详细内容（前10条）

1. ⭐ GSE317003 Kmt2c/Kmt2d 缺陷型胃癌的表观遗传和转录改变 [ChIP-Seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、ChIP-seq、epigenetic
• 📝 描述：Contributors : Dan Li ; Naitao Wang ; Yu ChenSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusKMT2C and KMT2D are two of the most frequently mutated genes in gastric adenocarcinoma, yet their function in cancer initiation remains poorly understood. In this study, we developed mouse models to investigate the molecular mechanism of Kmt2c/d loss in gastric tumorigenesis.
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2. ⭐ GSE316994 Kmt2c/Kmt2d 缺陷型胃癌的表观遗传和转录改变 [RNA-seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、RNA-seq、epigenetic
• 📝 描述：Contributors : Dan Li ; Naitao Wang ; Yu ChenSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusKMT2C and KMT2D are two of the most frequently mutated genes in gastric adenocarcinoma, yet their function in cancer initiation remains poorly understood. In this study, we developed mouse models to investigate the molecular mechanism of Kmt2c/d loss in gastric tumorigenesis.
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3. ⭐ GSE329359 无菌和SPF小鼠在LCMV Docile感染后16天，从SI-LP和脾脏中分选的gp33四聚体阳性CD8 T细胞的单细胞RNA测序[scRNA-Seq 10x]

• ✍️ 作者：未知作者
• 🏷️ 关键词：sequencing、scRNA、10x
• 📝 描述：Contributors : Miriam Kuhlmann ; Gustavo P de Almeida ; Wurmser Christine ; Dietmar ZehnSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusProlonged antigen exposure in chronic viral infections reduces the effector capacity of cytotoxic T cells - a phenomenon known as T cell exhaustion. Development of T cell exhaustion is driven by high viral titers, strong TCR stimulation, and high antigen concentrations associated with strong inflammatory signals. A largely unexplored factor has been the influence of the microbiome in these processes. Here, we report that T cell exhaustion progresses independently of the presence or absence of a microbiome in chronic lymphocytic choriomeningitis virus (LCMV) infections. Virus-specific CD8 T cells in germ-free mice showed high expression of the inhibitory receptor PD-1 and decreased cytokine production. Moreover, their global gene expression patterns, as determined by single-cell sequencing, were similar to those of cells in specific pathogen-free mice. In line with this, we observed similar pathogen loads with and without a microbiome. Thus, our study demonstrates that the microbiome is dispensable for the induction of T cell exhaustion and for the limited virus control seen in chronic LCMV infections.
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4. ⭐ GSE329173 整合单细胞和宏观转录组学以解码与重度子痫前期绒毛外滋养层侵袭停滞相关的转录和免疫微环境重塑

• ✍️ 作者：未知作者
• 🏷️ 关键词：immune、single-cell、transcriptomics
• 📝 描述：Contributors : Qihang Zhao ; Xiao Lin ; Juanmei Gao ; Linzhen WuSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensPreeclampsia is a pregnancy-specific systemic disorder that poses significant threats to maternal and perinatal health. The core pathological features of this condition involve shallow invasion of extravillous trophoblasts and defective vascular remodeling at the maternal-fetal interface during early pregnancy. Despite its clinical importance, the transcriptional reprogramming and dynamic cell-to-cell communication at single-cell resolution in severe preeclampsia remain insufficiently explored. This study aims to delineate the lineage shifts of extravillous trophoblasts and the associated immune microenvironment crosstalk
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5. ⭐ GSE316132 黑色素瘤表型可塑性和治疗耐药性的表观遗传调控[ATAC-seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：resistance、ATAC-seq、epigenetic
• 📝 描述：Contributors : Hongkuan Wang ; Hongwen Xuan ; Yucong Yu ; Xiaobing ShiSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensMelanoma progression and treatment failure are driven in part by the ability of tumor cells to undergo dynamic phenotypic state transitions. Here, we identify the SAGA chromatin-modifying complex as a critical epigenetic regulator that constrains melanoma phenotypic plasticity and preserves therapeutic vulnerability. Loss of SAGA-dependent epigenetic regulation disrupts lineage-associated chromatin states, leading to widespread transcriptional reprogramming and enhanced cellular adaptability. As a consequence, SAGA-deficient melanoma cells exhibit increased phenotypic heterogeneity and acquire resistance to targeted therapy. Mechanistically, SAGA loss impairs histone acetylation–dependent control of gene expression programs linked to differentiation and stress responses, enabling the emergence of drug-tolerant cell states. Together, these findings establish SAGA as an epigenetic safeguard against melanoma cell-state plasticity and reveal how disruption of chromatin regulatory complexes promotes therapeutic resistance.
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6. ⭐ GSE316110 黑色素瘤表型可塑性和治疗耐药性的表观遗传调控[ChIP-seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：resistance、ChIP-seq、epigenetic
• 📝 描述：Contributors : Hongkuan Wang ; Hongwen Xuan ; Yucong Yu ; Xiaobing ShiSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensMelanoma progression and treatment failure are driven in part by the ability of tumor cells to undergo dynamic phenotypic state transitions. Here, we identify the SAGA chromatin-modifying complex as a critical epigenetic regulator that constrains melanoma phenotypic plasticity and preserves therapeutic vulnerability. Loss of SAGA-dependent epigenetic regulation disrupts lineage-associated chromatin states, leading to widespread transcriptional reprogramming and enhanced cellular adaptability. As a consequence, SAGA-deficient melanoma cells exhibit increased phenotypic heterogeneity and acquire resistance to targeted therapy. Mechanistically, SAGA loss impairs histone acetylation–dependent control of gene expression programs linked to differentiation and stress responses, enabling the emergence of drug-tolerant cell states. Together, these findings establish SAGA as an epigenetic safeguard against melanoma cell-state plasticity and reveal how disruption of chromatin regulatory complexes promotes therapeutic resistance.
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7. ⭐ GSE311203 空间转录组学和组织病理学分析揭示杜氏肌营养不良症中 2a 型肌纤维的选择性丢失

• ✍️ 作者：未知作者
• 🏷️ 关键词：spatial、spatial transcriptomics、transcriptomics
• 📝 描述：Contributors : Clara Martinez Mir ; Paola Pisterzi ; Isabel De Poorter ; Jamilla Beek ; Anna Alemany ; Fanny Sage ; Niels GeijsenSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusDuchenne muscular dystrophy (DMD) features progressive muscle degeneration with extensive remodeling of fiber type composition and metabolism. To circumvent the lack of regional heterogeneity from bulk or small biopsies studies, we employed spatial transcriptomics, metabolic enzyme profiling, immunohistochemistry, and quantitative fiber-type analysis to map the tibialis anterior (TA) in dystrophic (hDMDdel52/mdx) and control mice. DMD muscles exhibited disrupted metabolic compartmentalization, with reduced central oxidative regions and lower oxidative gene expression. Histology confirmed decreased oxidative enzyme activity and MYH2 expression, the most oxidative type 2 fiber. Analysis across TA, extensor digitorum longus, and soleus muscles revealed consistent MYH2 fiber loss within a mosaic of localized pathological states. Modeling interactions between anatomy and disease highlighted spatially restricted transcriptional programs involving extracellular matrix remodeling, cytoskeletal disruption, and immune infiltration, indicating compartment-specific pathology. This multi-modal, spatially resolved framework advances understanding of muscle remodeling and guides biomarker discovery and therapeutic strategies that account for regional heterogeneity.
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8. GSE329327 Queuosine促进海洋细菌冰川希瓦氏菌(Shewanella glacialimarina)中wecB依赖性噬菌体抗性和生物膜形成

• ✍️ 作者：未知作者
• 🏷️ 关键词：regex:bacter(ia|ial|ium)、resistance
• 📝 描述：Contributors : Pavlina Gregorova ; Minna-Maria K Heinonen ; Nina Sipari ; Peter SarinSeries Type : Expression profiling by high throughput sequencingOrganism : Shewanella glacialimarinaTransfer RNA (tRNA) modifications critically fine-tune translational accuracy and efficiency, influencing bacterial adaptation to environmental challenges. Among these, the queuosine (Q) modification has recently emerged as a regulator of biofilm formation, yet its role during phage infection remains unknown. Here, we investigate how Q modification links host translational control to phage infection. We show that phage infection activates the Q biosynthetic pathway, leading to elevated Q levels and enhanced translation of NAT-biased genes. This shift drives two interconnected outcomes, namely increased biofilm formation and enhanced mutagenesis mediated by translesion synthesis polymerases. We further identify conserved, slippage-prone regions within surface-related genes that act as hotspots for adaptive variation. Together, our findings uncover a novel mechanistic link between tRNA modification and phage-driven bacterial diversification.
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9. GSE329316 在不同硬度基质上培养的海绵体成纤维细胞的转录组测序。

• ✍️ 作者：未知作者
• 🏷️ 关键词：sequencing、transcriptome
• 📝 描述：Contributors : Biao Liu ; Yuzhuo ChenSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensFibrotic diseases involve increased mechanical stress due to extracellular matrix deposition, significantly altering cellular metabolism. However, a systematic understanding of how mechanical force regulates lipid metabolism across different molecular layers remains limited. We employed an integrated multi-omics approach, including transcriptomics, Ribo-seq, proteomics, and lipidomics, to comprehensively assess the effects of mechanical stretch on lipid metabolism in human cavernous fibroblasts. Our analysis revealed that while mechanical force elicits complex multi-layered responses, post-translational regulation predominantly drives this lipid metabolic reprogramming. Lipidomics identified a significant reduction in fatty acids and an upregulation of ganglioside. Key genes central to this mechanosensitive metabolic shift were pinpointed. This study demonstrates that mechanical force hierarchically reprograms lipid metabolism. The shift from fatty acids to ganglioside underscores a key metabolic adaptation in fibroblasts. Targeting the identified critical genes may offer a promising therapeutic strategy for fibrosis-related diseases.
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10. GSE328107 PI3K 调控野生型 RAS 信号通路以赋予其对 KRAS 抑制剂的耐药性

• ✍️ 作者：未知作者
• 🏷️ 关键词：resistance、KRAS
• 📝 描述：Contributors : Xiangyu Ge ; Jaffarguriqbal Singh ; Wenxue Li ; Cassandra S Markham ; Christian F Ruiz ; Stites C Edward ; Moitrayee Bhattacharyya ; Yansheng Liu ; Mandar D MuzumdarSeries Type : OtherOrganism : Homo sapiensDespite the availability of RAS inhibitors and the dependence of >90% of pancreatic ductal adenocarcinomas (PDAC) on oncogenic KRAS mutations, resistance to KRAS inhibition remains a serious obstacle. We showed here that PI3K plays a major role in this resistance through upstream activation of wild-type RAS signaling – beyond its known KRAS effector function. The combination of proximity labeling, CRISPR screening, live-cell imaging, and functional assays revealed that PI3K orchestrates phosphoinositide-mediated GAB1 recruitment to the plasma membrane, nucleating assembly of RAS signaling complexes that activate MAPK in an EGFR/SHP2/SOS1-dependent manner. Inhibiting PI3K enhanced sensitivity to mutant-specific KRAS inhibitors in PDAC cells, including in cells with clinically identified PIK3CA mutations. These findings refine RAS-PI3K signaling paradigms, reveal that PI3K-driven wild-type RAS activation drives resistance to KRAS inhibition, and illuminate avenues for augmenting KRAS-targeted therapies in PDAC.
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1. ⭐ Takara Bio USA, Inc. 通过癌症研究基准研究验证了新型空间转录组学技术

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、spatial、spatial transcriptomics、transcriptomics
• 📝 描述：Takara Bio’s Trekker FX spatial transcriptomics improves single-cell resolution and detects more cell interactions, enhancing analysis of tumor microenvironments in cancer samples…
• 🔗 查看原文

2. scSurvival——基于细胞分辨率的临床癌症队列数据的单细胞生存分析

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、single-cell
• 📝 描述：RNA sequencing combined with single-cell analysis enables scSurvival to link specific tumor cell populations to patient risk, improving survival prediction and revealing drivers of cancer progression…
• 🔗 查看原文

3. 长链非编码RNA可能是一种有前景的癌症治疗靶点。

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer
• 📝 描述：RNA sequencing reveals how lncRNA IGF1R-AS1 drives MYC activation through chromatin looping, promoting tumor progression and highlighting a potential therapeutic target in prostate cancer…
• 🔗 查看原文

4. 维生素D可使乳腺癌治疗成功率提高79%。

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer
• 📝 描述：A daily vitamin D supplement may quietly supercharge chemotherapy. In a small study, women who took low doses alongside treatment were far more likely to see their cancer vanish than those who didn’t. Since vitamin D also supports immune function—and many patients are deficient—it could be playing a bigger role than expected. Scientists say this affordable approach deserves much deeper investigation.
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5. 麻省理工学院研究发现，儿童更容易受到水中致癌化学物质的影响。

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer
• 📝 描述：A troubling new study from MIT reveals that a common environmental contaminant, NDMA—found in polluted water, certain medications, and even processed foods—may pose a far greater cancer risk to children than adults. In experiments with mice, young animals exposed to the chemical developed significantly more DNA damage and cancer, despite experiencing the same initial exposure as adults. The key difference lies in how rapidly children’s cells divide, which turns early DNA damage into dangerous mutations much more easily.
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• GSE312942 STC-15 对 METTL3 的抑制诱导 RNA 错误加工，导致 dsRNA 形成并激活先天免疫 [RNA-seq]
• GSE288762 组蛋白高乙酰化对基因组组织的影响
• GSE324408 肌肉来源干/祖细胞的单细胞转录组图谱揭示衰老和再生的标志
• GSE299284 岩藻糖基转移酶 4 衍生的肽生物缀合物在碳纳米管上增强卵巢癌小鼠模型的抗肿瘤免疫力
• GSE298951 自身免疫抗体诱导的神经元过度活跃触发IgLON5疾病中的病理性Tau蛋白
• GSE295998 单细胞分析揭示帕金森病中边缘兴奋性神经元代谢通路失调
• GSE295307 促生长细菌肠杆菌属 CS8-gfp 增强水稻植株中莠去津-噻虫嗪降解的机制
• GSE291234 抗PD-1治疗后髓系特异性Trem2敲除对肝细胞癌的影响[ChIP-seq]
• GSE291032 抗PD-1治疗后髓系特异性Trem2敲除对肝细胞癌的影响[RNA-seq]
• GSE316797 Mediator复合物对黑色素瘤细胞可塑性的调控驱动治疗耐药性[ATAC-Seq]
• GSE316620 Mediator复合物对黑色素瘤细胞可塑性的调控驱动治疗耐药性[ChIP-Seq]
• GSE316133 黑色素瘤表型可塑性和治疗耐药性的表观遗传调控[CRISPR筛选]
• GSE315960 黑色素瘤表型可塑性和治疗耐药性的表观遗传调控
• GSE294392 大麦发育和萌发的空间转录组
• GSE329361 DNA修复驱动顺铂诱导的神经元死亡
• GSE300723 形态再生过程中细胞命运的渐进性决定 [scRNA-seq]
• GSE300721 形态再生过程中细胞命运的渐进性决定 [RNA-seq]
• GSE287341 WNT介导的肠上皮转化过程中基质Pdgfra表达细胞的动态重编程[图5]
• GSE287339 WNT介导的肠上皮转化过程中基质Pdgfra表达细胞的动态重编程[图3]
• GSE287338 WNT介导的肠上皮转化过程中基质Pdgfra表达细胞的动态重编程[图2]
• GSE287336 WNT介导的肠上皮转化过程中基质Pdgfra表达细胞的动态重编程[D8]
• GSE287335 肠上皮细胞WNT介导转化过程中基质Pdgfra表达细胞的动态重编程
• GSE326801 星形胶质细胞-小胶质细胞通过 CSF1 和 IFNβ 进行相互作用，促进中枢神经系统修复
• GSE319569 表观遗传早衰症将高甲基化与年龄相关病理联系起来
• GSE314244 抑制卵子生成 JNK 可预防 DNA 损伤性抗癌药物引起的原发性卵巢功能不全和不孕症
• GSE301598 急性缺氧条件下人原代胰岛和干细胞衍生胰岛的单细胞转录组比较分析
• GSE297745 IL-17A 中和作用可预防免疫检查点抑制剂相关性心肌炎，并协同增强免疫检查点阻断疗法的疗效
• GSE329041 DNA:RNA免疫沉淀（DRIP）测序数据，用于分析由WT和Dusp2-/- CD8+ T细胞体外诱导的虚拟记忆T细胞。
• GSE329039 跨损伤DNA聚合酶η绕过LANA-DNA交联，确保KSHV游离体持续存在和肿瘤生长
• GSE329037 RNA-seq 数据来自体外诱导的 WT 和 DUSP2-/- CD8+ T 细胞的虚拟记忆 T 细胞
• GSE329034 WT 和 Dusp2-/- 小鼠外周血 CD8+ T 细胞的单细胞转录组分析
• GSE329032 DNA:RNA免疫沉淀（DRIP）测序数据，用于分析由WT和Cd4-Cre Rpa1fl/fl CD8+ T细胞体外诱导的虚拟记忆T细胞。
• GSE328453 PGD2/DP2轴促进促炎反应，但减弱人类嗜碱性粒细胞的抗原呈递作用
• GSE327796 海鞘成体脑的空间转录组图谱：固着脊索动物脑的功能分区和细胞组成，以及对神经腺功能的新见解
• GSE313559 小鼠 HCC 中 TREM2⁺ 和 TREM2⁻ TAM 的转录组分析 [RNA-seq]
• GSE313557 凋亡细胞预处理前后 BMDM 分析 [RNA-seq]
• GSE311573 无序蛋白 LAT 编码 T 细胞活化中信号通路的相对水平
• GSE291286 慢性乙型肝炎的临床治愈取决于强大的 CD4+ T 细胞反应的激活和持续存在
• GSE291235 抗PD-1治疗后髓系特异性Trem2敲除对肝细胞癌的影响
• GSE329245 Polycomb 擦除器 BAP1 和 UTX 对于快速二价基因激活并非必需，但对于增强子建立至关重要 [RNA-seq]
• GSE329244 Polycomb 擦除蛋白 BAP1 和 UTX 对于快速二价基因激活并非必需，但对于增强子建立至关重要 [ChIP-seq]
• GSE319449 RNA-seq 分析 TADA2B KO A375 黑色素瘤细胞中 SOX10 过表达情况
• GSE319443 SOX10 敲除 A375 黑色素瘤细胞的 RNA-seq 分析
• GSE318799 RNA-seq 分析 B16F10 细胞中 Tada2b 敲除
• GSE318796 RNA-seq 分析 p300/CBO 敲除后 B16F10 细胞
• GSE318328 确定 Ce6@D4-EV 介导的光动力疗法后 TGF-β 激活的 CAFs 的转录组变化 (RNA-seq)
• GSE318327 通过RNA测序确定Ce6@D4-EV介导的靶向光动力疗法在皮下KPC肿瘤中诱导的转录变化
• GSE316930 连续的转录抑制和去抑制波允许古细菌细胞周期进程 [ChIP-Seq]
• GSE316929 连续的转录抑制和去抑制波允许古细菌细胞周期进程 [RNA-Seq]
• GSE316898 Mediator复合物对黑色素瘤细胞可塑性的调控驱动治疗耐药性[persister]
• GSE316897 Mediator复合物对黑色素瘤细胞可塑性的调控驱动治疗耐药性[crispr]
• GSE316474 介导复合物对黑色素瘤细胞可塑性的调控驱动治疗耐药性
• GSE302794：在气液界面培养条件下，对健康人、既往吸烟的慢性阻塞性肺病患者和目前吸烟的慢性阻塞性肺病患者的原代支气管上皮细胞进行单细胞RNA测序
• GSE302115：在气液界面培养条件下，对健康人、既往吸烟的慢性阻塞性肺病患者和目前吸烟的慢性阻塞性肺病患者的原代支气管上皮细胞进行ATAC-seq分析
• GSE301910：在气液界面培养条件下，对健康人、既往吸烟的慢性阻塞性肺病患者和目前吸烟的慢性阻塞性肺病患者的原代支气管上皮细胞进行转录组分析
• GSE300746：野生型和Angpt2基因敲除小鼠在接受3周腺嘌呤饮食后肾脏反应的RNA-Seq分析