详细内容（前10条）

1. ⭐ GSE331364 研究发现，产生脂肪酸乙醇酰胺的肠道细菌可缓解以腹泻为主的伴有胰岛素抵抗的肠易激综合征患者的胃肠道症状。

• ✍️ 作者：未知作者
• 🏷️ 关键词：bacteria、regex:bacter(ia|ial|ium)、resistance、gut、regex:gut(-?microbiome)?
• 📝 描述：Contributors : Shujun Xu ; Lixiang ZhaiSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusWe used fresh ileum tissue samples and performed single-cell RNA sequencing with the DNBelab C4 platform to investigate the mechanisms by which OEA treatment affects IBS-D-related symptoms in TNBS-treated mice. This approach enabled us to analyze cell-type-specific transcriptomic changes and to identify key cellular responses following OEA intervention in the context of TNBS-induced IBS-D symptoms
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2. ⭐ GSE328564 成纤维细胞-ILC3 相互作用抑制肠道炎症

• ✍️ 作者：未知作者
• 🏷️ 关键词：inflammation、gut、regex:gut(-?microbiome)?
• 📝 描述：Contributors : Qingxia Lin ; Ruichao E Liu ; Qiang Wang ; Lan Kang ; Gregory F Sonnenberg ; Coco Chu ; Lei ZhouSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusFibroblasts exhibit remarkable phenotypic and functional heterogeneity in chronic inflammatory diseases, but how these changes impact immune outcomes remain at early stages of investigation. Here we identify a unique fibroblast population that robustly expresses insulin-like growth factor 1 (IGF1) in the healthy intestine that are reduced in inflammatory bowel disease (IBD) patients and necessary to protect from experimental models of gut inflammation. In silico analyses reveal unexpected cross-talk between IGF1+ fibroblasts and group 3 innate lymphoid cells (ILC3s), which dominantly express the IGF-1 receptor (IGF1R) in the gut to protect from inflammation. Mechanistically, IGF1 limits ILC3 production of CXCL10 in inflammatory contexts to prevent recruitment of plasmacytoid dendritic cells (pDC) and restrain gut inflammation. Finally, IGF1 signaling reduces CXCL10 production in human ILC3s, but this pathway is altered in the inflamed intestine of IBD patients and inversely correlates with a higher frequency of pDC. Our results define an unexpected mechanism by which anti-inflammatory fibroblasts safeguard the gut by IGF1-dependent crosstalk with an innate lymphocyte-pDC axis.
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3. ⭐ GSE334973 全基因组表征染色体外环状 DNA 及其在结肠癌发生和发展中的功能作用 [RNA-seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、RNA-seq、genome
• 📝 描述：Contributors : Ji Wang ; Kehan Wang ; Wenbo JiaSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensExtrachromosomal circular DNAs (eccDNAs) are defined as distinct genomic entities of circular and mobile DNA molecules, but their molecular functions in and impact on breast cancer (BC) are rarely known. This study used Circle-seq to analyze eccDNAs from 19 BC tissues and 17 adjacent normal tissues. We found that eccDNAs are present on all chromosomes and enriched in seven eccDNA hotspot genes (HSGs) associated with the BC pathway. Several eccDNAs harboring entire genes (eccGenes) and eccDNAs harboring miRNAs (eccMIRs) were identified and linked to cancer-relevant pathways. Synthetic eccMIR6748, eccMIR6508, and eccMIR3142 elevated miRNA expression in MCF-7 cells, with eccMIR6748 promoting BC cell migration and invasion by upregulating miR-6748, which suppresses tumor suppressor candidate factor 5 (TUSC5) at the post-transcriptional level. eccMIR6748 also influences BC progression via the p38 mitogenactivated protein kinase (MAPK) signaling pathway. These findings suggest that eccDNAs, which contain functional genomic segments, play a role in BC initiation and progression, offering a dynamic source of genomic plasticity and potential as biomarkers and therapeutic targets.
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4. ⭐ GSE330797 结直肠癌（CRC）单细胞转录组学分析

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、single-cell、transcriptomics
• 📝 描述：Contributors : Fuduan Peng ; Haoyue Liu ; Florencia McAllisterSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensUnderstanding cellular processes underlying colorectal cancer (CRC) development is needed to devise intervention strategies. Here, we performed single-cell RNA sequencing (scRNA-seq) of human treatment-naive colorectal cancer.
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5. ⭐ GSE329693 微生物组衍生的代谢物影响慢性 HIV-1 感染中 CD4⁺ T 细胞的分化和免疫衰老 [RNA-Seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：immune、aging、RNA-seq
• 📝 描述：Contributors : Amanda C Da Silva ; Luke Flantzer ; Souheil-Antoine YounesSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensThe role of aromatic gut-derived bacterial metabolites (GDBMs) in shaping immune cell metabolism and function remains poorly explored. Using ex vivo metabolomic profiling of paired plasma and CD4⁺ T-cells from people living with HIV-1 (PLWH), we identified a network of aromatic GDBMs whose cell-associated abundance, rather than systemic levels, was linked to broad alterations in CD4⁺ T-cell metabolic and functional states. Among these metabolites, p- cresol sulfate (PCS) emerged as a mechanistic prototype investigated in depth. Ex vivo flow cytometry and single-cell RNA sequencing of CD4⁺ T-cells stratified by cell-associated PCS levels revealed dose-dependent enrichment of transcriptional programs associated with impaired differentiation capacity, regulatory-like identity, and cellular senescence. Consistently, in vitro transcriptomic and proteomic analyses of PCS-exposed CD4⁺ T cells demonstrated induction of cell-cycle arrest, mitochondrial dysfunction, and senescence-associated programs, including upregulation of p16 and p21. Integration of these immunometabolic features with measurements of HIV-1 reservoir size in PLWH revealed that CD4⁺ T-cell states defined by cell-associated GDBMs track with intact proviral DNA levels in vivo. Together, these findings define a microbiome-derived axis that reshapes CD4⁺ T-cell metabolism and fate and promotes immune aging–associated states in PLWH. Our data suggest that cell-associated GDBMs may foster immunometabolic CD4⁺ T-cell states previously linked to long-term HIV-1 reservoir persistence in vivo.
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6. ⭐ GSE328611 微生物组衍生的代谢物影响慢性 HIV-1 感染中 CD4⁺ T 细胞的分化和免疫衰老 [scRNA-seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：immune、aging、scRNA
• 📝 描述：Contributors : Amanda C Da Silva ; Luke Flantzer ; Shuya Kyu ; Ana C Santana ; Aarthi Talla ; Souheil-Antoine YounesSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensThe role of aromatic gut-derived bacterial metabolites (GDBMs) in shaping immune cell metabolism and function remains poorly explored. Using ex vivo metabolomic profiling of paired plasma and CD4⁺ T-cells from people living with HIV-1 (PLWH), we identified a network of aromatic GDBMs whose cell-associated abundance, rather than systemic levels, was linked to broad alterations in CD4⁺ T-cell metabolic and functional states. Among these metabolites, p- cresol sulfate (PCS) emerged as a mechanistic prototype investigated in depth. Ex vivo flow cytometry and single-cell RNA sequencing of CD4⁺ T-cells stratified by cell-associated PCS levels revealed dose-dependent enrichment of transcriptional programs associated with impaired differentiation capacity, regulatory-like identity, and cellular senescence. Consistently, in vitro transcriptomic and proteomic analyses of PCS-exposed CD4⁺ T cells demonstrated induction of cell-cycle arrest, mitochondrial dysfunction, and senescence-associated programs, including upregulation of p16 and p21. Integration of these immunometabolic features with measurements of HIV-1 reservoir size in PLWH revealed that CD4⁺ T-cell states defined by cell-associated GDBMs track with intact proviral DNA levels in vivo. Together, these findings define a microbiome-derived axis that reshapes CD4⁺ T-cell metabolism and fate and promotes immune aging–associated states in PLWH. Our data suggest that cell-associated GDBMs may foster immunometabolic CD4⁺ T-cell states previously linked to long-term HIV-1 reservoir persistence in vivo.
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7. ⭐ GSE314223 抗细胞因子生物制剂治疗的炎症性肠病患者对SARS-CoV-2 mRNA疫苗的T细胞免疫力强度和广度得以保留

• ✍️ 作者：未知作者
• 🏷️ 关键词：immunity、T cell、cytokine
• 📝 描述：Contributors : Michelle W Cheung ; Mark S Silverberg ; Tania H WattsSeries Type : Expression profiling by high throughput sequencing ; OtherOrganism : Homo sapiensThe widespread vaccination against SARS-CoV-2 offered an opporunity to investigate the effects of anti-cytokine biologics on the cellular responses to a specific vaccination. Previous research has demonstrated inflammatory bowel disease (IBD) patients treated with anti-TNF agents exhibit decreased Spike (S)-specific antibody responses compared to IBD patients treated with anti-IL-12/23 or healthy controls, even after four doses of mRNA vaccine (Cheung et al. JCI 2025). Less is known about the impacts of anti-TNF and anti-IL-12/23 therapy on T cell responses to vaccination, although previous research in our group has demonstrated that T cells responses in patients treated with anti-TNF or anti-IL-12/23 tend to wane quicker after two vaccine doses, compared to healthy controls (Dayam, Law, et al. JCI Insight 2023). To further examine the phenotype of and breadth of memory T cell responses to SARS-CoV-2 mRNA vaccination, here we performed immune profiling of S-specific memory T cells, isolated from anti-TNF treated- or anti-IL-12/23- treated IBD patients and healthy controls from timepoints after two and three vaccine doses, via 5’ single cell RNA-sequencing (with CITE-sequencing for hashtags only) and TCR-sequencing.
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8. ⭐ GSE296954 肿瘤浸润性 GZMK+ 效应记忆 T 细胞的分化与头颈癌新辅助免疫治疗的疗效相关

• ✍️ 作者：未知作者
• 🏷️ 关键词：tumor、cancer、regex:immuno(logy|therapy|suppression)
• 📝 描述：Contributors : Cem Sievers ; Clint AllenSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensWe performed single-cell RNA/VDJ-sequencing of sorted T cells from pre- and post-treatment tumor biopsies of patients with HPV-unrelated head and neck squamous cell carcinoma treated with either bintrafusp alfa alone or in combination with Tri-Ad5 vaccine.
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9. ⭐ GSE275014 肿瘤来源T细胞抗原的鉴定

• ✍️ 作者：未知作者
• 🏷️ 关键词：tumor、T cell、antigen
• 📝 描述：Contributors : Kensuke Shibata ; Yuka YamadaSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusTo identify Tumor-derived T cell ligands, MR1-overexpressing colon cancer cell line CT26_cl9 and its mutant CT26_cl9_M8 were compared.
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10. GSE330227 利用人体T细胞进行体内全基因组CRISPR筛选，以增强T细胞疗法对实体瘤的治疗效果

• ✍️ 作者：未知作者
• 🏷️ 关键词：T cell、genome
• 📝 描述：Contributors : Qi Liu ; Julia CarnevaleSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensLarge-scale CRISPR screening in human T cells holds significant promise for identifying genetic modifications that can enhance cellular immunotherapy. However, many genetic regulators of T cell performance in solid tumors may not be readily revealed in vitro. In vivo screening in tumor-bearing mice offers greater physiological relevance but has historically been limited by low intratumoral T cell recovery. Here, we developed a new model system that achieves substantially higher human T cell recovery from tumors, enabling genome-wide in vivo screens with relatively small numbers of mice. Tumor-infiltrating T cells in this model exhibit hallmarks of dysfunction compared to matched splenic T cells, creating an ideal context for screening for genetic modifiers of T cell activity in the tumor microenvironment. Using this platform, we performed two genome-wide CRISPR knockout screens to identify genes regulating T cell intratumoral abundance and effector function, as measured by IFN-γ production. The intratumoral abundance screen uncovered the P2RY8-Gα13 GPCR signaling axis as a negative regulator of human T cell infiltration into tumors. The effector function screen identified GNAS as a key regulator of T cell dysfunction in tumors. Its protein product, Gαs, acts as a convergent signaling node downstream of multiple GPCRs that sense different suppressive ligands. Targeted GNAS knockout rendered T cells resistant to multiple suppressive cues and significantly improved therapeutic performance across diverse solid tumor models in both CAR and TCR systems. Moreover, combinatorial knockout of P2RY8 and GNAS further enhanced overall tumor control, demonstrating that complementary screens with distinct in vivo readouts can nominate gene targets addressing orthogonal barriers, and that combining such edits can improve therapeutic potency. This flexible and scalable platform can be adapted to diverse tumor models and screening modalities, enabling systematic discovery of genetic strategies to equip T cell therapies for solid tumors.
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💡 该来源还有 12 条内容，详见 文末

• GSE291918 ORCA介导的多梳抑制复合物稳定化维持3D基因组结构并控制复制时间[ChIP-seq]
• GSE335106 野生型和 Pim1-/- 巨噬细胞的批量 RNA 测序分析
• GSE335072 LINEMAP：基于演化 CRISPR 条形码的单细胞谱系拓扑结构和分裂历史的定量时间重建
• GSE334988 PRMT2野生型和PRMT2敲除型KG-1a急性髓系白血病细胞的转录组分析
• GSE334783 支架蛋白AKAP79/150塑造对过敏原的先天免疫反应
• GSE327377 IKKα调控的microRNA miR-9-5p通过CDH1/Wnt/β-catenin信号通路介导肺癌的生长和侵袭
• GSE314620 ORCA介导的多梳抑制复合物稳定化维持3D基因组结构并控制复制时间[Cut & Run]
• GSE300311 PKM2 缺陷诱导的脂肪酸生物合成激活限制了非小细胞肺癌对奥希替尼的反应
• GSE296867 接受新辅助免疫治疗的 HNSCC 患者的治疗后外周血 T 细胞。
• GSE291919 ORCA介导的多梳抑制复合物稳定化维持基因组三维结构并控制复制时间
• GSE305276 骨细胞特异性敲除 Gasdermin D 通过促进软骨下骨的炎症和重塑驱动骨关节炎软骨退变
• GSE301329 骨细胞特异性缺失 Gasdermin D 通过促进软骨下骨的炎症和重塑驱动骨关节炎软骨退化。