详细内容（前10条）

1. ⭐ GSE302842 星形胶质细胞中髓系细胞中升高的基因-1/Metadherin (AEG-1/MTDH) 调节代谢功能障碍相关的脂肪性肝炎 (MASH) [空间转录组学]

• ✍️ 作者：未知作者
• 🏷️ 关键词：metabolic、spatial、spatial transcriptomics、transcriptomics
• 📝 描述：Contributors : Devanand Sarkar ; Suchismita Raha ; Rachel Mendoza ; Xufeng Qu ; Jinze LiuSeries Type : OtherOrganism : Mus musculusAstrocyte elevated gene-1/Metadherin (AEG-1/MTDH) plays an important role in regulating lipid metabolism and inflammation in hepatocytes, and promotes metabolic dysfunction-associated steatohepatitis (MASH). Myeloid cells, such as macrophages, play a key role in regulating inflammation. Here we investigated the role of AEG-1 in myeloid cells in regulating high fat/high sugar diet (HF/HSD)-induced MASH. Both male and female AEG-1MAC mice were significantly protected from MASH development compared to AEG-1fl/fl mice.
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2. ⭐ GSE313941 S1PR1 在介导肿瘤中 CD8 + T 细胞功能障碍中的非经典功能 [RNASeq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：tumor、T cell、RNAseq
• 📝 描述：Contributors : Debashree Basak ; Puspendu Ghosh ; Shilpak ChatterjeeSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusSphingosine-1-phosphate receptor 1 (S1PR1) signaling has been linked to the regulation of immunosuppressive cell populations within the tumor microenvironment (TME); however, its role in shaping anti-tumor CD8⁺ T cell responses remains poorly defined. Herein, we demonstrate that intratumoral CD8⁺ T cells express S1PR1, with expression predominantly enriched in the terminally exhausted subset. Transcriptomic profiling, combined with pharmacological inhibition and genetic knockdown, reveals that S1PR1-S1P signaling activates the PERK (protein kinase R (PKR)-like endoplasmic reticulum kinase)-CHOP (C/EBP homologous protein) axis of the endoplasmic reticulum stress response. CHOP, in turn, upregulates transcription of Map3k13 and Map3k15, triggering downstream MAPK signaling and culminating in activation of p38MAPK. Activation of this pathway impairs CD8⁺ T cell metabolism and effector function while increasing apoptotic susceptibility. This ultimately limits the persistence and accumulation of functional CD8⁺ T cells within the TME, thereby compromising their responsiveness to anti-PD-1 therapy. Targeting the S1PR1-S1P axis or its downstream effectors offers a promising strategy to improve cancer immunotherapy outcomes.
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3. ⭐ GSE311112 单细胞 RNA 测序分析揭示了接受伊布替尼治疗的 CLL 患者中不同的肿瘤和免疫抑制性 T 细胞表型

• ✍️ 作者：未知作者
• 🏷️ 关键词：tumor、RNA-seq、single-cell
• 📝 描述：Contributors : Shanmugapriya Thangavadivel ; Jami Shaffer ; Shrilekha Misra ; Samon Benrashid ; Britten K Gordon ; Alexander He ; Wantong Li ; Konur Oyman ; Annika Chura ; Shelby Cabrera ; Altan Turkoglu ; Tzung-Huei Lai ; Kerry A Rogers ; Seema A Bhat ; John C Byrd ; James S Blachly ; Jennifer A Woyach ; Bradley W BlaserSeries Type : Expression profiling by high throughput sequencing ; OtherOrganism : Homo sapiensThe development of Bruton tyrosine kinase inhibitors (BTKi) and their introduction into clinical practice represents a major advance in the treatment of chronic lymphocytic leukemia (CLL). However, monotherapy with ibrutinib or other BTKis generally does not induce complete remissions or undetectable minimal residual disease (MRD) even with extended therapy. Therefore, there is a need to understand the differences between ibrutinib sensitive and resistant CLL cells along with the immune microenvironment to identify novel therapeutic approaches for controlling residual disease during BTKi treatment. Here, we investigated the cellular heterogeneity of peripheral blood mononuclear cells from patients with CLL treated with ibrutinib using single-cell RNA sequencing. We identified unique transcriptional heterogeneity within the B cell cluster in the ibrutinib-sensitive and resistant patients. Ibrutinib sensitive cells showed enrichment of B cell populations with upregulation of MHC I molecules and TNF family members. Additionally, we observed that inflammatory response and metabolism related pathways were decreased, whereas cellular response to stress and DNA repair programs were increased in the ibrutinib resistance samples. T cells in ibrutinib-resistant patients showed expansion of Tregs and an exhausted CD8 effector T cell compartment. Furthermore, CD14+ and CD16+ monocytes from ibrutinib resistant patients preferentially expressed a gene expression program of antiviral immunity. At the single-cell level, our findings demonstrate a picture of transcriptional heterogeneity in the tumor compartment and immune milieu. Overall, these findings suggest that T cell exhaustion and monocyte functional polarization may have a crucial role in BTKi resistance.
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4. ⭐ GSE309226 上下文依赖性翻译抑制作为一种新型肿瘤治疗方式 [RNA-seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：oncology、regex:onco(logy|logist|gene|genic)、RNA-seq
• 📝 描述：Contributors : Paige D Diamond ; Paul V Sauer ; Mikael Holm ; Canessa J Swanson-Swett ; Lucas Ferguson ; Natalie M Bratset ; Grant W Wienker ; Justin S Sim ; Hailey K Adams ; Lillian Kenner ; Margot Meyers ; David Gygi ; Zef A Könst ; Sogole S Bahmanyar ; Lawrence G Hamann ; Anthony P SchullerSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensInhibitors of protein synthesis, including anisomycin, homoharringtonine, and other natural products bind in the peptidyl-transferase center (PTC) of the eukaryotic ribosome to inhibit translation. Recent work has demonstrated that some PTC-binding antibiotics act in a sequence-selective manner, inhibiting translation elongation at specific amino acids while the polypeptide is engaged in the PTC. However, this phenomenon has yet to be documented for compounds that inhibit translation by the human ribosome. Here we use structure-based design to guide synthesis of molecules called interdictors that bind to the human ribosome PTC and act in a context-selective manner to inhibit translation elongation. Using ribosome profiling, in combination with in vitro biochemistry and cryo-electron microscopy, we characterize the context selectivity of unique analogues and observe their preferred interactions with nascent chain residues with complementary properties. Furthermore, we present a structure for an interdictor bound to a portion of the MYC protein at ~ 1.9 Å resolution and identify resulting structural rearrangements in both the nascent chain and ribosomal RNA. Finally, we document how these compounds differentially impact the ribotoxic stress response pathway which monitors ribosome collisions and can lead to apoptosis. Together, our data establish sequence-selective inhibition of translation as a novel small-molecule therapeutic modality for historically difficult to address cancers by targeting translation of oncogenic dependency factors in the human ribosome PTC.
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5. ⭐ GSE303946 哈洛夫吉酮通过调节 p-eIF2α-S100A8/A9-钙信号传导、抑制整体蛋白质合成和逆转急性髓系白血病对伊达比星的耐药性发挥广谱细胞毒性作用 [RNA-Seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：leukemia、resistance、RNA-seq
• 📝 描述：Contributors : Liuzhi Shi ; Yigang Yuan ; Bin Zhou ; Shenmeng Gao ; Liu Shi ; Min Zhao ; Yue CaiSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusAlkaloid febrifugine., an herbal medicine in China, is prescribed routinely for malaria treatment. Halofuginone (HF), a natural product isolated from alkaloid febrifugine, exhibits anti-tumor and anti-inflammatory ability. Aim of the study: Acute myeloid leukemia (AML) is a heterogeneous hematological malignancy with low overall survival (OS). Resistance to chemotherapeutic drugs such as idarubicin (IDA) results in treatment failure. This study investigated the role of HF in anti-AML ability and in overcoming IDA resistance in AML cells.
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6. ⭐ GSE317755 成年墨西哥钝口螈与变态墨西哥钝口螈脑的空间转录组学比较

• ✍️ 作者：未知作者
• 🏷️ 关键词：spatial、spatial transcriptomics、transcriptomics
• 📝 描述：Contributors : Shuai Wang ; Sulei FuSeries Type : OtherOrganism : Ambystoma mexicanumThe Mexican axolotl (Ambystoma mexicanum) is an established model for studying tetrapod regeneration and development. Notably, axolotls exhibit remarkable brain regeneration as adults, a trait rarely observed in other adult vertebrates. Adult axolotls can undergo metamorphosis, a process that induces dramatic remodeling of multiple organs and is accompanied by a gradual decline in regenerative capacity and lifespan. However, systematic studies on whole-brain cellular dynamics and molecular mechanisms in both adult and metamorphosed individuals remain lacking. Here, we profiled five representative brain regions (olfactory bulb, telencephalon, diencephalon/mesencephalon, rhombencephalon, and pituitary) of the axolotl brain via spatial transcriptomics in both adult and metamorphosed individuals. Our work reveals metamorphosis-associated changes in cell types and molecular profiles across brain regions.
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7. GSE305869 表观遗传程序影响三阴性乳腺癌的肺特异性转移

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、epigenetic
• 📝 描述：Contributors : Diego M Marzese ; Pere Llinàs-Arias ; Andrés F Bedoya-LópezSeries Type : Methylation profiling by genome tiling arrayOrganism : Homo sapiensTriple-negative breast cancer (TNBC) is a major cause of cancer mortality, with distant metastases, particularly to the lung, presenting a significant clinical challenge. While epigenetic mechanisms like DNA methylation (DNAm) are known to influence TNBC progression, their specific role in driving metastasis remains underexplored. To address this gap, we present a comprehensive multi-omics analysis, integrating epigenomic and transcriptomic profiles from TNBC xenograft models and patient cohorts. Genome-wide DNAm profiling of primary tumors, lymph nodes, and lung metastases revealed pronounced global hypomethylation in lung lesions, consistent with clinical samples. Promoter-methylation changes were enriched in pathways linked to invasion and proliferation, and transcriptomic integration identified 22 epigenetically regulated genes. Among these, elevated AK1, SLC2A5, TPI1, and ZBTB17 expression correlated with a higher risk of lung dissemination. These findings highlight aberrant methylation as a driver of TNBC lung colonization and identify candidate prognostic markers, emphasizing the importance of epigenetic reprogramming in organ-specific metastasis.
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8. GSE279158 E蛋白Daughterless调控成年果蝇神经系统中的蛋白质翻译和记忆[RNA-seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：nervous、RNA-seq
• 📝 描述：Contributors : Laura Tamberg ; Carl Sander Kiir ; Jürgen Tuvikene ; Käthy Rannaste ; Mari Palgi ; Indrek Koppel ; Tõnis TimmuskSeries Type : Expression profiling by high throughput sequencingOrganism : Drosophila melanogasterDaughterless (Da), the Drosophila melanogaster homolog of mammalian E-protein transcription factor 4 (TCF4), is well studied in fruit fly embryonic development but its functions in adult nervous system are poorly understood. Mutations in human TCF4 gene lead to intellectual disabilities such as Pitt-Hopkins syndrome and TCF4 has also been linked to schizophrenia. Here, to explore the roles of Da in the Drosophila mature brain, we map Da DNA binding sites and study the transcriptomics of the brains where Da function is inhibited by pan-neuronal Extramacrohaete (Emc) overexpression, in both male and female Drosophila Our transcriptome analyses reveal that in the adult brain Da regulates the expression of genes involved in behavior, memory, synaptic signaling, protein translation, and metabolic processes. Moreover, combining the RNA sequencing data with Da ChIP sequencing results indicates that genes associated with neuronal projection guidance, metabolism, and translation are direct targets of Da. In addition, we validate the involvement of Da in memory formation. Overall, our results provide valuable information about the functions of Da in the adult brain and aid in better understanding the mechanisms of TCF4-related disorders.
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9. GSE317774 默克尔细胞癌中通过ATR抑制增强肿瘤免疫原性的机制

• ✍️ 作者：未知作者
• 🏷️ 关键词：tumor、carcinoma
• 📝 描述：Contributors : Rashmi Bhakuni ; Junghyun Lee ; Peter Goff ; Daniel Jones ; Long Nguyen ; Rongxiang Lin ; Evan Newell ; Evan Hall ; Oren Gilad ; Eric J Brown ; Paul NghiemSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensThere is an urgent unmet need to develop novel therapeutic strategies for tumors that do not respond to immune checkpoint inhibition (ICI) via PD-1 pathway blockade. The ATR-mediated DNA replication checkpoint has been reported to have immune-augmenting properties; however, the mechanisms underlying these properties are not well characterized. Here we explore the potential immunogenic effects of ATR inhibition in Merkel cell carcinoma (MCC), a cancer that is particularly relevant due to its high proliferative index and frequent response to anti-PD-(L)1 therapy. ATR inhibition induced tumor cell cytotoxicity in both Merkel cell polyomavirus-positive and UV-induced MCC cell lines in the absence of exogenous DNA damage. ATR inhibition alone or in combination with low-dose radiation induced numerous proinflammatory TNF-NF-κB signals as assessed via bulk transcriptomic profiling. These included increased expression of MHC class-I alleles, antigen processing machinery, interleukins, chemokines and interferon genes associated with anti-tumor immune responses in diverse tumor types. In parallel, we observed enhanced surface exposure of the “eat-me” signal calreticulin on MCC cells and subsequent phagocytosis by human monocyte-derived macrophages. Given that MCC tumors are often cGAS-STING-deficient (including two cell lines examined here), these ATRi-induced mechanisms are significant as they were activated regardless of cGAS-STING functional status. These data provide a mechanistic basis for the clinical evaluation of ATRi in advanced ICI-refractory MCC (NCT05947500), and suggest biomarkers that may be associated with response in human MCC tumors treated with ATRi.
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10. GSE317577 呼吸道病毒感染促进肺癌加速生长 [scATAC-Seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、scATAC
• 📝 描述：Contributors : Xiaoqin Wei ; Wei Qian ; Xiangyu Ye ; Jie SunSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusThe COVID-19 pandemic has highlighted long-term health consequences of viral pneumonia, yet its potential impact on cancer development and growth remains poorly understood. Here, we show that prior SARS-CoV-2 or influenza infection accelerates lung tumor progression by reprogramming the local immune landscape. To test whether heightened cytokine responses after tumor initiation reflect durable epigenetic priming, we performed scATAC-seq on total lung cells from SARS-CoV-2–infected mice (28 d.p.i.) and PBS controls. Across macrophages, epithelial cells, fibroblasts, and endothelial cells, infection induced mild-to-moderate increases in chromatin accessibility at the Csf3 promoter and putative enhancers, with similar accessibility gains at Il6, Il1b, Cxcl1, and Cxcl5 loci in multiple compartments. Motif enrichment and regulon analyses further indicated increased accessibility/activity of NF-κB and AP-1, along with elevated STAT3/STAT4 activity. Collectively, these data demonstrate that prior respiratory viral infection drives long-lasting epigenetic remodeling of cytokine loci in lung immune and structural cells.
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1. 比较单细胞RNA测序中样本多重化方法对下游分析的影响

• ✍️ 作者：未知作者
• 🏷️ 关键词：sequencing、single-cell
• 📝 描述：A head to head comparison of multiplexing strategies shows how workflow choice in RNA sequencing affects cell stress, transcript coverage, and data quality in cerebellar organoids…
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2. 最新研究发现野生蓝莓有益于心脏和肠道健康

• ✍️ 作者：未知作者
• 🏷️ 关键词：gut、regex:gut(-?microbiome)?
• 📝 描述：A sweeping scientific review highlights wild blueberries as a standout food for cardiometabolic health. The strongest evidence shows improvements in blood vessel function, with encouraging signs for blood pressure, cholesterol, blood sugar, gut health, and cognition. Researchers suggest these benefits may kick in within hours—or build over weeks—thanks to the berries’ unique mix of polyphenols and fiber.
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3. 研究人员开发深度学习工具，以变革癌症诊断和基因组研究。

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer
• 📝 描述：Deep-learning tools ClairS-TO and Clair3-RNA improve mutation detection from long-read DNA and RNA sequencing, enabling more accurate cancer diagnostics and RNA-level variant analysis…
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• GSE317576 呼吸道病毒感染促进肺癌加速生长 [scRNA-Seq]
• GSE297416 MitoPerturb-Seq 鉴定出基因特异性的单细胞对线粒体 DNA 耗竭和异质性的反应 [RNA-Seq]
• GSE294688 首次细胞分裂前细胞因子产生的早期爆发影响CD8 T细胞分化
• GSE285904 上下文依赖性翻译抑制作为一种新型肿瘤治疗方式
• GSE303795 哈洛夫吉酮通过调节 p-eIF2α-S100A8/A9-钙信号通路、抑制整体蛋白质合成以及逆转急性髓系白血病中伊达比星的耐药性，发挥广谱细胞毒性作用。
• GSE281054 表征成年果蝇感光细胞中组蛋白甲基化的年龄依赖性变化，并确定Trr和Trx在组蛋白甲基化中的作用
• GSE262534 鉴定 H3K4 甲基化对衰老果蝇感光细胞昼夜节律钟的影响
• GSE317485 循环中经模拟电穿孔处理的CD2野生型和CD2敲除型41BBzeta CART19细胞的单细胞RNA测序
• GSE315494 T细胞受体工程化T细胞靶向TP53R248Q新抗原在人类癌症模型中诱导抗肿瘤效应
• GSE302200 短时高强度流体剪切应力脉冲增强转移潜能并快速改变癌细胞代谢
• GSE303672 对 DMD 患者 HSkM 肌管进行 RNA 测序，发现全长肌营养不良蛋白 (DP427) 和肌营养不良蛋白 (utrophin) 均存在共同的转录组改变。
• GSE302723 星形胶质细胞中升高基因-1/Metadherin (AEG-1/MTDH) 在髓系细胞中调节代谢功能障碍相关脂肪性肝炎 (MASH)
• GSE289357 对缺乏肌营养不良蛋白和肌营养蛋白的 HeLa 细胞进行 RNA 测序，揭示了重叠的转录组改变
• GSE279107 E蛋白Daughterless调控成年果蝇神经系统中的蛋白质翻译和记忆
• GSE262182 RNA测序分析禁食小鼠的骨髓浆细胞
• GSE262108 RNA测序分析KD处理小鼠的骨髓浆细胞
• GSE317334 脑膜淋巴管功能障碍通过内质网和氧化应激途径加剧 CVST 小鼠的脑损伤。
• GSE313357 海马雌激素水平、受体类型和表观遗传学导致性别特异性记忆对同时发生的急性应激的脆弱性[RNA-Seq]
• GSE309403 CD4+ T 细胞介导 BCMA CAR 疗法后的 CAR 免疫相关不良事件 (CirAE)
• GSE299943 BCL-xL 作为西妥昔单抗耐药性结直肠癌的治疗靶点
• GSE297491 MitoPerturb-Seq 鉴定出基因特异性的单细胞对线粒体 DNA 耗竭和异质性的反应 [DamID]
• GSE297418 MitoPerturb-Seq 鉴定基因特异性单细胞对线粒体 DNA 耗竭和异质性的反应 [多组]
• GSE317733 snFLARE-seq 和 mrFRIGID 用于研究不同解剖起源的前列腺癌的转录组和代谢组图谱
• GSE270576 凝聚素-介体相互作用在有丝分裂染色体组织中的作用 [Hi-C]
• GSE270574 凝聚素-介体相互作用在有丝分裂染色体组织中的作用 [ChIP-Seq]
• GSE317681 接受帕博西尼治疗的 HR+/HER2- 转移性乳腺癌患者的基因组评估（PROMISE 研究）
• GSE317628 接受帕博西尼治疗的 HR+/HER2- 转移性乳腺癌患者的基因组评估（PROMISE 研究）配对
• GSE317499 海马CA2区神经元周围网状结构的退化解释了阿尔茨海默病中社会认知记忆的丧失
• GSE317494 靶向细胞生物能量学的双重疗法治疗胰腺癌
• GSE317469 YTHDC1敲低诱导的三阴性乳腺癌细胞基因表达变化
• GSE317443 多组学 SMR 和实验支持性分析揭示肝细胞癌的因果驱动因素
• GSE317433 前列腺癌骨转移中17q11.2高频缺失和癌症转移抑制microRNA miR-193a-3p的下调
• GSE317345 接受帕博西尼治疗的 HR+/HER2- 转移性乳腺癌患者的基因组评估（PROMISE 研究）
• GSE313168 突变的成纤维细胞生长因子受体 1 是高危神经母细胞瘤的致癌驱动因素和治疗靶点
• GSE308689 整合应激反应通​​过脂质运载蛋白2促进免疫逃逸
• GSE290122 用白色念珠菌感染的载体和 rmMETRNL 小鼠巨噬细胞的下一代测序分析。
• GSE290121 对经白色念珠菌处理的METRNL+/+(WT)和METRNL-/-(METRNL KO)巨噬细胞进行下一代测序分析
• GSE290120 外周血单核细胞的下一代测序分析（对照小鼠与全身性白色念珠菌感染小鼠）