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1. ⭐ GSE320372 双阳性斑点的空间转录组学分析

• ✍️ 作者：未知作者
• 🏷️ 关键词：spatial、spatial transcriptomics、transcriptomics
• 📝 描述：Contributors : Junichi Okada ; Li Liu ; Kosaku Shinoda ; Takeshi Saito ; Jeffrey E PessinSeries Type : OtherOrganism : Mus musculusIt is generally accepted that hepatic gluconeogenesis is active in the fasted state and inactive in the fed state. In contrast, de novo lipogenesis is active in the fed state and is inactive in the fasted state. We report a subset of periportal spots (hepatocytes) in spatial transcriptomics that are positive of both Pck1 and Fasn.
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2. ⭐ GSE327598 细胞周期蛋白依赖性激酶-9和氧化磷酸化抑制克服套细胞淋巴瘤的伊布替尼耐药性

• ✍️ 作者：未知作者
• 🏷️ 关键词：lymphoma、kinase、resistance
• 📝 描述：Contributors : Carly Roleder ; Xiaofan Zhao ; Vi Lam ; Edward C Dominguez ; Canping Chen ; Sonia Rodgriguez-Rodriguez ; Lili Wang ; Tycel Phillips ; Sonia Rodgriguez-Rodriguez ; Zheng Xia ; Alexey V DanilovSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensResistance to Bruton tyrosine kinase inhibitors (BTKi) is inevitable in mantle cell lymphoma (MCL). Cyclin-dependent kinase-9 (CDK9), a key regulator of oncogenic transcription, is a promising therapeutic target. Here we studied a selective CDK9 inhibitor, AZD4573, in MCL. AZD4573 suppressed growth of MCL cell lines and primary cells and reduced expression of key oncogenic programs including MYC and MCL1. However, CDK9 inhibition also induced metabolic adaptation, with increased oxidative phosphorylation (OxPhos), ATP production, and reactive oxygen species in ibrutinib-resistant models. In an ibrutinib-resistant MCL PDX model, AZD4573 produced modest survival benefit and suppressed TNFα/NF-κB and mTORC1 signaling, but OxPhos remained elevated. To define treatment-associated transcriptional changes at cellular resolution, we analyzed PBMCs from patients receiving AZD4573 using single-cell RNA sequencing. In a responding MCL patient, malignant B cells showed sustained downregulation of MYC targets and OxPhos, whereas refractory patients showed the opposite pattern, with upregulation of MYC-associated and OxPhos programs. Consistent with these findings, the OxPhos inhibitor IACS-010759 synergized with AZD4573 in vitro. Together, these results support CDK9 inhibition as a therapeutic strategy in BTKi-resistant MCL and highlight single-cell transcriptomics as a powerful approach to reveal response-associated malignant cell states and rational combination vulnerabilities.
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3. GSE326988 V(D)J 库重建基准测试：批量 RNA-Seq 与基于 PCR 的 RepSeq 对比，并通过 SMRT 测序验证 [SMRT]

• ✍️ 作者：未知作者
• 🏷️ 关键词：sequencing、RNA-seq
• 📝 描述：Contributors : Steve Genebrier ; Samuel Bastos Serra Trinca ; Ophélie Dézé ; Marie Cornic ; Maiwenn Pineau ; Karin Tarte ; Michel CognéSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensThe aim of this study is to benchmark methods for immunoglobulin repertoire profiling using human B-cell samples. We compare targeted VDJ mRNA sequencing and repertoire reconstruction from bulk RNA-seq data to PCR-independent full-length transcript sequencing using Single-Molecule Real-Time technology. The objective is to assess methodological biases and establish a robust reference framework for immunoglobulin repertoire analysis.
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4. GSE326979 V(D)J 基因库重建基准测试：批量 RNA-Seq 与基于 PCR 的 RepSeq 对比，并通过 SMRT 测序验证 [RNA-Seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：sequencing、RNA-seq
• 📝 描述：Contributors : Steve Genebrier ; Samuel Bastos Serra Trinca ; Ophélie Dézé ; Marie Cornic ; Maiwenn Pineau ; Karin Tarte ; Michel CognéSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensThe aim of this study is to benchmark methods for immunoglobulin repertoire profiling using human B-cell samples. We compare targeted VDJ mRNA sequencing and repertoire reconstruction from bulk RNA-seq data to PCR-independent full-length transcript sequencing using Single-Molecule Real-Time technology. The objective is to assess methodological biases and establish a robust reference framework for immunoglobulin repertoire analysis.
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5. GSE326977 V(D)J 基因库重建基准测试：批量 RNA-Seq 与基于 PCR 的 RepSeq 对比，并通过 SMRT 测序验证 [RACE_RepSeq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：sequencing、RNA-seq
• 📝 描述：Contributors : Steve Genebrier ; Samuel Bastos Serra Trinca ; Ophélie Dézé ; Marie Cornic ; Maiwenn Pineau ; Karin Tarte ; Michel CognéSeries Type : OtherOrganism : Homo sapiensThe aim of this study is to benchmark methods for immunoglobulin repertoire profiling using human B-cell samples. We compare targeted VDJ mRNA sequencing and repertoire reconstruction from bulk RNA-seq data to PCR-independent full-length transcript sequencing using Single-Molecule Real-Time technology. The objective is to assess methodological biases and establish a robust reference framework for immunoglobulin repertoire analysis.
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6. GSE324815 肿瘤内注射 CD40 激动剂 sotigalimab 与 pembrolizumab 联合治疗转移性黑色素瘤可快速激活抗原呈递细胞，并在非注射部位的肿瘤中驱动抗肿瘤反应：一项 1/2 期研究的结果

• ✍️ 作者：未知作者
• 🏷️ 关键词：tumor、antigen
• 📝 描述：Contributors : Kochat Veena ; Arslan Emre ; Rai Kunal ; Bentebibel Salah-Eddine ; Diab AdiSeries Type : Genome binding/occupancy profiling by high throughput sequencing ; Expression profiling by high throughput sequencingOrganism : Homo sapiensCheckpoint inhibitors (CPIs) benefit metastatic melanoma (MM) patients, but resistance remains a challenge. This phase 1/2 (NCT02706353) study evaluated intratumoral sotigalimab (an anti-CD40 agonistic antibody) with pembrolizumab in 32 CPI-naïve MM patients. Primary endpoints included determining safety and tolerability, the recommended phase 2 dose (RP2D) of sotigalimab, and the objective response rate (ORR). The most common adverse events (AEs) related to sotigalimab were injection-site reactions, pruritus, and fatigue. The ORR was 47% and the disease control rate (DCR) was 91% for all patients, and 50% and 92% at the RP2D, respectively. Multiomic biomarker analyses of tumor and blood samples collected before and during treatment demonstrated that sotigalimab effectively engaged the CD40 pathway, boosting the infiltration and activation of myeloid cells, including CD11c+DC-LAMP+ dendritic cells (DCs) and macrophages. The combination therapy activated both innate and adaptive immunity, in both injected and non-injected tumors. TCR sequencing analysis showed increased T-cell clonality with expanded new clones shared between injected and non-injected tumors. Clinical responses correlated with these immunologic changes, but not with baseline immunological features associated with response to anti-PD1 monotherapy. In the B16 melanoma mouse model, single- cell RNA sequencing analysis showed that the combination therapy enhanced antitumor immunity and reduced the immunosuppressive tumor environment. These findings suggest that intratumoral sotigalimab may enhance anti-PD1 therapy, supporting the need for further randomized phase 2 trials to better evaluate its therapeutic potential in the ‘in situ’ immunization approach.
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7. GSE302544 TRAPPC4 通过 TRIM55 调节 GPX4 蛋白稳定性来抵抗铁死亡并促进头颈部鳞状细胞癌的进展 [ATAC-seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：carcinoma、ATAC-seq
• 📝 描述：Contributors : Zhao Ding ; Yanxun Han ; Xiaojun ZhaSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensFerroptosis resistance continues to be a major challenge in the treatment of head and neck squamous cell carcinoma (HNSCC), yet the molecular mechanisms driving this resistance remain inadequately understood. Here, we conducted an unbiased genome-wide CRISPR-Cas9 knockout library screen and identified TRAPPC4 as a key protein that resists ferroptosis in HNSCC. Moreover, we conducted experiments using HNSCC cell lines, patient-derived organoids, cell-derived xenograft, patient-derived xenograft, conditional knockout mouse models, and popliteal lymph node and lung metastasis models, which confirmed that TRAPPC4 promotes HNSCC progression by inhibiting ferroptosis. Mechanistically, TRAPPC4 inhibits chromatin accessibility at the TRIM55 promoter, blocking FOS driven TRIM55 transcription, reducing TRIM55-mediated GPX4 degradation, and promoting ferroptosis resistance. We further identified pitavastatin calcium as a TRAPPC4 inhibitor and found that its combination with RSL3 effectively suppressed HNSCC progression. This work reveals the critical role of TRAPPC4-mediated ferroptosis in promoting HNSCC progression and provides a promising therapeutic target for treating HNSCC.
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8. GSE288724 对暴露于二甲双胍的正常结肠类器官进行网络分析，揭示了结直肠癌全基因组关联研究候选基因可能发挥调控作用

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、genome
• 📝 描述：Contributors : Matthew Devall ; Graham Casey ; Li LiSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensHere we aimed to define the effects of a three-day, 24-hour repeated dose exposure of metformin (90um) of colon epithelial cell gene expression through RNA-seq and network analysis (WGCNA) of 10 colon organoid lines derived from healthy individuals.
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9. GSE327265：20种环境条件下酿酒酵母祖先和进化菌株的单细胞RNA测序

• ✍️ 作者：未知作者
• 🏷️ 关键词：sequencing、single-cell
• 📝 描述：Contributors : Annisa Dea ; Yongqing Lan ; Valeryia Aksianiuk ; David Pincus ; Arjun S RamanSeries Type : Expression profiling by high throughput sequencingOrganism : Saccharomyces cerevisiaeWe performed single-cell RNA sequencing (scRNA-seq) of Saccharomyces cerevisiae cells across 20 environmental conditions using a lab w303 strain (ancestral) and an evolved strain grown in KCl under continuous directed evolution (derived). Cells were grown in each of 20 stress environments (18 for the derived strain) to log phase and harvested for scRNA-seq using the 10x Genomics Chromium platform. This dataset enables comparison of the variances in transcriptional responses across environments and between ancestral and evolved strains at single-cell resolution to reveal an adaptive hierarchy in stress response prioritization that collapses under continuous selection in a constant environment
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10. GSE306744 细胞分裂前 TCF1 下调决定长期效应和记忆 CD8 T 细胞的命运 [RNA-Seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：T cell、RNA-seq
• 📝 描述：Contributors : Mary Philip ; Natalie R FavretSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusRNA-SEQ analysis of antigen-specific CD8 T cells sorted from the spleens of Listeria-infected mice at different early timepoints following activation. As a control, we sequenced naive CD8 T cells prior to transfer into infected hosts.
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1. CRAN 上发布了新的 R 包 {bdlnm}：通过 INLA 在 R 中实现贝叶斯分布滞后非线性模型

• ✍️ 作者：未知作者
• 🏷️ 关键词：R package
• 📝 描述：CRAN, GitHub TL;DR: {bdlnm} brings Bayesian Distributed Lag Non-Linear Models (B-DLNMs) to R using INLA, allowing to model complex DLNMs, quantify uncertainty, and produce rich visualizations. Background Climate change is increasing exposure to extreme environmental conditions such as heatwaves and air pollution. However, these exposures rarely have immediate effects. … Continue reading: New R Package {bdlnm} Released on CRAN: Bayesian Distributed Lag Non-Linear Models in R via INLA
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1. 科学家发现肌萎缩侧索硬化症和痴呆症背后隐藏的肠道触发因素

• ✍️ 作者：未知作者
• 🏷️ 关键词：gut、regex:gut(-?microbiome)?
• 📝 描述：A new study reveals that gut bacteria may play a key role in triggering ALS and frontotemporal dementia. Harmful sugars produced by these microbes can spark immune responses that damage the brain. This breakthrough explains why some genetically at-risk people develop the diseases while others don’t. Even more promising, reducing these sugars improved brain health in experiments, hinting at new treatment possibilities.
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2. 一种常见的营养物质可能极大地增强癌症治疗效果

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer
• 📝 描述：A common eye-health nutrient, zeaxanthin, may also help the body fight cancer more effectively. Scientists discovered it strengthens T cells and enhances the impact of immunotherapy treatments. Found in everyday vegetables and supplements, it’s safe, accessible, and shows strong potential as a cancer therapy booster. Human trials are the next step.
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3. 科学家表示，我们一直以来对阿尔茨海默病的治疗都错了。

• ✍️ 作者：未知作者
• 🏷️ 关键词：Alzheimer
• 📝 描述：Alzheimer’s isn’t just one problem—it’s a tangled mix of biology, aging, and overall health. That’s why drugs targeting a single factor have fallen short, even as new treatments show modest benefits. Scientists are now pushing toward multi-pronged strategies, from gene editing to brain-cell rejuvenation and gut health interventions. The goal: stop treating Alzheimer’s as one disease and start tackling it as a complex system.
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4. 科学家终于揭开了前景看好的抗癌药物为何屡屡失败的秘密。

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer
• 📝 描述：Cancer drugs known as BET inhibitors once looked like a breakthrough, but in real patients they’ve often fallen short. New research reveals a key reason why: two closely related proteins, BRD2 and BRD4, don’t actually do the same job. Instead, BRD2 acts like a “stage manager,” preparing genes for activation, while BRD4 triggers the final step that turns them on. By blocking both at once, current drugs may be disrupting the process in unpredictable ways.
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• GSE306736 分裂前 TCF1 下调决定长期效应和记忆 CD8 T 细胞的命运 [ATAC-Seq]
• GSE306040 B12 促进炎症微环境、肠道菌群失调，并增强髓系偏向性克隆性造血。
• GSE327105 乐伐替尼通过抑制肠道血管内皮细胞 MAdCAM-1 介导的 B 细胞迁移来加剧结肠炎。
• GSE327044 研究显示，乐伐替尼通过抑制肠道血管内皮细胞 MAdCAM-1 介导的 B 细胞迁移而加剧结肠炎。
• GSE324031 肥大细胞特异性受体 Mrgprb2/X2 在泌尿道感染期间调节膀胱免疫
• GSE322974 利用 Xenium 5K 对人骨髓血凝块活检进行空间转录组分析
• GSE320303 血小板生成素缺乏细胞的单细胞RNA测序
• GSE319878 通过对正常结直肠活检组织进行基因表达分析，探究社区贫困与结直肠癌风险之间的机制联系
• GSE318083 BAF 复合物维持刺激反应染色质的可及性，是转录刺激反应所必需的 [RNA-seq]
• GSE318082 BAF 复合物维持刺激反应染色质的可及性，并且是转录刺激反应所必需的 [ATAC-seq]
• GSE314861 病原体特异性免疫反应可能是冠状病毒和流感病毒在自然猪宿主中感染后结果不同的潜在原因
• GSE308257 非编码RNA在EuroNet-PHL-C2研究中经典霍奇金淋巴瘤治疗中的作用
• GSE307384 无脊椎动物基因体甲基化的作用和遗传
• GSE302546 TRAPPC4 通过 TRIM55 调节 GPX4 蛋白稳定性来抵抗铁死亡并促进头颈部鳞状细胞癌的进展 [CRISPR 筛选]
• GSE302542 TRAPPC4 通过 TRIM55 调节 GPX4 蛋白稳定性来抵抗铁死亡并促进头颈部鳞状细胞癌的进展 [CUT&Tag]
• GSE302540 TRAPPC4 通过 TRIM55 调节 GPX4 蛋白稳定性，从而抵抗铁死亡并促进头颈部鳞状细胞癌的进展
• GSE319076 H3K4 甲基转移酶 KMT2D 是红系基因增强子处 GATA1 的必需辅助因子 [washout RNA-seq]
• GSE319075 H3K4 甲基转移酶 KMT2D 是红系基因增强子处 GATA1 的必需辅助因子 [GATA1 RNA-Seq]
• GSE314221 Reducing CETP activity prevents memory decline in an Alzheimer’s disease mouse model.
• GSE309721 H3K4 甲基转移酶 KMT2D 是红系基因增强子处 GATA1 的必需辅助因子 [ATAC-seq]
• GSE301517 地塞米松治疗的小梁网染色质拓扑动态分析鉴定出 78 个与眼压和原发性开角型青光眼相关的致病基因 [RNA-seq]
• GSE295056 LMNA 变异与常见多态性之间的基因-基因相互作用驱动早发性房颤 [ATAC-seq]
• GSE293474 KMT2D 介导的 H3K4 甲基化对于红细胞生成中 GATA1 转录激活至关重要 [ChIP-seq]
• GSE283485 G-四链体调控布鲁姆综合征中的染色质可及性和基因表达[RNA-seq]
• GSE283482 G-四链体调控布鲁姆综合征中的染色质可及性和基因表达[ChIP-seq]
• GSE283477 G-四链体调控布鲁姆综合征中的染色质可及性和基因表达[ATAC-seq]
• GSE269885 RNA-seq 分析过表达 RAB5 的人类 CD19 CAR T 细胞
• GSE327123 全基因组双重选择揭示人类基因组中新型自切割核酶