title: miRNA expression reveals a differential profile with moderate beer consumption in whole blood of healthy subjects

city: Barcelona

first: Lina

last: Badimon

state: BARCELONA

address: Carrer de Sant Antoni Maria Claret, 167

department: ICCC-Cardiovascular Program

institute: Research Institut- HSCSP

summary:
Affymetrix microarray (GeneChip microRNA 4.0) profilling of whole blood.
We used miRNA arrays to profile miRNAs isolated from whole blood samples of healthy subjects with or without moderate consumption of traditional beer

overall_design: We isolated miRNAs from whole blood samples of healthy subjects and profiled them to determine miRNA signature

first: Escate

last: Rafael

first: Camino

last: Sandra

first: Padró

last: Teresa

first: Badimon

last: Lina


title: Exploring differentially expressed lncRNAs between the osteosarcoma and adjacent normal tissues using RNA-Seq method

status: Public on Jan 01 2026

city: Jinan

first: Kailiang

last: Zhang

state: Shandong

address: 25 Shifan Raod

country: China

institute: the 960th Hospital of Joint Logistic Support Force

type: Non-coding RNA profiling by high throughput sequencing

summary: Osteosarcoma is one of the most commonly primary malignant tumors of bone, and the five-year survival rate for osteosarcoma patients is not satisfactory. Dysregulations of lncRNAs are frequently found in multiple cancers, including osteosarcoma, and these data reveal the critical involvement of lncRNAs in the tumorigenesis. Osteosarcoma tissues and adjacent normal tissues for controls were obtained and analyzed by high-throughput sequencing. Our data showed that hundreds of lncRNAs were identified, with LINC00673 ranking first among all the up-regulated lncRNAs. This study suggests that different expressions of lncRNAs may involve in the potential function in osteosarcoma and provide a novel insight for diagnosis of this disease.

overall_design: RNA-seq profiling of human osteosarcoma tissues and paired adjacent normal tissues was performed to identify differentially expressed lncRNAs.


title: Single-nucleus Multiome Profiling of Infant and Adult Human Spleen

city: New York

first: Siddhi

last: Nargund

state: NY

address: 3960 Broadway, Lasker 203A

department: Department of Systems Biology

country: USA

institute: Columbia University

type: Genome binding/occupancy profiling by high throughput sequencing

type: Expression profiling by high throughput sequencing

summary: We performed joint single-cell RNA and ATAC-seq on T cells from spleen of infant and adult donors.

overall_design: Multiome-seq: Single nuclei extracted form spleens of Infants and Adults. Joint snRNA and snATAC-seq libraries were prepared using the 10x Genomics platform

first: Peter A

last: Szabo

first: Donna L

last: Farber

last: Sims


title: Exposure of Ascaris suum larvae to red clover extract or biochanin A

city: Frederiksberg C

first: Andrew

last: Williams

address: Dyrlægevej 100

country: Denmark

institute: University of Copenhagen

summary: Transcriptomic analyses with the parasitic nematode Ascaris suum indicated that Biochanin A exerts its antiparasitic effect by interfering with membrane fluidity, while other compounds within the pulp extract may suppress its metabolism and expulsion, thereby generating a synergistic effect with potential to mitigate anthelmintic resistance

overall_design: Nematodes were exposed to 100 uM of biochanin A, 200 ug/mL red clover extract, or control solvent for three hour priors to RNA extraction. All samples were treated in triplicate.

middle: R


title: Mesangial cell-derived extracellular matrix protein 1 is essential for maintaining mesangial matrix homeostasis and glomerular architecture

city: 广东省

first: YU

middle: ansheng and southern medical

last: HU

state: 广东广东

address: 广东省广州市白云区京溪街道

institute: Nanfang Hospital

summary: Mesangial cells (MCs) and mesangial matrix (MM) constitute the mesangium, which is essential for maintaining normal glomerular structure and function. The mechanisms by which MCs regulate MM dynamics remain poorly understood. This study investigates the role of MC-derived extracellular matrix protein 1 (ECM1) in this process. To elucidate the mechanism, we collected kidney samples from  WT and Ecm1-KO mice at each time points (1, 2, and 4 weeks), with n = 3 per group and performed RNA-seq, aiming to capture the dynamic transcriptomic changes underlying the loss of ECM1.

overall_design: RNA-seq on kidney samples from  WT and Ecm1-KO mice at each time points (1, 2, and 4 weeks), with n = 3 per group.

first: Pei

last: Deng

first: Hui

last: Zhou

first: Jieli

last: Yu

first: Yinyin

last: Li

first: Fang

last: Yang

first: Miaomiao

first: Jiao

last: Luo

first: Jing

last: Nie

first: Bing

last: Sun

first: Fan Fan

last: Hou

first: Yu

last: Hu


title: S100A4-lineage Cells Contribute Modesty to Angiotensin II-mediated Thoracic Aortic Aneurysms Through Angiotensin II Type 1a Receptor in Mice

city: Lexington

first: Hisashi

last: Sawada

state: KY

address: 741 South Limestone BBSRB B251

institute: University of Kentucky

summary: Background: Angiotensin II (AngII) exerts a critical role in thoracic aortic aneurysm (TAA) formation via AngII type 1a receptor (AT1aR). However, the principal cell type mediating this process remains unclear. Our previous study demonstrated that S100A4-lineage cells are present in the aortic wall and involved in AngII-induced vascular remodeling. In the present study, we investigated whether S100A4-lineage cells contribute to AngII-mediated TAA formation through AT1aR. Methods: Proteomic, bulk RNA sequencing, and single-cell RNA sequencing data were analyzed to assess changes in S100A4 abundance in response to AngII infusion. Lineage tracing was performed to track S100A4-lineage cells during AngII-mediated TAA formation. Either saline or AngII was infused in mice with genetic deletion of AT1aR in S100A4-lineage cells and their wild-type littermates. Results: AngII infusion increased S100A4 protein and mRNA abundance significantly in the ascending aorta, particularly within smooth muscle cells and fibroblasts. Under basal conditions, S100A4-positive cells were localized to the media and adventitia. Following AngII infusion, these cells expanded markedly and populated the entire aortic wall. Deletion of AT1aR in S100A4-lineage cells modestly reduced AngII-induced TAA formation. Conclusions: S100A4-lineage cells modestly contribute to AngII-mediated TAA development through AT1aR in mice.

overall_design: Comparative gene expression analysis of RNA-seq data for ascending, descending, suprarenal abdominal, and infrarenal abdominal aortas of C57BL/6J male and femal mice with either saline or AngII infusion for 3 days.


title: A Porcine Model of Intervertebral Disc Injury Recapitulates Human Discogenic Pain via Notochordal Cell Loss and Pain-inducing Nucleus Pulposus Cell Emergence

city: Los Angeles

first: Dmitriy

last: Sheyn

address: 127 S San Vicente Blvd

institute: Cedars-Sinai Medical Center

summary: Lower back pain (LBP) is one of the most common causes of disability, with up to 40% of LBP cases attributed to intervertebral disc (IVD) degeneration. While small animal models are widely used to study IVD and LBP, the small size of their IVDs limits translational and biological relevance. Large animal models more accurately emulate human disease; however, methods of measuring LBP are not well established. Pigs were also considered unfit for LBP research, due to notochordal cells (NCs) persistence through life, unlike humans. We developed a comprehensive porcine model with quantitative measure of discogenic pain via biobehavioral testing (BBT), MRI, and multi-omics tissue analysis of IVD and DRGs. MRI demonstrated the progression of IVD degeneration beginning at 4 weeks post-injury. BBTs showed the development of significant pain responses by week 4 post-injury, supported by transcriptomics of injury matched DRGs. Single cell transcriptomics, trajectory and cell-cell communication analyses suggest that, with injury, NCs are differentiating to nucleus pulposus cells (NPCs). Furthermore, NPCs showed upregulation of cellular stress, neural outgrowth, and inflammation pathway, consistent with pain-inducing distress signals found in human samples. This study establishes novel MRI and BBT-based methods for quantifying LBP in pigs and supports its translational relevance to human discogenic LBP. The identification of LBP-associated clusters mirrors our previous finding in humans. Moreover, the shift of NC to NPC phenotype further supports that the porcine model is relevant to human pathology, as the injury induced accelerated aging and loss of NCs with IVD degeneration and discogenic pain.

overall_design: We performed performed a percutaneous needle puncture of lumbar discs under fluoroscopic guidance in female Yucatan minipigs. Degeneration and pain development were assessed longitudinally via MRI and biobehavioral testing. At 12 weeks post-injury, dorsal root ganglia (DRG) and IVD tissues were collected for bulk RNA-seq, and nucleus pulposus (NP) samples from injured and non-injured discs were harvested at 16 weeks for single-cell RNA-seq. Additional analyses included histology, immunofluorescence, proteomics, and serum biomarker quantification by ELISA. Integrated statistical analyses were performed to correlate imaging, behavioral, and molecular readouts of discogenic pain.

first: Kaneda

last: Giselle

first: Wechsler

last: Jacob

first: Chavez

last: Melissa

first: Sheyn

last: Julia

first: Cheema

last: Karandeep

first: Shen

last: Chushu

first: Rigo De Righi

last: Dante

first: Avalos

last: Pablo

first: Xie

last: Yibin

first: Tawackoli

last: Wafa

first: Floyd

last: Candace

first: Li

last: Debiao

last: Dmitriy


title: The SETD7–H3K4me1–APLNR Axis Couples Epigenetic Signaling to Orchestrate Endoderm Specification in Human Pluripotent Stem Cells

city: Guangzhou

first: shoupei

last: liu

address: 9th Floor, Building b, Huanyu 2nd Road, Haizhu District

department: Institute of Clinical Medicine

institute: Guangzhou First People's Hospital

summary: The differentiation of human pluripotent stem cells into definitive endoderm (DE), a pivotal event in embryonic development, remains incompletely elucidated with respect to its epigenetic control. Here, we identified SETD7, a histone H3K4 monomethyltransferase (H3K4me1), as dynamically upregulated during DE specification, with its expression correlating strongly with the key lineage marker SOX17. Genetic knockdown of SETD7 impaired DE formation, as evidenced by reduced expression of DE markers and disruption of APLNR-mediated PI3K/AKT/mTOR signaling—a phenotypic defect recapitulated by pharmacological inhibition of APLNR. Mechanistically, SETD7 facilitates H3K4me1 deposition at enhancer regions of APLNR, thereby promoting its transcriptional activation. Our findings unveil an epigenetic-regulatory axis wherein SETD7-mediated enhancer priming drives APLNR expression, ultimately activating the PI3K/AKT/mTOR cascade to promote endodermal commitment. Through an integrated approach incorporating doxycycline-inducible SETD7 knockdown in hESCs, pathway-specific pharmacology, ChIP-qPCR, and 3D organoid modeling, we decipher the spatiotemporal regulatory network governed by SETD7 during DE specification. This study highlights the critical crosstalk between histone modification landscapes and signal transduction during cell fate determination and establishes a novel strategy for manipulating differentiation trajectories.

overall_design: In this study, we revealed the molecular mechanism by which the SETD7-H3K4me1-APLNR axis regulates DE differentiation. Initially, during the epigenetic initiation phase, SETD7 mediates H3K4me1 modification at APLNR enhancer regions, thereby facilitating APLNR transcriptional activation. Subsequently, the APLNR protein is transported from the cytosol to the plasma membrane, where it becomes properly anchored within the lipid bilayer. Following membrane localization, the APLNR receptor engages with its cognate ligand Apelin, resulting in receptor activation and subsequent initiation of downstream PI3K/AKT/mTOR signaling cascade. This signal transduction ultimately converges on the transcriptional regulation of endodermal marker genes, orchestrating DE lineage specification.

first: Shoupei

last: Liu

first: Xiangting

last: Cao

first: Sen

last: Chen

first: Haibin

last: Wu

first: Yuyou

last: Duan


title: Effect of depletion of LINC00673 on gene expression in osteosarcoma.

first: Kailiang

last: Zhang

summary: Here, we report the importance of LINC00673 in osteosarocma. As important members of ceRNA networks, lncRNAs are well-known to serve as miRNA sponges, and then the lncRNA-miRNA-mRNA axis has been frequently reported in the literature. The ceRNA networks of LINC00673 have been reported in various types of cancers. In the current study, LINC00673 was proved to be primarily localized in the cytoplasm of osteosarcoma cells, and it is reasonable to speculate that LINC00673 may also act as a ceRNA to sponge the downstream miRNAs. So, our data provide potential downstream targets of LINC00673 and will help to find out the ceRNA networks of LINC00673 in osteosarcoma.

overall_design: Wildtype U2OS cells and U2OS cells stably transfected with LINC00673 shRNA were collected for miRNA-seq analysis.


title: Effect of depletion of LINC00673 on gene expression in osteosarcoma

overall_design: RNA-seq profiling of wildtype U2OS osteosarcoma cells and their derivatives with LINC00673 knockdown.


title: PARTAGE: Parallel analysis of replication timing and gene expression

city: Minneapolis

first: Quinn

last: Dickinson

state: MN

address: 100 Church Street SE

institute: University of Minnesota

summary: The human genome is partitioned into functional compartments that replicate at specific times during the S-phase. This temporal program, referred to as replication timing (RT), is co-regulated with the 3D genome organization, is cell type-specific, and changes during development in coordination with gene expression. Moreover, RT alterations are linked to abnormal gene expression, genome instability, and structural variation in multiple diseases, including cancer. However, mechanistic links between RT, large-scale 3D genome architecture, and transcriptional regulation remain poorly understood. A major limitation is that current approaches require the separate profiling of RT and transcriptomes from independent batches of samples, obscuring the complex co-regulation between the epigenome and transcriptome. Here, we developed PARTAGE, a multiomics approach that enables joint profiling of copy number variation (CNV), RT, and gene expression from the same sample, providing a more accurate integrative view of the complex relationships between RT and gene regulation.

overall_design: A novel multiomics approach for simultaneous analysis of RT and gene expression. We have collected cells at distinct stages of the cell cycle under conditions that preserve both nucleic acids, enabling joint profiling of RT (Repli-seq) and transcriptomes (RNA-seq).

first: Lakshana

last: Sruthi Sadu Murari

first: Silvia

last: Meyer-Nava

first: Juan Carlos

last: Rivera-Mulia


title: Hepatic transcriptomes reveal molecular mechanisms underlying weight divergence and growth regulation in Korean Ogye and Cornish Chickens

city: Mbarara

first: Andrew

middle: Wange

last: Bugenyi

address: N/A, N/A

department: Animal Resources Research Program

country: Uganda

institute: National Agricultural Research Organisation

summary: The Yeonsan Ogye, a culturally significant but small Korean chicken breed has been extensively studied for its fibromelanosis, leaving its low body weight and growth rate relatively unexplored. Here we present the first comparative hepatic transcriptome analysis of Ogye and the heavy, fast-growing Korean Brown Cornish breed at the critical stages of 5 and 10 weeks of age. Using RNA sequencing (RNA-seq) and bioinformatic analyses we uncovered significant and dynamic differences between the breeds. At 5 weeks, Ogye livers exhibited enriched inflammatory and energy-transfer processes (oxidoreductase activity, mitochondrial function), whereas in Cornish livers, translational and macromolecule biosynthesis pathways (ribosomal structure, RNA binding) were enriched. By 10 weeks, Ogye shifts further toward immune- and stimulus-response functions (cytokine/chemokine signaling, MAPK pathway, oxidative phosphorylation), while Cornish maintains elevated protein modification, intracellular transport, and RNA processing activities. Moreover, within the differentially expressed MAPK signaling pathway, genes involved in the regulation of cellular metabolism (FGF19, DUSP8, PTPRR, CACNA1C, CACNA1S, among others) were upregulated in Ogye while growth factor-related genes (IGF1, IGF2, EGFR, VEGFC, and FGFR3) stood out among the Cornish chicken. These patterns suggest contrasting metabolic signatures — a high maintenance, energy expending profile in Ogye versus a growth efficient, anabolic profile in Cornish — and reveal temporal switching of core pathways across development. Consequently, our findings provide a basis for future initiatives aimed at developing biotechnological solutions to enhance growth and weight gain in Ogye and potentially other small chicken breeds.

overall_design: This study investigates the hepatic transcriptomes of Ogye and Cornish chickens at 5 and 10 weeks of age, to unravel the molecular basis of their significant weight divergence

first: Andrew Wange

first: Jae-Rung

last: So

first: Ki-Duk

last: Song


title: Based on single-cell sequencing analysis of CD4+ T cells and B cells in patients with lupus nephritis, the heterogeneity of these cells was investigated.

city: Hefei

first: lili

last: cheng

state: Anhui Province

address: No. 117, Meishan Road

institute: The First Affiliated Hospital of Anhui University of Chinese Medicine

summary: Utilizing single-cell technology to analyze the heterogeneity of CD4+ T cells and B cells in patients with lupus nephritis.We have delineated the immune cell profile of PBMC in LN patients, and focused on describing the heterogeneity characteristics of CD4+ T cells and B cells. Some specific cell subtypes and ligand-receptor pairs were identified, which indicate potential therapeutic targets for lupus erythematosus.

overall_design: Under the condition of informed consent, this study conducted single-cell transcriptome sequencing on PBMC samples from 3 patients with LN and 3 healthy controls (HC), aiming to explore the conditions of LN CD4+ T cells and B cells. Firstly, the cells were classified into immune cell clusters through cell dimensionality reduction and clustering. Then, further subdivisions were made for CD4+ T and B cells. Using differential analysis and public data, the Maker genes that affected LN CD4+ T and B cells were identified. Subsequently, GO, KEGG, and GSEA enrichment analyses were used to conduct functional analysis of the differentially expressed genes in LN patients.

first: Lili

last: Cheng

first: Zhongfu

last: Tang

first: Ming

last: Li

first: Shuangshuang

last: Shang

first: Junjie

first: Sidi

first: Chuanbing

last: Huang


title: Expression profile of shNT and shPTX3 DAOY cells

city: Brescia

first: Roberto

last: Ronca

address: viale Europa 11

department: Molecular and Translational medicine

country: Italy

institute: University of Brescia

summary:
Sonic hedgehog-medulloblastoma (SHH-MB) represents a biologically diverse and clinically challenging subgroup, especially in high-risk variants characterized by metastatic dissemination. Identifying novel oncogenic mechanisms that can be therapeutically exploited is therefore a critical priority.  Here, we uncover Pentraxin-3 (PTX3) as a previously unrecognized, SHH-enriched oncogenic mediator that promotes proliferation, migration, clonogenicity, and angiogenesis. Mechanistically, we demonstrate that PTX3 activates a TLR4/IRAK1/PI3K-Akt/GSK-3/β-catenin signaling cascade, establishing a key regulatory axis essential for SHH-MB growth.
We used microarrays to detail the global programme of gene expression in DAOY shNT and shPTX3 cells.

overall_design: Expression profiles of shNT/shPTX3 DAOY cells using biological triplicates in each condition

first: Serena

last: Filiberti


title: Vitamin B12 promotes cefiderocol resistance and small-colony variants in carbapenem-resistant Acinetobacter baumannii.

city: Fullerton

first: M. S.

last: Ramirez

state: CA

address: 800 N. State College Blvd

institute: California State University Fullerton

summary: Carbapenem-resistant Acinetobacter baumannii (CRAB) is a global health threat with few effective treatment options remaining. Cefiderocol, a last-resort siderophore-cephalosporin antibiotic, exploits bacterial iron transport systems via TonB-dependent receptors (TBDRs) to gain cellular entry. However, treatment failures and emerging resistance highlight the complexity of its activity in vivo. In this study, we report an unanticipated cefiderocol resistance mechanism, where vitamin B12, a commonly used micronutrient supplement, modulates cefiderocol susceptibility. Vitamin B12 affect and interact with TBDRs and other metabolic and adaptation processes contributing to increases cefiderocol MIC level and emergence of persistence phenotypes. We show that vitamin B12 supplementations leads to strain-specific transcriptomic responses in the CRAB AB5075 and AMA17 strains, showing downregulation of siderophore transporters, stress responses, metabolic reprogramming, and biofilm-associated genes. Structural modeling and molecular docking reveal overlapping binding sites for vitamin B12 and cefiderocol within key TBDRs such as CirA and PirA, suggesting competitive inhibition. Additionally, vitamin B12 exposure increases cefiderocol MICs across a panel of clinical and reference strains, enhances survival in time-kill assays, and promotes emergence of small colony variants with persistent phenotypes. Notably, this effect is stable, dose-dependent and further seen to be increased in the presence of host-derived fluids. These findings describe a previously unrecognized host–pathogen–drug interaction with potential clinical implications, suggesting that vitamin B12 exposure could contribute to cefiderocol treatment failure. Our results underscore the urgent need to consider vitamin supplements potential contribution in antimicrobial therapy and CRAB management strategies.

overall_design: Total mRNA of Acinetobacter baumanii AB5075 or Acinetobacter baumannii AMA17 was isolated from bacteria incubated either in LB broth or in LB broth supplemented with vitamin B12 (methylcobalamin, 100 µg/mL).

first: Maria

middle: S

first: Rodrigo

last: Sieira


title: Single-cell RNA analysis reveals reduced frequency and activity of CXCR5+ atypical memory B cells in islet xenotransplantation treated with clinically applicable immunosuppressants including Belimumab

city: Seoul

first: Yuji

last: Lee

state: Soul-t'ukpyolsi

address: #308, Convergence building, Seoul National University College of Medicine, 103 D

country: South Korea

institute: Seoul National University

summary:
Background
Porcine-to-human islet xenotransplantation offers a promising solution to type 1 diabetes. This study investigates the use of belimumab, a human monoclonal antibody that inhibits B cell activating factor (BAFF) as part of an immunosuppressive regimen in porcine-to-non-human primate xenotransplantation.
Methods
Porcine islets were transplanted into Rhesus monkeys with an immunosuppressant regimen. Blood samples were collected from the monkeys pre- and post-treatment, and single-cell RNA sequencing was performed to investigate immune cell landscape changes, focusing on B cells.
Results
UMAP clustering of B cells identified five distinct subsets. Notably, belimumab treatment significantly reduced the proportion of both CXCR5+ and CXCR5- atypical memory B cells, which possess the potential to differentiate into antibody-secreting cells. Furthermore, differentially expressed gene (DEG) analysis revealed a comprehensive functional impairment, along with significant downregulation of activation markers such as CD69 and CD83, across all B cell subsets.
Conclusions
Our study elucidates the mechanism of action of belimumab in non-human primate models, serving as preclinical subjects for B-cell-targeted therapy research in a xenotransplantation context. Significantly, our data indicate that belimumab not only reduces the proportion of antibody-secreting atypical memory B cells but also induces functional impairment across all B cell subsets. Given the potential pathogenic roles of atypical memory B cells in autoimmunity and other related settings, their reduction by belimumab could play a crucial role in regulating B cell-mediated immune responses in pig-to-nonhuman primate pancreatic islet xenotransplantation. Thus, our findings highlight the prospective utility of belimumab as a B cell suppressant in future clinical xenotransplantation applications.

first: Ji-Hwan

last: Moon

first: Hyun-Je

last: Kim

first: Daesik

first: Yong-Hee

first: Jong-Min

first: Chung-Gyu

last: Park


title: MAPK1 mediates C/EBPβ phosphorylation to promote maturation and inhibit EMT process in hESC-derived hepatocytes [RNA-seq]

first: shoupei

last: liu

summary: Human pluripotent stem cell (hPSC)-derived hepatocytes exhibit progressive differentiation toward a phenotype resembling primary human hepatocytes (PHHs). Nevertheless, they still display persistent functional deficiencies in key mature hepatocyte properties, particularly in albumin secretion and ammonia metabolism, remain challenge compared to PHHs. In this study, we elucidated a critical regulatory role of CCAAT/enhancer-binding protein beta (C/EBPβ) in hepatocyte maturation. Forced expression of C/EBPβ significantly enhanced hepatic functionality, as evidenced by increased albumin secretion, upregulation of hepatic-specific genes, and suppression of epithelial-mesenchymal transition (EMT) markers. Mechanistically, we found that C/EBPβ directly binded to the promoter regions of E-cadherin (E-cad) and carbamoyl phosphate synthetase 1 (CPS1), enhancing their transcriptional activation. Furthermore, we identified a functional interaction between C/EBPβ and MAPK signaling, where MAPK1-mediated phosphorylation at Thr-235 potentiated C/EBPβ's transactivation capacity, thereby promoting hepatocyte differentiation and maturation. Our findings establish C/EBPβ as a master regulator of hepatic maturation, orchestrating transcriptional networks and post-translational modification. These insights provide a theoretical framework for optimizing stem cell-derived hepatocyte differentiation, facilitating their applications in various fields.

overall_design: Our previous work demonstrated that C/EBPβ overexpression in hepatic progenitor cells (HPCs) promoted mitotic activation through cell cycle regulator induction. This study would uncover a stage-specific functional duality of C/EBPβ in hESC-derived hepatocytes (hEHs). Quantitative assessments was used to determine how C/EBPβ activation enhance hepatic functionality while suppressing EMT process, and whether MAPK1-C/EBPβ regulatory axis also mechanistically play function in hPSC-derived hepatocytes by employing co-immunoprecipitation (Co-IP) assays to detect direct physical interaction between MAPK1 and C/EBPβ. Then, MAPK1-mediated phosphorylation at C/EBPβ Thr-235 to transcriptional activity of the downstream genes was further investigated, and finally CUT&Tag assays and luciferase activity was performed to confirm that C/EBPβ could enhance promoter occupancy at target genes. The results of these studies would demonstrate that C/EBPβ orchestrated hepatic maturation through dual mechanisms of transcriptional network regulation and dynamic post-translational modifications. These insights would provide a mechanistic basis for optimizing hPSC-to-hepatocyte differentiation strategies, offering new avenues for developing mature hepatocyte populations for applications in various fileds.

first: Shoupei

last: Liu

first: Xiangting

last: Cao

first: Haibin

last: Wu

first: Xueyan

last: Zhang

first: Sen

last: Chen

first: Huanhuan

last: Shan

first: Yuyou

last: Duan


title: NMN protects cisplatin induced AKI via NAD+/SIRT1 pathway

city: nantong

first: Zhaozhi

last: Wen

state: jiangsu

address: Seyuan Road 9

institute: Nantong University

summary: Acute kidney injury (AKI) is a critical public health concern with high morbidity and mortality.Using male mice and HK-2 cells, we found that the NAD⁺ precursor NMN restored renal NAD⁺ levels and activated SIRT1, markedly lowering plasma creatinine and BUN, reducing NGAL and KIM-1 expression, suppressing IL-6/IL-18 and neutrophil infiltration, and attenuating ROS and LDH release. Thus, NMN protects against CIS-AKI via the NAD⁺–SIRT1 pathway and represents a promising therapeutic strategy.

overall_design: RNA-seq profiling of saline-treated control and cisplatin-treated mouse kidneys at 72 h post-injection.

first: Yihang

last: Yang

first: Jiazeng

last: Wang

first: Longlong

first: Xiangge

last: Ji

first: Dong

first: Chongxu

last: Shi


title: CBTi-seq validates specialized alternative splicing patterns in gene-edited cells

city: nanjing

first: Liyong

last: He

state: Not US or Canada

address: 南京市玄武区东南大学

institute: State Key Laboratory of Digital Medical Engineering, School of Biological Science & Medical Engineering

summary: we compared the ability to reveal cell-specific splicing patterns between knockdown and control groups using CBTi-seq and 3’ targeting methods. The numbers of detected genes showed no significant difference between the two methods. However, gene body coverage distribution indicated differential genomic coverage patterns which CBTi-seq shows a uniform full-length coverage. CBTi-seq robustly identified pronounced exon skipping events spanning exon 4 to exon 6 in the knockdown group, contrasting with the constitutive splicing pattern observed in controls.

overall_design: establish Rrm2-knockdown and control cell groups, and then sequenced by CBTi-seq and 3’ targeting methods, respectively

first: Yan

last: Huang


title: CBTi-seq profiles cell type and splicing patterns in adult human testicular cells.

summary: Spermatogenesis is a highly complex and precisely regulated process. Moreover, alternative splicing (AS) is widely prevalent in the testis, but the regulations of AS in spermatogenesis is only little explored. As methodological validation, we performed random cell picking from two male donors with obstructive azoospermia (OA) and collected 192 adult testicular cells

overall_design: we performed random cell picking from two male donors with obstructive azoospermia (OA) and collected 192 adult testicular cells, then multiplexed sequencing by CBTi-seq

first: Qian

last: Sun

first: Wenbo

last: Li


title: AP2XI-3-dependent gene regulation in Toxoplasma gondii tachyzoites (Complementary data)

city: Wuhan

first: Fan

last: Fuqiang

address: 1 Shizishan St

institute: Huazhong Agricultural University

summary: Toxoplasma proliferation is governed by its flexible but tightly regulated cell division cycle, that remarkably depends on appropriate and temporal transcriptional waves throughout the division cycle although the underlying regulation network is still unclear. Here we reported the transcriptional factor, AP2XI-3, as an essential cell cycle related gene regulator in G1 progression. After AP2XI-3 depletion, tachyzoites growth was obviously arrested in G1 phage and daughter budding progression was also destroyed. Intriguingly, the growth arrest of mutant parasites was also observed in vitro. Combining analysis of RNA sequencing and Cut & TAG revealed the key regulatory role of AP2XI-3 in G1 phage related biomass accumulation and cellular competent. AP2XI-3 controlled and targeted a set of RNA transcription, metabolism or protein biosynthesis related genes, whose dysregulation functionally disrupted cell homeostasis and parasite division. Altogether, our finding demonstrated the functional role of AP2XI-3 in transcriptional controlling of G1 progression and revealed its potential ability as a drug design target.

overall_design: Toxoplasma gondii with AP2XI-3 tagged with (mAID-3HA) were treated with or without IAA and processed polyA-enriched RNAseq in tachyzoites

first: Fuqiang

last: Fan

first: Bang

last: Shen


title: GlycoRNA identification by rPAL enrichment from acute myeloid leukemia cell lines and derived extracellular vehicles

city: Thuwal

first: Jing

last: Kai

address: King Abdullah University of Science and Techonology

department: Biological and Environmental Science and Engineering Division

country: Saudi Arabia

summary: These data are used to identify the classes of glycoRNAs from AML cell lines and their derived EVs. GlycoRNAs were enriched from KG1a and HL60 cells, and their derived large/small EVs, using the corresponding total RNA as the input controls.

overall_design: Total RNAs were extracted from KG1a and HL60 cells, and their derived large and small EVs using RNAzol. GlyocRNA (sialyloglycoRNAs) were labeled with biotin using periodate oxidation and aldehyde ligation (rPAL) and enricehd, purfied and subjected to small RNA sequencing with their corresponsing total RNAs as the input controls. Small RNA libraries were prepared by MGIEasy Small RNA Library Prep Kit (BGI, Shenzhen, China), followed by sequencing on DNBSEQ-G400 platform by BGI-Shenzhen (China).

first: Jasmeen

last: Merzaban


title: Tmem45b Modulates itch via Endoplasmic Reticulum Calcium Regulation

city: Zhuhai

first: Liang

last: Chen

state: 广东Guangdong

address: 6th Building, No. 2515, Huan Dao North Road, Hengqin New Area, Zhuhai, Guangdong Province, China

institute: Guangdong Institute of Intelligence Science and Technology

summary: Chronic itch is detected by dorsal root ganglia (DRG) that severely impairs quality of  life. However, its underlying mechanisms remain poorly understood. We identified that  Tmem45b was contained in natriuretic peptide type B (Nppb)-, mas-related G-protein  coupled receptor member A3 (Mrgpra3)-, and Mrgprd-positive DRG neurons, which are  associated with itch sensation. The role of Tmem45b in itch sensation has not been  explored. Tmem45b conditional knockout (cKO) mice exhibited decreased scratching  to β-alanine, and increased scratching to chloroquine. Notably, Tmem45b cKO  alleviated chronic itch. Furthermore, Tmem45b cKO impaired the calcium response to  β-alanine and allyl isothiocyanate but not to chloroquine in dissociated DRG neurons.  Tmem45b deficiency led to significant downregulation of sarco/endoplasmic reticulum  calcium transport ATPase 1 (Serca1), impairing calcium storage capacity of  endoplasmic reticulum (ER). Inhibition of Serca1 in DRG neurons reduced intracellular  calcium release triggered by β-alanine and chloroquine. Together,Tmem45b deficiency  may reduce nonhistaminergic itch and disrupt ER calcium regulation, highlighting a  potential target for chronic itch therapy.

overall_design: RNA sequencing was performed on the dorsal root ganglia (DRG) tissues of Tmem45b-flox mice, Tmem45b-flox::Mrgprd-cre mice, CFA-induced Tmem45b-flox mice, and CFA-induced Tmem45b-flox::Mrgprd-cre mice to explore gene expression changes under different experimental conditions.

first: Sa-Shuang

first: Chen

last: Liang

first: Ruo-lin

first: Ze-lin

first: Peng-yu

last: Ren

first: Bin

last: Wu

first: Juan-juan

first: Li

last: Fu

first: Li-zu

last: Xiao

first: Wu-ping

first: Changlin Li


title: MAPK1 mediates C/EBPβ phosphorylation to promote maturation and inhibit EMT process in hESC-derived hepatocytes [CUT&Tag]

first: shoupei

last: liu

first: Shoupei

last: Liu

first: Xiangting

last: Cao

first: Haibin

first: Xueyan

last: Zhang

first: Sen

first: Huanhuan

last: Shan

first: Yuyou

last: Duan


title: Effect of embryonic thermal manipulation on gene expression in brain tissues of  chicken embryos

city: Beijing

first: Zixuan

address: No. 2 Yuanmingyuan West Road

department: College of Animal Science and Technology

institute: China Agricultural University

summary: This study investigated the transcriptomic effects of embryonic thermal manipulation (ETM) on brain development in White leghorn chicken. Fertilized eggs were incubated under control conditions (37.8 °C, 65% relative humidity, ED0–18) or subjected to ETM conditions (37.8 °C, ED0–12；39.5 °C, ED13–18).RNA sequencing was performed on hypothalamus and whole-brain tissues. Differential expression analysis identified 993 genes in the whole brain and 333 genes in the hypothalamus. Gene Ontology enrichment indicated that whole-brain DEGs were associated with gliogenesis, immune regulation, and cell proliferation, while hypothalamic DEGs were enriched in processes related to neural development, hormone secretion, immune function, and oxidative stress.

overall_design: RNA-seq was performed on hypothalamus and whole-brain tissues from embryos of White leghorn chicken at embryonic day 18 (ED18). Fertilized eggs were divided into control (CT) and embryonic thermal manipulation (ETM) groups, with three biological replicates per tissue per group. CT eggs were incubated at 37.8 °C and 65% relative humidity throughout, whereas ETM eggs were exposed to 39.5 °C from ED13 to ED18 and otherwise maintained under control conditions. Total RNA was extracted at ED18, libraries were prepared, and sequencing was conducted on the Illumina NovaSeq X Plus platform.

first: Fan

last: Zixuan

first: Jie

last: Yuchen

first: Niu

last: Bowen


title: CBTi-seq profiling spatially resolved single-cell transcriptomics in mouse brain functional areas

first: Liyong

last: He

summary: To evaluate the potential utility of the CBTi-seq for spatially resolved transcriptomics tissue analysis, we performed a proof-of-concept experiment by microneedle sampling and analyzing three typical mouse brain regions (cerebral cortex (Ccx), corpus callosum (Cc), and hippocampus (Hi)) under the specific zone. CBTi-seq enables spatially resolved transcriptomics analysis in the tissue microenvironment, and holds great potential for revealing the spatial and temporal characteristics and functional heterogeneity of cells.

overall_design: By microneedle sampling and analyzing three typical mouse brain regions (cerebral cortex (Ccx), corpus callosum (Cc), and hippocampus (Hi)) under the specific zone.

first: Kaitong

last: Dang


title: Nucleosome Positioning Shapes Cryptic Antisense Transcription.

city: Vienna

first: Jian Yi

last: Kok

address: Dr.-Bohr-Gasse 3

country: Austria

institute: GMI - Gregor Mendel Institute of Molecular Plant Biology

summary: Maintaining transcriptional fidelity is essential for precise gene regulation and genome stability. Despite this, cryptic antisense transcription, occurring opposite to canonical coding sequences, is a pervasive feature across all domains of life. How such potentially harmful cryptic sites are regulated remains incompletely understood. Here, we show that nucleosome arrays within gene bodies play a key role in suppressing cryptic transcription. Using the fission yeast Schizosaccharomyces pombe as a model, we demonstrate that CHD1-family chromatin remodelers coordinate with the transcription elongation machinery, specifically the PAF complex, to position nucleosomes at sites of cryptic transcription initiation within gene bodies. In the absence of CHD1, AT-rich sequences within gene bodies lose nucleosome occupancy, exposing promoter-like sequences that drive cryptic initiation. While cryptic transcription is generally detrimental, we identify a subset of antisense transcripts that encode critical meiotic genes, suggesting that cryptic transcription can also serve as a source of regulatory innovation. These findings underscore the essential role of nucleosome remodelers in maintaining transcriptional fidelity and reveal their broader contributions to cellular homeostasis and evolutionary adaptability.

overall_design: We aimed to characterize the diversity of antisense transcripts present in Schizosaccharomyces pombe (S. pombe). To achieve this, we employed Iso-Seq long-read sequencing to capture full-length transcripts. Our experimental design included two genetic backgrounds: wild-type (WT) S. pombe and an hrp1Δ hrp3Δ double mutant, which is known to exhibit increased levels of antisense transcription. Both genotypes were grown under standard laboratory conditions and subjected to two distinct stress treatments: caffeine and clotrimazole. This resulted in the following sample conditions for each genotype: untreated (control), caffeine-treated, and clotrimazole-treated. For sequencing, we multiplexed our samples in two separate runs. The first run included only the wild-type, untreated sample. The second run comprised all remaining conditions: both genotypes (WT and hrp1Δ hrp3Δ), each with and without the two stress treatments (caffeine and clotrimazole). This multiplexing strategy was chosen due to technical constraints.

first: Elin

last: Axelsson


title: RNA-seq analysis of mouse aortic endothelial cells of angiotensin II hypertensive mice

first: Sijia

last: Liang

address: 74 Zhongshan 2 Rd

department: Pharmacology

institute: Sun Yat-Sen University

summary: To explore the role of endothelial cells in hypertension, we developed an angiotensin II-induced mouse hypertension model. Eight-week-old C57BL/6 mice were anesthetized using 2% pentobarbital sodium, and osmotic pumps were subcutaneously implanted to deliver AngII at a constant rate of 1000 ng/kg/min over 14 consecutive days. Sham-operated mice underwent the identical procedure, with osmotic pumps containing 0.9% saline implanted subcutaneously instead. Subsequently, mouse aortic endothelial cells were isolated and subjected to RNA sequencing analysis.

overall_design: RNA-seq was performed to compare the mRNA expression level in mouse aortic endothelial cells from saline- and angiotensin II-infused mice.

first: Si-Jia


title: Distinct genomic and immunologic tumor evolution in germline TP53-driven breast cancers

city: Philadelphia

first: Kara

last: Maxwell

state: PA

address: 421 Curie Blvd

institute: University of Pennsylvania

summary: Pathogenic germline TP53 alterations cause Li-Fraumeni Syndrome (LFS), and breast cancer is the most common cancer in LFS females. We performed first of its kind multimodal analysis of LFS breast cancer (LFS-BC) compared to sporadic premenopausal BC. Nearly all LFS-BC underwent biallelic loss of TP53 with no recurrent oncogenic variants except ERBB2 (HER2) amplification. Compared to sporadic BC, in situ and invasive LFS-BC exhibited a high burden of short amplified aneuploid segments (SAAS). Pro-apoptotic p53 target genes BAX and TP53I3 failed to be up-regulated in LFS-BC as was seen in sporadic BC compared to normal breast tissue. LFS-BC had lower CD8+ T-cell infiltration compared to sporadic BC yet higher levels of proliferating cytotoxic T-cells. Within LFS-BC, progression from in situ to invasive BC was marked by an increase in chromosomal instability with a decrease in proliferating cytotoxic T-cells. Our study uncovers critical events in mutant p53-driven tumorigenesis in breast tissue.

overall_design: RNA-sequencing of RNA from formalin-fixed paraffin-embedded (FFPE) sections of breast tumors from LFS patients and age-matched nonLFS patients.

first: Nabamita

last: Boruah

first: Renyta

last: Moses

first: Ryan

last: Hausler


title: Pharmacological inhibition of the epigenetic enzyme EZH2 attenuates cardiac dysfunction and mitigates lipid metabolism perturbations in a murine model of myocardial infarction

city: Rouen

first: Sylvain

last: Fraineau

address: 22 Boulevard Gambetta

country: France

institute: Unversity of Rouen Normandy

summary: Rational: EZH2, an epigenetic enzyme, acts as a transcriptional repressor for genes dysregulated after myocardial infarction (MI). Objective: This study aims to assess the benefits of GSK-343 (EZH2 inhibitor) on cardiac function and lipid metabolism after MI. Methods: Mice were treated daily with vehicle or GSK-343 for 7 days after MI and we evaluated cardiac function (echocardiography), gene expression profiling (RNA-seq) and circulating lipidome (untargeted lipidomics). Results: The 28% MI decreased ejection fraction (EF) was improved by 20% with GSK-343. RNA-seq analysis revealed wide changes in MI normalized with GSK-343: 16 mitochondrial DNA-encoded genes, 57 genes related to mitochondrial function and 15 to lipid metabolism among the 561 down-regulated genes (FC 0.5 and 2; p=10-4). In plasma, while MI enhanced 18 triglycerides (1.24-2.43-fold; p<0.05) and decreased 32 choline glycerophospholipids (PC; 0.55-0.81-fold, p<0.05), GSK-343 normalized these perturbations. In MI, some of these lipids positively correlated with EF (e.g. PC40:6; R=0.84, p=0.004) or with cardiac hypertrophy (e.g. DG18:1_18:2; R=0.81, p=0.007) and GSK-343 abolished most of these correlations. Conclusion: Our study suggests that inhibiting EZH2 is of therapeutic interest to normalize lipid metabolism perturbations and improve cardiac function after MI.

overall_design: total RNA isolated from left ventricles of 5 independent sham or MI mice previously treated either with GSK-343 (20 mg/kg, Interchim Cat# XLR94D) or vehicle (20% captisol), 8 days post-MI, Poly-A mRNA-seq, sequencing length of 150 nt paired end (PE150) with the Illumina NovaSeq 6000 was performed.

first: Hugues

last: Boël

first: Matthieu

last: Ruiz


title: Paternal alcohol exposure leads to differential expression of sperm miRNA and disrupts offspring growth and metabolism

city: College Station

first: MICHAEL

middle: C.

last: GOLDING

state: Texas

address: 4466 TAMU

department: Veterinary Physiology & Pharmacology

institute: Texas A&M University

summary: Prenatal development is influenced by various paternal factors, including environmental exposures, lifestyle, and epigenetic modifications. This dissertation investigates the impact of chronic paternal alcohol (EtOH) consumption on offspring development, with a particular focus on placental function, mitochondrial health, and microRNA (miRNA) mediated epigenetic inheritance. Using a previously established mouse model, we explored how preconception paternal alcohol exposure alters sperm-inherited small RNA population and its downstream consequences on placental structure and function. Our findings demonstrate that chronic paternal EtOH consumption induces significant changes in sperm small RNA populations, particularly miRNAs known to regulate early embryonic development. These alterations correlate with disruptions in fetal growth and placental histology, suggesting an intergenerational transmission of stress-induced epigenetic modifications. Furthermore, we identified sex-specific differences in fetoplacental development, where male offspring exhibited pronounced placental inefficiencies and metabolic disruptions. A key aspect of this research involves the role of nuclear factor erythroid 2-related factor 2 (NRF2), a critical regulator of oxidative stress. We show that paternal NRF2 loss-of-function phenocopies the effects of chronic alcohol exposure, reinforcing the hypothesis that oxidative stress-induced epigenetic alterations mediate the observed developmental outcomes. Placental mitochondrial function, a vital determinant of fetal energy supply, was also significantly impaired in alcohol-exposed offspring. Notably, these defects persisted into adulthood, implicating long-term metabolic consequences. To assess the genetic and epigenetic basis of these outcomes, we conducted proteomic and transcriptomic analyses, revealing dysregulated pathways involved in mitochondrial bioenergetics, redox balance, and cellular metabolism. Our results highlight that paternal alcohol exposure not only disrupts placental architecture but also modifies the epigenetic landscape of the developing embryo, leading to systemic physiological alterations. These findings underscore the importance of considering paternal contributions to reproductive health and fetal development. By elucidating the mechanisms underlying alcohol-induced epigenetic inheritance, this research provides novel insights into the role of paternal environmental exposures in shaping offspring health trajectories. Ultimately, this work advocates for broader perspectives on preconception health, emphasizing the need for preventive strategies to mitigate paternal influences on developmental disorders.

overall_design: Sperm Small RNA, Controls, alcohol exposed, Nrf2 KO and Nrf2 liver KO. Various comparisons made

first: Sanat

last: Bhadsavle

first: Michael

last: Golding


title: Both enzymatic and non-enzymatic functions of BCAT1 confer malignant properties in human chondrosarcoma

city: Fukuoka

first: Eijiro

last: Shimada

state: Fukuoka

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

department: Orthopaedic Surgery

country: Japan

institute: Kyushu University

summary: Human chondrosarcoma is a malignant bone tumor with a poor prognosis due to its resistance to conventional therapies. In this study, we investigated the role of Branched-Chain Amino Acid Transaminase 1 (BCAT1) in chondrosarcoma pathogenesis.

overall_design: RNA profiling for human chondrosarcoma.

first: Yoshiki

last: Yamamoto

first: Makoto

last: Nakagawa

first: John

last: Glushka

first: Ayaka

last: Maeno

last: Tsunoda

first: Fumihiko

last: Nakatani

first: Kazuya

last: Ichihara

first: Akinobu

last: Matsumoto

first: Arthur

last: Edison

first: Hironori

last: Kaji

first: Junya

last: Toguchida

first: Benjamin

middle: A

last: Alman

first: Takahiro

last: Ito

first: Ayuna

last: Hattori


title: Unraveling Single-Cell Regulatory Networks in iPSC-Derived Neurons from Veterans with Gulf War Illness

first: James

last: Cai

state: TX

address: 4458 TAMU

department: Veterinary Intergrative Biosciences

summary: Gulf War Illness (GWI) is a complex condition affecting Veterans, and its underlying neuropathological mechanisms remain unclear. Patient-derived induced pluripotent stem cells (iPSCs) offer a platform to model the disease in vitro. Objective: To map transcriptomic landscapes and infer single-cell gene regulatory networks (scGRNs) in iPSC-derived neurons from symptomatic and non-symptomatic Gulf War Veterans to identify genes and pathways implicated in GWI pathophysiology and predisposition. Design, Setting, and Participants: This study utilized iPSCs generated from symptomatic GWI Veterans and non-symptomatic GWI Veteran controls. Neurons were differentiated from these iPSCs for analysis. Main Outcomes and Measures: Single-cell RNA sequencing (scRNAseq) was used to generate transcriptomic data. Machine learning algorithms were applied to infer and compare scGRNs between the symptomatic and non-symptomatic groups, identifying key regulatory differences. Results: Analysis of scRNAseq data revealed significant differences in gene expression profiles between neurons derived from symptomatic and non-symptomatic Veterans. scGRN inference identified distinct regulatory modules associated with GWI symptom status. Key transcription factors driving these differences were identified, along with target genes involved in neuroinflammatory responses, synaptic signaling, and stress response pathways. These findings point towards specific molecular dysregulations contributing to GWI neuropathology. Conclusions and Relevance: This study demonstrates the utility of iPSC-derived neurons coupled with single-cell transcriptomics and computational network inference for investigating GWI. The identified differences in scGRNs provide novel insights into the molecular underpinnings of the illness and highlight potential targets for future diagnostic and therapeutic strategies.

overall_design: RNA-seq profiling of forebrain organoids derived from veterans, both with and without Gulf War Illness, who were actively deployed during the first Gulf War. Both cells line derived organoids (case and control) were either treated with the toxicant regiment (hydrocortisone and diisopropyl fluorophosphate (DFP)) or the vehicle control (10% ethanol in ddH2O and isopropanol). Organoids were treated at 2.5 months and were fixed and collected for RNA-seq around 3 months of age.

first: Shreyan

last: Gupta

first: Kendra

last: Case

middle: J


title: EIF5A couples translational control with transcriptional reprogramming through chromocenter reorganization during spermiogenesis [ATAC-Seq]

city: Jinan

first: Yuling

address: Qianfoshan Street

department: CCenter of reproductive medicine

institute: Shandong University

summary: Translation initiation factor eIF5A facilitates protein synthesis and impacts diverse biological processes, yet its role in transcriptional regulation is poorly understood. Here we find eIF5A highly expressed in diverse spermatogenic cell types. Conditional knockout of Eif5a (SKO) causes complete infertility in male mice due to round spermatid arrest. Interestingly, eIF5A deletion severely compromises chromocenter integrity in round spermatids. Proteomic profiling reveals widespread dysregulation in eIF5A-deficient round spermatids, downregulated proteins are enriched for chromatin-associated functions, likely contributing to chromocenter dysfunction. Notably, ATAC-seq analysis shows increased chromatin accessibility upon eIF5A depletion, accompanied by transcriptional dysregulation of genes critical for acrosome and manchette formation. Our data underscore that eIF5A not only regulates the translation of chromatin-organizing proteins required for chromocenter stability but also influences transcriptional regulation by modulating chromatin landscape. These findings illuminate a novel, germ cell-specific pathway coupling translational control and transcriptional regulation via chromatin reorganization.

overall_design: Round spermatids were sorted by FCAS from three mice in each of the control and SKO groups. ATAC-seq was performed following the manufacturer's instructions (Vazyme, TD711). The library preparations were sequenced on an Illumina HiSeq platform and 150 bp paired-end reads were generated.


title: EIF5A couples translational control with transcriptional reprogramming through chromocenter reorganization during spermiogenesis [Ribo-Seq]


title: Temporal mapping of the anti-tumor effects of nanobody-based MSLN.CAR-T cell therapy in metastatic solid tumors [total RNA-Seq]

city: Bethesda

first: Mingming

last: Zhao

address: 9000 Rockville Pike

institute: national institutes of health

summary: Studies on the dynamic changes occurring in the tumor microenvironment (TME) following CAR-T cell therapy have been confounded by host lymphodepletion, multiple dosing and immunodeficient models. Here, a nanobody-based, mouse mesothelin-targeting CAR-T cell (A101) was developed, achieving effective primary tumor suppression, metastasis reduction, and improved survival after a single dose in immunocompetent, syngeneic mouse models without lymphodepletion. Temporal tumor profiling using RNA sequencing revealed initial downregulation of cell proliferation genes followed by upregulation of inflammation, epithelial-to-mesenchymal-transition (EMT) and extracellular matrix (ECM) modification genes in the CAR-T-treated tumors relative to mock-T-treated controls. This phenotype was reversed at a later timepoint which coincided with downregulation of immunosuppressive Cd274+ Lcn2+ neutrophils and upregulation of anti-tumor P2rx1+ Nrf2- neutrophils. At the same time, upregulation of Ccl2+ in fibroblasts and a more immunomodulatory macrophage phenotype was observed in CAR-T-treated tumors, indicating a tumor adaptation mechanism. This study demonstrates complex dynamic changes in the TME, and highlights time-dependent responses of solid tumors to CAR-T cell therapy. It further highlights Lcn2+ neutrophils and Ccl2+ fibroblasts as potential therapeutic targets for improving CAR-T cell anti-tumor efficacy for solid tumors.

overall_design: For totalRNA-seq, 344SQ tumors from saline-treated mice were harvested on day 0 post-treatment. 344SQ tumors from CAR-T- or mock-T-treated mice were harvested on day 2, 7 and 12 post-treatment. Tumors from 4-5 different mice were harvested per treatment group. Tumor tissue was stored in RNAlater Stabilization Solution (Invitrogen), homogenized and RNA was isolated using RNAeasy kit (Qiagen) according to the manufacturer’s instructions.

first: Chaido

last: Stathopoulou

first: Qun

last: Jiang

first: Jessica

last: Hong

first: Jing

last: Bian

first: Jingli

last: Zhang

first: Mitchell

last: Ho

first: Raffit

last: Hassan


title: EIF5A couples translational control with transcriptional reprogramming through chromocenter reorganization during spermiogenesis [RNA-Seq]

overall_design: We performed Smart-seq2 on FACS-isolated round spermatids from control and SKO mice at postnatal day 28 (primarily step 8 stage).For Smart-seq2, cell lysis, mRNA reverse transcription, and cDNA amplification were performed using the Discover-sc WTA Kit V2 (Vazyme, N711). Following this, cDNA fragmentation and adapter ligation were carried out with the TruePrep Flexible DNA Library Prep Kit for Illumina (Vazyme, TD504). All procedures were conducted in strict accordance with the manufacturer's protocols. The Smart-seq2 library sequencing was performed by Novogene on Illumina platforms, generating 150 bp paired-end reads.


title: Structural Basis of DNA-Dependent Coactivator Recruitment by the Tuft Cell Master Regulator POU2F3 [DMS_Screen]

city: Cold Spring Harbor

first: Damianos

last: Skopelitis

address: One Bungtown Rd

department: Cancer Biology

institute: Cold Spring Harbor Laboratory

summary: The transcription factor POU2F3 defines the identity of tuft cells and underlies a distinct molecular subtype of small cell lung cancer (SCLC). Although POU2F3 is considered undruggable, its activity critically depends on the coactivators OCA-T1 and OCA-T2. Here, we demonstrate that acute suppression of either POU2F3 or OCA-T1 induces regression of tuft cell-like SCLC xenografts in vivo. To explore the structural basis and druggability of this dependency, we solved crystal structures of POU2F3 bound to OCA-T1 or OCA-T2 in complex with DNA, revealing a tripartite, DNA-dependent interface. We further employed deep mutational scanning to systematically assess the functional impact of 4,218 missense variants in POU2F3 and OCA-T1, uncovering both mutation-sensitive hotspots and structurally constrained regions critical for tumor cell fitness. These findings define a unique transcriptional complex that integrates DNA recognition with coactivator recruitment and nominate POU2F3–OCA-T as a structurally tractable vulnerability in tuft cell-like carcinomas.

overall_design: Deep Mutational Scanning (DMS) of CRISPR-resistant OCA-T1 and POU2F3 cDNA libraries  co-expressing sgRNAs targeting the endogenous OCA-T1(sgOCA-T1) or POU2F3(sgPOU2F3) genes respectively. NCI-H211 Cas9+ cells were transduced with lentiviral DMS libraries at low MOI and cultured for 10 population doublings.

first: Aktan

last: Alpsoy

first: Jonathan

last: Ipsaro

first: Sujay

last: Pal

first: Frank

last: Chung

first: Shannon

last: Carpenter

first: John

last: Desmarais

first: Xiaoli

last: Wu

first: Kenneth

last: Chang

first: Matthew

middle: T

last: DiMare

first: Erin

last: Harten

first: Staci

last: Bergman

first: Justin

middle: B

last: Kinney

first: Jeffrey

last: Engelman

first: Hyo-Eun

middle: C

last: Bhang

first: Leemor

last: Joshua-Tor

first: Christopher

last: Vakoc


title: A novel Asrij-mNeonGreen reoprter mouse to investigate functional heterogeneity in hematopoietic stem cells

city: Bengaluru

first: Maneesha

last: Inamdar

state: Karnataka

address: JNCASR, Jakkur

department: MBGU

country: India

institute: JNCASR

summary: Hematopoietic stem cells (HSCs) within the bone marrow (BM) display significant molecular and functional heterogeneity. Deciphering intrinsic factors that govern HSC diversity is key to enriching specific HSC subtypes for predictable and clinically relevant differentiation outcomes. Here, we show that the mitochondrial protein Asrij/OCIAD1, a conserved regulator of hematopoietic homeostasis, contributes to HSC heterogeneity. Asrij depletion is known to cause loss of quiescence, myeloid bias and aging-like changes in mouse BM HSCs. Interestingly, Asrij expression is inherently heterogeneous and enriched in only 47% of the HSC population. To investigate whether Asrij expression levels influence HSC fate, we generated a novel Asrij-mNeonGreen knock-in reporter mouse using CRISPR-Cas9 technology. We show that the Asrij reporter faithfully recapitulates its heterogeneous expression in the BM HSCs, allowing isolation of cells based on Asrij expression levels. Ex-vivo culture of HSCs demonstrated that Asrijlow HSCs exhibit enhanced self-renewal capacity, whereas Asrijhigh HSCs are primed for differentiation. Transplantation assays further revealed that Asrijlow HSCs have enhanced reconstitution in the BM hematopoietic stem and progenitor cell (HSPC) and myeloid cell compartments. Transcriptomic analysis uncovered signatures of quiescence in Asrijlow HSCs, while Asrijhigh HSCs exhibit hallmarks of HSC activation. In summary, we show that Asrij levels impact the quiescence, self-renewal, and differentiation potential of HSCs, thereby contributing to the functional diversity of the HSC pool. Thus, the Asrij-mNeonGreen reporter mouse provides a powerful and versatile model for investigating the molecular underpinnings of functional diversity within the HSC compartment.

overall_design: Bulk RNA sequencing analysis of bone marrow long term (LT) hematopoietic stem cells expressing low and high levels of Asrij. Experiment was performed using 4 month old mice.

first: Aishwarya

last: Prakash

first: Souvik

last: Halder


title: Hepatocyte nuclear factor 4β protect zebrafish from dexamethasone-induced hepatobiliary syndrome and hepatobiliary syndrome complicated with GCRV-II infection by targeting Hsp70 and inhibiting autophagy

first: siyao

last: Zheng

address: No.7, Donghu South Road, Wuchang

institute: Institute of Hydrobiology, Chinese Academy of Sciences

summary: Hepatocyte nuclear factor 4β (Hnf4β), a nuclear receptor superfamily member, acts as a key regulator of functional gene expression and various cellular processes. The function of Hnf4β in metabolic diseases or infectious diseases had not yet defined in teleost. Here, we show that zebrafish Hnf4β plays a protective role in the host defense against dexamethasone (DEX)-induced hepatobiliary syndrome and hepatobiliary syndrome complicated with GCRV-II infection. Zebrafish Hnf4β deficiency have hepatomegaly, lipid deposition, impairs larvae survival and regulates the expression levels of many genes involved in oxidative phosphorylation and spliceosome during DEX treatment plus GCRV-II infection. In addition, Hnf4β gene disruption in zebrafish leads to induction of oxidative stress with the increased susceptibility to dexamethasone-induced hepatobiliary syndrome complicated with GCRV-II infection. Furthermore, we show that zebrafish Hsp70 promote the translocation of Hnf4β from the nucleus to the cytoplasm and interact with Hnf4β in the cytoplasm and nucleus at DEX + GCRV situation. Mechanistically, zebrafish Hnf4β mediates the beneficial effect for larvae survival and lipid metabolism in the case of DEX treatment plus GCRV-II infection is depending on the Hsp70-mediated autophagy. Collectively, our results identify that the mechanisms of zebrafish Hnf4β through targeting Hsp70 against dexamethasone-induced hepatobiliary syndrome complicated with GCRV-II infection.

overall_design:
At 4 dpf, the hatched larvae from WT and hnf4β-/- were either treated with 10 μM DEX or left untreated, or followed by either infection with 500 μL of 3.62 × 10^7 copies/mL GCRV-II. Forty larvae in triplicate per treatment at 48 hpi were collected for Illumina deep sequencing by Biomarker Technologies Ltd. Total RNA, mRNA, and cDNA libraries and were prepared following the same methods as our previous studies. The number of differentially expressed genes (DEGs) between two different samples was calculated according to the fragments per kilobase of exon per million mapped reads method. The DEGs in each group were identified via DESeq2, which was based on a fold change ≥ 1.5 and a false discovery rate < 0.05. Functional enrichment analysis, including Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses, was performed according to previously published methods.
Please note that WT data is available in GSE275683.

first: Mingxian

first: Siyao


title: Mn-MOF–Driven Enhanced Activation and Delivery of Pistol Ribozyme: A Strategy for Checkpoint Silencing and Cancer Immunotherapy

city: Tianjin

first: Yijin

last: Liu

address: Haihe Education Park, 38 Tongyan Road, Tianjin 300071, China

institute: Nankai University

summary: Checkpoint blockade targeting PD-L1 has transformed cancer immunotherapy but remains constrained by systemic immune-related toxicity and limited efficacy in poorly infiltrated tumors. Here, we report a manganese-enhanced ribozyme nanoplatform (PS473@NKMOF-101-[Mn]) that enables precise PD-L1 gene silencing and innate immune activation. PS473 is a rationally engineered variant of the natural Pistol ribozyme that exhibits high catalytic efficiency at GU-rich motifs, which is further potentiated by the use of Mn²⁺ as a cofactor. To overcome extracellular instability and ensure intracellular delivery, PS473 was encapsulated within a pH-responsive, Mn-doped metal–organic framework (NKMOF-101-[Mn]), which confers ribozyme protection and sustained Mn²⁺ release in the acidic tumor microenvironment. In vitro, PS473@NKMOF-101-[Mn] suppressed PD-L1 expression and macrophage activation. In vivo, the nanoplatform achieved over 90% tumor inhibition in a B16F10 melanoma model and enhanced CD8⁺ T-cell infiltration without systemic toxicity. Transcriptomic profiling further revealed the upregulation of type I interferon signaling and cGAS–STING pathway activation, indicating a synergistic mechanism combining gene knockdown and immunostimulation. This work presents a catalytically robust and immunologically active ribozyme-based nanotherapeutic, offering a promising strategy for targeted gene silencing and tumor immune reprogramming.

overall_design: Tumor tissues were obtained at 48 h after the last intratumoral injection dministration, and RNA-seq analysis was performed on the tumor tissues of the blank control roup and multiple treatment groups (FreePS473, PS473@CPs, NKMOF-101-[Mn], M5@NKMOF-101-[Mn], PS473@NKMOF-101-[Mn]).

first: Ming

last: Zhao


title: Structural Basis of DNA-Dependent Coactivator Recruitment by the Tuft Cell Master Regulator POU2F3 [RNA-seq]

first: Damianos

last: Skopelitis

overall_design: RNA-seq of stably expressed CRISPR-resistant cDNAs for POU2F3 (WT or L191A mutant) and an empty control, 5 days after infection with an sgRNA targeting endogenous POU2F3 (sgPOU2F3) or a negative control (sgROSA), in NCI-H211 Cas9+ cells.

first: Aktan

last: Alpsoy

first: Jonathan

last: Ipsaro

first: Sujay

last: Pal

first: Frank

last: Chung

first: Shannon

last: Carpenter

first: John

last: Desmarais

first: Xiaoli

first: Kenneth


title: Evolutionary adaptations to the hormonal regulation of vascular tissue development

city: ghent

first: Wei

last: Xiao

address: Technologiepark-Zwijnaarde 71 - 9052 Ghent - Belgium

country: Belgium

institute: VIB-UGent Center for Plant Systems Biology

summary: Vascular tissues connect shoot and root organs in the vascular plant lineage, providing significant adaptive advantages. Although the crosstalk between auxin and cytokinin in promoting both vascular cell proliferation and differentiation has been well studied in angiosperms such as Arabidopsis thaliana, little is known about this regulation in other vascular plant lineages. Here, we found that unlike the hormonal cross talk found in all other species under study, the lycophyte Selaginella moellendorffii shows clear task separation with auxin driving vascular cell proliferation only, and cytokinin specifically triggering cell differentiation. Using a cross-species transcriptomics approach, we found members of the AUXINs/INDOLE-ACETIC ACIDs (Auxs/IAAs) and CYTOKININ OXIDASEs (CKXs) gene families exhibited divergent expression patterns in response to auxin and cytokinin. Despite these regulatory differences, we show that AtIAA/SmIAA and AtCKX/SmCKX proteins are functionally conserved. Taken together, our findings suggest an evolutionary adaptation to the hormonal regulation of vascular tissue development in which core protein functions are conserved, but regulatory circuits diverged in Lycophytes.

sample_organism:
Arabidopsis thaliana
Selaginella moellendorffii

overall_design: For Arabidopsis thaliana, the plants (Col-0) were grown on 1/2 Ms plates for 4 days and transferred to mock, 10μM NAA or 10μM BAP for 2h. Next, the 0,2 cm root tips were harvested for RNA-seq. For Selaginella moellendorffii, the experimental setup 1: the plants (WT) were grown on 1/2 Ms plates for 14 days and transferred to mock, 10μM NAA or 10μM BAP for 2h. Next, the 0.2 cm root tips were harvested for RNA-seq. The experimental setup 2:  the plants (WT) were grown on 1/2 Ms plates for 14 days and transferred to 1μM NAA or Mock (directly harvest after the treatment) for 7d. Next, the plants were transferred to Mock for 0h, 3h, 6h, 12h, and 24h. The plants were harvest 0.2 cm root tips for RNA-seq in each indipendent time point.

first: Bert

last: De Rybel


title: Effect of the anitibiotic JNJ8464 on the transcriptome of Mycobacterium avium strain MAC101

city: Leiden

first: Herman

middle: Pieter

last: Spaink

address: Einsteinweg 55

department: Institute of Biology

country: Netherlands

institute: Leiden University

summary: The antibiotic JNJ8464-derivative 80998879 was added to the growth medium of cultures of M.avium strain MAC101 and RNA was islated after 1.5 hours of incubation. RNAseq was performed with Illumina sequencing. With a FDR rate threshold of 0.05 a number of 12 genes were identified that were upregulated and 1 gene was down regulated.

overall_design: Cells were grown in the presence (n=2) or absence (n=4) of the antibiotic JNJ8464 for 1.5 hours. Subsequently RNA was isolated and cDNA after depletion of rRNA was sequenced paired-end using Illumina technology.

middle: P


title: Structural Basis of DNA-Dependent Coactivator Recruitment by the Tuft Cell Master Regulator POU2F3 [CUT&Run]

overall_design: CUT&RUN-seq of stably expressed FLAG-tagged POU2F3 (WT or L191A mutant) and IgG isotype control in the NCI-H211 cell line.

last: Wu

last: Chang

first: Matthew

last: DiMare

first: Erin

last: Harten

first: Staci

last: Bergman

first: Justin

last: Kinney

first: Jeffrey

last: Engelman

first: Hyo-Eun

last: Bhang

first: Leemor

last: Joshua-Tor

first: Christopher

last: Vakoc


title: Temporal mapping of the anti-tumor effects of nanobody-based MSLN.CAR-T cell therapy in metastatic solid tumors [scRNA-Seq]

first: Mingming

last: Zhao

overall_design: For single cell RNA-FLEX sequencing: 344SQ tumors from CAR-T-, mock-T- and saline-treated 129S2/SvPasCrl mice were harvested on day 12 post-treatment. 3 mice were harvested per treatment group. CD45- and CD45+ cells were column sorted and fixed. Samples were 4x4 multiplexed and the pools were then loaded in 8 capture lanes. Biological replicates of CD45- or CD45+ samples were pooled together post-sequencing and analyzed.

first: Chaido

last: Stathopoulou

first: Qun

last: Jiang

first: Jessica

last: Hong

first: Jing

last: Bian

first: Jingli

last: Zhang

first: Mitchell

last: Ho

first: Raffit

last: Hassan


title: Dissecting transcriptional heterogeneity in sinonasal adenocarcinoma by single-cell RNA sequencing

city: Shenzhen

first: Zhewei

last: Lin

address: No. 33 Zhongyuan Road, Buji Subdistrict, Longgang District, Shenzhen City, Guangdong Province; Luohe Hospital Group Medical Center

institute: Medical Laboratory of the third affiliated hospital of Shenzhen university

summary: We have employed a single-cell RNA sequencing (scRNA-seq) approach using 10x Genomics scRNAseq to profile from 3 sinonasal adenocarcinoma (SNAC) tumors. It constructed a comprehensive single-cell transcriptional atlas, revealing profound cellular and molecular heterogeneity within the SNAC microenvironment.

overall_design: Three patients with recurrent sinonasal adenocarcinoma, each collected a primary tumor tissue sample through surgical resection or endoscopic biopsy, analyzed using scRNA-seq.

first: Dayang

last: Chen

first: Ru

first: Xiaowen

last: Dou

first: Wei

last: Wu

first: Haiyan

last: Yang

first: Jian

last: Li

first: Dan

last: Xiong


title: Single-cell RNA-seq of isolated non-parenchymal cells from imiquimod-induced psoriasis mouse model.

city: Mannheim

first: Volker

last: Ast

address: Theodor-Kutzer-Ufer 1-3

department: NGS Core Facility

country: Germany

institute: University Hospital Mannheim

summary: We applied 10x Genomics single-cell RNA sequencing to profile non-parenchymal liver cells (NPCs) in a psoriasis-like mouse model. The study focuses on immune and liver sinusoidal endothelial cell (LSEC) alterations along the skin–liver axis to elucidate mechanisms driving comorbid liver disease in psoriasis. Given that 30–50% of psoriasis patients develop liver involvement, this approach aims to identify maladaptive cellular crosstalk and potential therapeutic targets.

overall_design: 10 weeks old female C57BL/6J wild-type mice received topical imiquimod (5%, Aldara) on the shaved upper back for five consecutive days to induce psoriasis-like skin inflammation. Control mice were treated under the same conditions using petroleum jelly/Vaseline®.

first: Noor

last: Christiaens

first: Sina

middle: W

last: Kürschner-Zacharias

first: Manuel

last: Winkler


title: Supplemental deinoxanthin protects mice from irradiation-mediated systemic impairments by recovering hematopoietic and degenerative complications

city: Jeonbuk

first: JungChae

last: Lee

address: 567, Baekje-daero, Deokjin-gu, Jeonju-si, Jeollabuk-do, Republic of Korea

institute: Jeonbuk National University

summary: Total body irradiation (TBI) is used as curative therapy for cancer patients and in bone marrow (BM) transplantation. However, TBI impairs organs and BM and dysregulates the fates of BM-residing hematopoietic stem cells (HSCs) and mesenchymal stem cells (MSCs). Studies have suggested that TBI-mediated systemic injuries might be improved by preventing the overproduction of reactive oxygen species (ROS) and inflammatory mediators. In this work, we investigated whether Deinococcus radiodurans-derived deinoxanthin (DEIX) protects mice from sub-lethal TBI (5 Gy)-mediated complications and elucidated the associated mechanisms. Long-term oral supplementation with DEIX (25 mg/kg body weight, once per day for 42 consecutive days) protected mice against TBI-mediated decreases in organ and body weights, lifespan, and bone mass accrual. Supplemental DEIX inhibited TBI-mediated structural damage in the liver, kidney, and spleen and restored endogenous antioxidant defense systems in the liver and BM of TBI-exposed mice. Supplemental DEIX also suppressed BM impairment and the induction of senescence in BM-conserved HSCs and MSCs in TBI-exposed mice. That suppression involved the DEIX-induced restoration of TBI-stimulated disorder in osteogenic, osteoclastogenic, and adipogenic activation in BM. Additionally, supplemental DEIX recovered TBI-mediated defects in hematopoietic development and the multipotent functions of BM-derived cells. Moreover, the direct addition of DEIX in vitro diminished ROS accumulation and osteoclast formation and stimulated the proliferation and mineralization of BM-derived cells. Collectively, this study introduces the protective role of DEIX in TBI-mediated systemic defects and supports its clinical usefulness for patients who require TBI.

overall_design: RNA seq profiling of whole BM cells that were isolated 14 days post-total body irradiation (TBI) from four groups: 1) non-TBI mice (control group; 1-I, 1-II, 1-III), 2) TBI-exposed mice who received oral gavage of 100 μL of olive oil (vehicle) (TBI group; 2-I, 2-II, 2-III ), 3) TBI-exposed mice who were orally treated with DEIX (TBI+DEIX group; 3-I, 3-II, 3-III), and 4) the mice received DEIX only (DEIX group; 4-I, 4-II, 4-III). Here, the mice received DEIX (25 mg/kg body weight) once per day for 14 consecutive days after 5 Gy TBI with γ-rays by regulating the dosage time (0.66 Gy/min) using the radioactive half-life of γ-rays on a rotating platform (Model IR-221, MDS Nordion, Ottawa, Canada).

first: Jung-Chae


title: Antiandrogen treatment induces mitochondrial oxidative phosphorylation to promote castration resistance in prostate cancer [LNCaP]

city: Shanghai

first: Zehua

last: Ma

address: Pujian road 160

institute: Shanghai Jiaotong university

summary: Tumor recurrence and therapy resistance are generally accompanied by alterations in cellular metabolism. However, the mechanism by which metabolic conversion occurs and contributes to castration-resistant prostate cancer (CRPC) remains unclear. Here, we demonstrate that androgen receptor signaling inhibitors (ARSI)-induced mitochondrial oxidative phosphorylation (OXPHOS) is critical for CRPC development. Our findings indicate that prostate cancer cells exhibit increased mitochondrial OXPHOS following ARSI treatment; however, there is no significant change in glycolytic activity. Importantly, this metabolic conversion relies on increased glucose and glutamine utilization. Mechanistically, ARSI treatment induces oxidative stress, resulting in AMPK/PGC-1α-dependent metabolic conversion. High mitochondrial OXPHOS in turn renders prostate cancer cells resistant to ARSI. Pharmacological inhibition of mitochondrial OXPHOS shows promising treatment efficacy for CRPC and synergizes with ARSI to inhibit CRPC growth. Collectively, we demonstrate the metabolic plasticity of prostate cancer cells following ARSI treatment, identifying mitochondrial OXPHOS as a metabolic target for CRPC treatment.

overall_design: RNA-seq profiling of LNCaP cells and LNCaP-ENZR cells.

first: Kai

first: Chenggong

last: Luo

first: Heng

first: Tengda

last: Wang

first: Yong

last: Ban

first: Xuan

last: Liu

first: Lingyue

last: An

first: Guangheng


title: Uncovering glioblastoma origin cells: Isolation and characterization from the subventricular zone

city: Seoul

first: Kibyeong

last: Kim

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

institute: Yonsei University

summary: Glioblastoma (GBM), which has a poor prognosis despite aggressive treatments, likely originates from specific cells that acquire somatic mutations within the subventricular zone (SVZ), distant from the primary tumor site. However, the properties of GBM origin cells (OCs) residing in the SVZ remain largely unknown. In this study, we isolated and characterized GBM-OCs from the SVZ using a mouse model. Exome analyses of the mouse models revealed significant copy number alterations as GBM-OCs progressed to tumors in the model. RNA analysis of human SVZ samples from GBM patients identified chromosomal alterations (7 gain/10 loss), similar to those observed in early human GBM development. These alterations were predominantly found in neural stem cell-like (NSC-like), astrocyte-like (AC-like), and oligodendrocyte precursor cell-like (OPC-like) populations. This study identifies GBM-OCs in the SVZ of mice and humans, highlighting their distinct features, and suggests that these cells could serve as target cells for future GBM treatments.

overall_design: A total of 211 samples were obtained from 103 patients were collected, including 140 GBM tissue samples, 42 SVZ and 21 brain cortex samples from GBM patients, and 8 SVZ tissue samples from non-GBM patients. The samples underwent RNA sequencing to evaluate gene expression profiles and possible gene copy alterations of each GBM tissue.

first: Hyeong-Cheol

last: Oh

first: Ran Joo

last: Choi

first: Se-Young

last: Jo

first: Eunchae

last: Yeo

first: Jin-Kyong

last: Shim

first: Seo Jin

first: Hyejoung

last: Cho

first: Hyun Jung

first: Joo Ho

first: Seon-Jin

last: Yoon

first: Ryong Nam

first: Jeongsoo

last: Won

first: Jiho

last: Park

first: Seunghyun

last: Kang

first: Jihwan

last: Yoo

first: Ju-Hyung

last: Moon

first: Tae Hoon

last: Roh

first: Eui-Hyun

first: Se Hoon

first: Jong Hee

last: Chang

first: Albert H.

first: Hyun Seok

first: Jeong Ho

first: Hoon

first: Sangwoo

first: Seok-Gu


title: Epigenitic regular on effect of Hpb-colonized and -trained mice on peritoneal macrophage

city: xiamen

first: Qingxiang

last: Gao

address: Xiang'an south way

institute: Xiamen University

summary: Enteric helminth infections shape host immunity to other pathogens. However, it remains uncertain whether helminth infections following deworming treatment could induce long-term alterations in the host immune system. Here, we demonstrate that infection with Hpb, even after anthelmintic-mediated clearance, induces trained immunity to confer long-lasting cross-protection against lethal S. aureus challenge. This protective effect is associated with the prolonged expansion and functional reprogramming of peritoneal macrophages. Mechanistically, we identify the IL-4/IL-4Rα signaling axis, driven by Hpb-induced Th2 skewing, is essential for both peritoneal macrophage accumulation and Cybb-dependent reactive oxygen species (ROS) enrichment. Notably, Th2 cells, rather than eosinophils or basophils, serve as the predominant source of IL-4 and persist in the peritoneal cavity for at least three weeks post Hpb clearance. Collectively, these findings uncover a novel helminth-mediated trained immunity that promotes host resistance to systemic bacterial infection through Th2-dependent reprogramming of peripheral peritoneal macrophage.

overall_design: ATAC-seq profiling of peritoneal macrophages harvested from Hpb-colonized (11 days) and trained (dewormed and rested for 3 weeks) mice and its corresponding controls

first: Shih-Chin

last: Cheng

first: Jia

last: Zhang


title: CB2R downregulation drives trastuzumab resistance by reorganizing HER2 dimers to evade IFN-γ and enhance EGFR signaling

city: Madrid

first: Eduardo

last: Pérez-Gómez

state: Madrid

address: José Antonio Novais 12

department: Biochemistry and Molecular Biologý

country: Spain

institute: Universidad Complutense de Madrid)

summary: Despite the remarkable advances that have been implemented in HER2+ breast cancer treatment, especially upon the development of monoclonal antibodies like trastuzumab, resistance to HER2-targeted therapies remains a significant clinical challenge. Here, we investigated the role of the endocannabinoid system, specifically the cannabinoid CB2 receptor (CB2R), in trastuzumab resistance mechanisms. Analysis of human breast cancer samples revealed that a decreased expression of HER2-CB2R heterodimers following neoadjuvant treatment, primarily due to CB2R downregulation, is linked to poor long-term patient outcomes. Using various cellular and animal models, we demonstrate that trastuzumab resistance is dependent on CB2R expression, as it occurs upon CB2R downregulation and is rescued by CB2R re-expression. Mechanistically, CB2R loss enables cancer cells to evade antitumor IFN-γ signaling while promoting a shift from HER2-CB2R to HER2-EGFR heterodimers, thus reducing dependence on HER2 signaling and increasing reliance on EGFR-mediated pathways. Moreover, EGFR inhibition resensitized resistant cells to trastuzumab. In sum, our findings (a) identify a novel mechanism of trastuzumab resistance involving CB2R-mediated receptor heterodimerization and IFN-γ signaling modulation, (b) establish HER2-CB2R/EGFR heterodimer status and CB2R/EGFR expression as potential predictive biomarkers, and (c) support dual HER2/EGFR targeting as a promising strategy to overcome trastuzumab resistance in patients with HER2+ breast cancer.

overall_design: mRNA profile of the four BT474-derived cell lines (SCR, CB2 KO, trastuzumab sensible and trastuzumab resistance)

first: Marta

last: Seijo-Vila


title: Persistent cortical excitatory neuron dysregulation in adult Chd8 haploinsufficient mice [snRNA-Seq]

city: Davis

first: Stephanie

last: Lozano

address: 1544 Newton Ct

institute: University of California, Davis

summary: CHD8 mutations cause autism spectrum disorder, cognitive deficits, and macrocephaly. Chd8+/- mouse models exhibit macrocephaly and transcriptional pathology, with inconsistent findings regarding neurogenesis, neuron function, and behavior. Via stereology and single nuclei transcriptomics (snRNA-seq), we found increased Chd8+/- cortical volume was not explained by increase in neuron number. Differential expression (DE) was present across cortical cell types, with excitatory neurons exhibiting high DE burden and shared and subclass-specific DE signatures. Bulk RNA-seq DE of constitutive Chd8+/- and conditional Camk2a-Cre Chd8+/- mice identified shared transcriptional pathology. DE in synaptosomal versus nuclear mRNA identified overlapping DEGs, but also significant differences and exaggerated synaptosomal changes. Building on DE findings implicating glutamatergic neurons, we found Chd8+/- mice exhibited altered excitatory neuron spine density and dynamics, decreased GCaMP activity correlation, and sleep perturbation. Thus, Chd8 haploinsufficiency causes lasting excitatory neuron dysfunction, perturbs RNA regulation beyond transcription, and impacts neuronal properties, cortical microcircuits, and behavior.

overall_design: We profiled RNA expression of cortical dissections from adult wild-type and germline heterozygous Chd8 mutant mice. Single-nucleus RNA-sequencing (snRNA-seq) was performed on isolated cortical nuclei. Bulk RNA-sequencing was performed on whole cortical tissue from constitutive and conditional Chd8 mutant mice. Additional bulk RNA-sequencing was conducted on nuclear and synaptic fractions isolated from adult cortex to investigate compartment-specific expression changes.

first: Cesar

last: Canales

first: Nicholas

last: Frost

first: Karol

last: Cichewicz

first: Wellington

last: Amaral

first: Nicolas

last: Seban

first: Ethan

last: Fenton

first: Ayanna

last: Wade

first: Nickolas

last: Chu

first: Emily

last: Smith

first: Cory

last: Ardekani

first: Samuel

last: Frank

first: Jeffrey

last: Bennett

first: Pierre

last: Lavenex

first: Aspen

last: Kopley-Smith

first: Darlene

last: Rahbarian

first: Melissa

last: Corea

first: Daniela

last: Perla

first: Liam

last: Davis

first: Jiyuan

last: Zhu

first: Rebecca

last: Ortiz

first: Paris

last: Beauregard

first: Caitlin

last: Moyer

first: Jacob

last: Baker

first: Jingqi

last: Sun

first: Boxuan

last: Ma

first: Ju

last: Lu

first: Vikaas

last: Sohal

first: David

middle: G

first: Yi

last: Zuo

first: Alex

last: Nord


title: Anti-apoptotic and anti-oxidative effects of DDX24 through HO-1 transcriptional regulation

city: Taoyuan

first: Ming-Chih

last: Lai

address: No. 259, Wenhua 1st Road, Guishan District, Taoyuan City 333, Taiwan (R.O.C.)

department: Department of Biomedical Sciences

country: Taiwan

institute: Chang Gung University

summary: DEAD-box helicase 24 (DDX24) is a member of the DEAD-box protein family, which is essential for various aspects of RNA metabolism. DDX24 has been reported to play a role in ribosome biogenesis, transcription, and mRNA stability. Previous studies have implicated the functions of DDX24 in innate immunity, vascular malformation, cell growth, and cancer progression. Here, we describe a novel function of DDX24 in regulating the oxidative stress response and protecting cells from apoptosis. Our research revealed that DDX24 specifically regulates the expression of the heme oxygenase-1 (HO-1) gene, as determined by RNA sequencing analysis. HO-1 is responsible for degrading heme into carbon monoxide (CO), biliverdin, and ferrous ion (Fe2+), thereby exerting anti-apoptotic and anti-oxidative effects. We validated the regulation of HO-1 by DDX24 in both DDX24-depleted and DDX24-overexpressing HEK293 cells. Our findings indicate that DDX24 is involved in the induction of HO-1 expression under oxidative stress conditions. Importantly, DDX24 regulates the transcription of HO-1 instead of its mRNA stability, likely acting at the promoter and enhancer E1 region of the HO-1 gene. Furthermore, DDX24 depletion in HEK293T cells inhibits cell viability. DDX24 exerts both anti-apoptotic and anti-oxidative effects during oxidative stress. These results suggest that DDX24 plays a crucial role in protecting cells from oxidative stress-induced damage by regulating the transcription of HO-1.

overall_design: mRNA expression profiling by high throughput sequencing

first: Yu-Xiu

last: Lin


title: Persistent cortical excitatory neuron dysregulation in adult Chd8 haploinsufficient mice [RNA-Seq]

first: Stephanie

last: Lozano

first: Cesar

last: Canales

first: Nicholas

last: Frost

first: Karol

last: Cichewicz

first: Wellington

last: Amaral

first: Nicolas

last: Seban

first: Ethan

last: Fenton

first: Ayanna

last: Wade

first: Nickolas

last: Chu

first: Emily

last: Smith

first: Cory

last: Ardekani

first: Samuel

last: Frank

first: Jeffrey

last: Bennett

first: Pierre

last: Lavenex

first: Aspen

last: Kopley-Smith

first: Darlene

last: Rahbarian

first: Melissa


title: The PAR2/TRPV3/IL-33 Axis in Keratinocytes Drives Neuroimmune

city: Beijing

first: Zhou

last: Lingxuan

address: No. No.8, Xishiku Street, Xicheng District, Beijing

institute: Peking university first hospital

summary: Epidermal transient receptor potential (TRP) channels are involved in complex interactions between the peripheral nervous system and the immune system in atopic dermatitis (AD). Recently, we identified that TRPV3 interacts with protease-activated receptor 2 (PAR2) to mediate non-histaminergic itch. However, the downstream molecular mechanisms following TRPV3 activation in keratinocytes remain unclear.This study aims to investigate whether TRPV3 channels regulate mast cells in the context of AD.

overall_design: We developed a range of TRPV3 conditional knockout (cKO) mice and assessed the role of TRPV3 in mast cell density and migration. Additionally, we performed RNA sequencing analyses and used genetically encoded fluorescent sensor to investigate the downstream cytokines of the TRPV3-PAR2 pathway.

first: Jiahui

last: Zhao

first: Lingxuan

last: Zhou

first: Chenyu

last: Wang

first: Ziyan

last: Rao

first: Xiaohui

last: Yuan

first: Jun

last: Cui

first: Dongyu

first: Ying

last: Sun

first: Yan

last: Chen

first: Ruoyu

last: Li

first: Miao

last: Jing


title: The symbiotic system of ATP translocase-expressing bacteria (ATEB) and macrophages.

city: Hubei

first: 文

last: 李

address: Wuhan

institute: Wuhan University

summary: The endosymbiosis theory indicates that mitochondria evolved from free-living prokaryotes, which entered host cells and remained as endosymbionts. Here we have designed an Escherichia coli - macrophage symbiosis system. By engineering and modifying Escherichia coli to enter cells through membrane fusion, it can bypass lysosomes to avoid being degraded by cells and exist stably in macrophages. Moreover, it has been genetically engineered to express ATP. This symbiotic bacterium can serve as a mitochondrial substitute to provide the energy necessary for the metabolism of life activities of host macrophages. By up-regulating the genes related to tricarboxylic acid cycle and oxidative phosphorylation and down-regulating the genes related to glycolysis, it significantly enhances the metabolic activity of host macrophages. This symbiotic system can still exist within 60 hours and can still maintain certain functionality in the microenvironment of tumor nutritional deficiency.

overall_design: RAW264.7cells were co-cultured for 24 h. Total RNA was extracted using RNAiso plus reagent (TaKaRa Biomedical Technology Co., Ltd), and then RNA quality was determined by 5300 bioanalyzer (Agilent). RNA purification, reverse transcription, library construction, and sequencing were performed at Genecreate Biotechnology Co., LTD. (Wuhan, China) in accordance with the manufacturer's instructions. Cell transcriptomic data analysis was performed on the Genecreate Biotechnology cloud platform (China).


title: Genome wide mapping of sni445-HTP binding sites in yeast by CRAC

city: Toulouse

first: Hussein

last: HAMZE

address: 118 Route de Narbonne  31062 TOULOUSE Cedex France

institute: Toulouse university - cnrs

summary: We report the application of the Cross-Linking and cDNA (CRAC) technique to identify binding sites of sni445, ribosome assembly factor, on RNAs in vivo. Once sequenced, RNAs associated have been aligned to the yeast genome and enrichment of specific RNAs has been studied in more details. Specifically, apparition of Mutations/deletions in the reads is center of interest since they mostly correspond to precise site of cross-link between bait protein and target RNAs. Here sni445-HTP is mostly bound to two snoRNAs, SNR4 and SNR45.

overall_design: We analyse the sequence enrichment of RNAs associated to sni445-HTP compared to a mock (un-tagged) control after protein/RNA cross-link in vivo.

last: Hamze

first: Jutta

last: Hafner

first: Anthony

last: Henras

first: Brigitte

last: Pertschy


title: effect of Hpb-colonized and -trained mice on peritoneal macrophage gene expression

first: Qingxiang

last: Gao

overall_design: RNA-Seq profiling of peritoneal macrophages harvested from Hpb-colonized (11 days) and trained (dewormed and rested for 3 weeks) mice and its corresponding controls

first: Shih-Chin

last: Cheng

first: Jia

last: Zhang


title: Effect of circ72309 overexpression on gene expression related to gemcitabine sensitivity in pancreatic cancer cell lines

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

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

summary: Understanding the molecular characteristics of gemcitabine sensitivity in pancreatic cancer is essential for advancing individualized treatment strategies. This study identifies circ72309 as a potential contributor to improve gemcitabine sensitivity. circ72309 decreased cytidine deaminase, a nucleoside enzyme which transforms gemcitabine into an inactive form, via reactive oxygen species activity, and increased solute carrier family 29 member 1 (SLC29A1), a nucleoside transporter which imports gemcitabine into cells, by regulating targeted miRNAs.

overall_design: To identify the  changes of mRNA expression, gemcitabine-resistance pancreatic cancer cell line (GR3) was established and transfected with either circ72309 vector or negative control (scramble) oligonucleotides. Gene expression profiling was performed using RNA-seq data obtained from these two cell lines. A comparative analysis of the RNA-seq data was conducted to evaluate gene expression profiles between circ72309-transfected cells and scramble controls.

first: Naoko

last: Sekiguchi

first: Yoshito

last: Tomimaru

first: Hidenori

last: Takahashi

first: Hidetoshi

last: Eguchi


title: Gene expression profiles in failed-repair renal tubular epithelial cells of rats treated with ischemia/reperfusion operation or cisplatin administration

city: Tonomachi, Kawasaki-ku, Kawasaki City, Kanagawa, JAPAN

first: Kohei

last: Matsushita

institute: National Institute of Health Sciences

summary: The aim of this study is to investigate the gene expression profiles of renal tubules during maladaptive repair.

overall_design: n = 4/group. 6 groups (Total n = 24). Control_I/R, I/R_day 3, I/R_day 28, Control_cisplatin, cisplatin_day 5, cisplatin_day 28


title: RALP1 is critical for Plasmodium falciparum merozoite invasion of erythrocytes

city: Changsha

first: Xiaomin

last: Shang

state: Hunan Province

address: 172 Tongzipo Road

department: Department of Parasitology

institute: Central South University

summary: RALP1 plays critical roles in both Plasmodium falciparum development and host cell invasion. As an apical rhoptry-localized protein, RALP1 not only translocates to the tight junction to directly mediate invasion, but also regulates the expression of key invasion-related effectors, thereby orchestrating erythrocyte entry through multiple mechanisms. As conservation and specificity of RALP1 in Plasmodium species, elucidating its precise biological functions will not only deepen our understanding of erythrocyte invasion mechanisms but also provide novel therapeutic targets.

overall_design: RNA-seq profiling was performed on Plasmodium falciparum at distinct intraerythrocytic stages (ring and schizont).


title: Nascent transcript sequencing visualizes mouse preimplantation embryonic genome activation

first: Wenjie

last: Shu

address: Taiping Road 27

institute: Beijing Institute of Radiation Medicine

summary: Embryonic genome activation (EGA), a pivotal transcriptional event during preimplantation development, is accompanied by post-transcriptional regulation of maternal mRNAs. Disentangling the transcriptional output of the newly activated embryonic genome from concomitant post-transcriptional processing is important for decoding EGA dynamics.Here, using optimized low-input SLAM-seq (thiol(SH)-linked alkylation for the metabolic sequencing) in mouse embryos, we delineates the temporal hierarchy of EGA nascent transcription during mouse preimplantation embryogenesis and uncovers a mechanistic link between EGA and the first lineage specification, providing new insights into the regulatory architecture of early mammalian development.

overall_design: For the SLAM-seq profiling of mouse preimplantation embryos from nine stages, we adopted the criteria of 2 mM 4SU, 6-hour interval labeling and 10 embryos per sample for profiling; For the ATAC-seq, we selected the embryos from seven stages across the preimplantation development; For the function validation of KLF17, we collected contrl (ctrl), KO, mKO, pKO embryos at the M2C stage to perform SLAM-seq.

first: Yuxiang

last: Wang

first: Yue

last: Hu

first: Ran

last: Huo