详细内容（全部5条）

1. ⭐ GSE312604 CRATER 肿瘤微环境促进 CD8+ T 细胞参与并与免疫治疗成功相关 [空间转录组学]

• ✍️ 作者：未知作者
• 🏷️ 关键词：tumor、T cell、regex:immuno(logy|therapy|suppression)、spatial、spatial transcriptomics、transcriptomics
• 📝 描述：Contributors : Georgia Stirts ; Sophia Liu ; Qiyu Gong ; Irving Barrera ; Aya Ludin ; Leonard Zon ; Fei ChenSeries Type : OtherOrganism : Danio rerioT cell-mediated tumor killing underlies immunotherapy success. Here, we used long-term in vivo imaging and high-resolution spatial transcriptomics of zebrafish endogenous melanoma, as well as multiplex imaging of human melanoma, to identify domains facilitating the immune response during immunotherapy. We identified cancer regions of antigen presentation and T cell engagement and retention (CRATERs) as pockets at the stroma-melanocyte boundaries of zebrafish and human melanoma. CRATERs are rich in antigen-recognition molecules, harboring the highest density of CD8+ T cells in tumors. In zebrafish, CD8+ T cells formed prolonged interactions with melanoma cells within CRATERs, characteristic of antigen recognition. Following immunostimulatory treatment, CRATERs expanded, becoming the major sites of activated CD8+ T cell accumulation and tumor killing. In humans, elevation in CRATER density in biopsies following immune checkpoint blockade (ICB) therapy correlated with a clinical response to therapy. CRATERs are structures that show active tumor killing and may be useful as a diagnostic indicator for immunotherapy success.
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2. GSE307141 研究抗氧化剂表没食子儿茶素没食子酸酯在胎儿酒精谱系障碍中的治疗潜力：认知和RNA测序

• ✍️ 作者：未知作者
• 🏷️ 关键词：RNAseq
• 📝 描述：Contributors : Anna Ramos-Triguero ; Marta Astals-Vizcaino ; Elisabet Navarro-Tapia ; Melina Vieiros ; Adriana Bastons-Compta ; Leopoldo Martínez ; Vicente Andreu-Fernández ; Óscar García-AlgarSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensPrenatal alcohol exposure (PAE) impacts fetal development, leading to Fetal Alcohol Spectrum Disorders (FASD) characterized by cognitive, behavioral, and physical impairments. This study explores Epigallocatechin Gallate (EGCG), a potent antioxidant and modulator of neuronal plasticity, as a therapeutic intervention for FASD improvement. In a 12-month pilot study, patients with 40 FASD received 9 mg/kg/day of EGCG, with outcomes assessed through RNA sequencing of blood samples and neurocognitive evaluations (WISC-IV, CBCL 6-18, and NEPSY-II). Reduced levels of oxidative stress were observed after 6 months of daily treatment with EGCG, to maintain the bioavailability of the molecule in the body, with decreased levels of MDA and 8-isoprostane and increased activity of LDH. Significant neurocognitive improvements were shown after one year of treatment in Perceptual Reasoning Index (PRI) and Working Memory Index (WMI) using the WISC-IV test. CBCL test revealed an improvement in aggressive behavior scores after EGCG treatment. NEPSY-II assessment showed improvements in face memory, and delayed face memory. Interestingly, no significant improvements were observed in intelligence quotient, attention, anxiety, or depression, which affect a proportion of individuals diagnosed with FASD. Additionally, EGCG modulates molecular pathways associated with neuroinflammation, oxidative stress, immune response, and neurogenesis. This study highlights EGCG as a potential therapeutic candidate to ameliorate cognitive and behavioral deficits caused by PAE in children affected by FASD, revealing potential pathways and biomarkers that contribute to these improvements. These advancements ultimately aim to enhance the quality of life for FASD patients and their families.
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3. GSE314992 CXCR4 S338X 变体的表达提高了抗 CD19 CAR-T 细胞的抗白血病疗效

• ✍️ 作者：未知作者
• 🏷️ 关键词：leukemia
• 📝 描述：Contributors : Yushu Mao ; Zheng Hu ; Yong-guang YangSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensChimeric antigen receptor T (CAR-T) cell therapy has demonstrated remarkable success in treating hematological malignancies; however, antigen-positive relapse remains a significant obstacle to achieving sustained remission in B-cell acute lymphoblastic leukemia (B-ALL). To enhance the therapeutic efficacy of anti-CD19 CAR (CAR19)-T cells, we overexpressed CXCR4 in CAR19-T cells to improve their trafficking to bone marrow (BM), a key sanctuary for minimal residual disease. We engineered CAR19-T cells with overexpression of wild-type CXCR4 (CAR19/CXCR4WT-T) or gain-of-function CXCR4 S338X mutant (CAR19/CXCR4S338X-T). Both CAR19/CXCR4WT-T and CAR19/CXCR4S338X-T cells exhibited enhanced CXCR4 surface expression in vitro and in vivo compared to control CAR19-T cells, with the latter showing significantly superior improvements under all tested conditions, including engagement with CAR-specific antigens or CXCR4 ligand CXCL12. Upon engagement with CXCL12, CAR19/CXCR4S338X-T cells, but not CAR19/CXCR4WT-T cells, displayed significantly increased activation of ERK1/2 and AKT signaling pathways, as well as elevated transcription of TNF-α, IFN-γ, granzyme B, CDK6, and BCL2A1, along with strengthened effector functions, chemotaxis, and activation of anti-apoptotic pathways. Furthermore, CAR19/CXCR4S338X-T cells demonstrated significantly improved migration to and retention in the BM accompanied by increased CD45RA+CCR7+ memory T cell populations, which correlated with enhanced anti-leukemic effects following injection into B-ALL-bearing mice. This study offers a potentially effective strategy to improve the functionality and durability of CAR-T cell responses in hematological malignancies.
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4. GSE314919 Wnt 调控小鼠胃细胞分化和类视黄醇代谢基因

• ✍️ 作者：未知作者
• 🏷️ 关键词：metabolism
• 📝 描述：Contributors : Elizabeth Delgado ; Elise S Hibdon ; Theresa M Keeley ; Christopher Q Huynh ; Justin A Colacino ; Linda C SamuelsonSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusBackground & Aims: While recognized as a key regulator of gastrointestinal tissues, Wnt function in the stomach is poorly understood. This study aimed to define Wnt functions and identify Wnt-regulated genes in the stomach. Methods: Wnt signaling was localized using reporter mice. Proliferation was studied after canonical Wnt inhibition in vivo using Sox2-CreERT2; Ctnnb1fl/fl mice and in vitro using gastric organoid cultures. Wnt-regulated genes and potential effector pathways were identified by bulk RNAseq analysis of corpus and antral organoids 24 hours after Wnt inhibition. Retinoid metabolic components were localized in control and Wnt-inhibited mouse stomach by immunostaining. Results: Wnt signaling cells mapped to the base and proliferative region in both corpus and antrum. Wnt inhibition in vivo reduced proliferation and led to gastric stem cell loss. Cell signature analysis of RNAseq data revealed that gastric organoids adopt a surface cell transcriptional profile following Wnt inhibition instead of a basal cell profile. Furthermore, retinoid metabolism terms were differentially expressed after Wnt inhibition, with both corpus and antrum displaying decreased expression of retinoic acid target genes. Immunostaining mouse stomach showed differential localization of retinoid metabolic components in luminal pit cells (ALDH3A1), and basal chief/deep mucous cells (STRA6), with expression changes after b-catenin deletion consistent with the organoid analysis. Conclusion: Wnt signaling is required for gastric stem cell survival and promotes differentiation of cell types at the gland base. Retinoid metabolism is a candidate Wnt-regulated pathway, with cell-specific expression of key components. Localization of the retinol transporter STRA6 to high-Wnt cells at the gland base suggests that they are retinoic acid signaling cells.
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5. GSE314839 DOT1L介导的CDK9甲基化对于DNA双链断裂修复至关重要

• ✍️ 作者：未知作者
• 🏷️ 关键词：methylation
• 📝 描述：Contributors : Yugyeong Kim ; Hyebin Park ; Sang Beom SeoSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensP-TEFb is a key regulator of transcription elongation and is composed of cyclin-dependent kinase 9 (CDK9) and cyclin T1. DOT1L is a histone H3K79 methyltransferase. Here, we show that treatment with the DOT1L inhibitor EPZ-5676 induces transcriptome changes in HCT116 cells. We further demonstrate that DOT1L methylates CDK9 at lysine 56 and that CDK9 methylation-deficient mutant K56A reshapes genome-wide CDK9 occupancy. Notably, changes in CDK9 occupancy are particularly pronounced at double-strand break (DSB)-related genes and are associated with the regulation of their transcription. This idataset includes RNA-seq and ChIP-seq data generated from HCT116 cells.
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详细内容（全部1条）

1. 房间里的大象：空间数据科学中的图神经网络、嵌入和基础模型

• ✍️ 作者：未知作者
• 🏷️ 关键词：spatial
• 📝 描述：Slides: https://jakubnowosad.com/agforum2025 This presentation covered three interconnected deep learning concepts appearing in spatial data science work. Graph Neural Networks (GNNs) are a deep learning architecture that represents spatial dat… Continue reading: Elephant(s) in the room: Graph neural networks, embeddings, and foundation models in spatial data science
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详细内容（全部3条）

1. SARS-CoV-2感染改变肺细胞lncRNA的RNA甲基化

• ✍️ 作者：未知作者
• 🏷️ 关键词：methylation
• 📝 描述：When a virus infects a cell, it does more than just hijack the machinery to make new virus particles. It can also subtly reshape how the cell regulates its own RNA. Researchers from the Center for Medical Bioinformatics, Escola Paulista de Medicina, Federal University of São Paulo (UNIFESP) explored this idea by looking at …
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2. Hummingbird Diagnostics公司发表了关于液体活检中RNA生物标志物甲基化的研究报告

• ✍️ 作者：未知作者
• 🏷️ 关键词：methylation
• 📝 描述：Revealing a new layer in lung cancer diagnostics using direct RNA sequencing Hummingbird Diagnostics GmbH, a pioneer in harnessing blood-based small RNAs for early disease detection and characterization, today announced the publication of a new study in Nature Communications Medicine introducing an Oxford Nanopore Technologies (ONT)-based method for detecting small RNA modifications in blood The …
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3. 技术进步揭开了线粒体DNA之谜——我们的“另一个”基因组

• ✍️ 作者：未知作者
• 🏷️ 关键词：genome
• 📝 描述：About 1.8 billion years ago, one of our earliest ancestral cells engulfed a bacterial cell. Rather than being digested, the bacterium survived, and the two cells formed a partnership that persists to this day. Over time, that bacterium evolved into mitochondria, organelles found within cells whose role is echoed in science classrooms as being …
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