详细内容（前10条）

1. ⭐ GSE303150 空间转录组学揭示子宫腺肌症病变的混合分子特性、纤毛表型和免疫特征

• ✍️ 作者：未知作者
• 🏷️ 关键词：immune、spatial、spatial transcriptomics、transcriptomics
• 📝 描述：Contributors : Alison Maclean ; Emily Johnson ; Corie Rushworth ; Christopher J Hill ; Eva Caamano-Gutierrez ; Dharani K HapangamaSeries Type : OtherOrganism : Homo sapiensAdenomyosis is a common gynaecological condition characterised by ectopic endometrial tissue within the myometrium, causing debilitating symptoms with limited treatment options. Despite its prevalence, the pathogenesis of adenomyosis remains poorly understood, hindering the development of targeted therapies for true disease modification rather than symptom management. The objective of this study was to elucidate the spatial transcriptomic profile of adenomyosis lesions with matched eutopic endometrial subregions, with a focus on specific cell types and tissue compartments. The study was designed to identify differentially expressed genes, functionally enriched pathways, and cell-cell communication networks within adenomyosis lesions compared to matched endometrial subregions, and to nominate potential drug targets for future therapeutic development. We show that adenomyosis lesions exhibit a distinct transcriptome intermediate between matched endometrium and myometrium, with enhanced epithelial ciliation and altered biological pathways. We reveal that lesion transcriptome is more like the endometrial basalis than the functionalis, displaying increased olfactory signalling, altered oxidative phosphorylation and ATP synthesis, and an altered immune microenvironment suggestive of chronic inflammation. In silico drug screening identified potential compounds that can reverse the adenomyosis lesion transcriptome. These findings provide insights into the molecular landscape of adenomyosis lesions and pave the way for developing novel, lesion-specific treatments that could potentially spare the eutopic endometrium and offer alternatives to hysterectomy.
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2. ⭐ GSE310610 人类胎儿肺的空间转录组学

• ✍️ 作者：未知作者
• 🏷️ 关键词：spatial、spatial transcriptomics、transcriptomics
• 📝 描述：Contributor : Bhattacharya SoumyaroopSeries Type : OtherOrganism : Homo sapiensSpatial transcriptomic profiles were generated using lung tissue sections obtained from twelve prenatal human lung samples ranging in gestational age from 13 – 20 weeks, of which four were diagnosed with Trisomy 21, with defined hypoplasia.
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3. GSE283949 固有层肠道免疫细胞的单细胞测序

• ✍️ 作者：未知作者
• 🏷️ 关键词：immune、regex:intestin(e|al)
• 📝 描述：Contributors : Wolfram Ruf ; Jens Posma ; Dilraj Kaur ; Thati MadhusudhanSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusA point mutation in GPCR-protease activated receptor-2 (F2RL1) renders PAR2 insensitive to FXa/Matriptase-dependent activation. We characterized the of impact of the PAR-2 G37I mutation on immune cell populations and gene expression in the gut.
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4. GSE312748 人类血浆样培养基中的稳定同位素示踪揭示胶质母细胞瘤微环境的代谢和免疫调节

• ✍️ 作者：未知作者
• 🏷️ 关键词：immune、metabolic
• 📝 描述：Contributors : Milan R Savani ; Mohamad El Shami ; Bailey C Smith ; Samuel K McBrayerSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensBackground In vivo stable isotope tracing is useful for natively surveying glioma metabolism but can be difficult to implement. Stable isotope tracing is tractable using in vitro glioma models, but most models lack nutrient conditions and cell populations relevant to human gliomas. This limits our ability to study glioma metabolism in the presence of an intact tumor microenvironment (TME) and immune-metabolic crosstalk. Methods We optimized an in vitro stable isotope tracing approach for human glioma explants and glioma stem-like cell (GSC) lines that integrates human plasma-like medium (HPLM). We performed 15N2-glutamine tracing in GSC monocultures and human IDH-wildtype glioblastoma explants and developed an analytical framework to evaluate microenvironment-dependent metabolic features that distinguish them. We also conducted spatial transcriptomics to assess transcriptional correlates to metabolic activities. Results Human plasma-like medium culture preserved glioma explant viability and stemness while unmasking metabolic and immune programs suppressed by conventional culture conditions. Stable isotope tracing in HPLM revealed TME-dependent and TME-independent features of tumor metabolism. Tissue explants recapitulated tumor cell-intrinsic metabolic activities, such as synthesis of immunomodulatory purines. Unlike GSC monocultures, tissue explants captured tumor cell-extrinsic activities associated with stromal cell metabolism, as exemplified by astrocytic guanosine diphosphate mannose production in heterocellular explants. Finally, glioma explants displayed tumor subtype-specific metabolic reprogramming, including robust pyrimidine degradation in mesenchymal cells. Conclusions We present a tractable approach to assess glioma metabolism in vitro under physiologic nutrient levels and in the presence of an intact TME. This platform opens new avenues to interrogate glioma metabolism and its interplay with the immune microenvironment.
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5. GSE292908 抗CSF-1R疗法联合免疫化疗协调适应性免疫反应以消除富含巨噬细胞的三阴性乳腺癌

• ✍️ 作者：未知作者
• 🏷️ 关键词：immune、macrophage
• 📝 描述：Series Type : Expression profiling by high throughput sequencingOrganism : Mus musculusPatients diagnosed with metastatic triple negative breast cancer (mTNBC) have limited treatment options, are more prone to develop resistance and are associated with high mortality. A cold tumor immune microenvironment (TIME) characterized by low T cells and high tumor associated macrophages (TAMs) in mTNBC is associated with the failure of standard-of-care chemotherapy and immune checkpoint blockade (ICB) treatment. We demonstrate that the combination of immunostimulatory metronomic Cytoxan (CTX) coupled with anti-CSF-1R antibody targeted therapy (SNDX-ms6352) and anti-PD-1 (ICB), was highly effective against aggressive metastatic syngeneic Trp53 null TNBC genetically engineered mouse models (GEMMs) that present with high macrophage infiltration. Mechanistically, CSF-1R inhibition along with CTX disrupted the M-CSF/CSF-1R axis which upregulated IL-17, IL-15 and type II interferon and elevated B- and T cells. Addition of an anti-PD-1 maintenance dose was necessary to overcome de novo PD-L1 intra-tumoral heterogeneity (ITH) associated recurrence in lung and liver mTNBC.
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6. GSE303831 oHSV介导的JAG1阻断诱导胶质瘤衰老相关分泌表型，从而增强巨噬细胞活化并提高对西妥昔单抗介导的衰老细胞清除的敏感性 II

• ✍️ 作者：未知作者
• 🏷️ 关键词：macrophage、glioma
• 📝 描述：Contributors : Kimberly A Rivera-Caraballo ; Tae Jin Lee ; Arnoneel Sinha ; Marco Orecchioni ; Karina Vazquez-Arreguin ; Shilpa Sharma ; Kimya Jones ; Upasana Sahu ; Sara A Murphy ; Bangxing Hong ; Ravindra Kolhe ; Ashok Sharma ; Balveen KaurSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensOncolytic HSV-1 (oHSV) treatment induces Notch signaling and myelosuppression in the tumor microenvironment (TME) of preclinical models. In the clinic, upregulation of JAG1 gene expression was observed in recurrent high-grade glioma patients treated with CAN-3110. Since JAG1 is expressed on both glioma cells and tumor-associated macrophages (TAMs), and its expression correlated with a worse prognosis, we engineered a JAG1-antagonizing oHSV (OncoD-0J1) and interrogated its impact on the tumor and myeloid TME. OncoD-0J1 antagonized JAG1-mediated Notch signaling and had a significant therapeutic advantage in vivo, which relied on Notch signature in tumor cells. Kinome profiling revealed that OncoD-0J1 treatment suppressed CDK1, resulting in a G2/M cell cycle checkpoint as seen by cell cycle analysis. Cell cycle arrest led to senescence and correlated with increased reactive oxygen species, p62 accumulation, autophagosome accumulation, and senescence-associated beta-galactosidase activity. This resulted in increased production of inflammatory chemokines and DAMPs such as IL-1β and extracellular ATP. RNA sequencing of murine macrophages co-cultured with infected human tumor cells showed enrichment of chemotactic and pro-inflammatory pathways as well as increased Fc receptor activation following OncoD-0J1 infection. Single-cell RNA sequencing and flow cytometric analysis of F4/80+ cells isolated from infected tumors showed a shift from tumor-supporting TAMs to inflammatory macrophages upon OncoD-0J1 treatment. Senescent cells showed heightened EGFR activation as a mechanism to escape death, which created a unique vulnerability for cetuximab as a senolytic agent. Combination therapy reduced EGFR signaling and induced macrophage-mediated antibody-dependent cellular cytotoxicity, thereby increasing the anti-tumor therapeutic response of OncoD-0J1 as a monotherapy.
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7. GSE312113 急性去神经支配的肌肉细胞外囊泡通过逆行信号传导重塑神经元线粒体代谢，从而挽救周围神经损伤

• ✍️ 作者：未知作者
• 🏷️ 关键词：metabolism、Neuronal
• 📝 描述：Series Type : Expression profiling by high throughput sequencingOrganism : Rattus norvegicusPeripheral nerve injury causes muscle atrophy due to slow axonal regeneration, highlighting an unmet therapeutic need. Although neuromuscular interactions are classically viewed as unidirectionally nerve-dominated, we show that acutely denervated muscle (adMu) regulates nerve regeneration via a retrograde signaling pathway. adMu initiates a trans-tissue regulatory mechanism through extracellular vesicles (EVsadMu) that orchestrate neural energy homeostasis to accelerate regeneration. Functional profiling identifies IDH2 and CS as key metabolic enzymes within EVsadMu. Neurons treated with EVsadMu exhibit a 1.39-fold increase in NADPH/NADP+ ratio via IDH2, along with a 1.18- and 1.27-fold increase in NADH/NAD+ and FADH2/FAD ratios via CS, fueling the TCA cycle to enhance mitochondrial bioenergetics. This restores redox balance and energy supply, driving axonal regeneration. In sciatic nerve injury models, EVadMu-microneedle conduits significantly promote energy metabolism and functional recovery. Together, our findings position adMu as a metabolic signaling center enabling retrograde regulation for nerve regeneration, offering potential for clinical translation.
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8. GSE311272 SAFB1/SAFB2 敲除或 ERH 敲除对小鼠 Baf3 细胞 miRNA 转录组的影响

• ✍️ 作者：未知作者
• 🏷️ 关键词：transcriptome
• 📝 描述：Contributors : Sebastian Herzog ; Aschenwald SimonSeries Type : Non-coding RNA profiling by high throughput sequencingOrganism : Mus musculusMicroRNAs are small non-coding RNAs that mediate post-transcriptional silencing of most mammalian genes. They are generated in a multi-step process initiated by the Microprocessor, a protein complex composed of DROSHA and DGCR8. Recent studies have described the phenomenon of “cluster assistance”, in which a prototypic primary miRNA hairpin can license the Microprocessor-mediated processing of a clustered suboptimal hairpin in cis. Mechanistic analyses led to the identification of two critical factors for this process, SAFB2 (scaffold attachment factor B2) and ERH (enhancer of rudimentary homolog), but it remains unclear to which extent these factors contribute to and are required for cluster assistance. Here, we have used a previously established dual fluorescence reporter system (doi: 10.1016/j.molcel.2020.05.011) to generate loss-of-function clones for SAFB2 and its closely related family member SAFB1 as well as for ERH.Our data indicate that loss of SAFB1/2 and of ERH results in overlapping, but not identical defects in primary miRNA biogenesis.
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9. GSE305409 嗜酸性粒细胞维持 Treg 稳态，并在循环胸腺 Treg 的功能中发挥关键作用 [RNA-Seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：RNA-seq
• 📝 描述：Contributors : Xuan Xie ; Asya Khleborodova ; Tovah E Markowitz ; Ethan M ShevachSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusEos, a member of the Ikaros family of transcription factors, is expressed by T regulatory cells (Tregs) and has been postulated to play a role in Treg suppression and maintenance of Treg stability. We demonstrate that expression of Eos was limited to a subpopulation of thymus-derived, activated Tregs and is undetectable in resting or activated T conventional cells (Tconvs). Eos associates with Helios, Foxp3 and Hdac1 and binds directly to the CD25 locus at a site identical to the Foxp3 binding site resulting in enhancement of CD25 expression. Studies in heterozygous female mice demonstrate that Eos is critical for Treg survival and activation. Eos+ Tregs also represent the major population of recirculating thymic Tregs, in which Eos plays a critical role in regulating their migration and suppression of Treg precursors in the thymus by competing for IL-2 and depleting MHC II from thymic dendritic cells (DCs).
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10. GSE305408 Eos maintains Treg homeostasis and plays a critical role in the function of recirculating thymic Tregs [ChIP-Seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：ChIP-seq
• 📝 描述：Contributors : Xuan Xie ; Tovah E Markowitz ; Ethan M ShevachSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusEos, a member of the Ikaros family of transcription factors, is expressed by T regulatory cells (Tregs) and has been postulated to play a role in Treg suppression and maintenance of Treg stability. We demonstrate that expression of Eos was limited to a subpopulation of thymus-derived, activated Tregs and is undetectable in resting or activated T conventional cells (Tconvs). Eos associates with Helios, Foxp3 and Hdac1 and binds directly to the CD25 locus at a site identical to the Foxp3 binding site resulting in enhancement of CD25 expression. Studies in heterozygous female mice demonstrate that Eos is critical for Treg survival and activation. Eos+ Tregs also represent the major population of recirculating thymic Tregs, in which Eos plays a critical role in regulating their migration and suppression of Treg precursors in the thymus by competing for IL-2 and depleting MHC II from thymic dendritic cells (DCs).
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1. 肿瘤起始干细胞通过微调中性粒细胞的可塑性，塑造保护性生态位

• ✍️ 作者：未知作者
• 🏷️ 关键词：肿瘤
• 📝 描述：Secret hovertext: 肿瘤相关中性粒细胞（TAN）的异质性已被认识，但 TAN 的不同细胞状态如何出现、演化、分布并影响癌症免疫治疗疗效仍难以理解。通过单细胞 RNA 测序、空间转录组学和遗传作，我们表明抗 PDL1 + CD40 激动剂免疫疗法能够诱导 TANs 中的干扰素反应，使其在鳞状细胞癌（SCCs）中恢复抗肿瘤活性。相比之下，位于肿瘤-基质界面的 TAN 可以保持其免疫抑制状态。重要的是，我们在肿瘤-间质界面识别出一组 SOX2 高肿瘤起始干细胞（tSCs），它们上调脂肪酸去饱和酶 1（Fads1）生成花生四烯酸（AA）。该 tSC 特异性通路增强 TAN 中的前列腺素 E2（PGE2）信号，从而破坏干扰素反应，阻止 TANs 中干扰素诱导的抗肿瘤功能。通过微调中性粒细胞的可塑性，tSCs 塑造了中性粒细胞的异质性，塑造了一个保护性的微生态位，以在免疫治疗中存活并推动癌症复发。
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1. ⭐ Spatial Touchstone 为空间转录组学带来质量控制

• ✍️ 作者：未知作者
• 🏷️ 关键词：spatial、spatial transcriptomics、transcriptomics
• 📝 描述：The Spatial Touchstone dataset integrates RNA sequencing with imaging-based spatial transcriptomics, providing standardized metrics and tools to improve reproducibility and cross-platform comparisons across tissues….
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2. 利用基因条形码和单细胞转录组学解读细胞动力学

• ✍️ 作者：未知作者
• 🏷️ 关键词：single-cell、transcriptomics
• 📝 描述：Researchers used RNA sequencing to trace progenitor cells in esophageal preneoplasia, identifying markers that could aid early detection and therapy of esophageal cancer….
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3. 新一代抗癌药物展现出惊人的抗衰老功效

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、aging
• 📝 描述：A next-generation drug tested in yeast was found to extend lifespan and slow aging by influencing a major growth-control pathway. Researchers also uncovered an unexpected role for agmatinases, enzymes that help keep this pathway in balance. Diet and gut microbes may affect aging more than expected because they produce the metabolites involved.
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4. PERlncDB——用于探索植物长链非编码RNA表观遗传调控的新平台

• ✍️ 作者：未知作者
• 🏷️ 关键词：epigenetic
• 📝 描述：Researchers used RNA sequencing and epigenomic data to map plant lncRNAs, creating PERlncDB, a platform for exploring epigenetic regulation and functional roles across 19 plant…
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5. 阿尔茨海默病血液检测结果可能对肾脏有问题的人产生误导。

• ✍️ 作者：未知作者
• 🏷️ 关键词：Alzheimer
• 📝 描述：A large study found that people with impaired kidneys tend to have higher Alzheimer’s biomarkers, yet they don’t face a higher overall risk of dementia. For those who already have elevated biomarkers, kidney problems may speed up when symptoms appear. The findings show that kidney health can change how Alzheimer’s blood tests are read. Doctors may need to consider both organs to get a clearer picture.
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• GSE302854 Differential Transcriptome Features of Peripheral Blood Mononuclear Cells in Pulmonary Sarcoidosis with and without Extrapulmonary Lesions
• GSE294931 Transcriptome analysis of Drosophila melanogaster intestines upon knockdown of Tachykinin (Tk), the GPCR GulpR (CG32547), and bruchpilot (brp)
• GSE291168 高分辨率 HIV-1 m6A 表观转录组揭示了剪接依赖性甲基化簇和独特的 2-LTR 转录本修饰
• GSE275038 在预后不良的儿童 AML 中发现的特定间充质基质细胞亚群有利于白血病干细胞在骨髓中的持续存在 [scRNA-seq]
• GSE237261 RBM15B 调控 MLL 重排白血病的进展
• GSE194370 对经 KPC、4662、LLC 或 C26 细胞条件培养基处理 3 天和 5 天分化的 C2C12 细胞进行 RNA 测序。
• GSE312635 饮食限制期间，激素重塑免疫系统维持病原体控制和全身营养稳态
• GSE312316 母体西式饮食改变库普弗细胞比例，导致成年后再次接触西式饮食时出现代谢功能障碍相关的脂肪肝疾病
• GSE310125 人类大脑发育过程中的单细胞转录组分析（妊娠13、15和19周）
• GSE299721 重度子痫前期与脐带血细胞比例的显著DNA甲基化差异无关
• GSE298975 假青枯菌 LOV 结构域蛋白调控环境胁迫耐受性、铁稳态和细菌性枯萎病毒力
• GSE296213 LINE-1基因座转录促进致癌染色质结构的形成
• GSE294654 支架依赖性 CASP1 限制白血病中过度的细胞内在炎症信号传导 [THP1]
• GSE294653 支架依赖性 CASP1 限制白血病中过度的细胞内在炎症信号传导 [MDSL]
• GSE292848 IL-4、IL-13 和 IL-22 在特应性皮炎上皮屏障功能障碍和皮肤炎症中的不同作用
• GSE287039 围产期小鼠胸腺hAPC的单细胞转录组分析
• GSE291876 肾脏单核转录组学在慢性肾脏病临床前模型中鉴定出新的治疗靶点。
• GSE312035 PM2.5暴露对乳腺癌亚型恶性进展的影响机制
• GSE311225 人类造血的分子和表型蓝图将增殖应激与干细胞衰老联系起来。
• GSE289319 阿霉素生物合成的代谢工程：通过氧化还原伴侣优化和阿霉素A的结构分析推进P450催化
• GSE285957 基于高通量测序的创伤性增生性玻璃体视网膜病变兔模型中差异表达基因和microRNA的筛选
• GSE285439 RNA-Seq分析揭示了不同茎龄的细叶竹（Chimonocalamus delicatus）不同部位萜类化合物的表达情况。