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1. ⭐ GSE325671：用抗DKK3抗体治疗的DHT诱导的雄激素性脱发（AGA）小鼠模型的单细胞RNA测序分析

• ✍️ 作者：未知作者
• 🏷️ 关键词：antibody、RNA-seq、single-cell
• 📝 描述：Contributors : Jong-Hyuk Sung ; Minsoo Noh ; Seungchan An ; Hyunju Kim ; Mei Zheng ; In Guk Park ; Leegu SongSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusAndrogenetic alopecia (AGA) is characterized by progressive hair follicle miniaturization and remodeling of the skin microenvironment. To investigate cellular changes associated with AGA and the effects of DKK3 blockade, we performed single-cell RNA sequencing (scRNA-seq) of dorsal skin from a DHT-induced mouse model. Three experimental groups of male C3H/HeN mice were analyzed: vehicle control, DHT-treated AGA model, and DHT-treated mice receiving anti-DKK3 neutralizing antibody. Single-cell transcriptomic profiling identified cell population changes associated with DHT exposure and their modulation by anti-DKK3 treatment. This dataset provides a single-cell atlas of dorsal skin in the AGA model and following DKK3 inhibition.
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2. GSE287964 免疫排斥性血管屏障限制了神经内分泌肿瘤的免疫疗法疗效

• ✍️ 作者：未知作者
• 🏷️ 关键词：immune、regex:immuno(logy|therapy|suppression)
• 📝 描述：Contributors : Ailing Zhong ; Yiyun WangSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusSmall cell lung cancer (SCLC), a highly aggressive neuroendocrine malignancy, is among the most immune-desert tumor types and exhibits poor response to immunotherapy. However, the mechanisms underlying this immune resistance remain unclear. Here, we identify a unique immune-excluding vascular (IEV) barrier in SCLC, distinct from non-small cell lung cancer (NSCLC) and other cancers, composed of tightly connected endothelial cells, a thickened basement membrane, and dense pericyte coverage. Functionally, this barrier restricts immune cell infiltration, contributing to SCLC’s immunotherapy resistance. Mechanistically, we show that ASCL1, the master transcription factor of SCLC, is essential for IEV barrier formation. ASCL1 drives expression of insulin-like growth factor-binding protein 5 (IGFBP5), and depletion of IGFBP5 in tumor cells reduces IGF1 signaling in endothelial cells. Endothelial-specific disruption of IGF1R impairs barrier integrity. Importantly, targeting this axis either through IGFBP5 knockout or treatment with the IGF1R inhibitor OSI-906 enhances CD8+ T cell infiltration and synergizes with anti-PD1 therapy in SCLC. Furthermore, we demonstrate that this ASCL1-IGFBP5-IGF1R axis and the IEV barrier are conserved across multiple neuroendocrine cancers (NECs). Our findings reveal a previously unrecognized vascular barrier in NECs and propose novel therapeutic strategies to overcome immune exclusion and enhance immunotherapy efficacy in these recalcitrant cancers.
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3. GSE294216 对 KRASG12D 抑制剂 MRTX1133 的耐药性与异常组蛋白乙酰化和对 BET 抑制剂的敏感性增加有关

• ✍️ 作者：未知作者
• 🏷️ 关键词：resistance、histone
• 📝 描述：Contributors : Daniel R Principe ; Jeffrey H Becker ; Anastasia E Metropulos ; Alejandra M Marinelarena ; Thao D Pham ; Alexandre F Aissa ; Hidayatullah G MunshiSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiens ; Mus musculusAs many as 90% of human pancreatic ductal adenocarcinoma (PDAC) tumors harbor gain-of-function mutations in the KRAS oncogene. Recently, inhibitors of the most common KRAS mutation, KRASG12D, have entered the clinical arena. However, early evidence suggests that as monotherapy, KRASG12D inhibitors such as MRTX1133 at best provide brief periods of disease stabilization. Hence, there is a growing interest in understanding the mechanisms through which tumors acquire resistance to KRAS inhibition. In the present study, we generated in vitro models of MRTX1133 resistance and subjected parental and drug-resistant cell lines to RNA sequencing. This suggested that MRTX1133-resistant tumor cells undergo a global shift toward histone acetylation. Inhibition of the histone acetyltransferase EP300 reversed the drug-resistant phenotype in vitro, which subsequent RNA sequencing experiments determined was associated with the suppression of pro-survival FOSL1 signaling. Accordingly, siFOSL1 reversed the MRTX1133-resistant phenotype with similar effects on pro-survival signaling. Given the lack of clinically useful EP300 or FOSL1 inhibitors, we next explored whether inhibitors of the acetylation scanning BET proteins would be similarly effective. The addition of BET inhibitors re-sensitized several highly resistant cell lines to MRTX1133 and impaired FOSL1-mediated survival signaling in vitro. In murine models of MRTX1133-resistant PDAC, BET inhibition cooperated with MRTX1133 to markedly extend overall survival. As BET inhibitors are currently under clinical testing, the combination of MRTX1133 and BET inhibitors warrants further investigation, particularly in tumors that have developed resistance to KRAS inhibition.
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4. GSE325678 ATEVs对源自低免疫原性胰腺癌细胞克隆的胰腺肿瘤组织转录谱的影响

• ✍️ 作者：未知作者
• 🏷️ 关键词：tumor、cancer
• 📝 描述：Contributor : Mengying HuSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusAntigen processing and presentation (APP) is essential for adaptive immunosurveillance. We uncover a mechanism whereby activated T cell-derived extracellular vesicles (ATEVs) drive a positive feedback loop that enhances antigen presentation and immune responses in normal physiology and cancer. ATEV-induced immunogenicity relies on extracellular vesicular double-stranded DNA (EVDNA), which is notably abundant and primarily composed of genomic DNA enriched in immune-related genes, including those encoding APP machinery. Mechanistically, granzyme B (Gzmb) packaged by ATEVs disrupts the nuclear envelope of recipient cells, facilitating intranuclear transfer and subsequent transient expression of EVDNA encoding APP genes. DNase treatment removes most AT-EVDNA, abrogating APP upregulation and thus T cell activation and recruitment to tumors. Notably, ATEVs hold promise as an acellular immunotherapy, restoring APP and synergizing with checkpoint blockade in immunotherapy-refractory tumors. Collectively, our findings uncover a mechanism of transient, non-viral gene delivery by ATEVs which boosts APP and anti-tumor immunity while limiting autoimmunity.
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5. GSE325422 RNA-seq 分析丁酸钠对棕榈酸酯诱导的 HepG2 细胞胰岛素抵抗的影响

• ✍️ 作者：未知作者
• 🏷️ 关键词：resistance、RNA-seq
• 📝 描述：Contributors : Yinan Zhao ; Ping Jiang ; Yiwen Zhang ; Ya Wang ; Yige WangSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensObjective: Metabolic dysfunction-associated steatotic liver disease (MASLD) is characterized by hepatic insulin resistance (IR) and impaired lipid–glucose metabolism. Sodium butyrate (NaB), a short-chain fatty acid (SCFA), may improve metabolic homeostasis, but its actions in MASLD-related IR remain unclear. This study investigated the therapeutic effects and mechanisms of NaB in palmitate (PA)-induced insulin-resistant hepatocytes and high-fat diet (HFD)-induced MASLD mice. Methods: PA-treated HepG2 cells received NaB (0.5–1.5 mM). Lipid accumulation, glucose uptake, glycogen content, and metabolic gene and protein expression were analyzed using biochemical assays, staining, qPCR, Western blotting, and RNA-seq. In vivo, C57BL/6 mice were fed an HFD for 16 weeks and then treated orally with NaB (200 or 400 mg/kg/day) for 8 weeks. Metabolic phenotypes, liver histology, and major signaling pathways were analyzed. Results: In PA-induced HepG2 cells, NaB dose-dependently decreased triglyceride, total cholesterol, low-density lipoprotein cholesterol, and non-esterified fatty acid levels, while increasing high-density lipoprotein cholesterol, glucose uptake, and glycogen storage. NaB suppressed lipogenesis (↓SREBP1c, ↓FASN), enhanced fatty acid oxidation (↑PGC-1α, ↑PPARα, ↑CPT1A), restored GPR43–CaMKK2–adenosine monophosphate-activated protein kinase (AMPK)α–SIRT1 signaling, and activated PI3K/AKT signaling (↑p-IRS1, ↑p-PI3K, ↑p-AKT, ↑GLUT2), thereby reducing gluconeogenic markers (↓FOXO1, ↓PCK1, ↓G6PC1) and increasing glycogen synthase (↑GS). Transcriptomics confirmed enrichment of PPARα and metabolic pathways. In HFD-fed mice, NaB reduced body weight, improved lipid profiles, alleviated steatosis, improved glucose tolerance and insulin sensitivity, and restored liver glycogen, with greater effects at the higher dose. Conclusion: NaB alleviates hepatic steatosis and IR in MASLD by activating AMPK and PI3K/AKT pathways, promoting fatty acid oxidation, and enhancing glycogen synthesis. NaB may serve as a promising multi-target metabolic modulator for MASLD.
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6. GSE325379 转录组学分析表明，年龄通过表观遗传机制影响后代的生存能力。

• ✍️ 作者：未知作者
• 🏷️ 关键词：transcriptomics、epigenetic
• 📝 描述：Contributors : Chenggang Zou ; KeQin Zhang ; Yicheng Ma ; Qiu Zhao ; XinQian GongSeries Type : Expression profiling by high throughput sequencingOrganism : Caenorhabditis elegansUsing the nematode Caenorhabditis elegans as a model, we show that aging triggers transcriptional activation and repression of a large set of DNA repair genes and peroxisome-related genes, respectively in old worms.
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7. GSE303590 鞣花酸作为一种新型YTHDF抑制剂在三阴性乳腺癌中触发肿瘤抑制作用 II

• ✍️ 作者：未知作者
• 🏷️ 关键词：tumor、cancer
• 📝 描述：Contributors : Jianheng Zhou ; Jun ZhangSeries Type : Expression profiling by high throughput sequencing ; OtherOrganism : Homo sapiensThe m⁶A reader proteins YTHDF1–3 are key post-transcriptional regulators of m⁶A-modified transcripts in mammalian cells, and have emerged as critical contributors to the pathogenesis of triple-negative breast cancer (TNBC). Given their role in promoting tumorigenic phenotypes, YTHDF1–3 represent promising therapeutic targets. In this study, we identified ellagic acid (EA), a natural small molecule, as a pan-inhibitor of YTHDF proteins. To investigate the translational consequences of YTHDF inhibition, we performed ribosome profiling (Ribo-seq) to assess the global impact of EA on mRNA translation in TNBC cells.
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8. GSE303589 鞣花酸作为一种新型YTHDF抑制剂在三阴性乳腺癌中触发肿瘤抑制作用 I

• ✍️ 作者：未知作者
• 🏷️ 关键词：tumor、cancer
• 📝 描述：Contributors : Jianheng Zhou ; Jun ZhangSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensThe m⁶A reader proteins YTHDF1–3 are key post-transcriptional regulators of methylated transcripts and have been implicated in the progression of triple-negative breast cancer (TNBC). Owing to their roles in sustaining malignant phenotypes, YTHDF1–3 are attractive targets for therapeutic intervention. Here, we identify ellagic acid (EA), a naturally occurring polyphenol, as a pan-inhibitor of YTHDF proteins. To investigate the effect of YTHDF inhibition on mRNA stability, we performed RNA lifetime sequencing (RNA lifetime-seq) to profile transcriptome-wide RNA decay dynamics in EA-treated TNBC cells.
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9. GSE292359 黄芩苷通过与 AKT 结合，维持氧化还原平衡并抑制 PI3K/AKT 通路，从而改善 LPS 诱导的心脏损伤。

• ✍️ 作者：未知作者
• 🏷️ 关键词：cardiac、pathway
• 📝 描述：Contributors : Zhixuan Zhang ; Qiusheng Shen ; Xin Gu ; Xiaodong ZhangSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusPurpose The aim of this study was to investigate the effects of baicalin on septic cardiomyopathy and to elucidate the underlying mechanisms involved. Specifically, this study sought to determine the effects of baicalin on septic cardiomyopathy induced by AC16 cells and LPS in C57BL/6J mice and its underlying mechanisms.Methods: Echocardiography, histological staining, immunoblotting, qPCR, ELISA, RNA-seq, network pharmacology and molecular docking were performed. Changes in cardiomyocytes after LPS injection in mice were observed. The targets of baicalein in septic cardiomyopathy were screened using molecular docking and molecular dynamics, and the pathway of baicalein action was further elucidated by using RNA-seq and network pharmacology.Results: LPS stimulation induced apoptosis, an inflammatory response and oxidative stress in cardiomyocytes. In vivo experiments revealed that baicalin treatment attenuated septic myocardial injury, as evidenced by enhanced cardiac functional parameters, preservation of myocardial structure, and reduced inflammatory/apoptotic responses, and RNA-seq analyses revealed that the Pi3k/AKT signaling pathway was activated after the administration of baicalin, which was verified both in vitro and in vivo; this indicated that the protective effects of baicalin were related to the findings in vitro and in vivo, suggesting that the protective effect of baicalin is related to the activation of the PI3K/AKT pathway. Molecular docking studies revealed that baicalin inhibited cardiomyocyte inflammation and cardiomyocyte apoptosis, thereby ameliorating sepsis-induced cardiac injury, which may be related to the PI3K/Akt pathway.Conclusion: Baicalin activates the PI3K/AKT pathway and protects against sepsis-induced cardiac injury by binding with AKT.
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10. GSE278161 分层 Rorc(γt) 顺式调控级联协调 RORγt⁺ 先天免疫细胞的分化 [scRNA-seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：immune、scRNA
• 📝 描述：Contributors : Takuma Fukui ; Miyuki Watanabe ; Satoshi Kojo ; Eriko Sumiya ; Shinichiro SawaSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusAlthough ILC3s are known to differentiate in RORγt-dependent manner, besides ILC3s, RORγt-dependent developmental program is shared among several lymphocytes.However, little is known about the regulatory mechanism of RORγt expression specific to ILC3s. Our data newly idetified cell lineage-specific and two-step regulation of RORγt expression in ILC3 including LTi cells.
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1. R语言数字生物学：面向现代生命科学的高级生物信息学、预测建模和时间序列分析

• ✍️ 作者：未知作者
• 🏷️ 关键词：bioinformatics
• 📝 描述：Digital Biology with R Digital biology is no longer a niche intersection between biology and computation. It has become a core framework for how modern laboratories, biomedical teams, and translational researchers generate insight from complex biological systems. Whether the objective is to identify gene-expression signatures, model disease progression, classify patient … Continue reading: Digital Biology with R: Advanced Bioinformatics, Predictive Modeling, and Time Series Analysis for Modern Life Sciences
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1. Souporcell3：适用于高供体单细胞RNA测序数据集的稳健解复用

• ✍️ 作者：未知作者
• 🏷️ 关键词：RNA-seq、single-cell
• 📝 描述：RNA sequencing studies benefit from improved demultiplexing methods that accurately separate pooled single cell data, enabling scalable analysis across large numbers of…
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2. RNA测序揭示了密码子驱动的mRNA稳定性调控

• ✍️ 作者：未知作者
• 🏷️ 关键词：sequencing
• 📝 描述：RNA sequencing reveals how cells detect nonoptimal codons and regulate mRNA stability, uncovering mechanisms that control gene expression and translation efficiency…
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• GSE278157 分层 Rorc(γt) 顺式调控级联协调 RORγt⁺ 先天免疫细胞的分化 [ATAC-seq]
• GSE321657 吉西他滨耐药胆囊癌细胞和亲代细胞的差异表达谱
• GSE310340 利用小分子抑制剂 JQ1 干扰减数分裂前期 I 作为一种非激素男性避孕策略 [RNA-seq]
• GSE309960 早期和成年来源的B细胞群的可及染色质谱
• GSE303315 单细胞图谱揭示藻类生命周期转变的转录复杂性
• GSE297710 对 B6 和 8in4 (CD8 Dual) 小鼠淋巴结 T 细胞进行 RNA 测序分析
• GSE268413 回顾性分析揭示肺血管周围细胞的早期起源和发育 [scRNA-seq]
• GSE112918 结核分枝杆菌特异性记忆T细胞亚群反应的转录组特征
• GSE318596 人类血管生理灌注揭示了 YAP/TAZ-Apelin 开关将管腔内流动与内皮状态转变和血管重塑联系起来 [scRNA-seq]
• GSE318595 人类血管生理灌注揭示了 YAP/TAZ-Apelin 开关将管腔内流动与内皮状态转变和血管重塑联系起来 [批量 RNA 测序]
• GSE306990 胎儿毛滴虫的真性包囊形成：一种重新定义原生动物生物学的生存和耐药策略
• GSE304476 衰老组织中的炎症衰老驱动 CD8+ T 细胞群的重塑
• GSE291600 补体 C3aR 缺失不会减轻 tau 蛋白病模型中的神经退行性变，也不会改变急性炎症诱导的脑内基因表达变化
• GSE325428 病毒 SSB 结合的 ssDNA 激活细菌抗噬菌体防御系统 DARNA
• GSE325374 MUC21在口腔鳞状细胞癌中表达下调，且与不良预后相关
• GSE325370 核膜深内陷协调上皮细胞中染色质的空间组织（A 部分：培养 7 天和 2 小时的上皮细胞）
• GSE303283 eIF4E2 缺陷驱动非小细胞肺癌的顺铂耐药性
• GSE292812 脐带来源的 iNKT 细胞富含人 NKT10，并通过与 NRP1 相互作用发挥免疫抑制功能 [RNA-seq]
• GSE279022 RNA N6-甲基腺苷 (m6A) 调控弥漫性中线胶质瘤 (DMG) 的细胞周期进程并赋予其对 FTO 抑制剂的敏感性
• GSE278518 分层 Rorc(γt) 顺式调控级联协调 RORγt⁺ 先天免疫细胞的分化 [BulkRNA-seq_vitro]
• GSE278516 分层 Rorc(γt) 顺式调控级联协调 RORγt⁺ 先天免疫细胞的分化 [BulkRNA-seq_ChILP]
• GSE325739 微生物组在斑马鱼大肠杆菌和分枝杆菌血液感染模型中抵抗败血症过度炎症和细菌增殖
• GSE319617 利用 Renoir 进行高分辨率空间分析，推断人胎肝细胞间通讯
• GSE299815 消炎促进干细胞介导的骨再生
• GSE293269 禽类和鼠类胚胎面部信号中心的比较单细胞基因组学 [ME11_scRNA]
• GSE293268 鸟类和鼠类胚胎面部信号中心的比较单细胞基因组学 [ME11_scATAC-seq]
• GSE293264 禽类和鼠类胚胎面部信号中心的比较单细胞基因组学 [HH22_scRNA-seq]
• GSE293263 禽类和鼠类胚胎面部信号中心的比较单细胞基因组学 [HH22_scATAC-seq]
• GSE293083 CTHRC1促进前列腺癌骨转移
• GSE277118 卡介苗的 sRNA ncBCG427 可能通过抑制炎症反应和细胞凋亡来增强细胞内细菌的存活。
• GSE263781 解析稳态和衰老过程中造血干细胞的谱系决定