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1. ⭐ Nature Commun | 基于 WES、纳米孔及 scRNA-seq 的 I 期非小细胞肺癌术后复发机制解析

• ✍️ 作者：单细胞天地
• 🏷️ 关键词：TME、RNA-seq、RNAseq、scRNA
• 🔗 查看原文

2. ⭐ 一键启动RNA-Seq分析！EDASeq包，让基因数据自己说话！

• ✍️ 作者：云生信
• 🏷️ 关键词：RNA-seq、RNAseq、R包
• 🔗 查看原文

3. ⭐ 宁珖圣/Ping-Chih Ho团队TREIMM综述 | 线粒体脂质代谢在肿瘤免疫监视与免疫逃逸中的关键作用

• ✍️ 作者：CellPress全科学
• 🏷️ 关键词：肿瘤、免疫、代谢
• 📝 描述：该文总结和阐述了线粒体脂质代谢在肿瘤免疫监视和免疫逃逸中发挥的关键作用。
• 🔗 查看原文

4. ⭐ 代谢 | Nat.Rev.Cancer | 糖代谢酶及其代谢产物在癌症中的兼职功能

• ✍️ 作者：BioJournal Link
• 🏷️ 关键词：癌症、cancer、代谢
• 🔗 查看原文

5. 基于Signac的单细胞线粒体DNA分型与染色质可及性联合分析学习

• ✍️ 作者：单细胞天地
• 🏷️ 关键词：单细胞、scDNA
• 📝 描述：上周学习了基于Signac的scATAC-seq流程学习，这周学习一下单细胞线粒体DNA分型与染色质可及性的联合分析。
• 🔗 查看原文

6. 基于Signac的单细胞线粒体DNA分型与染色质可及性联合分析学习

• ✍️ 作者：生信方舟
• 🏷️ 关键词：单细胞、scDNA
• 📝 描述：上周学习了基于Signac的scATAC-seq流程学习，这周学习一下单细胞线粒体DNA分型与染色质可及性的
• 🔗 查看原文

7. 最新8+生信，多组学识别三级淋巴结构（TLS）结构并进行针对性分析。预测预后及免疫治疗疗效，值得借鉴！

• ✍️ 作者：生信小课堂
• 🏷️ 关键词：免疫、生信
• 📝 描述：点击查看详情
• 🔗 查看原文

8. Trends in Pharmacological Sciences编辑推荐的2024年度综述

• ✍️ 作者：CellPress全科学
• 🏷️ 关键词：TME、TCGA
• 📝 描述：本合辑旨在全面呈现药理学研究领域的重要议题与前沿突破。
• 🔗 查看原文

9. 河南农业大学陈震/姬祥团队Trends in Biotechnology综述 | AI点亮基因组编辑的未来图景

• ✍️ 作者：CellPress全科学
• 🏷️ 关键词：TCGA、基因组
• 📝 描述：该研究系统综述了深度学习技术在基因组编辑领域中的应用与发展。
• 🔗 查看原文

10. 综述 | Cancer Cell | 癌症中的衰老

• ✍️ 作者：BioJournal Link
• 🏷️ 关键词：癌症、cancer
• 🔗 查看原文

💡 该来源还有 7 条内容，详见 文末

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1. ⭐ GSE296373 人脐带间充质干细胞来源的细胞外囊泡通过调节基于 XBP1 的钙稳态来保护移植的胰岛免受内质网应激诱导的线粒体功能障碍

• ✍️ 作者：未知作者
• 🏷️ 关键词：tumor、cancer、oncology、carcinoma、lymphoma、immune、immunity、TME、metabolism、metabolic、metabolome、cardiac、glioma、resistance、TCGA、DepMap、depmap、Hi-C、single.cell、single-cell、scRNA、scDNA、scATAC、spatial、spatially、Visium、genome、genomics、transcriptome、transcriptomics、proteome、proteomics、Bioconductor、Seurat、Scanpy、epigenetic、epigenome、histone、clustering
• 📝 描述：Contributors : Baicheng Kuang ; Jimeng Ruan ; Hao Yan ; Shiqi Gu ; Tongwen Ou ; Nianqiao GongSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusIslet transplantation is an ideal option for diabetes while early graft lose serves as a major obstacle. Human umbilical cord mesenchymal stem cells (hucMSC) have multiple functions including the maintenance of cellular homeostasis. However, it is unknown whether extracellular vesicles (EVs) derived from hucMSC (hucMSC-EVs) provide protective effects against transplant-related trauma-induced islet injury. Here, we isolated and purified hucMSC-EVs, and found that hucMSC-EVs promoted grafted islet survival, and enhanced glycemic control following co-transplantation in a syngeneic streptozotocin (STZ)-induced mouse model of diabetes. After co-cultured for 12 h or 24 h, labelled hucMSC-EVs with PKH67 were readily internalized by NIT-1 β cells and islets. In tunicamycin (Tm) and thapsigargin (Tg) induced specific endoplasmic reticulum stress (ERS) cell injury models, hucMSC-EVs treatment improved cell viability and β cells function both in NIT-1 cells and ex vivo primary islets. Bulk RNA-seq demonstrated that hucMSC-EVs treatment significantly involved in ERS and the negative regulated mitochondrial apoptotic pathway. While ERS promoted interactions between endoplasmic reticulum (ER) and mitochondria, hucMSC-EVs alleviated ERS, maintained calcium homeostasis, and improved mitochondrial energy metabolism. Notably, the downregulation of XBP1 by hucMSC-EVs fine-tuned ER-mitochondria communication via reducing inositol-1,4,5-trisphosphate receptors at mitochondria-associated membranes (MAMs). Reduced XBP1 also activated Nrf2, restoring mitochondrial calcium homeostasis under ERS. miRNA analysis identified miR-182-5p enriched in hucMSC-EVs that specifically targeted XBP1 mRNA, leading to its degradation and downregulation. These findings demonstrate that hucMSC-EVs protect grafted islets by blocking XBP1 and restoring calcium homeostasis, thus suggesting their potential as a cell-free therapy for improving islet transplantation outcomes.
• 🔗 查看原文

2. ⭐ GSE281215 野生大豆种子发育的时空转录组和代谢组图谱揭示了营养积累的调控机制 [scRNA-Seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：tumor、cancer、oncology、immune、TME、metabolism、metabolic、metabolome、metabolomics、glioma、resistance、TCGA、RNA-seq、RNAseq、DNA-seq、ATAC-seq、scRNA、scDNA、scATAC、spatial、spatially、Visium、spatial transcriptomics、genome、genomics、transcriptome、transcriptomics、proteome、proteomics、Seurat、Scanpy、epigenetic、epigenome、histone、enrichment
• 📝 描述：Series Type : Expression profiling by high throughput sequencingOrganism : Glycine sojaSeed development is pivotal in soybean’s lifecycle, directly determining yield and nutritional quality related to oil and protein contents. However, spatiotemporally resolved mechanisms underlying cell differentiation and nutrient accumulation during seed growth remain elusive, especially in wild soybean (Glycine soja Sieb. et Zucc.), which harbors rich genetic diversity for quality traits. Here, spatial transcriptomics and metabolomics were combined to dissect their dynamics in G. soja seeds at the mid-maturity stage. Differential expression analysis characterized the distinct accumulation patterns between adaxial and abaxial embryo parenchyma cells, revealing abaxial cells are enriched in protein metabolism pathways while adaxial cells focus on lipid metabolism pathways, which is consistent with previous studies reporting spatial nutrient accumulation in G. soja seeds. Meanwhile, pseudotemporal trajectory analyses briefly supported a sequential transcriptional regulation pattern for these differences. Cell-cell communication analysis further uncovered potential signaling interactions mediating cell-type-specific differences across seed cells. Key genetic regulators and differential metabolites were identified through spatial transcriptomics and metabolomics co-expression analysis, with GsMAPK23-4 screened as a core candidate linked to cotyledon nutrient metabolism. Functional validation confirmed GsMAPK23-4 modulates seed quality: knockout mutants had significantly higher amino acids and proteins. These findings elucidate the cellular characteristics and differentiation processes in G. soja seeds at the mid-maturity stage, providing a molecular basis for understanding this phase and generating targets to improve soybean yield and quality.
• 🔗 查看原文

3. ⭐ GSE294561 YTHDF3 促进 m6A 富集的有丝分裂相关基因的翻译，从而减弱食管癌对新辅助化疗的反应 [RIP-seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：tumor、cancer、immune、immunity、TME、cardiac、glioma、resistance、TCGA、DepMap、depmap、RNA-seq、RNAseq、DNA-seq、ChIP-seq、ATAC-seq、Hi-C、scRNA、scDNA、scATAC、spatial、genome、genomics、proteome、proteomics、Seurat、Scanpy、epigenetic、epigenome、histone、enrichment
• 📝 描述：Contributors : Xiang Y Wang ; Ting wang ; Si M Zhao ; Zi G DongSeries Type : OtherOrganism : Homo sapiensNeoadjuvant chemotherapy (NACT) is a pivotal treatment strategy for esophageal cancer, significantly improving patient prognosis and 5-year survival rates. However, a substantial proportion of patients exhibit resistance to NACT and consequently fail to benefit from it. As NACT responsiveness is influenced by multiple distinct molecular pathways, it is essential to systematically investigate the mechanisms underlying poor therapeutic responses. In this study, we found that YTHDF3 directly enhances the m6A-dependent translation of key mitotic regulators, CDCA8 and INCENP, thereby reducing cellular sensitivity to NACT.
• 🔗 查看原文

4. ⭐ GSE281070 野生大豆种子发育的时空转录组和代谢组景观揭示营养积累的调控机制 [空间转录组学]

• ✍️ 作者：未知作者
• 🏷️ 关键词：tumor、cancer、oncology、immune、TME、metabolism、metabolic、metabolome、metabolomics、glioma、TCGA、DepMap、depmap、scRNA、scDNA、scATAC、spatial、spatially、Visium、spatial transcriptomics、genome、genomics、transcriptome、transcriptomics、proteome、proteomics、Seurat、Scanpy、epigenetic、enrichment
• 📝 描述：Series Type : OtherOrganism : Glycine sojaSeed development is pivotal in soybean’s lifecycle, directly determining yield and nutritional quality related to oil and protein contents. However, spatiotemporally resolved mechanisms underlying cell differentiation and nutrient accumulation during seed growth remain elusive, especially in wild soybean (Glycine soja Sieb. et Zucc.), which harbors rich genetic diversity for quality traits. Here, spatial transcriptomics and metabolomics were combined to dissect their dynamics in G. soja seeds at the mid-maturity stage. Differential expression analysis characterized the distinct accumulation patterns between adaxial and abaxial embryo parenchyma cells, revealing abaxial cells are enriched in protein metabolism pathways while adaxial cells focus on lipid metabolism pathways, which is consistent with previous studies reporting spatial nutrient accumulation in G. soja seeds. Meanwhile, pseudotemporal trajectory analyses briefly supported a sequential transcriptional regulation pattern for these differences. Cell-cell communication analysis further uncovered potential signaling interactions mediating cell-type-specific differences across seed cells. Key genetic regulators and differential metabolites were identified through spatial transcriptomics and metabolomics co-expression analysis, with GsMAPK23-4 screened as a core candidate linked to cotyledon nutrient metabolism. Functional validation confirmed GsMAPK23-4 modulates seed quality: knockout mutants had significantly higher amino acids and proteins. These findings elucidate the cellular characteristics and differentiation processes in G. soja seeds at the mid-maturity stage, providing a molecular basis for understanding this phase and generating targets to improve soybean yield and quality.
• 🔗 查看原文

5. ⭐ GSE305309 人胎盘来源间充质干细胞减弱老年小鼠海马衰老相关转录组谱

• ✍️ 作者：未知作者
• 🏷️ 关键词：tumor、cancer、carcinoma、immune、TME、cardiac、glioma、resistance、TCGA、DepMap、depmap、Hi-C、scRNA、scDNA、scATAC、spatial、spatial transcriptomics、genome、genomics、transcriptome、transcriptomics、proteome、proteomics、Seurat、epigenome、methylation、histone、enrichment、clustering
• 📝 描述：Series Type : Expression profiling by high throughput sequencingOrganism : Mus musculusBackground Intravenous human placenta–derived mesenchymal stem cells (hpMSCs) can improve tissue function through paracrine effects, but their impact on normal brain aging is not well defined. Methods Aged female mice (18–19 months) received three intravenous infusions of hpMSCs or PBS at six-week intervals. Hippocampal tissue was collected after the behavioral tests for RNA sequencing. Results RNA sequencing showed hpMSCs’ effectiveness in modulating aging-related neural pathways, particularly by downregulating age-specific genes in the hippocampus, indicative of neural reactivation. Conclusions Systemic hpMSC administration modulates neural pathways in aged mice.
• 🔗 查看原文

6. ⭐ GSE285920 Piezo1 的激活诱导 LSK 细胞异质性，导致 HSC 增殖和髓系造血 [scRNA-seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：tumor、cancer、carcinoma、TME、cardiac、glioma、kinase、resistance、TCGA、RNA-seq、RNAseq、DNA-seq、ChIP-seq、ATAC-seq、scRNA、scDNA、scATAC、spatial、genome、genomics、proteome、proteomics、Seurat、Scanpy、epigenetic、epigenome、histone
• 📝 描述：Contributors : Xinjiang Lu ; Tongyao Shang ; Li Zhao ; Shibo YingSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusBone marrow haematopoietic stem cells (HSCs) are mobilised into blood under various stresses. Although they are exposed to shear stress during circulation, the role of mechanical stimulation in regulating HSCs remains unknown. Piezo1, a mechanosensory ion channel, was implicated in regulation of haematopoietic cells. We analysed the transcriptional heterogeneity of LSK cells from mice treated with the Piezo1 agonist Yoda1 for 2 weeks. Our study demonstrated that activation of Piezo1 promoted HSC proliferation and differentiation toward the myeloid lineage, as evidenced by an increase in HSC numbers and the upregulation of myeloid transcription factors.
• 🔗 查看原文

7. ⭐ GSE289098 研究发现，炎症相关的微胶质细胞增殖会破坏海马胶质细胞网络通讯，从而导致术后神经认知功能障碍。

• ✍️ 作者：未知作者
• 🏷️ 关键词：tumor、cancer、carcinoma、immune、TME、cardiac、glioma、resistance、TCGA、DepMap、depmap、scRNA、scDNA、scATAC、spatial、Visium、genome、genomics、transcriptome、proteome、R package、Seurat、epigenetic、epigenome、histone、clustering
• 📝 描述：Contributors : Yuxiang Zheng ; Wenjie Xu ; Zizheng Suo ; Yinyin Qu ; Lina Lin ; Enze Zhang ; Dengyang Han ; Meikui Wu ; Hongyi Li ; Hui Zheng ; Ting Xiao ; Cheng NiSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusPostoperative neurocognitive impairment (PNCI) significantly affects the recovery and long-term outcomes of elderly patients, with central nervous system (CNS) inflammation serving as the key pathogenic driver of its development. As the resident immune cells of the CNS, microglia play a crucial role in regulating perioperative inflammation and maintaining homeostasis. However, the contribution, phenotypic heterogeneity, and communication network of perioperative microglia in the development of PNCI remain insufficiently characterized. In this study, 18-month-old mice underwent surgery and developed PNCI. Single-cell RNA sequencing was performed, which identified eight microglial subpopulations and six astrocytic subpopulations in hippocampus. Postoperatively, the percentage of microglial subpopulations underwent dramatic changes, with inflammation associated microglia (IAM) increasing more than 14-fold and transition state microglia (TSM) increasing more than 33-fold. These alterations were accompanied by a marked enhancement of intercellular communications among glial cells, particularly driven by the activation of TNF signaling pathway in IAM. This pathway, along with its associated regulatory network, critically modulated the function of astrocytes and endothelial cells, thereby playing a pivotal role in CNS inflammation and the subsequent development of PNCI. Notably, administration of TNF inhibitor etanercept attenuated IAM activation and glial network communication in the hippocampus, which was associated with improved cognitive performance in PNCI mice.
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8. ⭐ 对注射Ad-cre和接受他莫昔芬治疗后KrasLSL-G12D/+Lkb1fl/fl (KL)和KrasLSL-G12D/+Lkb1fl/flGpx4m/m (KLG4)小鼠肿瘤肺中的肿瘤细胞、TRM、MDM、单核细胞和CD8+ T细胞进行GSE281154 mRNA转录组测序

• ✍️ 作者：未知作者
• 🏷️ 关键词：tumor、cancer、carcinoma、leukemia、immune、TME、glioma、resistance、TCGA、sequencing、RNAseq、single.cell、scRNA、scDNA、scATAC、genome、genomics、transcriptome、transcriptomics、proteome、R package、Seurat、epigenetic、epigenome
• 📝 描述：Contributors : Peng Wang ; Shengdan Zhang ; Xin Chen ; Dandan Lin ; Bo ZhongSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusThe transcriptional profiling of tumor cells, TRMs, MDMs, Monocytes and CD8+ T cells from tumor lungs of KL and KLG4 mice
• 🔗 查看原文

9. ⭐ GSE140320 细胞外囊泡的功能和转录组分析发现钙保护蛋白是外周动脉疾病 (PAD) 的一种新的预后标志物

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、carcinoma、TME、cardiac、glioma、kinase、resistance、TCGA、DepMap、depmap、scRNA、scDNA、scATAC、10x、spatial、genome、genomics、transcriptome、transcriptomics、proteome、Seurat、Scanpy、clustering
• 📝 描述：Contributors : Goren Saenz-Pipaon ; Patxi San Martín ; Núria Planell ; Alberto Maillo ; Susana Ravassa ; Amaia Vilas-Zornoza ; Esther Martínez-Aguilar ; José A Rodriguez ; Daniel Alameda ; David Lara-Astiaso ; Felipe Prosper ; José A Paramo ; Josune Orbe ; David Gomez-Cabrero ; Carmen RoncalSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensRationale: Peripheral arterial disease (PAD) is associated with a high risk of cardiovascular events and death and is postulated to be a critical socioeconomic cost in the future. Extracellular vesicles (EVs) have emerged as potential candidates for new biomarker discovery related to their protein and nucleic acid cargo.Objective: To study prothrombotic activity, cellular origin and transcriptomic profile of circulating EVs and to assess them as prognostic and therapeutic targets in PAD.Methods and Results: This prospective study included control and PAD patients. Coagulation time (Procoag-PPL kit), EVs cellular origin and phosphatidylserine exposure were determined by flow cytometry in platelet-free plasma (n=45 PAD). Transcriptomic profiles of medium/large EVs were generated using the MARS-Seq RNA-Seq protocol (n=12/group). The serum concentration of the differentially expressed gene calprotectin was validated by ELISA in control (n=100) and PAD patients (n=317). Calprotectin was also determined in EVs and tissues of human atherosclerotic plaques (n=3). Circulating EVs of PAD patients were mainly of platelet origin, predominantly AnnexinV positive and were associated with the procoagulant activity of platelet-free plasma. Transcriptomic analysis of EVs identified 15 differentially expressed genes. Among them, serum calprotectin was elevated in PAD patients (pConclusions: We found that PAD patients release EVs, mainly of platelet origin, highly positive for AnnexinV and rich in transcripts related to platelet biology and immune responses. Amputation risk prediction improved with calprotectin and was significantly higher when combined with hs-CRP. Our results suggest that EVs can be a promising component of liquid biopsy with prognostic implications in PAD.
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10. ⭐ GSE276733 通过 FIRESCAPE 进行的生物分子追踪揭示了细胞外组蛋白 H3 的清除、损伤诱导和细胞摄取的不同模式

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、carcinoma、leukemia、immune、TME、metabolic、cardiac、glioma、kinase、resistance、TCGA、single.cell、scRNA、scDNA、scATAC、spatial、genome、genomics、bioinformatics、Bioconductor、Seurat、histone
• 📝 描述：Contributor : Adam P CribbsSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Rattus norvegicusThe study of chromatin has mostly been restricted to defining its function in the nucleus, where histone proteins fulfil vital roles in packaging genomic DNA and regulating transcription. However, chromatin components are often released into the extracellular space, either intentionally via cellular secretion or during disease or damage-induced cell death. These extracellular chromatin components, depending on the context, can consist of free histones, free DNA, intact nucleosomes (histone octamers wrapped by DNA), or heterogeneous, higher order structures such as neutrophil extracellular traps (NETs). They have been associated with diverse pathologies such as inflammation, cancer, and sepsis, and distinct toxic effects, most notably the damaging effects of free histones over intact nucleosomes. Extracellular chromatin components are emerging, suggested biomarkers for various associated diseases, yet there is a widely acknowledged lack of methods that distinguish between them and their unique functions in circulation. Here, we explore the fate and effects of extracellular free histone H3 by utilizing FIRESCAPE ([18F]-Fluorine Isotopic Radiolabeling Enabling Scanning of Clearance After Proteolytic Events), a novel radiolabeling concept that leverages the unique, high-sensitivity properties of the radioisotope 18F and residue-specific protein editing chemistry. By installing true 18F-containing protein sidechain mimics site-specifically into histone H3, FIRESCAPE enabled in vivo scanning of the half-lives, proteolytic susceptibility, and clearance of single residues in a protein of interest, at microdoses far below toxic levels (low nanomole). This now precisely reveals the remarkably distinct distribution, half-lives, damage-inducing abilities, and accumulation of free extracellular histones in cellulo and in vivo, comparing them to other chromatin states such as intact nucleosomes where appropriate. Free extracellular histones are rapidly cleared from circulation, first mediated by proteolysis of the histone tail. However, direct injection of free histones versus nucleosomes into tissue (brain) that is unprotected by such proteolysis provokes a starkly different response: free histones exhibited limited diffusion and swiftly promoted damage both in cell culture and in vivo, in contrast to the largely passive and benign nature…
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💡 该来源还有 26 条内容，详见 文末

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1. ⭐ 癌症中细胞死亡免疫串扰的治疗靶向以重新连接肿瘤免疫微环境

• ✍️ 作者：未知作者
• 🏷️ 关键词：肿瘤、癌症、免疫、免疫微环境
• 📝 描述：Secret hovertext: 免疫系统通过协调抑制恶性肿瘤的发生、进展和转移的抗肿瘤反应，在抗癌防御中发挥核心作用。新出现的证据强调了调节细胞死亡 （RCD） 途径与免疫激活（特别是免疫原性细胞死亡 （ICD））之间至关重要的相互作用。ICD 是指肿瘤细胞死亡并释放损伤相关分子模式（DAMP）和其他信号分子，从而重塑肿瘤免疫微环境（TIME）的一种特定形式的调节性细胞死亡。虽然规范的 RCD 途径已经很成熟，但 ICD 的诱导因子、TIME 动力学的时空调节以及免疫细胞的功能状态仍不完全清楚。我们彻底评估了利用 RCD 驱动的免疫调节作用机制的当代治疗方法，包括增强 ICD 和增强抗肿瘤免疫反应的策略。本综述的新颖之处在于其双重视角：描述肿瘤内在死亡程序如何重新编程肿瘤 TIME，以及免疫细胞死亡如何直接决定其向免疫刺激状态与免疫抑制状态的极化，最终影响治疗结果。我们深入分析了不同形式的 RCD 如何塑造抗原呈递、引导
• 🔗 查看原文

2. 微卫星稳定结直肠癌靶向治疗后获得性高肿瘤突变负荷和免疫治疗活性

• ✍️ 作者：未知作者
• 🏷️ 关键词：肿瘤、免疫
• 📝 描述：Secret hovertext: 目的：与微卫星不稳定性高 （MSI-H） CRC 相比，微卫星稳定 （MSS） 结直肠癌 （CRC） 突变很少，并且对免疫检查点阻断 （ICB） 不敏感。用靶向药物治疗的 CRC 在进展过程中通常会获得大量基因组改变。我们询问靶向治疗是否可用于在 MSS CRC 中产生高肿瘤突变负荷 （TMB） 并使这些肿瘤对 ICB 敏感。患者和方法：在接受靶向治疗的 MSS 转移性 CRC 患者中，我们评估了肿瘤发展为高 TMB 的患者的基线和进展 TMB 以及对 ICB 的反应。我们确定了在获得性高 TMB 病例中与紧急基因组改变相关的改变类型、突变特征、新抗原性和克隆性。结果：26 例病例中，9 例进展时 TMB 升高。其中三名患者接受了 ICB，但均无反应。在 TMB 高病例中，我们没有发现肿瘤浸润淋巴细胞的诱导或程序性死亡配体 1 表达。获得性基因组改变主要由单核苷酸变异组成，富集了单碱基取代
• 🔗 查看原文

3. 关于饮酒对美国成年人患癌症风险影响的信念。

• ✍️ 作者：未知作者
• 🏷️ 关键词：癌症
• 📝 描述：Secret hovertext:
• 🔗 查看原文

4. 免疫检查点抑制剂作为 SJS/TEN 的独立协同驱动因素。

• ✍️ 作者：未知作者
• 🏷️ 关键词：免疫
• 📝 描述：Secret hovertext:
• 🔗 查看原文

5. 欧洲战胜癌症计划因“立法不作为”而被推迟

• ✍️ 作者：未知作者
• 🏷️ 关键词：癌症
• 📝 描述：Secret hovertext: 暂无摘要
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6. 靶向前列腺癌细胞中的 CXCR2 可以阻断 TME 中 CD47-SIRPα相互作用并逆转 M2 巨噬细胞极化

• ✍️ 作者：未知作者
• 🏷️ 关键词：TME
• 📝 描述：Secret hovertext: 神经内分泌前列腺癌（NEPC）表现出很强的免疫逃避能力，在调节前列腺癌的代谢重编程中起着关键作用。CD36 + M2 肿瘤相关巨噬细胞 （TAM） 的高浸润和 NEPC 细胞中 CD47 表达升高通常与癌症患者的无进展生存期差有关。了解前列腺癌肿瘤微环境 （TME） 内肿瘤细胞中调节 CD36 + M2 TAM 浸润和高 CD47 表达的机制至关重要。使用细胞模型和两个动物模型，我们发现 IL-8/CXCR2 通路通过代谢重编程增加乙酰辅酶 A 水平，随后通过乙酰化增加 CD47 表达。此外，该途径通过刺激肿瘤细胞分泌棕榈酸并利用棕榈酰化机制来调节 CD47 的膜定位，从而保护肿瘤细胞免受巨噬细胞介导的吞噬作用。IL-8/CXCR2 通路还重塑了 TME 的代谢微环境，增加了 TME 中ω-3/6 多不饱和脂肪酸（PUFAs）的浸润，从而促进了 CD36 + M2 TAMs 的募集。NSG
• 🔗 查看原文

7. 人工智能在癌症中的应用、挑战和未来展望

• ✍️ 作者：未知作者
• 🏷️ 关键词：癌症
• 📝 描述：Secret hovertext: 人工智能 （AI） 正在迅速彻底改变肿瘤学研究的格局和个性化临床干预的进步。三个相互关联的领域的进展，包括训练人工智能模型的方法和算法的开发、专业计算硬件的发展以及成像、基因组学和临床信息等大量癌症数据的访问增加，已经融合在一起，导致人工智能在癌症研究中的新应用前景广阔。人工智能应用根据特定的癌症类型和临床领域进行系统组织，包括生物学机制的阐明和预测、临床数据中模式的识别和利用以改善患者预后，以及揭示流行病学、行为和现实世界数据集中固有的复杂性。当以道德和科学严谨的方式应用时，这些人工智能驱动的方法有望加速癌症研究的进展，并最终促进改善所有人群的健康结果。我们回顾了展示人工智能在肿瘤学中整合的例子，重点介绍了深度学习巧妙地解决了曾经被认为无法克服的挑战的案例，同时还讨论了为促进这些技术的更广泛采用而必须克服的障碍。
• 🔗 查看原文

8. I 型干扰素信号传导对癌症的背景依赖性影响

• ✍️ 作者：未知作者
• 🏷️ 关键词：癌症
• 📝 描述：Secret hovertext: 长期以来，I 型干扰素 （IFN） 一直被认为是分子机制的关键组成部分，该分子机制首先对多细胞真核生物中的病毒感染做出反应。最近，I 型干扰素信号传导也已成为自然发展的肿瘤以及对（免疫）治疗有反应的肿瘤的微环境中的常见过程。在这种情况下，稳健、急性但最终解决的 I 型干扰素反应似乎通过多种机制支持自然和治疗驱动的癌症免疫监测，包括恶性细胞阻止其增殖并经历凋亡细胞死亡的累积倾向，以及对 CD8+ 细胞毒性 T 淋巴细胞 （CTL）、自然杀伤 （NK） 细胞的广泛免疫刺激作用， 树突状细胞 （DC） 和肿瘤相关巨噬细胞 （TAM）。相反，微弱、惰性和最终无法解决的 I 型干扰素反应实际上促进了肿瘤进展，不仅通过促进恶性细胞的干性（这与转移性播散和治疗耐药性增加有关），而且还有利于建立高度免疫抑制的淋巴和髓系肿瘤微环境。在这里，我们对 I 型干扰素信号传导对癌症进展和治疗反应的背景依赖性影响进行
• 🔗 查看原文

9. Domvanalimab 联合 zimberelimab 在上尿路癌症中显示出前景

• ✍️ 作者：未知作者
• 🏷️ 关键词：癌症
• 📝 描述：Secret hovertext:
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10. 重新思考现代肿瘤学试验中的终点——超越 P 值。

• ✍️ 作者：未知作者
• 🏷️ 关键词：肿瘤
• 📝 描述：Secret hovertext:
• 🔗 查看原文

💡 该来源还有 6 条内容，详见 文末

详细内容（前10条）

1. ⭐ 当然，要构建可复现的数据科学流程，总得有人编写命令式代码。但这个人不一定是你。

• ✍️ 作者：未知作者
• 🏷️ 关键词：TME、metabolic、cardiac、scRNA、scDNA、scATAC、spatial、Seurat、Scanpy、histone
• 📝 描述：Last time I quickly introduced my latest package, {rixpress}, but I think that to really understand what {rixpress} brings to the table, one needs to solve the same problem without it. And incidentally, I think that this exercise also show… Continue reading: Of course, someone has to write imperative code to build reproducible data science pipelines. It doesn’t have to be you.
• 🔗 查看原文

2. ⭐ 利用有界调和平均值近似证据（以及具有已知体积的HPD区域）

• ✍️ 作者：未知作者
• 🏷️ 关键词：tumor、cancer、TME、Visium、genome、genomics、proteome、proteomics、histone
• 📝 描述：Following a suggestion by Christian Hennig at JSM 2024, I started working with my PhD student Dana Naderi on a detailed assessment of the method we proposed in 2009 with Darren Wraith for evidence approximation. (The method was briefly mentioned in a Physical Review paper and also briefly illustrated in our 2010 San … Continue reading: Approximating evidence via bounded harmonic means (and HPD regions with known volumes)
• 🔗 查看原文

3. ⭐ 使用 JavaScript API 简化 shinytest2 中复杂组件的交互

• ✍️ 作者：未知作者
• 🏷️ 关键词：TME、TCGA、scDNA、genome、genomics、epigenetic
• 📝 描述：When shinytest2’s set_inputs() won’t work, leverage widget APIs directly. Learn to write cleaner, faster and more robust tests using JavaScript APIs. Continue reading: Simplifying Interactions with Complex Widgets in shinytest2 Using JavaScript APIs
• 🔗 查看原文

4. ⭐ 驾驭波动：利用 H2O AutoML 对 STOXX 600 指数进行高性能预测

• ✍️ 作者：未知作者
• 🏷️ 关键词：TME、glioma、TCGA、Hi-C、Visium
• 📝 描述：Forecasting financial markets, such as the STOXX Europe 600 Index, presents a classic Machine Learning challenge: the data is inherently noisy, non-stationary, and highly susceptible to sudden market events. To tackle this, we turn to Automated Machine Learning (AutoML)—specifically the powerful, scalable framework provided by H2O.ai and integrated … Continue reading: Taming Volatility: High-Performance Forecasting of the STOXX 600 with H2O AutoML
• 🔗 查看原文

5. ⭐ 2025年9月排名前40的新CRAN软件包

• ✍️ 作者：未知作者
• 🏷️ 关键词：TME、scRNA、R package
• 📝 描述：Computational Methods fastfocal v0.1.3: Provides a fast moving-window (“focal”) and buffer-based extraction for raster data using the terra package. Automatically selects between a C++ backend and a Fast Fourier Transform (FFT) backend depend… Continue reading: September 2025 Top 40 New CRAN Packages
• 🔗 查看原文

6. 一些无用却有用的 R 函数——R 需求无用金字塔

• ✍️ 作者：未知作者
• 🏷️ 关键词：tumor、TME
• 📝 描述：What motivates human behaviour can be captured in the Maslow’s hierarchy of needs (source: Wiki). Maslow and psychologists have articulated these needs in a form of a Pyramid, and ever since the concept had been widely adopted (also criticised), and…Read more › Continue reading: Little useless-useful R functions – Useless Pyramid of R needs
• 🔗 查看原文

7. 改变是好事，所以别改变我的零钱。

• ✍️ 作者：未知作者
• 🏷️ 关键词：TME、TCGA
• 📝 描述：One of my former insurance colleagues once said, “When a company makes a change, it’s probably not going to benefit you.” Assuming the above photo is legitimate, and of course no… Continue reading: Change is good, so don’t change my change
• 🔗 查看原文

8. 普鲁士马踢 II：混合效应模型

• ✍️ 作者：未知作者
• 🏷️ 关键词：TME
• 📝 描述：Last time we used a quirky dataset to get acquainted with Generalised Linear Models. If you recall, the dataset is a count of deaths by horse kick, where every year all the corps in the army had some non-negative integer number of deaths and we … Continue reading: Prussian Horse Kicks II: Mixed Effects Models
• 🔗 查看原文

9. 奉献我的时间 VII

• ✍️ 作者：未知作者
• 🏷️ 关键词：TME
• 📝 描述：Here we go again! I ran the Mainova Frankfurt Marathon 2025 and wanted to look at the race results. How can we do this using R? I couldn’t see an easy way to download the data, so I used R to scrape them. Note that these times are currently provisional, … Continue reading: Pledging My Time VII
• 🔗 查看原文

10. 什么是基尼系数？如何计算基尼系数？

• ✍️ 作者：未知作者
• 🏷️ 关键词：scDNA
• 📝 描述：If this post is useful to you I kindly ask a minimal donation on Buy Me a Coffee. It shall be used to continue my Open Source efforts. You can send me questions for the blog using this form and subscribe to receive an email when there is a new … Continue reading: ¿Qué es el Índice de Gini y cómo calcularlo?
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💡 该来源还有 1 条内容，详见 文末

详细内容（全部10条）

1. ⭐ 生物信息学视角下的转录组学：批量和单细胞RNA测序分析的全面综述

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、immune、TME、cardiac、kinase、resistance、TCGA、sequencing、RNA-seq、RNAseq、ATAC-seq、Hi-C、single.cell、single-cell、scRNA、scDNA、scATAC、spatial、spatially、transcriptome、transcriptomics、bioinformatics、R package、Scanpy、pathway
• 📝 描述：Researchers from the Yucatan Scientific Research Center have published an insightful review examining how advances in RNA sequencing (RNA-seq) technologies are revolutionizing the field of transcriptomics, the study of all RNA molecules produced in a cell. The transcriptome provides a detailed snapshot of cellular activity, showing which genes are active, how strongly they are …
• 🔗 查看原文

2. ⭐ MultiGATE——基于图表示学习的空间多组学数据整合分析和调控推断

• ✍️ 作者：未知作者
• 🏷️ 关键词：tumor、TME、glioma、TCGA、DepMap、depmap、single.cell、scRNA、scDNA、scATAC、spatial、Visium、genome、genomics、Seurat、clustering
• 📝 描述：Researchers from the Chinese University of Hong Kong have introduced an innovative approach called MultiGATE, designed to integrate complex spatial multi-omics data. Spatial multi-omics combines information about where specific molecules are located in tissues with what genes or proteins they represent. By linking transcriptomics (RNA sequencing data) with other molecular features like proteins and …
• 🔗 查看原文

3. ⭐ RNA测序揭示了T细胞随年龄变化而发生的改变，这些改变会削弱疫苗反应。

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、cardiac、resistance、TCGA、sequencing、RNAseq、single.cell、single-cell、scRNA、scDNA、scATAC、Seurat、histone
• 📝 描述：Researchers used single-cell RNA sequencing to reveal how aging alters T cell function, explaining weaker vaccine responses in older adults and guiding future vaccine innovations…
• 🔗 查看原文

4. ⭐ 单细胞剪接估计——以单细胞分辨率解析剪接异质性

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、TME、TCGA、Hi-C、single.cell、single-cell、scRNA、scDNA、scATAC、spatial、Scanpy、epigenetic、histone
• 📝 描述：Researchers developed SCSES, a computational tool that enhances RNA sequencing data by accurately detecting alternative splicing and revealing hidden cellular diversity…
• 🔗 查看原文

5. ⭐ CytoTRACE 2 – 改进的单细胞发育潜能重建

• ✍️ 作者：未知作者
• 🏷️ 关键词：carcinoma、TME、TCGA、DepMap、depmap、single.cell、single-cell、scDNA、spatial、proteome
• 📝 描述：Researchers at Stanford University, have introduced a powerful new computational framework called CytoTRACE 2 that improves our ability to predict how individual cells develop and specialize. This innovation represents a major advance in single-cell biology and data-driven research. Understanding how cells transition from one type to another, such as how stem cells mature into …
• 🔗 查看原文

6. ⭐ sysVI——整合具有显著批次效应的单细胞RNA测序数据集

• ✍️ 作者：未知作者
• 🏷️ 关键词：resistance、RNA-seq、RNAseq、single.cell、single-cell、scRNA、scDNA、scATAC
• 📝 描述：Researchers at Helmholtz Munich developed sysVI, a machine learning method that improves integration of RNA sequencing data across diverse systems while preserving vital…
• 🔗 查看原文

7. ⭐ 在单个植物细胞中将基因表达与代谢物产生相匹配

• ✍️ 作者：未知作者
• 🏷️ 关键词：TME、metabolic、cardiac、TCGA、single.cell、genome、genomics、histone
• 📝 描述：A pioneering method enables simultaneous RNA and metabolite analysis To the point Gene activity and plant metabolites analyzed together in the same plant cell for the first time: Researchers have combined two techniques, single-cell RNA sequencing (scRNA-seq) and single-cell mass spectrometry (scMS), to measure gene expression and the metabolite profile in the same cell. A …
• 🔗 查看原文

8. ⭐ OpenPedCan 扩大了全球研究人员获取儿科癌症数据的途径。

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、scRNA、scDNA、scATAC、spatial
• 📝 描述：The OpenPedCan Project harmonizes genomic and clinical data from over 6,000 pediatric tumors across 100 cancer types, creating an open-access resource to advance collaboration and accelerate childhood cancer research. Modern cancer breakthroughs depend on collaboration and open data. The Open Pediatric Cancer (OpenPedCan) Project, published last month in GigaScience, is opening new doors for …
• 🔗 查看原文

9. P-body-seq 可以对 P 体成分进行全面分析。

• ✍️ 作者：未知作者
• 🏷️ 关键词：TME、Hi-C
• 📝 描述：A team led by researchers at Baylor College of Medicine has uncovered a surprising mechanism that helps determine how stem cells decide what type of cell they will become. Their work focuses on RNA condensates, tiny, droplet-like structures inside cells that organize and store RNA molecules. One type of RNA condensate, known as a …
• 🔗 查看原文

10. 2025 年单细胞方法新指南

• ✍️ 作者：未知作者
• 🏷️ 关键词：single.cell
• 📝 描述：New guide for emerging single cell methods: Methyl-Seq, CRISPR-Cas9 Screening, Gene Expression, ATAC-Seq, Multiomics, and more! Single cell sequencing is changing rapidly, with new methods that enable as many as 2.6 million cells to be sequenced at once at 62% lower cost*. Download the NEW Single Cell Methods Guide to learn about emerging techniques …
• 🔗 查看原文

• NPJ Precision Oncology | 你丢掉的增殖细胞，可能是区分肺癌免疫和化疗敏感性的关键？
• Nature：为何 74% 的 pMMR 免疫治疗仍无效？“纤维化”微环境或是元凶，新靶点指向 TGF-B！
• 26%！《自然》重大突破：pMMR 结肠癌“冷肿瘤”首次被激活，新辅助免疫治疗大获成功！
• metafor包: GOSH 图
• 10+生信，基于 Ro/e 发现不同治疗反应患者 CD8Teff 细胞比例差异。细胞丰度分析识别关键细胞目前在高分文章中很常见！
• 轻松一读 | 15分1区纯生信，机器学习：这次我连代码都没写，就上了标题？
• AI | Nature Methods | 用于发现质谱数据模式的通用语言

• GSE246906 选择性靶向B淋巴细胞中的MMP-12治疗严重过敏性气道疾病
• GSE305310 人胎盘间充质干细胞细胞外囊泡的 miRNA-Seq
• GSE302902 药物测序研究：结直肠癌患者体内高密度中性粒细胞 (HDN)、成熟低密度中性粒细胞 (M-LDN) 和未成熟低密度中性粒细胞 (IM-LDN)
• GSE275329 MeCP2 与超延伸复合物相互作用以调控转录（ChIP-Seq）
• GSE282854 靶向组蛋白甲基转移酶 DOT1L 可重塑 CD8 T 细胞并增强其对肿瘤细胞的固有细胞毒活性 [RNAseq_WT_KO_DMSO_EPZ]
• GSE307146 叶酸和甲基丙二酸对心血管疾病死亡率的独立交互作用
• GSE302900 药物测序研究：结直肠癌患者高密度中性粒细胞（HDN）的GM-CSF刺激与否
• GSE285919 Piezo1 缺陷诱导 HSC 转录组变化 [RNA-seq]
• GSE275332 MeCP2 与超延伸复合物相互作用以调控转录（RNA-Seq）
• GSE281010 PRC1介导POGZ在神经发育基因调控中的转录抑制功能
• GSE282853 靶向组蛋白甲基转移酶 DOT1L 可重塑 CD8 T 细胞并增强其对肿瘤细胞的固有细胞毒活性 [RNAseq_DMSO_SGC]
• GSE305755 RPA 直接刺激 Mer3/HFM1 解旋酶的持续活性，以确保减数分裂中正常的交叉形成
• GSE302903 12 例结直肠癌 (CRC) 患者肿瘤组织的单细胞 RNA 测序。
• GSE307042 保守的热激因子通过不同的机制控制大麦的热胁迫记忆 - 扩展重复
• GSE305194 细胞死亡波调节人类视网膜神经节细胞的数量和成熟度
• GSE301153 生酮饮食可改善 APOE4 阿尔茨海默病小鼠模型中雌性的记忆力。
• GSE152864 低剂量和高剂量腺病毒感染后肝脏 CD8 T 细胞群 mRNA 的 RNA 测序
• GSE282852 靶向组蛋白甲基转移酶 DOT1L 可重塑 CD8 T 细胞并增强其对肿瘤细胞的固有细胞毒活性 [ChIPSeq_DMSO_EPZ_SGC]
• GSE306015 循环细胞外囊泡在慢性肾脏病患者心力衰竭发病机制中的作用
• GSE275333 MeCP2 与超延伸复合物相互作用以调控转录
• GSE309506 利鲁唑对患者来源运动神经元的健康进行药理学挽救
• GSE281029 保守的热激因子通过不同的机制控制大麦的热胁迫记忆
• GSE271342 组蛋白2B单泛素化调控RNA聚合酶II转录的延伸-终止转换
• GSE300606 MNX1 通过抑制 PERCC1 来阻止人 β 细胞中生长抑素的表达
• GSE261266 TPO刺激介导iKMT2A-MLLT3 HSPC的基因表达
• GSE273186 抑制炎症小体可改善同源多囊肾病

• 重新思考现代肿瘤学试验中的终点——超越 P 值。
• RANKL 抗体狄诺塞麦在两组复发/难治性骨肉瘤患者中的 2 期试验，儿童肿瘤学组 （COG） 的报告
• 循环肿瘤 DNA 水平对参加 plasmaMATCH 试验的晚期乳腺癌患者的预后和预测影响
• 始终遵守身体活动指南和消化系统癌症风险和死亡率
• RAS-GTP 抑制克服非小细胞肺癌中由致癌和野生型 RAS 激活介导的对 KRASG12C 抑制剂的获得性耐药性
• 靶向 CDK12/13 可驱动有丝分裂停滞以克服对 KRASG12C 抑制剂的耐药性

• 注意时间