详细内容（前10条）

1. ⭐ GSE312235 肿瘤通过不同细胞类型劫持免疫豁免调节子，从而导致多种癌症中T细胞遗弃和免疫治疗耐药性

• ✍️ 作者：未知作者
• 🏷️ 关键词：immune、T cell、regex:immuno(logy|therapy|suppression)、resistance
• 📝 描述：Contributors : Bashir Lawal ; Akshat Gupta ; Renu Sharma ; Rohit Bhargava ; Yue Wang ; Xiaosong WangSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensImmune checkpoint blockade (ICB) has transformed oncology, yet most patients fail to respond, suffer from hyper-progressive disease, or face severe immune-related toxicities, underscoring the urgent need for biomarkers identifying non-responders. Here we show that tumors co-opt an immune-privileging regulon signature (IMPREG) mirroring transcriptional programs of immune-privileged organs — to enforce T-cell desertion and ICB resistance across cancer types. Single-cell and spatial transcriptomic analyses reveal that tumors activate IMPREG through three distinct cellular routes — malignant cells adopting immature neuronal states, cancer-associated fibroblasts assuming myofibroblast identities, or endothelial cells — each creating localized niches of immune suppression and antigen-presentation collapse. Across 4 discovery and 36 validation clinical datasets, IMPREG consistently predicts immunotherapy resistance in 14 distinct cancer types, functioning as an orthogonal marker independent of established biomarkers. Crucially, IMPREG-expressing tumors show enhanced sensitivity to EGFR inhibitors or anti-angiogenic therapies in specific tumor entities. These findings suggest IMPREG as a dual-utility predictive biomarker for personalized treatment stratification.
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2. ⭐ GSE319127 可喷涂纳米酶水凝胶通过表观遗传学重编程炎症促进糖尿病伤口再生 [GeoMX 空间转录组学]

• ✍️ 作者：未知作者
• 🏷️ 关键词：inflammation、spatial、spatial transcriptomics、transcriptomics
• 📝 描述：Contributors : Amal George Kurian ; Jeong-Hui Park ; Shanika Karunasagara ; Archita Gupta ; Shreyas Kumar Jain ; Tanza Baby ; Ueon Sang Shin ; Sak Lee ; Rajendra K Singh ; Jung-Hwan Lee ; Kam W Leong ; Hae-Won KimSeries Type : OtherOrganism : Rattus norvegicusChronic diabetic wounds present a critical clinical challenge due to persistent inflammation and compromised healing. Here we report a novel sprayable nanozyme hydrogel that epigenetically reprograms macrophages to suppress inflammation and coordinate regeneration. Ultrasmall copper-based nanozymes (CuNZ, ~4 nm) synthesized via an eco-friendly one-pot method demonstrated potent multi-radical scavenging activity. When integrated into gelatin methacryloyl (Gel), CuNZ@Gel exhibited excellent sprayability, conformal skin coverage, and long-term storage stability, offering substantial translatable potential. Notably, the nanozyme hydrogel induced distinct epigenetic modifications in macrophages by remodeling chromatin accessibility, effectively shifting gene expression from pro-inflammatory to anti-inflammatory profiles. This epigenetic modulation persisted under oxidative stress, actively suppressing inflammatory while facilitating regenerative responses. In diabetic wound models, CuNZ@Gel significantly accelerated healing through its coordinated antioxidant, anti-inflammatory, and pro-regenerative actions. Unlike conventional passive dressings, our sprayable nanozyme hydrogel proactively reprograms the wound microenvironment via epigenetic antioxidant mechanisms, offering novel insights and strategy for managing chronic diabetic wounds and inflammatory skin complications.
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3. GSE325176 大型基因组中顺式调控元件的全基因组发现 [scATAC-seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：scATAC、genome
• 📝 描述：Contributors : Gillian Forbes ; Emilia Skafida ; Michalis Averof ; Mathilde ParisSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Parhyale hawaiensisIdentifying non-coding regulatory elements in the genome poses a challenge in most organisms. Classical methods rely on trial and error to test the regulatory activities of DNA fragments using reporter constructs. In large eukaryotic genomes, where cis-regulatory elements can spread over long distances, separated by large stretches of non-functional DNA, this trial and error approach is particularly challenging. Here, we generate two types of resources that can be used to narrow the search for such cis-regulatory elements in the 3.6 Gbp genome of Parhyale hawaiensis (comparable in size to the human genome). First, we use bulk ATACseq to uncover genome-wide patterns of chromatin accessibility in embryonic and adult tissues of Parhyale (whole embryos and legs), and single-nucleus ATACseq to identify regions of open chromatin in diverse cell types recovered from adult legs, including epidermal, neuronal, muscle and blood cells. Second, by sequencing the genomes of three congeneric species of Parhyale hawaiensis – P. darvishi, P. aquilina and P. plumicornis – we identify islands of sequence conservation across the genome, corresponding to DNA elements that are functionally constrained during evolution. We present an approach by which low-coverage (10-15x) short-read genome sequencing, without genome assembly, is sufficient to provide reliable maps of sequence conservation. This approach cuts the cost and labour required to generate these maps, making the identification of cis-regulatory elements more widely accessible. We demonstrate the utility of these resources by identifying cis-regulatory elements that drive robust expression of fluorescent reporters ubiquitously and in specific cell types.
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4. GSE325175 大型基因组中顺式调控元件的全基因组发现 [bulk ATAC-seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：ATAC-seq、genome
• 📝 描述：Contributors : Gillian Forbes ; Emilia Skafida ; Çağrı Çevrim ; Michalis Averof ; Mathilde ParisSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Parhyale hawaiensisIdentifying non-coding regulatory elements in the genome poses a challenge in most organisms. Classical methods rely on trial and error to test the regulatory activities of DNA fragments using reporter constructs. In large eukaryotic genomes, where cis-regulatory elements can spread over long distances, separated by large stretches of non-functional DNA, this trial and error approach is particularly challenging. Here, we generate two types of resources that can be used to narrow the search for such cis-regulatory elements in the 3.6 Gbp genome of Parhyale hawaiensis (comparable in size to the human genome). First, we use bulk ATACseq to uncover genome-wide patterns of chromatin accessibility in embryonic and adult tissues of Parhyale (whole embryos and legs), and single-nucleus ATACseq to identify regions of open chromatin in diverse cell types recovered from adult legs, including epidermal, neuronal, muscle and blood cells. Second, by sequencing the genomes of three congeneric species of Parhyale hawaiensis – P. darvishi, P. aquilina and P. plumicornis – we identify islands of sequence conservation across the genome, corresponding to DNA elements that are functionally constrained during evolution. We present an approach by which low-coverage (10-15x) short-read genome sequencing, without genome assembly, is sufficient to provide reliable maps of sequence conservation. This approach cuts the cost and labour required to generate these maps, making the identification of cis-regulatory elements more widely accessible. We demonstrate the utility of these resources by identifying cis-regulatory elements that drive robust expression of fluorescent reporters ubiquitously and in specific cell types.
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5. GSE325124：未经处理和ConA处理小鼠肝脏免疫细胞的单细胞转录组分析

• ✍️ 作者：未知作者
• 🏷️ 关键词：immune、single-cell
• 📝 描述：Contributors : Wenyu Tian ; Weixuan Wang ; Dan LvSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusHepatic immune tolerance is essential for maintaining liver homeostasis, but its underlying cellular and molecular mechanisms remain poorly defined. In this study, we established a low-dose concanavalin A (ConA)-induced immune tolerance model in mice and performed single-cell RNA sequencing (scRNA-seq) on hepatic immune cells isolated from untreated (UT) and ConA-treated groups. Transcriptomic profiling revealed substantial remodeling of the hepatic immune microenvironment following low-dose ConA stimulation. Notably, we observed a pronounced activation of type II immune responses, characterized by enrichment of Th2-associated cytokine signatures and expansion of Th2, Tfh subsets. Further analysis identified B cells as potential key contributors to this process, exhibiting distinct transcriptional programs associated with humoral immunity that may play a role in the establishment of immune tolerance.
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6. GSE317333 NRasG12V/myrAKT驱动的肝细胞癌在Sepp1敲低和硒补充治疗下的单细胞转录组分析

• ✍️ 作者：未知作者
• 🏷️ 关键词：carcinoma、single-cell
• 📝 描述：Contributors : Jiazheng Jiao ; Lixing ZhanSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusThe immune microenvironment of hepatocellular carcinoma (HCC) is strongly influenced by tumor-infiltrating neutrophils, whose functional heterogeneity and regulatory mechanisms remain incompletely defined. Selenium metabolism, mediated by selenoprotein P (Sepp1), plays an important role in redox homeostasis and immune regulation in the liver.In this study, Ras/AKT-driven murine HCC models with Sepp1 knockdown were generated under control or selenium-supplemented conditions. Single-cell RNA sequencing was performed using the 10x Genomics Chromium platform to profile tumor tissues and the associated tumor microenvironment, with a particular focus on neutrophil populations.This dataset enables systematic analysis of neutrophil transcriptional states associated with selenium metabolism and immunoregulatory pathways in HCC. The data provide a resource for investigating how alterations in Sepp1 expression and selenium availability shape tumor-immune interactions at single-cell resolution.
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7. GSE320430 可喷涂纳米酶水凝胶通过表观遗传学方法重编程炎症以促进糖尿病伤口再生 [Chip-seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：inflammation、ChIP-seq
• 📝 描述：Contributors : Amal George Kurian ; Jeong-Hui Park ; Shanika Karunasagara ; Archita Gupta ; Shreyas Kumar Jain ; Tanza Baby ; Ueon Sang Shin ; Sak Lee ; Buuvee Bayarkhangai ; Rajendra K Singh ; Jung-Hwan Lee ; Kam W Leong ; Hae-Won KimSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusChronic diabetic wounds present a critical clinical challenge due to persistent inflammation and compromised healing. Here we report a novel sprayable nanozyme hydrogel that epigenetically reprograms macrophages to suppress inflammation and coordinate regeneration. Ultrasmall copper-based nanozymes (CuNZ, ~4 nm) synthesized via an eco-friendly one-pot method demonstrated potent multi-radical scavenging activity. When integrated into gelatin methacryloyl (Gel), CuNZ@Gel exhibited excellent sprayability, conformal skin coverage, and long-term storage stability, offering substantial translatable potential. Notably, the nanozyme hydrogel induced distinct epigenetic modifications in macrophages by remodeling chromatin accessibility, effectively shifting gene expression from pro-inflammatory to anti-inflammatory profiles. This epigenetic modulation persisted under oxidative stress, actively suppressing inflammatory while facilitating regenerative responses. In diabetic wound models, CuNZ@Gel significantly accelerated healing through its coordinated antioxidant, anti-inflammatory, and pro-regenerative actions. Unlike conventional passive dressings, our sprayable nanozyme hydrogel proactively reprograms the wound microenvironment via epigenetic antioxidant mechanisms, offering novel insights and strategy for managing chronic diabetic wounds and inflammatory skin complications.
• 🔗 查看原文

8. GSE315167 可喷涂纳米酶水凝胶通过表观遗传学重编程炎症以促进糖尿病伤口再生 [ATAC-seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：inflammation、ATAC-seq
• 📝 描述：Contributors : Amal George Kurian ; Jeong-Hui Park ; Shanika Karunasagara ; Archita Gupta ; Shreyas Kumar Jain ; Tanza Baby ; Ueon Sang Shin ; Sak Lee ; Rajendra K Singh ; Jung-Hwan Lee ; Kam W Leong ; Hae-Won KimSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusChronic diabetic wounds present a critical clinical challenge due to persistent inflammation and compromised healing. Here we report a novel sprayable nanozyme hydrogel that epigenetically reprograms macrophages to suppress inflammation and coordinate regeneration. Ultrasmall copper-based nanozymes (CuNZ, ~4 nm) synthesized via an eco-friendly one-pot method demonstrated potent multi-radical scavenging activity. When integrated into gelatin methacryloyl (Gel), CuNZ@Gel exhibited excellent sprayability, conformal skin coverage, and long-term storage stability, offering substantial translatable potential. Notably, the nanozyme hydrogel induced distinct epigenetic modifications in macrophages by remodeling chromatin accessibility, effectively shifting gene expression from pro-inflammatory to anti-inflammatory profiles. This epigenetic modulation persisted under oxidative stress, actively suppressing inflammatory while facilitating regenerative responses. In diabetic wound models, CuNZ@Gel significantly accelerated healing through its coordinated antioxidant, anti-inflammatory, and pro-regenerative actions. Unlike conventional passive dressings, our sprayable nanozyme hydrogel proactively reprograms the wound microenvironment via epigenetic antioxidant mechanisms, offering novel insights and strategy for managing chronic diabetic wounds and inflammatory skin complications.
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9. GSE325169 纠正由中性粒细胞驱动的小胶质细胞正反馈环路过度激活所扰乱的免疫微环境，可有效抑制病理性视网膜血管生成

• ✍️ 作者：未知作者
• 🏷️ 关键词：immune
• 📝 描述：Contributors : Ziyi Zhou ; Tianhao Yuan ; Guorui DouSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusDisrupting Galectin-3/NET-mediated microglia-neutrophil crosstalk suppresses retinal angiogenesis, revealing self-reinforcing immune mechanisms in advanced disease.
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10. GSE325146 体内靶向DNA甲基化编辑[小鼠脾脏]

• ✍️ 作者：未知作者
• 🏷️ 关键词：methylation
• 📝 描述：Contributors : Maria Kalomoiri ; Chiara Sorini ; Sebastiaan Vos ; Anderson Camargo ; Chandana Rao Prakash ; Per Svenningsson ; Majid Pahlevan Kakhki ; Lara Kular ; Maja JagodicSeries Type : Methylation profiling by arrayOrganism : Mus musculus ; Trametes gibbosaThe number of epigenome-wide association studies linking CpG DNA methylation with disease, traits and exposures, continues to rise. Establishing the causation of these associations, despite the rapid development of epigenome editing tools, remains challenging, particularly in vivo. In this study, we developed and characterized three Cre-dependent CRISPR-based mouse lines that enable locus-specific DNA methylation deposition by either constitutive or inducible dCas9-DNMT3A expression. We demonstrate robust locus-specific DNA methylation deposition of MHC class II (H2-Ab1) and interleukin 6 (Il6) genes in bone marrow-derived myeloid cells ex vivo. Moreover, neuron-specific targeting results in decreased cannabinoid receptor 1 (Cnr1) expression in striatal neurons in vivo. Notably, we demonstrate that the causal effect of DNA methylation on gene expression is locus-dependent, reinforcing the necessity of such editing tools for detailed understanding of the role of DNA methylation and for addressing the causality of disease-associated CpGs.
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1. 新型人工智能工具能以惊人的准确率预测癌症扩散。

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer
• 📝 描述：Researchers have discovered that cancer spread isn’t random—it follows a kind of biological “program.” By studying colon tumor cells, they identified gene patterns that signal whether a cancer is likely to metastasize. Their AI model, MangroveGS, can predict this risk with about 80% accuracy and even works across multiple cancer types. This could transform how doctors decide who needs aggressive treatment and who doesn’t.
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• GSE325144 体内靶向DNA甲基化编辑[小鼠脑]
• GSE307672 癌症干细胞通过FAM3C介导的SPIN1稳定化诱导脯氨酸合成以减轻ROS应激
• GSE315168 可喷涂纳米酶水凝胶通过表观遗传学重编程炎症促进糖尿病伤口再生 [mRNA-seq]