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1. ⭐ GSE318562 从核心到边缘绘制胶质母细胞瘤的空间结构图，描绘出特定微环境的肿瘤细胞状态和细胞间相互作用[空间转录组学]

• ✍️ 作者：未知作者
• 🏷️ 关键词：tumor、spatial、spatial transcriptomics、transcriptomics
• 📝 描述：Contributors : Saad M Khan ; Anthony Z Wang ; Rupen R Desai ; Colin R McCornack ; Rui Sun ; Sonika M Dahiya ; Jennifer A Foltz ; Ngima D Sherpa ; Lydia Leavitt ; Timothy West ; Alexander F Wang ; Aleksandar Krbanjevic ; Bryan D Choi ; Eric C Leuthardt ; Bhuvic Patel ; Albert H Kim ; Gavin P Dunn ; Allegra A PettiSeries Type : OtherOrganism : Homo sapiensTreatment resistance in glioblastoma (GBM) is largely driven by the extensive multi-level heterogeneity that typifies this disease. Despite significant progress toward elucidating GBM’s genomic and transcriptional heterogeneity, a critical knowledge gap remains in defining this heterogeneity at the spatial level. To address this, we employed spatial transcriptomics to map the architecture of the GBM ecosystem. This revealed tumor cell states that are jointly defined by gene expression and spatial localization, and multicellular niches whose composition varies along the tumor core-edge axis. Ligand-receptor interaction analysis uncovered a complex network of intercellular communication, including niche- and region-specific interactions. Finally, we found that CD8 +ve GZMK +ve T cells colocalize with LYVE1 positive CD163 positive myeloid cells in vascular regions, suggesting a potential mechanism for immune evasion. These findings provide novel insights into the GBM tumor microenvironment, highlighting previously unrecognized patterns of spatial organization and intercellular interactions, and novel therapeutic avenues to disrupt tumor-promoting interactions and overcome immune resistance.
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2. ⭐ GSE256045 IRG1/衣康酸轴通过磷酸戊糖途径调节肺肿瘤微环境

• ✍️ 作者：未知作者
• 🏷️ 关键词：tumor、tumor microenvironment、pathway
• 📝 描述：Series Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensThis SuperSeries is composed of the SubSeries listed below.
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3. ⭐ GSE256044 IRG1/衣康酸轴通过磷酸戊糖途径调节肺肿瘤微环境[sav25]

• ✍️ 作者：未知作者
• 🏷️ 关键词：tumor、tumor microenvironment、pathway
• 📝 描述：Contributors : Siavash Mansouri ; Rajkumar SavaiSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensTumor-associated macrophages (TAMs) are an important component of the immune milieu within the lung tumor microenvironment (TME) and have both tumor-promoting and tumor-inhibiting functions. However, the exact mechanisms underlying TAM-mediated inhibition of tumor development are still unknown. Itaconate is one of the main metabolites produced by the enzyme immune responsive gene 1 (IRG1) during a pro-inflammatory response. Single cell RNA-seq studies show that macrophages are the major immune cells for Irg1 expression in human and mouse lung tumors. Both Irg1-deficient mice and transplantation of Irg1-depleted bone marrow resulted in increased development of lung tumors in Kras and orthotopic mouse models, suggesting the anti-tumor function of Irg1-associated macrophages. On the other hand, 4-octyl-itaconate (octyl-Ita) reduces lung tumor development in lung cancer cell lines in vitro, in vivo models of lung cancer, and ex vivo using human tumor precision-cut lung slices. Mechanistically, IRG1/itaconate induces a metabolic shift in cancer cells and pro-tumor macrophages, specifically through inhibition of the pentose phosphate pathway (PPP). An integrative analysis of metabolomics, transcriptomics and proteomics identified glucose-6-phosphate dehydrogenase (G6PD) as the primary target for the antiproliferative effect of IRG1/itaconate. IRG1/Itaconate inhibited G6PD activity without affecting G6PD expression in Irg1-deficient mice and octyl Ita-treated lung cancer models. The novel inhibitory effects of IRG1/Itaconate and Octyl Ita on G6PD activity and PPP metabolism can not only suppress cancer cell proliferation in a non-cell-autonomous manner, but also re-educate pro-tumor macrophages into anti-tumor macrophages in a cell-autonomous manner. Our results suggest that octyl Ita is an effective anti-tumor metabolite with potential therapeutic application in lung cancer.
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4. ⭐ GSE256041 IRG1/衣康酸轴通过磷酸戊糖途径调节肺肿瘤微环境[sav24]

• ✍️ 作者：未知作者
• 🏷️ 关键词：tumor、tumor microenvironment、pathway
• 📝 描述：Contributors : Siavash Mansouri ; Rajkumar SavaiSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensTumor-associated macrophages (TAMs) are an important component of the immune milieu within the lung tumor microenvironment (TME) and have both tumor-promoting and tumor-inhibiting functions. However, the exact mechanisms underlying TAM-mediated inhibition of tumor development are still unknown. Itaconate is one of the main metabolites produced by the enzyme immune responsive gene 1 (IRG1) during a pro-inflammatory response. Single cell RNA-seq studies show that macrophages are the major immune cells for Irg1 expression in human and mouse lung tumors. Both Irg1-deficient mice and transplantation of Irg1-depleted bone marrow resulted in increased development of lung tumors in Kras and orthotopic mouse models, suggesting the anti-tumor function of Irg1-associated macrophages. On the other hand, 4-octyl-itaconate (octyl-Ita) reduces lung tumor development in lung cancer cell lines in vitro, in vivo models of lung cancer, and ex vivo using human tumor precision-cut lung slices. Mechanistically, IRG1/itaconate induces a metabolic shift in cancer cells and pro-tumor macrophages, specifically through inhibition of the pentose phosphate pathway (PPP). An integrative analysis of metabolomics, transcriptomics and proteomics identified glucose-6-phosphate dehydrogenase (G6PD) as the primary target for the antiproliferative effect of IRG1/itaconate. IRG1/Itaconate inhibited G6PD activity without affecting G6PD expression in Irg1-deficient mice and octyl Ita-treated lung cancer models. The novel inhibitory effects of IRG1/Itaconate and Octyl Ita on G6PD activity and PPP metabolism can not only suppress cancer cell proliferation in a non-cell-autonomous manner, but also re-educate pro-tumor macrophages into anti-tumor macrophages in a cell-autonomous manner. Our results suggest that octyl Ita is an effective anti-tumor metabolite with potential therapeutic application in lung cancer.
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5. ⭐ GSE318564 从核心到边缘绘制胶质母细胞瘤的空间结构图，描绘出特定微环境的肿瘤细胞状态和细胞间相互作用[scRNA-seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：tumor、scRNA、spatial
• 📝 描述：Contributors : Saad M Khan ; Anthony Z Wang ; Rupen R Desai ; Colin R McCornack ; Rui Sun ; Sonika M Dahiya ; Jennifer A Foltz ; Ngima D Sherpa ; Lydia Leavitt ; Timothy West ; Alexander F Wang ; Aleksandar Krbanjevic ; Bryan D Choi ; Eric C Leuthardt ; Bhuvic Patel ; Albert H Kim ; Gavin P Dunn ; Allegra A PettiSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensTreatment resistance in glioblastoma (GBM) is largely driven by the extensive multi-level heterogeneity that typifies this disease. Despite significant progress toward elucidating GBM’s genomic and transcriptional heterogeneity, a critical knowledge gap remains in defining this heterogeneity at the spatial level. To address this, we employed spatial transcriptomics to map the architecture of the GBM ecosystem. This revealed tumor cell states that are jointly defined by gene expression and spatial localization, and multicellular niches whose composition varies along the tumor core-edge axis. Ligand-receptor interaction analysis uncovered a complex network of intercellular communication, including niche- and region-specific interactions. Finally, we found that CD8 +ve GZMK +ve T cells colocalize with LYVE1 positive CD163 positive myeloid cells in vascular regions, suggesting a potential mechanism for immune evasion. These findings provide novel insights into the GBM tumor microenvironment, highlighting previously unrecognized patterns of spatial organization and intercellular interactions, and novel therapeutic avenues to disrupt tumor-promoting interactions and overcome immune resistance.
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6. ⭐ GSE303976 MInD：一种采用3D打印颗粒状弹性体的多器官侵入装置揭示了心脏对癌症转移的抵抗力

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、cardiac、resistance
• 📝 描述：Contributors : Amid Shakeri ; Dhana Abdo ; Matthew Ho Cheong Lei ; Sargol Okhovatian ; Richard Jiang ; Chuan Liu ; Karl T Wagner ; Daniel Vosoughi ; Jennifer Kieda ; Milica RadisicSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensDespite the systemic spread of cancer, the ventricular myocardium remains one of the least common sites of metastasis—a phenomenon that remains poorly understood. To investigate this, we developed the Multi-organ Invasion Device (MInD), a dynamic organ-on-a-chip platform that enables multi-organ culture under flow. Organ compartments are connected in MInD using PermeoTubes—3D-printed conduits with multi-scale fractal porosity fabricated from a granular poly(octamethylene maleate (anhydride) citrate) (POMaC) ink to impart viscoelasticity and ECM-mimetic permeability that supported cancer cell intravasation, migration, and extravasation. Highly aggressive breast cancer cells preferentially invaded hepatic tissue, while invasion into cardiac tissue was markedly suppressed in both co- and tri-organ culture. Cytokine profiling and RNA sequencing revealed that cardiac co-culture downregulated pro-metastatic and immunosuppressive cytokines and upregulated immune-activating and anti-invasive genes. In contrast, hepatic co-culture promoted matrix remodeling, angiogenesis, and immune suppression. Overall, this platform provides a new approach for uncovering organ-specific drivers of metastasis and cardiac resistance to metastasis, paving the way for future discovery of metastasis-inhibiting therapies.
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7. GSE333880 基质-免疫相互作用促进卵巢癌腹腔转移中的免疫抑制

• ✍️ 作者：未知作者
• 🏷️ 关键词：carcinoma、immune
• 📝 描述：Contributors : Neta Solomon ; Lea Monteran ; Dan Grisaru ; Neta ErezSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusHigh-grade serous (tubo-ovarian) carcinoma (HGSC) is the most lethal gynecological malignancy and the most common form of ovarian cancer. Most patients (75%) are diagnosed at advanced disease stages, with widespread peritoneal dissemination leading to poor prognosis. Cancer-associated fibroblasts (CAFs) were shown to modulate the immune microenvironment in multiple cancer types. However, their interactions with immune cells and their role in facilitating peritoneal metastasis in ovarian cancer are largely unresolved. Here, we characterized the interactions between fibroblasts and immune cells that facilitate the formation of a hospitable niche in metastatic peritoneal ovarian cancer. We isolated and characterized CAFs from HGSC patients and mouse models, and investigated the events that promote peritoneal metastases. Our findings reveal the reciprocal communication between fibroblasts and T cells in distinct peritoneal metastatic niches, positioning the TIGIT-CD155 immune checkpoint signaling axis as a target for therapeutic intervention in metastatic HGSC. Our study provides a potential novel avenue for therapeutic intervention to inhibit metastatic spread of ovarian carcinoma.
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8. GSE331146 肝脏和小肠转录组中酮己糖激酶缺失

• ✍️ 作者：未知作者
• 🏷️ 关键词：transcriptome、regex:intestin(e|al)
• 📝 描述：Contributor : Ming SongSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusDietary fructose is a major risk factor driving the progression of metabolic dysfunction-associated steatohepatitis (MASH) and hepatocellular carcinoma (HCC). However, the underlying fructose-induced nutrient-sensing pathway has remained unclear. Here, we report that fructose facilitates iron absorption through the (Ketohexokinase) KHK/PKM2/HIF-2α axis, driving MASH/HCC development. Fructose aberrantly stabilizes intestinal HIF-α compared to glucose; this effect is abrogated by a KHK inhibitor and genetic Khk deletion. Interestingly, reduced HIF-α stability in Khk deficient mice is rescued by a small-molecule inhibitor of pyruvate kinase M2 (PKM2). Conversely, Khk deficient mice exhibit spontaneous systemic iron deficiency, characterized by hypochromic anemia, and markedly reduced blood neutrophil numbers. Moreover, Khk deficiency inhibits iron absorption in a HIF-2α-dependent manner. Finally, fructose promotes MASH/HCC progression in an iron-dependent manner. This study reveals a unique nutrient-sensing pathway by dietary fructose that is therapeutically targetable.
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9. GSE180757 宿主对恶性疟原虫疟疾免疫反应的转录组学分析[第 2 年]

• ✍️ 作者：未知作者
• 🏷️ 关键词：immune、transcriptomics
• 📝 描述：Contributors : Abdrabou Wael ; Diawara Aïssatou ; Dieng Mame Massar ; Idaghdour YoussefSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensWe performed a genome-wide profiling of mRNA from human whole blood sample to identify mRNAs responsive to P.falciparum (P.f) infection and/or associated with parasite load.
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10. GSE330004 体内损伤相关非神经元细胞和损伤衍生反应性培养物的 RNA-seq 分析

• ✍️ 作者：未知作者
• 🏷️ 关键词：Neuronal、RNA-seq
• 📝 描述：Contributors : Dulce María Arzate ; Víctor Álvaro ; Ana Victoria Prádanos-Senén ; Lucía Gallego ; Alba Méndez-Alejandre ; Diana Manzano ; Celia Llorente-Sáez ; Rocío Bartolomé ; Alessia Ferrarini ; Juan Antonio López ; Elisa Murenu ; Benedikt Berninger ; Felipe Ortega ; Gabriel Piedrafita ; Magdalena Götz ; Christophe Heinrich ; Sergio GascónSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculus We performed RNA-seq analysis to compare lesion-derived reactive cultures (RCs) with non-neuronal cell populations isolated from injured and intact adult mouse cortex, providing a dataset to assess transcriptional similarities and differences between RCs and the in vivo cortical injury response.
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💡 该来源还有 38 条内容，详见 文末

• GSE279392：来自Degos病患者的皮肤、血液和脑脊液（CSF）样本的单细胞RNA和TCR测序
• GSE334503 绘制健康和免疫缺陷范围内的免疫细胞图谱和疫苗反应 [CITE-seq]
• GSE334385 i星形胶质细胞模型细胞因子对补体表达和神经元网络同步的影响。
• GSE334281 骨自体移植愈合的时间转录组分析揭示了动态的免疫、血管和成骨程序 [scRNA-seq]
• GSE316917 绘制胶质母细胞瘤从核心到边缘的空间结构图，揭示了肿瘤细胞微环境特异性状态和细胞间相互作用。
• GSE313739 Piezo1 调节造血稳态和慢性粒单核细胞白血病进展 [低通量 RNA 测序]
• GSE299682 核肌球蛋白1将基因组结构与小鼠脂肪组织重塑、代谢炎症和肥胖联系起来
• GSE335198 RNA-seq 和 ONT 全长转录组分析 HCT116 和 WiDr 细胞经 DMSO、GSK025 或 GS​​K715 处理
• GSE330886 复杂人体组织（胎盘）单细胞转录组学研究的挑战 [Xenium]
• GSE328358 斯卡巴嗪治疗三阴性乳腺癌的作用及靶点研究
• GSE320441 8-Me-PIQ 通过代谢抑制和核糖体生物合成抑制扩增脐带血造血干细胞
• GSE319236 母体和胎儿细胞对重度子痫前期的空间分辨贡献
• GSE310326 单细胞转录组学在复杂人体组织（胎盘）上的挑战
• GSE309671 小鼠异种移植瘤的转录组分析，该异种移植瘤源自 UMUC3 对照和 FASNKD 细胞，经 10%CSM（香烟烟雾培养基）和常规培养基处理。
• GSE308925 在香烟烟雾培养基和常规培养基条件下处理的 UMUC3 膀胱癌细胞系中 FASN 敲低后的染色质分析。
• GSE302516 人类前列腺肿瘤细胞系的转录组分析[2]
• GSE299630 近缘芽孢杆菌菌株对甜瓜种子早期诱导作用驱动其独特的代谢和防御程序
• GSE294756 CRL2-FEM1B 利用血红素募集 BACH1 进行降解并调节肺癌中的铁死亡
• GSE304044 重编程因子激活非经典氧化恢复通路，可使视网膜色素上皮细胞再生并恢复视力。
• GSE304043 重编程因子激活非经典氧化恢复途径，可使 RPE 恢复活力并恢复视力 [GSTA4_RNA-seq_6]
• GSE304042 重编程因子激活非经典氧化恢复途径，可使 RPE 恢复活力并恢复视力 [GSTA4_RNA-seq_5]
• GSE304041 重编程因子激活非经典氧化恢复途径，可使 RPE 恢复活力并恢复视力 [GSTA4_RNA-seq_4]
• GSE304040 重编程因子激活非经典氧化恢复途径，可使 RPE 恢复活力并恢复视力 [GSTA4_RNA-seq_3]
• GSE304039 重编程因子激活非经典氧化恢复途径，可使 RPE 恢复活力并恢复视力 [GSTA4_RNA-seq_2]
• GSE304038 重编程因子激活非经典氧化恢复途径，可使 RPE 恢复活力并恢复视力 [GSTA4_RNA-seq_1]
• GSE304037 重编程因子激活非经典氧化恢复途径，可使 RPE 恢复活力并恢复视力 [GSTA4_ATAC-seq]
• GSE302801 体内 CRISPR 敲除筛选揭示 Polr1a 是黑色素瘤转移的关键驱动因素和潜在治疗靶点 [RNA-Seq]
• GSE278753 SIK3 KO 对 CA1 区转录组的影响
• GSE335122：复发性外阴阴道念珠菌病患者和IL-17A治疗的健康对照组中性粒细胞的转录组分析
• GSE334728 巨噬细胞微环境重建揭示动态转录和通讯网络 肾脏巨噬细胞-上皮细胞通讯
• GSE334534 异质性抗原PL45细胞体液免疫的转录组决定因素
• GSE318816 基于血液的纤维化过敏性肺炎分子分型鉴定出两种具有不同临床结果的免疫亚型
• GSE313609 Piezo1 调节造血稳态和慢性粒单核细胞白血病进展
• GSE299673 心肌细胞特异性DNMT3A过表达后小鼠心脏的亚硫酸氢盐测序结果
• GSE249405 小鼠脑内RNA周转动力学的空间分布图
• GSE249403 小鼠脑内 RNA 周转动力学的空间映射 [空间 NT-seq]
• GSE249398 小鼠脑内 RNA 周转动力学的空间映射 [scNT-seq2]
• GSE335230 氧化应激通过 PARylation 和 DNA 损伤触发 RNAPII 停滞 [ChIP-seq]