详细内容（前10条）

1. ⭐ GSE334550 TNFR1在癌细胞上的表达对于免疫逃逸至关重要，并塑造了免疫抑制性肿瘤微环境

• ✍️ 作者：未知作者
• 🏷️ 关键词：tumor、cancer、immune、tumor microenvironment
• 📝 描述：Contributors : Elixabet Bolaños ; Lorena Cañas-Zabala ; Irene Olivera ; David Ruiz-Guillamón ; Enric Vercher ; Pedro Berraondo ; Ignacio MeleroSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusTNFα is an proinflammatory cytokine that can mediate immunosuppressive effects in cancer. Tumors in which we silenced TNFR1 by CRISPR/Cas9 showed disability of the TNFR1 KO variants to engraft in immunocompetent hosts, whilst engraftment in immunodeficient or CD8 T lymphocyte-depleted mice was preserved. The mechanism was mediated by secondary chemotactic inflammatory mediators elicited by TNFα in the malignant cells themselves. As a result, TNFR1 KO variants recruited drastically fewer myeloid-derived suppressor cells into the tumor microenvironment, thus explaining the immune escape of the WT variants. Interestingly, small amounts of TNFR1-sufficient tumor cells co-engrafted with the TNFR1 KO variants rescued tumorigenicity in the same tumor lesion but not in a distantly implanted TNFR1 KO tumor. Secondary mediators chiefly include CXCR1/2-acting chemokines, prostaglandin-E2 and TNFα itself. Knocking-down TNFR1 in a human tumor cell line rendered comparable results when xenografted. Analyses of scRNA-seq and spatial transcriptomics datasets from human solid tumors corroborate the role of TNFR1 on tumor cells in the induction of secondary pro-tumor inflammatory mediators.
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2. ⭐ GSE309307 TNFR1 在癌细胞上的表达对于免疫逃逸至关重要，塑造了免疫抑制性肿瘤微环境 [EO771]

• ✍️ 作者：未知作者
• 🏷️ 关键词：tumor、cancer、tumor microenvironment
• 📝 描述：Contributors : Elixabet Bolaños ; Lorena Cañas-Zabala ; Irene Olivera ; David Ruiz-Guillamón ; Ignacio MeleroSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusTNFα reportedly mediates multiple protumor and immunosuppressive functions acting on stromal cells in cancer-bearing hosts as a result of enhancing activation immune cell death of T lymphocytes, causing dysfunction of dendritic cells and/or eliciting chemokines which attract myeloid-derived suppressor cells. Experiments performed in transplantable tumors in which we silenced TNFR1 with CRISPR/Cas9 showed the inability of the TNFR1 KO variants to engraft in immunocompetent hosts, whilst engraftment in immunodeficient or CD8 T lymphocyte-depleted mice was preserved. The mechanism was related to secondary inflammatory mediators elicited by TNFα in malignant cells themselves, including CXCR1/2 chemokines and interestingly TNFα itself. As a result, TNFR1 KO variants recruited drastically fewer myeloid-derived suppressor cells into the tumor microenvironment, thus explaining the immune escape of the WT variants. Interestingly, TNFR1-sufficient tumor cells, when co-engrafted with the TNFR1 KO variants, rescued tumorigenicity of the same tumor lesion but not of a distantly implanted TNFR1 KO tumor. Secondary mediators chiefly include CXCR1/2-acting chemokines and prostaglandin E2 synthetase. Similar effects were observed upon knocking-down TNFR1 in a human tumor cell line. Moreover, human TNFR1 KO HT29 variants, when xenografted in immunodeficient mice, released lower levels of CXCL8 (IL-8) and recruited fewer murine myeloid cells into the tumor microenvironment. Analyses of scRNAseq data sets from human solid tumors corroborate the role of TNFR1 on tumor cells to induce secondary proinflammatory mediators. All together, we provide evidence for an essential role of TNFR1 expressed on the surface of tumor cells in immunoscape and further support TNF neutralization in the clinic to improve the efficacy and safety of approved immunotherapy approaches.
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3. ⭐ GSE309029 TNFR1 在癌细胞上的表达对于免疫逃逸至关重要，塑造了免疫抑制性肿瘤微环境。

• ✍️ 作者：未知作者
• 🏷️ 关键词：tumor、cancer、tumor microenvironment
• 📝 描述：Contributors : Elixabet Bolaños ; Lorena Cañas-Zabala ; Irene Olivera ; David Ruiz-Guillamón ; Ignacio MeleroSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensTNFα reportedly mediates multiple protumor and immunosuppressive functions acting on stromal cells in cancer-bearing hosts as a result of enhancing activation immune cell death of T lymphocytes, causing dysfunction of dendritic cells and/or eliciting chemokines which attract myeloid-derived suppressor cells. Experiments performed in transplantable tumors in which we silenced TNFR1 with CRISPR/Cas9 showed the inability of the TNFR1 KO variants to engraft in immunocompetent hosts, whilst engraftment in immunodeficient or CD8 T lymphocyte-depleted mice was preserved. The mechanism was related to secondary inflammatory mediators elicited by TNFα in malignant cells themselves, including CXCR1/2 chemokines and interestingly TNFα itself. As a result, TNFR1 KO variants recruited drastically fewer myeloid-derived suppressor cells into the tumor microenvironment, thus explaining the immune escape of the WT variants. Interestingly, TNFR1-sufficient tumor cells, when co-engrafted with the TNFR1 KO variants, rescued tumorigenicity of the same tumor lesion but not of a distantly implanted TNFR1 KO tumor. Secondary mediators chiefly include CXCR1/2-acting chemokines and prostaglandin E2 synthetase. Similar effects were observed upon knocking-down TNFR1 in a human tumor cell line. Moreover, human TNFR1 KO HT29 variants, when xenografted in immunodeficient mice, released lower levels of CXCL8 (IL-8) and recruited fewer murine myeloid cells into the tumor microenvironment. Analyses of scRNAseq data sets from human solid tumors corroborate the role of TNFR1 on tumor cells to induce secondary proinflammatory mediators. All together, we provide evidence for an essential role of TNFR1 expressed on the surface of tumor cells in immunoscape and further support TNF neutralization in the clinic to improve the efficacy and safety of approved immunotherapy approaches.
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4. GSE306617 胰腺腺鳞癌的临床、基因组和空间转录组特征

• ✍️ 作者：未知作者
• 🏷️ 关键词：carcinoma、spatial
• 📝 描述：Contributors : S D Haldar ; Meredith Wetzel ; Luciane T Kagohara ; Nilofer S AzadSeries Type : OtherOrganism : Homo sapiensPancreatic adenosquamous carcinoma (PASC) is a rare and aggressive disease variant, accounting for 1-4% of all exocrine pancreatic malignancies. Compared to conventional pancreatic ductal adenocarcinoma (PDAC), the clinical and molecular characteristics of PASC remain poorly defined due to its understudied nature. To investigate the spatial biology of PASC, we profiled resected tissue specimens from patients in our institutional cohort using the Visium spatial transcriptomics platform for compartment-specific differential gene expression and pathway enrichment analyses.
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5. GSE222790 一氧化氮供体对肿瘤浸润免疫细胞的影响。

• ✍️ 作者：未知作者
• 🏷️ 关键词：tumor、immune
• 📝 描述：Contributors : Chung-Yen Li ; Ming-Derg LaiSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusLow-dose nitric oxide donor, SNAP induced an anti-tumor effect through the immune modulation in tumor microenvironment. We isolated the lived CD45-positive immune cells from LL2 tumor tissue after the day 20 of 0.004 mg/kg SNAP treatment and performed single-cell RNA sequencing via BD Rhapsody Single-Cell analysis system.
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6. GSE342931 CK2–β-TrCP激酶–E3泛素连接酶级联反应是一种代谢传感器，可调节色氨酸2,3-双加氧酶的稳定性

• ✍️ 作者：未知作者
• 🏷️ 关键词：metabolic、kinase
• 📝 描述：Contributors : Alina S Thielen ; Bastian Bräuning ; Brenda A SchulmanSeries Type : OtherOrganism : Homo sapiensSmall molecules toggling the ubiquitin-proteasome system (UPS) are powerful regulators of protein degradation, yet how endogenous ligands gate UPS decisions in human biology remains poorly understood. Here we define control of UPS access to Tryptophan-2,3-dioxygenase (TDO2), which converts the essential amino acid tryptophan (Trp) to N-formylkynurenine. When Trp concentrations are limiting, TDO2 is degraded to avert tryptophanemia. We discovered that a CK2–β-TrCP kinase-E3 ligase cascade generates and recognizes phosphodegrons in TDO2 unless shielded by Trp binding to an exosite. Effects of Trp analogs on CK2–β-TrCP-dependent ubiquitylation indicated the indole, amino, and carboxylate groups collectively protect TDO2. Cryo-EM reveals these moieties organize a Trp-ordered flap that covers the exosite and thereby restricts generation of adjacent phosphodegrons. In the absence of Trp, the flap is flexible, enabling phosphorylation-coupled ubiquitylation. Overall, our data uncovered an endogenous small molecule conformationally stabilizing its own metabolizing enzyme through protection from a phosphorylation-ubiquitylation cascade.
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7. GSE343367 JAX scRNAseq 研究01 - PAX6 纯合缺失的雄性 KOLF2.2J hiPSC 衍生皮质脑类器官的单细胞 RNA 测序

• ✍️ 作者：未知作者
• 🏷️ 关键词：sequencing、single-cell
• 📝 描述：Contributors : Juliana A Diniz ; Bill Skarnes ; Paul RobsonSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensThis study characterizes the transcriptional dynamics underlying cortical brain organoid development in the absence of the transcription factor PAX6. A PAX6 null allele was engineered by introducing a premature termination codon causing a frameshift mutation (PTC+1). Single-cell RNA sequencing (scRNA-seq) was performed on samples collected at days 7, 8, and 9 following the initiation of differentiation from human induced pluripotent stem cells (hiPSCs), enabling a detailed temporal analysis of gene expression changes.
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8. GSE343347 COF-Tpy-Se-Cu 处理的癌细胞的转录组分析

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer
• 📝 描述：Contributor : Yuantong LiuSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusThis study profiled the transcriptional response of murine oral squamous cell carcinoma MOC1-R cells to COF-Tpy-Se-Cu combined with ionizing radiation. MOC1-R cells were maintained under control conditions or treated with COF-Tpy-Se-Cu (30 μg mL−1) plus 4 Gy X-ray irradiation, with three biologically independent replicates per condition. Total RNA was collected 24 h after treatment and subjected to paired-end RNA sequencing. The dataset was generated to identify differentially expressed genes and biological processes.
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9. GSE343058 果蝇亚沼泽种基因组的混合组装草图及注释

• ✍️ 作者：未知作者
• 🏷️ 关键词：genome
• 📝 描述：Contributors : William Dion ; Emily Washeleski ; Tessa E. Steenwinkel ; Emily Taylor ; Prajakta P. Kokate ; Aidan VanDrie ; Thomas Werner ; Paul D. GoetschSeries Type : Expression profiling by high throughput sequencingOrganism : Drosophila subpalustrisSpecies within the Drosophila quinaria group are models for ecological genetic studies on topics that include morphological diversity, color pattern development, and feeding behavior. Here, we performed bulk RNA-seq of mixed male and female adult flies to provide evidence for annotation of our hybrid assembly of the Drosophila subpalustris genome.
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10. GSE343057 沼泽果蝇基因组的混合组装草图及注释

• ✍️ 作者：未知作者
• 🏷️ 关键词：genome
• 📝 描述：Contributors : William Dion ; Emily Washeleski ; Tessa E. Steenwinkel ; Emily Taylor ; Prajakta P. Kokate ; Aidan VanDrie ; Thomas Werner ; Paul D. GoetschSeries Type : Expression profiling by high throughput sequencingOrganism : Drosophila palustrisSpecies within the Drosophila quinaria group are models for ecological genetic studies on topics that include morphological diversity, color pattern development, and feeding behavior. Here, we performed bulk RNA-seq of mixed male and female adult flies to provide evidence for annotation of our hybrid assembly of the Drosophila palustris genome.
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1. 长读长RNA测序的优势：减少等位基因失衡分析中的偏差

• ✍️ 作者：未知作者
• 🏷️ 关键词：RNA-seq
• 📝 描述：Long-read RNA sequencing combined with practical quality-control measures reduces mapping bias and improves the accuracy of allele-specific gene expression measurements…
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• GSE326436 FBXW5 过表达诱导三阴性乳腺癌细胞基因表达变化
• GSE308580 RNA ac4C 写入酶 NAT10 依赖的转录后调控是小鼠合子剪接激活的先决条件 [RNA-Seq]
• GSE304499 5XFAD;PS19 小鼠模型中独特的转录组改变与人类阿尔茨海默病相一致
• GSE341488 磷酸化保护致癌 RAS 免受 LZTR1 介导的损伤
• GSE342306 OM-sqPCR 可实现循环小 RNA 亚类的单步多重定量，用于结直肠癌分类
• GSE304834 顺铂处理的人卵巢颗粒细胞KGN转录组分析
• GSE274632 ChIP-Seq结果显示ut7细胞系中H3K27ac的表达水平较低
• GSE343368 NWU 研究 2 - KOLF2.2J hiPSC 在生长素诱导的特定基因产物蛋白降解后的 ATAC-seq 时间进程
• GSE343366 MSKCC 研究 4- LARRY 条形码标记的混合敲除 scRNA-seq (40KO)
• GSE343365 MSKCC 研究 5 - 胰岛分化过程中不同基因敲除型 ISL1 过表达的 RNA-seq 分析
• GSE342815 TLR7激动剂纳米药物通过重塑免疫微环境抑制骨肉瘤肺转移
• GSE314166 强力霉素诱导型NIH3T3细胞中3xFlag-MORC1 WT和dIDR-bpNLS的全基因组结合谱
• GSE291408 植物磺酰肽通过 CAMTA3 介导的转录信号传导调节拟南芥的生长-免疫权衡