详细内容（前10条）

1. ⭐ GSE326943 亚临床胆汁淤积是肠道菌群失调的标志，会导致癌症免疫疗法产生耐药性

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、regex:immuno(logy|therapy|suppression)、resistance、gut、regex:gut(-?microbiome)?
• 📝 描述：Contributors : Marine FIDELLE ; Miguel Araujo-VocesSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusGut dysbiosis compromises cancer immunosurveillance by downregulating ileal mucosal addressin cell adhesion molecule 1 (MAdCAM-1) but the metabolic landscape associated with gut dysbiosis remains elusive. Here, we show that antibiotics (ABX) or ABX-associated Enterocloster species, lead to the loss of secondary cholic acid-derived bile acids, BA (DCA) and the accumulation of tauro-conjugated primary BA (TCDCA, T-abo-MCA) in the plasma of patients and mice. DCA/GDCA (glyco-DCA) compensated dysbiosis bile acid abnormalities and circumvented primary resistance to PD-1 blockade. GDCA curtailed ABX-induced MAdCAM-1 downregulation and seemed to have an impact on anti tumor immunity. The single cell RNA sequencing in a mouse model of MCA205 fibrosarcoma helped us to characterize the effect of GDCA or DCA on anti tumor immunity and showed a decrease in T cell exhaustion in the TME.
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2. ⭐ GSE300445 空间肿瘤免疫生态系统影响抗 PD-1 免疫疗法在原发性皮肤黑色素瘤中的疗效 [空间转录组学]

• ✍️ 作者：未知作者
• 🏷️ 关键词：immune、regex:immuno(logy|therapy|suppression)、spatial、spatial transcriptomics、transcriptomics
• 📝 描述：Contributors : Pham Félix ; Dufeu Marion ; Benboubker Valentin ; Grimont Maxime ; Lhorisson Amélie ; Berthet Justine ; Donzel Marie ; Schneider Raphael ; Tonon Laurie ; Doffin Anne-Claire ; Boivin Félix ; Durand Simon ; Dubois Bertrand ; Lopez Jonathan ; Caux Christophe ; Valladeau-Guilemond Jenny ; Eberhardt Anaïs ; Dalle Stéphane ; Caramel JulieSeries Type : OtherOrganism : Homo sapiensIntra-tumoral heterogeneity in melanoma arises from dynamic cancer cell plasticity and underlies various mechanisms of immune escape. Here, we combined high-plex immunofluorescence imaging with spatially resolved transcriptomics to map the architecture of melanoma cell states and their interactions with the immune microenvironment in primary cutaneous tumours prior to adjuvant anti-PD1 immune checkpoint inhibitor (ICI) treatment. Computational analyses showed that melanoma cells organise into spatially restricted patches, with a preferential organisation of undifferentiated cells associated with poor ICI efficacy. Neighbouring immune cell composition varied according to cancer cell states, with a crucial involvement of specific subsets of tumour-associated macrophages, driven by signalling pathways involving tumour-derived and microenvironmental cues such as IFN-γ and hypoxia. Integrated spatial analyses further revealed tumour-immune ecosystems that stratify patient outcomes, delineating configurations either associated with ICI efficacy or metastatic relapse. These results uncover the spatial landscape of tumour ecosystems and identify signalling pathways as potential targets for improving the efficacy of ICI in melanoma.
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3. ⭐ GSE300793 空间肿瘤免疫生态系统影响抗 PD-1 免疫疗法在原发性皮肤黑色素瘤中的疗效 [RNAseq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：immune、regex:immuno(logy|therapy|suppression)、RNAseq、spatial
• 📝 描述：Contributors : Félix Pham ; Marion Dufeu ; Valentin Benboubker ; Maxime Grimont ; Amélie Lhorisson ; Justine Berthet ; Marie Donzel ; Raphael Schneider ; Laurie Tonon ; Anne-Claire Doffin ; Félix Boivin ; Simon Durand ; Bertrand Dubois ; Jonathan Lopez ; Christophe Caux ; Jenny Valladeau-Guilemond ; Anaïs Eberhardt ; Stéphane Dalle ; Julie CaramelSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensIntra-tumoral heterogeneity in melanoma arises from dynamic cancer cell plasticity and underlies various mechanisms of immune escape. Here, we combined high-plex immunofluorescence imaging with spatially resolved transcriptomics to map the architecture of melanoma cell states and their interactions with the immune microenvironment in primary cutaneous tumours prior to adjuvant anti-PD1 immune checkpoint inhibitor (ICI) treatment. Computational analyses showed that melanoma cells organise into spatially restricted patches, with a preferential organisation of undifferentiated cells associated with poor ICI efficacy. Neighbouring immune cell composition varied according to cancer cell states, with a crucial involvement of specific subsets of tumour-associated macrophages, driven by signalling pathways involving tumour-derived and microenvironmental cues such as IFN-γ and hypoxia. Integrated spatial analyses further revealed tumour-immune ecosystems that stratify patient outcomes, delineating configurations either associated with ICI efficacy or metastatic relapse. These results uncover the spatial landscape of tumour ecosystems and identify signalling pathways as potential targets for improving the efficacy of ICI in melanoma.
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4. ⭐ GSE335482 单细胞RNA测序揭示瘢痕疙瘩浸润区和细胞增生区中免疫主导的细胞异质性和基质可塑性

• ✍️ 作者：未知作者
• 🏷️ 关键词：immune、sequencing、single-cell
• 📝 描述：Contributors : Yuchen Cao ; Li Duan ; Dongxian Lin ; Yue Liu ; Mingzi YangSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensBackground Keloids are aggressive fibroproliferative disorders characterized by a sclerotic core and an actively invading margin, yet the cellular and molecular basis of this spatial heterogeneity remains poorly understood. The roles of immune-stromal crosstalk in driving peripheral invasion have not been systematically dissected. Methods Paired infiltrating and hypercellular zones were collected from anterior chest keloids of four patients. Single‑cell RNA sequencing was performed on 128,678 cells after rigorous quality control. Unbiased clustering, differential gene expression analysis, pseudotime trajectory reconstruction, and cell-cell interaction profiling were applied to compare the landscapes of cell composition, function, and differentiation/development trajectories between the two zones. Results The hypercellular zone was dominated by extracellular matrix‑producing myofibroblasts, whereas the infiltrating zone was enriched in mononuclear phagocytes and endothelial cells, exhibiting a loose collagen architecture permissive for cellular invasion. Infiltrating zone fibroblasts adopted an immunomodulatory, inflammatory cancer‑associated fibroblast‑like phenotype, while macrophages displayed a type I interferon signature and immunoglobulin‑mediated activation, indicating a chronic inflammatory state with features reminiscent of certain autoimmune conditions. Langerhans cells followed a three‑stage developmental trajectory from a stress‑responsive to a terminal NF‑κB‑driven effector state, orchestrating neutrophil and Th17 cell recruitment via chemokine and cytokine networks, with significant enrichment of the IL‑17 signaling pathway. Endothelial cells at the margin underwent endothelial‑to‑mesenchymal transition, and Schwann cells exhibited phenotypic plasticity, mirroring aggressive tissue remodeling. Conclusions In the context of this spatially resolved analysis, this study redefines the keloid margin as an immunology‑dominated niche characterized by profound cellular and spatial heterogeneity that is associated with features that could drive peripheral invasion. These findings suggest a shift of the paradigm of keloid pathogenesis from a fibroblast‑centric model to an immune‑driven integrated landscape in this cohort and provide a theoretical foundation for keloid precision therapies and zon…
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5. ⭐ GSE300446 空间肿瘤免疫生态系统影响抗 PD-1 免疫疗法在原发性皮肤黑色素瘤中的疗效 [snRNAseq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：immune、regex:immuno(logy|therapy|suppression)、spatial
• 📝 描述：Contributors : Pham Félix ; Dufeu Marion ; Benboubker Valentin ; Grimont Maxime ; Lhorisson Amélie ; Berthet Justine ; Donzel Marie ; Schneider Raphael ; Tonon Laurie ; Doffin Anne-Claire ; Boivin Félix ; Durand Simon ; Dubois Bertrand ; Lopez Jonathan ; Caux Christophe ; Valladeau-Guilemond Jenny ; Eberhardt Anaïs ; Dalle Stéphane ; Caramel JulieSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensIntra-tumoral heterogeneity in melanoma arises from dynamic cancer cell plasticity and underlies various mechanisms of immune escape. Here, we combined high-plex immunofluorescence imaging with spatially resolved transcriptomics to map the architecture of melanoma cell states and their interactions with the immune microenvironment in primary cutaneous tumours prior to adjuvant anti-PD1 immune checkpoint inhibitor (ICI) treatment. Computational analyses showed that melanoma cells organise into spatially restricted patches, with a preferential organisation of undifferentiated cells associated with poor ICI efficacy. Neighbouring immune cell composition varied according to cancer cell states, with a crucial involvement of specific subsets of tumour-associated macrophages, driven by signalling pathways involving tumour-derived and microenvironmental cues such as IFN-γ and hypoxia. Integrated spatial analyses further revealed tumour-immune ecosystems that stratify patient outcomes, delineating configurations either associated with ICI efficacy or metastatic relapse. These results uncover the spatial landscape of tumour ecosystems and identify signalling pathways as potential targets for improving the efficacy of ICI in melanoma.
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6. ⭐ GSE336281：促性腺激素处理和未处理小鼠卵巢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 : Seth Frietze ; Dimitry Krementsov ; Tia BrodeurSeries Type : Expression profiling by high throughput sequencing ; OtherOrganism : Mus musculusCD45+ immune cells were isolated from ovaries of adult female C57BL/6J mice treated with gonadotropin (n=5) or saline control (n=5). Individual mice were labeled with TotalSeq-B hashtag antibodies, pooled by treatment group, and subjected to 10x Genomics Chromium single-cell RNA sequencing. Hashtag oligonucleotide libraries were used for sample demultiplexing. The dataset was generated to characterize ovarian immune cell populations and their response to gonadotropin-induced hormonal stimulation.
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7. ⭐ GSE268014 HPV阳性和HPV阴性头颈部鳞状细胞癌肿瘤异质性的空间转录组分析

• ✍️ 作者：未知作者
• 🏷️ 关键词：tumor、carcinoma、spatial
• 📝 描述：Contributors : Thomas F Barrett ; Dor Simkin ; Itay Tirosh ; Sid PuramSeries Type : Other ; Expression profiling by high throughput sequencingOrganism : Homo sapiensHead and neck squamous cell carcinoma is the 6th most common malignancy worldwide. We performed spatial transcriptomics to profile intra- and inter-tumor heterogeneity. We identified recurring patterns of spatial gene expression that co-localize in subsets of tumors.
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8. GSE336230 抑郁症炎症的细胞和免疫代谢机制：单细胞RNA测序的初步发现

• ✍️ 作者：未知作者
• 🏷️ 关键词：inflammation、sequencing
• 📝 描述：Contributors : Mandakh Bekhbat ; Gulay B Bengü ; Manoj K Bhasin ; Jennifer C Felger ; Andrew H MillerSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensInflammation is associated with symptoms of anhedonia, a core feature of major depression (MD). We have shown that MD patients with high inflammation as measured by plasma C-reactive protein (CRP) and anhedonia display gene signatures of metabolic reprograming (e.g., shift to glycolysis) necessary to sustain cellular immune activation. To gain preliminary insight into the immune cell subsets and transcriptomic signatures that underlie increased inflammation and its relationship with behavior in MD at the single-cell (sc) level, herein we conducted scRNA-Seq on peripheral blood mononuclear cells from a subset of medically-stable, unmedicated MD out-patients. Three MD patients with high CRP (>3 mg/L) before and two weeks after anti-inflammatory challenge with the tumor necrosis factor antagonist infliximab and three patients with low CRP (≤3 mg/L) were studied. Cell clusters were identified using a Single Cell Wizard pipeline, followed by pathway analysis. CD14+ and CD16+ monocytes were more abundant in MD patients with high CRP and were reduced by 29% and 55% respectively after infliximab treatment. Within CD14+ and CD16+ monocytes, genes upregulated in high CRP patients were enriched for inflammatory (phagocytosis, complement, leukocyte migration) and immunometa-bolic (hypoxia-inducible factor [HIF]-1, aerobic glycolysis) pathways. Shifts in CD4+ T cell subsets included ~30% and ~10% lower abundance of CD4+ central memory (TCM) and naïve cells and ~50% increase in effector memory-like (TEM-like) cells in high versus low CRP patients. TCM cells of high CRP patients displayed down-regulation of the oxidative phosphorylation (OXPHOS) pathway, a main energy source in this cell type. Following infliximab, changes in the number of CD14+ monocytes and CD4+ TEM-like cells predicted improve-ments in anhedonia scores (r = 1.0, p < 0.001). In sum, monocytes and CD4+ T cells from MD patients with increased inflammation exhibited immunometabolic reprograming in association with symptoms of anhedonia. These findings are the first step toward determining the cellular and molecular immune pathways associated with inflammatory phenotypes in MD, which may lead to novel immunomodulatory treatments of psychiatric illnesses with increased inflammation.
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9. GSE336197 16S rRNA 数据集：基于支架的肠造口术和回肠造口术中肠道微生物群的前瞻性、开放标签、多中心随机对照试验

• ✍️ 作者：未知作者
• 🏷️ 关键词：gut、regex:gut(-?microbiome)?
• 📝 描述：Contributor : Zhongyu WuSeries Type : OtherOrganism : human feces metagenomeThis study performed gut microbiota 16s rDNA sequencing on patients receiving stent-based diversion technique (SDT) and temporary ileostomy surgery, with fecal samples collected at preoperative baseline and postoperative follow-up time points. This study aims to characterize perioperative gut microbial signatures, assess alterations in microbial alpha/beta diversity and differential taxa abundance, identify core microbial biomarkers affected by fecal diversion and surgical intervention, and map dynamic gut flora variation induced by SDT and ileostomy. Both ileostomy and minimally invasive SDT alter intestinal luminal conditions and fecal flow, thereby disrupting intestinal microecology and increasing risks of postoperative inflammation, stoma complications and gastrointestinal disorders; however, few studies have illustrated their effects on perioperative gut microbiota. This dataset fills the relevant microecological research gap, helps reveal microbial mechanisms of postoperative gastrointestinal complications, and provides evidence for targeted perioperative microecological intervention to optimize intestinal rehabilitation and reduce stoma-related adverse outcomes in this patient cohort.
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10. GSE329011 BMAL1 和 YAP 协同劫持增强子并促进衰老表皮的炎症 [ChIP-Seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：inflammation、ChIP-seq
• 📝 描述：Contributors : Camile Stephan Otto Attolini ; Guiomar Solanas ; Júlia Bonjoch ; Sandra Garcia MuleroSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusAgeing is characterised by persistent low-grade inflammation that is linked to impaired tissue homeostasis and functionality. However, the molecular mechanisms driving age-associated inflammation remain poorly understood. The mammalian skin is a clinically relevant site of ageing-driven inflammation associated with compromised barrier function, inefficient wound healing, elevated oxidative stress, and DNA damage accumulation. Here, we show that during ageing a previously uncharacterised BMAL1–YAP transcriptional complex displays enhanced binding at inflammation-related enhancers, amplifying the transcription of their target genes. Independent of its known role as a core circadian clock component, we report that BMAL1 partners with the mechanosensitive transcriptional cofactor YAP at enhancer regions to regulate epidermal identity genes. However, in aged skin, this BMAL1–YAP cooperative binding undergoes a functional shift, enhancing the activity of enhancers of inflammation-related genes, co-regulated by NF-κB. Interestingly, aged pro-inflammatory signals from the IL-17 pathway activate YAP in a Hippo-independent manner. These findings unveil a transcriptional mechanism underlying epidermal ageing, linking chromatin dynamics to inflammatory transcriptional programs through BMAL1–YAP-bound enhancer rewiring. By elucidating how ageing reprograms transcriptional networks, our work highlights potential strategies to counteract chronic inflammation and restore tissue homeostasis across age-related loss of functionality.
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1. 对单细胞RNA测序上游细胞保存方法进行多中心评估

• ✍️ 作者：未知作者
• 🏷️ 关键词：sequencing、single-cell
• 📝 描述：RNA sequencing workflows using preserved cells enable flexible sample collection and support reproducible single-cell analyses across multiple laboratories and processing platforms… The post Multisite assessment of methods for cell preservation upstream of single-cell RNA sequencing appeared first on RNA-Seq Blog.
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• GSE329010 BMAL1 和 YAP 协同劫持增强子并促进衰老表皮的炎症 [RNA-Seq]
• GSE327189 基于病毒的个体化新抗原疫苗作为切除的头颈部鳞状细胞癌的佐剂治疗：一项随机 I 期试验的免疫原性和疗效
• GSE315176 果蝇终生食用冻干的副拟杆菌（Parabacteroides distasonis）可改善肠道屏障完整性，延长其寿命和健康寿命。
• GSE303967 威尔姆斯肿瘤的 DNA 甲基化和转录组谱揭示了与肿瘤分层和治疗相关的新的失调基因和表观遗传过程。
• GSE303580 DNA甲基化和转录组谱分析揭示了Wilms肿瘤中与肿瘤分层和治疗相关的新的失调基因和表观遗传过程。
• GSE294070 BMAL1 和 YAP 协同劫持增强子并促进衰老表皮的炎症 [ChIP-Seq 2]
• GSE294069 BMAL1 和 YAP 协同劫持增强子并促进衰老表皮的炎症 [ChIP-Seq 1]
• GSE335215 体内双敲除 CAR-T 筛选鉴定出增强抗肿瘤免疫的协同基因对
• GSE336012 尼古丁和烟草烟雾从单细胞角度重塑神经元信号网络
• GSE335950 EO771乳腺癌细胞的批量RNA测序，包含3种条件
• GSE334781 “代谢陷阱”：近平滑念珠菌通过破坏 pH 值稳态和诱导过早迁移来抑制金黄色葡萄球菌生物膜的成熟
• GSE316678 主动脉瓣狭窄血清IGFBP2介导瓣膜肌成纤维细胞中女性特异性依格列汀耐药性
• GSE311890 患者外周血中长期存活的CD19 CAR-T细胞的单细胞转录组和TCR谱分析
• GSE336193 Zanidatamab治疗早期HER2阳性乳腺癌患者：NeoZanHER II期单臂开放标签试验
• GSE309897 调控线粒体代谢可增强急性髓系白血病对MCL-1抑制剂的敏感性
• GSE300940 多组学分析揭示病理性血流诱导的独特内皮基因表达谱 [RNA-Seq]
• GSE270318 ERK1/2抑制剂通过抑制Drp1依赖性线粒体分裂克服AML对维奈托克的耐药性
• GSE336192 配对 CRISPR 筛选以绘制顺式和反式基因调控图谱 (RNA-seq)
• GSE335980 超级维林敲除小鼠和超级维林突变小鼠的胰岛素作用、葡萄糖代谢和肌肉功能增强
• GSE335354 表面活性蛋白D (Sftpd) 敲除小鼠和野生型小鼠在阿霉素诱导的肠道毒性后空肠基因表达
• GSE334632 A549肺癌细胞在常氧、慢性或短暂缺氧条件下对碳离子的转录反应
• GSE334631 A549肺癌细胞在常氧、慢性或短暂性缺氧条件下对X射线的转录反应
• GSE334551 NAD+ 缺乏驱动代谢功能障碍相关性房颤
• GSE323120 将转录因子网络与染色质可及性整合为三阴性乳腺癌生存结果和药物反应的标志物
• GSE304991 先锋转录因子 TAL1 重塑染色质结构以指导红系细胞命运决定 [RNA测序]
• GSE304981 先锋转录因子 TAL1 重塑染色质结构以指导红系细胞命运决定 [ATAC-Seq]
• GSE300852 Sp8 和 Sp6 在肢芽外胚层中的调控功能 [RNA-seq]
• GSE300595 多组学测序发现髓系细胞与胰腺腺癌 (PDAC) 新辅助化疗治疗反应相关
• GSE293919 利用工程化蛋白质纳米笼对活细胞中细胞质RBP-RNA相互作用和转录组进行纵向监测
• GSE335657 酵母菌纲单细胞基因表达的比较分析
• GSE327794 核斑点的周边区域定义了一个在空间和时间上受到调控的长寿命内含子保留RNA区室，该区室在有丝分裂过程中会解体。