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1. ⭐ GSE325337 RANKL inhibits macrophage pro-inflammatory Toll-like receptor 2 and 4 signaling and impairs killing of intracellular bacteria

• ✍️ 作者：未知作者
• 🏷️ 关键词：bacteria、macrophage、Toll-like receptor、regex:bacter(ia|ial|ium)
• 📝 描述：Contributors : Clara D Si ; Christopher T Peek ; Sana R Fatah ; Andrew J Beaudoin ; Anton R Zhelonkin ; Kara R Eichelberger ; Stacy L Hahn ; Robert O Watson ; Denis A Mogilenko ; James E CassatSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusMonocyte-macrophage lineage cells, crucial components of the innate immune system, can uniquely form bone-resorbing osteoclasts upon exposure to the cytokine receptor activator of NF-κB ligand (RANKL) in the bone microenvironment. Recent studies have also begun to uncover extensive extraskeletal roles of RANKL. However, how monocyte-macrophage lineage cells respond to RANKL outside of the bone, and the impact that this signaling pathway exerts on the host immune response, is not fully understood. In this study, we sought to define how RANKL exposure shapes the macrophage inflammatory response to pathogens by using the model intracellular bacterium Salmonella enterica serovar Typhimurium (STm), which co-opts macrophages to cause life-threatening infections. We found that exposing both mouse and human macrophages to sub-osteoclastogenic levels of RANKL increased intracellular STm burdens and decreased pro-inflammatory cytokine production. RNA sequencing revealed downregulation of pattern recognition receptor (PRR) signaling pathways in RANKL-treated macrophages during the early stages of infection. Therefore, we hypothesized that RANKL impairs PRR-dependent signaling pathways that are important for pro-inflammatory cytokine production. We discovered that RANKL-treated macrophages exhibit reduced NF-κB and IRF3 activation, specifically in response to Toll-like receptor (TLR) 2 and TLR4 stimulation. We determined that prior RANKL exposure decreases abundance of the TLR2 and TLR4 adaptor proteins TRAM and TIRAP. Together, these data suggest that RANKL exposure negatively impacts the macrophage TLR-mediated inflammatory response to bacteria.
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2. ⭐ GSE289299 Syrah：最大化空间转录组数据输出的流程

• ✍️ 作者：未知作者
• 🏷️ 关键词：spatial、spatial transcriptomics、transcriptomics
• 📝 描述：Contributors : Carolyn E Brewster ; Frederick G Mann Jr ; Blair Benham-Pyle ; Alejandro Sánchez AlvaradoSeries Type : OtherOrganism : Schmidtea mediterraneaSpatial analysis of gene expression patterns has been a key technique for revealing the functions of genes. Traditionally, these analyses were constrained to examining only a few candidate genes per sample. However, the advent of spatial transcriptomic techniques like Slide-seqV2 has transformed this field, enabling unbiased and massively parallel exploration of gene expression patterns within their tissue contexts through RNA sequencing. Despite its potential, Slide-seq datasets often suffer from low read counts, loss of data points, and poor quality. We have identified that a significant source of these errors stems from the chemical synthesis of mRNA capture oligonucleotides used in Slide-seqV2. To address this issue, we have developed “Syrah,” an analysis pipeline designed to correct these errors. Syrah can dramatically enhance Slide-seqV2 datasets by recovering nearly 30% more reads. Unlike other dataset improvement methods that rely on complex mathematical imputation or single-cell RNA-seq references, Syrah operates independently, requiring no additional datasets or intricate calculations. This innovative technique promises to salvage previously unusable Slide-seq datasets by restoring valuable reads that were inadvertently discarded during analysis.
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3. ⭐ GSE285345 线粒体代谢和信号传导直接影响树突状细胞在抗肿瘤免疫中的功能 [ATAC-seq1]

• ✍️ 作者：未知作者
• 🏷️ 关键词：immunity、dendritic cell、metabolism
• 📝 描述：Contributors : Hao Shi ; Zhiyuan You ; Hongbo ChiSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusATAC-seq profiling of WT and OPA1-deficient cDC1s
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4. ⭐ GSE298128 蛋白质稳态维持 T 细胞分化潜能和肿瘤浸润淋巴细胞功能 [RNA-seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：tumor、T cell、RNA-seq
• 📝 描述：Contributors : Nicole E Scharping ; Ananda W GoldrathSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusCD8+ tumor-infiltrating lymphocytes (TIL) often fail to restrain tumor growth due to differentiation to T cell exhaustion. In healthy tissues, tissue-resident memory T cells (TRM) survey tissues and sustain protective capacity for years, and tumors that contain TIL with TRM-features are associated with better patient prognosis. We identified protein homeostasis (proteostasis) significant in distinguishing TRM and progenitor-exhausted TIL (TPEX) from terminally-exhausted TIL (TEX) by identifying multiple E3 ubiquitin ligases that maintain T cell differentiation potential. Sustained ligase-expression in TIL enhanced T cell accumulation, preserved stem-like TCF1+ populations, and improved anti-tumor function, whereas ligase loss-of-function impaired TIL and altered T cell differentiation in acute infection. TEX experience a loss of proteostasis, marked by unfolded protein accumulation despite functional proteasomes. Enforced ligase expression rescued this unfolded protein accumulation in TIL and improved immunotherapy responses, demonstrating the role of proteostasis in maintaining differentiation potential and identifying new avenues for advancing cancer immunotherapies.
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5. GSE313622 结合显微镜和蛋白质组学分析，对共生细菌 Candidatus Erwinia dacicola 与成年橄榄果蝇 Bactrocera oleae 的相互作用有了新的认识

• ✍️ 作者：未知作者
• 🏷️ 关键词：regex:bacter(ia|ial|ium)、proteomics
• 📝 描述：Contributors : Georgia Pantidi ; Ioannis Livadaras ; Evangelia Skoufa ; Emmanuel Spanoudakis ; Sofia Kaforou ; Christos Andronis ; John Vontas ; Inga Siden-KiamosSeries Type : Expression profiling by high throughput sequencingOrganism : Bactrocera oleaeThe olive fruit fly Bactrocera oleae is the major pest of olive production. The fly is dependent upon the symbiotic bacterium Candidatus Erwinia dacicola for the survival of the larvae in unripe olives, and in the adult stage they enhance fecundity. A major site of symbiont colonization is the esophageal bulb, yet the molecular interactions within this tissue remain poorly understood. To investigate host gene expression in this symbiont-bearing organ, we performed a transcriptomic analysis of B. oleae esophageal bulbs. This dataset provides a foundational resource for elucidating the functional biology of this organ and offers insights into insect–microbe symbiosis.
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6. GSE294258 细胞内铁稳态调控的表观遗传重编程导致 -7/del(7q) 白血病

• ✍️ 作者：未知作者
• 🏷️ 关键词：leukemia、epigenetic
• 📝 描述：Contributors : Yiman Peng ; Jianan Zheng ; Xintong Deng ; Zhongwang WangSeries Type : Expression profiling by high throughput sequencing ; Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusChromosome copy number variations (CNVs) are among the most critical yet poorly understood genetic drivers of human malignancies. -7/del(7q) is one of the most common CNVs in acute myeloid leukemia (AML) and is associated with poor prognosis. It has been proposed that there might be multiple tumor suppressor genes (TSGs) in these CNVs. Previously, we identified KMT2C, a histone methyltransferase, as a tumor suppressor gene in chromosome 7q. In this study, we performed a differentiation CRISPR screening of hematopoietic stem and progenitor cells (HSPCs) and discovered that ABCB8, encoding a mitochondrial iron transporter, is essential for HSPC differentiation. ABCB8 deficiency accelerated leukemogenesis in vivo and disrupted iron homeostasis, reducing cytoplasmic iron availability and impairing iron-dependent enzymes, including the histone demethylase KDM6A. Consequently, ABCB8 loss elevated H3K27me3 levels, repressing differentiation genes in an iron- and KDM6A-dependent manner. Notably, ABCB8 and KMT2C, neighboring genes on 7q, cooperatively regulated H3K27me3 to suppress leukemogenesis. Our findings reveal ABCB8 as a novel TSG in -7/del(7q) AML and uncover an unprecedented epigenetic collaboration between neighboring TSGs, driven by iron-mediated chromatin remodeling.
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7. GSE328504 CBFA2T3-GLIS2 融合介导的 mSWI/SNF 染色质重塑因子破坏在 AMKL 中产生癌症特异性依赖性 [ATAC-Seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、ATAC-seq
• 📝 描述：Contributors : Gabe Boyle ; Alexander W Ying ; Jay SarthySeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensTranscription factor (TF) fusion oncoproteins are frequently associated with poor prognosis and remain challenging therapeutic targets. Here we show that the CBFA2T3-GLIS2 (C/G) fusion oncoprotein present in lethal pediatric acute megakaryocytic leukemias (AMKLs) co-opts mSWI/SNF chromatin remodeling complexes, reprogramming regulatory element architecture to sustain aberrant cell cycle progression. The C/G fusion binds to and redistributes mSWI/SNF complexes via the SMARCD1 SWIFT domain and targets complexes to oncogenic enhancers including those bound by ETS family TFs and the G1 cyclin CCND2, a C/G AML-specific dependency. Pharmacologic inhibition of mSWI/SNF-mediated G1 cell cycle phasing via FHD-286 suppresses C/G-driven gene expression programs, induces G1 arrest and apoptosis in cells, and reduces leukemic burden and extends survival in aggressive C/G AML in vivo. These findings define an oncogenic mSWI/SNF–G1 axis in C/G AML and establish a therapeutic framework for targeting chromatin dysfunction-mediated cell cycle aberrancy in high-risk pediatric leukemias.
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8. GSE328503 CBFA2T3-GLIS2 融合介导的 mSWI/SNF 染色质重塑因子破坏在 AMKL 中产生癌症特异性依赖性 [RNA-Seq fhd286]

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、RNA-seq
• 📝 描述：Contributors : Gabe Boyle ; Alexander W Ying ; Jay SarthySeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensTranscription factor (TF) fusion oncoproteins are frequently associated with poor prognosis and remain challenging therapeutic targets. Here we show that the CBFA2T3-GLIS2 (C/G) fusion oncoprotein present in lethal pediatric acute megakaryocytic leukemias (AMKLs) co-opts mSWI/SNF chromatin remodeling complexes, reprogramming regulatory element architecture to sustain aberrant cell cycle progression. The C/G fusion binds to and redistributes mSWI/SNF complexes via the SMARCD1 SWIFT domain and targets complexes to oncogenic enhancers including those bound by ETS family TFs and the G1 cyclin CCND2, a C/G AML-specific dependency. Pharmacologic inhibition of mSWI/SNF-mediated G1 cell cycle phasing via FHD-286 suppresses C/G-driven gene expression programs, induces G1 arrest and apoptosis in cells, and reduces leukemic burden and extends survival in aggressive C/G AML in vivo. These findings define an oncogenic mSWI/SNF–G1 axis in C/G AML and establish a therapeutic framework for targeting chromatin dysfunction-mediated cell cycle aberrancy in high-risk pediatric leukemias.
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9. GSE328421 CBFA2T3-GLIS2 融合介导的 mSWI/SNF 染色质重塑因子破坏在 AMKL 中产生癌症特异性依赖性 [RNA-Seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、RNA-seq
• 📝 描述：Contributors : Gabe Boyle ; Alexander W Ying ; Jay SarthySeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensTranscription factor (TF) fusion oncoproteins are frequently associated with poor prognosis and remain challenging therapeutic targets. Here we show that the CBFA2T3-GLIS2 (C/G) fusion oncoprotein present in lethal pediatric acute megakaryocytic leukemias (AMKLs) co-opts mSWI/SNF chromatin remodeling complexes, reprogramming regulatory element architecture to sustain aberrant cell cycle progression. The C/G fusion binds to and redistributes mSWI/SNF complexes via the SMARCD1 SWIFT domain and targets complexes to oncogenic enhancers including those bound by ETS family TFs and the G1 cyclin CCND2, a C/G AML-specific dependency. Pharmacologic inhibition of mSWI/SNF-mediated G1 cell cycle phasing via FHD-286 suppresses C/G-driven gene expression programs, induces G1 arrest and apoptosis in cells, and reduces leukemic burden and extends survival in aggressive C/G AML in vivo. These findings define an oncogenic mSWI/SNF–G1 axis in C/G AML and establish a therapeutic framework for targeting chromatin dysfunction-mediated cell cycle aberrancy in high-risk pediatric leukemias.
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10. GSE284330 大规模并行功能表征揭示肠道菌群对调控DNA元件的调控

• ✍️ 作者：未知作者
• 🏷️ 关键词：gut、regex:gut(-?microbiome)?
• 📝 描述：Contributors : Chadmirah Zaratiana ; Tiffany Liu ; Yong-An Lee ; Agnes Ong ; Samantha Chang ; Torsten Wuestefeld ; Poshen B ChenSeries Type : OtherOrganism : Homo sapiens ; Mus musculusThe human genome contains millions of DNA cis-regulatory elements (CREs) that regulate gene expression across different cell types. In liver hepatocytes, CREs enable adaptation to environmental changes by modifying transcriptomes, particularly in response to gut microbiome signals, which are linked to liver diseases. However, our understanding of the functionality of CREs and their responses to gut microbiota signals in vivo remains limited. To address this, we conducted a genome-wide multiplexed reporter assay (MPRA) to map functional CREs in the liver. Using this functional catalog, we discovered a rare functional variant associated with hepatocellular carcinoma in the Asian population that disrupts CRE activity. Additionally, we identify functional CREs regulated by gut microbiota. Overall, this study enhances our understanding of functional CREs and highlights the complex interactions between the gut microbiome and host gene regulation.
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1. 单细胞总RNA测序拓展了我们对基因调控的认识。

• ✍️ 作者：未知作者
• 🏷️ 关键词：sequencing、single-cell
• 📝 描述：RNA sequencing captures both coding and noncoding RNAs at single-cell resolution, revealing complex regulatory programs and cellular identities across development and disease…
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2. 科学家发现驱动皮肤癌生长和免疫逃逸的隐藏“主开关”。

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、immune
• 📝 描述：A key protein, HOXD13, helps melanoma tumors grow and evade the immune system by boosting blood supply and blocking cancer-fighting T cells. Disabling it shrinks tumors and reopens the door for the immune system—offering a new path for treatment.
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3. 科学家发现一种能杀死耐药细菌的护肤化合物

• ✍️ 作者：未知作者
• 🏷️ 关键词：bacteria、regex:bacter(ia|ial|ium)
• 📝 描述：A popular Korean skincare ingredient may be far more powerful than anyone realized. Scientists have discovered that madecassic acid—derived from the herb Centella asiatica—can stop antibiotic-resistant bacteria in their tracks, including dangerous strains of E. coli. By targeting a bacterial protein that humans don’t have, the compound disrupts the microbes’ ability to survive, making it a promising new type of antibiotic.
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4. 在温泉中发现的环状RNA复制子扩展了微生物多样性

• ✍️ 作者：未知作者
• 🏷️ 关键词：regex:micro(b|be|bial|organism)
• 📝 描述：RNA sequencing reveals diverse circular RNA replicons in hot spring microbes, expanding understanding of Obelisk elements and their role in microbial ecosystems…
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5. Qlucore推出基于人工智能的膀胱癌检测

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer
• 📝 描述：RNA sequencing enables automated molecular subtyping and gene fusion detection in bladder cancer, improving risk assessment and reducing variability in tumor classification through AI-driven analysis…
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• GSE264595 XPO7-NPAT 轴代表 TP53 突变急性髓系白血病的关键脆弱性（RNA-Seq）
• GSE264594 XPO7-NPAT 轴代表 TP53 突变急性髓系白血病 (ATAC-Seq) 的关键脆弱性
• GSE328461 骨桥蛋白将获得性低氧诱导抗血管生成药物耐药性与乳腺癌抗PD-L1药物耐药性联系起来
• GSE328335 WSTF 敲低在结直肠癌细胞中的转录组和表观基因组分析 [ChIP-Seq]
• GSE298127 蛋白质稳态维持 T 细胞分化潜能和肿瘤浸润淋巴细胞功能 [CITE-seq]
• GSE320222 CBP突变型iPSC衍生脑类器官的scRNA-seq
• GSE319859 CBP突变型iPSC衍生脑类器官的RNA测序分析
• GSE318780 乳腺肿瘤组织及邻近正常组织的转录组分析
• GSE318510 人类多能干细胞中 I 型干扰素感知和信号传导的表观遗传锁定 [CUT&Tag]
• GSE318471 人类多能干细胞中 I 型干扰素感知和信号传导的表观遗传锁定。
• GSE312675 压力超负荷诱导的心室串扰激活新生小鼠对侧心室的再生机制 [RNA-Seq]
• GSE312674 压力超负荷诱导的心室串扰激活新生小鼠对侧心室的再生机制 [scRNA-Seq]
• GSE302892 利用单核 RNA 测序技术对对照组和心肌梗死后小鼠左心室进行转录组分析
• GSE302702 11 名意大利参与者的人类内脏脂肪组织活检的单核 RNA 测序。
• GSE302599 对 63 名意大利参与者的人类内脏脂肪组织活检进行单核 RNA 测序。
• GSE294457 TCA循环重编程是组蛋白乙酰化来源和细胞命运转变的基础，发生在细胞退出原始多能性状态的过程中
• GSE282556 冠状动脉疾病的单细胞变异到增强子到基因图谱[ChIP-seq]
• GSE328578 CBFA2T3-GLIS2 融合介导的 mSWI/SNF 染色质重塑因子破坏在 AMKL 中产生癌症特异性依赖性
• GSE328420 CBFA2T3-GLIS2 融合介导的 mSWI/SNF 染色质重塑因子破坏在 AMKL 中产生癌症特异性依赖性 [Cut & Tag 细胞系]
• GSE328419 CBFA2T3-GLIS2 融合介导的 mSWI/SNF 染色质重塑因子破坏在 AMKL 中产生癌症特异性依赖性 [Cut & Run M-07e]
• GSE328418 CBFA2T3-GLIS2 融合介导的 mSWI/SNF 染色质重塑因子破坏在 AMKL 中产生癌症特异性依赖性 [Cut&Tag WSU-AML]
• GSE328417 CBFA2T3-GLIS2 融合介导的 mSWI/SNF 染色质重塑因子破坏在 AMKL 中产生癌症特异性依赖性 [Cut & Tag blood]
• GSE328416 CBFA2T3-GLIS2 融合介导的 mSWI/SNF 染色质重塑因子破坏在 AMKL 中产生癌症特异性依赖性 [Cut & Run]
• GSE328387 LSD1 通过一种不依赖于去甲基酶的方式减弱结直肠癌细胞的铁死亡敏感性：一种通过靶向降解 LSD1 的创新抗肿瘤策略
• GSE328344 CB2R激动剂通过β-catenin/HoxA10环路保护肠上皮免受辐射损伤
• GSE328134 脂肪组织炎症由CCL19过表达介导，通过升高循环饱和脂肪酸和骨桥蛋白水平，加剧高脂饮食喂养小鼠的实验性牙周炎
• GSE327255 PTPRN2 低甲基化和 PHB2 调控的 miR-153-3p 成熟揭示了与肌痛性脑脊髓炎症状变异相关的双重表观遗传机制
• GSE295400 在芯片类器官中构建可灌注血管网络 [批量 RNA 测序]
• GSE294972 氯法齐明诱导宿主免疫系统的变化
• GSE294698 稳态成熟树突状细胞通过 Notch2 指导成纤维细胞分化以建立 T 细胞微环境
• GSE294697 稳态成熟树突状细胞通过 Notch2 指导成纤维细胞分化以建立 T 细胞微环境
• GSE294695 稳态成熟树突状细胞通过 Notch2 指导成纤维细胞分化以建立 T 细胞微环境
• GSE292820 脂肪变性使结直肠癌患者肝转移的组织病理学异质性向预后不良的替代性生长转变
• GSE264628 SIRT1参与人类干细胞的代谢和分化。
• GSE327851 跨神经元细胞因子递送通过下行回路可塑性促进脊髓挫伤严重程度不同的功能恢复
• GSE264747 DC-SIGN+巨噬细胞通过调节炎症细胞因子分泌缓解非酒精性脂肪性肝炎
• GSE255617 新型肝细胞癌药物的开发，JNK-IN-5A衍生物同时诱导细胞凋亡和坏死