详细内容（前10条）

1. ⭐ GSE316876 炎症性肠病期间肠道菌群触发的免疫反应的单细胞RNA测序分析

• ✍️ 作者：未知作者
• 🏷️ 关键词：immune、RNA-seq、single-cell、gut、regex:gut(-?microbiome)?
• 📝 描述：Contributors : Zichan He ; Xueying Li ; Huabin Liang ; Baofa Sun ; Lingyi ChenSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusWhether gut microbiota is pro-inflammation or anti-inflammation during the development of inflammatory bowel disease (IBD) remains controversial. To clarify this issue, using a dextran sodium sulfate (DSS) induced IBD mouse model, we showed that compared to specific pathogen free (SPF) mice, pseudo germ-free (pGF) mice exhibit milder IBD symptoms, suggesting a pro-inflammatory role of gut microbiota. We then employed single-cell RNA-sequencing to profile the immune cells in the colon of SPF and pGF mice at day 0, 2, and 7 of DSS treatment. DSS induces the increment of innate immune cells, including macrophages and dendritic cells, as well as proliferative CD8+ T cells, in SPF mice, while the numbers of innate immune cells and proliferative CD8+ T cells decline in DSS-treated pGF mice. Conversely, more prominent activation of T cells, especially CD4+ regulatory T cells (Tregs), was observed in DSS-treated pGF mice. Further analyses revealed that the major histocompatibility complex-class I (MHC-I) -CD8 and MHC-class II (MHC-II) -CD4 interactions promote the expansion of proliferative CD8+ T cells and CD4+ Tregs respectively. Moreover, we demonstrated that guanine deaminase (GDA) promotes inflammation through facilitating microtubule polymerization in macrophages. 7-methylguanine, a GDA inhibitor, mitigates DSS-induced IBD. In summary, our results demonstrate the pro-inflammatory function of gut microbiota during IBD pathogenesis, shed light on the regulatory mechanism of immune responses, and identify potential therapeutic targets for IBD.
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2. ⭐ GSE255517 通过体内 CRISPR 激活筛选肿瘤微环境调节剂，合理设计免疫基因治疗组合

• ✍️ 作者：未知作者
• 🏷️ 关键词：tumor、immune、tumor microenvironment
• 📝 描述：Series Type : Expression profiling by high throughput sequencing ; OtherOrganism : Homo sapiens ; Mus musculusThis SuperSeries is composed of the SubSeries listed below.
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3. GSE317187 一种新型吡咯烷查尔酮衍生物通过双重靶向MDM2-p53轴和铁死亡通路，表现出协同抗宫颈癌活性。

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、pathway
• 📝 描述：Contributor : Xinyi DengSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensCervical cancer remains a serious threat to women’s health, driving the need for effective and low-toxicity therapeutics.
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4. GSE317435 研究发现，葡萄糖和谷氨酰胺依赖的正交代谢状态相互解耦，独立维持癌细胞存活。

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、metabolic
• 📝 描述：Contributors : Elizabeth Mazzio ; Renee Reams ; Jean-Baptiste Lamango ; Zonnelle Hanley ; Karam SolimanSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensCancer metabolism is often framed as dependence on cooperative glucose-glutamine fuels; however, whether distinct nutrients enforce discrete metabolic states remains unclear. Glucose utilization is often interpreted under Warburg physiology, involving accelerated glycolysis and clockwise TCA rotation to generate reducing equivalents; yet, emerging evidence suggests that glutamine, under certain conditions, can drive anaplerotic pathways independent of glycolysis, involving a counterclockwise TCA linked to massive lipid biosynthesis. Here, we sought to define how glucose and glutamine independently govern adaptive metabolic states, rather than functioning as cooperative co-fuels, in MDA-MB-231 breast cancer cells. Briefly, cells were cultured under four defined nutrient conditions—full (+Glc,+Gln), deficient (−Glc,−Gln), glucose-only, and glutamine-only—and applied transcriptomic, metabolomic, and lipidomic analyses to resolve nutrient-enforced transcriptional and metabolic states.
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5. GSE317011 β-榄香烯通过抑制FLT1/PI3K/AKT信号通路将肿瘤相关巨噬细胞重编程为M1表型，从而增强PD-L1抑制剂在肺癌中的疗效

• ✍️ 作者：未知作者
• 🏷️ 关键词：tumor、cancer
• 📝 描述：Contributors : Jianmin Wang ; Yongxin YuSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusImmune checkpoint inhibitors (ICI), epitomized by PD-1/PD-L1 antibodies, have ushered in a new era in lung cancer treatment. However, ICI monotherapy is only applicable to a small subset of patients with high PD-L1 expression, while most patients with low expression require combination therapies. In this study, we found that β-elemene promotes M1 polarization of tumor-associated macrophages (TAM) and enhances the efficacy of PD-L1 antibody (aPD-L1) in C57BL/6 mice. RNA sequencing and surface plasmon resonance revealed that β-elemene directly binds to FLT1 and inhibits the PI3K/AKT/FOXO1 signaling pathway, thereby mediating TAM M1 polarization. Using FLT1 knockout mice, we further validated the critical role of FLT1 in TAM polarization and confirmed that M1 polarization synergizes with aPD-L1 treatment. Furthermore, co-immunoprecipitation demonstrated that the intracellular domain of FLT1 interacts with and phosphorylates the p85α subunit, initiating downstream signaling cascades. These findings elucidate the synergistic mechanism between β-elemene and aPD-L1. Importantly, as both agents are already clinically approved, we plan to conduct a clinical trial to evaluate the efficacy and safety of this combination therapy.
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6. GSE316872 ScRNA-seq 血液转录组学数据集揭示了枢纽基因在 NTM-PD 患者中的价值

• ✍️ 作者：未知作者
• 🏷️ 关键词：scRNA、transcriptomics
• 📝 描述：Contributors : Guoling Yang ; Li Wang ; Xubin Zheng ; Lan Yao ; Jianxia Chen ; Peng Wang ; Wei ShaSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensTo identify and validate peripheral blood mRNA signatures as non-invasive diagnostic biomarkers for nontuberculous mycobacterial pulmonary disease (NTM-PD), we performed an integrated transcriptomic analysis combining scRNA-seq and bulk RNA sequencing (RNA-seq), followed by experimental validation.Peripheral blood samples were collected from a total of 8 participants, including 3 patients with Mycobacterium avium complex pulmonary disease (MAC-PD), 3 patients with Mycobacterium abscessus pulmonary disease (MAB-PD), and 2 healthy controls (HC). All samples were subjected to scRNA-seq to dissect the single-cell transcriptomic landscape of peripheral blood, and paired bulk RNA-seq was conducted simultaneously to achieve comprehensive transcriptomic profiling.Integrated analysis of scRNA-seq and bulk RNA-seq datasets revealed that eight core genes were significantly upregulated in NTM-PD patients compared with HCs. Notably, this gene signature exhibited superior specificity relative to other candidate gene combinations, highlighting its potential as a diagnostic biomarker for NTM-PD.
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7. GSE307840 组学辅助设计基因组编辑策略用于具有挑战性的永生化细胞模型

• ✍️ 作者：未知作者
• 🏷️ 关键词：genome
• 📝 描述：Contributors : Patricia Mendoza-Garcia ; Benjamin Keith ; Xiang ZhangSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensCRISPR-Cas9 has become a popular genome editing tool for biomedical research and drug development due to its capability to enable precise correction or integration of genetic mutations in the genome. However, precise genome editing competency varies dramatically between cell types depending on their capabilities for DNA damage. In this proof-of-concept study, we took the example of HepG2 and MCF7 to show that omics profiling identifies bottlenecks that are associated with poor precise knock-in (KI) efficiency in hard-to-engineer cells. These bottlenecks include previously described factors such as the predominance of non-homologous end joining (NHEJ) repair and impaired homologous recombination (HR) capability, but also reveals apoptotic priming status of the cells as a limiting factor. Upon further comparative analysis between HepG2 and MCF7 cells, we pinpointed and validated the proliferating cell nuclear antigen (PCNA) as a target to overexpress to enhance precise KI efficiency in MCF7. Overall, we describe how employing a multi-omics approach to characterize cell models of interest can facilitate an in-depth understanding of their editability molecular signature, empowering us to manipulate the activity of key pathways for precise editing, and therefore increase efficiency of desired editing outcomes.
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8. GSE291732 胰腺癌原位模型中β-catenin依赖性和非依赖性基因的鉴定

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer
• 📝 描述：Contributors : Nathan Harmston ; David Virshup ; Babita MadanSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensWnt signaling regulates metazoan development and homeostasis, in part by β-catenin dependent activation and repression of a large number of genes. However, Wnt signaling also regulates genes independent of β-catenin, genes that are less well characterized. In this study, using a pan-Wnt inhibitor we performed a comprehensive transcriptome analysis in a Wnt-addicted orthotopic cancer model to delineate the β-catenin-dependent and independent arms of Wnt signaling. We find that while a large percentage of Wnt-regulated genes are regulated by β-catenin, ten percent of these genes are regulated independent of β-catenin. Interestingly, a large proportion of these β-catenin independent genes are Wnt-repressed.
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9. GSE290575 G549 EP300_KO RNA-seq

• ✍️ 作者：未知作者
• 🏷️ 关键词：RNA-seq
• 📝 描述：Contributors : Fatemeh Molaei ; Graham MacLeod ; Stephane AngersSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensEP300 was identified as potential regulator of Injury-response/Mesenchymal state in Glioblastoma stem cells. Our objective was to identify the effect of EP300 KO on transcriptomic signature of Injury-response/Mesenchymal GSC.
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10. GSE273354 利用 ATAC-seq 检测方法研究 VHL 对 Caki-1 细胞染色质可及性的潜在影响。

• ✍️ 作者：未知作者
• 🏷️ 关键词：ATAC-seq
• 📝 描述：Contributors : Kenan Zhang ; Lin HeSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensTo investigate the potential impact of VHL on chromatin accessibility, the assay for transposase-accessible chromatin with high throughput sequencing (ATAC-seq) was performed in renal cell carcinoma cells.The VHL wild-type Caki-1 cells were used to generate control or VHL knockout cells by CRISPR/Cas9-mediated genome editing (sgCTR and sgVHL Caki-1 cells).Following ATAC-seq, DNAs were amplified using non-biased conditions, labeled, and sequenced with Illumina NovaSeq 6000.
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1. ⭐ 化疗会重塑肠道菌群以阻止转移。

• ✍️ 作者：未知作者
• 🏷️ 关键词：bacteria、regex:bacter(ia|ial|ium)、gut、regex:gut(-?microbiome)?
• 📝 描述：Chemotherapy’s gut damage turns out to have a surprising upside. By changing nutrient availability in the intestine, it alters gut bacteria and increases levels of a microbial molecule that travels to the bone marrow. This signal reshapes immune cell production, strengthening anti-cancer defenses and making metastatic sites harder for tumors to colonize. Patient data suggest this immune rewiring is linked to better survival.
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2. GENCODE CLS项目——通过捕获长读长RNA测序大规模扩展lncRNA目录

• ✍️ 作者：未知作者
• 🏷️ 关键词：sequencing
• 📝 描述：An expanded GENCODE lncRNA catalog built using long-read RNA sequencing reveals thousands of new human and mouse genes, improving genome interpretation and disease…
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3. 这一个基因或许可以解释大多数阿尔茨海默病病例。

• ✍️ 作者：未知作者
• 🏷️ 关键词：Alzheimer
• 📝 描述：Alzheimer’s may be driven far more by genetics than previously thought, with one gene playing an outsized role. Researchers found that up to nine in ten cases could be linked to the APOE gene — even including a common version once considered neutral. The discovery reshapes how scientists think about risk and prevention. It also highlights a major opportunity for new treatments aimed at a single biological pathway.
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4. 新型催化剂使塑料升级回收效率比铂金催化剂高10倍。

• ✍️ 作者：未知作者
• 🏷️ 关键词：10x
• 📝 描述：Scientists are finding new ways to replace expensive, scarce platinum catalysts with something far more abundant: tungsten carbide. By carefully controlling how tungsten carbide’s atoms are arranged at extremely high temperatures, researchers discovered a specific form that can rival platinum in key chemical reactions, including turning carbon dioxide into useful fuels and chemicals. Even more promising, the same material proved dramatically better at breaking down plastic waste, outperforming platinum by more than tenfold.
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• GSE314870 HIV 损害并利用肺部 Th17 和 Th22 细胞介导的针对结核分枝杆菌的免疫反应
• GSE312319 拉斯穆森脑炎受累脑组织的免疫图谱
• GSE317317 内源性逆转录病毒合成异源嵌合RNA以增强人类早期胚胎发育[新生RNA测序]
• GSE317191 妊娠期糖尿病（GDM）中的胎盘重塑扰乱脂质代谢
• GSE317176：野生型猴和Tau-P301L转基因猴多种组织的单核RNA测序数据集
• GSE299243 人类胎儿发育胃与多能干细胞衍生胃类器官的单细胞转录组比较
• GSE288070 放射疗法联合新辅助和同步IL-13Rα2靶向免疫毒素疗法治疗弥漫性内生性脑桥胶质瘤
• GSE264095 osfkbp20-1b突变体与野生型(ZH11)水稻在PEG处理下可变剪接的转录组分析