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1. GSE302161 肿瘤尊严谱的极端：两种常见犬肛周肿瘤的转录组图谱与癌症的标志相一致 [3’ RNA-Seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、RNA-seq
• 📝 描述：Contributors : Alexander F Haake ; Alina K Loriani Fard ; Vladimir M Jovanovic ; Michael Hummel ; Sandro Andreotti ; Achim D GruberSeries Type : Expression profiling by high throughput sequencingOrganism : Canis lupus familiarisThe hallmarks of cancer describe stepwise changes in cellular functions and molecular pathways of tumour cells that undergo malignant progression. Although 14 hallmarks have been proposed, their manifestation at the molecular level across different tumour types remains incompletely understood. Here, we hypothesised that hallmark-associated transcriptomic signatures reflect the contrasting biological behaviours of a pair of a benign and a highly malignant tumour. To this end, we compared the two most common canine perianal tumours, the highly malignant apocrine gland anal sac adenocarcinoma (AGASAC) and the benign hepatoid gland adenoma (HGA). Spontaneous tumours were analysed using 3’ RNA-Seq (AGASAC n = 15, HGA n = 10) and a direct mRNA hybridisation panel (AGASAC n = 33, HGA n = 12). Large transcriptomic differences were observed in both the number of differentially expressed genes and enriched pathways. Hallmarks such as “sustaining proliferative signalling”, “evading growth suppressors”, and “tumour-promoting inflammation” were prominent in AGASACs, while HGAs showed enrichment for “deregulating cellular metabolism” and “resisting cell death”. Surprisingly, some transcriptomic differences were not as clearly differentiating or evident, such as “activating invasion and metastasis” or “inducing or accessing vasculature”. Additionally, our data point towards a subgrouping of AGASACs associated with the inflammatory landscape, supporting the notion that it is a promising candidate for immune checkpoint inhibitor therapy. Overall, the transcriptomes of these two extremes on the tumour dignity spectrum clearly contrasted each other in select aspects of the hallmarks. Still, their malignant or benign behaviours could not generally be mirrored on the mRNA level.
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2. GSE312117 RNA-seq 分析了体外培养的野生型 E-mu-Myc 细胞和体内用 Vehicle 和 ASNase 处理的 E-mu-Myc 细胞衍生的 B 细胞淋巴瘤。

• ✍️ 作者：未知作者
• 🏷️ 关键词：lymphoma、RNA-seq
• 📝 描述：Contributors : Johanna Chiche ; Nicolas Nottet ; Jean-Ehrland RicciSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusThis dataset contains RNA-seq profiles of wild-type E-mu-Myc-lymphoma cells in two experimental contexts. First, E-mu-Myc-cells isolated from 12 individual transgenic Eµ-MycTg/+ mouse were cultured in vitro under standard growth conditions. Second, RNA-seq was also performed on bulk B-cell lymphomas of wild-type C57BL/6 mice engrafted with E-mu-Myc-#506 cells and treated with either Vehicle or L-asparaginase (ASNase) until disease endpoint. This dataset enables the comparison of transcriptional programs between in vitro–cultured E-mu-Myc-cells. It also evaluates the transcriptional responses to ASNase treatment in vivo in established B-cell lymphomas grown in C57BL/6 mice (n=1 BCL/group).
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3. GSE311260 不同调节性T细胞亚群在结直肠癌中的相反功能

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、T cell
• 📝 描述：Contributors : Xiao Huang ; Dan Feng ; Sneha Mitra ; Emma S Andretta ; Nima B Hooshdaran ; Aazam P Ghelani ; Eric Y Wang ; Joe N Frost ; Victoria Lawless ; Aparna Vancheswaran ; Qingwen Jiang ; Christina S Leslie ; Alexander Y RudenskySeries Type : Expression profiling by high throughput sequencing ; OtherOrganism : Mus musculusRegulatory T (Treg) cells are considered major contributors to the growth of solid organ tumors, with the notable exception of colorectal cancer (CRC), despite the documented abundance of Treg cells in CRC. Here, we demonstrate that IL-10⁺ and IL-10⁻ Treg cells constitute two distinct subsets with opposing functions: IL-10⁺ Treg cells counteract, while IL-10⁻ Treg cells promote, the growth of genetically engineered CRC tumors. Our findings suggest that the tumor-suppressive function of IL-10⁺ Treg cells is mediated by their suppression of effector CD4⁺ T cell production of IL-17, a cytokine that directly stimulates CRC tumor cell proliferation. Consistently, IL-10⁺ Treg cells were more abundant in both mouse and human CRC tumors than in tumor-adjacent normal colon tissue, whereas IL-10⁻ Treg cells exhibited the opposite distribution. Furthermore, gene expression signatures associated with IL-10⁺ and IL-10⁻ Treg cells correlated with better and worse disease prognoses in human CRC, respectively. This functional dichotomy between Treg subsets provides a rationale for therapeutic strategies aimed at selectively targeting pro-tumoral Treg cells while preserving their anti-tumoral counterparts across various barrier tissue cancers that harbor both subsets.
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4. GSE304867 慢性压迫重现了与促肿瘤表型相关的巨噬细胞的转录、代谢和功能状态变化

• ✍️ 作者：未知作者
• 🏷️ 关键词：tumor、metabolic
• 📝 描述：Contributors : Alice A Burchett ; Hao Chen ; Julian Najera ; Sc ott Howard ; Meenal DattaSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusMacrophages comprise a significant portion of the glioblastoma tumor microenvironment and are essential in promoting immunosuppression and tumor progression. Solid tumors such as glioblastoma generate solid stress as they expand, creating a compressive microenvironment for mechanosensitive immune cells including macrophages. Macrophages are known to respond to various mechanical stimuli but have not yet been studied in the context of chronic compression observed in growing tumors. Here, we used a custom in vitro compression system to elucidate the effects of compressive solid stress on murine macrophages. We found that macrophages have significant morphological, transcriptional, metabolic, and functional responses to compression. These changes corresponded to both canonical pro- and anti-inflammatory macrophage states. The gene expression signatures of compressed macrophages more closely resembled those of glioma-associated macrophages known to be associated with worse patient outcomes. These results indicate that compression alone, independent from tumor cell-derived biochemical factors, may contribute to the pathological tumor-associated macrophage phenotype. This could represent a vicious cycle of tumor immunomechanics and mechano-immunology. Targeting solid stress in tumors or the response to solid stress by macrophages may interrupt this feedback loop to help normalize the tumor immune microenvironment and improve glioblastoma response to immunotherapy.
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5. GSE291751 Profling of breast cancer cells using single-cell triomics analysis of DNA, RNA, and proteins with Tapestri chemistry

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、single-cell
• 📝 描述：Contributors : Emma Jonasson ; Stefan Filges ; Anna Gustafsson ; Anders StåhlbergSeries Type : Expression profiling by high throughput sequencing ; OtherOrganism : Homo sapiensCancer displays large heterogeneity both between and within tumors where intratumor heterogeneity can occur at genetical, transcriptional and translational level. The variability results in tumor cell subpopulations with distinct molecular and cellular characteristics, some of which can have therapy-resistant properties. To date it has been experimentally challenging to study tumor cell heterogeneity. Here, we present a single-cell triomics approach to assess DNA, RNA and protein simultaneously in thousands of single cells using microfluidics. First, we profiled two breast cancer cell lines, MCF7 and T-47D, cultured in monolayer with and without 5-fluorouracil treatment. Next, we generated cell-free patient-derived scaffolds (PDS) that we repopulated with MCF7 cells for 21 days. This experimental model system mimics in vivo tumor cell growth and is suitable for drug testing, such as chemotherapies. We profiled individual MCF7 cells cultured in different PDSs with and without 5-fluorouracil treatment using triomics. Our approach and data demonstrate that single-cell triomics is feasible, which opens up new means to decipher tumor heterogeneity at different layers.
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6. GSE290623 不同调节性T细胞亚群在结直肠癌中的相反功能

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、T cell
• 📝 描述：Contributors : Xiao Huang ; Dan Feng ; Sneha Mitra ; Emma S Andretta ; Nima B Hooshdaran ; Aazam P Ghelani ; Eric Y Wang ; Joe N Frost ; Victoria R Lawless ; Aparna Vancheswaran ; Qingwen Jiang ; Cheryl Mai ; Karuna Ganesh ; Christina S Leslie ; Alexander Y RudenskySeries Type : Expression profiling by high throughput sequencing ; Genome binding/occupancy profiling by high throughput sequencing ; OtherOrganism : Homo sapiens ; Mus musculusThis SuperSeries is composed of the SubSeries listed below.
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7. GSE290622 不同调节性T细胞亚群在结直肠癌中的相反功能

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、T cell
• 📝 描述：Contributors : Xiao Huang ; Dan Feng ; Sneha Mitra ; Emma S Andretta ; Nima B Hooshdaran ; Aazam P Ghelani ; Eric Y Wang ; Joe N Frost ; Victoria Lawless ; Aparna Vancheswaran ; Qingwen Jiang ; Christina S Leslie ; Alexander Y RudenskySeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensRegulatory T (Treg) cells are considered major contributors to the growth of solid organ tumors, with the notable exception of colorectal cancer (CRC), despite the documented abundance of Treg cells in CRC. Here, we demonstrate that IL-10⁺ and IL-10⁻ Treg cells constitute two distinct subsets with opposing functions: IL-10⁺ Treg cells counteract, while IL-10⁻ Treg cells promote, the growth of genetically engineered CRC tumors. Our findings suggest that the tumor-suppressive function of IL-10⁺ Treg cells is mediated by their suppression of effector CD4⁺ T cell production of IL-17, a cytokine that directly stimulates CRC tumor cell proliferation. Consistently, IL-10⁺ Treg cells were more abundant in both mouse and human CRC tumors than in tumor-adjacent normal colon tissue, whereas IL-10⁻ Treg cells exhibited the opposite distribution. Furthermore, gene expression signatures associated with IL-10⁺ and IL-10⁻ Treg cells correlated with better and worse disease prognoses in human CRC, respectively. This functional dichotomy between Treg subsets provides a rationale for therapeutic strategies aimed at selectively targeting pro-tumoral Treg cells while preserving their anti-tumoral counterparts across various barrier tissue cancers that harbor both subsets.
• 🔗 查看原文

8. GSE290619 不同调节性T细胞亚群在结直肠癌中的相反功能

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、T cell
• 📝 描述：Contributors : Xiao Huang ; Dan Feng ; Sneha Mitra ; Emma S Andretta ; Nima B Hooshdaran ; Aazam P Ghelani ; Eric Y Wang ; Joe N Frost ; Victoria Lawless ; Aparna Vancheswaran ; Qingwen Jiang ; Christina S Leslie ; Alexander Y RudenskySeries Type : Expression profiling by high throughput sequencing ; OtherOrganism : Mus musculusRegulatory T (Treg) cells are considered major contributors to the growth of solid organ tumors, with the notable exception of colorectal cancer (CRC), despite the documented abundance of Treg cells in CRC. Here, we demonstrate that IL-10⁺ and IL-10⁻ Treg cells constitute two distinct subsets with opposing functions: IL-10⁺ Treg cells counteract, while IL-10⁻ Treg cells promote, the growth of genetically engineered CRC tumors. Our findings suggest that the tumor-suppressive function of IL-10⁺ Treg cells is mediated by their suppression of effector CD4⁺ T cell production of IL-17, a cytokine that directly stimulates CRC tumor cell proliferation. Consistently, IL-10⁺ Treg cells were more abundant in both mouse and human CRC tumors than in tumor-adjacent normal colon tissue, whereas IL-10⁻ Treg cells exhibited the opposite distribution. Furthermore, gene expression signatures associated with IL-10⁺ and IL-10⁻ Treg cells correlated with better and worse disease prognoses in human CRC, respectively. This functional dichotomy between Treg subsets provides a rationale for therapeutic strategies aimed at selectively targeting pro-tumoral Treg cells while preserving their anti-tumoral counterparts across various barrier tissue cancers that harbor both subsets.
• 🔗 查看原文

9. GSE290618 不同调节性T细胞亚群在结直肠癌中的相反功能

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、T cell
• 📝 描述：Contributors : Xiao Huang ; Dan Feng ; Sneha Mitra ; Emma S Andretta ; Nima B Hooshdaran ; Aazam P Ghelani ; Eric Y Wang ; Joe N Frost ; Victoria Lawless ; Aparna Vancheswaran ; Qingwen Jiang ; Christina S Leslie ; Alexander Y RudenskySeries Type : Expression profiling by high throughput sequencing ; Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusRegulatory T (Treg) cells are considered major contributors to the growth of solid organ tumors, with the notable exception of colorectal cancer (CRC), despite the documented abundance of Treg cells in CRC. Here, we demonstrate that IL-10⁺ and IL-10⁻ Treg cells constitute two distinct subsets with opposing functions: IL-10⁺ Treg cells counteract, while IL-10⁻ Treg cells promote, the growth of genetically engineered CRC tumors. Our findings suggest that the tumor-suppressive function of IL-10⁺ Treg cells is mediated by their suppression of effector CD4⁺ T cell production of IL-17, a cytokine that directly stimulates CRC tumor cell proliferation. Consistently, IL-10⁺ Treg cells were more abundant in both mouse and human CRC tumors than in tumor-adjacent normal colon tissue, whereas IL-10⁻ Treg cells exhibited the opposite distribution. Furthermore, gene expression signatures associated with IL-10⁺ and IL-10⁻ Treg cells correlated with better and worse disease prognoses in human CRC, respectively. This functional dichotomy between Treg subsets provides a rationale for therapeutic strategies aimed at selectively targeting pro-tumoral Treg cells while preserving their anti-tumoral counterparts across various barrier tissue cancers that harbor both subsets.
• 🔗 查看原文

10. GSE290617 不同调节性T细胞亚群在结直肠癌中的相反功能

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、T cell
• 📝 描述：Contributors : Xiao Huang ; Dan Feng ; Sneha Mitra ; Emma S Andretta ; Nima B Hooshdaran ; Aazam P Ghelani ; Eric Y Wang ; Joe N Frost ; Victoria Lawless ; Aparna Vancheswaran ; Qingwen Jiang ; Christina S Leslie ; Alexander Y RudenskySeries Type : Other ; Expression profiling by high throughput sequencingOrganism : Mus musculusRegulatory T (Treg) cells are considered major contributors to the growth of solid organ tumors, with the notable exception of colorectal cancer (CRC), despite the documented abundance of Treg cells in CRC. Here, we demonstrate that IL-10⁺ and IL-10⁻ Treg cells constitute two distinct subsets with opposing functions: IL-10⁺ Treg cells counteract, while IL-10⁻ Treg cells promote, the growth of genetically engineered CRC tumors. Our findings suggest that the tumor-suppressive function of IL-10⁺ Treg cells is mediated by their suppression of effector CD4⁺ T cell production of IL-17, a cytokine that directly stimulates CRC tumor cell proliferation. Consistently, IL-10⁺ Treg cells were more abundant in both mouse and human CRC tumors than in tumor-adjacent normal colon tissue, whereas IL-10⁻ Treg cells exhibited the opposite distribution. Furthermore, gene expression signatures associated with IL-10⁺ and IL-10⁻ Treg cells correlated with better and worse disease prognoses in human CRC, respectively. This functional dichotomy between Treg subsets provides a rationale for therapeutic strategies aimed at selectively targeting pro-tumoral Treg cells while preserving their anti-tumoral counterparts across various barrier tissue cancers that harbor both subsets.
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1. 房间里的大象：空间数据科学中的图神经网络、嵌入和基础模型

• ✍️ 作者：未知作者
• 🏷️ 关键词：spatial
• 📝 描述：Slides: https://jakubnowosad.com/agforum2025 This presentation covered three interconnected deep learning concepts appearing in spatial data science work. Graph Neural Networks (GNNs) are a deep learning architecture that represents spatial dat… Continue reading: Elephant(s) in the room: Graph neural networks, embeddings, and foundation models in spatial data science
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1. 哈佛大学肠道研究成果或将改变我们治疗肥胖症和糖尿病的方式

• ✍️ 作者：未知作者
• 🏷️ 关键词：gut、regex:gut(-?microbiome)?
• 📝 描述：Scientists found that certain molecules made by gut bacteria travel to the liver and help control how the body uses energy. These molecules change depending on diet, genetics, and shifts in the microbiome. Some even improved insulin response in liver cells when tested in the lab. The findings could open the door to new ways of preventing or managing obesity and diabetes.
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2. 天然化合物可显著增强对侵袭性白血病的治疗效果

• ✍️ 作者：未知作者
• 🏷️ 关键词：leukemia
• 📝 描述：Forskolin, a plant-derived compound, shows surprising potential against one of the most aggressive forms of leukemia. Researchers discovered that it not only stops cancer cells from growing but also makes them far more vulnerable to chemotherapy by preventing them from pumping out the drugs meant to kill them. Experts say this dual action could help create safer, more powerful AML treatments with fewer harsh side effects.
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3. 一位研究生的奇思妙想引发了衰老研究的重大突破。

• ✍️ 作者：未知作者
• 🏷️ 关键词：aging
• 📝 描述：Senescent “zombie” cells are linked to aging and multiple diseases, but spotting them in living tissue has been notoriously difficult. Researchers at Mayo Clinic have now taken an inventive leap by using aptamers—tiny, shape-shifting DNA molecules—to selectively tag these elusive cells. The project began as an offbeat conversation between two graduate students and quickly evolved into a collaborative, cross-lab effort that uncovered aptamers capable of binding to unique surface proteins on senescent cells.
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• GSE290616 不同调节性T细胞亚群在结直肠癌中的相反功能
• GSE267256 批量 RNA-seq 分析揭示了胶原蛋白三螺旋重复序列包含蛋白 1 (Cthrc1) 心脏成纤维细胞在心肌梗死后心室重塑中的关键作用
• GSE261428 单细胞 RNA 测序分析揭示了胶原蛋白三螺旋重复序列包含蛋白 1 (Cthrc1) 心脏成纤维细胞在心肌梗死后心室重塑中的关键作用
• GSE221363 单细胞多组学研究揭示了衰老过程中破骨细胞生成增加所需的新型调控因子
• GSE312054 脂肪量和肥胖相关（FTO）/SOCS6-m⁶A轴表观遗传修饰通过调节角质形成细胞功能将肥胖与特应性皮炎联系起来
• GSE313501 用于下一代 RNA 测序和小 RNA 定量分析的无凝胶文库制备
• GSE313494 Heterogeneity of senescent cells underlies resistance to ABT263 and ARV825
• GSE309178 保守小蛋白 SniP3 参与蓝藻的氮胁迫反应和代谢调控
• GSE309005 CDK8/19激酶抑制剂SNX 631对OV90亲本和抗失巢凋亡同源系的影响
• GSE301538 良恶性肿瘤谱的极端情况：基于癌症特征的两种常见犬肛周肿瘤之间不同的转录组图谱 [nCounter®]
• GSE295151 线粒体蛋白酶 Afg3l2 通过 Mmadhc 调节小鼠造血干细胞和祖细胞的稳态 [蛋白质组学]
• GSE295143 线粒体蛋白酶 Afg3l2 通过 Mmadhc 调节小鼠造血干细胞和祖细胞的稳态 [RNA-Seq]
• GSE293224 对健康对照组和系统性红斑狼疮患者的人类中性粒细胞进行 RNA 测序分析
• GSE291539 HIF-1α+ CD4 T 细胞协调肺部组织驻留免疫细胞网络 [Xenium]
• GSE291386 HSPC 衍生红细胞分化的染色质可及性分析 ​​[ATAC-seq]
• GSE288110 TBP 调控小鼠早期胚胎中转座元件的表达 [RNA-seq]
• GSE282321 KDM3A 催化组蛋白 H3K9 上羟乙酰赖氨酸的形成
• GSE265828 揭示心肌梗死后修复性心脏成纤维细胞的分子激活机制
• GSE255766 MCF-7 ESR1 药物反应 scRNA
• GSE247440 小鼠器官衰老基因表达特征
• GSE65632 甲氨蝶呤孵育HT29人结肠癌细胞基因表达的时间进程分析