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1. ⭐ GSE332556 肿瘤相关巨噬细胞 GnT-V 通过分支 N-糖基化促进 M1 极化，从而增强对肿瘤免疫疗法的敏感性

• ✍️ 作者：未知作者
• 🏷️ 关键词：tumor、macrophage、regex:immuno(logy|therapy|suppression)
• 📝 描述：Contributor : Depeng YangSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensTumor tissues with differential sensitivity to immunotherapy were sequenced using The DNBelab C4 /DNBelab TaiM4 Series Single-Cell Library Prep Set (MGI) was used for sequencing and sequenced on the DNBSEQ-T7 sequencer with pair-end sequencing. Immunotherapy based on immune checkpoint inhibitors (ICIs) has become one of the most successful clinical treatment strategies and has marked a milestone in the field of cancer therapy. Regrettably, the complex immunosuppressive network within the tumor microenvironment (TME), characterized by imbalanced immune cell subsets and suppressed immune cell function, represents a major cause of ICI treatment failure. This study, through single-cell analysis, provides mechanistic insights into TAM polarization and establishes the therapeutic feasibility of targeting this regulatory axis, thereby introducing a novel treatment strategy to benefit cancer patients.
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2. ⭐ GSE328313 SLC15A3 介导的二肽代谢通过 mTORC1 激活赋予淋巴瘤抗代谢物耐药性 [Ribo-seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：lymphoma、metabolism、resistance
• 📝 描述：Contributors : Haojun Yang ; Sohit Miglani ; Davide RuggeroSeries Type : Expression profiling by high throughput sequencing ; OtherOrganism : Mus musculusAntimetabolites, chemotherapy targeting nucleotide biosynthesis, are among the oldest and most widely used cancer treatments, yet resistance remains a daunting barrier, especially in the fight against B-cell lymphomas. However, the underlying mechanisms of this resistance have long remained elusive. Using an innovative, integrated omics approach, we unexpectedly identified that the accumulation of dipeptides and upregulation of the dipeptide transporter SLC15A3 underlie resistance to nucleotide deficiency in a Myc-driven large B cell lymphoma mouse model. A similar mechanism occurs after long treatment of human B cell lymphoma cells with the chemotherapeutic purine synthesis inhibitor 6-mercaptopurine (6MP). Mechanistically, we demonstrate that dipeptides containing essential amino acids activate the growth and survival mTORC1 signaling pathway. Notably, SLC15A3 specifically interacts with mTOR on the lysosome, boosting mTORC1 activity selectively in resistant lymphoma cells but not in the parental cancer cells. Silencing SLC15A3 diminishes mTORC1 activity and restores resistant lymphoma sensitivity to 6MP. Strikingly, resistant lymphomas, but not primary tumors, exhibit heightened sensitivity to the clinical mTOR inhibitor, rapamycin, in culture and in vivo. We extend these findings in human lymphoma biopsies, which reveal increased SLC15A3 expression following antimetabolite therapy. Together, our study uncovers a previously unrecognized metabolic adaptation that fuels cancer resistance to nucleotide deficiency and positions mTORC1 inhibitor, rapamycin, as a potential therapeutic strategy for transforming the management of chemotherapy-resistant lymphomas.
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3. ⭐ GSE297912 利用类器官-免疫共培养平台开发预测结直肠癌肿瘤免疫反应性的AI模型

• ✍️ 作者：未知作者
• 🏷️ 关键词：tumor、cancer、immune
• 📝 描述：Contributors : Misun Park ; Jiyeon Kim ; Jinguen Rheey ; Jihwan Park ; Ji-yeon ParkSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensThis study aimed to functionally assess tumor immune responsiveness in colorectal cancer using a co-culture platform combining patient-derived organoids (PDOs) with autologous tumor-reactive T cells. The following samples were classified as immune-responsive based on significant T cell–mediated cytotoxicity and IFN-γ production in co-culture assays. RNA sequencing was performed to identify transcriptional signatures associated with immune activation. These immune-responsive PDOs served as the discovery cohort for biomarker identification, enabling the integration of functional immunogenicity data with transcriptomic profiling to develop explainable AI models for predicting immunotherapy response in colorectal cancer.
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4. GSE318836 甲状腺激素激活驱动皮肤鳞状细胞癌中成纤维细胞的特性和肿瘤重塑

• ✍️ 作者：未知作者
• 🏷️ 关键词：tumor、carcinoma
• 📝 描述：Contributors : Emery Di Cicco ; Stefano Sol ; Fabiana Boncimino ; Monica Dentice ; Anna MandinovaSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusCutaneous squamous cell carcinoma (cSCC) is a major cause of cancer-related mortality, with Cancer-Associated Fibroblasts (CAFs) acting as central drivers of tumor progression and immunotherapy resistance. We identified Type 2 deiodinase (D2)-mediated thyroid hormone signaling as a critical regulator of CAF activation. To elucidate the molecular mechanisms governing this reprogramming, we performed RNA-sequencing on CAFs isolated from fibroblast-specific D2 knockout (Col1a2-Cre; D2fl/fl) and wild-type mice (Col1a2-Cre; D2wt/wt). Furthermore, we assessed transcriptional rescue by treating D2-deficient CAFs with exogenous T3. This dataset defines the D2-dependent gene signatures associated with metabolic remodeling and collagen-rich matrix deposition, identifying thyroid hormone signaling as a driver of fibroblast heterogeneity and a potential therapeutic vulnerability in cSCC.
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5. GSE332566 研究基因组、转录组和表观遗传生物标志物在接受 PD-1/PD-L1 抑制剂治疗的复发和/或转移性头颈部鳞状细胞癌患者中的预测价值

• ✍️ 作者：未知作者
• 🏷️ 关键词：carcinoma、epigenetic
• 📝 描述：Series Type : Methylation profiling by genome tiling arrayOrganism : Homo sapiensImmune checkpoint inhibitors have improved survival in several solid tumors, including head and neck squamous cell carcinoma (HNSCC). However, current use of PD-1/PD-L1 inhibitors relies on PD-L1 expression, which does not reliably predict patient response. Therefore, better predictive biomarkers are needed to identify which patients benefit from immunotherapy. Previous studies suggest that genomic and transcriptomic features may help predict treatment response.
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6. GSE331466 Hp1bp3 缺失将染色质重组与胶质瘤的代谢脆弱性联系起来 [ATAC-LOF]

• ✍️ 作者：未知作者
• 🏷️ 关键词：metabolic、glioma
• 📝 描述：Contributors : Brittney Lozzi ; Benjamin DeneenSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusNuclei were isolated from freshly collected GFP+ tumor tissue and processed for transposase-accessible chromatin profiling using standard ATAC-seq protocols. Tumors were generated through in utero electroporation of triple guide casset targeting Nf1, p53, and Pten (3xCr) plus or minus a guide targeting heterochromatin protein 1 binding partner 3 (Hp1bp3) to assess differences in chromatin accessibility associated with Hp1bp3 deficiency. Sequencing libraries were generated following Tn5 transposition and PCR amplification, then sequenced on an Illumina platform to produce paired-end reads. Raw sequencing data were quality filtered, aligned to the mouse reference genome, and analyzed to identify regions of differential chromatin accessibility between genotypes. These datasets were generated to characterize epigenetic and regulatory landscape alterations associated with Hp1bp3 loss in the context of 3xCr high-grade glioma tumors.
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7. GSE331351 单细胞多组学揭示蛋白酶 3-ANCA 阳性肉芽肿性血管炎中 T 细胞亚群中 STAT3-PIM1 轴的激活

• ✍️ 作者：未知作者
• 🏷️ 关键词：T cell、single-cell
• 📝 描述：Contributors : Nanthicha Inrueangsri ; Carlo G Bonasia ; Kevin P Mennega ; Matthew A Jackson-Wood ; Samuel J Bullers ; Oliver Wood ; Malte Borggrewe ; Petya D Marinova ; Rindert R Venema ; Theo Bijma ; Rosanne D Reitsema ; Wayel H Abdulahad ; Jan-Stephan F Sanders ; Abraham Rutgers ; Peter HeeringaSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensGranulomatosis with polyangiitis (GPA) is an autoimmune disease marked by relapses and treatment-related morbidity. CD4⁺ T cells play a central role in GPA pathogenesis, but their molecular profile remains incompletely defined. This study aimed to characterize CD4⁺ T cells in proteinase 3-ANCA-positive GPA (PR3-GPA) patients using single-cell multi-omics to identify molecular signatures associated with disease activity. Peripheral blood mononuclear cells were obtained from PR3-GPA patients during active disease, remission, and healthy controls. Single-cell RNA sequencing and CITE-seq were used to define transcriptional and protein expression profiles of CD4⁺ T cell subsets. Findings were validated using RT-qPCR, flow cytometry–based assays, including phospho-flow cytometry, and in vitro inhibition assay. scRNA-seq and CITE-seq revealed upregulated PIM1 expression in CD4⁺ T cell subsets in active GPA compared to controls. Pim kinase inhibition reduced CD4⁺ T cell activation, proliferation, and cytokine production. These findings indicate that circulating CD4⁺ T cells in active PR3-GPA are characterized by activation of the STAT3–PIM1 axis, potentially driven by upstream IL-6 signaling.
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8. GSE268368 单核细胞重编程和发育的改变增强脓毒症幸存小鼠的脂多糖诱导的肺损伤 [ATAC-Seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：monocyte、ATAC-seq
• 📝 描述：Contributors : Scott J Denstaedt ; Breanna McBean ; Alan P Boyle ; Brett Arenberg ; Matthias Mack ; Bethany B Moore ; Michael W Newstead ; Benjamin H Singer ; Jennifer Cano ; Hallie C Prescott ; Helen S Goodridge ; Rachel L ZemansSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusSepsis is the leading cause of infection-related hospitalization. Persistent inflammation after sepsis is associated with poor long-term outcomes including rehospitalization for new injurious lung conditions. Prior infection can elicit durable epigenetic changes in immune cells and their progenitors leading to inflammatory reprogramming, but the role of persistent immune programming in mediating complications in sepsis survivors remains unclear. We previously established that survival of murine polymicrobial sepsis is associated with enhanced lung injury responses to lipopolysaccharide. This is associated with enhanced cytokine expression in classical (Ly6Chi) monocytes in the lungs, suggesting a role for monocytes in enhancing lung injury in sepsis survival. We performed monocyte depletion and adoptive transfer in mice three weeks and three months after sepsis. We establish that Ly6Chi monocytes are persistently reprogrammed to enhance lung injury and identify neutrophil degranulation as a potential mechanism. Three weeks after sepsis, murine monocytes show persistently altered transcription and chromatin alterations enriched for TLR4, HIF1α, and JAK-STAT signaling and AP-1 binding consistent with persistent immune reprogramming. As novel Ly6Chi monocyte subsets have been recently identified, but functional relevance remains unknown, we evaluated the presence of monocyte subsets and their association with sepsis and acute lung injury. We show for the first time, to our knowledge, that sepsis provokes an ontogenic shift in monocytes towards a granulocyte-monocyte progenitor-derived neutrophil-like lineage in mice and humans. These data suggest that altered myelopoiesis in sepsis survival may be predictive of poor long-term outcome, to this end we show that monocyte and neutrophil counts are associated with 90-day mortality and are complimentary in predicting outcome. Taken together this work supports a conceptual model whereby prior sepsis elicits durable changes in bone marrow progenitors and a shift in monocyte subsets leading to a predisposition to lung injury. This study highlights gaps in our knowledge relating to the interact…
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9. GSE268367 单核细胞炎症程序和发育的改变介导脓毒症幸存者肺损伤加剧 [RNA-Seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：monocyte、RNA-seq
• 📝 描述：Contributors : Scott J Denstaedt ; Breanna McBean ; Alan P Boyle ; Brett Arenberg ; Matthias Mack ; Bethany B Moore ; Michael W Newstead ; Benjamin H Singer ; Jennifer Cano ; Hallie C Prescott ; Helen S Goodridge ; Rachel L ZemansSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusPersistent inflammation after sepsis is associated with poor long-term outcomes including rehospitalization for new injurious lung conditions. Prior infection elicits durable reprogramming in myeloid cells and their progenitors in other contexts. We previously established a murine model of sepsis survival induced by cecal ligation and puncture which results in enhanced lung injury responses to lipopolysaccharide. In this model, classical (Ly6Chi) monocytes in the lungs of post-sepsis mice expressed more inflammatory cytokines, suggesting a primed phenotype and direct role in enhancing lung injury. Therefore, we hypothesized that persistent inflammatory reprogramming of monocytes predisposes to lung injury in sepsis survivors. Here, deplete and/or adoptively transfer monocytes three weeks and three months after sepsis in mice. We evaluate transcriptomic and epigenomic pathways associated with monocyte reprogramming and explore the effect of sepsis on novel monocyte subsets in mice and humans. We find that monocytes from sepsis survivor mice mediate enhanced lung injury responses to LPS and promote neutrophil degranulation. Sepsis elicits durable changes monocytes characterized by JAK-STAT signaling and AP-1 binding and shifts in monocytes and progenitors toward the neutrophil-like subset. We confirm a similar monocyte subset shift in humans with acute sepsis and show that monocyte counts are predictive of 90-day mortality in a cohort of adult sepsis patients. We conclude that sepsis induces inflammatory memory affecting bone marrow progenitors and monocyte subsets predisposing to lung injury. This study sheds light on the interaction of monocyte subsets and immune reprogramming from prior stimuli in governing secondary organ injury responses.
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10. GSE331535 拟南芥幼苗对水分胁迫的TOR依赖性转录组响应

• ✍️ 作者：未知作者
• 🏷️ 关键词：transcriptome
• 📝 描述：Contributors : Dhriti Singh ; Ashverya LaxmiSeries Type : Expression profiling by arrayOrganism : Arabidopsis ; Arabidopsis thalianaTo assess the role of TOR kinase, Col-0 and TOR RNAi (tori 35-7) seedlings were subjected to water-deficit treatment and analyzed using Affymetrix microarrays.Comparative transcriptome profiling of Col-0 and TOR RNAi seedlings was used to identify gene expression changes associated with TOR-regulated responses to water-deficit stress.
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1. 科学家表示，家猫或许能帮助人类找到新的癌症治疗方法。

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer
• 📝 描述：Scientists have cracked open the “black box” of feline cancer in a landmark study that genetically analyzed nearly 500 cat tumors from around the world. The research uncovered striking similarities between cancers in cats, dogs, and humans — including shared cancer-driving genes tied to aggressive breast cancers.
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• GSE331507 I-BRD9 处理的胶质瘤细胞的多组学分析
• GSE319771 心脏结节病炎症和自身免疫信号的整合分子分析 [Xenium]
• GSE310741 表征三维加载模型中乳腺癌细胞对流体剪切的生化反应
• GSE304836 人类真皮成纤维细胞测序
• GSE266396 Cx43介导的MSC线粒体转移通过PGC1-α激活减轻IRI-AKI中的氧化应激-炎症轴
• GSE72325 全基因组微阵列分析鉴定受白色念珠菌 TAF12 变体调控的基因
• GSE303202 营养基因组学和心血管研究揭示了枣（Ziziphus jujuba）的降血压主要健康效应