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1. ⭐ GSE328726 老年猪心血管-肾脏-代谢（CKM）综合征新模型的肾脏单核转录组学研究

• ✍️ 作者：未知作者
• 🏷️ 关键词：aging、metabolic、cardiovascular、transcriptomics
• 📝 描述：Contributors : A R Chade ; S K Sivasankaran ; R Sitz ; E A McCarthy ; S Martin ; A EirinSeries Type : Expression profiling by high throughput sequencingOrganism : Sus scrofaBackground: CKM syndrome is characterized by pathophysiological interactions among the heart, the kidneys, and metabolic derangements. CKM syndrome is more prevalent in the elderly, but the specific cell populations implicated in renal injury have yet to be identified. We leveraged a new translational model of CKM syndrome in aging swine and single-nucleus RNA sequencing (snRNA-seq) to investigate the renal cell-specific transcriptomic profile, thereby setting the stage for future testing of potential new targets.
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2. ⭐ GSE344976 肠道细菌色氨酸酶活性抑制乙醇诱导的肝损伤

• ✍️ 作者：未知作者
• 🏷️ 关键词：regex:bacter(ia|ial|ium)、gut、regex:gut(-?microbiome)?
• 📝 描述：Contributors : Marko Mrdjen ; Anthony J Horak ; Amy C Burrows ; Megan R McMullen ; Emily Huang ; Semanti Ray ; Tejul Dafria ; Kristen E Kay ; Nour Mouannes ; Vai Pathak ; Greg Brubaker ; Nathan I Johns ; Min Wang ; Xianfeng Zeng ; Daniel M Rotroff ; Naseer Sangwan ; Jonathan D Smith ; Michael A Fischbach ; Laura E Nagy ; Jonathan M BrownSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusAlcohol consumption leads to disruptions to the gut microbiota including a depletion of tryptophan-derived indole metabolites. Disrupted tryptophan metabolism is clearly associated with alcohol-associated liver disease, yet our understanding of the specific role of gut microbe-driven tryptophan metabolism has been hampered due to lack of mouse models. To address this, we created a defined synthetic microbial community with either intact or genetically deleted tryptophanase activity for in vivo studies. Gnotobiotic mice lacking bacterial tryptophanase activity are more susceptible to ethanol-induced liver injury. Interestingly, mice with intact microbial tryptophanase activity have a robust induction of IL-6 and acute phase proteins when challenged with ethanol. Furthermore, bacterial tryptophanase activity promoted a spatial reorganization of the gut microbiome and colonization of Akkermansia muciniphila within the ileum. Collectively, this study highlights the functional importance of bacterial tryptophan metabolites in shaping ethanol-driven reorganization of the gut microbiome and host immune response to promote liver injury.
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3. ⭐ GSE302812 表观遗传紊乱驱动干性、衰老逃逸和肿瘤异质性 批量RNA测序

• ✍️ 作者：未知作者
• 🏷️ 关键词：tumor、RNAseq、epigenetic
• 📝 描述：Contributors : Kirsten C Sadler ; Elena MagnaniSeries Type : Expression profiling by high throughput sequencingOrganism : Danio rerioHeterogeneity is largely attributed to distinct genetic changes within each cell population but the widespread epigenome repatterning that characterizes most cancers is also highly heterogenous within tumors, and can generate cells with diverse identities and malignant features. We show that overexpressing high levels of the epigenetic regulator and oncogene, human UHRF1, in zebrafish hepatocytes rapidly induced changes in the DNA methylome and disordering, DNA damage, cell cycle arrest, senescence, and acquisition of progenitor like features. These changes are observed within 1 day of human UHRF1 overexpression (at 80 hours post fertilization; hpf) and is fully evident at 120 hpf. Reducing UHRF1 expression transitions these cells from senescent to proliferation-competent. Removing demonstrated that UHRF1 overexpression at 80 hpf already induced DNA damage response, senescence and decrease of hepatocyte specific pathways and this is further exhanced at 120 hpf. Deletion of tp53 from UHRF1 overexpressing line completely rescued cellular senescence and some of the key senescence-associated genes but do not abrograte the major transcriptomic changes caused by UHRF1 overexpression.
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4. GSE328196 研究模拟了 IDH 突变型胶质瘤的治疗顺序，结果表明突变型 IDH 抑制剂 vorasidenib 可改善放化疗疗效。

• ✍️ 作者：未知作者
• 🏷️ 关键词：glioma、sequencing
• 📝 描述：Contributors : Diana Shi ; Ester Calvo Fernandez ; Mario L. Suva ; Samuel K. McBrayerSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusThe mutant IDH1/2 inhibitor (mIDHi) vorasidenib was recently incorporated into clinical treatment guidelines for IDH-mutant gliomas, although its impact on chemoradiation is unclear. Specifically, it is unknown whether upfront mIDHi exposure alters subsequent chemoradiation efficacy. Addressing this critical question has been challenging due to limited clinical data and a paucity of mIDHi-responsive preclinical glioma models. We aggregated 29 patients across three institutions who were among the earliest to receive mIDHi prior to radiation+/-chemotherapy. We report outcomes of these patients compared to a similarly treated mIDHi-naïve cohort. To empirically address how mIDHi affects chemoradiotherapy efficacy, we used a mIDHi-responsive genetic mouse model of IDH-mutant astrocytoma. Mice that received vorasidenib before chemoradiation (vorasidenib–>chemoradiation) had improved survival compared to control mice (vehicle–>chemoradiation). In sum, we find no evidence from emerging real-world clinical data that upfront mIDHi therapy diminishes efficacy of subsequent chemoradiation. Moreover, preclinical modeling demonstrates that prior vorasidenib treatment enhances, rather than impairs, chemoradiation sensitivity of IDH-mutant glioma.
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5. GSE317475 斑马鱼肝脏在120 hpf时，肝细胞中hUHRF1-EGFP过表达的全基因组DNA甲基化

• ✍️ 作者：未知作者
• 🏷️ 关键词：genome、methylation
• 📝 描述：Contributors : Kirsten C Sadler ; Filippo Macchi ; Elena MagnaniSeries Type : Methylation profiling by high throughput sequencingOrganism : Danio rerioWe investigated DNA methylation changes in preneoplastic zebrafish livers following hepatocyte-specific overexpression of the epigenetic regulator UHRF1. Genome-wide DNA methylation profiling was performed using low-input reduced representation bisulfite sequencing (RRBS) on pooled livers dissected from wild-type sibling larvae and Tg(fabp10a:hUHRF1-EGFP^high) zebrafish at 5 days post fertilization. Across all samples, approximately 10× coverage was achieved at more than 1.5 million CpG sites. These were compared to profiling carried out in parallel on wild-type samples present in GSE173792. Hepatocyte-specific hUHRF1 overexpression altered methylation levels at nearly one-third of all CpGs analyzed, with ~15% of CpGs exhibiting loss of methylation; hypomethylation occurred predominantly at CpGs that were fully methylated in controls, whereas CpGs that gained methylation were enriched among sites that were partially methylated in control livers. Analysis of WT samples was published in PMID: 34356097.
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6. GSE303361 表观遗传紊乱驱动干性、衰老逃逸和肿瘤异质性 [scRNAseq_hUHRF1]

• ✍️ 作者：未知作者
• 🏷️ 关键词：tumor、epigenetic
• 📝 描述：Contributors : Kirsten C Sadler ; Elena Magnani ; Patrice M DelaneySeries Type : Expression profiling by high throughput sequencingOrganism : Danio rerioHeterogeneity is largely attributed to distinct genetic changes within each cell population but the widespread epigenome repatterning that characterizes most cancers is also highly heterogenous within tumors, and can generate cells with diverse identities and malignant features. We show that high levels of the epigenetic regulator and oncogene, UHRF1, in zebrafish hepatocytes rapidly induced methylome disordering, loss of heterochromatin, and DNA damage, resulting in cell cycle arrest, senescence, and acquisition of stemness. Reducing UHRF1 expression transitions these cells from senescent to proliferation-competent. The expansion of these damaged cells results in hepatocellular carcinomas (HCC) that have immature cancer cells intermingled with fibroblasts, immune and senescent cells expressing high UHRF1 levels, which serve as reservoirs for new cancer cells. Here, we performed scRNAseq in zebrafish livers with UHRF1 overexpressing hepatocytes and controls, in which membrane ocalized EGFP was expressed, at time points in which we observe senescence, senescence escape and HCC formation.
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7. GSE342133 Actβcat、SHH OE 和 Gli3 cKO 条件下 E13.5 和 E14.5 小鼠皮肤真皮的单细胞 RNA 测序

• ✍️ 作者：未知作者
• 🏷️ 关键词：RNA-seq、single-cell
• 📝 描述：Contributor : Peggy MyungSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusMouse embryonic skin samples were collected at E13.5 or E14.5. For each condition, dorsolateral skin from littermate control and mutant embryos was dissected and dissociated for single-cell RNA-seq. Conditions include constitutive dermal β-catenin activation (Actβcat, E13.5), SHH overexpression (SHH OE, E13.5), and Gli3 conditional knockout (Gli3 cKO, E13.5), each with paired littermate controls. An additional E14.5 wildtype replicate was included.
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8. GSE334294 通过单细胞测序研究HuR在小鼠PDAC肿瘤中的功能

• ✍️ 作者：未知作者
• 🏷️ 关键词：sequencing、single-cell
• 📝 描述：Contributors : Yifei Guo ; Katherine R Prlz ; Hen Halamish ; Jonathan R BrodySeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusThe tumor microenvironment (TME) of pancreatic ductal adenocarcinoma (PDAC) is characterized by heterogeneous stroma and immune populations. The role of tumor-intrinsic post-transcriptional gene regulation in driving tumor-immune crosstalk has been relatively unexplored. Here, we report that the RNA-binding protein, HuR (ELAVL1), is enriched in human PDAC and that genetic disruption of HuR impaired tumor growth. Comprehensive spatial and flow cytometry profiling of the PDAC TME revealed that genetic disruption of HuR in PDAC enhanced both T cell number and functional state. Mechanistically, single-cell RNA sequencing in vivo showed that HuR stabilizes mTOR pathway transcripts critical for metabolic adaptation in PDAC. HuR-driven metabolic reprogramming promotes tumor nutrient dominance and limits nutrient consumption by neighboring tumor-reactive T cells. Overall, we find that the post-transcriptional regulator HuR facilitates immune evasion in PDAC by constraining T cell function, identifying HuR blockade as a promising therapeutic strategy in combination with immunotherapies.
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9. GSE260804 IRF2 降解调节先天免疫反应 [RNA-seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：immune、RNA-seq
• 📝 描述：Contributor : R RejaSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusThe transcription factor IRF2 protects against skin inflammation in mice and humans but, paradoxically, promotes pyroptosis by inducing Gsdmd. How IRF2 activates some proinflammatory genes, but suppresses others is unclear. We show that skin inflammation in Irf2-deficient mice is driven by IRF1 activation of interferon-stimulated genes (ISGs). Chromatin profiling revealed that IRF1 and IRF2 occupy the same ISG regulatory sites, but as a weaker transcriptional activator, IRF2 limited ISG transcription by IRF1. Toll-like receptor signaling favored IRF1-driven transcription by inducing Irf1. In addition, IRF1 recruited the ubiquitin ligase SPOP to ISG sites, resulting in proteasomal degradation of IRF2. This shift from IRF2 to IRF1 occupancy enhanced ISG transcription. Collectively, these findings define a hierarchical transcriptional circuit in which IRF2 limits IRF1 activity under homeostatic conditions but is displaced during an immune response, allowing IRF1-dependent gene programs central to innate immunity and autoinflammation.
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10. GSE345045 比较转录组学和免疫分析发现透明细胞牙源性癌和透明细胞透明癌具有共同的分子特征 [1]

• ✍️ 作者：未知作者
• 🏷️ 关键词：carcinoma、immune
• 📝 描述：Contributors : Helen X Hou ; Bidish K Patel ; Emily E Ackerman ; Tom Bisson ; Samyukta Singh ; Peter M Richieri ; A J IafrateSeries Type : OtherOrganism : Homo sapiensClear cell odontogenic carcinoma (CCOC) and hyalinizing clear cell carcinoma (HCCC) are rare head-and-neck malignancies with recurrent EWSR1::CREB family fusions that show overlapping morphology and immunophenotype, but whose molecular relationship to each other and to relevant differential diagnoses has remained poorly defined due to tissue rarity. No standardized systemic therapy exists for either tumor. We performed spatial transcriptomic profiling (NanoString GeoMx Whole Transcriptome Atlas), multiplex immunofluorescence, and RNA in situ hybridization on 80 FFPE tumor samples spanning CCOC, HCCC, clear cell sarcoma, and six additional head-and-neck comparator tumors (squamous cell carcinoma, ameloblastoma, adenoid cystic carcinoma, myoepithelial carcinoma, Ewing sarcoma, and prostate carcinoma as an outgroup). CCOC and HCCC showed highly concordant, overlapping global transcriptomic profiles and converged on a shared epithelial-secretory program, with strong enrichment of IGF2 and candidate therapeutic targets including TACSTD2 (TROP2), FGFR2, FOLR1, KDR, MSLN, and MUC1. Clear cell sarcoma, despite sharing the same fusion family, remained transcriptomically distinct. Immune profiling revealed a cold tumor microenvironment in CCOC/HCCC, with low B2M and HLA class I expression, sparse lymphoid infiltration, and minimal PD-L1 expression, consistent with impaired antigen presentation. These findings indicate that CCOC and HCCC share a common molecular identity distinct from other relevant head-and-neck tumors, particularly myoepithelial carcinoma and squamous cell carcinoma, providing a framework to improve diagnostic classification and prioritize therapeutic targets for these exceptionally rare cancers.
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1. ExoShorkie——利用迁移学习预测酵母中外源基因组的RNA-seq覆盖率

• ✍️ 作者：未知作者
• 🏷️ 关键词：RNA-seq
• 📝 描述：ExoShorkie uses RNA sequencing data and transfer learning to predict expression from exogenous DNA, supporting more accurate gene-regulation models and synthetic biology…
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2. 长读长测序会议，乌普萨拉，2026年11月2-4日

• ✍️ 作者：未知作者
• 🏷️ 关键词：sequencing
• 📝 描述：The LRUA26 meeting highlights advances in long-read RNA sequencing, including full-length isoform analysis, genome assembly, structural variation, epigenetics, and emerging research applications…
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3. 超强“自然杀伤”细胞或将成为一种强大的新型抗癌武器

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer
• 📝 描述：Researchers have found a way to supercharge natural killer cells, powerful immune cells that can attack cancer, so they can penetrate solid tumors and keep fighting once inside. In mice, these specially prepared tissue-resident cells slowed the growth of several tumors, including melanoma and head and neck cancers, and worked even better when paired with the antibody drug cetuximab.
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4. 带状疱疹疫苗与痴呆风险降低24%有关

• ✍️ 作者：未知作者
• 🏷️ 关键词：vaccine
• 📝 描述：Older adults who received the Shingrix shingles vaccine were 24% less likely to be diagnosed with dementia over four years in a study of more than 500,000 people. Researchers estimate the difference could amount to roughly one dementia case prevented for every 17 people vaccinated.
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5. 活过110岁的人体内拥有异常丰富的杀伤性免疫细胞。

• ✍️ 作者：未知作者
• 🏷️ 关键词：immune
• 📝 描述：People who reach 110 and beyond appear to have unusually large numbers of rare immune cells capable of killing abnormal cells. These CD4 cytotoxic T cells became more common with age and often expanded into large groups of nearly identical cells, suggesting the immune system was repeatedly responding to persistent threats.
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• GSE331342 持久的细胞外基质修饰重塑肠道干细胞命运并促进慢性炎症
• GSE306733 EZH2-TTP-mTORC1 轴驱动致命性前列腺癌的表型可塑性和治疗脆弱性 [ChIP-Seq]
• GSE306580 EZH2-TTP-mTORC1 轴驱动致命性前列腺癌的表型可塑性和治疗脆弱性 [RNA-seq]
• GSE304648 胶质母细胞瘤脑膜免疫图谱的单细胞RNA测序
• GSE338951 转录组和表观遗传变化促进骨髓纤维化中脾脏髓外造血的发展 [scRNA-3prime]
• GSE338587 热应激泌乳荷斯坦奶牛骨骼肌、脂肪、肝脏和外周血单核细胞的多组织mRNA测序、miRNA测序和单细胞RNA测序
• GSE338205 转录组和表观遗传变化促进骨髓纤维化中脾脏髓外造血的发展 [scATAC-seq]
• GSE266636 小鼠胚胎原肠胚形成期单细胞RNA测序图谱
• GSE344918 H3K9me3异染色质的完整性和功能由H3K9me3甲基转移酶-HP1依赖性维持[H3K27me3 ChIP-seq]
• GSE344597 鉴定 DFNB1 位点参与 GJB2 调控的促进因子 [Hi-C]
• GSE344167 腹主动脉瘤中内皮细胞特性的维持依赖于血小板衍生的 TGF-β1 [scRNA-Seq]
• GSE328723 RNA测序数据集，包含骨关节炎样条件下用caspase-1和caspase-8抑制剂处理的人类软骨细胞。
• GSE312424 单细胞基因组条形码揭示人类和鸟类脊髓的层级谱系结构
• GSE343110 TurbOmics：一个基于网络的平台，用于使用多组学整合方法分析代谢组学数据。
• GSE338940：特定病原体清除小鼠和暴露于 IMPACT4 的小鼠全血白细胞的批量 RNA 测序
• GSE333837 前列腺癌中THRAP3的磷酸化依赖性基因表达调控和选择性剪接
• GSE333232 祖细胞 T 细胞维持慢性 2 型肺部炎症
• GSE321684 肠道上皮内淋巴细胞迁移和组织稳态受 Ga13 调控
• GSE310293 前列腺癌中磷酸化依赖的THRAP3 RNA结合
• GSE309558 NEAT1 结构重塑重连 MYC 降解通路 [MYC_CLIP_seq]
• GSE309557 NEAT1 结构重塑重连 MYC 降解通路 [RNA_seq_ASO_24]
• GSE309556 NEAT1 结构重塑重连 MYC 降解通路 [RNA_seq_NEAT1_gapmer]
• GSE309555 NEAT1 结构重塑重连 MYC 降解通路 [MYC_RIP_seq]
• GSE304046 食管过敏性炎症调控神经免疫回路的鉴定
• GSE260808 IRF2降解调节先天免疫反应
• GSE344678 人类壳核单细胞RNA测序
• GSE344602 木犀草素-7-O-β-D-葡糖醛酸苷通过抑制AKT/mTOR和JAG1/NOTCH1信号通路改善银屑病样皮肤炎症
• GSE344591 艾灸可改善CFA小鼠的疼痛样行为，并与初级体感皮层的DNA甲基化和转录变化相关
• GSE344344 Foxo1缺失后内侧前额叶皮层小白蛋白中间神经元的核糖体相关RNA测序
• GSE343877 eIF5A K49乙酰化状态对弓形虫转录组的影响
• GSE338680 基因组编辑对体内基因表达调控的抵抗
• GSE306584 靶向 PAR2 可重编程髓系细胞，增强抗原呈递并增强 PD-1 检查点阻断疗法的疗效
• GSE306561 基于计算机转录组学的药物重定位研究在大鼠模型中发现伏立诺他（Vorinostat）可作为调节神经囊虫病神经炎症的候选药物。
• GSE293039 肝移植后亚临床至临床T细胞介导的排斥反应中JAK-STAT/IFN信号通路的动态变化
• GSE343730 me31B H333R突变对果蝇卵巢转录组的影响
• GSE342194 EV-Tracer 能够对癌细胞-成纤维细胞共培养中的细胞外囊泡相关信号进行谱系分辨检测和分子分析。
• GSE338952 转录组和表观遗传学改变促进骨髓纤维化中脾脏髓外造血的发生
• GSE325581 Mest 转录本延伸至 Mestxl 维持但不启动神经分化中趋同基因 Copg2 的母系等位基因偏向（RNA-seq Dnmt3l−/+）
• GSE325578 Mest 转录本延伸至 Mestxl 维持但不启动神经分化中趋同基因 Copg2 的母系等位基因偏向（区域捕获 Hi-C）
• GSE309172 结直肠癌 (CRC) 细胞系的基因表达谱。
• GSE305584 ZEB1-IL-6轴促进乳腺癌干细胞特性
• GSE302084 人类 T 细胞中的 AAV 衣壳进化鉴定出一系列靶向 CD7 的变体，可用于高效 T 细胞和 NK 细胞工程改造 [CRISPR 筛选]