详细内容（前10条）

1. ⭐ GSE320041 利用空间生态型对肿瘤微环境进行高分辨率、非侵入性分析 [Visium]

• ✍️ 作者：未知作者
• 🏷️ 关键词：tumor、tumor microenvironment、spatial、Visium
• 📝 描述：Contributors : Wubing Zhang ; Erin L Brown ; Abul Usmani ; Aadel A Chaudhuri ; Aaron M NewmanSeries Type : OtherOrganism : Homo sapiensMulticellular programs in the tumor microenvironment (TME) drive cancer pathogenesis and response to therapy but remain challenging to identify and profile clinically. Here, we present a machine learning framework for multi-analyte profiling of spatially dependent cell states and multicellular ecosystems, termed spatial ecotypes (SEs). By integrating 10M single-cell and spot-level spatial transcriptomes from diverse human carcinomas and melanomas, we identified nine SEs with broad conservation—each with unique biology, geospatial features, and clinical outcome associations, including several linked to immunotherapy response. Notably, SEs were distinguishable by DNA methylation profiling and recoverable from plasma cell-free DNA (cfDNA) using deep learning. In cfDNA from nearly 100 melanoma patients, SE levels exhibited striking associations with immunotherapy response. Our data reveal fundamental units of TME organization and demonstrate a multimodal platform for solid and liquid TME profiling, with implications for improved risk stratification and therapy personalization.
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2. ⭐ GSE320040 利用空间生态型对肿瘤微环境进行高分辨率、非侵入性分析 [scRNA-seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：tumor、tumor microenvironment、scRNA、spatial
• 📝 描述：Contributors : Wubing Zhang ; Erin L Brown ; Abul Usmani ; Aadel A Chaudhuri ; Aaron M NewmanSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensMulticellular programs in the tumor microenvironment (TME) drive cancer pathogenesis and response to therapy but remain challenging to identify and profile clinically. Here, we present a machine learning framework for multi-analyte profiling of spatially dependent cell states and multicellular ecosystems, termed spatial ecotypes (SEs). By integrating 10M single-cell and spot-level spatial transcriptomes from diverse human carcinomas and melanomas, we identified nine SEs with broad conservation—each with unique biology, geospatial features, and clinical outcome associations, including several linked to immunotherapy response. Notably, SEs were distinguishable by DNA methylation profiling and recoverable from plasma cell-free DNA (cfDNA) using deep learning. In cfDNA from nearly 100 melanoma patients, SE levels exhibited striking associations with immunotherapy response. Our data reveal fundamental units of TME organization and demonstrate a multimodal platform for solid and liquid TME profiling, with implications for improved risk stratification and therapy personalization.
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3. ⭐ GSE320038 高分辨率、无创的肿瘤微环境空间生态型分析 [RNA-seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：tumor、tumor microenvironment、RNA-seq、spatial
• 📝 描述：Contributors : Wubing Zhang ; Erin L Brown ; Abul Usmani ; Aadel A Chaudhuri ; Aaron M NewmanSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensMulticellular programs in the tumor microenvironment (TME) drive cancer pathogenesis and response to therapy but remain challenging to identify and profile clinically. Here, we present a machine learning framework for multi-analyte profiling of spatially dependent cell states and multicellular ecosystems, termed spatial ecotypes (SEs). By integrating 10M single-cell and spot-level spatial transcriptomes from diverse human carcinomas and melanomas, we identified nine SEs with broad conservation—each with unique biology, geospatial features, and clinical outcome associations, including several linked to immunotherapy response. Notably, SEs were distinguishable by DNA methylation profiling and recoverable from plasma cell-free DNA (cfDNA) using deep learning. In cfDNA from nearly 100 melanoma patients, SE levels exhibited striking associations with immunotherapy response. Our data reveal fundamental units of TME organization and demonstrate a multimodal platform for solid and liquid TME profiling, with implications for improved risk stratification and therapy personalization.
• 🔗 查看原文

4. ⭐ GSE284695 肥胖介导的肿瘤内神经支配增加胰腺癌的肿瘤发生 [空间转录组学]

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、spatial、spatial transcriptomics、transcriptomics
• 📝 描述：Contributors : Prasenjit Dey ; Shyamananda S Mayengbam ; Aftab Alam ; Matthew Witkowski ; Sharon Senchanthisai ; Elif I Bektas ; Min MaSeries Type : OtherOrganism : MusThe incidence of pancreatic ductal adenocarcinoma (PDAC) is on the rise, and host factors like obesity increase risk by 60% and mortality by two-fold; however, the mechanisms that drive obesity-associated tumorigenesis are poorly understood. Here, we showed that obesity-mediated pancreatic steatosis was associated with a higher level of neo-innervation in PDAC. Neo-innervation mostly comprised sympathetic neurons that released catecholamines, which ligated the adrenergic receptor on both tumor and immune cells, subsequently activating a downstream signaling cascade that led to a pro-tumorigenic type 2 immune microenvironment accelerating tumorigenesis. Further, we identified NgCAM-related cell adhesion molecule (NrCAM) and nerve growth factor (NGF) as major mediators secreted by adipocytes that drove neurogenesis. Targeting neuro-adrenergic signaling by nerve ablation or pharmacologic approaches abolished obesity-related tumor progression. Overall, this study advances our understanding of the fundamental biology underpinning obesity-mediated neo-innervation and its causal link to exacerbating PDAC development, providing new avenues for therapeutic intervention.
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5. ⭐ GSE306996 高度非整倍体衰老细胞的转录组揭示了其与肿瘤微环境的相互作用以及Yorkie蛋白的促生存作用

• ✍️ 作者：未知作者
• 🏷️ 关键词：tumor、tumor microenvironment、transcriptome
• 📝 描述：Contributors : Kaustuv Ghosh ; Marco Milán ; Camille Stephan-Otto AttoliniSeries Type : Expression profiling by high throughput sequencingOrganism : Drosophila melanogasterChromosomal instability (CIN), an increased rate of changes in chromosome structure and number, is observed in most human carcinomas. Drosophila epithelial tumor models have been instrumental in demonstrating that, beyond the generation of genomic copy number heterogeneity, CIN can act as a source of tumor growth, metastasis and malignancy through the production of aneuploidy-induced senescent cells. Here we characterized the transcriptional program of these cells. We present evidence that most cellular responses to aneuploidy and senescence, such as cell cycle arrest, autophagy induction, activation of the actin cytoskeleton and upregulation of genes involved in secretion, are reflected at the transcriptional level. Besides those secreted proteins mediating tumor growth, metastasis and malignancy, we unravel a role of Upd1 cytokine in driving the death of the nearby tumor microenvironment through activation of the JAK/STAT pathway and induction of autophagy. We also demonstrate a pro-survival role of the hippo-Yorkie pathway in tumor cells. Our data contribute to the identification of potential therapeutic strategies to block CIN-induced tumorigenesis by targeting senescent cells and blocking their ability to interact with the tumor microenvironment.
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6. ⭐ GSE329919 肿瘤微生物负荷通过调节干扰素信号传导驱动免疫反应

• ✍️ 作者：未知作者
• 🏷️ 关键词：tumor、immune、regex:micro(b|be|bial|organism)
• 📝 描述：Series Type : Expression profiling by high throughput sequencingOrganism : Mus musculusTo investigate the mechanisms involved in tumor microbial-associated immunotherapy sensitivity, we performed RNA sequencing on mouse MC38 tumor tissues upon local microbial depletion.
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7. ⭐ GSE325323 补体因子B缺乏通过FOS介导的色氨酸代谢和免疫抑制促进肺癌进展

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、immune、metabolism
• 📝 描述：Contributor : chenglu HeSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensTo investigate the molecular consequences of CFB deficiency in lung adenocarcinoma, we conducted RNA-sequencing on CFB-silenced (sh-CFB) and control (sh-NC) NCI-H1299 cells.
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8. GSE324604 磷酸乙醇胺胞苷酰转移酶 2 整合 DAG 代谢和 TBK1 激活以调节抗病毒先天免疫

• ✍️ 作者：未知作者
• 🏷️ 关键词：immunity、metabolism
• 📝 描述：Contributors : Wencong Lai ; Zengjie Liu ; Qinghui Ai ; Kangsen MaiSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusPhosphatidylethanolamine (PE) biosynthesis is critical for membrane biology and cellular homeostasis. However, its specific role in antiviral innate immunity remains poorly understood. Here, we demonstrate that inhibition of phosphoethanolamine cytidylyltransferase 2 (PCYT2), a key enzyme in PE biosynthesis, promotes TBK1 activation to enhance antiviral immune response. Mechanistically, PCYT2 deficiency leads to the accumulation of diacylglycerol (DAG), which activates protein kinase C δ (PKCδ). We identify PKCδ as a direct kinase for TBK1, and demonstrate that it binds to and phosphorylates TBK1 at Ser716. This Ser716 phosphorylation facilitates subsequent canonical phosphorylation at Ser172, resulting in hyperactivation of the TBK1–IRF3 axis. Our findings uncover a novel link between phospholipid metabolism and antiviral innate immunity, suggesting that targeting the PE biosynthesis pathway could be a potential therapeutic strategy against viral infections.
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9. GSE304021跨癌分析鉴定出转移特异性肿瘤内微生物群特征，其中链球菌属是关键微生物枢纽

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、regex:micro(b|be|bial|organism)
• 📝 描述：Contributors : Nevena Todorovic ; Sara Bertorello ; Serena Pillozzi ; Simonetta Bianchi ; Maria Raffaella Ambrosio ; Giulia Nannini ; Simone Baldi ; Amedeo AmedeiSeries Type : OtherOrganism : Homo sapiensCancer remains one of the leading global health challenges, with lung (LC), breast (BC), and colorectal (CRC) cancers among the most prevalent and deadly malignancies. The intratumoral microbiota (IM), a distinct microbial ecosystem within tumor tissues, has emerged as a potential modulator of carcinogenesis, immune responses, and metastatic progression; however, comparative cross-cancer analyses are very scarce. In this study, we profiled and compared the IM composition and diversity in FFPE samples from an Italian cohort of BC (GSE212891), CRC (GSE216589), and LC patients. BC samples exhibited the highest genus-level richness, whereas CRC samples showed significantly greater overall alpha diversity, consistent with the microbial complexity of the gut environment. LC samples displayed the most balanced microbial distribution, as indicated by the highest Shannon index value. Stratification by metastatic condition revealed distinct microbial signatures: 16 genera were exclusive to metastatic tumors and 49 to non-metastatic ones. In BC specifically, the class Clostridia and family Burkholderiaceae were enriched in non-metastatic samples, accompanied by distinct functional shifts in pantothenate and coenzyme A biosynthesis and lysine and lipid A pathways. Microbial network analysis further uncovered differences in ecological community structure and keystone taxa: Streptococcus spp. predominated as hubs in metastatic tumors, whereas Neisseria spp. were central in non-metastatic networks. Overall, our findings highlight cancer-type– and metastasis-specific microbial signatures, supporting a potential role for the IM in tumor progression and offering avenues for biomarker development and therapeutic targeting.
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10. GSE288868 X连锁癌症相关多肽，由假定的非编码RNA编码，调控乳腺癌中的基因表达和细胞通路[RNA-seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、RNA-seq
• 📝 描述：Contributors : Shrikanth S Gadad ; Cristel V Camacho ; Xuan Gong ; Micah Thornton ; Venkat S Malladi ; Anusha Nagari ; Aishwarya Sundaresan ; Tulip Nandu ; Sneh Koul ; Yan Peng ; W L KrausSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensLong noncoding RNAs (lncRNAs) have been found to play a critical role in cancer biology and other prevalent diseases. While most lncRNAs are poorly conserved and not evolutionarily neutral, they regulate biological processes at the RNA level. Recent studies have suggested that a subset of lncRNAs produce functional proteins, and in this study, we have discovered a protein named XCP ((X-linked Cancer-associated Polypeptide). XCP is encoded by a pancreas- and testis-specific RNA annotated as a putative long noncoding RNA by Sun and Gadad et al. (lncRNA1456, aka RHOXF1P3), located on chromosome X. We found that lncRNA1456 and XCP are upregulated in luminal A, luminal B, and HER2 molecular subtypes of breast cancer, and XCP modulates estrogen-dependent as well as estrogen-independent growth of MCF-7 cells by regulating cancer pathways in xenograft models. We find that XCP shares homology with homeodomain-containing proteins and interacts with PHF8, which is also an X-linked gene, and demethylates H3K9me2 to activate transcription. Mechanistically, XCP positively regulates histone demethylase activity of PHF8 in vitro to regulate gene expression in breast cancer cells. These findings identify XCP as a coregulator of transcription and emphasize the need to interrogate the potential functional roles of open reading frames originating from noncoding RNAs.
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详细内容（全部5条）

1. RNA测序可识别炎症性乳腺癌的血液生物标志物

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、sequencing
• 📝 描述：RNA sequencing using TGIRT technology reveals blood-based RNA biomarkers that may improve diagnosis and monitoring of inflammatory breast cancer through liquid biopsy…
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2. 科学家发现一种预防牙龈疾病的新方法，该方法不会杀死有益细菌。

• ✍️ 作者：未知作者
• 🏷️ 关键词：bacteria、regex:bacter(ia|ial|ium)
• 📝 描述：Scientists have uncovered a surprising way to influence the bacteria living in our mouths — not by killing them, but by interrupting how they “talk” to each other. Researchers found that dental plaque bacteria use chemical signals to coordinate growth, and by blocking those signals, they were able to encourage healthier bacteria while reducing disease-linked microbes tied to gum disease. Even more intriguing, the bacterial conversations changed depending on oxygen levels above and below the gums, revealing an entirely new layer of complexity inside the mouth.
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3. RNA测序揭示ATF6α如何支持糖尿病中β细胞的存活

• ✍️ 作者：未知作者
• 🏷️ 关键词：sequencing
• 📝 描述：RNA sequencing reveals how ATF6α supports pancreatic beta cell survival and proliferation under chronic stress, offering insight into diabetes-related beta cell loss…
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4. 吃鸡蛋可降低患阿尔茨海默病风险27%。

• ✍️ 作者：未知作者
• 🏷️ 关键词：Alzheimer
• 📝 描述：Eating eggs might do more than just start your day—it could help protect your brain. Researchers found that people 65 and older who eat eggs regularly have a significantly lower risk of developing Alzheimer’s disease, with daily or near-daily consumption linked to up to a 27% reduction. Even modest egg intake showed benefits, suggesting that small dietary changes could make a meaningful difference over time.
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5. 医生警告说，这种广受欢迎的维生素可能会悄无声息地干扰癌症治疗。

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer
• 📝 描述：Many cancer patients turn to biotin supplements hoping to restore hair lost during treatment, but experts warn the popular vitamin may do more harm than good. While biotin is often marketed for stronger hair and nails, there’s little evidence it actually helps cancer-related hair loss—and it can dangerously interfere with lab tests. Doctors say the supplement can distort key blood markers, potentially masking cancer recurrence or delaying treatment decisions.
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• GSE287423 X连锁癌症相关多肽，由假定的非编码RNA编码，调控乳腺癌中的基因表达和细胞通路[ChIP-seq]
• GSE233321：健康人类免疫系统终生单细胞图谱揭示婴儿独特的免疫特征
• GSE305224 共价泛TEAD抑制剂阻断YAP活性，并在Hippo依赖性癌症模型中表现出脑渗透性[RNA-seq]
• GSE284697 肥胖介导的肿瘤内神经支配增加胰腺癌的肿瘤发生 [RNA-seq]
• GSE284696 肥胖介导的肿瘤内神经支配增加胰腺癌的肿瘤发生 [scRNA-seq]
• GSE330178 人类母胎界面中表型相似但功能不同的NK细胞群
• GSE330176 人类母胎界面中表型相似但功能不同的 NK 细胞群 [bulkRNA-seq]
• GSE329880 突变型 IDH1 通过抑制髓系祖细胞程序阻断中性粒细胞生成 [纳米孔测序]
• GSE329878 突变型 IDH1 通过抑制髓系祖细胞程序阻断中性粒细胞生成 [bulk RNA-Seq]
• GSE329858 突变型 IDH1 通过抑制髓系祖细胞程序阻断中性粒细胞生成 [ATAC-seq]
• GSE310622 肝脏特异性抑制PLA2G6/iPLA2β可通过磷脂重塑改善高脂饮食喂养小鼠的葡萄糖和脂质代谢
• GSE288983 X连锁癌症相关多肽，由假定的非编码RNA编码，调控乳腺癌中的基因表达和细胞通路
• GSE326332 具有三糖抗原敲除 (3KO) 或不具有多个人类转基因 (HTG) 的肾脏异种移植的转录组反应和存活率
• GSE319089 人类神经干细胞来源的细胞外囊泡补充剂对脑癌放化疗后转录组的影响
• GSE305254 共价泛TEAD抑制剂阻断YAP活性，并在Hippo依赖性癌症模型中表现出脑渗透性
• GSE305227 共价泛TEAD抑制剂阻断YAP活性，并在Hippo依赖性癌症模型中表现出脑渗透性[定量测序]
• GSE298907 IKZF2 在 TLX3 和突变型 IL7R 存在的情况下表达下调：白血病中转录失调的新轴
• GSE298727 NADPH氧化酶4与Dahl盐敏感性大鼠肾脏的代谢应激
• GSE329565 通过 RNA-Seq 分析对携带内耳条件性敲除 Esrrg 的小鼠进行基因表达谱分析。
• GSE327572 乳腺肿瘤肺转移的免疫微环境分析
• GSE297144 研究发现，胰腺癌中的 HFE H63D 变异体通过抑制细胞周期促进上皮间质转化。
• GSE296679 研究表明，一种新型衰老治疗剂高三尖杉酯碱能够减轻饮食和年龄相关的肥胖和胰岛素抵抗，并延长小鼠的寿命。
• GSE275711 创伤性脑损伤后及抗CD9抗体治疗后小鼠丘脑免疫细胞单细胞水平的基因表达谱
• GSE260805 创伤性脑损伤后小鼠海马和丘脑单细胞水平免疫细胞基因表达谱