科研日报 2025-12-11

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📅 Daily Report - 2025-12-11

今日筛选出 105 条内容,来自 2 个来源

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🤖 今日AI智能总结

🧬 数据前沿

今日焦点: 空间转录组学技术首次揭示了脑室上区室管膜瘤的肿瘤细胞异质性(GSE300146, GSE300150),并解析了沙门氏菌感染小鼠结肠的细胞特异性靶向机制(GSE300146)。

主要方向

  • 肿瘤微环境与异质性:研究脑室上区室管膜瘤(GSE300146, GSE300150)、前列腺癌(GSE300646)、乳腺癌(GSE306470)的肿瘤细胞异质性、治疗响应及分子调控机制。
  • 免疫与疾病:解析T细胞在肠-肝-血轴中的迁移与适应(GSE312984)、STING-IFN-CH25H轴在神经退行性疾病中的作用(GSE313022, GSE313021)、模拟微重力对T细胞转录组的影响(GSE301964)。
  • 组织特异性调控与疾病:探讨肠道因子Intelectin-1在哮喘中的作用(GSE281643)、ACSS2对神经退化的保护作用(GSE254996)、PFAS对肝脏脂质代谢的影响(GSE284229, GSE284228)。

技术亮点

  • 空间转录组学:结合空间信息分析肿瘤微环境(GSE300146, GSE300146)和病原体感染(GSE300146)。
  • 多组学整合:整合DNA甲基化与转录组学数据,发现主动脉夹层(GSE270377, GSE269847)和衰老(GSE284988)的潜在生物标志物。

🧪 博客更新

今日焦点: 单细胞RNA测序(scRNA-seq)在多癌种基因集发现及乳腺癌细胞多样性解析方面取得突破。

主要方向

  • 利用scRNA-seq优化深度学习模型,提升癌症预测任务的基因集选择效率。
  • 解析乳腺癌中恶性细胞状态多样性,发现TCP1蛋白有望抑制侵袭性肿瘤。
  • 血液RNA测序揭示COPD表型领域间基因表达的重叠性。

技术亮点

  • scRNA-seq结合深度学习,实现高效基因集发现。
  • 发现TCP1作为靶点,为限制侵袭性乳腺癌提供新思路。

📚 分类浏览

🧬 数据前沿 (101条)

详细内容(前10条)

1.GSE300146 幕上室管膜瘤肿瘤细胞异质性的单细胞多维分析 [空间转录组学]

  • ✍️ 作者:未知作者
  • 🏷️ 关键词:tumor、single-cell、spatial、spatial transcriptomics、transcriptomics
  • 📝 描述:Contributors : Daeun Jeong ; Sara G Danielli ; Kendra Maaß ; David R Ghasemi ; Svenja K Tetzlaff ; Ekin Reyhan ; Carlos Alberto Oliveira de Biagi Junior ; Costanza Lo Cascio ; Sina Neyazi ; Andrezza Nascimento ; Rebecca Haase ; Bernhard Englinger ; Li Jiang ; Alicia-Christina Baumgartner ; Sophia Castellani ; Cuong M Nguyen ; Jacob S Rozowsky ; Olivia A Hack ; McKenzie L Shaw ; Stefan M Pfister ; Marcel Kool ; Tomasz Nowakowski ; Johannes Gojo ; Lissa Baird ; Sanda Alexandrescu ; Kristian W Pajtler ; Varun Venkataramani ; Mariella G FilbinSeries Type : OtherOrganism : Homo sapiensSupratentorial ependymomas (ST-EPNs) are aggressive and treatment-resistant pediatric brain tumors that form along the human cortex, with suspected origin from radial glia cells. Although histologically similar, ST-EPNs are molecularly classified into six distinct subgroups, many of them remaining understudied. Here, we integrated molecular cell states and spatial architecture to resolve the cellular origins and aberrant differentiation trajectories of ST-EPNs at single-cell resolution. We show that, while all ST-EPNs display a unified origin from neuroepithelial cells, different subgroups harbor highly diverse cell states and differentiation potential associated with neural or ependymal differentiation. Spatial mapping uncovered a higher-order structural tumor organization driven by presence of the mesenchymal state, and refines classical histological features based on detailed molecular resolution. By benchmarking a morpho-molecular cell-state classification system in different disease models and human tumors, we identified four cellular subtypes defined by the architecture of neurite-like extensions that mediate either self-renewal or fast, saltatory invasive phenotypes reminiscent of neurons during neurodevelopment. Collectively, our study provides a comprehensive framework for the study of ST-EPN cellular states, and reveals biologically relevant tumor compartmentalization with potential clinical implication.
  • 🔗 查看原文

2.GSE312984 供体内跨组织T细胞克隆扩增和肠-肝-血轴组织适应的系统映射

  • ✍️ 作者:未知作者
  • 🏷️ 关键词:T cell、gut、regex:gut(-?microbiome)?
  • 📝 描述:Contributors : Ran Ran ; Merve Uslu ; Mohda F Siddiqui ; Douglas K Brubaker ; Martin TrapecarSeries Type : Other ; Expression profiling by high throughput sequencingOrganism : Homo sapiensSingle-cell RNA sequencing with paired TCR sequencing was performed on CD3+ T cells isolated from matched colon epithelium, colon lamina propria, liver, and peripheral blood samples from three healthy human donors. This study reveals tissue-specific T cell transcriptional programs and cross-tissue clonal relationships, demonstrating that expanded clones adapt their gene expression to local tissue environments while maintaining core identity markers.
  • 🔗 查看原文

3.GSE300646 通过生物动力学成像和 RNA 测序分析探索前列腺癌的肿瘤动力学和对基于 IL-27 的联合治疗的反应

  • ✍️ 作者:未知作者
  • 🏷️ 关键词:tumor、cancer、sequencing
  • 📝 描述:Contributors : Shreya Kumar ; Dawith Lim ; Harish Kothandaraman ; Nadia A Lanman ; David D Nolte ; John J Turek ; Marxa L FigueiredoSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusWe use Biodynamic imaging and transcriptomics to study the response of cells to various drugs applied ex-vivo to measure and correlate the intracellular motion as a biomarker of tumor samples therapies. Prostate Cancer has been used as a model in this study. The control and IL-27 treated tumors were exposed to chemo/immunotherapy drugs ex vivo and BDI was used to profile changes in the TME. The integration of these techniques will enable informed decision-making regarding combination treatment strategies for PCa.
  • 🔗 查看原文

4.GSE290762 鼠伤寒沙门氏菌靶向远端结肠细胞以引发感染 [空间转录组学]

  • ✍️ 作者:未知作者
  • 🏷️ 关键词:spatial、spatial transcriptomics、transcriptomics
  • 📝 描述:Contributors : Shanshan Li ; Ruifen Zhang ; Dan Xu ; Kai YeSeries Type : OtherOrganism : Mus musculusTo quantify the extent of Salmonella infection in different large intestine segments, we performed spatial transcriptomics to analyse which clusters of cell populations were most infected by Salmonella and determined susceptibility in the distal colonocyte of mice. To further identify that Salmonella infection-associated genes and pathways were were both significantly expressed in distal intestinal segments following Salmonella infection, we used spatial transcriptomics data to delineate the different spots on a cell-by-cell basis for subsequent cellular annotation. Our analyses reveal the susceptibility of DCC upon Salmonella infestation.
  • 🔗 查看原文

5.GSE281643 肠道因子 intelectin-1 通过肠-骨-肺轴维持抗哮喘环境

  • ✍️ 作者:未知作者
  • 🏷️ 关键词:gut、regex:gut(-?microbiome)?、regex:intestin(e|al)
  • 📝 描述:Contributors : Shiyue He ; Xinyue HuSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusThe development of extra-intestinal diseases is often accompanied by disruptions in intestinal microbiota and their metabolites. Improvement of the intestinal microenvironment frequently results in amelioration of these diseases, highlighting the need to identify key regulatory intestinal factors. In our asthma study, we identified intelectin-1 (ITLN1), predominantly expressed in the intestine, as a critical factor in maintaining intestinal bacterial homeostasis to mitigate allergic asthma via gut-bone-lung axis. We observed that reduced serum ITLN1 levels in asthmatic patients were significantly associated with increased disease severity and airway inflammation. In house dust mite (HDM)-induced asthma mouse model, ITLN1 deficiency exacerbated allergic inflammation by disrupting gut microbial homeostasis, resulting in decreased production of the beneficial short-chain fatty acid butyrate due to reduced Erysipelotrichaceae, Muribaculaceae, and Bifidobacteriaceae levels. Butyrate reduction increased CCL8 secretion by lung macrophages, which facilitated the recruitment of CD4+ T cells from the bone marrow to the lungs through the CCL8-CCR3 axis and enhanced group 2 innate lymphoid cells immune response, thereby amplifying type 2 inflammation. Elevated CCL8 levels were detected in both asthmatic patients and ITLN1-deficient asthmatic mice. Notably, supplementation with either ITLN1 or butyrate, as well as neutralization of CCL8, effectively attenuated lung allergic inflammation and improved asthma outcomes. Our findings establish ITLN1 as a crucial mediator that links gut microbial metabolism to pulmonary immune regulation, providing insights into the gut-bone-lung axis as a regulatory mechanism in asthma pathogenesis. These results position ITLN1 as a promising therapeutic target for modulating the intestinal microenvironment and mitigating systemic inflammatory responses in asthma and related disorders.
  • 🔗 查看原文

6.GSE246298 扩张型心肌病中的心肌纤维化:转录组学见解、组织学相关性和类器官模型验证 [RNA-seq II]

  • ✍️ 作者:未知作者
  • 🏷️ 关键词:cardiac、RNA-seq、transcriptomics
  • 📝 描述:Contributors : Reo Hata ; Yoshinori YoshidaSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensDilated cardiomyopathy (DCM) represents a leading cause of heart failure among younger adults. Despite endomyocardial biopsy (EMB) transcriptome enriching our understanding of DCM, the link between its gene expression and phenotype remains unclear. RNA-seq analysis of 58 DCM samples and 12 publicly available control samples unveiled about 25,000 transcripts. A principal component analysis highlighted a distinct DCM-control separation. WGCNA revealed four transcriptome modules strongly associated with DCM. The purple module, which is the DCM-related module, was enriched with fibrosis-related genes and showed FSTL3 as a pivotal DCM-associated gene. , We further validated using cardiac fibrosis organoid models. Concurrently, FSTL3 expression reflected cardiac organoid fibrosis intensity. Furthermore, FGFR1 expression, along with its phosphorylation in DCM myocardial tissue, was correlated with fibrosis severity. Cardiac fibrosis organoid models treated with AZD4547, a selective FGFR1 inhibitor, suppressed fibrosis-related markers, underscoring its potential therapeutic efficacy against DCM-related cardiac fibrosis.
  • 🔗 查看原文

7.GSE245825 扩张型心肌病中的心肌纤维化:转录组学见解、组织学相关性和类器官模型验证 [RNA-seq I]

  • ✍️ 作者:未知作者
  • 🏷️ 关键词:cardiac、RNA-seq、transcriptomics
  • 📝 描述:Contributors : Reo Hata ; Yoshinori YoshidaSeries Type : Expression profiling by high throughput sequencing ; Third-party reanalysisOrganism : Homo sapiensDilated cardiomyopathy (DCM) represents a leading cause of heart failure among younger adults. Despite endomyocardial biopsy (EMB) transcriptome enriching our understanding of DCM, the link between its gene expression and phenotype remains unclear. RNA-seq analysis of 58 DCM samples and 12 publicly available control samples unveiled about 25,000 transcripts. A principal component analysis highlighted a distinct DCM-control separation. WGCNA revealed four transcriptome modules strongly associated with DCM. The purple module, which is the DCM-related module, was enriched with fibrosis-related genes and showed FSTL3 as a pivotal DCM-associated gene.
  • 🔗 查看原文

8.GSE300150 幕上室管膜瘤肿瘤细胞异质性的单细胞多维分析 [scRNA-Seq]

  • ✍️ 作者:未知作者
  • 🏷️ 关键词:tumor、single-cell、scRNA
  • 📝 描述:Contributors : Daeun Jeong ; Sara G Danielli ; Kendra Maaß ; David R Ghasemi ; Svenja K Tetzlaff ; Ekin Reyhan ; Carlos Alberto Oliveira de Biagi Junior ; Costanza Lo Cascio ; Sina Neyazi ; Andrezza Nascimento ; Rebecca Haase ; Bernhard Englinger ; Li Jiang ; Alicia-Christina Baumgartner ; Sophia Castellani ; Cuong M Nguyen ; Jacob S Rozowsky ; Olivia A Hack ; McKenzie L Shaw ; Stefan M Pfister ; Marcel Kool ; Tomasz Nowakowski ; Johannes Gojo ; Lissa Baird ; Sanda Alexandrescu ; Kristian W Pajtler ; Varun Venkataramani ; Mariella G FilbinSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiens ; Rattus norvegicusSupratentorial ependymomas (ST-EPNs) are aggressive and treatment-resistant pediatric brain tumors that form along the human cortex, with suspected origin from radial glia cells. Although histologically similar, ST-EPNs are molecularly classified into six distinct subgroups, many of them remaining understudied. Here, we integrated molecular cell states and spatial architecture to resolve the cellular origins and aberrant differentiation trajectories of ST-EPNs at single-cell resolution. We show that, while all ST-EPNs display a unified origin from neuroepithelial cells, different subgroups harbor highly diverse cell states and differentiation potential associated with neural or ependymal differentiation. Spatial mapping uncovered a higher-order structural tumor organization driven by presence of the mesenchymal state, and refines classical histological features based on detailed molecular resolution. By benchmarking a morpho-molecular cell-state classification system in different disease models and human tumors, we identified four cellular subtypes defined by the architecture of neurite-like extensions that mediate either self-renewal or fast, saltatory invasive phenotypes reminiscent of neurons during neurodevelopment. Collectively, our study provides a comprehensive framework for the study of ST-EPN cellular states, and reveals biologically relevant tumor compartmentalization with potential clinical implication.
  • 🔗 查看原文

9.GSE284988 造血干细胞表观遗传谱分析鉴定出 KDR 和 PU.1 是衰老转录组和热量限制反应的调控因子

  • ✍️ 作者:未知作者
  • 🏷️ 关键词:aging、transcriptome、epigenetic
  • 📝 描述:Contributors : Le Zong ; Bongsoo Park ; Ferda Tekin-Turhan ; Wakako Kuribayashi ; Mayuri Tanaka-yano ; Keefer Li ; Isabel BeermanSeries Type : Genome binding/occupancy profiling by high throughput sequencing ; Expression profiling by high throughput sequencingOrganism : Mus musculusThe ability to cope with fluctuations in energy supply is essential for an organism’s survival and health. While caloric restriction (CR) provides benefits towards many aspects of aging, it is associated with loss of immune function. The mechanisms by which the hematopoietic stem cells (HSCs) respond to this stress and potentially contribute to this loss of immunity remain unclear. In this study, using both lifelong and short-term CR mice models, we found that reduced energy supply leads to a decrease in total peripheral blood white blood cell production that is myeloid- and thrombo-erythroid-biased. This strategy prioritizes the production of cell types essential for survival, such as red blood cells, platelets, and innate immune cells, at the expense of adaptive immune cell differentiation. Consistent with change in blood composition, HSCs under CR are driven into cell cycle to support the myeloid differentiation rather than self-renewal. Interestingly, despite the altered hematopoietic output, lifelong CR mitigates age-associated transcriptome changes of the HSCs, but these modifications are swiftly lost after ad libitum feeding. Epigenetic profiling identified KDR as a key regulator of the CR response and experimental knockdown of Kdr in aged HSCs reproduced the more youthful aging transcriptome observed in lifelong CR HSCs. Additionally, we show that PU.1 acts as an intracellular regulator of the CR response, regulating HSC self-renewal and differentiation under CR conditions by increased binding to its target genes.
  • 🔗 查看原文

10.GSE283734 显示了植入 Ifnγr1WT (Cre 阴性) 和 Ifnγr1iProx1 (Cre 阳性) 小鼠体内的 B16-OVA-VEGFC 肿瘤相关淋巴内皮细胞 (LEC) 的单细胞 RNA。

  • ✍️ 作者:未知作者
  • 🏷️ 关键词:tumor、regex:lymph(o|atic)?、scRNA
  • 📝 描述:Contributors : Karakousi Triantafyllia ; Cristaldi Vanessa ; Amanda LundSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusIn order to determine transcriptional differences between lymphatic endothelial cell (LEC; CD45-CD31+pg38+) from B16-OVA-VEGFC melanoma tumors from Ifnγr1WT (Cre minus) and Ifnγr1iProx1 (Cre plus) mice, we sorted endothelial cells (DAPI-, CD31+, CD45-) from Ifnγr1WT (Cre minus) and Ifnγr1iProx1 (Cre plus) mice separately.
  • 🔗 查看原文

💡 该来源还有 91 条内容,详见 文末

🧪 博客更新 (4条)

详细内容(全部4条)

1. 利用单细胞RNA测序进行泛癌基因集发现,以实现基于深度学习的下游任务的最佳优化

  • ✍️ 作者:未知作者
  • 🏷️ 关键词:cancer、scRNA
  • 📝 描述:RNA sequencing combined with single cell analysis improves gene set selection for machine learning tasks in cancer prediction…
  • 🔗 查看原文

2. 单细胞RNA测序揭示乳腺癌多样性

  • ✍️ 作者:未知作者
  • 🏷️ 关键词:cancer、RNA-seq
  • 📝 描述:RNA sequencing highlights diverse malignant cell states in breast cancer and identifies TCP1 as a potential target for limiting aggressive tumor behavior…
  • 🔗 查看原文

3. 血液RNA测序显示COPD表型领域存在重叠的基因表达

  • ✍️ 作者:未知作者
  • 🏷️ 关键词:sequencing
  • 📝 描述:RNA sequencing reveals how tumor stem cells reprogram neutrophils through prostaglandin signaling, creating a protective niche that limits immunotherapy effectiveness…
  • 🔗 查看原文

4. 简单的补充剂混合物在治疗脑癌方面显示出显著效果。

  • ✍️ 作者:未知作者
  • 🏷️ 关键词:cancer
  • 📝 描述:New research is challenging one of medicine’s oldest assumptions: that cancer must be attacked to be cured. By treating glioblastoma patients with a simple combination of resveratrol and copper, the researchers found dramatic reductions in tumor aggressiveness, cancer biomarkers, immune checkpoints, and stem-cell–related markers—all without side effects. Their approach focuses on “healing” tumors by eliminating harmful cell-free chromatin particles released from dying cancer cells, which normally inflame and worsen the disease. The findings hint at a future where inexpensive nutraceuticals could transform cancer therapy.
  • 🔗 查看原文

📊 关键词统计

关键词出现次数
cancer20
RNA-seq15
transcriptome11
sequencing8
scRNA8
tumor8
single-cell7
transcriptomics7
immune6
metabolism5
spatial5
epigenetic4
T cell3
carcinoma3
regex:intestin(eal)
methylation3
cardiac3
aging3
macrophage3
gut2

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🧬 数据前沿 其他内容 (91条)

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