid homeostasis, and this reorganization is reversed when flux through the CDP-Etn pathway is restored. Together, these results suggest that lipid recycling to be an additional tool in the p53 arsenal supporting cellular fitness.

overall_design: KPnull cells engineered to express a doxycycline-inducible vector without cDNA (Vector) or p53 cultured with or without doxycycline for two days. Chromatin immunoprecipitation DNA-sequencing (ChIP-Seq) for P53 was performed.

first: J

last: Yashinskie

first: L


title: Gene expression profile at single cell level of rotavirus specific CD4+ T cells

city: Toronto

first: Kei

last: Haniuda

state: Ontario

address: 1 King’s College Circle, MSB7310

department: Department of Immunology

institute: University of Toronto

summary: IgA is the dominant antibody isotype secreted into the mucosal lumen. Mucosa-resident IgA+ plasma cells (PCs) generated following enteric infection can persist as long-lived plasma cells (LLPCs) in the gut, ensuring durable protection against reinfection. However, little is known about how virus-specific IgA+ PCs are generated and maintained. Upon infection with mouse rotavirus (RV) via the oral route, we found that antigen (Ag)-specific IgG+ and IgA+ PCs are generated in a follicular helper T (TFH) cell-dependent manner that involves CD40 signaling and MHC class II (MHCII) restricted Ag-presentation by B cells. Unexpectedly, although the RV-specific IgG response requires Ag-presentation by conventional dendritic cells, Ag-presentation by B cells is sufficient for the generation of RV-specific IgA. The accumulation of RV-specific IgA+ PCs in the small intestinal lamina propria (SILP) was found to depend on a type 1 TFH (TFH1) cell subset, which requires B cell Ag-presentation for their development and co-expresses Bcl-6 and T-bet. IFNγ receptor signaling is required for the expression of CXCR3 on RV-specific IgA+ PCs, which in turn promotes their migration to the SILP. Moreover, TFH1 cells are also required for the optimal development of IgA+ LLPCs in the upper and lower respiratory tracts in response to intranasal influenza A virus (IAV) infection. However unlike with RV, expression of MHCII on B cells was not sufficient for generating an IAV-specific IgA response in the airways, suggesting the operation of mucosal site-specific priming mechanisms. Collectively, our data reveal that unconventionally primed TFH1 cells support IgA responses to mucosal viral infections.

overall_design: Following mouse RV ECw infection, VP4-specific, VP6-specific and total CD4+ T cells were purified from pooled Peyer's patches (PPs) and mesenteric lymph nodes (MLNs) by magnetic sorting and flow cytometric sorting, and analyzed using scRNA-seq.

first: Jennifer

last: Gommerman


title: Transcriptomic effects of PFBA and PFHxA exposure on RPMI2650 cells

status: Public on Nov 16 2025

city: Shanghai

first: Ting

last: Xu

address: No. 1239 Road Siping

institute: Tongji University

summary: This study investigated the toxicological effects of two short-chain per- and polyfluoroalkyl substances (PFAS), including perfluorobutanoic acid (PFBA) and perfluorohexanoic acid (PFHxA), on the transcriptome of human nasal RPMI2650 cells. Gene annotation enrichment analysis highlighted neurofactor, synaptic, solute carrier, and ribosome signaling pathways in common pathways of widespread transcriptional changes in RPMI2650 cells. Systematic analysis of RNA-seq data revealed that PFAS-treated RPMI2650 cells are encoded to participate in cell proliferation (H3C14), nerve regeneration (L1CAM, P2RY1), and solute transport (SLC17A7, LRRK2). TOP 10 GO analysis showed that DEGs was mainly concentrated in synaptic regulation, cell division correlation and solute carrier transport. For example, in the PFBA treatment group, typical terms include synaptic vesicular membrane (GO:0030672), synaptic transmission, glutaminergic energy (GO:0035249), and interneuronal synaptic transmission (GO:0007270), while in the PFHxA treatment group, DEGs is mainly enriched in nucleosomes (GO:0000786). Microtubule binding (GO:0008017) and neuronal differentiation in the central nervous system (GO:0021953). In KEGG enrichment pathway, PFBA-treated differential genes were mainly concentrated in synaptic related pathways, such as serotonergic synapses (hsa04726), glycerophospholipid metabolism (hsa00564), and GABAergic synapses (hsa04727). In addition to neuron-related pathways, PFHxA processing enrichedneurotransmitter related pathways such as sphingolipid biosynthesis-Globo and isoglobo series (hsa00603), GABaergic synapses (hsa04727), and neuroactive ligand-receptor interactions (hsa04080).

overall_design: To investigate the transcriptomic effects of PFAS of different chain lengths on nasal epithelial cells, RPMI2650 cells cultured at the air-liquid interface were exposed to 1μM PFBA and PFHxA for 7 days, and the cells were collected for transcriptome sequencing.

first: Huan

last: Wang


title: The role of EHMT2 in uveal melanoma progression

city: Birmingham

first: Narendra

last: Wajapeyee

state: AL

address: 720 20th Street South, Kaul 540A

department: Department of Biochemistry and Molecular Genetics

institute: University of Alabama at Birmingham

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

overall_design: Refer to individual Series


title: p53 mediates phospholipid headgroup scavenging [RNA-seq]

overall_design: KPnull cells engineered to express a doxycycline-inducible vector without cDNA (Vector) or various forms of p53 (WT, wild-type; TAD1m, TAD1 p53 mutant; TAD2m, TAD2 p53 mutant; TAD1/2m, TAD1/2 p53 mutant) cultured with or without doxycycline for two days. KPsh cells grown on or off doxycycline for ten days. Cells were collected in duplicate or triplicate, followed by total RNA extraction using TRIzol.

first: K

last: Paras


title: siRNA mediated knockdown of ABCA1 in murine bone marrow derived macrophages

city: Urbana

first: Erik

middle: Russell

last: Nelson

state: IL

address: 407 S. Goodwin Ave

department: Molecular and Integrative Physiology

institute: University of Illinois at Urbana-Champaign

summary: RNA sequencing of murine bone marrow derived macrophages after transfection with control siRNA or siRNA against ABCA1

overall_design: RNAseq profiling of murine bone marrow macrophages. Control siRNA versus siRNA against ABCA1

first: Shruti

middle: V

last: Bendre


title: Tailoring a CRISPR/Cas-based Epigenome Editor for Programmable Chromatin Acylation and Decreased Cytotoxicity

city: Houston

first: Isaac

middle: B

last: Hilton

state: Texas

address: 6500 Main St., BRC Rm 660

institute: Rice University


title: Distinct transcription factor interactions drive HOXB13 activity in different stages of prostate cancer

city: Vancouver

first: Nathan

last: Lack

address: 2260 Oak st.

institute: Vancouver Prostate Centre

first: Shreyas

last: Lingadahalli

first: Betul

last: Ersoy Fazlioglu

first: Umut Berkay

last: Altintas


title: Cellular and Molecular Profiling of Collagenous Gastritis

city: Boston

first: Stephanie

last: Dougan

address: 450 Brookline Ave

institute: Dana Farber Cancer Institute

summary: Collagenous gastritis (CG) is a rare disease characterized by thick bands of subepithelial collagen within the stomach and presents with a variety of symptoms ranging from anemia to vomiting. Gastric biopsies were collected from six CG patients, including one patient before and after glucocorticoid steroid treatment, and several matched controls. Single-cell RNA- and T-cell receptor (TCR)-sequencing was performed on gastric biopsies.

overall_design: Control or CG patient biopsies were processed fresh and unsorted or frozen and CD45+ live flow-sorted. Single cell suspensions where processed in the 10x Genomics pipeline for scRNA- and scTCR-sequencing.

first: Michael

last: Walsh

first: Lestat

last: Ali

first: Jamie

last: DiCarlo

first: Enoch

last: Chung

first: Li

last: Qiang

first: Jiao

last: Shen

first: C

last: Keleher

first: Mary

last: Thompson

first: Keri

last: Sullivan

middle: K


title: Multi-omic integration identifies mechanisms of Broad Drug Resistance and opportunities for therapeutic reprogramming cancer cells

status: Public on Nov 15 2025

city: Notre Dame

first: Ian

last: Mersich

state: Indiana

address: 54417 Leahy Dr, Notre Dame, IN 46556

department: Chemistry and Biochemistry

institute: University of Notre Dame

summary: Broad drug resistance in cancer arises through diverse transcriptional, metabolic, and genetic adaptations, yet the shared molecular programs that sustain cross-resistant phenotypes remain incompletely defined. This study integrates PRISM drug-response data with transcriptomic, metabolomic, and mutational profiles to characterize the molecular features associated with broad drug resistance and to identify compounds capable of reversing resistance-associated gene signatures. Resistant cell lines exhibited coordinated activation of extracellular matrix remodeling, stress-adaptation pathways, and survival signaling, with NFE2L2 emerging as a central regulatory hub linking upstream mutations to oxidative-stress transcriptional programs. Multi-omic integration further revealed metabolic reprogramming as a conserved hallmark of resistance, and analyses of clinical cohorts demonstrated that resistance-associated alterations were associated with reduced progression-free survival.  Computational perturbagen screening nominated compounds predicted to counteract resistance-associated transcriptional signatures. Experimental validation confirmed that rosiglitazone suppressed NFE2L2-associated gene expression programs and restored chemotherapy sensitivity in resistant models, supporting a scalable framework for rational phenotypic reprogramming.  This GEO submission provides raw RNA-seq data generated from compound-treated OE19 cells used to experimentally validate candidate re-sensitization strategies.

overall_design: OE19 esophageal adenocarcinoma cells were treated with 1 µM rosiglitazone, halcinonide, methylprednisolone or 0.1% DMSO (control) , each in biological duplicate, alongside two untreated control samples. Total RNA was extracted using the Qiagen RNeasy Mini Kit according to the manufacturer’s instructions. RNA-seq libraries were prepared by the University of Notre Dame Genomics Core and sequenced on an Illumina NextSeq 2000 platform (paired-end, PE50), generating ~30 million reads per sample. Raw FASTQ files were aligned to the GRCh38/hg38 reference genome using HISAT2, and gene-level read counts were produced using featureCounts. FASTQ files (R1 and R2 for each biological replicate) are provided as supplementary data to support reproducibility and downstream analysis.


title: Mapping of Nab3 RNA-binding sites in Saccharomyces cerevisiae with suboptimal expression of PIC2.

city: Edinburgh

first: Sander

last: Granneman

address: Mayfield Road, Kings Buildings, Waddington building, room 3.06

department: Centre for Synthetic and Systems Biology

institute: University of Edinburgh

summary: Using CRAC, we compared the transcriptomic occupancy of Nab3 in a Saccharomyces cerevisiae BY4741 parental strain (PIC2-GFP, i.e., WT) and two derived mutants overexpressing (pTEF1-PIC2) or lacking (KO) PIC2. The purpose of the experiment was to check whether overexpressing or preventing the expression of PIC2 (an established Nab3 mRNA target which, when overexpressed or deleted, causes severe cellular defects) would cause a re-distribution of Nab3 binding among its other target transcripts. Sequencing outputs were processed using the pyCRAC pipeline and peak calling was performed with DBPeaks, our newly developed package for identification and comparison of binding sites defined by RNA-binding footprinting techniques (e.g., CRAC, iCLIP, PAR-CLIP, etc.).

overall_design: Two biological replicates of CRAC experiments performed in a parental Saccharomyces cerevisiae BY4741 strain (PIC2-GFP) and two derived mutants: pTEF1-PIC2 and KO. While pTEF1-PIC2 encodes a LEU2 plasmid coding for the coding and untranslated region of PIC2 under the pTEF1 promoter, the KO strain has a kanMX6 cassette replacing the entire PIC2 gene. All strains encoded NAB3-HTF (HIS6-TEV-3xFLAG). PIC2-GFP and KO were transformed with the pRS415 LEU2 vector to allow for B13medium uniformity. When SC-Leu cultures containing 1% (w/v) raffinose reached an OD600 of 1, cells were UV cross-linked (254 nm; 500 mJ/cm2) in the Vari-X-linker (UVO3) and rapidly filtered on 0.8 μm membranes (Merck) using a filtration device connected to a vacuum pump. Membranes were collected in 50 mL tubes, flash frozen by submersion into liquid nitrogen and stored at -80ºC until the day of the experiment.  On the day of the experiment, pellets were resuspended in a volume of lysis buffer (150 mM NaCl, 50 mM Tris pH 7.8, 0.1% (v/v) Nonidet P-40, 1 EDTA-free protease inhibitor cocktail (Roche) per 50 mL and 5 mM β-mercaptoethanol) corresponding to twice their mass. Lysates were then transferred to a fresh 50 mL tubes, where they were mixed with 2 volumes of 0.5 mm zirconia beads (Thistle Scientific), and vortexed at maximum speed for five 1-minute intervals alternated with 1-minute incubations on ice. An additional volume of lysis buffer was pipetted into each sample before partitioning the cell debris by centrifugation at 4ºC (4000 rpm, 15 minutes) and spinning down lighter impurities in an additional centrifugation step (10000 rpm, 20 minutes) at 4ºC. Immunoprecipitation of the labelled protein from the supernatant was achieved during a two-hour incubation of the sample with 75 µL of anti-FLAG® M2 magnetic beads (Sigma-Aldrich, M8823-5ML) which had been previously washed three times with 1 mL TN150 buffer. Immobilised beads underwent three 5-minute washes with TN1000 buffer (50 mM Tris pH 7.8, 1 M NaCl, 0.1% (v/v) Nonidet P-40 and 5 mM β-mercaptoethanol) and three additional 5-minute washes in 2 mL TN150 buffer (150 mM NaCl, 50 mM Tris pH 7.8, 0.1% (v/v) Nonidet P-40 and 5 mM β-mercaptoethanol). Afterwards, beads were resuspended in 550 µL of TN150 and incubated with 1 µL of a 1:100 dilution of RNace-It™ for exactly 5 minutes at 37 °C. To prevent overdigestion of co-immunoprecipitated transcripts and elute the bait proteins from the anti-FLAG beads, the solution was mixed with 0.4 g of guanidium hydrochloride (Gu-HCl) and the necessary volume of NaCl and imidazole (pH 8.0) to reach a final concentration of 300 mM and 10 mM respectively. After removing the beads, samples were pipetted onto 50 µL of Ni-NTA agarose resin (Qiagen) equilibrated with wash buffer I (6 M Gu-HCl, 10 mM imidazole, 300 mM NaCl, 50 mM Tris-HCl pH 7.8, 0.1% (v/v) Nonidet P-40 and 5 mM β-mercaptoethanol) and incubated at 4 °C overnight while rotating at 12 rpm.  Upon Ni-NTA binding, beads were transferred to Pierce columns (Thermo Fisher Scientific) and washed twice with 500 µL of wash buffer I before undergoing three additional washes of 500 µL with NP-PNK buffer (10 mM MgCl2, 50 mM Tris-HCl pH 7.8, 0.1% (v/v) Nonidet P-40, 5 mM β-mercaptoethanol). Alkaline phosphatase treatment was performed by resuspending immunoprecipitated RNA-protein conjugates in 80 µL of NP-PNK buffer containing 4 units of FastAP thermosensitive alkaline phosphatase (Thermo Fisher Scientific) and 80 units of RNasin® ribonuclease inhibitor (Promega) and incubating the samples at 37 °C for 1 hour. Dephosphorylation was stopped upon addition of 500 µL of wash buffer. Having equilibrated the Ni-NTA agarose with three washes of 500 µL with NP-PNK, we performed adapter ligation by resuspending the beads 80 µL of reaction mix containing 0.6 µM of the applicable App-PE 3′ adapter (5’App-NAGATCGGAAGAGCACACGTCTG-ddC 3’), 30 units of T4 RNA ligase 2 truncated K227Q (New England Biolabs), 60 units RNasin® (Promega) and 10% (w/v) polyethylene glycol 8000 (PEG 8000). The reaction took place at 25 °C for six hours.  After washing once with 500 µL of wash buffer I and three times with 500 µL of NP-PNK buffer, we 5’end radiolabelled co-immunoprecipitated RNAs by incubating the Ni-NTA resin with 60 µL of NP-PNK buffer containing 30 µCi 32P-γATP (PerkinElmer) and 30 units of T4 polynucleotide kinase (New England Biolabs). After a 40-minute incubation of the reaction at 37ºC, ATP (Roche) was supplemented to a final concentration of 1 mM and the reaction continued for another 20 minutes. The reaction was stopped by washing three times with 500 µL of wash buffer I and three 500 µL washes of NP-PNK buffer followed before the addition of the 5′ linker ligation mix. The reaction took place in a volume of 80 µL of NP-PNK buffer supplemented with 1.25 µM of the fitting adapter, 40 units of T4 RNA ligase 1 (New England Biolabs), 80 units of RNasin® and 10 mM ATP (Roche).  5’ adapter ligation was left to proceed overnight at 16 °C for all bait proteins. The adapter sequences were 5’-ACACGACGCTCTTCCGATCTNNNTAAGCN-3’ and 5’-ACACGACGCTCTTCCGATCTNNNATTAGCN-3’ for PIC2-GFP (WT) repeats 1 and 2 respectively; 5’-ACACGACGCTCTTCCGATCTNNNTGGAGCN-3’ and 5’-ACACGACGCTCTTCCGATCTNNNACTCAGCN-3’ for pTEF1-PIC2 replicates 1 and 2 respectively;  and 5’-ACACGACGCTCTTCCGATCTNNNTGTCACN-3’ and 5’-ACACGACGCTCTTCCGATCTNNNGCACTAN-3’ for both mut-NNS-BS libraries. After pooling suitable libraries together, the samples and its corresponding traces were sequenced using a benchtop MiniSeq system (Illumina), which performed single-end sequencing of 150 bp-reads.

first: Sofia

last: Esteban-Serna