详细内容（前10条）

1. ⭐ GSE334323 基于定制探针的空间转录组学技术实现了FFPE结直肠癌组织中微生物组的检测

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、spatial、spatial transcriptomics、transcriptomics
• 📝 描述：Contributors : Rayyan Aburajab ; Jennifer Karmouch ; Robert Jenq ; David W CraigSeries Type : OtherOrganism : Homo sapiensWe describe a custom probe design pipeline targeting the variable regions of bacterial 16S rRNA, compatible with the probe-based chemistry of the 10X Genomics Visium CytAssist platform, enabling spatially resolved bacterial profiling in FFPE tissue. Applied to a cohort of six FFPE colorectal cancer tumor and normal adjacent tissue specimens, we demonstrate the feasibility of a probe-based spatial metatranscriptomics for simultanous profiling of host gene expression and the intratumoral bacterial communities.
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2. ⭐ GSE294273 肿瘤驻留 T 细胞和树突状细胞在黑色素瘤中形成免疫治疗反应的原位原型 [scRNA-seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：tumor、regex:immuno(logy|therapy|suppression)、scRNA
• 📝 描述：Contributors : Andrea Di Pietro ; Patrick Crock ; Niko Thio ; Sara Alei ; David Yoannidis ; Timothy SempleSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensTumor-resident (TR) T cells participate in immunosurveillance of melanoma, but their role in determining response to immune checkpoint inhibitors (ICI) has not been comprehensively explored. We performed spatial and single-cell profiling on 32 metastatic melanoma lymph node samples, from treatment-naïve, ICI-resistant, or ICI-responsive patients. In responders, we found enrichment for early differentiation (TCF1+) CD8+ and CD4+ TR which co-localized with melanoma cells. CD8+ TR were hyperexpanded, and both CD8+ and CD4+ TR upregulated cytotoxicity-related gene expression, suggesting functional anti-tumor immunity. Conversely, ICI-resistant tumors displayed chronic IFN-γ responses within the tumor microenvironment to potentiate T cell exhaustion. In ICI-responsive melanoma tumors, CD8⁺ TR interact with CD4⁺ TR cells (via the CCL4-CCR5 axis) and engage with type-3 dendritic cells (DC3) (via IL15-IL15R interaction). This intratumoral immune triad (CD8⁺ TR – CD4⁺ TR – DC) is exclusive to responders. This study illustrates the role of TR cells and their crosstalk with DCs in effective ICI responses.
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3. ⭐ GSE294272 肿瘤驻留 T 细胞和树突状细胞在黑色素瘤中形成免疫治疗反应的原位原型 [bulk RNA-seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：tumor、regex:immuno(logy|therapy|suppression)、RNA-seq
• 📝 描述：Contributors : Andrea Di Pietro ; Patrick Crock ; Niko Thio ; Angela Pizzolla ; Thu Ngoc Nguyen ; Sean Macdonald ; Stuart BencraigSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensTumor-resident (TR) T cells participate in immunosurveillance of melanoma, but their role in determining response to immune checkpoint inhibitors (ICI) has not been comprehensively explored. We performed spatial and single-cell profiling on 32 metastatic melanoma lymph node samples, from treatment-naïve, ICI-resistant, or ICI-responsive patients. In responders, we found enrichment for early differentiation (TCF1+) CD8+ and CD4+ TR which co-localized with melanoma cells. CD8+ TR were hyperexpanded, and both CD8+ and CD4+ TR upregulated cytotoxicity-related gene expression, suggesting functional anti-tumor immunity. Conversely, ICI-resistant tumors displayed chronic IFN-γ responses within the tumor microenvironment to potentiate T cell exhaustion. In ICI-responsive melanoma tumors, CD8⁺ TR interact with CD4⁺ TR cells (via the CCL4-CCR5 axis) and engage with type-3 dendritic cells (DC3) (via IL15-IL15R interaction). This intratumoral immune triad (CD8⁺ TR – CD4⁺ TR – DC) is exclusive to responders. This study illustrates the role of TR cells and their crosstalk with DCs in effective ICI responses.
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4. ⭐ GSE317411 巨噬细胞驱动腹股沟脂肪垫和淋巴结重塑以应对外周炎症。

• ✍️ 作者：未知作者
• 🏷️ 关键词：lymph、inflammation、regex:lymph(o|atic)?
• 📝 描述：Contributors : Robin Bartolini ; Deepika Sharma ; Gillian J Wilson ; Gillian Dunphy ; Jonathan Cavanagh ; Heba A Halawa ; John Cole ; Stefan Weidt ; Jennifer Barrie ; Kirstyn Gardner-Stephen ; Gerard J GrahamSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusAdaptive immune responses are intensely energy-dependent and rely on a local source of fuel-producing molecules which have been proposed to be derived from fat pads in which mammalian lymph nodes are embedded. However, the trigger for their release has not been identified. Here we demonstrate that cutaneous inflammation is directly correlated with rapid atrophy of perinodal fat pads and increase in embedded lymph node size. We further demonstrate that the fat pad atrophy is associated with influx of a CCR2-independent, lipid metabolising, macrophage population and that macrophage depletion ameliorates fat pad atrophy, and lymph node expansion, downstream of inflamed sites. Our data therefore identify peripheral inflammation as an antigen-independent trigger of downstream fat pad and lymph node remodelling and contributes to the release of essential nutrients to drive the energetic requirements of the adaptive immune response.
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5. GSE310989 双特异性抗体工程化细胞外囊泡重定向 T 细胞以预防术后硬膜外纤维化 [scRNA-seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：antibody、scRNA
• 📝 描述：Contributors : Zheng Zhang ; Wei Xiong ; Liang Huang ; Shanwei Ye ; Qian XuSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusEpidural fibrosis (EF) is a frequent and debilitating complication that impairs recovery following spinal surgery, yet effective targeted therapies are lacking. Here we observe enrichment of FAP⁺ fibroblasts at surgical sites in patients after laminectomy. To therapeutically target this subset, we develop bispecific antibody–decorated extracellular vesicles (BsAb EVs), which redirect endogenous T cells to eliminate FAP⁺ fibroblasts in situ. In a preclinical model, BsAb EVs selectively eliminate pathogenic fibroblasts, reduce fibrotic collagen accumulation, and prevent the development of postoperative epidural fibrosis without detectable systemic toxicity under the tested conditions. Single-cell RNA sequencing reveals that FAP⁺ fibroblasts represent a transcriptionally distinct subset from α-SMA⁺ myofibroblasts, characterized by enhanced extracellular matrix remodeling and TGF-β production. Together, these findings highlight a critical stromal subset in EF pathogenesis and position BsAb EVs as a promising immunotherapeutic strategy for targeting pathogenic stromal cells in fibrotic and tissue-remodeling disorders.
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6. GSE334376 成人腹部皮肤健康人表皮细胞的单细胞RNA测序

• ✍️ 作者：未知作者
• 🏷️ 关键词：RNA-seq、single-cell
• 📝 描述：Contributors : Hannes Kühtreiber ; Polina Kalinina ; Michael MildnerSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensSingle-cell RNA sequencing was performed on viable epidermal cells isolated from healthy adult human abdominal skin samples obtained during abdominoplasty. Epidermal cell suspensions were generated by enzymatic dissociation, viability sorting, and 10x Genomics Chromium-based single-cell library preparation. Libraries were sequenced on an Illumina HiSeq 3000/4000 platform.
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7. GSE333970 WNT抑制诱导的人类心肌生成转录反应（单细胞RNA测序）

• ✍️ 作者：未知作者
• 🏷️ 关键词：RNA-seq、single-cell
• 📝 描述：Contributors : Victor Velecela ; Antoine Bassil ; Ellen Smith ; Dimitris Konstantopoulos ; Fredrik Salmén ; Andreia S Bernardo ; Stefan HopplerSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensSince embryonic cardiac development in vivo and in vitro cardiomyocyte differentiation protocols both require WNT inhibition, our study focussed on how inhibition of WNT signalling guides the transcriptional landscape towards human cardiomyocyte differentiation. We uncovered transcriptional responses using single-cell RNA sequencing. with bioinformatics analysis defining cell identities, reconstructing differentiation trajectories, dissecting WNT inhibition-dependent gene expression and inferring Gene Regulatory Networks (GRN) driving cardiomyocyte specification. We found that WNT inhibition (WNTi) redirects early mesoderm precursors towards a cardiomyocyte fate while limiting alternative lineages.
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8. GSE333960 绘制健康和免疫缺陷范围内的免疫细胞图谱和疫苗反应 [TCR-seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：immune、vaccine
• 📝 描述：Contributors : Davide Vespasiani ; James Lancaster ; Hamish W KingSeries Type : OtherOrganism : Homo sapiensImmune responses to infection and vaccination exhibit diversity between individuals that can be shaped by differences in their immune cell landscapes and the signalling, transcriptional, and genetic mechanisms that coordinate immune cell function. Specific antibody deficiency (SAD) and common variable immunodeficiency (CVID) are common forms of predominantly antibody deficiencies that result in poor responses to vaccination. While molecular and cellular causes of the immune dysfunction and poor vaccination responses for individuals with CVID have been reported, immune cell or molecular defects have not yet been identified in SAD. Here, we have used single-cell multi-omics to define the cellular landscapes, transcriptional states, adaptive immune repertoires and protein expression of patients with SAD and CVID before and after polysaccharide vaccination. We discovered that while SAD and CVID exhibit overlapping immune defects, including accumulation of exhausted NK memory cells and dysregulated expression of genes that mediate lipopolysaccharide sensing and clearance by monocytes, individuals with SAD have a unique expansion of cytotoxic CD4+ T cells that correlates with reduced regulatory T cells. In response to vaccination, we observed rapid changes in gene expression associated with lipopolysaccharide responses by monocytes and NF-kB pathway activation in B cells, and an apparent expansion of a CD95+ class-switched memory B cell population that does not occur in patients with lower antigen-specific responses. Together, our findings reveal cellular and molecular factors that underpin variability in vaccine responses and define SAD in a broader spectrum of immune dysfunction.
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9. GSE333955 绘制健康和免疫缺陷范围内的免疫细胞图谱和疫苗反应 [BCR-Seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：immune、vaccine
• 📝 描述：Contributors : Davide Vespasiani ; James Lancaster ; Hamish W KingSeries Type : OtherOrganism : Homo sapiensImmune responses to infection and vaccination exhibit diversity between individuals that can be shaped by differences in their immune cell landscapes and the signalling, transcriptional, and genetic mechanisms that coordinate immune cell function. Specific antibody deficiency (SAD) and common variable immunodeficiency (CVID) are common forms of predominantly antibody deficiencies that result in poor responses to vaccination. While molecular and cellular causes of the immune dysfunction and poor vaccination responses for individuals with CVID have been reported, immune cell or molecular defects have not yet been identified in SAD. Here, we have used single-cell multi-omics to define the cellular landscapes, transcriptional states, adaptive immune repertoires and protein expression of patients with SAD and CVID before and after polysaccharide vaccination. We discovered that while SAD and CVID exhibit overlapping immune defects, including accumulation of exhausted NK memory cells and dysregulated expression of genes that mediate lipopolysaccharide sensing and clearance by monocytes, individuals with SAD have a unique expansion of cytotoxic CD4+ T cells that correlates with reduced regulatory T cells. In response to vaccination, we observed rapid changes in gene expression associated with lipopolysaccharide responses by monocytes and NF-kB pathway activation in B cells, and an apparent expansion of a CD95+ class-switched memory B cell population that does not occur in patients with lower antigen-specific responses. Together, our findings reveal cellular and molecular factors that underpin variability in vaccine responses and define SAD in a broader spectrum of immune dysfunction.
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10. GSE322776 牛奶体细胞转录组对荷斯坦奶牛饲料转化率和免疫力的多效性影响

• ✍️ 作者：未知作者
• 🏷️ 关键词：immunity、transcriptome
• 📝 描述：Contributors : Victoria Asselstine ; Flavio Schenkel ; Filippo Miglior ; Christine Baes ; Paul Stothard ; Angela CánovasSeries Type : Expression profiling by high throughput sequencingOrganism : Bos taurusIn the livestock industry, feed is the largest expense, driving interest in breeding more feed-efficient animals. Residual feed intake (RFI) is a widely used measure of feed efficiency, accounting for actual feed intake versus expected requirements for maintenance and production. Because feed efficiency is highly polygenic, associated genes may have pleiotropic effects on traits such as immunity, complicating breeding strategies. One way to study pleiotropy is through -OMICs technologies, including transcriptomics, which uses RNA-Sequencing (RNA-Seq) to analyze the transcriptome at specific tissue levels and time points. This study used RNA-Seq to identify differentially expressed (DE) genes between Low RFI (n = 22) and High RFI (n = 17) Holstein cows. A total of 36 genes were DE between groups, enriched in 28 metabolic pathways (FDR < 0.01), most of which were immune-related, including the RIG-I-like receptor signaling pathway. QTL annotation and enrichment analyses were also performed for the DE genes. Within these gene regions, 646 previously annotated QTL were identified, of which 26.7% were related to milk traits. Notably, 10 QTL were associated with feed efficiency, while 4 were linked to host immunity. QTL enrichment further revealed 387 significantly enriched QTL, with the majority of the top associations related to health. In summary, this research identified candidate genes and QTL regions suggesting potential pleiotropic relationships between feed efficiency and immunity in Holstein dairy cows. These findings highlight the need for further investigation to balance productivity and health in genetic improvement programs.
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💡 该来源还有 15 条内容，详见 文末

• GSE294441 基于纳米串的黑色素瘤淋巴结转移基因表达谱分析
• GSE294274 肿瘤驻留 T 细胞和树突状细胞在黑色素瘤中形成免疫治疗反应的原位原型 [scTCR-seq]
• GSE322542 果蝇不同睡眠-觉醒调控下的脑转录组学揭示多种稳态通路
• GSE288137 单细胞多组学揭示控制不同 EMT 肿瘤状态的转录网络
• GSE334384 增强的血管活性肠肽信号传导通过抑制 NF-κB 信号传导来预防杜氏肌营养不良症相关心肌病的发展
• GSE334345 探索性研究美泊利单抗治疗哮喘后血液转录组的变化
• GSE334289 宿主转录反应揭示猪神经囊虫病免疫调节和血脑屏障重塑的分子特征
• GSE334223 整合多组学分析表明，外源吲哚-3-乳酸通过调节浮萍培养物中的多种代谢途径促进其生长
• GSE334222 基于全转录组芯片测序的脑瘫生物标志物筛选及人鼠跨物种保守靶点分析_circRNA-seq
• GSE334081 IL10RA缺失重塑牛乳腺上皮细胞对胞内金黄色葡萄球菌1小菌落变异株的免疫反应
• GSE317848 组蛋白H3的可用性对发育比H3.2与H3.3亚型的区分更重要
• GSE317810 组蛋白H3的可用性对发育比H3.2与H3.3亚型的区分更重要
• GSE303605 Rbm5 通过 Myc 驱动的转录回路维持白血病干细胞
• GSE269450 结合多组学和分子动力学揭示黄曲霉毒素B1通过SCP2介导的肠道毒性
• GSE292576 XPO1 R749Q 突变通过激活 HIF-1/2α–AXL–PI3K/MAPK 信号通路驱动子宫内膜癌进展