详细内容（前10条）

1. ⭐ GSE301720 整合的单细胞和空间分析揭示了头颈癌免疫检查点阻断反应中依赖于上下文的髓系-T细胞相互作用

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、immune、T cell、single-cell、spatial
• 📝 描述：Contributors : Athena E Golfinos-Owens ; Taja Lozar ; Parth Khatri ; Rong Hu ; Paul M Harari ; Paul F Lambert ; Megan B Fitzpatrick ; Huy Q DinhSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensBackground Approximately 15-20% of head and neck cancer squamous cell carcinoma (HNSCC) patients respond favorably to immune checkpoint blockade (ICB). Previous single-cell RNA-Seq (scRNA-Seq) studies identified immune features, including macrophage subset ratios and T-cell subtypes, in HNSCC ICB response. However, the spatial features of HNSCC-infiltrated immune cells in response to ICB treatment need to be better characterized.Methods Here, we perform a systematic evaluation of cell interactions between immune cell types within the tumor microenvironment using spatial omics data using complementary techniques from both 10X Visium spot-based spatial transcriptomics and Nanostring CosMx single-cell spatial omics with RNA gene panel including 435 ligands and receptors. In this study, we used integrated bioinformatics analyses to identify cellular neighborhoods of co-localizing cell types in single-cell spatial transcriptomics and proteomics data. In addition, we used both publicly available scRNA-Seq and in-house spatial RNA-Seq data to identify spatially constrained Ligand-Receptor interactions in Responder patients.Results With 522,399 single cells profiled with both RNA and protein from 26 patients, in addition to spot-resolved spatial RNA-Seq from 8 patients treated with ICB together with bioinformatics analysis of publicly available single-cell and bulk RNA-Seq, we have identified a spatial and cell-type specific context-dependency of myeloid and T cell interaction difference between Responders and Non-Responders. We defined further cellular neighborhood and the sources of chemokine CXCL9/10-CXCR3 interactions in Responders, emerging targets in ICB, as well as CXCL16-CXCR6, CCL4/5-CCR5, and other underappreciated and potential markers and targets for ICB response in HNSCC. In addition, we have contributed a rich data resource of cell-cell Ligand Receptor interactions for the immunotherapy and HNSCC research community.Discussion Our work provides a comprehensive single-cell and spatial atlas of immune cell interactions that correlate with response to ICB in HNSCC. We showcase how integrating multiple technologies and bioinformatics approaches can provide new insights into potential immune-based biomarkers of ICB response. Our …
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2. ⭐ GSE319270 多组学揭示维生素D在炎症性肠病中对免疫-肠道微生物群相互作用和耐受性通路的影响

• ✍️ 作者：未知作者
• 🏷️ 关键词：immune、gut、regex:gut(-?microbiome)?
• 📝 描述：Contributor : John GubatanSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensLoss of immune tolerance to the gut microbiome plays a pathogenic role in inflammatory bowel disease (IBD). How dietary factors alter host immune-gut microbiome interactions in IBD is unclear. Here, we apply multi-omics (IgA-SEQ, IgG-SEQ, blood scRNA-seq and immune repertoire sequencing) to investigate the effects of 12 weeks of vitamin D on host immune microbe interactions in patients with IBD. Vitamin D treatment associates with decreased disease activity and inflammatory markers and increased IgA-bound and decreased IgG-bound gut microbiota. Vitamin D alters the profiles of IgA-bound (increased Lachnospiraceae, Blautia) and IgG-bound (decreased Proteobacteria, Enterococcaceae) gut bacteria. Vitamin D increases BAFF signaling between plasmacytoid dendritic cells and B cells, alters BCR and TCR clonotypes that associate with Ig-bound gut microbiota, and increases α4β7+ B and T regulatory cells. Our results demonstrate that vitamin D promotes immune tolerance to gut microbiota in patients with IBD. Clinical trial is registered under NCT04828031
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3. ⭐ GSE319268 多组学揭示维生素 D 调节炎症性肠病中的免疫-肠道微生物群相互作用和耐受途径 [16S rRNA-seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：immune、gut、regex:gut(-?microbiome)?
• 📝 描述：Contributor : John GubatanSeries Type : OtherOrganism : human feces metagenomeLoss of immune tolerance to the gut microbiome plays a pathogenic role in inflammatory bowel disease (IBD). How dietary factors alter host immune-gut microbiome interactions in IBD is unclear. Here, we apply multi-omics (IgA-SEQ, IgG-SEQ, blood scRNA-seq and immune repertoire sequencing) to investigate the effects of 12 weeks of vitamin D on host immune microbe interactions in patients with IBD. Vitamin D treatment associates with decreased disease activity and inflammatory markers and increased IgA-bound and decreased IgG-bound gut microbiota. Vitamin D alters the profiles of IgA-bound (increased Lachnospiraceae, Blautia) and IgG-bound (decreased Proteobacteria, Enterococcaceae) gut bacteria. Vitamin D increases BAFF signaling between plasmacytoid dendritic cells and B cells, alters BCR and TCR clonotypes that associate with Ig-bound gut microbiota, and increases α4β7+ B and T regulatory cells. Our results demonstrate that vitamin D promotes immune tolerance to gut microbiota in patients with IBD. Clinical trial is registered under NCT04828031
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4. ⭐ GSE319142 多组学揭示维生素D对炎症性肠病中免疫-肠道微生物群相互作用和耐受途径的调控

• ✍️ 作者：未知作者
• 🏷️ 关键词：immune、gut、regex:gut(-?microbiome)?
• 📝 描述：Contributor : John GubatanSeries Type : OtherOrganism : Homo sapiensLoss of immune tolerance to the gut microbiome plays a pathogenic role in inflammatory bowel disease (IBD). How dietary factors alter host immune-gut microbiome interactions in IBD is unclear. Here, we apply multi-omics (IgA-SEQ, IgG-SEQ, blood scRNA-seq and immune repertoire sequencing) to investigate the effects of 12 weeks of vitamin D on host immune microbe interactions in patients with IBD. Vitamin D treatment associates with decreased disease activity and inflammatory markers and increased IgA-bound and decreased IgG-bound gut microbiota. Vitamin D alters the profiles of IgA-bound (increased Lachnospiraceae, Blautia) and IgG-bound (decreased Proteobacteria, Enterococcaceae) gut bacteria. Vitamin D increases BAFF signaling between plasmacytoid dendritic cells and B cells, alters BCR and TCR clonotypes that associate with Ig-bound gut microbiota, and increases α4β7+ B and T regulatory cells. Our results demonstrate that vitamin D promotes immune tolerance to gut microbiota in patients with IBD. Clinical trial is registered under NCT04828031
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5. ⭐ GSE319486 组蛋白甲基转移酶 G9a 抑制可增强免疫检查点抑制剂在实验性肝细胞癌中的疗效

• ✍️ 作者：未知作者
• 🏷️ 关键词：carcinoma、immune、histone
• 📝 描述：Contributors : Elena Adan-Villaescusa ; Borja Castello-Uribe ; Iker Uriarte ; Eva Santamaria ; Roberto Barbero ; Miriam Belzunce ; Amaya López-Pascual ; Maria Ujue Latasa ; Jasmin Elurbide ; Emiliana Valbuena-Goiricelaya ; Agavni Mesropian ; Guillem Cano-Segarra ; Ana Hernández de Sande ; Lorenzo Nevi ; Simone Carotti ; Umberto Vespasiani-Gentilucci ; Felipe Prosper ; Antonio Pineda-Lucena ; Bruno Sangro ; Josepmaria Argemi ; Pedro Berraondo ; Pablo Sarobe ; Albert Gris-Oliver ; Roser Pinyol ; Josep M Llovet ; Maria Arechederra ; Carmen Berasain ; Alexis Cocozaki ; Veronica Gibaja ; Matias A Avila ; Maite G Fernandez-BarrenaSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiens ; Mus musculusImmune checkpoint inhibitors (ICIs) have improved cancer therapy, but their efficacy in hepatocellular carcinoma (HCC) remains limited, partly associated with tumor-intrinsic mechanisms of immune evasion. To investigate potential epigenetic drivers of immune resistance, this study evaluated transcriptional changes following pharmacological inhibition of the histone methyltransferase G9a (EHMT2). Bulk RNA sequencing was performed on the murine NM53 and human PLC/PRF/5 HCC cell lines treated with G9a inhibitors. NM53 cells were treated with CM272 with or without interferon gamma (IFN-gamma), and PLC/PRF/5 cells were treated with EZM8266. Gene-level expression was quantified for both cell lines, and transposable element (TE) family-level expression was quantified for NM53 samples.
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6. GSE293444 STAT1 和 STAT3 信号通路在卵巢癌中的作用：预后生物标志物和治疗靶点 [RNA-seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、RNA-seq
• 📝 描述：Contributors : Esther Rodman ; John HawseSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensEpithelial ovarian cancer is the 7th most common cancer in women worldwide and is the most fatal of all female reproductive cancers. JAK/STAT signaling is oncogenic in ovarian cancer and has been reported to be constitutively active in a proportion of chemotherapy resistant ovarian cancer cell lines and tumors. However, the precise molecular mechanisms by which STAT1 and STAT3 function in ovarian cancer are not well understood and the consequences of their specific inhibition have yet to be determined. Methods: To delineate the specific functions of STAT1 and STAT3 in high grade serous and endometrioid ovarian cancer cell lines, we treated OVSAHO and MDAH cells with IFNγ or IL6, canonical STAT1 and STAT3 activators respectively, with and without STAT1 or STAT3 specific siRNAs. We conducted RNA-sequencing and ChIP-sequencing following treatment to delineate direct and indirect target genes for STAT1 and STAT3. We generated a STAT1 and STAT3 specific gene signature and applied them to publicly available datasets to test their predictive and prognostic ability. Results: Using these global and unbiased datasets, we identified STAT1 and STAT3 specific pathways, developed STAT1 and STAT3 specific gene signatures, and applied these signatures to publicly available ovarian cancer patient data. We determined the STAT1 and STAT3 signature’s associations with tumor development, chemotherapy responsiveness and long-term patient outcomes. Conclusions: Our studies have further informed the precise mechanisms of STAT1 and STAT3 action in the two most common subtypes of ovarian cancer and have defined gene signatures that are both prognostic and predictive.
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7. GSE285714 NIK 驱动的髓系细胞 IL-23 产生是自身免疫性炎症发展的关键因素 [scRNA-seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：inflammation、scRNA
• 📝 描述：Contributors : Nishada Ramphal ; Matthias Klein ; Ari WaismanSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusWe have employed a single cell sequencing approach with BD Rhapsody to study the differences within myeloid cells in the draining lymph nodes four days after MOG immunisation between NIKfl/fl control mice and NIK^CX3CR1 mice
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8. GSE313697 高脂饮食重塑肠道宿主-微生物群关系，导致艰难梭菌感染后预后更差

• ✍️ 作者：未知作者
• 🏷️ 关键词：gut、regex:gut(-?microbiome)?
• 📝 描述：Contributors : Kumar Archit ; Nguyen Nhu T Q ; O’Brien Martin ; Young Vincent B ; Yung RaymondSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusHigh-fat diet rewires gut host-microbiota relationship to derive worse outcomes following Clostridioides difficile infection
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9. GSE302930 膀胱癌表观遗传图谱揭示管腔型和基底鳞状分子亚型中的主要转录因子和风险相关调控元件

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、epigenetic
• 📝 描述：Contributors : Elio Adib ; Amin H. Nassar ; Sarah Abou Alaiwi ; Toni K. Choueiri ; David J. Kwiatkowski ; Matthew L. FreedmanSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensWe performed histone ChIP-seq, the Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq), and RNA sequencing (RNA-seq) on 28 fresh frozen bladder/upper tract tumor samples. We integrated 64 unique data sets to gain a holistic view of gene regulation in bladder cancer expression/molecular subtypes and nominated candidate subtype-specific master transcription factors (TF) driving expression differences. We also integrated bladder GWAS risk SNPs with H3K27ac ChIP-seq and ATAC-seq data and revealed that risk variants were significantly enriched in genetically determined peaks
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10. GSE317145：用GRK2活性调节剂治疗Tg2576阿尔茨海默病小鼠后的全转录组微阵列基因表达谱分析

• ✍️ 作者：未知作者
• 🏷️ 关键词：Alzheimer、transcriptome
• 📝 描述：Contributors : Joshua Abd Alla ; Ursula QuittererSeries Type : Expression profiling by arrayOrganism : Mus musculusWith increased aging of the global society, the prevalence of Alzheimer’s Disease (AD) is on the rise worldwide. This study aimed to identify AD-related transcript changes in frontal cortex specimens of 18-month-old Tg2576 mice which were used as an experimental model of AD. This study analyzed frontal cortex specimens of two groups of 18-month-old Tg2576 AD mice. The first group was treated for 6 months with the GRK2 activity modulated, CPD10 [1-(1,3-Benzodioxol-5-yl)-4-(cyclopropanecarbonyl)-3-hydroxy-2-phenyl-2H-pyrrol-5-one] in drinking water (8 mg/kg/d) and the untreated control group of 18-month-old Tg2576 mice received tap water. The whole transcriptome microarray gene expression analysis identifies transcripts which were altered by treatment with the GRK2 activity modulator.
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1. 靶向单细胞RNA测序技术的实用指南

• ✍️ 作者：未知作者
• 🏷️ 关键词：sequencing、single-cell
• 📝 描述：This review examines biases in RNA sequencing at the single cell level and outlines targeted strategies to improve transcript detection, coverage of internal regions, and experimental decision making…
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2. 研究人员在肺癌前病变中发现了潜在的免疫逃逸机制

• ✍️ 作者：未知作者
• 🏷️ 关键词：immune
• 📝 描述：Using RNA sequencing, researchers identified miR-149-5p as a driver of immune evasion in progressive bronchial lesions, revealing a potential pathway for early lung cancer…
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3. 脑部炎症可能是导致强迫行为的原因。

• ✍️ 作者：未知作者
• 🏷️ 关键词：inflammation
• 📝 描述：For years, compulsive behaviors have been viewed as bad habits stuck on autopilot. But new research in rats found the opposite: inflammation in a key decision-making brain region actually made behavior more deliberate, not more automatic. The change was linked to astrocytes, brain support cells that multiplied and disrupted nearby circuits. The discovery hints that some compulsive behaviors may arise from excessive, misdirected control rather than a loss of it.
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4. 这种新的血液检测方法可以在癌症扫描结果出来之前就检测出癌症。

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer
• 📝 描述：A new light-based sensor can spot incredibly tiny amounts of cancer biomarkers in blood, raising the possibility of earlier and simpler cancer detection. The technology merges DNA nanotechnology, CRISPR, and quantum dots to generate a clear signal from just a few molecules. In lung cancer tests, it worked even in real patient serum samples. Researchers hope it could eventually power portable blood tests for cancer and other diseases.
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• GSE319431 人鼻咽癌细胞在 BALF2​​-LR 和 BALF2​​-HR 过表达组中的 RNA-seq
• GSE289832 脾神经 NE-β2AR 轴通过调节中性粒细胞免疫抑制加剧脓毒症急性肾损伤 [RNA-seq]
• GSE289831 脾神经 NE-β2AR 轴通过调节中性粒细胞免疫抑制加剧脓毒症急性肾损伤 [scRNA-seq]
• GSE285229 了解含乳脂饮食对肠道上皮稳态的影响。
• GSE280985 免疫胆道单细胞图谱揭示了胆管炎中 2 型常规树突状细胞与 γδ T 细胞之间的相互作用 [scRNA-seq]
• GSE280852 免疫胆道单细胞图谱解析胆管炎中 2 型常规树突状细胞与 γδ T 细胞之间的相互作用 [RNA-seq]
• GSE307866 阿尔茨海默病风险因素和局部神经黑色素含量对人类蓝斑转录组图谱的影响
• GSE307403 人类前额叶皮层皮质层和细胞微环境中与精神分裂症相关的基因表达变化 [Visium]
• GSE300206 异染色质蛋白 1 (HP1) 的相分离控制恶性疟原虫毒力基因沉默 [RNA-seq]
• GSE293317 STAT1 和 STAT3 信号通路在卵巢癌中的作用：预后生物标志物和治疗靶点
• GSE227793 对一组患有心房颤动和健康窦性心律的个体的配对左心房和右心房进行 H3K27ac 和 H3K4me3 ChIP-Seq 分析
• GSE304355 人类特异性增强子调节染色体相互作用以促进神经发生 [小鼠 RNA-seq]
• GSE304354 人类特异性增强子调节染色体相互作用以促进神经发生 [人类单细胞RNA测序]
• GSE318047 胶质母细胞瘤患者（第3组）人脑皮层标本的全转录组微阵列基因表达谱分析
• GSE318046 胶质母细胞瘤患者大脑皮层标本的全转录组微阵列基因表达谱分析（第 2 组）
• GSE318045 胶质母细胞瘤患者大脑皮层标本的全转录组微阵列基因表达谱分析（第1组）
• GSE309790 异常DNA甲基化与产前暴露和新生儿及儿童期肥胖增加有关
• GSE309460 有丝分裂后转录激活和 3D 调控相互作用对黏连蛋白耗竭表现出位点和分化特异性敏感性 [ChIP-seq]
• GSE288300 有丝分裂后转录激活和 3D 调控相互作用对黏连蛋白耗竭表现出位点和分化特异性敏感性 [RNA-seq]
• GSE208730 RNA测序：小鼠背部皮肤、尾部皮肤和口腔上皮中慢速和快速循环表皮干细胞与毛囊干细胞的比较
• GSE319500 卵巢癌无进展生存期的可预测性
• GSE319460 糖尿病和脓毒症小鼠肠道转录组分析 [miRNA-seq]
• GSE311681 免疫胆道单细胞图谱解析胆管炎中2型常规树突状细胞与γδ T细胞之间的相互作用
• GSE297569 保守的非编码序列 CNS11 是 17 型免疫细胞中 Rorc 转录的主控区 [4C-Seq]
• GSE297567 保守非编码序列 CNS11 是 17 型免疫细胞中 Rorc 转录的主控区 [CUT&Tag]
• GSE281197 免疫胆道单细胞图谱解析胆管炎中 2 型常规树突状细胞与 γδ T 细胞之间的相互作用 [multiplex_and_CITE_seq]
• GSE281196 免疫胆道单细胞图谱揭示了胆管炎中 2 型常规树突状细胞与 γδ T 细胞之间的相互作用 [Multiome]
• GSE277350：帕金森病患者来源的iPSCs中少突胶质细胞谱系细胞的单细胞转录组变化（LRRK2-G2019S突变）
• GSE174547 血管线粒体兴奋效应将 Mfn2 与改善的系统代谢和健康寿命联系起来