title: Tissue-specific mRNA m6A reprogramming unveils vitamin-driven post-transcriptional regulation in mice

city: Guangzhou

first: Xiaoyun

last: Wang

state: Guangdong

address: 190 Kaiyuan Avenue, Huangpu

department: Infection and Immunity

institute: Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences

summary: Vitamins are critical regulators of cellular processes, yet their influence on mRNA modifications, particularly N6-methyladenosine (m6A), remains poorly understood. This study investigates the effects of various vitamins (VB2, VB6, and VB12) on the mRNA m6A epitranscriptome in multiple mouse tissues (brain, liver, and testis). Clustering analyses revealed closer similarity between brain and testis m6A profiles, while the liver exhibited a unique signature, reflecting tissue-specific regulatory dynamics. Notably, over 90% of vitamin-specific m6A sites did not correlate with mRNA abundance, highlighting the role of m6A as a post-transcriptional regulator. Pathway enrichment analyses further revealed tissue- and vitamin-specific adaptations. Key genes responsive to vitamin treatments emerged as central regulators of m6A dynamics, aligning with the known roles of vitamins in metabolism, neural plasticity, and gene expression.

overall_design: To explore the impact of vitamins on epigenetic regulation, we profiled the mRNA m6A epitranscriptome in mouse brain (representing the nervous system), liver (representing the digestive and defense system), and testis (representing the reproductive system). Using the m6A-seq2 protocol, we constructed MeRIP-seq libraries designed to profile m6A modifications. Both input and immunoprecipitation (IP) libraries were prepared from the three tissues (brain, liver, testis) treated with three different vitamins (VB2, VB6, and VB12) and subjected to sequencing.

first: Jia

last: Li

first: Anrui

last: Liu


title: Mitochondrial L-2-hydroxyglutarate is a physiologic signaling metabolite [CUT&Run]

status: Public on Apr 02 2026

city: Chicago

first: Yuki

last: Aoi

state: IL

address: 303 E Superior St. SQBRC 7-300

department: Biochemistry & Molecular Genetics

country: USA

institute: Northwestern University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: L-2-hydroxyglutarate (L-2-HG) is a low-abundance metabolite in mammals due to the mitochondrial enzyme L-2-HG dehydrogenase (L2HGDH), which oxidizes L-2-HG to 2-oxoglutarate (2-OG) to prevent its accumulation1. In humans lacking L2HGDH activity, L-2-HG builds up, leading to L-2-HG aciduria, a rare childhood neurometabolic disorder2. Thus, L-2-HG is often classified as a toxic metabolite2–5. Furthermore, L-2-HG is produced in response to hypoxia, acidic pH, and electron transport chain (ETC) impairment6–10. However, whether L-2-HG has a physiological function is unclear. Here, we investigated whether L-2-HG qualifies as a physiological signaling metabolite by testing three criteria: regulated levels, defined molecular targets, and a measurable physiological function. We report that elevated mitochondrial NADH/NAD⁺ ratio drives malate dehydrogenase 2 (MDH2) to reduce 2-oxoglutarate (2-OG) into L-2-HG, while L-2-hydroxyglutarate dehydrogenase (L2HGDH) reversibly oxidizes L-2-HG to 2-OG within the mitochondrial matrix, independently of the ETC. Proteome integral solubility alteration (PISA) assays revealed KDM4 family of H3K9 demethylases as L-2-HG-responsive targets. Consistent with the targets, elevated L-2-HG repressed nascent transcription of specific gene sets and promoted accumulation of the repressive histone mark H3K9me3 at those loci. In vivo, early embryonic L2HGDH overexpression lowered L-2-HG broadly, reduced postnatal growth, and caused postnatal mortality. Despite systemic lowering, kidneys displayed a unique vulnerability, developing fibrosis and functional decline. Mechanistically, L-2-HG depletion in the postnatal kidney resulted in a specific loss of H3K9me3 at L1MdTf retrotransposons, leading to their de-repression and coinciding with activation of the integrated stress response and inflammation pathways. Our findings establish mitochondrial L-2-HG as a physiological signaling metabolite that couples mitochondrial redox to chromatin regulation and is essential for postnatal kidney development and survival. These findings suggest that metabolites previously regarded as toxic may also serve critical physiological functions.

overall_design: To study the impact of L2HGDH overexpression on epigenetic modifications and transcription in mouse kidney, CUT&RUN assays for H3K9me3 and RNA Polymerase II were performed.

first: Ram

middle: P

last: Chakrabarty

first: Navdeep

middle: S

last: Chandel


title: HDAC inhibition unlocks tumor plasticity and enhances immunotherapy response in Myc- Driven Small Cell Lung Cancer [ATAC-Seq]

city: Baltimore

first: Linying

last: Zhu

state: Maryland

address: 20 Penn St

department: School of Medicine

institute: University of Maryland, Baltimore

summary: Small Cell Lung Cancer (SCLC) is a highly aggressive malignancy, accounting for approximately 15% of all lung cancer cases. Characterized by low immunogenicity, SCLC may utilize epigenetic mechanisms to evade immune detection. Here, we demonstrate that entinostat, a class I histone deacetylase inhibitor (HDACi) upregulates immune-related genes in human SCLC cells. In vivo, we confirmed entinostat treatment increased expression of immunecheckpoint ligands and antigen presentation machinery in Myc-driven tumors in a Rb1/Trp53/MycT58A (RPM) SCLC mouse model, while shifting tumors from a neuroendocrine(NE)-high to a NE-low phenotype. Notably, combining entinostat with anti-PD-1 immunotherapy significantly enhances T-cell infiltration, suppresses tumor growth, and prolongs survival in RPM allograft models. These findings underscore the potential of entinostat to reprogram the immunological landscape and NE status of SCLC, enhance immune checkpoint blockade efficacy, and improve therapeutic outcomes.

overall_design: ATAC-seq profiling of Rb1/Trp53/MycT58A (RPM) induced lung tunor and normal lung tissue. And the induced tumors treated with vehicle, IgG, anti-PD-1 antibody, entinostat and the combination of anti-PD-1 and entinostat.

first: Azam

last: Ghafoor

first: Lorinc

last: Prongor

first: Haoxuan

last: Ying


title: HDAC inhibition unlocks tumor plasticity and enhances immunotherapy response in Myc- Driven Small Cell Lung Cancer

type: Expression profiling by high throughput sequencing

overall_design: RNA-seq profiling of Rb1/Trp53/MycT58A (RPM) induced lung tumor and normal lung tissue.


title: HDAC inhibition unlocks tumor plasticity and enhances immunotherapy response in Myc- Driven Small Cell Lung Cancer.

overall_design: RNA-seq profiling of Rb1/Trp53/MycT58A (RPM) induced lung tunor and normal lung tissue (GSE309192). The induced tumors treated with vehicle, IgG, anti-PD-1 antibody, entinostat and the combination of anti-PD-1 and entinostat.


title: Elevated Labile Iron Contributes to Membrane Repair Deficits in FSHD

city: Washington,DC

first: Chen

last: Yi Wen

state: Washington,DC,

address: Sheikh Zayed Campus,111 Michigan Avenue,

department: Center for Precision Medicine and Genomics Research

institute: Childrens National Hospital

summary: Facioscapulohumeral muscular dystrophy (FSHD) is an autosomal dominant muscle disease caused by expression of the transcription factor DUX4, which we previously found to be associated with plasma membrane (PM) repair deficits. However, the molecular mechanisms associated with poor membrane repair are not clear. Here, we show PM injury itself results in mild but significant increase in DUX4 mRNA expression, as well dysregulation of genes enriched in pathways critical for membrane repair. We find these dysregulated genes to be sensitive classifiers of FSHD status in human muscle biopsies, indicating their potential utility as novel biomarkers. In addition, FSHD myoblasts show dysregulation of genes in the ferroptosis cell death signaling pathway in response to membrane damage. Subsequent experiments indicated FSHD myoblasts present with hallmark features of ferroptotic stress, including elevated labile ferrous (Fe2+) iron, and lipid peroxidation at baseline and post-injury. Furthermore, we demonstrate that the expression of ferroptosis biomarkers is elevated in FSHD muscle biopsies, which is predictive of the presence of inflammation and positively correlates with the degree of fatty infiltration in FSHD skeletal muscle.  Increasing labile iron and lipid peroxidation worsens membrane repair in FSHD myoblasts, while treatment with the iron chelator 2,2′-Bipyridyl and ferroptosis inhibitor ferrostatin-1 improve repair. These data are the first to identify signs of ferroptotic stress in FSHD myoblasts, and demonstrate the potential therapeutic benefit of iron chelation and ferroptosis inhibition to improve membrane repair capacity in FSHD.

overall_design:
To investigate the transcriptional response to plasma membrane injury, we  performed single cell RNAseq of immortalized human myoblast cell lines from 2 donors with FSHD, and 2 healthy siblings
2 myoblast cell lines from individuals with FSHD and two myoblast cell lines from Healthy individuals were collected prioor to membrane injury (baseline), and at 6-hours post-injury. A total of  8 samples were obtained

first: Adam

middle: J

last: Bittel

first: Surajit

last: Bhattacharya

first: Lulya

last: Okubamariam

first: Yi-Wen

last: Chen


title: Circulating cell populations as response predictors and targets to improve immunotherapy in metastatic lung cancer

city: Sao Paulo

first: Kenneth

last: Gollob

address: Albert Einstein Ave, 627/701

country: Brazil

institute: Hospital Israelita Albert Einstein

summary: Immunotherapy efficacy varies among patients with advanced non-small cell lung cancer (NSCLC). Here, we profiled baseline systemic immunity in patients with stage IV NSCLC treated with anti-PD-1 plus chemotherapy to identify immune mechanisms and circulating biomarkers associated with response. We prospectively enrolled 33 treatment-naive patients, including 22 responders and 11 non-responders at week 9, and 17 responders and 16 non-responders at 6 months. Responders showed increased frequencies of circulating T cells expressing CD69, TCF-1, and CXCR3. In contrast, non-responders exhibited higher frequencies of CTLA-4-, CD161-, and IL-10-expressing CD4+ and CD8+ T cells. These systemic immune profiles were mirrored in the tumor microenvironment in an independent cohort. Importantly, combined CTLA-4 and PD-1 blockade reactivated anti-tumor T cell features in non-responders in vitro, highlighting CTLA-4 as a potential driver of resistance. Together, these findings support personalized immunotherapy strategies guided by systemic immune biomarkers in advanced NSCLC.

overall_design: We included patients of both sexes aged 18 years or over, histologically confirmed diagnosed of stage IV NSCLC that were treated with the combination of pembrolizumab + chemotherapy. Patients with disease progression were included in the “non-responder” group and patients with complete or partial response or stable disease were included in the “responder” group. Responses were assessed 9 weeks or 6 months after starting treatment. Peripheral blood was collected in EDTA tubes at the time of diagnosis, before starting the treatment, and PBMC were purified using a Ficoll gradient and cryopreserved in FBS / DMSO.

first: Amanda

middle: B

last: Figueiredo


title: Discovery of kidney disease targets using multimodal human podocyte injury models

city: Durham

middle: D

last: Barreto

address: 1427 Fitzpatrick Center

institute: Duke University

summary: Podocyte injury is a hallmark of chronic kidney disease (CKD), but whether different injury signals perturb unified or distinct molecular targets remains unclear. Using human induced pluripotent stem cell (hiPSC)-derived podocytes, we modeled cellular injury via exposure to diabetic, inflammatory, chemical toxin, biomechanical, and infectious stressors. Transcriptomic analysis revealed both shared and unique changes in gene expression across injury modes. While drug-induced injuries triggered broader transcriptional responses, conserved pathways related to lysosome function, RNA metabolism, and immune activation were identified across models. Importantly, we discovered that NEU1, CD82, ABI3BP, and ADAM17 as targets of human podocyte injury. We confirmed enrichment of these targets in kidney disease patient biopsies, underscoring their in vivo relevance and potential as therapeutic targets. These findings highlight the value of human-relevant experimental models and provide insight into podocyte injury responses, offering a framework for future precision medicine approaches.

overall_design: Human iPSC lines were cultured under standard conditions and used for podocyte differentiation. hiPSCs were grown on a Matrigel matrix in mTeSR1 medium and induced into podocytes through a stepwise differentiation protocol involving mesoderm induction followed by intermediate mesoderm and podocyte induction. After differentiation, the podocytes were exposed to various injury conditions, including high glucose, high glucose with inflammatory cytokines, Adriamycin, cytochalasin D, and lipopolysaccharide. RNA was isolated from three biological replicates per condition, and RNA quality was assessed. RNA sequencing was performed per sample for differential gene expression analysis.

first: Bowen

last: Jiang

first: Morgan

middle: A

last: Burt

first: Nikolaos

last: Dimitrakakis

first: Samira

last: Musah


title: Single-nucleus RNA sequencing of human subcutaneous adipose tissue biopsies from 59 Finnish participants.

city: Los Angeles

first: Kyla

last: Gelev

email: kylagelev@gmail.com, kzg@g.ucla.edu

address: 695 Charles E. Young Drive South

institute: University of California, Los Angeles

summary: We performed single-nucleus RNA-sequencing on subcutaneous adipose tissue biopsies from 59 Finnish donors from the Kuopio OBesity Surgery study (KOBS) cohort.

overall_design: Frozen subcutaneous adipose tissue (SAT) biopsies (n=59) were pooled and batched into 8 batches with 7-8 SAT samples per batch. We randomly assigned samples to batches to minimize correlations between phenotypes of interest and batch. We took 100mg from each sample prior to pooling the samples together for nuclei isolation and applied the 10x Genomics nuclei isolation protocol. Library construction was performed using the Single Cell 3’ v3.1 chemistry. All libraries were equally distributed across two lanes and sequenced on the Novaseq X Plus 25B to target 70,000 reads per nucleus.

middle: Z

first: Päivi

last: Pajukanta

first: Jussi

last: Pihlajamäki


title: AATF supports proliferation of glioblastoma cells by sustaining mitochondrial respiration through an NRF-1-dependent mechanism [RNA-seq]

city: Rome

first: Stefano

last: Di Giovenale

address: Via Elio Chianesi,  53

country: Italy

institute: IRCCS National Cancer Institute Regina Elena

summary: The ability of cancer cells to promote cellular proliferation by preferentially using glycolysis as primary source of energy, has long been considered a hallmark of tumour metabolism. However, emerging evidence suggests a more complex situation with many tumours exhibiting a pronounced dependence on mitochondrial respiration through oxidative phosphorylation (OXPHOS) for their development and maintenance. In line with this, numerous studies have reported an upregulation of mitochondrial genes and OXPHOS components across multiple cancer types. Glioblastoma (GBM) is the most frequent and malignant brain tumour in adults, characterized by rapid proliferation, resistance to therapy and ability to recur. In addition to a profound genetic and molecular heterogeneity, GBM also exhibits strong metabolic heterogeneity with different grade of dependence from mitochondrial activity. Notably, the transcription factor Nuclear Respiratory Factor 1 (NRF-1), a key regulator of OXPHOS gene expression and mitochondrial functions, has recently been linked to GBM progression and poor prognosis. Che-1/Apoptosis Antagonizing Transcription Factor (AATF) is a transcriptional regulator with a crucial role in several cancer types where it contributes to tumorigenesis by promoting cell cycle arrest and apoptosis, as well as resistance to therapy. Here, we show that AATF expression is correlated with clinical outcome in GBM patients. Moreover, we demonstrate that its depletion leads to cell cycle arrest, impaired mitochondrial respiration, and disrupted mitochondrial architecture in GBM cells. In particular, we provide evidence that AATF interacts with NRF-1 and it is essential for NRF-1-mediated transcription of the OXPHOS genes by affecting RNA polymerase II recruitment and chromatin structure. Overall, our findings highlight a previously unrecognized role of AATF in GBM proliferation and mitochondrial metabolism and suggest it as a potential target for therapeutic intervention.

overall_design: RNAseq experiment of U138 cell lines with control and interfirence of AATF conducted in triplicates.

first: Cristina

last: Sorino

first: Italia

last: Falcone

first: Francesca Romana

last: Auciello

first: Claudio

last: Pulito

first: Federica

last: Lo Sardo

last: Scalera

first: Francesca

last: De Nicola

first: Valeria

last: Catena

first: Ludovica

last: Ciuffreda

first: Brindusa Ana Maria

last: Arteni

last: Giuliani

first: Bruno

last: Amadio

first: Giovanni

last: Blandino

first: Maurizio

last: Fanciulli

first: Simona

last: Iezzi


title: AATF supports proliferation of glioblastoma cells by sustaining mitochondrial respiration through an NRF-1-dependent mechanism [ChIP-seq]

overall_design: ChIPseq experiment targeting NRF1 in U138 cell in control and interfired AATF.


title: MK2/p38/p53 negatively regulate basal IL-1β and noncanonical NF-κB signaling

city: Hannover

first: Sarah

middle: Maria

last: Herr

address: Carl-Neuberg-Str. 1

country: Germany

institute: Medizinische Hochschule Hannover

summary: Interleukin (IL)-1β is a pro-inflammatory cytokine implicated in sterile inflammation and tumor development. Investigating the role of MAPKAP kinase 2 (MK2) in IL-1β processing, we found that Il1b mRNA and IL-1β protein levels were elevated in resting MK2-knockout (KO) macrophages and in the serum of MK2/3 double-KO mice. This was linked to activation of the non-canonical NF-κB pathway in the absence of MK2 or its activator, p38α. Rescue by MK2, its kinase-inactive mutant MK2K79R, or p38α suppressed this pathway and reduced Il1b expression. We also observed decreased basal protein levels of tumor suppressor p53 in MK2- or p38α-deficient cells. Mechanistically, p53 interacts with caspase-3, promoting cleavage of RelB, thereby inhibiting non-canonical NF-κB signaling and subsequent Il1b and TP53 expression. These findings explain elevated basal IL-1β levels in MK2-KO macrophages and uncover a new autoregulatory mechanism of TP53 expression. Additionally, they reveal a new mechanism that contributes to the long-discussed link between cancer and inflammation, wherein the tumor suppressor p53 inhibits cytokine production in parallel.

overall_design: RNA-seq profiling of untreated or IL-1α treated immortalized MK2-KO macrophages rescued with either MK2 (iMK2-KO+MK2) or an empty vector (iMK2-KO+GFP)

first: Sarah Maria

first: Matthias

last: Gaestel


title: Met32 governs transcriptional control of sulfur metabolic flexibility and resistance to reactive sulfur species in the human fungal pathogen Candida albicans

city: Montreal

first: Adnane

last: Sellam

address: 5000, rue Bélanger

country: Canada

institute: Universite de Montreal

summary: Although considerable advances were made in understanding the metabolic machinery that enable bacteria to utilize alternative sulfur sources, many aspects of this process remain understudied in fungi. To explore the genetic circuit by which the highly prevalent opportunistic yeast Candida albicans control sulfur utilization, we characterized the transcriptional atlas associated with sulfur starvation in this yeast. We identified many putative desulfonation enzymes that were differentially transcribed and showed that Jlp12, an α-ketoglutarate dioxygenase, was critical for the utilization of different sulfur sources found in many niches of the human host. We also uncovered that the Zinc-finger transcription factor Met32 acts as a master transcriptional regulator, that modulates genes of sulfur utilization including Jpl12. Importantly, we found that the C. albicans Met32 functions exclusively in the control of sulfur utilization genes, while it governs methionine biosynthesis in the S. cerevisiae lineage. This work also identified Seo13 as the first major facilitator superfamily transporter in fungi that transports the alternative sulfur source glutathione, under the direct control of Met32. Furthermore, we showed that Met32 modulates C. albicans tolerance sulfite excess by tuning the basal transcriptional level of the superoxide dismutase Sod1. This underscores the dual role of Met32 in the breakdown of sulfur-containing metabolites and the neutralization of the resulting reactive sulfur species (RSS). Our study delineates a new mechanism by which fungal pathogens utilize sulfur sources and neutralize RSS, and underscores its importance for fungal fitness in vivo.

overall_design: In this study, we identified transcripts modulated under sulfur starvation by comparing the transcriptome of cells growing in sulfur-lacking medium (SLD) to those growing in sulfur-replete medium (SLD supplemented with either taurine, mixture of methionine/cysteine, ammonium sulfate or glutathione) in the pathogenic yeast Candida albicans. We also identified transcripts that were modulated in the mutant of the transcription factor Met32 (met32). The transcriptional profile of met32 grown in sulfur-free (SLD) or sulfur-supplemented medium (SLD + taurine or SLD + glutathione) was compared to that of the wild-type (WT) strain grown under similar conditions.

first: Anagha C

last: Menon

first: Faiza

last: Tebbji

first: Antony T

last: Vincent


title: MDM2 degradation overcomes feedback regulation of p53 signaling in Merkel cell carcinoma

city: Boston

first: Andrew

last: Cherniack

state: Mass

address: 450 Brookline Ave

department: Molecular Oncology

institute: Dana Farber Cancer Institute

summary: This study explored the efficacy of MDM2 degraders, KTX-049 and KT-253, in treating Merkel cell carcinoma (MCC), an aggressive skin cancer. MCC tumors often exhibit clonal integration of Merkel cell polyomavirus, with virus-positive (MCCP) and virus-negative  (MCCN) tumors showing distinct molecular profiles. MDM2, a target of the ST-MYCL- Tip60 complex in MCCP, inhibits p53-mediated tumor suppression. Our results  demonstrate that KTX-049 is over 100 times more potent than the MDM2 inhibitor DS- 3032 in MCC cell lines with wild-type p53, effectively degrading MDM2 and activating the  p53 response. Mathematical modeling indicates that KTX-049 collapses the p53-MDM2 feedback loop, enhancing its potency. In vivo, KT-253 induced robust and durable p53 pathway activation, producing deep tumor regressions in patient-derived xenograft models. However, the observed resistance was linked to TP53 mutations. These findings highlight the potential of MDM2 degraders as a therapeutic strategy for MCC and other tumor types with wild-type p53 and underscore the need for further investigation of resistance mechanisms and combination therapies.

overall_design: This study includes 1) RNA-seq profiling of Merkel cell carcinoma established cell lines MKL-1 and WaGa treated with DMSO, an MDM2 degrader KTX-049 or an MDM2 inhibitor DS-3032. 2)RNA-seq profiling of Merkel cell carcinoma PDX and CDX derived cell lines treated with DMSO or KTX-049.

first: Varsha

last: Ananthapadmanabhan

first: Simone

last: Bruno

first: Leonard

last: Vonk

first: Yu-Chen

last: Cheng

first: Abeba

last: Teshager

first: Benjamin

middle: K

last: Eschle

first: Charles

middle: L

last: Howarth

first: Joana

last: Rodrigues

first: Julia

last: Schnabel

first: Ananya

last: Kodali

first: Prafulla

middle: C

last: Gokhale

first: Rujuta

last: Kshirsagar

first: Susanne

last: Breitkopf

first: Kirti

last: Sharma

first: Joao

last: Paulio

first: Yvonne

last: Li

first: Franziska

last: Michor

first: Yogesh

last: Chutake

first: Joyoti

last: Dey

first: James

last: DeCaprio


title: Mitochondrial L-2-hydroxyglutarate is a physiologic signaling metabolite [PRO-seq]

first: Ali

last: Shilatifard

address: 320 E Superior St

department: Department of Biochemistry and Molecular Genetics

institute: Northwestern University Feinberg School of Medicine

summary: L-2-hydroxyglutarate (L-2-HG) is a low-abundance metabolite in mammals, due to the mitochondrial enzyme L-2-HG dehydrogenase (L2HGDH), which oxidizes L-2-HG to 2-oxoglutarate (2-OG) to prevent its accumulation1. In humans lacking L2HGDH activity, L-2-HG builds up, leading to L-2-HG aciduria, a rare childhood neurometabolic disorder2. Thus, L-2-HG is classified as a toxic metabolite2–5. Furthermore, L-2-HG is produced in response to hypoxia, acidic pH, and electron transport chain (ETC) impairment6–10. We investigated the regulation of L-2-HG levels, its impact on gene expression, and whether it has a physiological role in mice. Here, we report that elevated mitochondrial NADH/NAD+ triggers malate dehydrogenase 2 (MDH2) to produce L-2-HG from 2-OG. By contrast, L2HGDH converts L-2-HG to 2-OG in the mitochondrial matrix without requiring a functional ETC. Nascent gene expression analysis in mouse embryonic stem cells (mESCs) demonstrated that the majority of genes were downregulated by elevated L-2-HG levels. To identify proteins involved in L-2-HG-dependent gene regulation, we used proteome integral solubility alteration assays (PISA), which showed that L-2-HG engages the RNA demethylase FTO and H3K9 demethylases KDM4A/B/C in mESC nuclear extracts. The L-2-HG-dependent accumulation of m6A in mRNAs and H3K9me3 at the gene loci negatively correlated with gene expression. Importantly, mitochondrial L2HGDH overexpression during early embryogenesis lowered basal L-2-HG levels and resulted in viable mice at birth but triggered reduced growth, impaired kidney function, and post-natal mortality. Thus, L-2-HG primarily downregulates gene expression and is a signaling metabolite necessary for post-natal mammalian growth and survival. These findings suggest that other previously considered toxic metabolites might also play physiological roles.

overall_design: PRO-seq (Precision Run-On Sequencing) to investigate whether L-2-HG metabolite has a physiological role in mice.

first: Ram

last: Chakrabarty

first: Jonathan

middle: G

last: van Vranken

first: Yuki

last: Aoi

first: Marta

last: Iwanaszko

first: Navdeep

last: Chandel


title: Transcriptomic analysis of human induced stem cell-derived endothelial cells and retianl endothelial cells

first: Ying-Yu

last: Lin

address: 534 Research Drive

summary: This study conducts a comprehensive transcriptome analysis to compare human induced pluripotent stem cell-derived endothelial cells (iECs) with retinal endothelial cells (iRECs). By examining gene expression profiles, we aims to identify molecular distinctions and similarities between these cell types. With an increasing need to develop tissue-specific endothelial cells for more accurate disease modeling and personalized therapies, this work highlights the unique features of retinal endothelial cells. Understanding these differences is crucial, as retinal endothelial cells play a key role in ocular diseases such as diabetic retinopathy and aged-related macular degeneration. Insights from this study could enhance the development of targeted therapies for retinal vascular disorders.

overall_design: RNA-seq profiling of iECs and matched differentiation of iRECs derived from the same iPSC line (WTC-TJP1) and analyzed at passage1

first: Parker

last: Esswein

first: Sharon

last: Gerecht


title: Mitochondrial L-2-hydroxyglutarate is a physiologic signaling metabolite [ChIP-seq]

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) of H3K9me3 to investigate whether L-2-HG metabolite has a physiological role in mice.


title: in vivo human embryonic spinal cord atlas validates stem cell-derived human dorsal interneurons and reveals ASD spinal signatures [day43NMP_scRNAseq]

status: Public on Apr 01 2026

first: Samantha

last: Butler

state: California

address: 610 Charles E Young Drive East

department: Neurobiology

institute: University of California, Los Angleles

summary: Spinal cord injuries (SCI) result in the loss of motor and sensory function. We are working towards restoring sensation by developing directed differentiation protocols to generate dorsal spinal interneurons (dIs; dI1-dI6) from human embryonic stem cells (hESCs). Here, we present an improved method that produces human dIs via a neuromesodermal progenitor state, the physiological intermediate for spinal cord development. We show that retinoic acid (RA), bone morphogenetic protein 4 (BMP4) and growth differentiation factor (GDF) 11 direct dI identity, while GDF11 and extended time in culture promotes posterior spinal identities. Together, these protocols generate the full complement of dorsal subtypes along the entire anterior-posterior axis of the spinal cord. To benchmark in vitro-derived dIs, we constructed a single-cell RNA-Seq atlas of the human embryonic spinal cord and used it to show that hESC-derived dIs closely match their endogenous counterparts. The atlas also reveals that the dI4/dI5 populations dramatically expand in comparison with the other spinal lineages. Moreover, they have mechanosensory circuit signatures linked to autism spectrum disorder, implicating spinal circuits in autistic phenotypes.

overall_design: Single-cell sequencing of embryonic bodies (EBs) generated from H9 hESC-derived NMPs induced for 2, 4, or 10 days. EBs were treated with RA, RA+BMP4, or RA+GDF11 to induce relevant spinal neuron cell types. At 43 days, a single cell suspension was obtained from the EBs and sent for scRNA-seq.

first: Sandeep

last: Gupta

first: Eric

last: Heinrichs

first: Cristian

last: Rodriguez

first: Emily

last: Friedman

first: Salena

last: Gallardo

first: Talin

last: Dermirjie

first: Teny

last: Panosian

first: Keith

last: Phan

first: Anooshik

last: Tahmasian

first: Yahir

last: Veridin


title: Distinct cytokines regulate gene expression and anti-tumor activity in regenerated CD8+ T cells derived-from induced pluripotent stem cells.

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

country: Japan

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

summary: Adoptive T cell therapy can induce tumor regression in cancer patients. Tumor-specific CD8+ T cells regenerated from induced pluripotent stem cells (iPSCs), termed regenerated cytotoxic T lymphocytes (CTLs), are promising resources for adoptive T cell therapy. However, it remained unclear what kinds of cytokines enhance the anti-tumor activity of regenerated CTLs. In this study, we examined the effects of exogenous cytokines on the characteristics of regenerated CTLs. We found that IL-15- or IL-21-treatment in vitro enhanced the anti-tumor activity of regenerated CTLs, presumably by different mechanisms. IL-15-treated regenerated CTLs showed early-effector-like characteristics, whereas IL-21-treated regenerated CTLs showed both naïve- and effector-like characteristics. These findings provide useful insights for the clinical application of regenerated CTLs in the future.

overall_design: WT1-specific regenerated CD8+ T cells derived from induced pluripotent stem cells (iPSCs) were stimulated with WT1 peptide-pulsed lymphoblastoid cell line (LCL) in the presence of indicated cytokines for 7 days. RNA of the cytokine-treated cells was extracted and analyzed by RNA-seq.

first: Kenta

last: Kondo

first: Nobuhito

last: Nitta

first: Koji

last: Terada

first: Yusuke

last: Sano

first: Mina

last: Kumode

first: Seiji

last: Nagano

first: Kyoko

last: Masuda

last: Okuzaki

first: Toru

last: Miyake

first: Masaji

last: Tani

first: Hiroshi

last: Kawamoto

first: Yasutoshi

last: Agata


title: in vivo human embryonic spinal cord atlas validates stem cell-derived human dorsal interneurons and reveals ASD spinal signatures [day27NMP_scRNAseq]

first: Samantha

last: Butler

overall_design: Single-cell sequencing of embryonic bodies (EBs) generated from H9 hESC-derived NMPs induced for 2, 4, or 10 days that were treated with RA, RA+BMP4, or RA+GDF11 for a total of 14 days.

first: Sandeep

last: Gupta

first: Eric

last: Heinrichs

first: Cristian

last: Rodriguez

first: Emily

last: Friedman

first: Salena

last: Gallardo

first: Talin

last: Dermirjie

last: Panosian


title: mRNA m6A modifications and the RNA-binding protein YTHDF1 affect translational control in both normal and pathological learning

first: Chuan

last: He

state: Illinois

address: 929 E 57th St, Room E319B

institute: University of Chicago

summary: Animals learn and adapt to environmental changes. However, neural plasticity can also become maladaptive, leading to neurological and psychiatric disorders. How do we use known molecular mechanisms to harness the power of neural plasticity to prevent and treat diseases? Consolidating learning is known to require new protein synthesis. We found that mRNA m6A modifications and the RNA-binding protein YTHDF1 are required for molecular, cellular, and behavioral adaptations in response to environmental changes. Deletion of Ythdf1 in dopamine D1- or D2 receptor-expressing neurons selectively impaired D1- or D2-dependent learning, respectively, including both adaptive and maladaptive learning. This highlights YTHDF1 as a potential therapeutic target for preventing pathological plasticity. YTHDF1 recognizes m6A modifications on transcripts and regulates their translation. Elevated cAMP triggered increased protein synthesis in control striatal neurons but not in Ythdf1-deficient neurons. Behaviorally, cell-type-specific Ythdf1 deletion resembled learning phenotypes caused by deletion of the m6A methyltransferase gene Mettl14, suggesting YTHDF1 as the main mediator of m6A-dependent regulation in the striatum.

overall_design: Mouse brain tissue was frozen in liquid nitrogen and then thawed in ice-cold RIPA buffer. Tissue was lysed with a douncer and then crosslinked with 245 nm UVC at 45,000 J/m2 total dose. Standard CLIP-seq was performed with monoclonal anti-YTHDF1 antibody (Abcam, ab220162) and RIPA buffer as lysis buffer.

first: Zhuoyue

last: Shi

first: Zhongyu

last: Zou


title: in vivo human embryonic spinal cord atlas validates stem cell-derived human dorsal interneurons and reveals ASD spinal signatures [day0NMP_bulk RNAseq]

overall_design: RNA-seq profiling of H9 hESCs induced for 2, 4, or 10 days (in triplicate) with FGF and CHIR, alongside an undifferentiated hESC control.

first: Teny

first: Keith

last: Phan

first: Anooshik

last: Tahmasian

first: Yahir

last: Veridin


title: in vivo human embryonic spinal cord atlas validates stem cell-derived human dorsal interneurons and reveals ASD spinal signatures [day0NMP_scRNAseq]

overall_design: Single cell-seq profiling of H9 hESCs induced for 2, 4, or 10 days with FGF and CHIR.


title: Distinct Dynamics and Composition of Endogenous Neuronal RNA Granules

city: Bronx

first: Ronald

last: Cutler

state: NY

address: 1300 Morris Park Ave

department: Genetics & Biochemistry

institute: Albert Einstein College of Medicine

summary: RNA granules are essential regulators of post-transcriptional gene expression, enabling mRNA transport, localization and local translation in neurons. The localized transcriptome is diverse; however, how different mRNAs are organized into granules for efficient localization and translation remains unknown. Here, we combine real time single RNA imaging with protein and RNA proximity labeling to investigate two endogenous neuronal mRNA granule populations, Actb and Arc, in stimulated primary hippocampal neurons. Using orthogonal RNA labeling systems in a dual knock-in mouse model, we show that Actb and Arc mRNAs are packaged into spatially segregated granules with distinct trafficking dynamics, localization kinetics, and responses to synaptic stimulation. While Actb granules displayed rapid and sustained localization, whereas Arc granules showed delayed, transient recruitment, consistent with their respective roles in structural and activity-dependent plasticity. Proximity labeling reveals that these granules are entirely distinct in their RNA signatures, despite sharing core RNA-binding proteins. Using motif analysis, we propose that shared cis-regulatory elements may drive selective co-packaging of mRNAs into unique granules. Together, these findings demonstrate that neuronal mRNAs are differentially sorted into molecularly and functionally distinct granules, providing a framework for understanding how precise spatio-temporal control of mRNA localization and translation is achieved across complex neuronal arbors.

overall_design: Primary hippocampal neurons derived from Actb:24xMBS and Arc:24xPBS transgenic mice were used to characterize the RNA composition of mRNA-containing granules following chemical long-term potentiation (cLTP) stimulation. To identify RNAs in proximity to Actb or Arc transcripts, an APEX2-based RNA proximity biotinylation approach was employed. APEX2 was targeted to specific RNAs via MCP–MBS and PCP–PBS systems, with neurons transduced with lentiviruses expressing MCP-APEX2 or PCP-APEX2 fusion proteins.  Proximity labeling was induced by a 1-minute H₂O₂ treatment at 1 hour post-cLTP stimulation, a time point corresponding to peak cytoplasmic accumulation of Arc mRNA. Following labeling, total RNA was extracted, and biotinylated RNAs were enriched באמצעות streptavidin pulldown and prepared for high-throughput sequencing.  Control conditions included uninfected neurons and scrambled targeting controls (MCP-APEX2 expressed in Arc:24xPBS neurons and PCP-APEX2 expressed in Actb:24xMBS neurons) to account for non-specific labeling.

first: Rogow

last: Jackson

first: Cutler

last: Ronald

first: Das

last: Sulagna


title: Rat somatic genome editing enables ER+ breast cancer modeling

city: Houston

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

summary: Genetically engineered mouse models have advanced cancer research but often fail to capture key features of certain human tumors. Rats, with distinct physiology and tumor biology, offer a powerful alternative, yet their use has been constrained by technical barriers to genome editing. Here, we report efficient somatic genome editing in rats, enabling both Indel and substitution mutations. We then apply this approach to model estrogen receptor (ER)-positive breast cancer, which accounts for ~70% of human cases but remains poorly represented in mice. The resulting rat tumors reproduce hallmarks of human ER+ breast cancer, including ductal histology, hormone responsiveness, and immune-microenvironmental features. By contrast, identical genetic alterations in mice failed to yield ER+ tumors, underscoring critical species differences in tumorigenesis. Together, this work establishes a versatile platform for rapid generation of clinically relevant rat tumor models, opening new avenues to dissect tumor biology, therapeutic response, and immune interactions in previously inaccessible cancer subtypes.

overall_design: Multiple group comparison. We compared the transcriptomes of different rat models, involving six genotypes in all.

first: Wen

last: Bu

first: Yi

last: Li


title: Essential lncRNAs in the human transcriptome

city: New York

first: Wen-Wei

last: Liang

address: 101 Avenue of the Americas

institute: New York Genome Center

summary: Mammalian genomes host a diverse array of RNA that includes protein-coding and noncoding transcripts. However, the functional roles of most long noncoding RNAs (lncRNAs) remain elusive. Using RNA-targeting CRISPR-Cas13 screens, we probed how loss of ~5,500 lncRNAs impacts cell fitness across five human cell lines and identified 788 lncRNAs with context-specific or broad essentiality. We confirm their essentiality with individual perturbations and find that the majority of essential lncRNAs operate independently of their nearest protein-coding genes. Using transcriptome profiling in single cells, we discover that loss of essential lncRNAs impair cell cycle progression and drive apoptosis. Many essential lncRNAs demonstrate dynamic expression across tissues during development. Using ~9,000 primary tumors, we pinpoint those lncRNAs whose expression in tumors correlates with survival, yielding new biomarkers and potential therapeutic targets. This transcriptome-wide survey of functional lncRNAs advances our understanding of noncoding transcripts and demonstrates the potential of transcriptome-scale noncoding screens with Cas13.

overall_design: To identify essential lncRNAs, we engineered five human cell lines, HAP1, HEK293FT, K562, MDA-MB-231 and THP1, to express the nuclear-localized RfxCas13d effector under doxycycline-inducible control. Next, we transduced each cell line with the lentiviral gRNA library at a low multiplicity-of-infection to ensure each cell received only a single perturbation and induced Cas13 expression via doxycycline addition. We harvested genomic DNA from these cells at 0, 7, and 14 days post-Cas13 induction and computed changes in gRNA abundance via amplicon sequencing.


title: Oxygen-generating microparticles enhance viability and functionality of human pluripotent stem cell-derived cardiomyocytes

city: Cincinnati

first: JIALIANG

last: LIANG

address: 231 Albert Sabin Way

department: Department of Pathology and Laboratory Medicine

institute: University of Cincinnati

summary: Human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) represent a promising therapy for myocardial infarction (MI), but their survival is severely limited by the hypoxic infarct environment. The optimal oxygen levels required to maintain the viability and functionality of hiPSC-CMs remain poorly defined. This study aimed to develop a controlled oxygen-delivery system to support engineered heart tissue (EHT) for cardiac regeneration. Oxygen-generating particles (OGPs) were engineered using peroxide (sodium percarbonate) and antioxidant (β-carotene) components encapsulated in PLGA microparticles. The effects of OGPs on hiPSC-CMs were evaluated through oxidative stress assays, cell viability analysis, and contractility measurements. RNA-seq was performed to investigate gene expression changes in hiPSC-CMs in response to OGPs and hypoxic stress. Transcriptomic analysis revealed that genes associated with CM maturation and contractile function were upregulated following OGP pretreatment. RNA-seq further demonstrated activation of oxygen-responsive metabolic pathways that facilitated cellular adaptation to hypoxic stress. OGP-mediated oxygen delivery offers a promising strategy for oxidative preconditioning and significantly improves the regenerative efficacy of hiPSC-CM-based cardiac therapies.

overall_design: Experiment 1: hiPSC-CMs were generated using a Wnt activation/inhibition protocol. Following 10 days of induction, cells were treated with OGPs or vehicle control for 24 hours. Total RNA was then isolated from undifferentiated hiPSCs, vehicle-treated hiPSC-CMs, and OGP-treated hiPSC-CMs for RNA sequencing. Experiment 2: After 10 days of differentiation and subsequent purification, hiPSC-CMs were treated with OGPs or vehicle control and exposed to hypoxic conditions (1% O₂). After 24 hours, total RNA was extracted from both groups for RNA sequencing.

first: Jialiang

first: Xingyu


title: Glypican-1 upregulation elicited in response to a cell-impermeable kinase inhibitor and its overexpression enhance HIV infection

summary: Studies of herpes simplex virus (HSV) entry revealed a previously unrecognized "outside-in" signaling pathway involving phosphatidylserine (PS) scrambling and associated translocation and subsequent extracellular activation of canonical intracellular proteins, including Akt. We hypothesized that HIV-1, which activates a different scramblase, TMEM16F, to induce PS externalization, may similarly trigger an "outside-in" signaling response to promote viral entry. To study this process, we utilized a cell-impermeable staurosporine analog, alkyl-CIMSS, which is a broadly active kinase inhibitor that blocks HSV-induced exofacial Akt phosphorylation, and HSV entry. We show that TMEM16F-mediated PS externalization in response to HIV is not associated with Akt translocation; however, surprisingly, pretreatment of cells with alkyl-CIMSS enhanced HIV-1 infection post-entry. To identify potential biological processes that mediated this enhancement, we performed whole-cell total and phosphoproteomics, and bulk RNA sequencing. Cells treated with alkyl-CIMSS exhibited increased cyclin-dependent kinase (CDK) activity, resulting in higher levels of phosphorylated SAMHD1. Further, alkyl-CIMSS treatment robustly upregulated the cell surface density of the proteoglycan glypican-1 (GPC1). Lentivirus-driven GPC1 overexpression or shRNA knockdown demonstrated that, independent of alkyl-CIMSS treatment, GPC1 expression promotes HIV infection. Collectively, these findings demonstrate that alkyl-CIMSS modulates the exofacial plasma membrane to promote susceptibility to HIV infection by increasing CDK activity and upregulating GPC1.

overall_design: RNA-Seq profiling of Jurkat-CCR5 cells and the effect of alkyl-CIMSS in the context of HIV-1BaL infection.

first: Vinzant

last: Kelsey

first: Herold

last: Betsy


title: Gene Expression Profiling of T- and NK-cell Lymphoma Cell Cultures

city: Chapel Hill

first: Jacob

last: Pantazis

state: NC

address: 116 Manning Drive

department: Pharmacology

institute: University of North Carolina at Chapel Hill

summary: RNA-seq gene expression profiling was performed on 30 established T- and NK-cell lymphoma cell cultures. These data were collected to for the measurement of correlations between gene expression profiling and the sensitivities of T- and NK-cell lymphoma cultures to small molecule therapies used in the treatment of T- and NK- lymphomas.

overall_design: RNA was extracted from 1 M cultured cells, taken after cells had been grown up to a high densitv, >400,000 live cells per mL in RPMI. Total RNA was extracted using Rneasy extraction kit from QIAGEN. Samples were shipped to Novogene corporation where cDNA library perparation and sequencing were performed. NovaSeq 6000 was used (A01426) in one lane of an S4 Flow Cell (ID#H73WJDSX2).

first: Pantazis

last: Jacob

first: Pomeroy

last: Amy

first: Palmer

last: Adam


title: Nuclear basket subunits Nup211 and Rsm1 influence RNA 3'-processing and  transcription termination in fission yeast

first: Ana

middle: M

last: Sanchez

address: 430 E 67th Street, RRL-865

department: Molecular Biology

institute: Memorial Sloan Kettering Cancer Center

summary: RNA-seq analysis compares gene expression of rsm1∆ and nup211-1435* mutants to the wild-type fission yeast (Schizosaccharomyces pombe)

overall_design: Two test samples and 1 control sample were processed (each sample has 3 replicate experiments).

first: Lauren

last: Bednor

first: Aleksei

last: Innokentev

first: Angela

last: Sem

first: Beate

last: Schwer

first: Stewart

last: Shuman


title: EGF-induced EMT in MDA-MB-468 breast cancer cell line

city: Trondheim

first: Ellen Marie

middle: Botne

last: Quinsgaard

address: Erling Skjalgsons gate 1

country: Norway

institute: Norwegian University of Science and Technology

summary: The Epithelial-Mesenchymal Transition (EMT) is an early  metastatic process found to promote disease progression and poor prognosis in cancer. Here, EMT was induced in the breast cancer cell line MDA-MB-468 using epidermal growth factor (EGF). Gene expression data was used to determine effects on metabolic pathways, as well as to assess the degree of EMT induction.

overall_design: MDA-MB468 cells were seeded, serum-starved and treated with 50ng/mL Epidermal Growth Factor (EGF) for 0h, 12h, 24h, 48h and 72h respectively before lysis and RNA-extraction.


title: Glioblastoma cells imitate neuronal excitability in humans

city: Copenhagen

first: Joachim

last: Weischenfeldt

address: Ole Maaløes Vej 5

department: BRIC

country: Denmark

institute: University of Copenhagen

summary: Background: Glioblastomas are renowned for their pronounced intratumoral heterogeneity, characterized by a diverse array of plastic cell types. However, the physiological and transcriptomic features of the cells residing in the invasive leading edge (LE), including both neurons and glioblastoma cells (GBCs), remain unclear, challenging our comprehension of the glioblastoma pathophysiology. Methods: To elucidate molecular and morphophysiological features of LE cells, we established an experimental workflow enabling the investigation of GBCs and neurons within cancer-infiltrated organotypic tissue specimens from the same patients. With this approach, we characterized the electrophysiological properties of cells in the neocortical tumor LE (LE cells). We further performed single-cell Patch-seq experiments, enabling transcriptomic analysis of electrophysiologically recorded LE cells. Results: Upon depolarization, 58% of LE cells exhibited aberrant action potentials (aAPs). Electrophysiological assessment showed that a subset of GBCs generated aAPs, with no significant differences in aAP propertiescompared to LE neurons. Transcriptomic analysis of 144 LE cells revealed four transcriptomic clusters, including two GBC populations and two neuronal populations. LE GBCs exhibited diverse cellular states, including mesenchymal-like, astrocyte-like, neural progenitor-like, and oligodendrocyte-precursor cell-like phenotypes.  Notably, LE GBCs exhibiting aAPs displayed reduced mitotic pathway activity and developmental regulatory ionchannel CaV1.2. Cell-cell interaction analysis illustrates a higher signaling interaction between aAP LE cells compared to no-aAP LE cells. Conclusion: In summary, we find comparable electrical properties between neurons and a subset of GBCs in the leading edge, suggesting an active electrophysiological role of GBCs in the tumor's pathophysiology.

overall_design:
Acute and cultured slices of human glioblastoma tumors were prepared, and whole-cell patch-clamp recordings were performed, followed by nucleus extraction for transcriptomic analysis. RNA was reverse-transcribed, amplified, and sequenced using the SMART-seq v2 protocol.

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

first: Tong

last: Tong

first: Josephine

last: Hendriksen

first: Kirstine

last: Elbæk

first: Attila

last: Ozsvar

first: Jens

middle: T

last: Eschen

first: Francisco

last: Rodríguez-González

first: Ilayda

last: Pusat

first: Emilie

last: Littau Christensen

first: Mads

last: Rahbæk

first: Kathrine

last: Pii Frederiksen

first: Søren

middle: O

last: Cortnum

first: Ann

last: Sindby

first: Kaare

last: Meier

first: Nikola

last: Mikic

last: Sørensen

first: Jonathan

last: Ting

first: Marco

last: Capogna

first: Bjarne

middle: W

last: Kristensen

first: Wen-Hsien

last: Hou

first: Anders

middle: R

last: Korshøj


title: Single-cell RNA sequencing reveals M2-like macrophage signatures associated with mesenchymal stem cell treatment in a murine sepsis model

city: Chiba

first: Takahisa

last: HISHIYA

state: Chiba

address: 1-8-1,inohana, chuo-ku

institute: Chiba university

summary: Mesenchymal stem cells (MSCs) have shown therapeutic potential in preclinical sepsis models, but the mechanisms remain unclear. Using a murine cecal ligation and puncture model, we performed single-cell RNA sequencing of CD45+ immune cells 6 hours after MSC administration. MSC treatment improved survival and induced transcriptional reprogramming of macrophages toward an M2-like phenotype, accompanied by reduced inflammatory signatures. These findings provide mechanistic insight into MSC-mediated immune modulation in sepsis.

overall_design: In vivo murine sepsis model induced by cecal ligation and puncture (CLP). Human adipose-derived MSCs were administered intravenously. Peripheral blood CD45+ immune cells were collected 6 hours post-CLP and analyzed using single-cell RNA sequencing to evaluate immune cell composition and transcriptional changes.

first: Takehiko

last: Oami

last: Hishiya

first: Seiji

last: Miyauchi

first: Chiaki

last: Iwamura

first: Kiyoshi

last: Hirahara

first: Taka-aki

last: Nakada


title: Nuclear FGF2, Androgen Receptor and Wnt Pathway Activation Define a Targetable Subset of Antiprogestin-Resistant Luminal Breast Cancer

city: La Plata

first: Martin

middle: Carlos

last: Abba

state: Buenos Aires

country: Argentina

institute: School of Medical Sciences - UNLP

summary: We used PR+ T47D and T47D‑YA cell lines engineered to overexpress FGF2 to investigate FGF2‑driven antiprogestin resistance. Transcriptome profiling, qRT-PCR, immunohistochemistry, and in vivo assays were performed to assess hormone receptor expression, pathway alterations, and therapeutic response. We evaluated nuclear androgen receptor (AR) and FGF2 in luminal breast cancer specimens. RNA-seq showed that FGF2 overexpression dysregulated Wnt signaling, downregulated estrogen receptor (ER) and PR, and upregulated AR expression. PR isoform B (PRB) predominated over isoform A, consistent with an antiprogestin-resistant phenotype. FGF2-overexpressing xenografts showed antiprogestin resistance, increased proliferation, and lung metastasis. AR and Wnt pathway blockade impaired tumor growth, and combined treatment further reduced tumor and metastatic burden. In clinical samples, nuclear FGF2 correlated with elevated AR levels in ER+PR− and PRB-high tumors.

overall_design: Total RNA was isolated from T47D-YA cells overexpressing the 18 or 22.5 kDa FGF2 isoforms, and from empty vector controls (MOCK) for further RNA-sequencing.

first: Caroline

last: Lamb

first: Claudia

last: Lanari


title: The phytosterol 24 (S)-saringosterol alters lipid homeostasis and inflammatory pathways in a cell-specific manner.

city: St. Louis

first: Jinsheng

last: Yu

state: MO

address: 660 S. Euclid Ave.

department: Genetics

institute: Washington University School of Medicine

summary: Liver X receptors (LXR alpha/beta) are nuclear receptors that play a crucial role in regulating various biological processes, including lipid metabolism and inflammation. Activation of these receptors using synthetic pan LXR agonists, such as T0901713 and GW3965 has demonstrated neuroprotective effects, making them promising therapeutic targets for neurodegenerative disorders like Alzheimer’s Disease (AD). However, the clinical applications of synthetic pan-LXR agonists are limited by adverse hepatic effects including hypertriglyceridemia and steatosis. Thus, dissociating the beneficial effects of LXR agonism from the deleterious side effects in the liver will be required for the development of LXR agonists as better potential therapeutics. In this study, we investigated 24(S)-saringosterol, a phytosterol derived from the seaweed Sargassum fusiforme, which has previously been reported to exhibit LXR agonist activity without inducing hepatic steatosis. To elucidate its effects on lipid metabolism and inflammatory pathways, we used two distinct cell lineages-myeloid and hepatic cells. Our results demonstrate that 24(S)-saringosterol exhibits a stronger activation of LXR regulated gene expressions leading to dose-dependent upregulation of the cholesterol efflux transporter ABCA1 in both cell types. In myeloid cells, including microglia and bone marrow-derived macrophages, like GW3965, 24(S)-saringosterol exhibited anti-inflammatory effects by downregulating genes involved in interferon- pathways and promoted cholesterol efflux by upregulating ABCA1 via LXR activation. In myeloid as well as hepatic cells, 24(S)-saringosterol reduced the expression of cholesterol biosynthesis genes as well as LDLR via SREBP2, in contrast to GW3965, which upregulated expression of lipid synthesis genes via SREBP1. These findings highlight the therapeutic potential of 24(S)-saringosterol as a dissociated LXR agonist that effectively mitigates the adverse effects associated with synthetic LXR agonists. This compound represents a promising candidate for further investigation in the context of AD and other metabolic and inflammatory disorders.

overall_design: Primary mouse microglia, bone derived macrophages, and hepatocytes were cultured and treated with either Vehicle (Etoh), 1 micromolar of GW3964 or 10 micromolar of 24(S)-saringosterol . Post 24 hr treatment, cells were washed and RNA was extracted using Zymo Research Quick RNA Miniprep Plus kit (cat#R1058). The extracted RNA was submitted for bulk RNA sequencing.

first: Manmeet

last: Singh

first: Monique

last: Mulder

first: Anil

last: Cashikar

first: Steven

last: Paul


title: Machine Learning Analysis of the Human Initiator Region Reveals Key Features of Different Types of Core Promoters

city: La Jolla

first: James

middle: T.

last: Kadonaga

address: 9500 Gilman Dr

institute: University of California, San Diego

summary: The initiator (Inr) is the starting point for the transcription of many genes. Here, we generated highly predictive machine learning models of the human Inr region, and determined that the Inr is present in about 60% of focused human promoters, identified a novel TATA-specific Inr, and detected the overlapping but functionally distinct TCT motif. Quantitative genome-wide analyses revealed a strict and synergistic interaction between the Inr and DPR, an inverse relationship between the TATA and DPR, a flexible and sometimes independent function of the TATA box in relation to the Inr, and different properties of the TCT motif in humans versus Drosophila.

overall_design: HARPE (high-throughput analysis of randomized promoter elements) and SVR (support vector regression) analyses of the human initiator (Inr) region. HARPE was performed in vitro and in human (HeLa) cells.

first: Torrey

middle: E

last: Rhyne-Carrigg

first: Long

last: Vo ngoc

last: Medrano

first: Kassidy

last: Gillespie


title: Multimodal profiling reveals a Notch-responsive regenerative subpopulation of cochlear supporting cells [2]

city: Omaha

first: Litao

last: Tao

state: NE

address: 2500 California Plaza

department: Biomedical Sciences

institute: Creighton University

summary: Regeneration enables organisms to repair damaged tissues, yet this capacity is strikingly limited in the cochlear sensory epithelium, essential for sound detection. A major cause of hearing loss arises from the irreversible loss of sensory hair cells (HCs) in the cochlea. While supporting cells (SCs) have a latent ability to trans-differentiate into HCs, this regenerative potential is rapidly lost after development. Using live imaging and single-cell multiomics of cochlear explants, we uncovered the cellular and molecular heterogeneity underlying the limited regenerative capacity of the neonatal mouse cochlea. Notch repression broadly silenced key SC genes, yet only a rare subpopulation of Deiters cells (DC), termed responsive DCs, initiated the trans-differentiation into HC fate. These cells underwent coordinated transcriptional and enhancer remodeling, linking epigenetic priming with morphological plasticity, while other SCs remained refractory despite robust Notch targets downregulation. Our study provides a molecular definition of a fate-primed SC state, revealing Notch inhibition as a selective trigger that unmasks rare regenerative competence.

overall_design: RNA-seq profiling of supporting cells (SC) isolated from murine cochlear explants after 24h of Notch inhibition treatment, and corresponding control samples. Two developmental time points, P0 and P6. Four replicates per treatment/control at P0 and three replicates at P6.

first: Lama

last: Khalaily

first: Shahar

last: Kasirer

first: Katherine

last: Domb

first: Mi

last: Zhou

first: Buwei

last: Shao

last: Taiber

first: Ran

last: Elkon

first: David

last: Sprinzak

first: Karen

middle: B

last: Avraham


title: Targeting LPAR4 overcomes stress adaptation to CDK4/6 inhibition in soft tissue sarcoma [RNAseq]

first: Jlenia

last: Guarnerio

address: 6767 Bertner Ave

institute: MD Anderson Cancer Center

summary: CDK4/6 inhibitors are under active clinical evaluation in sarcoma, yet the mechanisms governing sensitivity and resistance remain unclear. We show that the CDK4/6 inhibitor abemaciclib not only suppresses tumor cell proliferation but also induces robust type I interferon signaling driven by dsRNA accumulation, which is essential for its anti-tumor activity. Abemaciclib reshapes the sarcoma immune microenvironment by increasing T cell infiltration and enhancing intratumoral interferon-producing monocytes. Integrated transcriptomic and proteomic analyses identified Lysophosphatidic Acid Receptor 4 (LPAR4) as an adaptive stress-response factor upregulated in tumor cells upon treatment and associated with poor patient prognosis. Functionally, LPAR4 mitigates interferon-induced mitochondrial stress, limiting reactive oxygen species accumulation and apoptosis, while its silencing exacerbates mitochondrial dysfunction and promotes tumor cell death. In vivo, LPAR4 loss synergizes with abemaciclib to inhibit tumor growth and prolong survival. These findings establish LPAR4 as a key regulator of stress adaptation and a promising target to potentiate CDK4/6-based therapies.

overall_design: Transcriptomic profiling of mouse undifferentiated sarcoma cells (p53 k.o. Ccne1 o.e.) with or without treatment with the CDK4/6 inhibitor abemaciclib, and with or without knock-down of Lpar4.

first: Jin-Fen

last: Xiao

first: Emily

middle: Y

last: Ko


title: Targeting LPAR4 overcomes stress adaptation to CDK4/6 inhibition in soft tissue sarcoma [CITEseq]

overall_design: Mice bearing undifferentiated pleiomorphic sarcoma (UPS) tumors were treated with vehicle or with the CDK4/6 inhibitor abemaciclib (n=4 mice per group, 8 mice total). Live cells were isolated from tumors for single-cell RNA-sequencing.


title: Heterochronic activation of TGF-β signaling drives the diversity of the avian sterna

city: Fukuoka

first: Seung June

last: Kwon

state: Fukuoka

address: 744 Motooka, Nishi-ku

department: Graduate School of Systems Life Sciences

institute: Kyushu University

summary: Adaptive evolution has driven the diversification of vertebrate skeletal morphology, enabling a wide array of locomotor modes and lifestyles. In volant birds (carinates), the sternum develops a ventral keel that provides an attachment site for massive pectoral muscles essential for powered flight. In contrast, flightless ratites have lost both flight capability and the keel, resulting in a striking morphological contrast between their sterna. Here, we interrogated the cellular and molecular basis underlying this morphological divergence by using chicken embryos as a carinate model and emu embryos as a ratite model. Through a series of analyses including spatiotemporal transcriptomics and a spheroid culture system, we found that TGF-β signaling, which promotes proliferation of ventral sternal chondroprogenitors, is activated in both species until the stage when the left and right sternal progenitors meet; however, in chicken this activation persists beyond this stage, driving ventral extension of the keel primordium, whereas in emu it shuts off early, culminating in the absence of a protruding keel. Together, our findings suggest that skeletal morphological changes associated with behavioral transitions can arise from heterochrony in developmental signaling, thereby deepening our understanding of the evolutionary logic shaping skeletal diversification.

sample_organism:
Dromaius novaehollandiae
Gallus gallus

platform_organism:
Dromaius novaehollandiae
Gallus gallus

overall_design: RNA-Seq (combined with photo-isolation chemistry) profiling of chicken and emu sternal progenitors at developmental stage 24 and stage 36: dorsal and ventral. For each conditions, 4 biological replicates were prepared.

first: Yuji

last: Atsuta


title: MYST acetyltransferases are a targetable therapeutic vulnerability in SETBP1-mutant leukemia [CUT&Run]

city: Portland

first: Julia

last: Maxson

state: Oregon

address: 3181 SW Sam Jackson Park Rd

institute: Oregon Health and Science University

summary: Mutations in SET binding protein 1 (SETBP1) are associated with an adverse prognosis in myeloid malignancies. These mutations stabilize SETBP1 protein, driving increased expression of a progenitor-associated gene expression program through incompletely described mechanisms. A proteomic screen revealed interactions between SETBP1 and members of the MYST acetyltransferase complexes, including the catalytic subunits—KAT6A and KAT7. Mutant SETBP1 increases the localization of MYST complexes at known SETBP1 target genes, including the Hoxa cluster, where they drive increased histone acetylation and gene expression. Treatment of SETBP1D868N-expressing myeloid progenitors with MYST inhibitors reduced target gene expression. To establish the efficacy of MYST inhibition in vivo, we treated mice harboring a syngeneic SETBP1-mutant leukemia with the clinical-grade MYST inhibitor—PF-9363. This resulted in complete hematologic control and increased survival. MYST inhibition was also highly effective against a SETBP1-mutant PDX model. These studies identify MYST acetyltransferases as promising therapeutic targets in SETBP1-mutant malignancies.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: CUT&RUN on human cell line: Doxycycline-inducible SETBP1 expression in K562 cells. CUT&RUN on mouse primary cells: lentivirally transduced control (luciferase) or SETBP1D868N mutant into mouse bone marrow lineage-negative (Lin-) cells and GFP sorting positive cells.

first: Hanqian

last: Carlson

first: Thai

last: Nguyen


title: Expression data of microRNAs captured by OAA from plasma of NSCLC patients treated with nivolumab

city: Maebashi

first: EIJI

last: Narusawa

address: Showa-machi, Maebashi, Gunma 371-8511,

institute: Department of General Surgical Science, Gunma University Graduate School of Medicine

summary: Background: Predictive biomarkers for immune checkpoint inhibitors (ICIs) in non-small cell lung cancer (NSCLC) are limited. High-mannose glycans, enriched in tumors, can be selectively captured using OAA1 (recombinant OAA), a novel lectin. This study investigates whether plasma microRNAs (miRNAs) enriched by OAA1 serve as predictive markers of response to anti-PD-1 therapy.  Methods: Pre-treatment plasma samples from 48 NSCLC patients treated with nivolumab were processed using OAA1 lectin columns. Levels of circulating miR-320a, miR-320b, and miR-3613-5p , which were identified as resistance associated miRNAs by microarray, were quantified with and without OAA1 enrichment. Associations with therapeutic response and overall survival were analyzed.  Results: The three miRNAs were significantly upregulated in patients with stable or progressive disease compared to partial responders, but only after OAA1 enrichment. ROC and survival analyses showed improved predictive and prognostic power with OAA1-enriched miRNAs. For example, miR-3613-5p’s AUC improved from 0.837 to 0.897, and its hazard ratio increased from 3.386 to 7.815.  Conclusion: OAA1-captured plasma miRNAs are associated with resistance to nivolumab and poor prognosis in NSCLC. This glycan-based enrichment strategy enhances the clinical value of circulating miRNAs and may complement tissue-based ICI biomarkers.

overall_design: Paired pre-treatment and post-treatment blood samples collected from two NSCLC patients were utilized for microRNA isolation and RNA microarray as recently described. Briefly, miRNA was isolated from plasma by lectin column. RNA extraction was performed using the OAA-lectin column and the QIAzol® Lysis Reagent (Qiagen) followed by purification in the NucleoSpin® miRNA Plasma (MACHEREY-NAGEL GmbH & Co.). Biotinylated cRNA preparation was performed with the FlashTag™ Biotin HRS RNA Labeling Kit (Thermo Fisher Scientific, Walthmam, MA, USA) and the biotin-labeled sample were hybridized on GeneChip miRNA 4.0 Array. GeneChips were washed and stained in the Affymetrix GeneChips Fluidics Station 450. GeneChips were scanned using the Affymetrix GeneChip™ Scanner 3000 7G with AutoLoader.

first: Yukiko

last: Nakano

first: Eiji

first: Tadataka

last: Kamiyama

first: Takehiko

last: Yokobori

first: Yoshihiro

last: Taguchi


title: MYST acetyltransferases are a targetable therapeutic vulnerability in SETBP1-mutant leukemia [RNA-Seq]

overall_design: RNA-seq profiling of mouse bone marrow lineage-negative (Lin-) primary cells lentivirally transduced with control (luciferase) or SETBP1D868N mutant. To study MYST inhibitor effects, RNA-seq profiling was also performed on mouse bone marrow lineage-negative (Lin⁻) primary cells lentivirally transduced with the SETBP1D868N mutant followed by treatment with DMSO or PF-9363.


title: Transcriptome of TACI KO and WT mouse marginal zone and follicular B cells

city: London

first: Victor

last: Tybulewicz

address: 1 Midland Road

country: United Kingdom

institute: Francis Crick Institute

summary: The mature peripheral B cell compartment consists of follicular (FO) and marginal zone (MZ) B cells, which mature from transitional B cells in the spleen and mount T-dependent and T-independent antibody responses, respectively. TACI (Tnfrsf13b) is a member of the TNF-receptor superfamily expressed on mature and transitional B cells, with highest expression on MZ B cells and plasma cells, which is activated by the cytokines BAFF and APRIL. BAFF also stimulates the related receptor BAFFR, which provides signals that are essential for mature B-cell survival. Previous studies of TACI-/- mice have observed that TACI-deficiency leads to an expansion of mature B cells, and therefore it has long been thought that TACI is a negative regulator of mature B-cell survival. However, TACI-/- mice also have elevated levels of BAFF, therefore the B-cell hyperplasia phenotype in TACI-/- mice is most likely a cell-extrinsic effect due to increased BAFF-BAFFR signalling in TACI-/- B cells. To investigate the cell-intrinsic role of TACI, we generated mouse mixed bone marrow chimeras from TACI-/- and WT mice and studied the effect of TACI loss in vivo, without the confounding factor of increased BAFF. Here, we have analysed the transcriptomes of TACI KO and TACI WT marginal zone and follicular B cells by RNAseq.

overall_design: Mouse splenic follicular and marginal zone B cells of the genotype Tnfrsf13b-/- CD45.2+ (TACI KO), Tnfrsf13b+/+ CD45.2+ (TACI WT), or wildtype CD45.1+ were isolated by FACS from adult mixed bone marrow chimeras, with 6 biological repeats for each genotype, and analysed by RNAseq.

first: Daisy

middle: H

last: Luff

first: Stefan

last: Boeing


title: Intracellular Aβ42 Sequestration by a Serine Protease Mitigates Neurotoxicity

city: hunan province

first: yang

last: meng

address: lusan

country: China

institute: hunan normal university

summary: The repeated failures in developing disease-modifying therapies for Alzheimer's disease (AD) by targeting extracellular Aβ have urged a complete reassessment of the cellular mechanisms underlying Aβ neurotoxicity. Emerging evidence suggests that intraneuronal Aβ accumulation represents an early pathogenic event in AD, preceding extracellular plaque formation and neuroinflammatory responses. However, whether targeting intracellular Aβ can halt disease progression and how this can be achieved remain unknown. While investigating the brain transcriptional responses to Aβ pathology, we identified a neuroprotective role for the serine protease Yip7 in a Drosophila AD model. Neuronal overexpression of yip7 alleviated multiple Aβ42- induced deficits, including declines in locomotor activity, impaired proteostasis, increased brain ageing and neuronal death, and reduced lifespan. Unlike canonical digestive proteases, Yip7 is not secreted but instead localizes to the endosomal/lysosomal compartments via a putative transmembrane domain initially predicted as a signal peptide. Crucially, Yip7’s neuroprotective function depends on its proper subcellular localization rather than the catalytic triad of serine proteases. Mechanistically, rather than directly eliminating Aβ, Yip7 increased neuronal retention of Aβ, supporting a model in which Yip7 reduces Aβ42 toxicity by limiting its degradation/secretion. Notably, yip7 overexpression also conferred protection in a Huntington's disease model, underscoring its broader relevance. Together, these findings introduce a novel concept that intracellular Aβ sequestration by a serine protease can mitigate neurotoxicity, and propose targeting intracellular amyloid as a promising therapeutic strategy for AD.

overall_design: Flies from Drosophila models with different genes were reared at 29°C and fed normally. Using Drosophila head transcriptome data to detect gene expression changes between wild-type and AD (Alzheimer’s disease) model flies.

first: Jingyun

last: Su

first: Xinfeng

last: Wang

first: Pa

last: Wu

first: Zongzhao

last: Zhai

first: Meng

last: Yang


title: Therapeutic Potential of ASO-Mediated KCNT1 Knockdown in KCNT1 Epileptic Encephalopathy

city: Boston

first: Timothy

last: Yu

state: MA

address: 300 Longwood Ave

institute: Boston Children's Hospital

summary: KCNT1-related epileptic encephalopathy, including Epilepsy of Infancy with Migrating Focal Seizures (EIMFS), is a severe neurodevelopmental disorder associated with refractory seizures, profound neurologic impairment, and premature death. It is caused by de novo genetic variants in KCNT1 which alter the function of Slack, an evolutionarily conserved sodium-gated potassium channel that modulates neuronal firing patterns and excitability. Pathogenic KCNT1 variants lead to overactive Slack channels, boosting total neuronal potassium currents by up to 40%, driving cortical hyperexcitability and causing seizures. Here we investigate antisense oligonucleotide (ASO)-mediated KCNT1 knockdown as a therapeutic strategy for patients with EIMFS. Intrathecal delivery of an experimental, non-allele-specific, KCNT1-targeting ASO by lumbar puncture in two patients with KCNT1 p.R474H, a severe, recurrent pathogenic variant, led to a significant reduction in seizure frequency and intensity, supporting the potential efficacy of suppression of KCNT1 expression as a therapeutic strategy for EIMFS. However, investigational treatment was also associated with development of ventricular enlargement or hydrocephalus in both patients, prompting in one case redirection of goals of care. This finding was not clearly related to EIMFS itself, drawing attention to an important possible toxicity of some intrathecal antisense oligonucleotides.

overall_design: RNA-seq of WT iPS-neurons with four treatment conditions: no treatment, Tofersen ASO, Tominersen ASO, and Valeriasen ASO


title: Characterization of Persistency of Lay in Laying Hens

city: Ithaca

first: Laurie

last: Francoeur

address: 507 Tower Rd

department: Animal Science

institute: Cornell University

summary: Selective breeding in laying hens has resulted in a laying rate of approximately one egg per day during their first year. Due to variability within a flock, this rate declines after the first year, leading producers to cull hens. The aim of this study was to identify physiological and molecular differences between persistent (PL, egg-laying rate = 100%) and non-persistent layers (NPL, egg-laying rate ≤ 82%) after the first year. Forty laying hens were reared from 16 to 76 weeks of age and a subset was maintained until 96 weeks. Throughout the study, egg-laying data were recorded daily. At 76 weeks, ovarian tissue was collected from PL (n=3) and NPL (n=4) hens for RNA-sequencing. Ovarian RNA-sequencing analysis revealed 279 differentially expressed genes between PL and NPL hens and analysis predicted the estrogen receptor as an upstream regulator. A greater understanding of the physiology and molecular patterns of persistent hens could enhance production efficiency and provide insights into ovarian aging in women.

overall_design: RNA-sequencing of ovarian samples from persistent and non-persistent laying hens.

first: Deena

last: Scoville

first: Jaclyn

last: Ahern

first: Patricia

middle: A

last: Johnson


title: Transcriptional analysis of direct NSD2 target genes in t(4;14) multiple myeloma reveals H3K36me2-dependent regulation and H3K27me3 antagonism [SLAM-seq]

city: Miami

first: sanxiong

last: liu

state: FL

address: 1501 NW 10th Avenue

department: Human Genetics

institute: University of Miami Miller School of Medicine

summary: This study aimed to identify the direct transcriptional targets of the H3K36me2 methyltransferase NSD2 in t(4;14) multiple myeloma (MM), where its aberrant expression drives oncogenesis, and to elucidate the molecular mechanisms underlying its regulatory role. To achieve this with precise temporal control and minimize cellular adaptation artifacts, we established an inducible dTAG-mediated acute NSD2 degradation system in the KMS-11 t(4;14) MM cell line. Using this model, we performed time-resolved SLAM-seq to measure newly synthesized mRNA levels at 7, 14, and 21 days post-NSD2 degradation, enabling the identification of primary transcriptional targets. Further SLAM-seq datasets were generated under conditions of NSD2 depletion followed by reconstitution with either wild-type NSD2 (NSD2WT) or a catalytically inactive mutant (NSD2Y1179A) to evaluate the requirement for SET domain activity. The contribution of H3K27me3 antagonism to NSD2-mediated gene regulation was investigated by performing SLAM-seq on NSD2-depleted cells treated with distinct PRC2 inhibitors (EPZ-6438 and MAK-658). Complementing the transcriptomic data, we performed CUT&Tag to map the genomic distribution of the H3K27me3 histone mark following NSD2 depletion relative to control conditions. Analysis of these datasets revealed 308 primary NSD2 transcriptional targets, predominantly downregulated upon NSD2 loss and enriched for functionally relevant transcription factors. Reconstitution experiments demonstrated that NSD2's transcriptional effects are almost entirely dependent on its SET domain catalytic activity. Furthermore, PRC2 inhibition partially rescued the downregulation of approximately half of the NSD2 target genes, highlighting a significant role for H3K27me3 antagonism. Importantly, CUT&Tag analysis showed that the compensatory increase in H3K27me3 upon NSD2 loss occurred primarily across genome-wide intergenic regions, rather than directly at the promoters or gene bodies of NSD2 target genes. Collectively, these deposited transcriptomic (SLAM-seq) and epigenomic (H3K27me3 CUT&Tag) data support a model where NSD2 regulates target gene transcription via H3K36me2 deposition, which, in part, functions by antagonizing H3K27me3 deposition at distal regulatory elements to foster a permissive chromatin environment, providing a valuable resource for understanding NSD2 function in t(4;14) MM and Wolf-Hirschhorn syndrome.

overall_design: SLAM-seq profiling was performed on two independent clones of human t(4;14) multiple myeloma KMS-11 cells engineered for inducible dTAG-mediated degradation of endogenous NSD2 (NSD2dTAG cells) to assess the impact of acute NSD2 depletion on newly synthesized and total mRNA levels. The experimental variables investigated include: 1) A time course of NSD2 depletion following dTAGV-1 treatment for 0 (control), 7, 14, or 21 days; 2) Reconstitution of NSD2-depleted cells with doxycycline-induced wild-type NSD2 (NSD2WT) or catalytically inactive NSD2 (NSD2Y1179A), compared to NSD2-depleted controls without induction; and 3) Treatment of NSD2-depleted cells with PRC2 inhibitors EPZ-6438 or MAK-658, compared to NSD2-depleted cells treated with a DMSO vehicle control. Each condition and time point includes data from the two biological replicate NSD2dTAG clones.

first: Yubao

first: Sanxiong

last: Liu

first: Gareth

last: Morgan


title: NeuID is a novel neuron-specific lncRNA that regulates neuronal function in Alzheimer’s disease

city: Göttingen

first: Andre

last: Fischer

state: NDS

address: Von-Siebold-Str. 3a

department: Epigenetics and Systems Medicine in Neurodegenerative Diseases

institute: DZNE Göttingen

summary: Non-coding RNAs are transcripts that do not encode proteins and comprise 98.5% of the human transcriptome. Among these, long non-coding RNAs (lncRNAs) have been implicated in various biological functions, including the control of gene expression and translation. The central nervous system (CNS) harbors a diverse array of lncRNA transcripts, yet the functions of many remain largely unexplored. In this study, we employed FANS with total RNA-sequencing and single-nuclei RNA sequencing approaches using human and mouse brain tissue to identify novel lncRNAs specific to neurons, and potentially associated with neurodegenerative diseases. We discovered a novel brain-specific lncRNA, the we named 'NeuID', that is specifically expressed in neuronal cells in the mouse and human brains. NeuID expression was found to be reduced in the brains of Alzheimer’s disease (AD) patients. Knockdown (KD) of NeuID resulted in the downregulation of synaptic plasticity genes. Additionally, NeuID KD led to decreased dendritic spine density and reduced neuronal network activity in MEA recordings. Furthermore, we demonstrate that NeuID interacts with EZH2, a component of the PRC2 complex, and mediates the h3k27me3 levels of Olig2 transcription factor. Notably, CRISPRa mediated overexpression of NeuID resulted in the rescue of functional impairment caused by AD-related pathological Aβ oligomers. Overall, our findings identify a novel brain and neuron-exclusive lncRNA that regulates neuronal function, is dysregulated in AD, and might be a potential therapeutic target against neuronal pathology in AD.

overall_design: RNA-seq profiling from primary hippocampal neurons treated with either control gapmers or NeuID gapmers to knockdown NeuID

first: Ranjit

last: Pradhan

first: Sadman

last: Sakib

first: Iga

last: Grzadzielewska

first: Eren

last: Diniz

first: Dennis

last: Krueger

first: Sophie

last: Schroeder

first: Susanne

last: Burkhardt

first: Anna-Lena

last: Schuetz

first: Jelena

last: Radulovic

first: Farahnaz

last: Sananbenesi

first: André


title: Effect of decitabine on therapeutic response in doxorubicin- and paclitaxel-resistant breast cancer cell lines

city: Brno

first: Core Facility

last: Bioinformatics

address: Kamenice 5

country: Czech Republic

institute: CEITEC - Masaryk University

summary: Breast cancer is the most commonly diagnosed malignancy in women worldwide, yet treatment success is frequently compromised by the development of therapeutic resistance. The complex nature of this resistance necessitates in-depth investigation to identify the mechanisms underlying the resistant phenotype of tumor cells and to develop effective therapeutic strategies. This study details the derivation and comprehensive functional and molecular characterization of doxorubicin- and paclitaxel-resistant breast cancer cell lines representing three distinct subtypes. Additionally, a triple-negative breast cancer (TNBC) cell line was used to explore the potential of the DNA methyltransferase inhibitor decitabine in reversing aberrant DNA methylation patterns associated with chemotherapy resistance. The study also evaluates decitabine's ability to enhance therapeutic efficacy in treatment-resistant TNBC.

overall_design: We established a paclitaxel-resistant breast cancer (BC) cell line from the MDA-MB-231 cell line, which represents the triple-negative BC subtype. Both the paclitaxel-resistant and parental MDA-MB-231 cell lines were used to generate tumor xenografts in SCID-beige immunodeficient mice. These tumors were then used for RNA sequencing (RNA-seq) to investigate whether chemotherapy resistance is linked to DNA methylation-induced transcriptomic changes, and to evaluate the potential of the DNA methyltransferase inhibitor decitabine (DAC) to reverse these alterations, thereby sensitizing resistant cells to chemotherapy. Mice harboring tumors from either the parental or paclitaxel-resistant cell lines were treated for a total of 26 days with vehicle, doxorubicin, decitabine, or a combination of doxorubicin and decitabine. The treatment regimen consisted of two 12-day cycles, separated by 2-day rest period. In each cycle, 4 mice were treated with decitabine on days 1-4 and 10-11, 4 mice were treated with doxorubicin on days 5 and 12, 4 mice received a combination of both agents (decitabine on days 1-4 and 10-11, doxorubicin on days 5 and 12), and 4 mice were treated with vehicle solution at the specified timepoints.

first: Lenka

last: Trnkova

first: Nicolas

last: Blavet


title: MRPGRX2 Antagonist Treatment Prevents Inflammation and Disease in a Mouse Model of Atopic Dermatitis Dataset 2

city: San Diego

first: Joshua

last: Wollam

address: 9761 W. Canyon Ter. Unit 1

institute: Escient Pharmaceuticals

summary: The Mas-Related G-Protein Coupled Receptor X2 (MRGPRX2) is a promiscuous receptor expressed on mast cells that mediates IgE-independent mast cell activation and degranulation in response to a variety of diverse agonists and has been implicated in numerous inflammatory conditions, including atopic dermatitis. We investigated if the small molecule MRGPRX2 antagonist, INCB000262, improves disease phenotype in the house dust mite + Staphylococcus aureus enterotoxin type B (HDM+SEB) mouse model of atopic dermatitis and further characterized mast cell-mediated aspects of disease. MRGPRX2 knock-in mice were sensitized to HDM+SEB and orally dosed once daily with either vehicle or INCB000262 for 4 weeks, and efficacy and skin transcriptional changes evaluated. INCB000262 attenuated HDM+SEB-induced atopic dermatitis in vivo with improvements observed in skin thickness, transepidermal water loss, tissue weight, and overall clinical score. In addition, transcriptome changes induced by HDM+SEB exhibited a mast cell activation signature consistent with human atopic dermatitis lesional skin, which was attenuated by antagonist treatment.  Overall, the MRGPRX2 antagonist, INCB000262, attenuated HDM+SEB-induced atopic dermatitis disease phenotypes and mast cell-associated transcriptional changes, supporting further evaluation of INCB000262 as an oral treatment for atopic dermatitis and other mast cell-mediated diseases.

overall_design: RNAseq profiling of skin from HDM+SEB treated or vehicle-treated MRGPRX2 knock-in mice treated with or without the MRGPRX2 antagonist INCB000262

first: Swetha

last: Srinivasan


title: MRPGRX2 Antagonist Treatment Prevents Inflammation and Disease in a Mouse Model of Atopic Dermatitis Dataset 1

overall_design: RNAseq profiling of skin from HDM+SEB treated or vehicle-treated MRGPRX2 knock-in mice (without drug treatment)


title: Whole genome CRISPR drop-out screen in THP-1 cells exposed to mebendazole

first: Owen

last: Williams

address: 30 Guilford Street

department: Cancer section

institute: UCL GOS ICH

summary: We previously reported that mebendazole is an effective anti-AML therapeutic and acts via induction of MYB degradation. The present experiemnt was performed in order to uncover pathways of potential resistance in AML cells to mebendazole exposure. A whole genome CRISPR drop-out screen was performed on THP-1 AML cells exposed to 1 micromolar mebendazole or DMSO in order to identify genes that decreased AML sensitivity to this drug.

overall_design: THP-1 cells were transduced with the pooled sgRNA library, 2 ug/ml puromycin added after 48 h. Multiplicity of infection was calculated after 4 days puromycin selection, at which point the culture contained 29%  viable cells by flow cytometry. Cells were selected for 10 days in puromycin after which either 1 uM mebendazole or DMSO was added to the cultures and 10 days later viable cells enriched by density centrifugation and genomic DNA isolated.

first: Alexia

last: Tsakaneli

first: Noelia

last: Che


title: PTPMT1-dependent regulatory T cells mediate immunological tolerance to gut pathobionts

city: Cologne

first: Mauro

last: Corrado

address: Joseph-Stelzmann-Str. 26

institute: University of Cologne

summary: Mitochondrial dysfunctions are emerging as key drivers of gut inflammation, colitis, and IBD, yet their role in regulating immune tolerance remains unclear. Meanwhile, pathobiont infections, such as those caused by Helicobacter species, affect nearly half the global population, with symptoms manifesting in only 20%, adding a new layer of complexity. The genetic and environmental factors that disrupt gut tolerogenic mechanisms, tipping the balance toward disease in symptomatic infections, are not fully understood. Here, we show that PTPMT1 impairs tolerance to Helicobacter via Treg cells, independently from T cell-generated Type I or Type II interferons. Without cardiolipin, Treg cells lose metabolic fitness and immunosuppressive potential, unleashing pro-inflammatory myeloid cells in the gut. As a result, PTPMT1 ΔT mice are highly vulnerable to pathobiont infections even without microbiome imbalance. Inflammation and helper T cell imbalance are conserved in Barth syndrome, linked to cardiolipin deficiency from TAFAZZIN mutations. Overall, we propose that T cell-specific PTPMT1 governs the balance between tolerance and inflammation in the gut, dictating outcomes in pathobiont infections.

overall_design: CD45+ cells obtained from 3 pooled wild type and 3 pooled PTPMT1 deficient animals were used in scRNAseq

first: David

last: Sanin


title: MVI-targeted carbon-ion radiotherapy combined with immunotherapy for advanced hepatocellular carcinoma: Phase Ib DEPARTURE trial

city: Chiba-shi

first: Makoto

last: Fujiya

address: 1-8-1 Inohana, Chuo-ku

institute: Chiba university

summary: Hepatocellular carcinoma (HCC) with macrovascular invasion carries a poor prognosis, necessitating novel therapeutic strategies. This phase Ib trial evaluated the safety and preliminary efficacy of combining carbon-ion radiotherapy with immune checkpoint inhibitors in patients with advanced HCC. RNA-seq was conducted to investigate changes in the tumor microenvironment, aiming to identify molecular signatures predictive of response or resistance to the combination therapy. The reduction group showed enrichment of pathways related to inflammation, complement activation, which are often associated with immune activity. In contrast, the progression group exhibited enrichment of pathways linked to mesenchymal characteristics and angiogenesis, processes that may correlate with reduced therapy efficacy.

overall_design: RNA-seq was performed on pre-treatment biopsy specimens from nine patients enrolled in the DEPARTURE trial, with follow-up analysis conducted on non-irradiated lesions from three patients 42 days after treatment initiation.

first: Sadahisa

last: Ogasawara

first: Keisuke

last: Koroki

first: Hiroaki

last: Kanzaki


title: T, NK, NKT cells in the brain from WT or 15q dup mice [brain]

first: Minako

last: Ito

address: 3-1-1 Maidashi, Higashi-ku

summary: Autism Spectrum Disorder (ASD) is a neurodevelopmental disorder with no effective treatment, caused by genetic factors such as copy number variations (CNVs) and immunological factors such as maternal infection. The role of immunity in genetic ASD remains unclear. Here, we investigated the immun cells in the brains of a mouse model of ASD (15q11-13 duplication), a common CNV associated with ASD.

overall_design: T cells, NK cells, and NKT cells in the brain were sorted from WT and 15q dup mice at embryonic day 16 and 1, 2, 3, 4, and 6 weeks of age (E16; n = 8 (WT); n = 7 (15q), 1w; n = 11 (WT); n = 8 (15q), 2w; n = 10 (WT); n = 13 (15q), 3w; n = 7 (WT); n = 10 (15q), 4w; n = 9 (WT); n = 9 (15q), 6w; n = 7 (WT); n = 7 (15q)) and performed scRNA-seq.

first: Natsumi

last: Takayama


title: Regenerative potential of neonatal tendon cells is regulated by intrinsic resistance to inflammation and supportive T cell-secreted factors

city: New York

first: Alice

middle: H.

last: Huang

department: Orthopedic Surgery

institute: Columbia University

summary: Tendons mediate force transmission from muscle to bone to allow movement. Upon injury, adult tendons heal by scar formation with persistent functional deficits. While the immune response is a key regulator of healing, the roles of specific immune cells and their interactions with resident tendon cells remain understudied. While it is well appreciated that macrophages drive both inflammation and its resolution, other immune cells such as T cells have also been implicated. Here, we apply in vitro culture of CD4+ helper T cell supernatants to determine the role of neonatal vs adult T cells in regulating key tendon cell properties previously associated with neonatal tendon regeneration. While T cells were dominated by inflammatory Th1 cells regardless of source, neonatal T cells were less inflammatory compared to adult. Proliferation and migration potential were also properties intrinsic to neonatal tendon cells. While adult tendon cells were more sensitive to secreted T cell factors, neonatal T cell factors generally supported regenerative properties in adult tendon cells. Using RNA sequencing, we further identified a role for JAK/STAT signaling specific to treatment with adult T cell supernatants; using a small molecule inhibitor of JAK/STAT, we confirmed that suppression of adult tendon cell migration by adult T cell factors can be rescued by JAK/STAT inhibition. Altogether, these data show that regenerative tendon healing in neonates is due to both intrinsic neonatal tendon cell resistance to T cell-mediated inflammation as well as a more favorable immunological environment induced by neonatal CD4+ T cells.

overall_design: 25K thawed tendon cells cultured for 3 days were treated with 1ml of complete DMEM + 1ml of either T cell media alone (+1% P/S) or adult/neonatal stimulated supernatants, before RNAseq processing. Samples adult.1-3 are adult tendon cells treated with T cell media, adult.4-6 are adult tendon cells treated with adult stimulated supernatant, adult.7-9 adult tendon cells treated with neonatal stimulated supernatant. Neo.1-3 are neonatal tendon cells treated with T cell media, neo.4-6 are neonatal tendon cells treated with adult stimulated supernatant and neo.7-9 are neonatal tendon cells treated with neonatal stimulated supernatant.

first: Giulia

last: Crosio

first: Emily

last: King


title: IFN-γ and TLR9 signaling reprogram tumor-associated macrophages to promote antitumor immunity in melanoma

status: Public on Jul 06 2026

city: Tokyo

first: Ruslan

last: Deviatiiarov

address: Hongo 2-1-1, Bunkyo-ku

department: Intractable Disease Research Center

institute: Juntendo University

summary: Tumor-associated macrophages (TAMs) often adopt immunosuppressive phenotypes that promote tumor progression and limit the efficacy of immunotherapy. Although Toll-like receptor 9 (TLR9) agonists and interferon-γ (IFN-γ) possess immunostimulatory properties, their antitumor efficacy as monotherapy remains limited, particularly in poorly immunogenic tumors. Here, we investigated whether coordinated activation of innate immune pathways could reprogram macrophages and enhance antitumor immunity in melanoma. Using cap analysis of gene expression (CAGE), we found that combined CpG DNA and IFN-γ stimulation induced extensive transcriptional reprogramming in macrophages, characterized by activation of M1-associated genes, enhancer remodeling, alternative transcription start site usage, and induction of transcription factors associated with inflammatory and cytotoxic responses. Functionally, this combination also markedly enhanced macrophage-mediated phagocytosis of live tumor cells.

overall_design: Total RNA was extracted from bone marrow–derived macrophages (BMDM) treated with IFN-γ, CpG DNA, or their combination for 0, 3, 9, and 15 h using TRIzol reagent (Invitrogen). Two biological replicates were generated for each condition.

first: Oleg

last: Gusev

first: Sofia

last: Dubovskova