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1. ⭐ GSE319722 空间动态将PD-L1和肿瘤相关巨噬细胞富集微环境与微卫星稳定型结直肠癌的免疫和间质状态联系起来

• ✍️ 作者：未知作者
• 🏷️ 关键词：tumor、cancer、immune、macrophage、spatial
• 📝 描述：Contributors : Carolina Martínez-Ciarpaglini ; Brenda Palomar de LucasSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensMicrosatellite-stable colorectal cancer comprises a heterogeneous group of tumors generally considered “immune cold” due to limited neoantigen generation and T-cell exclusion or inactivation. Current evidence indicates that the composition of T and B immune cells within the tumor microenvironment represents a prognostically relevant factor, significantly associated with both tumor expression profiles and molecular subtypes. We conducted an exploratory analysis to identify prognostically relevant immune cell components in this group of tumors and to investigate corresponding differences in RNA-based bulk expression and high-resolution spatial transcriptomic profiles. A total of 254 cases of localized mismatch repair–proficient colorectal cancer cases were evaluated. Our findings revealed PD-L1 expression as a robust, independent prognostic biomarker associated with favorable outcomes in this specific population. Bulk RNA expression analysis showed that PD-L1–negative tumors exhibited an expression profile consistent with abundant cancer-associated fibroblast infiltration, increased matrix stiffness, and impaired immune activation—features aligned with tumor progression and poorer clinical outcomes. In contrast, PD-L1–positive tumors displayed stromal programs enriched in immune activation and controlled remodeling, consistent with an immunologically active microenvironment. Spatial transcriptomics added an additional layer of evidence, revealing that epithelial-to-mesenchymal transition–related programs can dominate stromal niches in PD-L1–negative tumors, particularly within macrophage-enriched stromal regions. In conclusion, our observations suggest a crosstalk link between PD-L1 expression on immune cells and immune-activated vs mesenchymal-dominant states driven within tumor-associated macrophage-enriched stromal niches. These results provide insight into the biological mechanisms underlying disease progression and highlight tumor-associated macrophages as a potential therapeutic target to overcome immune resistance particularly in PD-L1–negative MSS-CRC tumors.
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2. ⭐ GSE327985 慢性不可预测轻度应激 (CUMS) 小鼠癌症模型中肿瘤内 CD45+ 免疫细胞的单细胞 RNA 测序

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、immune、sequencing、single-cell
• 📝 描述：Contributors : Julia A Brown ; Hilal Bashir ; Melody Y ZengSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusWe performed single-cell RNA sequencing (scRNA-seq) of intratumoral CD45+ Immune cells from mice subjected to chronic unpredictable mild stress (CUMS) or control conditions. Cells were multiplexed using hashtag oligonucleotides (HTO1-HTO4, TotalSeq-C) and sequenced using the 10x Genomics 5-prime Gene Expression + Feature Barcode + B cell receptor (BCR) V(D)J workflow (Well 3). This dataset contains GEX profiles of intratumoral B cells from 4 samples (2 conditions x 2 biological replicates; 29,456 cells total). BCR V(D)J sequencing data (IGH/IGK/IGL; 1,107 contigs from 604 B cells) from the same tumor well are also provided.
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3. ⭐ GSE292567 癌症干细胞是肿瘤微环境的超敏传感器，在调控转移动力学中发挥作用

• ✍️ 作者：未知作者
• 🏷️ 关键词：tumor、cancer、tumor microenvironment
• 📝 描述：Series Type : Expression profiling by high throughput sequencing ; Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensThis SuperSeries is composed of the SubSeries listed below.
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4. ⭐ GSE292485 癌症干细胞是肿瘤微环境的超敏传感器，在调控转移动力学中发挥作用

• ✍️ 作者：未知作者
• 🏷️ 关键词：tumor、cancer、tumor microenvironment
• 📝 描述：Contributors : Binwu Tang ; Howard Yang ; Maxwell Lee ; Lalage M WakefieldSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensCancer stem cells (CSCs) are key drivers of metastasis and therapy resistance but have been challenging to visualize and study in situ. Using a fluorescent CSC reporter, we observed very different population dynamics for CSCs and nonCSCs during metastatic lung colonization in breast cancer models. CSC expansive self-renewal drives early lesion formation before switching to a maintenance mode of balanced self-renewal and differentiation, whereupon nonCSC proliferation takes over as the main driver of metastatic expansion. Mechanistic analyses showed that CSCs are hyper-responsive to microenvironmental cues such as cell crowding and nutrient availability, suggesting a novel role for CSCs as sensors and early responders to fluctuating local conditions in the tumor. Most inputs converge on YAP/TAZ/TEAD, with heightened CSC sensitivity and response supported by elevated receptor expression and increased chromatin accessibility around enhancers with TEAD binding sites. Targeting inputs to the YAP/TAZ/TEAD node reversed chemotherapy-induced enrichment of CSCs in lung metastases.
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5. ⭐ GSE292476 癌症干细胞是肿瘤微环境的超敏传感器，在调控转移动力学中发挥作用

• ✍️ 作者：未知作者
• 🏷️ 关键词：tumor、cancer、tumor microenvironment
• 📝 描述：Contributors : Binwu Tang ; Howard Yang ; Maxwell Lee ; Lalage M WakefieldSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensCancer stem cells (CSCs) are key drivers of metastasis and therapy resistance but have been challenging to visualize and study in situ. Using a fluorescent CSC reporter, we observed very different population dynamics for CSCs and nonCSCs during metastatic lung colonization in breast cancer models. CSC expansive self-renewal drives early lesion formation before switching to a maintenance mode of balanced self-renewal and differentiation, whereupon nonCSC proliferation takes over as the main driver of metastatic expansion. Mechanistic analyses showed that CSCs are hyper-responsive to microenvironmental cues such as cell crowding and nutrient availability, suggesting a novel role for CSCs as sensors and early responders to fluctuating local conditions in the tumor. Most inputs converge on YAP/TAZ/TEAD, with heightened CSC sensitivity and response supported by elevated receptor expression and increased chromatin accessibility around enhancers with TEAD binding sites. Targeting inputs to the YAP/TAZ/TEAD node reversed chemotherapy-induced enrichment of CSCs in lung metastases.
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6. ⭐ GSE253850 人类和小鼠肾上腺具有物种特异性和性别二态性异质性以及组织更新的特征[空间转录组学]

• ✍️ 作者：未知作者
• 🏷️ 关键词：spatial、spatial transcriptomics、transcriptomics
• 📝 描述：Contributors : Maria E Kastriti ; Denis Maksimov ; Julian Petersen ; Julia Krupinova ; Marina Utkina ; Sergei Popov ; Dmitry Beltsevich ; Anna Roslyakova ; Olga Glazova ; Samira Kaziakhmedova ; Alina Ryabova ; Anna Kuznezova ; Anastasia Shcherbakova ; Ekaterina Bondarenko ; Zoia Antysheva ; Eugene Albert ; Lilia Urusova ; Anastasia Lapshina ; Anastassia Chevais ; Ekaterina Avsievich ; Valentin Trofimov ; Galina Melnichenko ; Natalya Mokrysheva ; Ivan Dedov ; Oleg Gusev ; Andreas Heinzel ; Rainer Oberbauer ; Mary Woroncow ; Pavel Volchkov ; Peter V Kharchenko ; Igor AdameykoSeries Type : Expression profiling by high throughput sequencing ; OtherOrganism : Homo sapiensThe adrenal gland is a fundamental endocrine organ exhibiting constant renewal. Despite extensive work in rodents, human-specific aspects of hormone-producing cell populations, stem cells, and self-renewal mechanisms are not fully understood. To fill this knowledge gap and address species-specific features, we generated high density single-cell and spatial transcriptomics atlases of adult human and mouse adrenal glands using Visium, VisiumHD and Stereo-seq, covering a spectrum of sexes and ages. Our comparisons between human and murine adrenal gland revealed significant evolutionary divergence despite homology in function of specific regions, which questiones the applicability of mouse models in studies of human adrenal disorders. Self-renewal mechanisms in adrenocortical populations that were previously discovered in mice also revealed human-specific features or were confronted by human-specific transitions not evident in rodents. The latter included specific perivascular mesenchymal progenitors, and dispersed SF1+/EZH2+ progenitor cells, which implies that human adrenocortical cells may be renewed in a localized manner in addition to the centripetal model. We also engaged in cross-comparison of our adult human adrenals with fetal stages to reveal developmental strategies still operating as a part of self-renewal in adults. Unexpectedly, human SF1+/EZH2+ progenitors turned out to be operating during adrenocortical development and later during adult stages, albeit in different degrees. At last, we revealed sex-specific differences in human cholesterol metabolism and other features reflecting human and mouse sexual dimorphism in adrenal glands. Overall, our new comparative mouse-human atlases shall provide an additional resource for further molecular interrogations of adrenal gland biology and p…
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7. ⭐ GSE330526 靶向αvβ5整合素可改变胰腺癌富含TGF-β的肿瘤微环境

• ✍️ 作者：未知作者
• 🏷️ 关键词：tumor、cancer、tumor microenvironment
• 📝 描述：Series Type : Expression profiling by high throughput sequencingOrganism : Mus musculusPancreatic ductal adenocarcinoma (PDAC) is notorious for its aggressive, therapy-resistant nature that is in part driven by the desmoplastic, hypo-perfused, and immunosuppressive tumor microenvironment (TME). Here, we demonstrated that the αv integrin- and neuropilin-1 (NRP-1)-dual targeting iRGD peptide reverses some of these TME features by inhibiting transforming growth factor-β (TGF-β) activation in the tumor, a process mediated by the αvβ5 integrin. In addition to PDAC epithelial cells and fibroblasts, regulatory T cells (Tregs) in PDAC tumors also expressed the αvβ5 integrin and NRP-1. The αvβ5+ Tregs potently inhibited T cell proliferation, and systemic iRGD therapy not only depleted αvβ5+ Tregs from PDAC tumors but also reduced their αvβ5- counterparts. Mechanistically, iRGD inhibited the activation of TGF-β mediated by the αvβ5-rich TME, thereby depriving Tregs of the cytokine essential for their development and maintenance. NRP-1-dependent tumor penetration was required for this effect because a traditional RGD peptide without an NRP-1-binding motif failed to inhibit TGF-β signaling or deplete Tregs in vivo. Treatment with iRGD induced a series of additional TME changes, such as improved vascular patency and perfusion, reduced stromal fibers, and increased CD8+ T cell entry into the core of the tumors. Combining iRGD with immune checkpoint blockade led to an enhanced anti-tumor effect. Together, these findings support targeting the αvβ5 integrin with affinity ligands such as iRGD as a potential approach to enhance immunotherapy efficacy against PDAC and other desmoplastic tumors with high TGF-β and αvβ5 expression.
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8. ⭐ GSE319419 粒子重编程 TLR-铁死亡轴和免疫代谢途径抑制髓系抑制以改善前列腺癌中的检查点阻断 [RNA-Seq Hi-Myc 小鼠]

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、TLR、RNA-seq
• 📝 描述：Contributors : Nabil A Siddiqui ; Michelle S BradburySeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusThe limited efficacy of immunotherapies (IT) in advanced prostate cancer (PCa) stems from a tumor microenvironment where myeloid-driven immune suppression, stromal remodeling, and metabolic barriers converge to limit antitumor immunity. We highlight the immuno-metabolic properties of an ultrasmall PSMA-targeting silica particle therapy as a first-in-class strategy to reprogram the Toll-like receptor (TLR)–ferroptosis axis in Myc-driven PCa. As single agents, these particles suppress lipid and steroid biosynthesis, disrupt lipid peroxidation control, and impair nutrient flux, sensitizing tumors to ferroptosis. Coordinated redox remodeling, stromal reprogramming, and innate immune activation reverse myeloid suppression and promote CD8⁺ T cell infiltration. When combined with CSF-1R inhibition and/or immune checkpoint blockade, particles suppress tumor growth, extend survival beyond 100 days, and achieve up to 50% complete remissions in Myc-overexpressing models. These findings position TLR–ferroptosis axis remodeling as a mechanistic blueprint for rational, particle-driven ITs with broad translational potential in PCa and other immunologically refractory malignancies.
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9. ⭐ GSE301231 结肠 Treg 的单细胞 RNA 测序分析：由对食物、微生物或自身抗原有反应的不同 TCR 驱动的天然 Treg 或 pTreg

• ✍️ 作者：未知作者
• 🏷️ 关键词：regex:micro(b|be|bial|organism)、RNAseq、single-cell
• 📝 描述：Contributors : Xinxin Chi ; Diane Mathis ; Christophe BenoistSeries Type : Expression profiling by high throughput sequencing ; OtherOrganism : Mus musculusAntigen-specific regulatory T cells (Tregs) in the gut are essential for maintaining immune tolerance, yet the contributions of different antigen sources and TCR identities to peripheral Treg (pTreg) differentiation remain poorly understood. In this study, we replaced endogenous TCRs in CD4⁺ Tconv cells (CD45.2⁺) with defined TCRs using an AAV-based system. Tconv cells expressing TCRs reactive to food (TF2.2, TF2.7, TF2.6), E. coli Nissle (TM3.5, TM2.3, TM1.2), or self antigens (TS2.3, TS2.1) were transferred into CD45.1⁺ hosts carrying the corresponding antigens. Ten days post-transfer, we performed single-cell RNA sequencing on donor-derived pTreg cells sorted from pooled mesenteric lymph nodes (mLNs), based on Foxp3-GFP expression. In parallel, we profiled TCR-edited transferred cells that did not convert to Foxp3⁺. As negative controls, we included non-edited and TCR-negative donor cells that had undergone the same in vitro culture and transfer process but did not receive differentiation-inducing signals. For comparison with endogenous T cell populations, we also included host-derived CD25hi Tregs as well as GFP⁺ and GFP⁻ cells from age-matched Foxp3-GFP mice.
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10. ⭐ GSE330256 肿瘤来源的 miR200a 通过 Wnt5a/IL-6/B7-H4 轴抑制卵巢癌转移 [RNA-seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：tumor、cancer、RNA-seq
• 📝 描述：Contributors : He Fei ; Lina Yang ; Fengyin JiangSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensGene expression analysis in human Ovarian Cancer cells(HEY) treated with gain of function of miR200a.
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1. 科学家表示，这种常见的甜味剂可能正在悄然改变你的新陈代谢。

• ✍️ 作者：未知作者
• 🏷️ 关键词：metabolism
• 📝 描述：Researchers say fructose is not just “empty calories” — it may actively push the body toward fat storage and metabolic disease. A new review found that fructose affects the body differently from glucose, disrupting normal energy regulation and promoting processes linked to obesity, insulin resistance, and cardiovascular problems.
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2. 用于下一代RNA测序和小RNA定量分析的无凝胶文库制备

• ✍️ 作者：未知作者
• 🏷️ 关键词：sequencing
• 📝 描述：RNA sequencing sensitivity improves with gel-free library preparation, reducing primer dimer artifacts and enhancing small RNA quantification from lower sample inputs…
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• GSE309174 器官培养中的干细胞激活揭示了子宫平滑肌瘤中代谢、纤维化、血管和免疫失调的新型转录程序
• GSE326299 扩增的驻留心脏巨噬细胞数量对疾病病理的影响
• GSE319397 TLR-铁死亡轴和免疫代谢通路的粒子重编程抑制髓系抑制，从而改善前列腺癌的检查点阻断治疗
• GSE307775 心脏巨噬细胞亚型在心脏中的功能作用 [snRNA-Seq]
• GSE307501 心脏巨噬细胞亚型在疾病和稳态中的功能作用
• GSE292888 骨来源的骨形成细胞（osterix+）是乳腺癌中促肿瘤肌成纤维细胞癌相关成纤维细胞的来源
• GSE138498 应激诱导的 CXCL13 调节胰腺外分泌稳态、年龄相关的慢性炎症和癌症进展
• GSE330249 GATA4 缺失促进突变 Kras 驱动的胰腺导管腺癌，而无典型前体病变 [ChIP-Seq]
• GSE330245 GATA4 缺失促进突变 Kras 驱动的胰腺导管腺癌，而无典型前体病变 [上皮 RNA 测序]
• GSE330243 GATA4 缺失促进突变 Kras 驱动的胰腺导管腺癌，而无典型前体病变 [bulk RNA-Seq]
• GSE330223 常见变异型免疫缺陷伴炎症并发症中细胞因子失调和抗体缺乏的汇合
• GSE329938 ALK 融合肺腺癌的全面分析揭示了突变 p53 驱动的 DNA 复制和修复失调在靶向治疗耐药中的作用 [RNA-Seq]
• GSE321717 用于识别细胞重编程最小网络的组合转录因子筛选方案 [scRNA-seq]
• GSE319821 生酮饮食作为SETD1B相关癫痫的表观遗传疗法
• GSE312967 SOX10敲低葡萄膜黑色素瘤的转录组和miRNA表达谱
• GSE270113 胸腔呼吸道感染后继发流感感染可增强巨噬细胞反应和肺损伤 II
• GSE253849 人类和小鼠肾上腺的特征是物种特异性和性别二态性异质性和组织更新[scRNA-seq]
• GSE166962 PARP 抑制通过激活内源性逆转录病毒诱导 mESC 细胞毒性 [ATAC-seq]
• GSE330580：酒精复发大鼠模型中前额叶皮层和伏隔核神经元和胶质细胞的区域和性别依赖性单细胞转录组特征
• GSE329323 建立感觉神经元作为多聚谷氨酰胺扩增的 ATXN3 驱动的周围神经病变的治疗靶点 [Advil RNA-seq]
• GSE324934 体外个性化治疗头颈癌：3D-OTC模型
• GSE322779 转录因子 TFEB 通过增强溶酶体容量和线粒体功能来拮抗心脏肥大和心力衰竭
• GSE320100 建立感觉神经元作为多聚谷氨酰胺扩增的 ATXN3 驱动的周围神经病变的治疗靶点 [11937-RNA-seq]
• GSE247745 拟南芥病毒感染下转录重编程相关的异染色质重组 [RNA-seq]
• GSE247744 拟南芥病毒感染下转录重编程相关的异染色质重组 [ChIP-seq]
• GSE330325 糖原贮积症 1a 型和健康对照成纤维细胞的 Epic 甲基化分析
• GSE330233 CHD8 单倍体不足会损害人类腹侧前脑类器官中腹侧祖细胞的增殖和抑制性神经元的成熟
• GSE330201 PEDV不连续转录产生一种新型亚基因组RNA，以增强免疫逃逸和病毒适应性
• GSE330159 对 53 hpf 野生型和 iqgap1-/- 出血阳性突变体胚胎进行批量 RNA 测序
• GSE330158 单个 6 日龄野生型和 osgep G177A 纯合子幼虫的批量 RNA 测序
• GSE329962 致病性 IgG 唾液酸化通过 Siglec-1–FcγR–VDAC1 轴驱动巨噬细胞免疫代谢功能障碍和肺部免疫病理
• GSE297517 磁场通过 RSRP1 介导的分泌信号轴抑制非小细胞肺癌 [KO]
• GSE297180 磁场通过RSRP1介导的分泌信号轴抑制非小细胞肺癌
• GSE330586 发光杆菌 ANT-2200 发光态和低发光态的比较转录组学
• GSE327619 小鼠内皮染色质重塑酶调节纤溶酶活性和无菌性炎症以防止致命性胚胎肝脏恶化
• GSE304521 性别依赖性 I 型干扰素信号传导加剧阿尔茨海默病病理
• GSE292568 花生四烯酰牛磺酸可预防饮食诱导的肝脂肪变性和炎症
• GSE289872 嗜酸性粒细胞促进肠绒毛中出生后平滑肌细胞的第二波分化
• GSE214352 PM20D1衍生疗法诱导小胶质细胞与淀粉样斑块结合，并改善阿尔茨海默病病理。