title: Differential microRNA expression profile identified by microarray analysis in anaplastic thyroid cancer cells after valproic acid and gamma rays combined treatment

city: Buenos Aires

first: Marina

last: Perona

address: Avenida General Paz 1499

department: Radiobiología

country: Argentina

institute: Comisión Nacional de Energía Atómica

summary:
We analyzed the effect of valproic acid (VA) in radioresistant anaplastic thyroid cancer (ATC) cells at the expression level of microRNA (miRs) by microarray analysis. The regulated miRs by VA and irradiation, enriched in processes like DNA damage response, reveal a novel miR expression profile.
We used the Affymetrix The GeneChip® miRNA 4.0 Array that ensures a complete measurement of small non-coding  RNA transcripts involved in gene regulation. These Affymetrix miRNA Arrays provide 100% miRBase v20 coverage; 30,424 mature miRNA (all organisms); 5,214 human, mouse, and rat miRNA; 1,996 human snoRNA, scaRNA;  3,770 probe sets unique to human, mouse, and rat  pre-miRNA hairpin sequences.

overall_design:
MicroRNA expression profiling by microarray analysis in anaplastic thyroid cancer cells after valproic acid and gamma rays combined treatment.
MiRNA expression was profiled on Affymetrix GeneChip® miRNA-4_0-st-v1 Array,  representing 723 human and 76 human viral miRNAs in 40 normal and 40 cancerous gastric tissues.

first: Irene

middle: L

last: Ibañez

first: Hebe

last: Durán

first: Guillermo

last: Juvenal


title: A dynamic gene regulatory code drives synaptic development of hippocampal granule cells [RNA-Seq]

status: Public on Sep 21 2025

city: leuven

first: Danie

last: Daaboul

address: Herestraat 49

department: Department of Neuroscience

country: Belgium

institute: KU Leuven

type: Expression profiling by high throughput sequencing

summary: Connecting neurons into functional circuits requires the formation, maturation, and plasticity of synapses. While advances have been made in identifying individual genes regulating synapse development, the molecular programs orchestrating their action during circuit integration of neurons remain poorly understood. Here we have employed a bulk RNA sequencing method (RiboTag) to study the development of hippocampal GCs. GCs represent the first relay in the hippocampal tri-synaptic loop, and play an essential role in processing spatial representations and memory acquisition. This study provides a high temporal resolution analysis of the translatome of GCs during early postnatal development (P5, P7, P10, P15, P21, and P28). Together, these findings highlight the networks of key TFs and target genes orchestrating GC synapse development.

overall_design: Hippocampi from Rbp4-Cre:RiboTag mice were homogenized and the homogenate was incubated with anti-HA magnetic beads for RPL22-HA pull down. Ribosome-bound mRNA was separated from ribosomes, RNA was isolated and libraries prepared for bulk RNA sequencing. This process was repeated at post-natal day (P)5, P7, P10, P15, P21 and P28.

first: Blanca

last: Lorente-Echeverría

first: Jeroen

last: Vandensteen

first: Gabriele

last: Marcassa

first: Willem

last: Naert

first: Joris

last: Vandenbempt

first: Elke

last: Leysen

first: Malou

last: Reverendo

first: Ine

last: Vlaeminck

first: Lise

last: Vervloessem

first: Jochen

last: Lamote

first: Suresh

last: Poovathingal

first: Kristofer

last: Davie

first: Keimpe

last: Wierda

first: Dan

last: Dascenco

first: Stein

last: Aerts

last: De Wit


title: Butylphthalide may inhibit blood-brain barrier disruption through complement-related pathways to alleviate cognitive impairment in epileptic mice

city: Wenzhou

first: Shihao

last: Chen

address: Shangcai Village, Nanbaixiang Street

department: Department of Neurology

country: China

institute: The First Affiliated Hospital of Wenzhou Medical University

summary: To investigate the effect of butylphthalein (NBP) on gene expression after epileptic seizures, we used RNA sequencing (RNA seq) to analyze the mRNA expression after NBP treatment. The volcano plots between Sham, KA, and KA+NBP groups clearly show different gene distributions. Finally, we found that 754 shared genes overlapped between these differentially expressed genes, which was reversed by NBP treatment.

overall_design: Randomly divide the experimental mice into three groups: sham surgery group, KA group, and KA+NBP group. After 30 days of different treatments, 3 mice were randomly selected from each group for RNA sequencing.


title: Platelet-rich fibrin induces an inflammatory phenotype of U937 macrophages

city: Vienna

first: Reinhard

last: Gruber

address: Sensengasse 2a

country: Austria

institute: Medical University Vienna

summary: Platelet-rich fibrin (PRF) is widely used to support local healing, a process that requires the transient polarization of macrophages towards an inflammatory phenotype. PRF and blood clot components, in general, can potentially incite this macrophage response. To test this hypothesis, we performed a screening assay to identify the overall response of macrophages to PRF. To this aim, U937, a histiocytic lymphoma cell line, and THP1, a leukemia cell line, both commonly used bioassays to study macrophage responses, were exposed to PRF lysates. Transcriptomic changes were identified by bulk RNA sequencing. Analysis was based on significantly regulated genes with an adjusted p-value of p<0.05. In U937 macrophages, consistent with our hypothesis, the clustering of increased genes revealed chemokine activity (CCL2, CCL3, CCL4, CCL5, CCL7, CCL8, CCL20, CCL23, CCL26, CXCL5, CXCL6, CXCL8, CXCL16, and PPBP), RAGE receptor binding (FPR1, S100A8, S100A9, and S100A12), IgG binding (FCGR1A, FCGR2A, FCGR2B, FCGR3A), prostaglandin biosynthetic process (CBR1, CD74, EDN1, FABP5, IL1B, MIF, PTGES, PTGS1) and collagen catabolic process (CTSL, FAP, MMP3, MMP7, MMP9, MMP12, MMP14, MMP19 and MRC2). In THP1 cells, clustering highlighted only steroid biosynthesis. These findings emphasize U937 as an appropriate bioassay to study inflammatory macrophage polarization upon PRF exposure, being consistent with clinical macrophage signatures during early wound healing and holding the potential to recover inflammatory macrophages in chronic wounds.

overall_design: We proposed using THP-1 and U937, as THP-1 is a leukemia cell line, and U937 originates from the pleural effusion of a patient with histiocytic lymphoma, both widely established monocytic cell lines, exposed to PRF lysates, to identify the overall response of macrophages to PRF. Transcriptomic changes were determined by bulk RNA sequencing. In the indicated experiments, RT-PCR was conducted to verify some gene expression changes relevant to the RNA-seq.

first: Panahipour

last: Layla

first: Xiaoyu

last: Huang


title: OTUD4 regulates pancreatic cancer progression via Hippo/YAP axis

city: Shenyang

first: Shuaike

last: Qu

address: Liaoning Province,Shenyang city,Shenbei New District,79 Puhe Road

institute: China Medical University

summary: The over-activation of Hippo/YAP axis was often observed in pancreatic adenocarcinoma (PAAD), while the detailed mechanism is not totally understood. Recent studies demonstrated that the ubiquitin modification, which controlled the protein stability of YAP, played important roles in Hippo signaling and PAAD progression. In order to understand the underlying link between YAP protein stability and Hippo activity in PAAD progression, we carried out GSEA bioinformatic analysis coupled with siRNA screening and identified OTUD4 as an important effector for Hippo signaling in PAAD. OTUD4, which was highly expressed in PAAD tissue, correlated with Hippo target gene expression in PAAD tissues. Depletion of OTUD4 significantly reduced the activity of Hippo/YAP axis and hampered PAAD progression. Mechanism studies revealed that OTUD4 could interact with YAP and promote YAP K48-linked poly-ubiquitination and degradation in PAAD. In conclusion, our study identified an interesting regulation mechanism between OTUD4 and Hippo signaling in PAAD, while targeting OTUD4 could be a plausible strategy for PAAD therapy.

overall_design: RNA-seq profiling of AsPC-1 cells transfected with siControl or siOTUD4 for 48h


title: Single-cell simultaneous metabolome and transcriptome profiling revealing metabolite-gene correlation networ

city: Nanjing

first: Songtao

last: Yuan

state: Jiangsu

address: 300 Guangzhou Road

department: Department of Ophthalmology

institute: The First Affiliated Hospital of Nanjing Medical University

summary: Metabolic studies at single cell level could directly define the cellular phenotype closest to physiological or disease states. However, the current single cell metabolome (SCM) study using mass spectroscopy has the difficulty to give a complete view of the metabolic activity in the cell, while the prediction of metabolism-phenotype relationship is limited by the potential inconsistency between transcriptomic and metabolic levels. Here, single-cell simultaneous metabolome and transcriptome profiling method (scMeT-seq) is developed, based on sub-picoliter sampling from the cell for the initial metabolome profiling followed by single cell transcriptome sequencing. This design does not only provide sufficient cytoplasm for SCM, but also nicely keeps the cellular viability for the accurate transcriptomic analysis in the same cell. Diverse relationships between the two omics are revealed in macrophages with the stimulation of lactate and lactate transporter (MCT1) antagonist. Moreover, we mapped metabolite states to the single-cell differentiation trajectory and gene correlation network of macrophages, which allows the unsupervised functional interpretation of metabolome. Thus, the established scMeT-seq should lead to a new perspective in metabolic research by transforming metabolomics from metabolite snapshot to functional approach.

overall_design: The scRNA-seq library was constructed following a modified Smart-seq2 protocol(21). In detail, 4ul lysed sample was incubated at 72C for 3 min. The first-strand cDNA was reverse-synthesized using oligo(dT) and template-switching oligonucleotides. The synthesized first-strand cDNAs were amplified by 20 cycles. After purification, 0.1 ng of cDNA was used for Nextera tagmentation (Illumina) and library construction. Sequencing was then performed on Illumina HiSeq 4000.Single-cell samples were consolidated and subjected to sequencing on the Illumina Novaseq 6000 platform, targeting an average of 3 million reads per library in a paired-end 150-bp format. The raw sequencing data underwent demultiplexing and were subsequently processed with the fastp software (version 0.20.0) for quality trimming. The quality-trimmed reads were then aligned to the mouse reference genome mm10 using the HISAT2 aligner (version 2.1.0) with standard settings. The counts of reads per gene were quantified utilizing the StringTie package. The processed data matrix was import into Seurat (version 4.0). We took the transcriptome matrix as input and then scaled it before using dimensionality reduction techniques. Next, we performed PCA on the scaled data and selected the top principal components to preserve biological variation and remove technical noise. We added the quality-controlled metabolic matrices to the new assay and performed data standardization and normalization. We used a graph-based clustering method to cluster macrophages. We selected gene sets in GSEA (https://www.gsea-msigdb.org/gsea/index.jsp) and assessed the pathway activity of the cells using the GSVA method. We combined the pathway matrix and the normalized metabolome matrix, calculated the correlation between pathways and metabolites using the spearman method, and visualized the results by scatter plot in ggplot2. Based on the grouping information, Wilcoxon rank sum test was performed using FindMarkers function. Genes with |LogFC|>0.25 and P<0.05 were considered as signature genes, and the results were visualized by volcano plots of ggplot2.The Monocle2 package was used to analyze macrophage trajectories. We imported the transcriptome and metabolite matrices into Monocle and used the feature genes and metabolites to sort the pseudotemporal trajectories of the cells. The "DDRTree" was applied to reduce the space to two dimensions and the trajectories in the reduced dimensional space were visualized using the function "plot_cell_trajectory". Cells were divided into three states based on the trajectories, and Gene Ontology (GO) enrichment analysis was performed for the differentially expressed genes of each state using the ClusterProfiler package. The GENIE3 (https://bioconductor.org/packages/release/bioc/html/GENIE3.html) package was used to analyze the metabolite-gene covariance network. We imported the merged matrix of bi-omics and performed functional enrichment analysis for the genes in the three selected modules using the above software and visualized them by bar plot of ggplot2. The schematic was drawn by the BioRender Graphics Tool (http://BioRender.com).


title: Nanoscale Dynamics of Enhancer-Promoter Interactions during Exit from Pluripotency

city: Goettingen

first: Dimitra

last: Tsouraki

state: Lower Saxony

address: Am Fassberg 11

country: Germany

institute: Max Planck Institute for Multidisciplinary Sciences

summary: While compelling genetic evidence supports the role of enhancers in regulating promoter activity even over large genomic distances, it remains unclear to what extent physical proximity to promoters is required. To address this, we combined fluorescence in situ hybridization with super-resolution microscopy and Tri-C to examine enhancer–promoter (E–P) distances and regulatory element clustering at important loci (Nanog, Dppa3, Dnmt3a, Sox2, Prdm14) during the transition from naive to primed pluripotency in mouse embryonic stem cells. Despite transcriptional changes of several orders of magnitude, most genes show no major alterations in median E–P distances or in the probability of multiway contacts across states. However, Tri-C reveals a weak enrichment of multiway contacts at Nanog in naive cells, where it is highly expressed. Because transcription often occurs in transient bursts within a subset of cells, we combined RNA and DNA FISH to identify active alleles. For Nanog and Dppa3, reduced E–P distances correlate with more recent transcriptional activity. Together, these findings support models in which transcription is associated with transient E–P proximity and suggest that multiway contact formation among regulatory elements may contribute to gene regulation.

overall_design: Tri-C experiments. Study of multi-way chromatin interactions from key viewpoints during the exit of mouse embryonic stem cells from pluripotency.

first: Gabriela

last: Stumberger

first: David

last: Hörl

first: Clemens

last: Steinek

first: Marieke

middle: A

last: Oudelaar

first: Heinrich

last: Leonhardt

first: Hartmann

last: Harz


title: N6-methyladenine DNA demethylase ALKBH1 promotes gastric carcinogenesis via disrupting NRF1 binding capacity [ALKBH1-RNA-seq]

status: Public on Sep 22 2025

city: Beijing

first: Xiaohong

last: Wang

address: Haidian district

institute: Peking university cancer hospital

summary: DNA N6-methyladenine (6mA) is an emerging epigenetic modification that regulates various biological processes. Here, we demonstrated the role of DNA 6mA modification in gastric cancer (GC). GC cells and tumors displayed a marked reduction in 6mA levels compared with normal gastric tissues and GES1 cells. 6mA-IP-seq revealed that 6mA was abundant in the surrounding transcription start sites and occurred at consensus motifs. Among the 6mA regulators, ALKBH1, a demethylase, was significantly overexpressed in GC tissues compared to adjacent normal tissues (n=32, P<0.05). Moreover, high ALKBH1 expression was associated with poor survival of patients with GC in three independent GC cohorts (cohort I: n=276, P=0.0093; cohort II: n=136, P=0.001; TCGA dataset: n=381, P=0.0061). Functionally, ALKBH1 knockout increased DNA 6mA and suppressed GC cell growth and cell migration in vitro, and inhibited tumorigenicity and metastasis in vivo. ALKBH1 knockout in mice impairs chemically induced gastric carcinogenesis. Mechanistically, ALKBH1 mediates DNA 6mA demethylation to repress gene expression. In particular, the 6mA sites were enriched in NRF1 binding sequences and targeted for demethylation by ALKBH1. ALKBH1-induced 6mA demethylation inhibited NRF1-driven transcription of downstream targets, including multiple genes involved in the AMPK signaling pathway. Accordingly, ALKBH1 suppressed AMPK signaling, causing a metabolic shift towards the Warburg effect that facilitates tumorigenesis. In conclusion, we revealed, for the first time, that ALKBH1 plays an oncogenic role in GC. ALKBH1 demethylates 6mA within the NRF1-binding regions of tumor suppressor genes to attenuate the binding of NRF1, which subsequently inactivates AMPK signaling and promotes the “Warburg” phenotype.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for BGC823 cells and its ectopic expression derivatives (BGC823-ALKBH1).

first: Chi

middle: C

last: Wong

first: Huarong

first: Kaili

last: Fu

first: Lingxue

last: Shi

first: Hao

last: Su

first: Shang

last: Guo

first: Hongyan

last: Gou

first: Xiaoxu

last: Hu

first: Lianhai

last: Zhang

first: Jiafu

last: Ji

first: Jun

last: Yu


title: A dynamic gene regulatory code drives synaptic development of hippocampal granule cells [SS2]

first: Danie

last: Daaboul

summary: Connecting neurons into functional circuits requires the formation, maturation, and plasticity of synapses. While advances have been made in identifying individual genes regulating synapse development, the molecular programs orchestrating their action during circuit integration of neurons remain poorly understood. Here, we have employed a single-cell RNA sequencing (scRNAseq) method (Smart-seq2) to study the development of hippocampal GCs. GCs represent the first relay in the hippocampal tri-synaptic loop and play an essential role in processing spatial representations and memory acquisition. This study provides a high temporal resolution analysis of the transcriptome of GCs during early postnatal development (P5, P7, P10, P15, and P28). Together, these findings highlight the networks of key TFs and target genes orchestrating GC synapse development.

overall_design: We performed scRNAseq on GCs from Rbp4-Cre:Ai9 mice at key timepoints during synapse development. Brain slices from Rbp4-Cre:Ai9 mice were made using a 500 μm brain matrix, and the dentate gyrus (DG) was dissected. Next, the DG was chopped in smaller pieces and digested using Pronase. Following the digestion, the tissue pieces were homogenized using two-size Pasteur pipettes and the mix was loaded in a 20% Percoll solution to remove debris. Following centrifugation, the pellet was resuspended in OptiMEM-trehalose, and DAPI was added. Fluorescence Activated Cell Sorting (FACS) was done based on DAPI and tdTomato signal, into 96-well plates containing lysis buffer

first: Blanca

last: Lorente-Echeverría

first: Jeroen

last: Vandensteen

first: Gabriele

last: Marcassa

first: Willem

last: Naert

first: Joris

last: Vandenbempt

first: Elke

last: Leysen

first: Malou

last: Reverendo

first: Ine

last: Vlaeminck

first: Lise

last: Vervloessem

first: Jochen

last: Lamote

first: Suresh

last: Poovathingal

first: Kristofer

last: Davie

first: Keimpe

last: Wierda

first: Dan

last: Dascenco

first: Stein

last: Aerts

last: De Wit


title: DNA methyltransferase Dnmt3ba-mediated epigenetic modulation of Integrin signaling is essential for hematopoietic stem and progenitor cell development

city: Jinan

first: kang

last: ai

address: 44 Wenhua West Road

institute: Shandong University

type: Methylation profiling by high throughput sequencing

summary: In vertebrate embryonic development, hematopoietic stem and progenitor cells (HSPCs) originate from a subset of arterial endothelial cells in the ventral wall of the dorsal aorta through endothelial-to-hematopoietic transition (EHT). Despite extensive research efforts, gaps persist in understanding the establishment of EHT and HSPC generation. In this study, we demonstrate that DNA methyltransferase 3ba (Dnmt3ba), highly expressed in the hemogenic endothelial cells (HECs), plays a crucial role in HEC generation and HSPC development. Depletion of Dnmt3ba impairs HEC survival, which ultimately affects the generation and differentiation of HSPCs in zebrafish. Mechanistically, Dnmt3ba deficiency leads to hypomethylation at the itgα3b and itgα7 loci, diminishing the expression of these Integrins and downstream Akt signaling and Mdm2 phosphorylation, while concurrently triggering HEC apoptosis by upregulation of P53 activity. Manipulation of DNMT3B in an iPSC-derived human hematopoietic differentiation system indicates functional conservation. Collectively, our findings unveil an epigenetic mechanism governed by Dnmt3ba, orchestrating HEC survival through epigenetic modulation of Integrin signaling.

overall_design: Whole-genome bisulfite sequencing (WGBS) and RNA-seq were performed on hematopoietic endothelial cells (HECs) isolated from Danio rerio embryos at 36 hours post-fertilization (hpf). For each experiment, the number of embryos in each group was determined based on the amount required to obtain sufficient RNA or DNA from approximately 5,000 cells for RNA-seq and WGBS, respectively. Three biological replicates were prepared for both the control and dnmt3ba morphant groups. All samples that met the quality and quantity requirements were included in the sequencing analysis.

first: Kang

last: Ai

first: Lei

last: Li

first: Lu

last: Wang


title: Enhancer remodeling activates Notch signaling to confer chemoresistance in advanced nasopharyngeal carcinoma

city: guangzhou

first: Lizhen

last: Liu

address: 106 ZhongShan Er Road

institute: 1.	Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: PRR14 mediates mechanotransduction and regulates myofiber identity via MEF2C in skeletal muscle

city: Changsha

first: Mei

last: Yang

address: 139 Middle Renmin Road

institute: The Second Xiangya Hospital, Central South University

summary: Sarcopenia, characterized by the loss of muscle mass, strength, and function, predisposes adverse outcomes and its mechanism is waiting to reveal. Here, we report decrease of PRR14, a nuclear protein, in skeletal muscle results in sarcopenia. Genetically, genome-wide association studies (GWAS) identified multiple single nucleotide polymorphisms (SNPs) in PRR14 locus associated with body mass index (BMI) and total body lean mass, which indicated its association with sarcopenia; Specific knockout of skeletal muscle Prr14 in mice confirmed the causal effect; Biochemical analysis and high-throughput sequencing, including both transcriptome and approaches for the study of the epigenome (CUT&Tag sequencing and ATAC sequencing), revealed that Prr14 was required for myofiber homeostasis in skeletal muscle: Prr14 loss altered chromatin structure and reduced Mef2c activity, which in combination resulted in failure of maintaining myofiber identity and therefore sarcopenia. Our findings demonstrate that PRR14 orchestrates critical epigenetic changes and transcription factor activity to maintain myofiber identity, thereby providing novel therapeutic avenues for skeletal muscle pathologies associated with dysregulation of these mechanisms.

overall_design: CUT&Tag of samples from the quadriceps femoris from both Prr14-KO and Prr14-WT mice


title: Enhancer remodeling activates Notch signaling to confer chemoresistance in advanced nasopharyngeal carcinoma [RNA-Seq]

summary: Acquired resistance to chemotherapy is one of the major causes of mortality in advanced nasopharyngeal carcinoma (NPC). However, effective strategies are limited and the underlying molecular mechanisms remain elusive. Using an established NPC cellular model, we demonstrated that the acquisition of chemoresistance was accompanied by massive enhancer remodeling, resulting in aberrant hyperactivation of Notch signaling pathway in NPC. Transcriptomic profiling analysis showed that hyperactivity of Notch signaling pathway was associated with chemoresistance in advanced NPC patients. In addition, overexpression of Notch3-slug axis was correlated with relapses and metastasis of NPC. Importantly, we showed that genetic or pharmacological perturbation of Notch3 could overcome the chemoresistance of NPC in both in vitro and in vivo models. Together, our study indicated that genome-wide enhancer reprogramming activates Notch signaling pathway to confer chemoresistance of NPC, suggesting that targeting Notch3 could provide a potential therapeutic strategy to effectively treat advanced chemoresistant NPC.

overall_design: RNA-seq for 5-8F parental (5-8F P) cells and 5-8F paclitaxel-resistant (5-8F R) cell

first: Peng

last: Deng

first: Sailan

first: Jinghan

last: Hong


title: Enhancer remodeling activates Notch signaling to confer chemoresistance in advanced nasopharyngeal carcinoma [ChIP-Seq]

summary:
Acquired resistance to chemotherapy is one of the major causes of mortality in advanced nasopharyngeal carcinoma (NPC). However, effective strategies are limited and the underlying molecular mechanisms remain elusive. Using an established NPC cellular model, we demonstrated that the acquisition of chemoresistance was accompanied by massive enhancer remodeling, resulting in aberrant hyperactivation of Notch signaling pathway in NPC. Transcriptomic profiling analysis showed that hyperactivity of Notch signaling pathway was associated with chemoresistance in advanced NPC patients. In addition, overexpression of Notch3-slug axis was correlated with relapses and metastasis of NPC. Importantly, we showed that genetic or pharmacological perturbation of Notch3 could overcome the chemoresistance of NPC in both in vitro and in vivo models. Together, our study indicated that genome-wide enhancer reprogramming activates Notch signaling pathway to confer chemoresistance of NPC, suggesting that targeting Notch3 could provide a potential therapeutic strategy to effectively treat advanced chemoresistant NPC.
1. Chromatin immunoprecipitation DNA-sequencing (ChIP-seq ) for H3K27Ac, H3K4me3 in 5-8F P and 5-8F R cells

overall_design: Lizhen Liu


title: Gene expression profile at single cell level of cells from the motor cortex after spinal cord injury (SCI)

city: Nantong

first: Xinghui

address: 19 Qixiu Road

institute: Nantong University

summary: We used single cell RNA sequencing (scRNA-seq) to analyze the diversity of cells in the motor cortex after SCI.

overall_design: Motor cortex cells of the Sprague-Dawley rats were extracted by nuclei isolation according to the localization of the brain atlas and analyzed using scRNAseq.

first: Ruirui

last: Zhang

first: Xiaoxiao

last: Han

first: Qi

last: Shan

first: Mengru

last: Zheng

first: Xiaosong

last: Gu

first: Songlin

last: Zhou


title: Effect of disruption of  STAT3 Y705 phosphorylation on lung gene expression in mice during influenza virus infection

city: Fuzhou

first: Shasha

address: Shangxia Dian Road 15#

institute: Fujian Agriculture and Forestry University

type: Non-coding RNA profiling by high throughput sequencing

summary:
To investigate the functional relevance of the STAT3 Y705 in antiviral immunity, we established STAT3 705 tyrosine site mutation (STAT3Y705F/+) mice and infected them with influenza virus for 24 h, then collected the lungs.
We then performed gene expression profiling analysis using data obtained from RNA-seq of 3 different samples.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for  lungs of in WSN-infected WT mice and STAT3Y705F/+ mice.

first: Siya

first: Ziding

last: Yu

first: Wenzhuo

first: Ji-Long

last: Chen


title: Protective effects of swimming exercises on murine tumor-induced cardiac inflammation and apoptosis by suppressing PI3K-AKT pathway

status: Public on Sep 20 2025

first: Jun

last: Peng

state: Fujian

address: 1 Qiuyang Road, Minhou Shangjie

department: Academy of Integrative Medicine

institute: Fujian University of Traditional Chinese Medicine

summary: o investigate the intervention effect of aerobic exercise on cardiac dysfunction caused by tumor growth, and to explore its mechanism of action. Animals were implanted with CT-26 metastatic tumors in mice. The exercise method was swimming, with two daily interventions of 30 minutes each. 6 days a week for 4 weeks; To investigate the impact of swimming exercise intervention on cardiac function caused by tumor growth, we conducted experiments such as transcriptome sequencing, cardiac ultrasound, and protein detection to explore the mechanism of its effect.

overall_design: We conducted an animal experiment using CT-26 transplanted tumor mice and combined it with swimming exercise intervention to observe the effect of aerobic exercise on the intervention of cardiac dysfunction caused by tumor growth, and to explore its mechanism.

first: Jiapeng

first: Lei


title: Scaffolding element rewires genome architecture during differentiation at the Zfp608 locus [ATAC-Seq and Hi-C]

city: Montpellier

first: Ivana

last: Jerkovic

state: Occitanie

address: 141 rue de la Cardonille

country: France

institute: IGH, CNRS

summary: Upon differentiation chromatin rewires in order to reflect its new cellular identity and function. Zfp608 locus is rewired following the differentiation from the ESCs to the NPCs. During this process the local chromatin content is remodelled with activating marks littering the region, local 3D chromatin conformation compacts the region through local chromatin contacts and the Zfp608 expression amplifies. This study investigates the cis genetic elements as well as trans elements that drive this process in order to better understand how differentiation rewiring occurs.

overall_design: ATAC-seq experiments of mouse NPC wt cells. cHi-C experiments of deletion of CTCF motif at the element A in NPC cells.

last: Jerković

first: Marco

last: Di Stefano

first: Hadrien

last: Reboul

first: Michael Florian

last: Szalay

first: Davide

last: Normanno

first: Flora

last: Paldi

first: Giorgio Lucio

last: Papadopoulos

first: Quentin

last: Szabo

first: Frederic

last: Bantignies

first: Giacomo

last: Cavalli


title: Trancriptome-wide mapping of TET2-regulated m5C sites in mouse embryonic stem cells (mESCs)

city: philadelphia

first: Fange

last: Liu

state: PA

address: 415 curie blvd, Clinical Research Building Rm 350

country: USA

institute: UPENN

summary: We mapped the transcriptome-wide distribution of m5C sites, which are under the regulation TET2, using immunoprecipitation with specific anti-5mC antibodies followed by next-generation high-throughput sequencing in Tet2 KO mESCs in comparison to wild-type mESCs. Our data revealed that TET2-mediated m5C modifications primarily localize in 3’UTR of mRNA.  Moreover, transcripts containing TET2-regulated m5C sites are stabilized with longer lifetime in Tet2 deficiency mESCs, indicated by the lifetime-seq.

overall_design:
m5C profiling and lifetime-seq in wild-type and Tet2 KO mESCs

Bisulfite sequencing in Tet2 KO and wild-type mESCs

first: Kathy

last: Fange Liu

first: Hui

last: Shen


title: Essentiality and dynamic expression of the human tRNA pool during viral infection

city: Rehovot

first: Noa

last: Aharon-Hefetz

address: 234 Herzl Street

country: Israel

institute: Weizmann Institute of Science


title: Dual edged mechanisms of a tomatine in hepatocellular carcinoma by suppression of Wnt/b Catenin signaling versus RelB driven resistance in tumor therapy

city: Shanghai

first: Tianzhen

last: Wang

address: No.500, Dongchuan Road

institute: East China Normal University

summary: Background: The plant-derived steroidal alkaloid α-tomatine has emerged as a promising pan-cancer therapeutic agent, its multifaceted biological effects in HCC remain unexplored. This study aims to decipher α-tomatine’s molecular duality in HCC, resolving its paradoxical capacity to simultaneously activate tumor-suppressive signaling and provoke chemoresistance networks, ultimately establishing synergistic phytotherapy strategies. Methods: HepG2 hepatocellular carcinoma cells were exposed to α-tomatine to evaluate dose-dependent effects on proliferation, migration/ invasion, and cell cycle distribution. Transcriptomic pro ling via RNA sequencing identi ed dysregulated pathways. Pharmacological interventions using Wnt3a (activation) and XAV939 (inhibition) modulated Wnt/β-catenin signaling, while CRISPR/Cas9-mediated RelB knockout and plasmid-based overexpression established isogenic cell models. These interventions were subsequently applied in BALB/c nude mouse xenografts, where tumor volume was longitudinally monitored during α-tomatine treatment. Results: α-Tomatine demonstrated dose-dependent suppression of hepatocellular carcinoma cell proliferation, migration, and invasion, concomitant with G2/M phase arrest. Mechanistically, it exerted Wnt/β- catenin inhibition via β-catenin phosphorylation/degradation while paradoxically inducing RelB-mediated reduction of anti-tumor activity. Wnt activation attenuated therapeutic effects, whereas Wnt inhibitors enhanced ef cacy. Genetic RelB ablation potentiated α-tomatine’s anti-tumor activity, contrasting with resistance in RelB-overexpressing models. Xenografts con rmed enhanced suppression in RelB-de cient tumors. Conclusion: This plant-derived alkaloid exerts anti-HCC effects through Wnt pathway modulation, while compensatory RelB activation constrains therapeutic outcomes. Strategic RelB co-targeting establishes a dual pathway phytotherapy paradigm, synergistically merging botanical pharmacodynamics with precision

overall_design: HepG2 cells were treated with 2uM α-tomatine for 6h, 12h and 24h. The bulk RNA-seq profiling was done to identify the differential expressed genes.

first: Chenyue

last: Xu

first: Yanling

last: Yuan

first: Bianhong

last: Zhang


title: Extended PRF: impact of heat on gene expression in gingival fibroblasts

first: Reinhard

last: Gruber

summary: Extended platelet-rich fibrin (e-PRF) combines the prolonged resorption properties of heat-coagulated platelet-poor plasma (PPP), becoming an albumin gel (Alb-gel) that is mixed back with the respective native cell-rich buffy coat layer (BC), the concentrated PRF (C-PRF). E-PRF or Alb-PRF is utilized as a barrier membrane in various clinical applications, such as guided tissue regeneration. Heating of PPP might lower its biological activity, but testing this hypothesis is necessary. To this end, we exposed gingival fibroblasts to lysates of regular PPP, heated PPP (hPPP), and BC, followed by bulk RNA sequencing. Gingival fibroblasts respond to PPP lysates with a total of 153 up- and 71 down-regulated genes when considering a minimum 3.0-fold log2 expression change and a significance level 2.0 log-10. In sharp contrast, the response to hPPP was characterized by only five up-regulated and five down-regulated genes, clearly indicating that heating almost completely abolished the biological activity of PPP. As expected, BC was more potent than PPP and broadened the spectrum of regulated genes. RT-PCR and immunoassays confirmed the heat sensitivity of PPP as exemplified by IL11 and other genes. Moreover, PPP, but not hPPP, drives the phosphorylation of p65, representing NF-κB signaling. Taken together, these findings extend previous observations that PPP causes a robust response in gingival fibroblasts and also strengthen the hypothesis that this response is heat-sensitive. These operations support the clinical concept of e-PRF by mixing back the heated inactive PPP with the bioactive buffy coat C-PRF layer.

overall_design: We exposed gingival fibroblasts to 30% lysates of regular PPP, heated PPP (hPPP), and BC, followed by bulk RNA sequencing, to identify changes in the genetic signatures of fibroblasts. In the indicated experiments, RT-PCR and immunoassays were conducted to verify some gene expression changes relevant to the RNA-seq. Moreover, the Western blot assay was applied to confirm that hPPP loses the capacity to induce NF-κB signaling.

first: Xiaoyu

last: Huang

first: Panahipour

last: Layla


title: Study of Conserved Motifs in Senecavirus A Genome

city: Qingdao

first: Fuxiao

address: 700 Changcheng Road, Chengyang District

institute: Qingdao Agricultural University

summary: Ribosome sequencing (Ribo-seq) technology was employed to analyze key sequences regulating translation elongation in the Senecavirus A (SVA) genome and to evaluate their impact on viral replication, thereby providing a theoretical foundation for elucidating the molecular mechanisms of SVA.First, the translation rate of the whole genome of SVA was analyzed using rSVA-GFP as a model via Ribo-seq technology. Based on the significant ribosome enrichment peaks detected by Ribo-seq, synonymous mutations were introduced into the corresponding sequences. After chemical synthesis, these sequences were substituted into the full-length cDNA backbone to obtain recombinant plasmids. Subsequently, reverse genetics was employed to transfect the plasmid into BHK-21 cells to rescue the replication-competent recombinant virus. A series of experiments, including blind passage, RT-PCR, Sanger sequencing, and growth curve analysis, were conducted on the recombinant virus to characterize its biological properties. Representative recombinant viruses were selected for secondary Ribo-seq analysis to elucidate the effects of the modification site on viral replication and protein translation.Ribo-seq data revealed significant ribosomal translation -stall peaks in VP1, 2C, and 3D genes, suggesting that key motifs impeding ribosomal translocation may be present in these regions. It was hypothesized that these regions may contain key motifs that impede ribosomal translocation. To test this hypothesis, these regions were further synonymously mutated to construct recombinant viruses. The results indicated that only the mutant in the 3D region successfully rescued replication-competent viruse that remained genetically stable through 20 passages and had no significant impact on viral growth kinetics. It suggested that the motifs in the 3D region were nonessential for viral replication. In contrast, the motifs, corresponding to the Ribo-seq-specific peaks in the VP1 and 2C regions, were essential for viral replication. The further Ribo-seq analysis of the rescued virus revealed the absence of ribosomal stalling peaks in both the 2C and 3D regions. This suggested that the key motifs in the 2C region, if any, were not the sole determinant of the translation rate of viral proteins. In contrast, disrupting any such structures in the 3D region did not impact viral replication but could affect the rates of viral protein translation.

overall_design: Ribo-seq profiling of Senecavirus A expressing green fluorescent protein (rSVA-GFP) and genetically modified rSVA-GFP at 24h post-infection in BHK-21 cells

first: Yan

last: Li

first: Xiaoxiao

last: Duan

first: Jie

first: Zhijuan

first: Qianqian


title: ACVR1-mediated glycolytic reprogramming promotes histone lactylation and neuronal pyroptosis in neuropathic pain {ChIP-seq]

first: xiaowei

middle: xiaowei

last: zhao

address: No.16 Jiangsu Road, Shinan District, Qingdao, China

institute: Qingdao University

summary:
Chronic neuropathic pain arises from intricate neuroimmune interactions, yet the molecular mechanisms remain poorly defined.
Here, we identify activin A receptor type 1 (ACVR1) as a key neuronal driver of a metabolic-epigenetic program in the spinal dorsal horn following peripheral nerve injury. Nerve injury induced ACVR1 upregulation, which enhanced glycolytic flux and lactate production. Lactate served as a substrate for ACVR1-dependent histone H3 lysine 18 lactylation (H3K18la), an epigenetic modification enriched at promoters of pro-nociceptive genes, thereby activating a neuroinflammatory transcriptional program. Multi-omics integration and functional assays revealed that this pathway engaged the NLRP3 inflammasome and triggered neuronal pyroptosis. Pharmacological inhibition of ACVR1 or blockade of lactylation suppressed inflammasome activation, reduced neuroinflammation, and alleviated pain hypersensitivity in vivo. These findings delineate a pivotal neuronal ACVR1-glycolysis-H3K18la axis that orchestrates neuroimmune cross-talk in neuropathic pain, providing a potential metabolic-epigenetic target for therapeutic intervention.

overall_design: Spinal cord in three treatment groups: sham, SNI, SNI+LDN193189

first: Xiaowei

last: Zhao


title: Autophagy acts as a brake on obesity-related fibrosis by controlling purine nucleoside signalling

city: Oxford

first: Klara

last: Piletic

address: Roosevelt Drive

country: United Kingdom

institute: University of Oxford

summary: A hallmark of obesity is a pathological expansion of white adipose tissue (WAT), accompanied by marked tissue dysfunction and fibrosis. Autophagy promotes adipocyte differentiation and lipid homeostasis, but its role in obese adipocytes and adipose tissue dysfunction remains incompletely understood. Using a mouse model, we demonstrate that autophagy is a key tissue-specific regulator of WAT remodelling in diet-induced obesity. Importantly, loss of adipocyte autophagy substantially exacerbates pericellular fibrosis in visceral WAT. Change in WAT architecture correlates with increased infiltration of macrophages with tissue-reparative, fibrotic features. We uncover that autophagy restrains purine nucleoside metabolism in obese adipocytes. This ultimately leads to a reduced release of the purine catabolites xanthine and hypoxanthine. Purines signal cell-extrinsically for fibrosis by driving macrophage polarisation towards a tissue reparative phenotype. Our findings in mice reveal a novel role for adipocyte autophagy in regulating tissue purine nucleoside metabolism, thereby limiting obesity-associated fibrosis and maintaining the functional integrity of visceral WAT. Purine signals may serve as a critical balance checkpoint and therapeutic target in fibrotic diseases

overall_design: Gonadal white adipose tissue was isolated from lean C57BL/6J mice, mechanically and enzymatically digested. For primary cell culture, the stromal vascular fraction was enriched for CD11b+ cells with CD11b MicroBeads (Miltenyi Biotec) according to manufacturers’ instructions after red blood cell lysis. 350,000 cells were seeded in 24-well plates in RPMI containing 10 % FBS and 1 % P/S and incubated overnight to allow macrophages to attach. The following day, macrophages were enriched by washing the wells with room temperature PBS and treated with experimental conditions. Macrophages were cultured in RPMI containing 10 % FBS and 1 % P/S and 50 ng/ml M-CSF and treated with 100 µM of either hypoxanthine or xanthine over 72 hours. RNA was extracted using RNeasy Plus Micro Kit (Qiagen) and gene expression profiling analysis was performed on RNA-seq macrophage data.


title: ACVR1-mediated glycolytic reprogramming promotes histone lactylation and neuronal pyroptosis in neuropathic pain [RNA-Seq]


title: Changes in RNA levels following inhibition of mechanistic target of rapamycin

city: Chicago

first: Sejeong

last: Shin

state: IL

address: 909 S Wolcott Ave.

institute: University of Illinois at Chicago

summary: This study aimed to identify changes in RNA levels after inhibiting the mechanistic target of rapamycin using RNA sequencing.

overall_design: A375 cells were treated with inhibitors of the mechanistic target of rapamycin for 24 hours.

first: Sang-Oh

last: Yoon


title: A human pluripotent stem cell tri-culture platform to elucidate microglial regulation of retinal ganglion cells in neuroinflammation

city: Indianapolis

first: Jade

last: Harkin

state: Indiana

address: NB Building, 320 W 15th St #414

institute: Indiana University School of Medicine

summary: Optic neuropathies, including glaucoma, are characterized by the progressive degeneration of retinal ganglion cells (RGCs), ultimately leading to irreversible vision loss. Increasing evidence implicates microglia, the resident immune cells of the central nervous system, as key modulators of RGC health and disease progression. However, the precise mechanisms by which microglia influence RGCs remain poorly understood, particularly in the human context. In this study, we established human pluripotent stem cell (hPSC)-derived co-culture systems incorporating microglia, astrocytes, and RGCs to explore how microglia shape RGC growth and maturation under physiological conditions. We first examined the impact of homeostatic microglia on RGCs in both co-culture and tri-culture systems, revealing distinct influences of cell types in co-culture compared to when they were grown individually. We then modeled inflammatory states by activating microglia with lipopolysaccharide (LPS) and evaluated their effects on RGCs both directly and in the context of astrocyte co-culture. This stepwise, reductionist approach enabled us to dissect the cellular interactions driving RGC vulnerability in inflammatory conditions relevant to optic neuropathies. Our findings provide new insight into the complex neuroimmune landscape that underlies RGC degeneration and identify key pathways that may serve as therapeutic targets across a range of optic nerve diseases

overall_design:
We performed single-cell RNA sequencing on iPSC-derived RGCs, astrocytes, and microglia to compare their transcriptional profiles in monoculture versus tri-culture. To assess the impact of neuroinflammation, we further profiled cells from lipopolysaccharide (LPS)-treated and homeostatic control tri-cultures. Cells were dissociated using Accutase prior to sequencing.

TC_control: Triple Culture Untreated Control
TC_LPS: Triple Cultured treated with LPS (Lipopolysaccharide)
IC_control: Individual Culture (Monoculture) untreated Control which includes all 3 cell types combined but grown in monoculture


title: The farnesoid X receptor (FXR) antagonist 7β-isopropylchenodeoxycholic acid improves glucose metabolism in mice on Western diet

city: Hradec Kralove

first: Josef

last: Skoda

state: Czech Republic

address: Akademika Heyrovského 1203

department: Department of Pharmacology and Toxicology

country: Czech Republic

institute: Faculty of Pharmacy in Hradec Kralove, Charles University, Czech Republic

summary: The roles of the farnesoid X receptor (FXR) and Takeda G protein-coupled receptor 5 (TGR5) in regulating metabolic pathways were highlighted recently. Nevertheless, the impact of FXR inhibitors on glucose metabolism remains unclear. In this study, we explored the effects of 7β-isopropylchenodeoxycholic acid (7β-ipCDCA), a combined FXR antagonist and TGR5 agonist, on impaired glucose metabolism in mice fed Western diet. A dual FXR antagonistic/TGR5 agonistic activity of 7β-ipCDCA was confirmed on gene reporter assays. Its effects on glucose homeostasis were evaluated using a glucose tolerance test in C57BL/6J mice mimicking metabolic syndrome condition induced by Western diet with additional sugar in drinking water for 24 weeks. The glucose-lowering mechanism was investigated by measuring glucagon-like peptide 1 (GLP-1) release, mRNA expression of glucose transporters and genes involved in glucose metabolism in intestinal, hepatic, white adipose, and kidney tissues, and in human intestinal NCI-H716 and murine GLUTag cells. Additionally, bile acid metabolome and liver lipidome were determined. 7β-ipCDCA restored blood glucose homeostasis altered by Western diet in mice via enhanced GLP-1 release and inhibition of glucose transporters in the ileum. While changes in the liver function were marginal, 7β-ipCDCA augmented taurocholic acid plasma concentration. 7β-ipCDCA increased liver triglycerides exclusively in mice fed a chow diet, whereas mice on the Western diet were protected from hepatic triglyceride accumulation. This study revealed a novel role of FXR in regulating intestinal glucose transporters and GLP-1 secretion, emphasizing the potential of FXR antagonists/TGR5 agonists in modulating hyperglycemia.

overall_design: Mice fed with HFD for 25 weeks were for last 6 weeks treated with vehicle (control) or 7β-ipCDCA (MI172 group). After end of the experiment, livers were used for RNA-seq (4 replicates per group).

first: Alzbeta

last: Stefela

last: Dohnalova

first: Hana

last: Lastuvkova

first: Stanislav

last: Micuda

first: Otto

last: Kucera

first: Petr

last: Pavek


title: Development of AptCD4-LNT for selective mobilization and activation CD4+ T cells to enhance anti-tumor immunity in triple-negative breast cancer

city: Hangzhou

first: Yalin

last: Xiong

state: Zhejiang

address: No. 150, Dongfang Street, Xiasha Street, Qiantang District

institute: Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences

summary: CD8+ T cells are well-established primary effectors in anti-tumor immunity, but increasing evidence underscores the critical and multifaceted role of CD4+ T cells, which can function both as helper cells and direct tumor killers. However, the clinical potential of CD4+ T cells has been limited by poor tumor infiltration and the challenges posed by an immunosuppressive tumor microenvironment. To address these limitations, we developed a CD4 aptamer-engineered liquid nitrogen-treated cancer cell system (AptCD4-LNT) designed to selectively activate and recruit CD4+ T cells for improved anti-tumor immunity. This system leverages the CD4 aptamer's specificity for CD4+ T cells and the homing properties of LNT cells to drive targeted infiltration and activation of CD4+ T within the tumor microenvironment. Activated CD4+ T cells, in turn, enhance the infiltration and activity of NK cells, B cells, and dendritic cells, reshaping the immune landscape and potentiating anti-tumor responses in triple-negative breast cancer. Our findings highlight the pivotal role of CD4+ T cells in TNBC immunotherapy and present a promising strategy for advancing CD4-targeted treatments in clinical settings.

overall_design: After receiving AptCD4-LNT administration every 3 days with a dose of 5 × 10^6 cells, 4 × 10^6 cells, and 3 × 10^6 cells, sequentially, triple negative breast cancer  (4T1) bearing mice were sacrificed at 9 days, and tumor tissues were obtained for scRNA-Seq. The untreated mice bearing triple negative breast cancer received PBS as the control.

first: Heming

last: Tang

first: Shaoju

last: Gan

first: Liyan

last: Fei

first: Lu

last: Guo

first: Kejing

last: Zhang

first: Haowen

first: Ting

last: Fu

first: Qin

last: Wu

first: Weihong

last: Tan


title: Germline cell identity maintenance by a pair of zinc finger proteins C3H14 and C3H15 in flowering plants

first: Chenjiang

last: You

state: Shanghai

address: 2005 Songhu Rd

institute: Fudan University

summary: In the anther of flowering plants, innermost germline cells (meiocytes) and surrounding somatic cells (tapetum) are differentiated from the same precursor archesporial cells (ARs), and these cells after specification acquire distinct cell identities. However, the maintenance of meiocyte identity is elusive. Here we demonstrate a conserved surveillance mechanism governed by Arabidopsis zinc-finger proteins C3H14 and C3H15, which regulate mRNA homeostasis to safeguard the meiocyte identity. C3H14/C3H15 interacts with P-body proteins and CCR4-NOT deadenylase complex, and is required for eliminating unwanted transcripts. Their deficiency induces ectopic accumulation of mRNAs essential for AR differentiation and tapetum development in meiocytes, thus resulting in a confused meiocyte identity with subsequently tapetum-like reactive oxygen species (ROS) bursts and programmed cell death (PCD). Furthermore, CRISPR-Cas9-induced mutations in AtC3H14/15 paralogs in soybean and rice caused similar defects in meiocyte identity maintenance, indicating that germline cell maintenance by post-transcriptional RNA elimination is conserved in flowering plants.

overall_design: meiocytes from Arabidopsis col-0, c3h14, c3h15, and c3h14 c3h15 with two replicates; inflorescence meristem and anther at stage 2 from col-0 with three replicates; 21-day old leaves from col-0 and c3h14 c3h15 with three replicates.

first: Yingxiang

last: Wang

first: Cong

first: Zhiyu

last: Chen


title: An interdisciplinary research pipeline, representing the infant gut environment, to evaluate gut health benefits of early life nutrition ingredients

city: Zeist

first: Marjolein

last: Meijerink

state: Utrecht

address: Utrechtseweg 48

department: RAPID

country: Netherlands

institute: TNO

summary:
- Background: Optimized diets during the first period of life may be most effective for improving gut and overall health. Here, we set up an interdisciplinary research pipeline to evaluate gut health benefits of early life nutrition ingredients through advanced integration of in vitro and modeling technologies that represent the infant gut environment.
- Methods: In our InTESTine platform (TM), biopts of piglet gut tissue (Jejunum or Colon) were exposed (0-6h) to various infant/piglet-formula-milk based food matrices (-/+ prebiotics; -/+ predigestion by infant/piglet fecal microbiome). RNA expression of the piglet gut tissue biopts was measured by RNAseq.
- Results: To be published in various papers.
- Conclusion: To be published in various papers.

overall_design: RNAseq expression of piglet (age 3wk) gut tissue biopts (J=jejunum or C=colon) after 0-6h exposure to various infant/piglet formula-milk based food matrices (IFM = 10% Infant Formula Milk, PMR = 10% Piglet Milk Replacer) -/+ addition of prebiotics (2'FL=2'-fucosyllactose, LGG = Lactobacillus rhamnosis Goldin Gorbach, GOS = Galacto-oligosaccharide, ZnO = Zinc oxide) and -/+ predigestion of the milk-based foodmatrices (-/+ prebiotics) by microbiome from either breast/formula-fed human infants (BfH = microbiome Brest-fed Human infants, FFH = microbiome Formula-fed Human infants) or healty/dysbiotic piglets (DysP = microbiome dysbiotic piglets, HeaP = microbiome healthy piglets) in our i-screen platform (TM; i = i-screen = predigested foodmatrix -/+ prebiotic). 0 = no added: prebiotic, food matrix or microbiome. SIEM = blanc microbiome medium of the i-screen platform (no addiditons of prebiotic, food matrix and microbiome).

first: Joanne

last: Donkers

first: Sabina

last: Bijlsma

first: Kirina

last: van der Bijl

first: Nicole

last: Plomp

first: Bo

last: Heming

first: Martien

last: Caspers

first: Xavier

last: Sa Castro Pinho

first: Margreet

last: Heerikhuisen

first: Klaudyna

last: Borewicz

first: Erik

last: Eckhardt

first: Regiane

last: Santos

first: Maria

last: Wiese


title: Nivolumab plus ipilimumab for potentially resectable hepatocellular carcinoma: long-term efficacy and biomarker exploration

city: Taipei

first: Chia-Lang

last: Hsu

address: No. 7, Zhongshan S. Rd.

department: Department of Medical Research

country: Taiwan

institute: National Taiwan University Hospital

summary: Immune checkpoint inhibitor-based combination therapy produced high objective response for patients with hepatocellular carcinoma (HCC) and may improve clinical outcome as neoadjuvant or peri-operative therapy. This study evaluated efficacy and safety of nivolumab plus ipilimumab for patients potentially resectable HCC and explored potential predictive biomarkers for efficacy.

overall_design: Transcriptomics analysis was performed to investigate the biomarkers associated with the response of immune checkpoint inhibitor therapy

first: Chiu

first: Da-Liang

last: Ou

first: Yung-Yeh

last: Su


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

city: Nanjing

first: yan

last: chen

address: 163 Xianlin Road, Qixia District

institute: Nanjing university

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

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

first: Yan

last: Chen

first: Chenming

last: Xu

first: Wu

last: Yin


title: Adipocyte autophagy-mediated signals in the control of macrophage phenotype during diet-induced obesity

first: Klara

last: Piletic

summary: A hallmark of obesity is a pathological expansion of white adipose tissue (WAT), accompanied by marked tissue dysfunction and fibrosis. Autophagy promotes adipocyte differentiation and lipid homeostasis, but its role in obese adipocytes and adipose tissue dysfunction remains incompletely understood. Using a mouse model, we demonstrate that autophagy is a key tissue-specific regulator of WAT remodelling in diet-induced obesity. Importantly, loss of adipocyte autophagy substantially exacerbates pericellular fibrosis in visceral WAT. Change in WAT architecture correlates with increased infiltration of macrophages with tissue-reparative, fibrotic features.

overall_design: To investigate the role of adipocyte autophagy in diet-induced obesity, we used Adipoq-Cre ERT2 Atg7fl/fl mice, where autophagy was inducibly depleted with administration of tamoxifen specifically in adipocytes, followed by 16 weeks of high fat diet feeding with a 60kcal% fat diet. Gonadal white adipose tissue was isolated from these mice, mechanically and enzymatically digested and macrophages were isolated using flow-assisted cell sorting (CD11b+ F4/80+ CD64+ markers). We then performed gene expression profiling analysis using data obtained from RNA-seq of macrophages isolated from either WT or adipocyte autophagy KO white adipose tissue.


title: Overexpression of the fructose transporter SLC2A5 (GLUT5) in association with PHGDH splicing dynamics is a venetoclax resistance mechanism in acute myeloid leukemia

city: Köln

first: Stuart

middle: James

last: Blakemore

state: NRW

address: Robert-Koch-Str. 21

department: TRIO

institute: University Hospital Cologne

summary:
Background: The combination of hypomethylating agents (HMA) with the Bcl-2 inhibitor venetoclax (VEN) has significantly advanced acute myeloid leukemia (AML) treatment. This therapy is approved for older patients and those with comorbidities.
Objectives: We aimed to identify resistance mechanisms to HMA-VEN therapy using scRNA-Seq on primary AML samples. GLUT5 expression on AML progenitors from resistant and non-resistant patients was evaluated through immunoblotting and immunofluorescence. Seahorse and CRISPR experiments were conducted to validate the phenotype in the THP-1 AML monocyte cell line.
Findings: scRNA-Seq revealed an upregulation of Leukemia Stem Cell (LSC) 17 scores in pre-treatment samples compared to HMA-VEN relapse samples. RNA velocity analysis indicated that LSCs in pre-treatment samples were the root cell population, while HMA-VEN relapse cells, specifically AML Blast 1, showed preferential splicing of PHGDH, a key serine synthesis pathway member, resulting in the overexpression of SLC2A5. GLUT5 was more frequently and intensely expressed on the cell surface in patients resistant to HMA-VEN. Seahorse assays demonstrated that fructose uptake via GLUT5 suppressed oxygen consumption in THP-1 cells following siRNA-mediated knockdown.
Conclusions: Aberrant GLUT5 expression by leukemia progenitors represents a metabolic adaptation contributing to VEN resistance in AML.

overall_design: Bone marrow specimens from two AML patients who initially achieved a complete remission to the combination of hypomethylating agents with the Bcl-2 inhibitor venetoclax (HMA-VEN), (CR, defined as less than 5% marrow blasts by morphology) then became refractory to HMA-VEN (HMA-VEN-Refractory) were analyzed by scRNA-Seq.

middle: J

first: Martin

last: Peifer

first: Lukas

middle: P

last: Frenzel


title: Novel function of NUP153 in HNF4α transcriptional upregulation contributes to promoting HBV replication

city: Beijing

first: Qianqian

last: Jiang

address: No.11 Xizhimen South Street

institute: Peking University

summary: Background & Aims: Nucleoporin 153 (NUP153) is known to facilitate the nuclear entry of the human immunodeficiency virus (HIV) nucleocapsid. Studies had also showed that immature hepatitis B virus (HBV) nucleocapsids can be arrested by NUP153, allowing them to further mature. In this study, we investigated the impact and specific mechanisms of NUP153 on HBV replication. Methods: NUP153 was knocked down using RNA interference or over-expressed through an expression plasmid in HBV cell models or in vivo in HBV-replicating mice. Luciferase reporter assays were employed to assess the activities of viral or host factor promoters. Cytoplasmic and nuclear fractionation experiments were conducted to analyze the subcellular distribution of proteins and HBV RNA. Results: In the present study, we found that HBV induced significant upregulation of NUP153 mRNA and protein in HBV cell models and HBV infected patients. Overexpression of NUP153 would markedly increase covalently closed circular DNA (cccDNA) transcription activity and progeny virus production, while downregulation of NUP153 could significantly inhibit HBV replication without affecting HBV cccDNA level directly. Similar results were observed in mice model hydrodynamically injected (HDI) with 1.2×HBV plasmid. HBV promoter assays revealed that NUP153 could promote HBV core promoter activity, likely in a hepatocyte nuclear factor 4α (HNF4α) dependent manner. Mechanistically, ERK signaling was required for NUP153-mediated promotion of HNF4α and HBV replication. Conclusions: The study here suggested that host factor NUP153 which reciprocally upregulated by the virus, is an important positive regulator of HBV replication. It also suggested that the NUP153-HBV positive feedback loop could serve as a potential therapeutic target.

overall_design: To further investigate whether endogenous NUP153 exerts a functional effect on HBV transcription and replication, we downregulated NUP153 expression using siRNA targeting NUP153 (siNUP153), followed by the transfection of prcccDNA/Cre.

first: Fengmin

last: Lu


title: Investigate the role of B cell in response to anti-PD1 + anti-CTLA in hepatocellular carcinoma

summary: B cells may play a critical role in the response to immune checkpoint inhibitor treatment. To investigate the mechanisms, we performed RNA-seq analysis on mouse hepatocellular carcinoma by depleting B-cells and treating with anti-PD1 and anti-CTLA4.

overall_design: Mouse HCC model (Hepa1-6 cell, C57BL/6) was developed and treated with isotype or anti-PD1 plus anti-CTLA4 under the candition of WT and B-cell depleition.

first: D

first: C


title: 1α,25(OH)2D3 remodels γδ T cell metabolism and ameliorates insulin resistance

city: Guangzhou

first: Peng

last: Li

address: The Biomedical Translational Research Institute, Faculty of Medical Science, Jinan University

institute: Jinan University

summary: Epidemiological studies have showed that vitamin D deficiency was correlated with increased risk of insulin resistance and type 2 diabetes. Although immune cells triggered chronic inflammation as a central link between obesity and insulin resistance, how vitamin D affects metabolic remodeling in immune cells to control inflammation and insulin resistance has not been well characterized. Here we defined a critical role of 1α,25(OH)2D3 in regulating glycolysis metabolism, protecting against inflammation and alleviating insulin resistance. Mechanistically, 1α,25(OH)2D3-VDR promote fructose-1,6-bisphosphatase (FBP1) expression to repress glycolysis in γδ T cells, thereby inhibiting Akt/p38 MAPK phosphorylation and reducing inflammatory cytokines production. Notably, therapeutic administration of 1α,25(OH)2D3 restrains inflammation in adipose-resident γδ T cells and ameliorates systemic insulin resistance in obesity mice. Collectively, these findings show that 1α,25(OH)2D3 has an important role in maintaining γδ T cells homeostasis via orchestrating metabolic programs, and is highly promising target for preventing obesity, inflammation and insulin resistance.

overall_design: Human healthy γδ T cells (Control, n=3; Treatment, n=3).

first: Ke

first: Wenhui

last: Yuan

first: Yunfei

last: Gao


title: Transcriptional changes mediated by the HDACi panobinostat in IDH-wildtype and IDH-mutant gliomas

status: Public on Sep 19 2025

first: Thomas

middle: Kieran

last: Sears

address: 303 E. Superior St.

department: Neurological Surgery

institute: Northwestern University

summary: IDH1/2 mutations (IDHmut) increase methylation of DNA and histones in gliomas. IDHmut inhibitors are effective against low-grade IDHmut gliomas, but new strategies against high grade IDHmut gliomas are needed. Although histone deacetylase inhibitors (HDACi) are ineffective against IDHwt glioblastoma (GBM), their potential in IDHmut gliomas has not been extensively studied. We previously established that IDHmut gliomas are more sensitive to HDACi than IDHwt GBM. Here, we show that IDHmut is associated with unique transcriptional changes mediated by the HDACi panobinostat in glioma, providing insight into the mecahnism of increased HDACi sensitivithy..

overall_design: IDH1/2 wildtype glioma cultures (0827, 0923, 0211, GBM12, GBM43) and IDH1/2 mutant (0905, BT142, TS603, TB09) were treatred with 10 nM panobinostat and evaluated for unique transcriptional signatures that would indicate why IDH1/2 mutant gliomas are more sensitive to HDACi

middle: K

first: Craig

middle: M

last: Horbinski


title: Transcriptional changes mediated by the HDACi belinostat  in IDH-mutant glioma cultures with YAP and TAZ overexpression

summary: IDH1/2 mutations (IDHmut) increase methylation of DNA and histones in gliomas. IDHmut inhibitors are effective against low-grade IDHmut gliomas, but new strategies against high grade IDHmut gliomas are needed. Although histone deacetylase inhibitors (HDACi) are ineffective against IDHwt glioblastoma (GBM), their potential in IDHmut gliomas has not been extensively studied. We previously established that IDHmut gliomas are more sensitive to HDACi than IDHwt GBM. Here we show that IDHmut is associated with greater sensitivity to HDACi only in glioma, not in IDHmut chondrosarcoma or cholangiocarcinoma.  Two mediators of HDACi resistance, YAP and TAZ, were methylated and suppressed in IDHmut gliomas, but not in other IDHmut cancers. Inducing YAP or TAZ expression in IDHmut gliomas conferred resistance to HDACi. Here, we report the transcriptional changes mediated by the HDACi belinostat in IDHmut glioma with and without YAP or TAZ expression.

overall_design: RNA seq profiling of belinostat-treated 0905 and TS603 IDH mutant glioma cultures, with and without YAP 5SA and TAZ 4SA expression.


title: ExoChew-Seq: An in vitro method for investigating singlestranded DNA-protein interactions

city: Blacksburg

first: Ramu

last: Anandakrishnan

state: VA

address: 1410 Prices Fork Rd., Lab 101

department: Biomedical Sciences

institute: Edward Via College of Osteopathic Medici

summary: During various cellular DNA transactions such as DNA replication and repair, genomic doublestranded DNA (dsDNA) is transiently unwound to generate single-stranded DNA (ssDNA). Several proteins interact with ssDNA, site- and/or structure-specifically, to regulate key cellular processes. Investigating these processes requires genome-wide identification of these ssDNA sequences. However, because of the transient nature of ssDNA in vivo techniques cannot reveal all such sequences requiring an in vitro alternative. Traditionally, ssDNA libraries are prepared by boiling or alkali-treatment of dsDNA libraries, but these techniques have their limitations as ssDNA can rapidly reanneal to generate dsDNA. We present here ExoChew, a novel enzymatic technique, which generates persistent ssDNA libraries from dsDNA libraries. In ExoChew, T7 exonuclease (T7 exo) or E. coli exonuclease III (Exo III), which binds and cleaves dsDNA in a specific direction, generates ssDNA libraries from dsDNA libraries. To validate the technique and demonstrate its applications, we conducted a genome-wide search for hnRNP K binding sites in an ExoChew-generated ssDNA library from mouse genomic DNA. The hnRNP K-bound ssDNA fragments were sequenced (ExoChew-seq) and a consensus hnRNP K binding motif was identified. Two other potential uses of ExoChew are the generation and genome-wide identification of ssDNA secondary structures and protein-ssDNA interactions.

sample_organism:
Escherichia coli
Mus musculus

platform_organism:
Escherichia coli
Mus musculus

overall_design: Mouse cell line, NMuMG, and human cell lines, A549 and HeLa cells,  were grown in DMEM with a high glucose medium containing 10% FBS. Cells were grown to sub-confluency in 10 cm plates, trypsinized, washed with PBS, and finally, lysed by adding 10 mM Tris (pH 7.4), 1 mM EDTA (pH 8), and 1% SDS. Chromosomal DNA was prepared using a Quick-DNA Midiprep Plus Kit. s. The Oxford Nanopore Ligation Sequencing Kit was then used to ligate adapters and prepare the dsDNA, according to the manufacturer’s instructions. The dsDNA conversion products were then loaded and sequenced using an ONT MinION flow cell. MinKNOW software was used for controlling the device, data acquisition, and real-time basecalling using the manufacturer’s recommended settings.


title: Spatial dynamics of brain development and neuroinflammation [Epigenomic_data]

city: New Haven

first: Di

last: Zhang

address: 55 Prospect St

institute: Yale University

summary: Spatially mapping multiple omics layers across time enables dissection of mechanisms underlying brain development, differentiation, arealization, and disease.  Here, we deploy spatial tri-omics to chart spatiotemporal remodeling in development and neuroinflammation.  We generate a tri-omic atlas of mouse brain from postnatal day P0–P21 and compare corresponding regions in developing human brain.  In cortex, a subset of layer-defining transcription factors shows temporally persistent and spatially spreading chromatin accessibility.  In corpus callosum, myelin genes exhibit dynamic chromatin priming across subregions, and layer-specific projection neurons appear to coordinate axonogenesis and myelination.  In a lysolecithin (LPC) model, we observe molecular programs shared between development and neuroinflammation.  Microglia display conserved and distinct inflammatory and resolution programs and are transiently activated both at lesion cores and at distal sites, presumably via neuronal circuitry.  These data reveal common and divergent mechanisms and provide a resource for studying brain development, function, and disease.

overall_design: Samples consist of mouse brain tissue sections collected across normal postnatal development (P0, P2, P5, P7, P10, P21) as well as from a lysolecithin (LPC)-induced demyelination model at multiple recovery stages (5, 10, 21 days post-lesion). Each sample was processed for spatial multi-omic profiling using DBiT-seq. Biological replicates are included for each developmental stage and lesion condition. Experimental variables under investigation include developmental timepoint, brain region, and lesion status (lesion core, distal white matter, and control). These samples enable comparative analyses of spatiotemporal dynamics in brain development and demyelination.

first: Zhang

last: Di

first: Kirby

last: Leslie


title: Spatial dynamics of brain development and neuroinflammation [Spatial Transcriptomics]

summary: Spatially mapping multiple omics layers across time enables dissection of mechanisms underlying brain development, differentiation, arealization, and disease. Here, we deploy spatial tri-omics to chart spatiotemporal remodeling in development and neuroinflammation. We generate a tri-omic atlas of mouse brain from postnatal day P0–P21 and compare corresponding regions in developing human brain. In cortex, a subset of layer-defining transcription factors shows temporally persistent and spatially spreading chromatin accessibility. In corpus callosum, myelin genes exhibit dynamic chromatin priming across subregions, and layer-specific projection neurons appear to coordinate axonogenesis and myelination. In a lysolecithin (LPC) model, we observe molecular programs shared between development and neuroinflammation. Microglia display conserved and distinct inflammatory and resolution programs and are transiently activated both at lesion cores and at distal sites, presumably via neuronal circuitry. These data reveal common and divergent mechanisms and provide a resource for studying brain development, function, and disease.

first: Leslie

last: Kirby


title: Transcriptomic analysis of budding yeast with re-engineering acetyl coenzyme A metabolic pathways that prevent senescence

city: Cambridge

first: Laura

last: Biggins

address: Babraham Research Campus

department: Bioinformatics

institute: The Babraham Institute

summary: mRNA sequencing was performed on young and 48h aged MEP yeast in wild type, over-expressed SAK1, and ALD6 deletion cells

overall_design: MEP cells were collected at log or aged (48h) before being collected, ethanol fixed, and purified using the MEP protocol.

first: Hanane

last: Hadj-Moussa

first: Megan

last: Ulusan

first: Dorottya

last: Horkai

first: Jonathan

last: Houseley


title: Bilayer Heterogeneous Methacrylated-Silk Fibroin Scaffold with Antibacterial and Osteoinductive Functions for Treating Infectious Bone Defects

city: 成都市

first: Zhuojun

last: Xie

state: 四川省

address: 成都市人民南路三段14号

institute: Sichuan University

summary: Infectious bone defects (IBDs) pose a significant clinical challenge due to the simultaneous requirements for effective infection control and robust bone regeneration, and guided bone regeneration (GBR) using multifunctional scaffolds offers a promising therapeutic strategy. Herein, we developed a bilayer hydrogel scaffold (DSHM) based on methacrylated silk fibroin (SilMA) integrated with hydroxyapatite (HA) and minocycline hydrochloride (MH) to address these demands. By precisely optimizing the concentrations of SilMA, photoinitiator, HA, and MH, we engineered a bilayer structure featuring a porous HA-loaded layer (PSH, ~432.1 μm) to enhance mechanical strength and support osteogenic differentiation, and a dense MH-loaded layer (DSM, ~34.6 μm) to act as a barrier against fibrous tissue ingrowth and provide sustained antibacterial effects. The interface-crosslinked DSHM scaffold exhibited a well-defined heterogeneous architecture, improved mechanical properties, tunable degradation, and excellent biocompatibility. Notably, DSHM demonstrated synergistic multifunctionality, including inhibition of fibroblast infiltration, promotion of bone tissue regeneration, and effective infection control. Overall, the DSHM scaffold presents a robust approach for localized and targeted treatment of IBDs, with strong potential for clinical translation.

overall_design: To explore the potential antibacterial and osteogenic mechanisms of the materials, whole-transcriptome RNA sequencing (RNA-seq) was performed on tissue samples using high-throughput transcriptomic analysis. Six SD rats (aged 6–8 weeks) were used to establish infectious cranial defect models as previously described and were randomly assigned to two groups: one receiving DSHM implantation and the other serving as a blank control. Two weeks post-implantation, the rats were euthanized, and tissues from the defect regions were carefully dissected, rinsed with pre-chilled sterile PBS, blotted dry, and immediately transferred into cryovials containing RNA-later (5 mL, Beyotime). Samples were snap-frozen in liquid nitrogen and sent to Suzhou Genewiz Biological Technology Co., Ltd. (China) for high-throughput RNA sequencing and subsequent bioinformatics analysis.

first: Mengqi

last: Luo

first: Wenjie

first: Liming

last: Ge

first: Changdao

last: Mu

first: Defu

first: Zhilang

last: Xu

first: Ye

last: Tian

first: Xianglong

last: Han


title: RRBS-seq of single-cell clones of four cell Lines reveals highly-conserved methylated sites in DNA

city: Shanghai

first: Yicen

last: Ding

address: 800 Dongchuan Road, Shanghai, China

institute: Shanghai Jiao Tong University

summary: DNA methylation is one of the most studied epigenetics, and its effects on embryonic development, cell differentiation, cell development, aging, apoptosis, carcinogenesis, and genomic stability are all im-portant. In the classical epigenetic model, cytosine methylation is steadily transmitted to daughter cells with fidelity as DNA replicates. However, a large number of studies have shown that there are detectable changes in DNA methylation at many CpG sites during DNA replication. In this study, we selected four different types of cell lines, A549, ARPE-19, Jurkat and SW1353. For a single CpG site in a single cell, there are only three methylation states, 100% methylation, 50% methylation, and 0% methylation, and any DNA methylation that deviates from these three results indicates a methylation change. We used reduced representative bisulfite sequencing (RRBS)  to screen out methylation sites.

overall_design: RRBS-seq combined with RNA-seq analysis to find high-fidelity methylation CpG sites in four kinds of cell lines

first: Fei

first: Mengju

last: He

first: Yani

last: Kang


title: RRBS-seq of single-cell clones of four cell Lines reveals highly-conserved methylated sites in DNA [RNA-Seq]

last: Zhang


title: A regulator of amino acid catabolism controls Acinetobacter baumannii gut colonization

first: Lauren

middle: D

last: Palmer

address: 835 S Wolcott Ave

department: Microbiology and Immunology

institute: University of Illinois Chicago

summary: Asymptomatic gut colonization increases the risk of clinical infection and transmission by the multidrug-resistant pathogen Acinetobacter baumannii. Ornithine utilization was shown to be critical for A. baumannii competition with the resident microbiota to persist in gut colonization, but the regulatory mechanisms and cues are unknown. Here, we identify a transcriptional regulator, AstR, that specifically activates the expression of the A. baumannii ornithine utilization operon astNOP. Phylogenetic analysis suggests that AstR was co-opted from the Acinetobacter arginine utilization ast(G)CADBE locus and is specialized to regulate ornithine utilization in A. baumannii. Reporter assays showed that astN promoter expression was activated by ornithine but inhibited by glutamate and other preferred amino acids. astN promoter expression was similarly activated by incubation with fecal samples from conventional mice but not germ-free mice, suggesting AstR-dependent activation of the astN promoter responds to intermicrobial competition for amino acids. Finally, AstR was required for A. baumannii to colonize the gut in a mouse model. Together, these results suggest that pathogenic Acinetobacter species evolved AstR to regulate ornithine catabolism, which is required to compete with the microbiota during gut colonization.

overall_design: RNA-seq profiling of A. baumannii wildtype and ∆astR strains grown to mid-log phase and then washed and incubated in minmal M9 medium with ornithine, succinate, or NH4Cl as the sole carbon or nitrogen sources (succinate/NH4; ornithine/NH4; succinate/ornithine)


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

city: Glasgow

first: Kathryn

last: Gilroy

address: Garscube

institute: CRUK Scotland Institute

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

overall_design: Organoids derived from either small intestinal tumours or liver metastasis, from mice with mutations in either Kras/P53/Notch1 or Apc/Kras/P53/Tgfbr1, were sequenced using Gem-X flex single cell technology.

first: Mark

last: White

first: Megan

last: Mills

first: Laura

last: Millett

first: Owen

last: Sansom


title: Changes in Histone H3 acetylation in panobinostat-treated IDH-wildtype and IDH-mutant glioma cultures

first: Thomas

last: Sears

summary: IDH1/2 mutations (IDHmut) increase methylation of DNA and histones in gliomas. IDHmut inhibitors are effective against low-grade IDHmut gliomas, but new strategies against high grade IDHmut gliomas are needed. Although histone deacetylase inhibitors (HDACi) are ineffective against IDHwt glioblastoma (GBM), their potential in IDHmut gliomas has not been extensively studied. We previously established that IDHmut gliomas are more sensitive to HDACi than IDHwt GBM. Here we show that IDHmut is associated with greater sensitivity to HDACi in glioma. While HDACi induced more histone acetylation and gene regulation in IDHmut glioma than in IDHwt GBM, ChIP-Seq studies show such acetylation was mostly within gene deserts, whereas IDHmut glioma promoters paradoxically lost histone acetylation.

overall_design: H3KAc ChIP-Seq on IDH wildtype (0827, 0923) and IDH mutant (0905, BT142) treated with and without the HDACi panobinostat

first: Craig

last: Horbinski


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

overall_design: Following treatment with either vehicle or a combination of Braf and EGFR inhibition, tumours in mice with mutations in Braf, P53 and Rnf43 were sequenced by Gem-X flex single cell sequencing after 1 or 3 days.


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

overall_design: Mice were induced with a single 70uL injection of 100uM 4-OH tamoxifen into the colonic submucosa. When an established tumour was identified on colonoscope (beginning weekly two weeks post injection), mice were placed on a treatment regime. Mice were treated once  daily with AZD4625 (OG 100uL 100mg/kg) or vehicle (0.5% HPMC 0.1% Tween 80) for 4 days and sampled two hours post dose on the fourth day.


title: Transcriptome profiling of porcine valvular interstitial cells undergoing mesenchymal-to-endothelial transition under osteogenic induction

city: shanghai

first: Binglin

last: Li

state: 上海

address: 241 Huaihai West Road, Xuhui District, Shanghai, China

institute: shanghai chest hospital

summary: Calcific aortic valve disease (CAVD) is a progressive disorder characterized by fibrosis, calcification, and endothelial dysfunction. Valvular interstitial cells (VICs) are the predominant cell type within the aortic valve and play key roles in valve remodeling. Recent evidence suggests that VICs exhibit phenotypic plasticity and may undergo mesenchymal-to-endothelial transition (MEndT) under calcific conditions. To explore the transcriptional landscape of this process, we performed RNA sequencing on primary porcine VICs cultured in growth medium (GM), osteogenic medium (OM) for 8 days, and primary porcine valve endothelial cells (pVECs). This dataset provides a resource for understanding the molecular mechanisms underlying MEndT and its potential contribution to CAVD pathogenesis.

overall_design: Primary porcine aortic valve interstitial cells (pVICs) and valve endothelial cells (pVECs) were isolated from healthy pig aortic valves. Three experimental groups were established: pVICs cultured in growth medium (GM) (n = 4 biological replicates), pVICs cultured in osteogenic medium (OM) for 8 days (n = 4 biological replicates), pVECs cultured in growth medium (GM) (n = 4 biological replicates). RNA was extracted from each sample, and sequencing libraries were prepared and sequenced on the Illumina platform. Each group contained four independent biological replicates, yielding a total of 12 samples.

first: Dan

last: zhu


title: cGAS-STING Pathway Mediation in Osteoclast Function and Bone Fracture Healing

first: miaomiao

last: zheng

address: No. 168 Changhai Road, Yangpu District

institute: Changhai Hospital

summary: Inflammation, as a crucial initial phase of bone healing, typically commences in the early stages of fracture repair. The cGAS-STING pathway serves as a key mediator of inflammation. The aim of this study is to explore the biological role and molecular mechanisms of the cGAS-STING pathway in the fracture healing process, with a particular focus on its function during the early inflammatory phase.

overall_design: A murine femoral fracture model was utilized to investigate the activation of the cGAS-STING pathway during the early and late stages of bone healing. The methodologies encompassed transcriptome sequencing and immunohistochemistry. Pathway modulation was accomplished through the application of the STING inhibitor H-151 and the activator SR-717, with the effects being assessed via in vivo experiments (transcriptome sequencing, microCT, safranin O-fast green staining, and TRAP staining) and in vitro assays (TRAP staining, F-actin ring formation, bone resorption tests, qPCR, and Western blot analysis).

first: Miaomiao

last: Zheng


title: Spatial dynamics of brain development and neuroinflammation

first: Di

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

The full dataset is available via the NeMO Archive, including controlled-access human data and mouse data. This GEO Series provides a mirror of the mouse subset.

overall_design: Refer to individual Series

first: Leslie

last: Kirby


title: The Rip1 cytochrome bc1 catalytic subunit modulates antifungal tolerance in Candida auris

city: Vienna

first: Trinh

last: Phan-Canh

email: phancanht99@univie.ac.at, phancanhtrinh@gmail.com, karl.kuchler@univie.ac.at, karl.kuchler@univie.ac.at

state: Vienna

address: Dr.-Bohr-Gasse 9

department: Max Perutz Labs Vienna, Campus Vienna Biocenter

institute: Medical University of Vienna

summary: Comparative transcriptomic profiling of Candida auris rip1∆ and WT

overall_design: RNA Sequencing was conducted on a Candida auris B8441 and its rip1∆. The cells were cultivated to the exponential phase in YPD and YP-2% Glycerol at 37°C with agitation at 200rpm. Subsequently, cultures were harvested, and RNA isolation was performed, followed by the preparation of sequencing libraries for three biological replicates.

first: Karl

last: Kuchler


title: Targeting fatty acid synthase suppresses tumor development in NF2/CDKN2A-deficient malignant pleural mesothelioma

city: Nagakute

first: Karnan

last: Sivasundaram

state: Aichi

address: Yazakokarimata

department: Biochemisy

country: Japan

institute: Aichi Medical University

summary: To investigate the effect of cerulenin in NF2/p16 on gene expression, we have emoloyed whole genomic microarray expression profiling using HOMC-B1 and MeT-5Acells

overall_design: The HOMC-B1 and MeT-5A cells were plated at 80% confluence and cultured for 24 hours in vitro.

first: Akinobu

last: Ota

first: Sivasundaram

last: Karnan


title: Dual-Targeted Ping-Pong CAR T Cells: Leveraging Peripheral Expansion to Improve Solid Tumor Immunotherapy

city: Philadelphia

first: Regina

middle: M.

last: Young

state: Pennsylvania

address: 3400 Civic Center BLVD

department: CCI

institute: University of Pennsylvania

summary: Clinical responses to CD19-directed CAR T cell therapy in B cell malignancies are strongly associated with robust CAR T cell expansion in the peripheral blood. In contrast, CAR T cells targeting solid tumors do not encounter cognate antigen in the periphery, resulting in limited expansion and subtherapeutic peak concentrations. To overcome this, we engineered dual-targeted and dual-co-stimulated CAR T cells (CD19/28ζ-M5BBζ) that recognize CD19+ B cells, thereby promoting peripheral expansion and increasing the pool of solid tumor-directed CAR T cells available for tumor infiltration without the need for lymphodepletion. In immunocompetent C57BL/6 mouse models of pancreatic ductal adenocarcinoma and melanoma, these dual-targeted CAR T cells demonstrated enhanced peripheral expansion, improved anti-tumor efficacy, and increased survival without added dysfunction or toxicity compared to single antigen-targeted CAR T cells. We translated our findings to human CAR T cells by developing a novel pancreatic/xenograft model with CD19⁺ B cells in the periphery and again demonstrated that treatment with dual CAR T cells showed significantly enhanced tumor clearance and survival compared to single antigen-targeted CAR T cells. In conclusion, we demonstrate that dual-targeted CAR T cells boost peripheral expansion, and anti-tumor efficacy, providing a strategy for enhancing outcomes for patients treated with clinical CAR T products targeting solid tumors.

overall_design: Bulk RNA-seq of CD45.1+ CAR T cells in the spleen of mice engrafted with PDAC 7940b tumors at day 6 to compare dual-co-stimulated CAR T cells (CD19/28ζ-A03BBζ) to control CAR T cells (A03BBζ).

first: Amanda

middle: V

last: Finck

first: Ziming

last: Wang

first: Linhui

last: Chen

first: Carl

middle: H

last: June


title: Bone Marrow Failure (BMF) Model Mimics Aplastic Anemia (AA) Patients: Single-Cell Landscape of Immune Response Reveals Novel Mechanisms of Immune Imbalance in AA

first: yumeng

address: Changchun street.

department: Xuanwu hospital

institute: Capital Medical University

summary: Background: the pathogenesis of HSPCs impairment in aplastic anemia (AA) remains unclear.We focused on CD8+ T cells, and investigated platelets, CD4+ T cells, macrophages, and mitochondrial energy metabolism, aiming to elucidate the cellular atlas changes associated with bone marrow failure (BMF). Methods: We have successfully established a mouse model of bone marrow failure and analyzed the immune response at the single-cell level. Results: platelets regulate CD4+/CD8+ T cells, and macrophages by releasing PF4. CXCR3/CXCR5 bind to PF4, activating mitochondrial signaling pathways. The decrease of Treg, weakening immunosuppression. Additionally, there is a significant increase in CD8+ effector T cells. Increased energy metabolism was observed in CD8+ stress T cells. It should be noted that, platelet reduction itself in AA weakens energy metabolism, subsequently impairing the hemostatic and thrombotic functions. However, platelets' regulatory function in immune cells remains significant. An imbalance in M1 and M2 macrophage polarization is observed. While a phenotype macrophage and CD8+ naive T cells are important cell phenotypes in marrow aging, not contribute to pathology failure. Conclusion: the possible mechanisms of BMF in AA: based on PF4, platelet-T cell/macrophage crosstalk leads to immune overactivation and the release of cytokines such as IFN-γ and TNF-α, which attack the marrow. Therefore, transforming imbalanced CD8+ effector T cells, stress T cells, Treg cells, and M1/M2 macrophages into CD8+ naive T cells and a phenotype of macrophages via inhibiting platelet immune regulatory function, may provide a promising strategy to reverse BMF.

overall_design: The mice were divided into four groups: The BMF group (experimental group), the total-body irradiation (TBI) group (control group), the normal young mouse group (wild type, WT), and the normal aged mouse group (Aged). Bone marrow samples were collected from all four groups, with one sample from each group, for a Single Cell RNA-seq Workflow (WTA for whole-transcriptome amplification and ABseq for antibody sequencing) (Fig 1A). The study was approved by the Experimental Animal Welfare Ethics Committee of Xuanwu Hospital, Capital Medical University (approval number: XW-20210531-1). The more details were in "Supplementary materials-METHODS", and the Fig 1A for the experimental design.

first: Shuai

last: Tan

first: Fang

last: Fang

first: Jing

last: Sun

first: Yumeng

first: Yaochi

first: Wanling

last: Sun*


title: Characterization of SARS-CoV-2–Specific B Cell Responses in Breakthrough and Multiple Infection Cohorts

city: New York

first: Patrick

last: Wilson

state: NY

address: 413 E 69th St

department: Drukier Institute

institute: Weill Cornell Medicine

summary: We analyzed the B cell responses after infection in two cohorts: individuals with breakthrough infections following SARS-CoV-2 vaccination and individuals with multiple SARS-CoV-2 infections.

overall_design: SARS-CoV-2–specific B cells were sorted from PBMCs obtained from both the breakthrough infection cohort and the multiple-infection cohort, and LIBRA-seq was used to assess their antigen reactivity to SARS-CoV-2 and gene expression profiles.

first: Siriruk

last: Changrob

first: Atsuhiro

last: Yasuhara

first: Jordan

last: Chervin

first: Chloe

last: Troxell


title: Proliferative diabetic retinopathy subtypes defined by immune defense and endothelial mitochondrial dysfunction

city: Chicago

first: Andrius

last: Kazlauskas

address: 1855 W Taylor Street

department: Ophthalmology & Visual Sciences

summary: Proliferative diabetic retinopathy (PDR) is a major complication of diabetes characterized by pathological angiogenesis in the retina. Standard treatment includes vitrectomy to remove these abnormal vessels, and the resulting clinical specimens provide an opportunity to define drivers of PDR. Here, we profiled endothelial and immune cells from such samples to identify disease mechanisms. In some patients, endothelial cells were more abundant, whereas in others, immune cells predominated. Immune cells exhibit gene expression programs directed against pathological endothelium, suggesting an endogenous defense that may explain the scarcity of endothelial cells in certain cases. Preoperative anti-vascular endothelial growth factor (VEGF) therapy altered transcriptional programs in both endothelial and immune cells, indicating that its effects extend beyond the vasculature. A comparison of endothelial signatures from PDR patients and nondiabetic donor retinas revealed a distinct molecular program in PDR, prominently marked by mitochondrial dysfunction. In contrast, endothelial cells from the murine oxygen-induced retinopathy (OIR) model lacked mitochondrial dysfunction, although other features of pathological angiogenesis were shared. These findings suggest that PDR is not a uniform disease but comprises distinct types characterized by either immune-mediated clearance of pathological vessels or endothelial mitochondrial dysfunction. They also revealed that anti-VEGF therapy influences both endothelial and immune compartments, with implications for treatment strategies. Finally, the data clarify both the relevance and limitations of the OIR model for preclinical testing of new therapeutic targets.

overall_design: RNA-Seq analysis of CD31+ cells isolated from vitreous removed from patients with proliferative diabetic retinopathy during vitrectomy.

first: Maximilian

last: McCann

first: Basma

last: Baccouche

first: Yueru

last: Li

first: Priti

last: Roy

first: Neil

last: Sheth

first: Jennifer

last: Lim

first: William

last: Mieler

first: Felix

last: Chau

first: Lawrence

last: Ulanski

first: Paul

last: Chan

first: Monique

last: Munro

first: Robert

last: Hyde

first: Caitlin

last: Berek

first: Anna

last: Ong

first: Sudeshna

last: De

first: Barbara

last: Siedlecki

first: Ru-Ik

last: Chee

first: Yannek

last: Leiderman

first: Michael

last: Heiferman