详细内容（前10条）

1. ⭐ GSE316477 肿瘤细胞聚集通过调控H3K36组蛋白去甲基化酶KDM2A增强转移能力

• ✍️ 作者：未知作者
• 🏷️ 关键词：tumor、histone、clustering
• 📝 描述：Contributors : Carolyn Kravitz ; Kiran D Patel ; Emily Wingrove ; Dejian Zhao ; Tang Tang ; Sampada Chande ; Yuchen Huo ; Thomas F Westbrook ; Qin Yan ; Don X NguyenSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensDisseminated tumor cells can form clusters via cell-cell adhesion, which increases their capacity to initiate metastasis. Metastatic clusters are characterized by distinct changes in transcription, suggesting that epigenetic mechanisms underlie their unique phenotypic state. By performingfunctional epigenomic studies in models of non-small-cell lung cancer, we identified the histone H3 lysine 36 (H3K36) demethylase KDM2A as being differentially required for the fitness of metastatic cell clusters. This contextual dependency on KDM2A is predicated by tumor cell-cell aggregation, which specifically induces KDM2A binding to CpG island enriched promoters. At these defined genomic loci, KDM2A maintains H3K36 monomethylation, which preferentially correlates with transcriptional activation. KDM2A directly targets oxidative phosphorylation genes and KDM2A activity is required for optimal mitochondrial respiration and apical cell junction integrity in cell clusters. Consequently, suppressing KDM2A reduces metastatic seeding and colonization in multiple organs, including in the brain. These findings reveal a chromatin regulatory mechanism by which homotypic cell communication instructs the epigenome of disseminated tumor cells to potentiate their metastatic competence.
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2. ⭐ GSE313511 肾移植活检和匹配外周血中CD45+免疫细胞的单细胞RNA测序

• ✍️ 作者：未知作者
• 🏷️ 关键词：immune、sequencing、single-cell
• 📝 描述：Contributors : Dawei Zou ; Stephanie Yi ; Yulin Dai ; Wenhao ChenSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensT cells are central mediators of transplant rejection, yet the differentiation trajectories that sustain this process remain incompletely defined. To delineate the differentiation trajectory of CD8+ T cells, we performed single-cell transcriptomic profiling of matched allograft and peripheral blood mononuclear cell (PBMC) samples obtained from the same patient.
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3. ⭐ GSE315993 比较多组学分析揭示鳍和肢体再生的保守和衍生机制[空间转录组学 II]

• ✍️ 作者：未知作者
• 🏷️ 关键词：spatial、spatial transcriptomics、transcriptomics
• 📝 描述：Contributors : Josane F Sousa ; Gabriela Lima ; Louise Perez ; Hannah Schof ; Igor SchneiderSeries Type : OtherOrganism : Ambystoma mexicanumComparative studies of vertebrate appendages offer a powerful framework for uncovering shared components of an ancestral regeneration toolkit. Here, we employed a multi-omics comparative approach leveraging the regenerative capacity of the axolotl, zebrafish, and Polypterus senegalus, a fish capable of full fin regeneration. We identified conserved markers of proximal and distal blastema territories, shared activation of DNA damage repair, hif1a-mediated hypoxia response, and sequential activation of pro- and anti-inflammatory program. Apical epithelial ridge markers were expressed in both the wound epidermis and distal mesenchyme during limb and fin regeneration. Notably, hif4a-expressing erythrocytes were uniquely associated with proximal limb and fin amputations but not fin rays, while epidermal myoglobin expression was upregulated only in Polypterus and zebrafish fins. Genome-wide chromatin profiling identified candidate regeneration-responsive elements and a conserved enrichment for AP-1 transcription factor binding. Together, these finding identify shared and derived mechanisms of limb and fin regeneration.
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4. ⭐ GSE315990 比较多组学分析揭示鳍和肢体再生的保守和衍生机制[空间转录组学]

• ✍️ 作者：未知作者
• 🏷️ 关键词：spatial、spatial transcriptomics、transcriptomics
• 📝 描述：Contributors : Josane F Sousa ; Gabriela Lima ; Louise Perez ; Hannah Schof ; Igor SchneiderSeries Type : OtherOrganism : Polypterus senegalusComparative studies of vertebrate appendages offer a powerful framework for uncovering shared components of an ancestral regeneration toolkit. Here, we employed a multi-omics comparative approach leveraging the regenerative capacity of the axolotl, zebrafish, and Polypterus senegalus, a fish capable of full fin regeneration. We identified conserved markers of proximal and distal blastema territories, shared activation of DNA damage repair, hif1a-mediated hypoxia response, and sequential activation of pro- and anti-inflammatory program. Apical epithelial ridge markers were expressed in both the wound epidermis and distal mesenchyme during limb and fin regeneration. Notably, hif4a-expressing erythrocytes were uniquely associated with proximal limb and fin amputations but not fin rays, while epidermal myoglobin expression was upregulated only in Polypterus and zebrafish fins. Genome-wide chromatin profiling identified candidate regeneration-responsive elements and a conserved enrichment for AP-1 transcription factor binding. Together, these finding identify shared and derived mechanisms of limb and fin regeneration.
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5. ⭐ GSE309775 TET2突变克隆造血中先天免疫激活的代谢控制[ChIP-seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：immune、metabolic、ChIP-seq
• 📝 描述：Contributors : Peter G Kim ; Christopher Hergott ; Aidan Miller ; Amy Deik ; Meaghan Boileau ; Kevin Bullock ; Kerry Pierce ; Angeline Choy ; Wesley Shin ; Marie McConkey ; Justin Loke ; Birgitta Ryback ; Michael Trinh ; Hong Yue ; Hojong Yoon ; Paul Park ; Shourya Burman ; Matthew Vander Heiden ; Eric Fisher ; Scott Armstrong ; Clary Clish ; Benjamin EbertSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiens ; Mus musculusTET2 mutations drive inflammation in clonal hematopoiesis of indeterminate potential (CHIP), but the mechanism by which TET2 inactivation leads to inflammation is not understood. Here, we used in vivo genome-wide genetic perturbations in primary wildtype (WT) or Tet2 knockout (KO) Cas9+ hematopoietic stem-progenitor cells (HSPCs) in a model of zymosan peritonitis to elucidate the basis of Tet2 KO inflammation. We found that Tet2 restrains O-linked N-acetylglucosamine (O-GlcNAc) glycosyltransferase (Ogt), a Tet2 binding partner and metabolic sensor that integrates nutrient availability. Tet2 loss disrupts this Tet2-Ogt interaction, and dysregulated Ogt facilitates widespread H3K4 trimethylation including lipid-related gene loci and inflammatory lipid droplet formation. We identified ATP citrate lyase (Acly) as a critical node for lipid accumulation, inflammation, and myeloid expansion in Tet2 deficiency. In summary, we reveal that Tet2 serves as a negative regulator of the nutrient sensor Ogt, and that Tet2 inactivation leads to aberrant lipid droplet formation and inflammation.
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6. GSE296587 对共存染色质特征的DNA甲基化和羟甲基化进行测序

• ✍️ 作者：未知作者
• 🏷️ 关键词：sequencing、methylation
• 📝 描述：Contributors : Rafael D C Tavares ; Somdutta Dhir ; Xuan He ; Jack Monahan ; Minna Taipale ; Paula Golder ; Aldo Ciau-Uitz ; Walraj Gosal ; David Tannahill ; Shankar BalasubramanianSeries Type : Genome binding/occupancy profiling by high throughput sequencing ; OtherOrganism : Mus musculusEpigenetic modifications govern chromatin dynamics and cell state. However, current methods cannot simultaneously resolve the presence of multiple DNA modifications at co-occurring chromatin-associated features. It is thus not clear how these features are physically coupled and how their combinations regulate genome function. To address this key question, we report 6-base-CUT&Tag, a method for simultaneous 6-base sequencing at target chromatin features. Using 6-base-CUT&Tag to profile 5mC and 5hmC at co-occurring histone modifications in mouse embryonic stem cells, we identify histone mark-specific signatures of methylation and hydroxymethylation to improve discrimination of different functional enhancer states.
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7. GSE312873 巨噬细胞组织驻留所需的多胺介导的翻译后修饰 [scRNA-seq 2]

• ✍️ 作者：未知作者
• 🏷️ 关键词：macrophage、scRNA
• 📝 描述：Contributors : Erika L Pearce ; David E Sanin ; Gustavo CarrizoSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusTissue-resident macrophages (RTMs) form during embryogenesis, self-renew locally, and regulate tissue homeostasis by clearing dead cells and debris. During tissue damage, however, bone marrow-derived monocytes enter tissue sites and differentiate into RTM, repairing the tissue and replenishing macrophages in the niche. Universal cell-intrinsic mechanisms that control the monocyte to RTM transition remain elusive. We investigated mice with myeloid cell deletions in deoxyhypusine synthase (DHPS), an enzyme that mediates the polyamine-dependent hypusine modification of the translation factor eIF5A, and found that DHPS is required for cell adhesion and signaling programs critical for RTMs. Without DHPS expression, immature tissue macrophages form, but RTM and associated homeostatic functions are lost. Thus, the polyamine-hypusine pathway is a global, tissue-agnostic program driving the differentiation trajectory of monocyte-derived macrophages into RTM.
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8. GSE290686 巨噬细胞组织驻留所需的多胺介导的翻译后修饰 [RNA-Seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：macrophage、RNA-seq
• 📝 描述：Contributors : Erika L Pearce ; David E Sanin ; Gustavo CarrizoSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusTissue-resident macrophages (RTMs) form during embryogenesis, self-renew locally, and regulate tissue homeostasis by clearing dead cells and debris. During tissue damage, however, bone marrow-derived monocytes enter tissue sites and differentiate into RTM, repairing the tissue and replenishing macrophages in the niche. Universal cell-intrinsic mechanisms that control the monocyte to RTM transition remain elusive. We investigated mice with myeloid cell deletions in deoxyhypusine synthase (DHPS), an enzyme that mediates the polyamine-dependent hypusine modification of the translation factor eIF5A, and found that DHPS is required for cell adhesion and signaling programs critical for RTMs. Without DHPS expression, immature tissue macrophages form, but RTM and associated homeostatic functions are lost. Thus, the polyamine-hypusine pathway is a global, tissue-agnostic program driving the differentiation trajectory of monocyte-derived macrophages into RTM.
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9. GSE290571 巨噬细胞组织驻留所需的多胺介导的翻译后修饰 [scRNA-seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：macrophage、scRNA
• 📝 描述：Contributors : Erika L Pearce ; David E Sanin ; Gustavo CarrizoSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusTissue-resident macrophages (RTMs) form during embryogenesis, self-renew locally, and regulate tissue homeostasis by clearing dead cells and debris. During tissue damage, however, bone marrow-derived monocytes enter tissue sites and differentiate into RTM, repairing the tissue and replenishing macrophages in the niche. Universal cell-intrinsic mechanisms that control the monocyte to RTM transition remain elusive. We investigated mice with myeloid cell deletions in deoxyhypusine synthase (DHPS), an enzyme that mediates the polyamine-dependent hypusine modification of the translation factor eIF5A, and found that DHPS is required for cell adhesion and signaling programs critical for RTMs. Without DHPS expression, immature tissue macrophages form, but RTM and associated homeostatic functions are lost. Thus, the polyamine-hypusine pathway is a global, tissue-agnostic program driving the differentiation trajectory of monocyte-derived macrophages into RTM.
• 🔗 查看原文

10. GSE283746 婴儿单细胞比较分析揭示了 RSV 特异性 NK 细胞反应下降和 COVID-19 特异性炎症反应增加 [COVID_RSV_scRNA]

• ✍️ 作者：未知作者
• 🏷️ 关键词：NK cell、single-cell
• 📝 描述：Contributors : Asa Thibodeau ; Asunción Mejías ; Djamel Nehar-Belaid ; Radu Marches ; Virginia Pascual ; Jacques Banchereau ; Octavio Ramilo ; Duygu UcarSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensThe clinical phenotype of infants infected with respiratory syncytial virus (RSV) differs from that of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. RSV is the leading cause of hospitalization for lower respiratory tract infection and carries a significant higher risk of respiratory failure compared to SARS-CoV-2, which has been generally linked to fever and croup in young infants. The underlying mechanisms these differences remain unclear. We analyzed peripheral blood mononuclear cells (PBMCs) and serum from infants infected with SARS-CoV-2 (n=30), RSV (n=19), and healthy controls (n=17) using single-cell RNA sequencing, single-nucleus ATAC sequencing and cytokine profiling. Both viruses triggered type I interferon responses across PBMC subsets but differed in their NK cell and inflammatory responses. Severe RSV cases were characterized by lower NK cell percentages, lower IFNG expression and diminished chromatin accessibility at T-BET and EOMES binding sites in NK cells. Furthermore, RSV infections were associated with increased frequencies of CD4+ TEMRA and memory Treg cells. In contrast, SARS-CoV-2 infections were marked by more pronounced pro-inflammatory signatures, including increased transcriptional and epigenetic activity at NFKB factors and higher serum TNF concentrations. These findings highlight distinct immune response pathways in RSV and SARS-CoV-2 infections that may inform future therapeutic strategies.
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1. ⭐ 西北大学医学院研发的新型抗体可激活免疫系统对抗胰腺癌

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、immune、antibody
• 📝 描述：Pancreatic cancer uses a sugar-coated disguise to evade the immune system, helping explain why it’s so hard to treat. Northwestern scientists discovered this hidden mechanism and created an antibody that strips away the tumor’s protective signal. In animal tests, immune cells sprang back into action and tumors grew much more slowly. The team is now refining the therapy for future human trials.
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2. 评估全转录组测序在临床融合检测中的应用

• ✍️ 作者：未知作者
• 🏷️ 关键词：sequencing、transcriptome
• 📝 描述：Clinical RNA sequencing using whole transcriptome sequencing reliably detects gene fusions and splice variants when strict quality thresholds are applied, while also uncovering…
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3. iTP-seq——一种可扩展的体外细菌翻译图谱表征分析工作流程

• ✍️ 作者：未知作者
• 🏷️ 关键词：regex:bacter(ia|ial|ium)
• 📝 描述：A new iTP-seq workflow uses RNA sequencing to map bacterial ribosome positions with codon-level precision, revealing how sequence context and antibiotics shape translation dynamics…
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4. 餐后血糖飙升可能会增加患阿尔茨海默病的风险。

• ✍️ 作者：未知作者
• 🏷️ 关键词：Alzheimer
• 📝 描述：Spikes in blood sugar after eating may be more dangerous for the brain than previously thought. In a massive genetic study, people with higher post-meal blood sugar had a much greater risk of Alzheimer’s disease. The effect couldn’t be explained by visible brain damage, suggesting hidden biological pathways may be involved. Researchers say managing blood sugar after meals could become a key strategy for reducing dementia risk.
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5. 后代数量少，寿命更长：哺乳动物衰老的隐秘规律

• ✍️ 作者：未知作者
• 🏷️ 关键词：aging
• 📝 描述：A large international study reveals that mammals tend to live longer when reproduction is suppressed. On average, lifespan increases by about 10 percent, though the reasons differ for males and females. Castrated males avoid the harmful effects of testosterone, while females gain longevity by sidestepping the intense physical demands of pregnancy and nursing. The results underscore a powerful biological trade-off between making offspring and staying alive longer.
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• GSE283744 婴儿单细胞比较分析揭示了 RSV 特异性 NK 细胞反应下降和 COVID-19 特异性炎症反应增加 [COVID_RSV_snATAC]
• GSE274462 ACSL4相关脂质代谢是KMT2A重排急性髓系白血病的一个独特治疗弱点
• GSE309504 组合表型图谱使细菌能够抵抗噬菌体感染
• GSE298064 TET2突变克隆造血中先天免疫激活的代谢控制
• GSE295041 患者匹配的卵巢癌样本中复发性肿瘤特异性标志物的鉴定
• GSE316220 对照组和 DHEA 处理组小鼠的多组织转录组批量 RNA 测序（卵巢、子宫、胸腺、脑、心脏、肠、肾、肝和脾）
• GSE300298 保守的水杨酸信号通路通过地钱中独特的TGA转录因子控制植物对假单胞菌的免疫力
• GSE286337 五种物质粉（含茯苓）通过调节肠道菌群来调节胃抑制多肽的释放，从而改善肥胖小鼠的脂质代谢紊乱。
• GSE282942 鸢尾素通过 IL-33-ST2 通路改善肥胖和葡萄糖耐受不良
• GSE316651 一项针对雌雄小鼠的纵向研究，旨在识别与年龄无关的衰弱相关的DNA甲基化特征。
• GSE316630 RNA结合蛋白NOVA-1调控秀丽隐杆线虫的环状RNA表达、选择性剪接和衰老
• GSE316055 阿尔茨海默病相关 TREM2 或其衔接蛋白 TYROBP/DAP12 缺失的小胶质细胞中下游信号传导的差异
• GSE313065 巨噬细胞组织驻留所需的多胺介导的翻译后修饰
• GSE290459 巨噬细胞组织驻留所需的多胺介导的翻译后修饰 [核糖体测序]
• GSE230606 肾移植受者外周血单核细胞 (PBMC) 和同种异体移植活检样本中 CD45+ 免疫细胞的单细胞水平基因表达谱
• GSE315999 比较多组学分析揭示鳍和肢体再生的共同和衍生机制 [ATAC-seq]
• GSE315989 多组学比较分析揭示鳍和肢体再生的保守和衍生机制 [批量 RNA 测序]
• GSE315636 阻断T型Ca²⁺通道通过抑制PI3K/AKT通路破坏线粒体功能和卵泡发育
• GSE270670 无细胞基因组学揭示结核分枝杆菌转录周期的基本调控原理
• GSE316449 H3K27me3α-酮戊二酸通过选择性减少 H3K27me3 驱动牙周膜成纤维细胞的成骨和细胞外基质基因程序 [RNA-Seq]
• GSE316447 H3K27me3α-酮戊二酸通过选择性减少 H3K27me3 驱动牙周膜成纤维细胞中的成骨和细胞外基质基因程序 [ATAC-Seq]
• GSE311420 小鼠二倍体ES细胞的单细胞基因组结构[CUT&Run]
• GSE305052 从蓼科植物中鉴定出的独特 miRNA319a 介导跨界抑制宫颈癌，靶向 ITGA3