title: Plasmacytoid dendritic cells are dispensable or detrimental in murine systemic or respiratory viral infections [RNA-Seq 2]

city: Marseille

first: Bertrand

last: Escaliere

address: 163 avenue de Luminy

institute: CIML

summary: Plasmacytoid dendritic cells (pDCs) are major producers of type I/III interferons. Since these cytokines are crucial for antiviral defense, it is assumed to be also the case for pDCs. However, robust evidence supporting this dogma is scarce. Genetic mutations or pharmacological manipulations causing pDC loss or disrupting their interferon production affect other immune cells, which could confound interpretation. To overcome this bottleneck, we engineered pDC-less mice, specifically and constitutively devoid of pDCs because expressing diphteria toxin under coordinated control by the Siglech and Pacsin1 genes co-expressed only in pDCs. pDC-less mice mounted protective intrinsic and innate immune responses against systemic infection with mouse cytomegalovirus, and were more resistant to intranasal infection with influenza virus and SARS-CoV2. Thus, contrary to dogma, pDCs and their interferon production proved dispensable or deleterious during systemic or respiratory viral infections. pDC-less mice will enable rigorously revisiting the roles of pDCs in health and disease.

overall_design: Lungs were isolated from control and pDC-less mice unifected (D0) or at day 3 (D3) or 6 (D6) after intranasal IAV infection. RNA extracted from lungs was used to prepare libraries for RNA-seq. For each mouse strain 3 replicates at D0, 4 at D3 and D6.

first: Clemence

last: Ngo

first: Khalissa

last: Rahmani

last: Valente

first: Marc

last: Dalod

first: Elena

last: Tomasello


title: Bioinspired non-expansive biodegradable matrix promotes blood vessel organoid development for ischemic stroke repair

status: Public on Sep 19 2025

city: Chongqing

first: Yue

last: Sun

address: gaotanyan street

department: Department of Anatomy

country: China

institute: Third Military Medical  University

type: Expression profiling by high throughput sequencing

summary: Tissue engineering-based vascular reconstruction represents a promising therapeutic strategy for ischemic stroke. However, in the confined stroke cavity, conventional implants are unable to simultaneously provide swelling-resistant support and growth-permissive internal space, which are crucial for effective revascularization. To address this limitation, we develop a bioinspired, non-expansive biodegradable matrix (NEBM) through covalent/non-covalent assembly of commercially available, clinical-grade natural polymers. We show that NEBM recapitulates key features of brain ECM—including porous microstructure and tissue-matched stiffness—to deliver structural stability. Moreover, its progressively degradable structure establishes a dynamic remodeling niche that directs cellular behavior toward promoting angiogenesis. Compared to commercial Matrigel-based matrix, NEBM fosters blood vessel organoids (BVOs) development with higher vascular density, larger vessel diameters, and more distinct arterial features. In both subcutaneous and stroke transplantation models, we find that NEBM facilitates the integration of BVOs with the host vasculature. Strikingly, this revascularization in stroke cavity stimulates neurogenesis, contributing to significant functional recovery. As such, our study provides valuable guidance to design clinically translatable matrices for organ repair and regeneration in confined environments.

overall_design: The differentiation of hiPSCs into vascular spheroids was carried out according to a  previously established protocol.These vascular spheroids were then encapsulated in either HS, a bio-hybrid matrix composed of HT (hyaluronic acid) and SF (Silk Fibroin), or Matrigel-based matrices and cultured in a vascular maturation medium.The development of the BVOs was monitored daily using an optical microscope until day 6 and analyzed using scRNA-seq.

first: Dongling

last: Xiao

first: Guanyuan

last: Yang

first: Yinghao

last: Li

first: Chuhong

last: Zhu


title: RIPPLY1 suppresses cancer cell stemness via targeting TBX19 in CTNNB1-mutated hepatocellular carcinoma

city: Shanghai

first: Guangyan

last: Zhangyuan

state: Shanghai

address: 197 Ruijin Er Road

department: Department of General Surgery, Pancreatic Disease Center

institute: Ruijin Hospital, Shanghai Jiao Tong University School of Medicine

summary: Background & Aims CTNNB1-mutated HCCs exhibit a relatively low stem-like and well-differentiated phenotype. However, the mechanism remains unclear. Ripply transcriptional repressor 1 (RIPPLY1), a transcriptional repressor required for somite segmentation, has hardly been studied in cancer. Here, we aim to unveil the role of RIPPLY1 in the regulation of cancer cell stemness in CTNNB1-mutated HCCs. Approach and Results RIPPLY1 was found to be transactivated by the Wnt/β-Catenin signal pathway. Human sample analysis confirmed that RIPPLY1 was significantly upregulated in CTNNB1-mutated HCC tissues and positively correlated with better prognosis of HCC patients. Hepatocyte-specific deletion of RIPPLY1 promoted tumorigenesis and progression in DEN/PB-induced CTNNB1-mutated HCC mouse model and hydrodynamic tail-vein injection (HDTVi)-induced CTNNB1-mutated HCC mouse model. RIPPLY1 knockout tumor cells displayed upregulated levels of stem cell makers and enhanced cancer stem cell properties. Co-IP and MS identified TBX19 as the target protein of RIPPLY1. RIPPLY1 suppressed the transcriptional activity of TBX19 via recruiting TLE1 and promoting proteasome-dependent degradation of TBX19. TBX19 deficiency abolished the effect of RIPPLY1 loss on cancer cell stemness in CTNNB1-mutated HCCs. Conclusion： Loss of RIPPLY1 promotes cancer cell stemness via facilitating the TBX19 transcriptional activity in CTNNB1-mutated HCCs.

overall_design: Ripply1 exons 1 to 3 were flanked with loxP sites to generate floxed Ripply1 (Ripply1F/F) mice. Ripply1F/F mice were further crossed with Alb-Cre transgenic mice to generate mice with hepatocyte-specific deletion of RIPPLY1 (Ripply1Hep) .The male Ripply1F/F and Ripply1ΔHep mice were intraperitoneally injected with a single dose of DEN (90 μg/g) at 6 weeks of age. After a treatment-free interval of 3 weeks, mice were kept on a diet containing 0.05% PB for 27 weeks. The primary hepatocytes were isolated from DEN/PB induced liver tumors of Ripply1F/F and Ripply1Hep mice 30 weeks after DEN injection and subjected to RNA-sequencing.

first: Weiwei

last: Yu

first: Wenfang

last: Tian

first: Junjie

last: Xie

first: Jun

last: Wang

first: Xiayang

last: Ying

first: Fei

first: Yufei

last: Shao

first: Xiuxiang

last: Tan

first: Hao

last: Qian

first: Baiyong

last: Shen


title: Oral Vutiglabridin mitigates retinal degeneration by targeting mitochondrial dysfunction and retinal pigment epithelium senescence in mouse models

city: Seoul

first: Hyewon

last: Chung

address: 120 Neungdong-ro, Gwangjin-gu

country: South Korea

institute: Konkuk University

summary: Age-related macular degeneration (AMD) is a leading cause of vision loss in the elderly, driven by retinal pigment epithelium (RPE) dysfunction, mitochondrial impairment, oxidative stress, chronic inflammation, and cellular senescence. Vutiglabridin, an orally available derivative of glabridin, has been reported to enhance mitochondrial function and mitigate metabolic stress, suggesting potential therapeutic utility in retinal aging. Here, we evaluated the efficacy and mechanism of Vutiglabridin in multiple models, including naturally aged mice representing age-associated retinal degeneration, sodium iodate (NaIO3)-induced geographic atrophy (GA), and laser-induced choroidal neovascularization (CNV). Retinal morphology and function were assessed by fundus photography, autofluorescence imaging, and electroretinography, while molecular, histological, and transcriptomic analyses were employed to investigate senescence, mitochondrial function, and inflammation. Pharmacokinetic profiling demonstrated prolonged ocular distribution of Vutiglabridin. In parallel, Paraoxonase 2 (PON2) knockdown mice were used to determine the mechanistic dependency. Vutiglabridin attenuated senescence and inflammatory markers, reduced mitochondrial ROS, and preserved retinal thickness in aged mice, while bulk RNA sequencing demonstrated partial reversal of aging-associated transcriptional signatures. In the NaIO3 model, Vutiglabridin restored mitochondrial membrane potential, enhanced mitophagy, and improved retinal function. In CNV models, it suppressed lesion growth and oxidative stress with efficacy comparable to aflibercept. Importantly, Vutiglabridin increased PON2 protein levels in vivo, and its protective effects were abolished in PON2-deficient mice, confirming a PON2-dependent mechanism. These findings establish Vutiglabridin as a promising oral therapeutic candidate for both dry and neovascular AMD, acting through PON2-mediated enhancement of mitochondrial resilience and suppression of oxidative, inflammatory, and senescent pathways.

overall_design: Bulk RNA-seq profiling of RPE cells from aged-mice (24 month), aged-mice treated with Vutiglabridin for 6 months (24 month), and young mice (9 month).

first: Jae-Byoung

last: Chae

first: Chul-Woo

last: Park

first: Hyung Soon

first: Hyeong Min

last: Lee

first: Soonje

first: Purum

last: Kim


title: CASSIA: a multi-agent large language model for reference free, interpretable, and automated cell annotation of single-cell RNA-sequencing data

city: Madison

first: Yixuan

state: Wisconsin

address: 320 East Wilson Street, 602

department: Department of Biostatistics and Medical Informatics

country: USA

institute: University of Wisconsin - Madison

summary: Cell type annotation is an essential step in single-cell RNA-sequencing analysis, and numerous annotation methods are available. Most require a combination of computational and domain-specific expertise, and they frequently yield inconsistent results that can be challenging to interpret. Large language models have the potential to expand accessibility while reducing manual input and improving accuracy, but existing approaches suffer from hyperconfidence, hallucinations, and lack of reasoning. To address these limitations, we developed CASSIA for automated, accurate, and interpretable cell annotation of single-cell RNA-sequencing data. As demonstrated in analyses of 970 cell types, CASSIA improves annotation accuracy in benchmark datasets as well as complex and rare cell populations, and also provides users with reasoning and quality assessment to ensure interpretability, guard against hallucinations, and calibrate confidence.

overall_design: Single-cell RNA-sequencing was performed on human brain metastasis tissues obtained during the clinical trial NCT03398694. Samples were collected from patients with confirmed brain metastases originating from non-small cell lung cancer. Tissues were resected, dissociated, and processed using the 10x Genomics Chromium platform. Resulting scRNA-seq profiles were clustered, and marker genes were identified using the FindAllMarkers function in Seurat. These markers were used as input to CASSIA for cell type annotation. Final annotations were validated with quality scores and consensus-based confidence assessments.

first: Elliot

first: Lingxin

last: Cheng

first: Jack

last: Shireman

first: Yujia

last: Cai

first: Jihua

last: Liu

first: Chitrasen

last: Mohanty

first: Mahua

last: Dey

first: Christina

last: Kendziorski


title: Oncogenic MAPK signalling induces epithelial cell state change and therapeutic resistance in vivo IV

city: Glasgow

first: Kathryn

last: Gilroy

address: Garscube

country: United Kingdom

institute: CRUK Scotland Institute

summary: The colorectal epithelium is a rapidly renewing tissue, with a remarkable capacity to regenerate following injury. In colorectal cancer (CRC), this regenerative capacity can be co-opted to drive epithelial plasticity. Activation of oncogenic MAPK signalling in CRC is common, with mutations frequently found in both KRAS (40-50%) and BRAF (10%), alongside other mechanisms of EGFR pathway upregulation. Nonetheless, inhibition of this pathway is often linked to rapid therapeutic resistance in patients. Given the recent development of KRAS inhibitors and the licensing of BRAF+EGFR inhibitor combinations we have investigated mechanisms of resistance to these agents in complex mouse models of CRC. Here we show that MAPK signalling supports the regenerative/revival stem cell phenotype in vivo, while its inhibition leads to rapid remodelling of both Kras and Braf mutant mouse models to a high Wnt activity canonical stem cell phenotype marked by expression of Lgr5. This results in acute therapeutic resistance in Kras driven, and delayed resistance in Braf driven models. Importantly, where therapeutic MAPK targeting is applied in the presence of a single regenerative epithelial population, such as early metastatic disease, or where plasticity is restrained, for example through Wnt pathway restriction, a marked impact on tumourigenesis is observed. Modelling of an BRAF and RNF43-mutant patient population, clinically super-responders to BRAF/EGFR inhibitor therapy, demonstrates excellent response to therapy due to restricted epithelial plasticity, highlighting the criticality of cellular plasticity in therapeutic response. Together, our data provide clear insight into the mechanisms underpinning resistance to targeting oncogenic MAPK signalling in CRC. Moreover, we demonstrate that strategies that aim to restrict epithelial plasticity or corral into or intervene when tumours are in a regenerative cell fate may improve efficacy of MAPK targeting agents in CRC.

overall_design: Following treatment with either EGFR inhibitor or vehicle control, mouse colonic tumours with loss of Apc were sequenced by Gem-X flex single cell sequencing.

first: Mark

last: White

first: Megan

last: Mills

first: Laura

last: Millett

first: Owen

last: Sansom


title: Plasmacytoid dendritic cells are dispensable or detrimental in murine systemic or respiratory viral infections [RNA-Seq 1]

first: Bertrand

last: Escaliere

country: France

overall_design: Lungs were isolated from K18-hACE mice unifected (D0) or at day 1 (D1), day 2 (D2), day 4 5D4) or 6 (D6) after intranasal SARS-CoV2 infection. RNA extracted from lungs was used to prepare libraries for RNA-seq. 3 replicates at D0 and D1, 5 at D2 and  D4 and 2 at D6.

first: Clemence

last: Ngo

first: Khalissa

last: Rahmani

first: Michael

last: Valente

first: Marc

last: Dalod

first: Elena

last: Tomasello


title: Transcriptional Rewiring of BET Inhibitor Treated Ewing Sarcoma Cells Augments their Dependency on Focal Adhesion Kinase

city: Seattle

first: Research

middle: Scientific

last: Computing

state: WASHINGTON

address: 818 Stewart Street

department: Research Scientific Computing

institute: Seattle Children's Research Institute

summary: Epigenetic dysregulation is a hallmark of cancer. Small molecule inhibitors such as bromodomain and extraterminal (BET) protein inhibitors developed to target epigenetic dependencies have demonstrated significant promise in preclinical models. However, clinical success with epigenetic drugs as single agents has been limited by emergence of tumor cell tolerance and escape, which often occurs due to transcriptional rewiring. Ewing sarcoma (EwS), a bone and soft tissue tumor driven by the EWS::FLI1 fusion oncoprotein, is characterized by profound oncogene-dependent enhancer reprogramming. Thus, epigenetic modifying therapies are of high therapeutic interest. In this study, we sought to elucidate how EwS cells escape BET inhibition to identify biologically informed drug combinations that could be advanced to clinical trials. As expected, EwS cells and xenografts initially responded to BMS-986158, a pharmaceutical grade BET inhibitor, but proliferation was rapidly restored. A kinase inhibitor screen showed that BMS-986158 drug tolerant persister (DTP) cells were sensitive to inhibitors of Focal Adhesion Kinase (FAK), a critical signaling node downstream of extracellular matrix (ECM) engagement. RNA sequencing revealed that DTP cells had been transcriptionally rewired and that mesenchymal signature and ECM remodeling genes were specifically upregulated. Combining BMS-986158 with the FAK inhibitor Defactinib had synergistic effects on EwS cell proliferation, survival, and invasion in vitro, and significantly inhibited tumor outgrowth in vivo. Our studies identify BET and FAK inhibition as a rational combination therapy worthy of further investigation for EwS, and demonstrate that defining emergent mechanisms of epigenetic drug tolerance can identify new vulnerabilities that can be therapeutically targeted.

overall_design: Poly(A)-capture RNAseq (Novaseq) was performed on RNA extracted (Qiagen Rneasy kit) from EwS cell lines A673, CHLA10 and TC32 exposed to 5nM BMS-986158 for 72 hrs and A673 and CHLA10 cells exposed to 5nM BMs-986158 for 20 days.

first: Shireen

last: Ganapathi

first: Beth

last: Lawlor


title: Obesity promotes urinary tract infection by disrupting urothelial immune defenses

city: Columbus

first: John

middle: David

last: Spencer

state: OH

address: 700 Children's Drive

institute: Nationwide Children's Hospital

summary: Obesity is a significant public health concern associated with increased infection risk, but the mechanisms remain unclear. Using a diet induced obesity mouse model, we investigate how obesity impacts urinary tract infection (UTI) susceptibility and bladder urothelial defenses. High fat diet-fed female and male C57BL/6 mice exhibit increased susceptibility to uropathogenic E. coli (UPEC) following experimental UTI. Transcriptomic analysis of bladder urothelial cells reveals sex-specific gene expression changes, but both sexes share activation of focal adhesion and extracellular matrix signaling. Western blot and immunostaining confirm activation of focal adhesion kinase (FAK), a central component of the focal adhesion pathway, in the bladders of obese female and male mice. Mechanistically, primary human urothelial cells overexpressing FAK exhibit increased UPEC invasion. These findings demonstrate that obesity enhances UTI susceptibility and identify FAK as a conserved pathway disrupted by obesity, contributing to increased UPEC vulnerability.

overall_design: Urothelium was isolated from bladders of female and male mice fed standard chow or high-fat diet for 8 or 12 weeks. RNA-seq was performed on urothelium, and comparisons were made between high-fat and standard chow-fed mice of the same sex and/or diet duration.

last: Schwartz

first: John David


title: Heritable fetal protection against MLL::ENL-driven leukemogenesis depends on MLL3 [Bulk RNA-seq]

city: St Louis

first: Jeffery

last: Magee

state: Missouri

address: 660 South Euclid Ave

institute: Washington University In St Louis

summary: MLL rearrangements (MLLr) are the most common cause of congenital and infant leukemias. MLLr arise prior to birth and require very few cooperating mutations for transformation, yet congenital leukemias are 10-fold less common than infant leukemias and >100-fold less common than childhood leukemias overall. This raises the question of whether mechanisms exist to suppress leukemic transformation during fetal life.  Here, we show that in mice, fetal MLL::ENL exposure creates a heritable, leukemia-resistant state. MLL::ENL imposes a negative selective pressure on fetal hematopoietic progenitors that persists after birth to suppress transformation. These changes do not occur when MLL::ENL is induced shortly after birth, and transformation proceeds efficiently in that context. The fetal barrier to transformation is enforced by MLL3. It can be bypassed by cooperating mutations or inactivation of MLL3. Heritable, fetal protection against leukemic transformation may explain the low incidence of congenital leukemias in humans despite prenatal MLL rearrangement.

overall_design: We performed bulk RNA-seq to identify expression of human MLL::ENL in the mouse Tet-off-ME model, we sorted Lineage-KIT+ fetal liver or bone marrow progenitors. 4 biological replicates were used  per age of induction and age of analysis.

first: Jonny

last: Mendoza-Castrejon

first: Jeffrey

middle: A


title: Heritable fetal protection against MLL::ENL-driven leukemogenesis depends on MLL3 [scATAC-seq]

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: To assess changes in chromatin accessibility, we performed scATAC-seq. We sorted Lineage-KIT+ progenitors from fetal liver or Postnatal (P28) bone marrow. scATAC-seq was performed on P28 LK cells following fetal or postnatal MLL::ENL induction and on E18 LK progenitors following fetal MLL::ENL induction.


title: Heritable fetal protection against MLL::ENL-driven leukemogenesis depends on MLL3 [scRNA-seq]

overall_design: To assess changes in transcriptional responses to MLL::ENL, we performed CITE-seq. We sorted Lineage-KIT+ progenitors from fetal liver (E14 and E18), neonatal liver (P0), or Postnatal (P28) bone marrow. CITE-seq was performed on P28 LK cells following fetal or postnatal MLL::ENL induction and on  E14, E18, and P0 LK progenitors following fetal MLL::ENL induction.


title: HIF2-driven PTHrP Mediates Cachexia and Hypercalcemia in Renal Cell Carcinoma: Successful Treatment with HIF2 Inhibitors [polysome-seq]

city: Boston

first: Qinqin

last: Jiang

state: Ma

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary: Kidney cancer frequently causes paraneoplastic syndromes, including hypercalcemia and cachexia, but the underlying mechanisms are incompletely understood.  The most common form of kidney cancer, clear cell renal cell carcinoma, is frequently caused by loss of the pVHL tumor suppressor protein and the resulting upregulation of the HIF2 transcription factor.  We show that PTHLH, which resides on a ccRCC amplicon on chromosome 12p, is a direct HIF2 transcriptional target in ccRCC.  Further, we show that the increased PTHLH expression is both necessary and sufficient for the induction of hypercalcemia and cachexia in preclinical orthotopic cell line tumor models.  Consistent with these observations, two different allosteric HIF2 inhibitors, belzutifan and NK-2152, rapidly ameliorated hypercalcemia and cachexia in ccRCC patients, including in patients who did not exhibit objective tumor shrinkage.

overall_design: We aim to systematically identify HIF-responsive genes by RNA-Seq in OS-RC-2 cells. We generated two isogenic comparisons to create HIF2 high and low status, for which cells 1) were treated with 2 uM PT2399 (PT) or vehicle (Veh) for 72 hours, 2) underwent CRISPR-based gene editing with a HIF2a sgRNA or a contrl sgRNA (sgCtrl). We then performed RNA-Seq experiments to quantify gene expression for each condition in triplicates.

first: Muhannad

last: Abu-Remaileh

first: Zachary

middle: T

last: Herbert

first: William

middle: G

last: Kaelin Jr


title: Effect of depletion of KDM4D, NFIB, and MLL1 on gene expression during adipogenic differentiation of C3H10T1/2 mesenchymal stem cells [RNA-Seq]

city: Paris

first: Catherine

last: Coirault

address: 47 bd de l'Hôpital

institute: Inserm

summary: To investigate the effects of A-type lamins on chromatin accessibility during mechanical loading in human skeletal muscle, we established 72h differentiated muscle cells in which each target gene has been knocked down by siRNA.

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of 4 different cells in two conditions: baseline and after 4h cyclic mechanical stretch. Comparative gene expression profiling analysis of RNA-seq data for control and  siRNA known down myotubes.

first: Saline

last: Jabre


title: Effect of depletion of KDM4D, NFIB, and MLL1 on gene expression during adipogenic differentiation of C3H10T1/2 mesenchymal stem cells

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of 4 different cells in two conditions: baseline and after 4h cyclic mechanical stretch.Comparative gene expression profiling analysis of RNA-seq data for control and siRNA knockdown myotubes.


title: The Ashkenazi-centric G334R variant of TP53 is severely impaired for transactivation but retains tumor suppressor function in a mouse model [ChIP-Seq]

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

summary: Mutations in the TP53 tumor suppressor gene are the most abundant genetic occurrences in cancer.  Some of these mutations lead to loss of function of p53 protein, some are gain of function, and some variants are hypomorphic (partially-functional).  Currently, there is no clinical distinction between different p53 mutations and cancer therapy or prognosis.  Mutations in the oligomerization domain of p53 appear to be quite distinct in function, compared to mutations in the DNA binding domain.  Here we show that, like other p53 oligomerization domain mutants, the Ashkenazi-specific G334R mutant accumulates to very high levels in cells and is significantly impaired for the transactivation of canonical p53 target genes.  Surprisingly, we find that this mutant retains the ability to bind to consensus p53 target sites.  A mouse model reveals that mice containing the G334R variant show increased predisposition to cancer, but only a fraction of these mice develop cancer at late onset.  We show that the G334R variant retains the ability to interact with the SP1 transcription factor and contributes to the transactivation of joint SP1-p53 target genes.  The combined evidence indicates that G334R is a unique oligomerization domain mutant that retains some tumor suppressor function.

overall_design: Chromatin immunoprecipitation DNA sequencing (ChIP-seq) for p53, SP1 and H3K27Ac in HCT116 cells with either WT p53 or G334R before and after exposure to nutlin-3a treatment.

first: David

middle: C

last: Stieg

first: Katilyn

last: Casey

first: Bhanu

last: Karisetty

first: Julia

middle: I

last: Leu

first: Fiona

last: Larkin

first: Peter

last: Vogel

first: Jozef

last: Madzo

first: Maureen

last: Murphy


title: UV-induced (6-4)PP and CPD XR-seq data for L1 stage wildtype, csb-1 and xpc-1 C.elegans

city: Chapel Hill

first: Cansu

last: Kose

state: NC

address: 120 Mason Farm Rd.

department: Biochemistry and Biophysics

institute: UNC-Chapel Hill

summary: XR-seq was performed to map the repair of UV-induced photoproducts.

overall_design: XR-seq was performed 5 minutes, 1 hour, 8 hours, 24 hours and 48 hours after UVB 4 kj/m2 in each strain in L1 stage. Either anti (6-4)PP or anti CPD antibodies used to purified excised oligonucleotides.


title: Time series single-nuclei RNA sequencing experiments of the early stages of Arabidopsis flower development

city: Berlin

first: Jose

middle: M.

last: Muino

address: Max-Dohrn-Str. 8-10

country: Germany

institute: German Federal Institute for Risk Assessment

summary: To understand the gene expression dynamics of flower development in the early stages at single cell level,  we performed time series single-nuclei RNA sequencing (snRNA-seq) experiments using Arabidopsis thaliana flowers of developmental stages.

overall_design: Nuclei were isolated from pAP1:AP1-GR ap1-1 cal-1 Arabidopsis thaliana flower tissues after 0, 2, 4, 8 days of DEX induction. After DAPI staining, nuclei were collected by fluorescence-activated cell sorting (FACS) based on the DAPI peaks. SnRNA-seq library were then generated by SMARTer ICELL8 single-cell system

first: Xiaocai

last: Xu

first: Peilin

last: Chen

first: Kerstin

last: Kaufmann

middle: M


title: CD137L+Macrophage Resolves Acute Cystitis Induced by UPEC Infection through Regulatory T Cells Activation

city: Jinan

first: Yaxiao

last: Liu

state: Shandong

address: Wenhuaxi Road 107

institute: Qilu hospital of Shandong University

summary: Urinary tract infections (UTIs) typically evoke prompt and vigorous innate immune responses in bladder, but the specific mechanisms that resolute acute inflammation remain unclear. In this study, single-cell RNA sequencing and analysis of immune cells from the bladder at early stage of uropathogenic Escherichia coli (UPEC) infection was performed. The increased hyperactivated CD137L+macrophage response and decreased immunosuppressive Treg cells are elucidated in the bladder microenvironment of UPEC infection. Conditional depletion of CD137L in macrophage aggravates inflammatory reaction, bacterial load and urothelium destruction. Deletion of Treg cells also aggravated inflammation while promoting urothelial injury after UPEC infection. Additionally, Treg cells were increased in infected bladder which can be reversed by a myeloid-CD137L deletion. We thought activation of Treg cells by CD137L+macrophage is a key mechanism for suppressing acute inflammatory reaction after UPEC infection. The present study provided new insights into the functions of myeloid-CD137L dependent Treg cells in the immune response to UPEC infection.

overall_design: CD45+ bladders immune cell of C57BL6 mice with UPEC infection or not by Fluorescence-activated cell sorting and analyzed using ScRNAseq.


title: Gpnmb⁺ Microglia Represent a Distinct Subtype Reacting to Neuronal Loss induced by Prion Disease

city: Zurich

first: Davide

last: Caredio

state: Switzerland

department: Institute of Neuropathology

country: Switzerland

institute: University Hospital of Zurich

summary: Of all neurodegenerative pathologies, prion diseases exhibit one of the most extensive neuroinflammatory phenotypes, yet the impact of neuroinflammation on the course of the disease is anything but clear . Prions trigger conspicuous proliferation of microglial cells, which may contribute to neuronal damage but are also involved in prion clearance . We approached these questions by establishing a spatial-transcriptomic atlas of the progression of prion disease, and identified GPNMB gene as the most enriched one in a subset of microglial cells with enhanced phagocytic activity present only in prion-infected mice. This cell type responded to ongoing apoptosis in distinct brain regions from 30 weeks post-prion inoculation and progressively increased up to the terminal stage of the disease.

overall_design: Prion infected animals (RML6) and related (NBH) controls were sacrificed at 3 different timepoints during disease progression: 27 weeks post intraperitoneal injection (wpi), 30 wpi and terminal stage. OCT embedded brains were cut to generate 10 um thin-cryosections. Spatial transcriptomics was then performed by using 10x Genomics protocol.


title: Transcriptomic profiles of biopsy-derived colon epithelial organoids from pediatric patients with ulcerative colitis

city: Palo Alto

first: Michael

middle: J.

last: Rosen

state: CA

address: 1701 Page Mill Rd, #262

institute: Stanford University

summary: Colon epithelial organoid lines were developed from pediatric patients with endoscopically active ulcerative colitis, inactive ulcerative colitis, and those without endoscopic or histologic evidence of colon inflammation (non-IBD controls). From each organoid line, RNA was processed from undifferentiated organoids (spheroids) and parallel organoids differentiated for 3 days (colonoids). Paired-end sequencing of poly-A enriched RNA libraries was carried out on the Illumina NovaSeq PE150 platform and the reads were aligned to the human reference hg38 genome. To determine differentially expressed genes, transcripts with Log2FC ≥ ±1, FDR P ≤ 0.1 were considered statistically significant.

overall_design: Bulk RNA-sequencing of colon epithelial organoid lines from eight pediatric patients with active UC, inactive UC, and non-IBD controls.

first: Babajide

last: Ojo

first: Lyong

last: Heo


title: Epigenetic scars in regulatory T cells are retained after successful treatment of chronic hepatitis C with direct-acting antivirals [ATAC-Seq]

city: Daejeon

first: So-Young

last: Kim

state: Daejeon

address: GSMSE, 291, Daehak-ro, Yuseong-gu, Daejeon, Rep, E18-1

institute: KAIST

summary: During chronic HCV infection, several immune components are altered both quantitatively and qualitatively. The recent introduction of DAAs led to a high cure rate of chronic HCV infection. Nevertheless, we have demonstrated that inflammatory features of TREG cells are maintained at phenotypic, transcriptomic, and epigenetic levels even after successful DAA treatment.

overall_design: Bulk ATAC sequencing using isolated human peripheral blood TREG cell population (CD4+ CD25+ CD127-)  TREG cell was isolated from patients with chronic HCV infection before DAA treatment, at SVR, and from long-term follow-up (2.3 years to 6.3 years since SVR12, mean = 2.9 years)

first: June-Young

last: Koh

first: Dong

last: Lee

first: Jun

last: Park

first: Won

first: Eui-Cheol

last: Shin


title: Epigenetic scars in regulatory T cells are retained after successful treatment of chronic hepatitis C with direct-acting antivirals [RNA-Seq]

overall_design: Bulk RNA sequencing using isolated human peripheral blood TREG cell population (CD25+ CD127-)  TREG cell was isolated from patients with chronic HCV infection before DAA treatment, at SVR, and from long-term follow-up (2.3 years to 6.3 years since SVR12, mean = 2.9 years)


title: A Time-dependent Glia cell-Mediated Neuroprotective Effects of Kv7/KCNQ channel opener QO-83 in Ischemic Stroke: Mechanisms of Action and Therapeutic Potential

city: Shijiazhuang

first: Huiran

last: Zhang

state: Hebei

address: 361 Zhongshan East road

institute: Hebei Medical University

summary: This study investigates the protective role of Kv7 channel opener QO-83 in mouse brain injury induced by ischemia-reperfusion and permanent ischemia. QO-83 shows promise in enhancing survival rates, reducing infarction area, cerebral edema, and maintaining the blood-brain barrier. Furthermore, QO-83 administration correlates with enhanced cognition, memory, and fibrotic scar mitigation. Notably, these protective effects extend beyond the 4-6-hour post-reperfusion window. Single-nucleus RNA sequencing unveils distinct microglial and astrocyte clusters influenced by QO-83, potentially mediated via KCNQ3/5 targets. Notably, QO-83's influence on nestin-positive cell differentiation underscores its potential in limiting fibrotic scar formation. This study highlights QO-83 as a protective agent against ischemic brain injury, showcasing its multifaceted effects and potential as a therapeutic strategy.

overall_design: C57 wide type mice were subjected to 90 min middle cerebral artery occlusion and then reperfusion. 3 days later, ischemic brains were collected from 1 sham mouse, 2 model-βCD mice and 2 model-QO-83 mice and analyzed using single-nuclear RNA sequencing.

first: Yanfei

last: Tian

first: Yan

first: Jinlong

last: Qi

first: Xiangyu

last: Wang

first: Yi

last: Yuan

first: Rong

first: Yupeng

last: Zhao

first: Chang

first: Najing

last: Zhou

first: Xinyu

first: Jing

last: Yang

first: Xiaona

last: Du

first: Hailin

first: Jiyao

last: Xiao


title: Binding events of tobacco MatK on plastid transcripts

first: Jose

last: Muino

summary: Binding sites of tobacco MatK on the plastid transcripts were found by RIP-seq

overall_design: RIP-seq experiments were performed using an antibody versus HA for 3 biological replicates on HA tagged MatK tobacco line and on non-tagged MatK line as a control

first: Yujiao

last: Qu

first: Christian

last: Schmitz-Linneweber


title: Novel biomarker for prostatic ductal adenocarcinoma identified using spatial transcriptomic analysis

status: Public on Sep 18 2025

city: Tokyo

first: Yuto

last: Baba

address: 35 Shinanomachi Shinjuku-ku

country: Japan

institute: Keio University School of Medicine

summary: Prostatic ductal adenocarcinoma (PDA) is a rare but clinically aggressive variant of prostate cancer. We performed spatial transcriptomic analysis on PDA tissues and identified a PDA-specific biomarker.

overall_design: For this study, three PDA and three non-PDA tissues were analyzed. Differentially expressed genes (DEGs) were identified from PDA lesions in each specimen, and the commonly upregulated genes were selected as candidates for PDA-specific markers. Among these candidates, those showing lower expression in non-PDA tissues were considered potential novel markers for PDA.

first: Yutaka

last: Suzuki

first: Takeo

last: Kosaka


title: Identifying Potential Biomarkers Associated with Sebum Production, Pore Enlargement, and Comedones Using Transcriptomic Approaches

city: Beijing

first: Qitian

last: Fu

state: Beijing

address: Liangxiang Campus, Beijing Technology and Business University, Gongchen Sub-district, Fangshan District, Beijing

department: Department of Cosmetics, School of Light Industry Science and Engineering

institute: Beijing Technology and Business University, Beijing, China

summary: The molecular mechanisms underlying skin pore issues—excessive sebum secretion, pore enlargement, and comedone formation—remain poorly defined. We collected skin samples from four groups—dry skin without enlarged pores (DNEP), oily skin without pores (ONEP), oily skin with enlarged pores (OEP), oily skin with pores and comedones (OEPC)—measured physiological parameters, identified differentially expressed genes (DEGs) via RNA sequencing, conducted KEGG/GO enrichment analysis for DEGs, and used canonical correlation analysis to explore gene expression-physiological parameter relationships. Group comparisons revealed key genes and pathways: sebum production (DNEP vs. ONEP) involved lipid synthesis and inflammation, with ADM and PLAUR correlating with sebum content. Pore enlargement (ONEP vs. OEP) implicated ECM remodeling and immune processes, with IL27RA, MTOR, and PTAFR linked to skin roughness and elasticity. Comedogenesis (OEP vs. OEPC) involved lipid metabolism and differentiation, with ACADVL and CHST11 correlating with sebum and roughness. This study highlights seven core genes (ADM, PLAUR, IL27RA, MTOR, PTAFR, ACADVL, CHST11) and immune-inflammatory/ECM-receptor pathways as critical drivers of pore phenotypes, suggesting promising therapeutic targets.

overall_design: Microbiopsy collection  Facial skin biopsies on the cheekbone were extracted using microbiopsy tools (Trajan Scientific and Medical, Melbourne, Australia, described by Lin et al14.) by trained staff for gene expression assessments. Next, the microbiopsy device lancet was sterily removed and stored at –80°C. RNA extraction and sequencing  Total RNA was isolated from samples using Trizol reagent. RNA concentration and quality were assessed with a NanoDrop spectrophotometer. Starting from three micrograms of total RNA, sequencing libraries were prepared. mRNA was enriched using poly-T oligo-attached magnetic beads and fragmented. Double-stranded cDNA was synthesized, end-repaired, adenylated, and ligated with Illumina adapters. Library fragments were size-selected (400-500 bp) using AMPure XP system. Enrichment PCR (15 cycles) was performed, followed by purification and quality assessment on a Bioanalyzer 2100 system. Raw data were sequenced and generated in FASTQ format on the Illumina NovaSeq 6000 platform of Shanghai Personal Biotechnology Co., LTD. Fastp (0.22.0) software was used to get high quality sequence (Clean Data) for further analysis. The filtered reads were mapping to the reference genome using HISAT2 (v2.1.0). Pathway Enrichment Analysis  Pathway enrichment analysis shows the gene expression information and classifies DEGs for gene annotation. ClusterProfiler (v4.6.0) software was used to perform Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis16-18 and Gene ontology (GO) analysis of differential genes19,20. GO analysis can be divided into three parts: biological progress (BP), cellular component (CC) and molecular function (MF). KEGG is a database that integrates genomic information and biological pathways, signaling pathways, diseases, and drugs. The p-value was calculated by hypergeometric distribution method. Bonferroni-corrected p-value<0.05 was considered to be statistically significant.

first: Ying

last: Ye

first: Yanan

last: Li

first: Peiwen

last: Sun

first: Yao

last: Pan


title: Lactate promotes cholesterol uptake by facilitating SCARB1 expression through histone H3K18 lactylation

city: GUANGZHOU

first: jiamin

last: chen

address: WAIHUAN EAST ROAD

institute: SOUTH CHINA UNIVERSITY OF TECHNOLOGY

summary: Metabolic reprogramming supports the proliferation of cancer cells under hypoxic stress, including enhanced glycolysis and altered fatty acid metabolism. However, the mechanism underlying its regulation of cholesterol metabolism remains incompletely understood. Here, we show that lactate-induced cholesterol accumulation activates mammalian target of rapamycin complex 1 (mTORC1) signaling under hypoxic conditions, thereby promoting hepatocellular carcinoma (HCC) progression. Mechanistically, lactate upregulates scavenger receptor class B type 1 (SCARB1) expression by enhancing histone H3 lysine 18 lactylation (H3K18la), leading to increased cholesterol levels. We furthermore demonstrate that SCARB1-mediated cholesterol uptake is essential for the activation of mTORC1, which promotes tumor growth by preventing HCC cells from excessive autophagy. Importantly, analysis of clinical HCC samples showed a positive correlation between H3K18la and SCARB1 expression. Taken together, these findings provide novel insights into hypoxia-driven metabolic reprogramming and reveal a previously unrecognized connection between lactate and cholesterol metabolism, suggesting a potential innovative cancer therapy for HCC.

overall_design: RNA-Seq profiling of Hep3B cells cultured under normoxia, hypoxia, hypoxia treated with oxamate sodium for 48 hours

first: Jiamin

last: Chen

first: Kengcheng

last: Liu

first: Mingyue

first: Shengqi

last: Shen

first: Shi-Ting

first: Jin

last: Cai

first: Guanxu

last: Ji

first: Linchong

first: Ping

last: Gao

first: Tong

last: Zhang


title: KLF7 is a general inducer of human pluripotency

city: Padua

first: Elena

last: Carbognin

state: --- Select One ---

address: via Ugo Bassi 58b

department: Biology

country: Italy

institute: University of Padua

summary: Pluripotency is the capacity to give rise to all differentiated cells of the body and the germ line and is governed by a self-reinforcing network of transcription factors. The forced expression of only some of these factors enables the reprogramming of somatic cells to pluripotency. In murine cells, several kruppel-like factors (KLFs) have been identified as stabilisers and inducers of pluripotency. Human somatic cells are routinely reprogrammed by expression of KLF4 in combination with OCT4, SOX2 and cMYC (OSKM). An extensive transcriptome analysis revealed, however, that KLF4 is barely expressed in conventional human pluripotent stem cells (PSCs). Here we show that KLF7 is robustly expressed in conventional human PSCs and it allows transcription factor-mediated somatic reprogramming. Moreover, we find that KLF7 is highly expressed in naive PSCs and its forced expression in conventional hPSCs induces upregulation of naive markers and boosts efficiency of chemical resetting to naive PSCs, overall suggesting that KLF7 is a general human pluripotency factor and an inducer of pluripotency.

overall_design: Transcriptional analysis of human fibroblasts reprogrammed to iPSCs with OSKM or OSK7M reprogramming cocktails (samples 1-22) and transcriptional analysis of human iPSC expressing KLF7 or an EMPTY control (KiPS KLF7 and KiPS EMPTY) subjected to chemical resetting to naive PSCs (samples 23-47). Samples analysed for reprogramming: 3 replicates of BJ human fibroblasts (fibroblasts controls), 3 replicates of H9 hESCs (conventional PSCs controls), 4 replicates of OSKM P4 (iPSCs obtained with OSKM reprogramming cocktail and stabilised in colture for 4 passages), 4 replicates of OSKM P7 (iPSCs obtained with OSKM reprogramming cocktail and stabilised in colture for 7 passages), 4 replicates of OSK7M P4 (iPSCs obtained with OSK7M reprogramming cocktail and stabilised in colture for 4 passages), OSK7M P7 (iPSCs obtained with OSK7M reprogramming cocktail and stabilised in colture for 7 passages). Samples analysed for chemical resetting: 3 replicates of HPD00 primed-iPSCs (primed controls), 3 replicates of HPD01 naive-iPSCs (naïve controls), 3 replicates of HPD06 naive-iPSCs (naïve controls), 4 replicates of KiPS EMPTY, 4 replicates of niPSC EMPTY (KiPS EMPTY post-chemical resetting), 4 replicates of KiPS KLF7, 4 replicates of niPSC KLF7 (KiPS KLF7 post-chemical resetting).

first: Mattia

last: Arboit

first: Irene

last: Zorzan

first: Paolo

last: Martini

first: Graziano

last: Martello


title: Transcriptome Profile Analysis Reveals the Regulation Mechanism of Pistil Abortion in Handeliodendron bodinieri

city: nanning

first: tianfeng

last: liu

address: Xixiangtang Street

institute: guangxi university

summary: To elucidate the molecular mechanism of pistils abortion underlying sex differentiation from transcriptomic aspects in Handeliodendron bodinieri, we use abnormal pistils before and after abortion in male flowers and normal pistils in female flowers at the same stage as control material. Key genes regulating pistil abortion was identified by using RNA-seq technique. The results show that it was abortion from the two-nucleate embryo sac to four-nucleate embryo sac at stage one (the diameters of the flower buds were 1.3–1.6 mm), at the same time, 12 genes related to ovule development, such as INO, BEL1, and CRC,  24 genes related to plant hormones, such as AHP6, ARF, ERF, and GID1, and 12 genes related the ROS, such as POD, SOD, CAT and RBOH might be involved in the regulation of pistil abortion. Therefore, this study will provide a theoretical foundation for the conservation, breeding, and application of H. bodinieri in the future.

overall_design: Flower buds and pistils mRNA profiles of  male and female flowers in Handeliodendron bodinieri

first: Tianfeng

first: Song

last: Guo

first: Zailiu

first: Chaoyang

last: Ma

first: Feifei

last: Liao


title: Genome-wide DNA methylation assay of allopurinol-induced SCAR

city: Changsha

first: Yu

address: 139# Road Renmin

institute: The Second Xiangya Hospital of Central South University

type: Methylation profiling by genome tiling array

summary: To further explore the mechanisms of allopurinol-induced SCAR, we conducted a genome- wide DNA methylation analysis of the allopurinol-induced SCAR patients and tolerant controls. The study individuals were divided into four groups as SCAR patients with HLA-B*58:01, tolerant controls with HLA-B*58:01, SCAR patients without HLA-B*58:01, and tolerant controls without HLA-B*58:01. After bioinformatics analysis of the methylation data, we found that aberrant DNA methylation status of HLA molecules, including HLA-B, cell-cell adhesion molecules and anti- apoptotic molecules contribute to the pathogenesis of allopurinol-induced SCAR. We also recovered some promising epigenetic markers with high sensitivity and specificity for allopurinol-induced SCAR.

overall_design: Bisulphite converted DNA from the 62 samples were applied to the Illumina Infinium MethylationEPIC BeadChip (850K)

first: Ming

last: Zhao

first: Qian-Jin

last: Lu


title: A protocol for high-throughput microplate-based CUT&Tag

city: Saint Louis

first: Michael

middle: P

last: Meers

address: 660 Euclid Ave

institute: Washington University School of Medicine

summary: Cleavage Under Targets & Tagmentation (CUT&Tag) is a versatile method for measuring genomic occupancy of chromatin-associated proteins with high sensitivity and specificity. CUT&Tag has low sequencing requirements and is therefore suitable for highly multiplexed experiments, but methods to process samples at throughput without specialized equipment are lacking. Here we present a method for simultaneous parallel processing of 96 CUT&Tag samples in a standard microplate. Plate-CUT&Tag can be carried out in a similar time frame to benchtop CUT&Tag and yields data of comparable quality. We present data from cell culture and patient leukemia samples processed with Plate-CUT&Tag to illustrate its utility in large-scale preclinical and translational studies.

overall_design: CUT&Tag-Direct and Plate-CUT&Tag on K562 and RS4-11 cell lines and in AML patient samples.


title: Rhabdomyosarcoma transformation dictated by presence of primary cilia and hedgehog signaling in endothelial progenitor cells

city: Memphis

first: Hongjian

last: Jin

state: TN

address: 262 Danny Thomas Place

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hospital

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

overall_design: Refer to individual Series


title: The LHX1 Gene Regulatory Network Represses Pluripotency to Specify the Embryonic Head

city: Westmead

first: Riley

last: McMahon

address: 214 Hawkesbury Road

country: Australia

institute: Children's Medical Research Institute

summary: The development of the embryonic head in mice relies on the activity of the transcription factor LIM homeobox 1 (LHX1) in the anterior epiblast.  In this study, we sought to unravel the molecular role of LHX1 during and immediately following gastrulation. We utilized  CRISPR-Cas9 gene editing in embryo models as well as DamID-seq, RNA-seq, and ATAC-seq in mouse embryos. These techniques enabled us to reveal the genome wide targets of LHX1 for the first time in gastrulation stage mouse embryos. Integrated analysis of the omics datasets uncovered that LHX1 is instrumental in decommissioning the pluripotency network and determining the anterior fate of the precursor tissue of the embryonic head. We found that LHX1 directly binds to and regulates genes involved in WNT and FGF signaling pathway inhibition. We also identified a downstream target of LHX1, Kctd1, expressed in the anterior tissue, which acts to modulate canonical WNT activity. These findings identified a component of the gene regulatory network anchored by LHX1 that governs the development of the embryonic head.

overall_design: RNA-seq was run on day zero, two, four and six embryoid bodies derived from wild type (R1 ESC) or Lhx1-knockout Lhx1KO mouse embryonic stem cells.


title: RNA sequencing of PDX-AML samples using prime-seq

city: Munich

first: Irmela

last: Jeremias

address: Feodor-Lynenstr. 21

department: Research Unit Apoptosis in Hematopoietic Stem Cells

institute: Helmholtz Zentrum München, German Center for Environmental Health (HMGU), Munich, Germany

summary: We established serially transplantable and robust, genetically engineered patient derived xenograft (PDX) models of acute myeloid leukemia (AML).

overall_design:
Patients'  primary AML cells were transplanted into NSG mice. Models which engrafted were serially passaged and isolated from murine bone marrow. PDX cells were lysed and mRNA was extracted. mRNA read counts were determined by prime-seq.

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

first: Binje

last: Vick

first: Tobias

last: Herold

first: Wolfgang

last: Enard

first: Johannes

last: Bagnoli


title: A NEW DYSTROPHIN DEFICIENT RAT MODEL MIRRORING EXON SKIPPING IN PATIENTS WITH DMD EXON 45 DELETIONS

city: EVRY-COURCOURONNES

first: Tao

last: WANG

state: France

address: 1 bis, rue de l’Internationale

department: R & D

institute: genethon

summary: Mutations in the dystrophin (DMD) gene can cause muscle-wasting disorders ranging from the milder Becker muscular dystrophy (BMD) to the more severe Duchenne muscular dystrophy (DMD). Exon 45 deletion is the most frequently reported single-exon deletion in DMD patients worldwide. In this study, we generated a novel rat model with an exon 45 deletion using the CRISPR/Cas9 technology. The DmdΔ45 rat recapitulate key clinical and molecular features of DMD, including progressive skeletal muscle degeneration, impaired muscle and cardiac function, cognitive deficits, elevated circulating muscle damage biomarkers and an overall reduced lifespan. Transcriptomics analyses confirmed the deletion of exon 45 and revealed gene expression patterns consistent with dystrophin deficiency. In the skeletal muscle, RNA-seq profiles demonstrated a transition from early stress responses and regenerative activity at 6 months to chronic inflammation, fibrosis, and metabolic dysfunction by 12 months. Similarly, the cardiac transcriptomic shifted from an early inflammatory and stress-responsive state to one characterized by fibrotic remodelling and metabolic impairment. Despite these pathological features, the DmdΔ45 rats exhibited a milder phenotype than other DMD rat models. This attenuation may be attributed to spontaneous exon 44 skipping, which partially restores the reading frame and results in an age-dependent increase in revertant dystrophin-positive fibres. Further analysis indicated downregulation of spliceosome-related genes, suggesting a potential mechanism driving exon skipping in this model. In summary, the DmdΔ45 rat represents a valuable model for investigating both the molecular determinants of phenotypic variability and the endogenous mechanisms of exon skipping. These findings offer important insights for the development of personalized exon-skipping therapies, particularly for DMD patients with exon 45 deletions.

overall_design: To profile the transcriptome of a DMD exon 45 deletion rat model, we performed RNA-seq on four muscle types (diaphragm, heart, psoas, and soleus) from wild-type and mutant rats at 6 and 12 months of age, with three biological replicates per group.


title: Proteoglycofili are glycosaminoglycan-containing fibrillar components released by neutrophils to neutralize bacteria

city: Strasbourg

first: Benoit

last: Marteyn

address: 2 allée Konrad Roentgen

institute: CNRS - Institut de Biologie Moléculaire et Cellulaire (IBMC)

summary: Here we uncover that neutrophils release a previously unidentified fibrillar complex, named proteoglycofili (PGF) under hypoxic conditions or upon bacterial infection, using Shigella as a model. PGF are preferentially released by neutrophils over NETs upon bacterial infection. We demonstrated that PGF are released by living neutrophils, do not contain DNA and are mainly composed of granule proteins. We revealed that the fibrillar structure of PGF is sustained by two glycosaminoglycans (GAGs), hyaluronic acid and chondroitin sulfate, firstly identified here to be released by neutrophils. We demonstrated that PGF are potent antimicrobials, which degrade virulence factors of Shigella and block its growth, similarly with E. coli or Salmonella. We confirmed that GAGs were essential for PGF antimicrobial activity in vitro and in vivo. Beyond bacterial infections, our results strongly suggest that GAGs may be released by neutrophils in a broad range of inflammatory diseases to be further explored.

overall_design: RNA-seq was performed at T0 (neutrophils freshly purified) and HG (neutrophils incubated for 18h at 37°C under anoxic conditions). Four replicates were generated for each condition.

first: Antonin

last: Andre

first: Marina

middle: V

last: Barroso

first: Jurate

last: Skerniskyte

first: Lorine

last: Debande

first: Vanessa

last: Paul

first: Nathan

last: Broussaudier

first: Ahmad

last: Sabbah

first: Jules

last: Tritschler

first: Melina

last: Siegwald

first: Caroline

last: Ridley

first: Isabelle

last: Svahn

first: Amber

middle: D

last: Bowler

first: Valerie

last: Demai

first: Katia

last: Boniface

first: Stephane

last: Rigaud

first: Jean-Yves

last: Tinevez

first: Philippe

last: Sansonetti

first: Freddy

last: Radke

first: Romain

middle: R

last: Vives

first: David

last: Thornton

middle: S


title: Aberrant fibro-adipogenic progenitor subpopulations drive volumetric muscle loss-induced fibrosis

city: Atlanta

first: Lauren

last: Hymel

state: GA

address: 315 Ferst Dr NW

institute: Georgia Institute of Technology

summary: Volumetric muscle loss (VML) injuries result in chronic fibrosis, inflammation, and persistent functional deficits. Fibro-adipogenic progenitor (FAP) cells are a heterogeneous, muscle-resident stromal cell population that play a crucial role in muscle regeneration but also contribute to fibrosis in muscle disease. The role of FAPs in VML is not well established and may be a critical target to ensure functional muscle regeneration after VML. We utilized a critical VML model in the mouse quadriceps, compared with subcritical injuries and uninjured controls, to study the single-cell transcriptional profile of FAPs after VML. Our findings establish an aberrant FAP subpopulation that is elevated in VML injury and provide novel targets for future scarless muscle regeneration in VML.

overall_design: Subcritical injuries and critical VML defects were created in the mouse left quadriceps, and animals were euthanized 7 days post-injury. Uninjured quadriceps were used as naïve controls. Single cells from quadriceps were isolated, processed, and stained for CITE-seq study. Four animals were included in each group.

first: Edward

last: Botchwey

first: Emily

last: Greenwood

first: Seul

last: Lee


title: Engineered Nanobodies Targeting Endogenous Digoxin-like Substances Function as Novel Immune Checkpoints Inhibitors and Enhance Immunotherapy against Cancer Metastasis

city: Nanjing

first: chenming

last: xu

address: 163 Xianlin Road, Qixia District

institute: Nanjing university

summary: Digoxin is a well-recognized cardiovascular medication; however, epidemiological investigations have associated its clinical application with an elevated risk of malignancy. To elucidate it, we discovered, for the first time, that therapeutic digoxin can facilitate tumor metastasis by acting as an inducer of immune checkpoints, including PD-1, PD-L1/2, CTLA-4, LAG-3, ICOS, TIM-3, and TIGIT, among others. The PD-1/PD-L1 axis plays a pivotal role. Digoxin upregulates PD-L1 production in cancer cells through multiple mechanisms, including digoxin-PKM2 interaction, liquid-liquid phase separation, and Na,K-ATPase degradation. Notably, endogenous digoxin (ED) was significantly upregulated in breast cancer, correlating with increased metastasis. When specific nanobodies (Nbs) were developed to functionally inhibit ED in vivo, pulmonary tumor metastasis was reduced. However, the efficacy of ED-targeting Nbs was limited by endogenous ouabain (EO), another hormone structurally similar to digoxin. To address this, Nbs co-targeting ED and EO demonstrated an increased anti-metastatic effect and a notable reduction in immune checkpoint expression. Furthermore, Nbs simultaneously targeting ED, EO, and PD-1 exhibited significant synergy in suppressing tumor progression with a favorable safety profile. In conclusion, therapeutic digoxin and ED are potent inducers of immune checkpoints. Engineered nanobodies co-targeting cardiotonic hormones (ED, EO) and immune checkpoints present a promising novel approach in the treatment of breast cancer metastasis.

overall_design: RNA-seq profiling of LLC tumors treated with high and low doses of digoxin.

first: Yan

last: Chen

first: Chenming

last: Xu

first: Wu

last: Yin


title: Transcriptomic Insights into the Host Response to MPXV Infection in Human Neuronal Cells

city: Kunming

first: Zhengcun

last: Wu

address: No. 935, Jiaoling Road, Wuhua District, Kunming, Yunnan Province

institute: Institute of Medical Biology, Chinese Academy of Medical Sciences

summary: The Monkeypox virus (MPXV) is a neurotropic zoonotic pathogen, as evidenced by neurological symptoms in patients and its demonstrated neuroinvasive potential in both in vitro and in vivo models. However, the host responses and mechanisms underlying MPXV-induced neural damage remain poorly understood. To address this gap, we performed transcriptomic profiling and functional validation across three human neuronal cell lines (U87MG, SH-SY5Y, and HMC3) to investigate MPXV-induced molecular alterations. Among these cell types, U87MG cells exhibited the most pronounced transcriptional changes. Specifically, MPXV infection activated the MAPK signaling pathway (ERK1/2 and p38) and elicited a strong pro-inflammatory response, characterized by elevated TNF-α, IL-16, IL-17, and IL-1β. In parallel, immune evasion signatures were detected, including upregulation of MOGS, DICER1, and VPS13A, along with downregulation of STAT1 and IFIT family genes. Notably, MPXV markedly suppressed ADAR1, a key RNA-editing enzyme essential for neural homeostasis and antiviral defense, thereby implicating ADAR1 dysregulation as a driver of virus-induced neuroinflammation and injury.

overall_design: Building on these findings, network and drug-target analyses identified core transcriptional regulators (e.g., EGR, ZBTB7A, POU2F2) and candidate compounds modulating ADAR1. Consistently, in human iPSC-derived astrocytes, MPXV triggered inflammatory and apoptotic phenotypes accompanied by ADAR1 downregulation. Crucially, functional assays demonstrated that two ADAR-targeting compounds—Prosaptide and Neuropeptide Head Activator—effectively suppressed MPXV replication. In conclusion, our study provides the first integrative transcriptomic and functional characterization of MPXV infection in neuronal cells, and identifies ADAR1 as a pivotal mediator of MPXV-induced neuropathogenesis and a promising therapeutic target.

first: Qiangming

last: Sun

first: Haiting

last: Long

first: Tingfu

last: Du


title: RiboTag-based profiling of actively translating transcripts in Nrf2-deficient and wildtype Müller cells in a mouse model of oxygen-induced retinopathy

city: Baltimore

first: Zhenhua

state: MD

address: 400 North Broadway Smith BLDG 3001 Smith BLDG 3001

institute: Johns Hopkins University

summary: Müller cells play a critical role in retinal angiogenesis and inflammation, particularly in ischemic retinopathies such as oxygen-induced retinopathy (OIR).  Here, we employed actively translating transcriptome profiling using RiboTag technology to selectively examine gene expression in Müller cells with and without Nrf2, a master regulator of oxidative stress responses, during OIR. Conditional deletion of Nrf2 in Müller cells exacerbated retinal avascular areas and pathological neovascularization in the OIR model, without altering Müller cell number or viability. RiboTag-based RNA sequencing and pathway analysis identified dysregulation of oxidative phosphorylation and acute phase signaling, along with suppression of pathways related to neuronal signaling. Müller cell Nrf2 deficiency resulted in dysregulation of multiple genes involved in acute-phase response, inflammation, and angiogenesis. These findings uncover a critical role for Nrf2 in maintaining Müller cell homeostasis and identify molecular signatures by which its loss amplifies retinal gliosis and pathological angiogenesis.

overall_design: RNA-seq profiling of wildtype and Muller cell-specific Nrf2 cKO at OIR P14

first: Jie

last: Wang

first: Jiang

last: Qian

first: Elia

last: Duh


title: Characterising the effect of age and sex on post-transcriptional regulation in synovial joint tissues

city: Liverpool

first: Ufuk

last: Ersoy

address: William Henry Duncan Building

institute: University of Liverpool

summary: We investigated how age and sex affected mRNA kinetics in chondrocytes isolated from young female and male horses, as well as from older females. We chose to focus on this cell type due to its critical role in articular cartilage maintenance and to the relative ease of isolating appropriate cell numbers from equine metacarpophalangeal joint to permit prompt analysis and avoid cell dedifferentiation. Chondrocytes plated at high density were analysed with SLAM-Seq, which uses the chemical conversion of 4-thiouridine (4sU) labelled RNA, allowing for the detection of newly synthesised and pre-existing RNA within one sample. We used four-hour pulse of 4sU immediately prior to RNA extraction. Based on the findings from Erhard et al., this duration is expected to provide sufficient labelling time to accurately estimate the half-life of genes ranging from approximately one to 10 hours. To increase the detection of a sufficient number of conversions per transcript, we used 500 μM 4sU and sequenced to the libraries 150bp from both ends. Our results demonstrated progressive degradation of unlabelled, pre-existing RNA and concurrent transcription of 4sU-labelled, newly synthesised RNA over time.

overall_design: RNA-seq profiling of 4-thiouridine (4-sU) labeled chondrocytes isolated from young female, young male, and old female equines

first: Sam

last: Haldenby

first: Ioannis

last: Kanakis

first: Julie

last: Aspden

first: Mandy

last: Peffers

first: Simon

last: Tew


title: Distinct Colitis-Associated Macrophages Drive NOD2-Dependent Bacterial Sensing and Gut Homeostasis

city: La Jolla, CA 92093

first: Pradipta

last: Ghosh

address: 9500 Gilman Drive (MC 0651)

department: Departments of Medicine and Cellular and Molecular Medicine

institute: University of California San Diego

summary: In this study, to investigate the role of macrophage GIV in the colon, Katkar et al. employed a myeloid-specific GIV-KO (Ccdc88afl/fl/LysMCre) mouse model to analyze colon transcriptomic data from wild-type (WT) and macrophage-specific GIV-KO mice treated with dextran sulfate sodium (DSS) colitis, with or without muramyl dipeptide (MDP) treatment.

overall_design: To induce colitis, mice were fed with drinking water containing 2.5% dextran sulfate sodium (DSS, w/v) (MP Biomedicals, MW 36–50 kDa) for five days and then replaced normal drinking water as described. For treatment study, MDP (100 mg/mouse/day) was administered via intraperitoneal route in 100 ml total volume sterile saline every alternate day starting from day 0 of experiment. Mice were sacrificed on the 14th day, and colon length was assessed. Colon samples were collected for assessing gene expression the levels of mRNA (by qPCR). To induce colitis, 8–10-week-old mice were administered 2.5% (w/v) dextran sulfate sodium (DSS; MW 36,000–50,000) in drinking water for 5 consecutive days, followed by regular water for an additional 2 days. Control mice received regular drinking water throughout the experiment. Colonic tissues were harvested on day 7 for RNA extraction. Total RNA was isolated using TRIzol reagent (Life Technologies) and Quick-RNA MiniPrep Kit (Zymo Research, USA), and RNA integrity was assessed using a RNA ScreenTape (Agilent Technologies).

first: Katkar

last: Gajanan

first: Mahitha

last: Anandachar

first: Saptarshi

last: Sinha


summary: Our analysis determined the effect of age on polyadenylation site usage in joint tissues. Using total RNA purified from articular cartilage or synovium, we performed QuantSeq-Rev 3’ end RNA sequencing to identify polyadenylation sites utilised in all transcripts. This 3’ end sequencing method reads 3’ to 5’, starting in the polyA tail of the transcript, and so every read identifies a polyadenylation site. We then utilised PolyAminer software, with adaptations made to the code to identify and mask genomic polyA regions so that they would contribute to the site comparisons following read alignment. We found evidence that age affected polyadenylation site usage in both of these tissues

overall_design: Frozen tissue samples from young and old horses were homogenised using a Braun Mikrodismembrator and extracted in TRIzol (Thermo Fisher Scientific, Waltham, MA, USA, #15596018). Following the addition of chloroform and phase separation, the aqueous layer was removed and processed through RNeasy mini kits (Qiagen, Manchester, UK, #74104), including on-column DNase digestion. QuantSeq-Reverse library preparation and NextSeq 75 cycle[M1] [TS2] High Output sequencing with V2chemistry was performed by Lexogen (Vienna, Austria).


title: Cell-extrinsic controls over neocortical neuron fate and diversity [PatchSeq]

city: Geneva

first: Denis

last: Jabaudon

address: Rue Michel-Servet 1

institute: University of Geneva

summary: Neocortical cellular diversity emerges gradually during development. Cell-extrinsic interactions shape this extended maturation, yet cell-type-specific dependence on such cues has not been systematically examined. To address this, we compared how cell identity and diversity unfolds in different conditions during neocortical development. Conditions were modified in vivo using genetically modified mice models in which position or innervation are altered and in vitro using two-dimensional cultures. This approach revealed a molecular hierarchy in which cell class-distinguishing features emerge first, followed by subclass- and type-related characteristics. Acquisition of cellular identity and diversity remained stable across in vivo models. In contrast, in vitro glutamatergic neurons showed decreased expression of identity-defining genes, reduced diversity and alterations in connectivity. Cellular identity and diversity were closest to in vivo values in organotypic cultures. These findings reveal population-specific responses to environmental conditions and highlight the role of extracellular context in shaping cell diversity in the maturing neocortex.

overall_design: Chronic optogenetic stimulation of primary cultures, cultures were prepared from E16 brains electroporated at E14 with pCAG-tdTomato plasmid alone or with a mix of pCAG-tdTomato plasmid and pAAV CAG 439 ChR2 E123T T159C 2A tDimer plasmid. Starting at DIV1 cultures were chronically optogenetically stimulated by applying a protocol of train stimulation of blue LED (train of 20 stimulations; 10ms stimulation duration; 50ms stimulation interval; 30s inter-train interval) until Patchseq at DIV17.

first: Natalia

last: Baumann

first: Sabine

last: Fièvre

first: Ilaria

last: Morassut

first: Esther

last: Klingler

first: Giorgia

last: Bartolini

first: Sergi

last: Roig Puiggros


title: Global transcriptome analysis of early and terminal erythropoiesis in newly diagnosed with multiple myeloma patients associated anemia

city: Zhengzhou

first: Shihui

last: Wang

state: Henan

address: No. 7 Weiwu Road, Zhengzhou, Henan, China

department: Institute of Hematology

institute: Henan Provincial People’s Hospital

summary: In NDMM anemia patients, erythroid progenitors show downregulation of growth factor response pathways (e.g., SPHK1), while terminal erythroblasts have upregulation of mitochondrial oxidative phosphorylation and p53-related genes, with increased cellular ROS levels. Mechanistically, genes like COX6C, UQCRB, UQCRH, PMAIP1, and MYCT1 are up-regulated in terminal erythroblasts.

overall_design: RNA was extracted from sorted BM erythroid progenitors and terminal erythroblasts, followed by Illumina NovaSeq 6000 sequencing. After quality control, reads were aligned to hg38 using kallisto, with differential expression analysis performed by DESeq2. PCA and GO enrichment analyses were conducted.

first: Huizhi

last: Zhao


title: Cell-extrinsic controls over neocortical neuron fate and diversity [snRNAseq]

overall_design: Single nucleus transcriptomics of in vivo and invitro models of extrinsic factors of mouse neuronal maturation


title: RNA tomography reveals spatial gene expression maps of Arabidopsis thaliana roots infected with Heterodera schachtii

city: Wageningen

first: Jose

last: Lozano-Torres

state: Gelderland

address: Radix, Building no. 107, Droevendaalsesteeg 1

department: Plant Sciences

country: Netherlands

institute: Wageningen University & Research

summary: Plant-parastic nematodes cause substantial crop losses worldwide. The sedentary endoparasite nematode Heterodera schachtii induces specialized feeding structures in host roots. The molecular mechanisms underlying feeding structure initiation and development remain poorly understood. High-resolution, spatially resolved transcriptomics is required to study localized gene expression patterns underlying feeding structure formation. Here, we introduce RNA tomography for plants, a powerful untargeted spatial transcriptomics technology that allows studying gene expression at cellular resolutions. We applied RNA tomography to Arabidopsis thaliana roots infected with H. schachtii at 1 and 2 days post inoculation. Our findings provide novel insights into early nematode parasitism.

overall_design: Four-day-old Arabidopsis seedlings grown in RoPod microscopic chambers were inoculated with ~20 H. schachtii infective stage juveniles (J2) per 3 seedlings. Roots with a single nematode infection at 1 and 2 days post inoculation were selected for RNA tomography library preparation.

first: Anna

last: Pijnacker

first: Yuhao

first: Jaap-Jan

last: Willig

first: Jonas

last: Mars

first: Steffen

last: Werner

first: Kelvin

last: Adema

first: Geert

last: Smant

first: Hendrik

last: Korswagen

middle: L


title: Astrocyte CCN1 stabilizes neural circuits in the adult brain

city: La Jolla

first: Laura

last: Sancho

address: 10010 N Torrey Pines

institute: Salk Institute for Biological Studies

summary: We have used single-nucleus (sn) RNA sequencing through a 10x Genomics platform to examine the impact of overexpressing CCN1 in astrocytes during the critical period. We transcriptionally profiled all cell types in the visual cortex after bilateral injection AAV-CCN1 or AAV-tdTomato as a control.

overall_design: 14 days after AAV injection into the visual cortex bilaterally, the visual cortices were dissected out, nuclei were extracted and FACS was performed on Hoechst-labeled nuclei. 2 visual cortices per mouse were dissected and 2 mice were pooled per sample. 1 tdT sample and 1 CCN1 sample were considered 1 replicate. Replicates were sequenced at different times but samples were processed the same way.

last: Sancho Fernandez

first: Nicola

last: Allen


title: Genetic, Hormonal, and Transcriptomic Analyses Highlight the Crucial Role of Phytohormones in First Branch Angle (FBA) Regulation in Pepper

city: Nanchang

first: Xinjie

last: Yuan

state: Jiangxi

address: No. 602, Nanlian Road

department: Institute of Vegetables and Flowers

institute: Jiangxi Academy of Agricultural Sciences

summary:
Background The first branch angle (FBA) is a critical trait influencing plant architecture, yield, and mechanized harvesting efficiency in pepper (Capsicum annuum L.). However, the genes and regulatory processes involved remain largely unclear.
Results The phenotypic evaluation of 220 pepper accessions revealed significant genetic variation in FBA, with a broad-sense heritability of 93.26%, indicating a strong genetic foundation and making it a stable trait for selection. A genome-wide association study (GWAS) with mixed linear model and FarmCPU detected 25 significant SNPs related to FBA. Several candidate genes were identified, encompassing components of brassinosteroid signaling, gibberellin signaling, serine/threonine-protein kinase signaling, and cell wall modification. To functionally contextualize these genetic findings, two accessions with divergent FBAs (compact B010 and loose B003) were selected for cytological and hormonal analyses. The paraffin sections stained with Periodic Acid-Schiff showed that the compact B010 exhibits more starch granules in endodermal amyloplasts, while the loose B003 has larger cell size on the adaxial side. Hormonal analysis based on HPLC-MS/MS revealed higher auxin levels in the compact B010 and higher gibberellin, cytokinin, brassinosteroid, and strigolactone levels in the loose B003. These results suggest a mechanism whereby brassinosteroid/gibberellin-mediated cell expansion, potentially through the action of cell wall modification genes, drives the loose architecture of B003. Furthermore, RNA-Seq and qRT-PCR confirmed the coordinated regulation of the key phytohormone pathways (auxin signaling; cytokinin, gibberellin, and brassinosteroid biosynthesis) and serine/threonine-protein kinase signaling. Therefore, our work integrates multi-layered analyses to propose a regulatory framework for FBA in pepper: genetic loci associate with alterations in phytohormone regulation, kinase activity, and cellular traits, which orchestrate the transcriptomic, hormonal, and cytological changes that collectively determine branch architecture.

overall_design: At the early flowering stage, the first branch sites of B010 and B003 were sampled for RNA sequencing, with three biological replicates for each accession.


title: RNA-Seq of PBMC of FAP patient before and after a low-inflammatory diet

city: Orbassano

first: Giulio

last: Ferrero

state: TO

address: Regione Gonzole, 10

department: Dept. Clinical and Biological Sciences

institute: University of Turin

summary:
Long-term dietary fat intake influences cancer development through metaflammation, a state of chronic low-grade inflammation driven by dysregulated lipid metabolism. Patients with Familial Adenomatous Polyposis (FAP), who carry hereditary APC gene mutations and have a 100% risk of developing colorectal cancer (CRC), currently rely on prophylactic colectomy and anti-inflammatory therapies targeting key pathways such as prostaglandin-COX for chemoprevention. The emerging concept of metabolic-associated immune reprogramming prompted us to investigate whether a nutritional intervention aimed at reducing metaflammation could restore an effective immune response.
To address this, we studied 28 FAP patients who followed a low-inflammatory diet (LID) for six months. Multiomics analyses, including multiparametric immune profiling, transcriptomics, lipidomics, and proteomics at both systemic and local levels, revealed that LID reshaped proinflammatory-associated lipid species and modulated immune cell function. This was confirmed by a reduction in inflammatory and myeloid responses in PBMC transcriptional programs and decreased cytokine secretion following ex vivo TLR agonist stimulation. In the intestine, LID reduced polyp size and induced transcriptional changes associated with the restoration of innate immune memory. Additionally, LID decreased the abundance of dyslipidemic macrophages, a negative prognostic factor in CRC. These immunometabolic changes correlated with improved patient quality of life. Overall, these findings highlight LID as a promising immune-modulating strategy capable of reshaping local immunity, reducing FC accrual, and promoting antitumor immune responses, positioning dietary interventions as a viable approach for CRC prevention in high-risk individuals.

overall_design: RNA-Seq was performed on PBMC samples from 30 FAP patients before a low-inflammatory diet (LID) and after three and six months after the dietary intervention.

first: Elena

last: Daveri


title: A gene regulatory element modulates myosin expression and alters cellular response to stress [mouse]

city: Durham

first: Taylor

last: Anglen

address: 101 Science Drive, CIEMAS Rm. 2323

department: Biomedical Engineering

institute: Duke University

summary: A hallmark of heart disease is gene dysregulation and reactivation of fetal gene programs. Reactivation of these fetal programs can provide cardioprotective or compensatory effects during heart failure depending on the type and stage of the underlying cardiomyopathy. Many putative cardiac gene regulatory elements have been identified that may control these programs, but their functions are largely unknown. We profile genome-wide changes to gene expression and chromatin structure in cardiomyocytes derived from human pluripotent stem cells. We identify and characterize a gene regulatory element important for the regulation of MYH6 that encodes human fetal myosin and is critical to the pathogenesis of hypertrophic and dilated cardiomyopathies. Using chromatin conformation assays in combination with epigenome editing, we find that gene regulation is mediated through direct interaction between MYH6 and the enhancer. We also find that activation of the enhancer alters cardiomyocyte response to the hypertrophy-inducing peptide endothelin-1. Collectively, these results identify regulatory mechanisms of cardiac gene expression programs that act through critical developmental factors and modulate cellular response to stress.

overall_design: Differential analysis of chromatin looping after repression of an MYH6/MYH7 enhancer in mouse HL-1 cardiomyocyte line, assessed using HiCAR protocols.

first: Irene

last: Kaplow

first: Baekgyu

last: Choi

first: Kevin

last: Hagy

first: Duc

last: Tran

first: Megan

middle: E

last: Ramaker

first: Svati

last: Shah

first: Ravi

last: Karra

first: Yarui

last: Diao

first: Charles

last: Gersbach


title: GLP-1 receptor agonism results in reduction in hepatic ethanol metabolism

city: New Haven

first: Frhaan

last: Zahrawi

state: CT

address: 300 cedar st

department: Internal Medicine

institute: Yale University

summary: Glucagon-like peptide 1 receptor (GLP-1R) agonists are used along with ethanol consumption, but their interactions are not understood. Our aim was to determine the effects of GLP-1R agonism on the liver in mouse models of high ethanol consumption. We identified that GLP-1R agonism reduced ethanol consumption, mitigated ethanol-induced upregulation of several liver metabolizing enzymes, including Cyp2e1 and also reduced Cyp2e1 independent of ethanol intake. As expected from a reduction in Cyp2e1, GLP-1R agonism resulted in increased blood ethanol levels. This occurred after a single dose of ethanol when given by gavage, and by the intraperitoneal route. This suggests that GLP-1R agonism can reduce ethanol-mediated hepatotoxicity despite continued ethanol consumption and elevate blood alcohol levels

overall_design: 24 mice were divided into four groups—1) Control (CT), 2) Alcohol-fed (ALC), 3) Alcohol + GLP-1R agonist (ALC + GLP), 4) Control + GLP-1R agonist (CT + GLP). The semaglutide dosage regimen was escalated from 1 to 30 nmol/kg over 16 days. On day 16, mice in the alcohol groups received alcohol gavage, and control groups received dextrin.

first: Suyavaran

last: Arumugam

first: Bubu

last: Banini

first: Wajahat

last: Mehal


title: Heritable fetal protection against MLL::ENL-driven leukemogenesis depends on MLL3

city: St Louis

first: Jeffery

last: Magee

state: Missouri

address: 660 South Euclid Ave

institute: Washington University In St Louis

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

overall_design: Refer to individual Series


title: A gene regulatory element modulates myosin expression and alters cellular response to stress

state: NC

overall_design: Differential analysis of chromatin looping after repression of an MYH6/MYH7 enhancer in cardiomyocytes derived from human pluripotent stem cells, assessed using HiCAR protocols.


title: A gene regulatory element modulates myosin expression and alters cellular response to stress [ATAC-seq]

overall_design: To identify cis-regulatory elements important for regulating fetal cardiomyocyte gene expression we profiled genome-wide changes to chromatin structure in cardiomyocytes derived from human pluripotent stem cells following GSK3 inhibition.


title: A gene regulatory element modulates myosin expression and alters cellular response to stress [RNA-seq]

overall_design: To identify differentially expressed fetal cardiomyocyte genes we profiled changes to gene expression in cardiomyocytes derived from human pluripotent stem cells following GSK3 inhibition.


title: RNA-seq analysis of human iPSC derived hepatocyte and stellate cell surround organoids (iHSOs)

city: bunkyo-ku

first: Masato

last: Miyoshi

address: yushima

department: Gastroenterology

institute: Tokyo Medical and Dental University

summary: To investigate the interaction between hepatocytes and hepatic stellate cells in iHSOs, we established contact co-culture organoids using iPSC-derived HSCs and hepatocytes; termed iPSC-derived hepatocyte-stellate cell surround organoids (iHSOs). Sorting based on fluorescent labeling (GFP/tdTomato) of the iPSCs used in iHSOs allowed analysis of each cell type. A comprehensive RNA-seq analysis was conducted.

overall_design: In addition to preparing RNA-seq samples from hepatocytes and HSCs sorted from iHSOs using FACS (CoSp-SortHep, n=3; CoSp-SortHSC, n=3), we also prepared RNA-seq samples from iPSCs (n=1), iPS-Heps (n=2), iPS-HSCs (n=2), iPS-Hep mono-spheroids (iPS-Hep-Sph, n=2), and iPS-HSC mono-spheroids (iPS-HSC-Sph, n=2).

first: Tomohiro

last: Mochida

first: Sei

last: Kakinuma


title: Identification of transcriptional targets for Dif and Dorsal in intestinal cells of fly

city: Changsha

first: peng

middle: guo

last: fan

state: Hunan

address: Lushan Road

institute: Hunan University

summary: The regulation of Toll signalling pathway in non-immune functions remains unclear. In this study, we found that Toll pathway regulates intestinal stem cells activity of drosophila. To further explore the potential regulation mechanism, we performed cleavage under target and tagmentation (Cut&Tag) analysis to identify candidate genes regulated by Dif and Dorsal (core transcription factors in Toll pathway) in total intestinal cells.

overall_design: Using transgenic flies with Dif-GFP or Dorsal-GFP fusion protein, the transcriptional targets for Dif and Dorsal in total intestinal cells were examined.

first: Guofan

last: Peng

first: Jun

last: Zhou


title: The effects of early systemic neuroinflammation on the brain’s response to further inflammatory insults in the hipppcampus at the single-cell level

city: Shanghai

first: Ping

last: Yang

address: 800 Rd dong chuan

institute: Shanghai Jiao Tong University

summary: To identify how an early life first neuroinflammatory challenge affects th brain's response to subsequent challenges.

overall_design: We estabilished a neontal two-hit model: for the first hit, mice were injected subcutaneously at P3 with 5mg/kg lipopolysaccharides (L) or saline (S);for the second hit,  mice received 5mg/kg LPS (L) or saline (S) intraperitoneally. Animals were divided into four groups: SS, SL, LS, LL. Mice were sacrificed at P15, 24 hours after the second hit.  Hippocampal tissue was prepared for single-cell sequencing.

first: Xiang

last: Yu


title: Integrated miRNA-mRNA Analyses of Triple-Negative Breast Cancer in Black and White Patients with or Without Obesity

city: New Orleans

first: Jovanny

last: Zabaleta

state: LA

address: 1700 Tulane Ave

department: Interdisciplinary Oncology

institute: LSUHSC

type: Non-coding RNA profiling by high throughput sequencing

summary: Triple-negative breast cancer (TNBC) is an aggressive, heterogeneous subtype of breast cancer. miRNAs play an essential role in TNBC pathogenesis and prognosis. Obesity is linked with an increased risk for several cancers, including breast cancer. Obesity is also related to the dysregulation of miRNA expression in adipose tissues. However, there is limited knowledge about race- and obesity-specific differential miRNA expression in TNBC. We performed miRNA sequencing of 48 samples (24 tumor and 24 adjacent non-tumor tissues) and RNA sequencing of 24 tumors samples from Black (AA) and White (EA) TNBC patients with or without obesity. We identified 55 miRNAs exclusively associated with tumors in obese EA patients and 33 miRNAs in obese AA patients, each capable of distinguishing tumor tissues from obese from lean individuals within their respective racial groups. In EA, we detected 41 significant miRNA–mRNA correlations. Notably, miR-181b-5p and miR-877-5p acted as negative regulators of tumor-suppressor genes (e.g., HEY2, MCL2, HAND2), while miR-204-5p and miR-143-3p appeared to indirectly target oncogenes (e.g., RAB10, DR1, PTBP3, NCBP1). Among AA patients, we found 28 significant miRNA–mRNA interactions. miR-195-5p, miR-130a-3p, miR-130a-5p, miR-424-5p, miR-148a-3p, miR-374-5p, and miR-30a-5p each potentially downregulated two or more genes (e.g., CLCN4, PLCB1, CDC25B, AEBP2, ERBB4). Pathway enrichment analysis highlighted KRAS, ESR1, ESR2, RAB10, TNRC6C, and NCAN as the most commonly differentially expressed in EA, whereas ERBB4, PLCB1, and SERPINE1 were most frequently in AA. These findings highlight the importance of considering race-specific miRNA–mRNA signatures in understanding TNBC in the context of obesity, offering insights into biomarker-driven patient stratification for targeted therapeutic strategies.

overall_design: To determine the relationship between the levels of microRNA (miRNA) expression and obesity in breast cancer, we perfomed miRNA-seq in tumor and adjacent non-tumor tissues in Triple Negative Breast Cancer (TNBC) samples of African American and Caucasian women dignosed with the disease.

first: Fokhrul

last: Hossain

first: Martha

last: Gonzalez-Ramirez

first: Jone

last: Garai

first: Diana

last: Polania-Villanueva

first: Li

last: Li

first: Farzeen

last: Nafees

first: Md

last: Manirujjaman

first: Bolin

last: Bolin

first: Samarpan

last: Majumder

first: Xiao-Cheng

last: Wu

first: Chindo

last: Hicks

first: Luis

last: Del Valle

first: Denise

last: Danos

first: Augusto

last: Ochoa

first: Lucio

last: Miele


title: Disrupting YAP phase separation attenuates the development of primary liver cancer in animal models

city: Xiamen

first: Lijun

last: Cai

address: No. 668, Jinhu Road

department: Central Laboratory,

institute: Zhongshan Hospital (Xiamen), Fudan University

summary: In these murine liver cancer samples, we used specific antibody detection to find endogenous YAP formation condensates in the focal area, a phenomenon also observed in human liver cancer tissues. Deletion, mutagenesis and replacement assays of the coiled-coil (CC) domain demonstrate a critical role of activated YAP condensation in c-Myc-induced hepatoma, myr-AKT-induced intrahepatic cholangiocarcinoma, and N90-CTNNB1-induced hepatoblastoma. Transcriptome sequencing revealed that YAP phase separation inhibits AMPK activation and promotes c-Myc-induced hepatoma development. Our research indicates that condensates driven by YAP phase separation enrich TAK1, an AMPK-activated upstream kinase, potentially creating a physical barrier to AMPK phosphorylation activation. In addition, we further demonstrated that a specific peptide derived from TEAD1 disrupts the formation of YAP condensates and attenuates the development of these primary liver cancers.

overall_design: Transcriptomic sequencing was conducted on liver cancer tissues induced by YAP-S127A/c-Myc and YAP-S127A-4LE/c-Myc.

first: Shuang-zhou

last: Peng

first: Fu-quan

last: Jiang

first: Jia-jia

last: Liang


title: Suppressing A549 lung cancer cells by targeting FOXM1 with a 71-residue self-derived region.

city: Hsinchu

first: Chia-Chan

last: Hsu

address: 101, Section2, Kuan-Fu Road

department: Institute of Biotechnology

country: Taiwan

institute: National Tsing Hua University

summary: High FOXM1 expression levels have been associated with poor prognosis in patients across various cancer types. FOXM1 plays a multifunctional role in tumorigenesis, including proliferation, anti-apoptosis, and metastasis, making it a potential marker and attractive therapeutic target. We screened FOXM1 truncations and identified a 71-residue region (51-121) from N-terminal repression domain (NRD) that effectively targets FOXM1 transcriptional activity in luciferase reporter assays. Specifically, FOXM1 transcriptional activation domain (TAD) interacted with NRD 51-121 in immunoprecipitation assays. Further analysis showed that mutations hindering hydrophobicity or mimicking PLK1 phosphorylation within TAD blocked the association between NRD 51-121 and TAD. Additionally, expressing NRD 51-121 in A549 cells resulted in reduced proliferation, increased apoptosis, and enhanced senescence compared to controls. RNA sequencing indicated that FOXM1 is a key factor influencing gene expression profiles in A549 cells expressing NRD 51-121. Collectively, our study suggests a potential cancer therapy targeting FOXM1. This approach suppresses FOXM1 by expression of NRD 51-121, which supposedly binds to TAD, thereby inactivating its transcriptional networks and limiting cancer growth.

overall_design: Transcriptome analysis was pferformed on Ad-mCherry A549 cells and Ad-mCherry NRD 51-121 A549 cells, both in triplicate.

first: I-Ching

last: Wang


title: SDR42E1 modulates vitamin D absorption and cancer pathogenesis: insights from an in vitro model

city: Doha

first: Georges

middle: Michel

last: Nemer

state: Qatar

department: CHLS

country: Qatar

institute: HBKU

summary:
Introduction: Vitamin D is a pleiotropic hormone essential for bone health and overall physiological function. Despite its significance, vitamin D deficiency remains widespread and is often influenced by genetic factors.
Methods: This study investigates the role of SDR42E1, a gene encoding a short-chain dehydrogenase/reductase enzyme, in vitamin D regulation and sterol metabolism. Using CRISPR/Cas9 gene-editing, we generated an SDR42E1 knock-in model in HCT116 colorectal cells, which exhibit high endogenous SDR42E1 expression, harboring a nonsense variant associated with vitamin D deficiency.
Results: Integrated transcriptomic and proteomic analyses revealed significant dysregulation of sterol absorption and metabolism (fold change (FC) = 1.8, P = 0.007) and cancer-related signaling pathways (FC = −1.7, P = 0.02). Notably, key differentially expressed genes included upregulated LRP1B and ABCC2, alongside downregulated WNT16 and SLC7A5. Proteomic profiling confirmed alterations in cell proliferation-related proteins, including reduced ALDOA expression (FC = −0.37, P = 0.0005). Functionally, SDR42E1 deficiency reduced cell viability by 53% (P = 0.0001), an effect reversed by transient SDR42E1 overexpression with restoring ABCC2 expression.
Conclusion: These findings establish SDR42E1 as a key modulator of vitamin D-related pathways and highlight its potential as a therapeutic target for addressing vitamin D deficiency and associated pathologies, including cancer.

overall_design: To investiage global transcriptomic changes associated with SDR42E1, a suggested modulator of serum vitamin D levels, we performed bulk RNA sequencing on HCT116 cell lines subjected to CRISPR/Cas9-induced SDR42E1 knock-in and transient overexpression of the wild-type SDR42E1 gene, alongside wild-type HCT116 cells serving as negative controls, all sampled simultaneously. Each sample in this study comprises three biological replicates.

first: Nagham

middle: N

last: Hendi


title: Genomic characterization and transcriptomic profile of Candida krusei in a neonatal intensive care unit in Delhi, India

city: Nutley

first: Neeraj

last: Chauhan

state: New Jersey

address: 111 ideation way

institute: Center for Discovery and Innovation, Hackensack Meridian Health

summary: In the last decade, Candida krusei has caused multiple outbreaks of candidemia in Neonatal Intensive Care Units (NICUs) in low-and middle-income countries such as Brazil, India, and South Africa. In India, C. krusei ranks as the sixth cause of candidemia in adult ICUs. Additionally, sporadic outbreaks of nosocomial candidemia in the NICUs are widely reported from India. However, the genetic population of C. krusei causing outbreaks remain largely unknown.  In the present study, we used whole genome sequencing to examine the genetic structure of C. krusei population causing candidemia spanning a period of five years (2015-20) in a single NICU in Delhi, India. Further, to evaluate the mechanisms of azole antifungal resistance in C. krusei, we compare the transcriptomic profiles of fluconazole susceptible (FLU-S) and resistant (FLU-R) isolates. Transcriptomic assay was performed in logarithmically growing C. krusei clinical isolates 123/P/19 and 1390/P/18 strains. STAR aligner v.2.5.2b was used to sequence the trimmed reads with the specified reference genome of P. kudriavzevii  to determine the unique gene hit counts. A total of 178 genes were differentially expressed by at least 1.5-fold in 1390/P/18 as compared to 123/P/19 isolate. Principal component analysis (PCA) of normalized read counts also depicted almost similar transcriptomic profile between the two C. krusei strains with 53 % variance at principal component 1. Out of 178 differentially expressed genes, 72 were up-regulated and 106 were down-regulated in 1390/P/18 strain compared to 123/P/19 strain. Functionally, genes associated with transport (n=10), mitogen activated protein kinase signaling (MAPK; n=8), transcription factors (TF; n=6) and ergosterol biosynthesis (n=3) were expressed differentially.

overall_design: We performed RNA-seq analysis of logarithmically growing Candida krusei isolates in the Yeast Extract Peptone Dextrose broth medium (YPD; 1% yeast extract, 2% peptone, and 2% dextrose) at 30°C. We sequenced 123/p/19 and 1390/p/18 strains in biological duplicates.

first: Raju

last: Shivarathri

first: Kusum

last: Jain

first: Jianping

last: Xu

first: Anuradha

last: Chowdhary


title: Chronic Obstructive Submandibular Adenitis

city: chengdu

first: li

last: honglin

address: No.14, Section 3, Renmin South Road

institute: sichuan university

summary:
To investigate the unique mechanism of chronic obstructive submandibular adenitis , we obstructed the right submandibular duct in eight-week-old C57BL/6J female mice.
We then collected submandibular glands 7 days after operation for transcriptome sequencing.

overall_design: Control group;Sialadenitis group   five mice each

first: Yubin

last: Cao

first: Honglin

last: Li