详细内容（前10条）

1. ⭐ GSE312026 肉瘤中的表观遗传重塑通过调节 Hippo 通路促进 T 细胞浸润（人类）

• ✍️ 作者：未知作者
• 🏷️ 关键词：T cell、epigenetic、pathway
• 📝 描述：Contributors : Lundqvist Andreas ; Cruz De los Santos MireiaSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensImmunotherapy in osteosarcoma remains limited by insufficient T cell infiltration. Considering the importance of epigenetics in sarcomagenesis, the impact of histone modifications in shaping the immune microenvironment was investigated. Using patient-derived ex vivo spheroids and in vivo metastatic osteosarcoma models, we found that pharmacological elevation of H3K27ac by the histone deacetylase 1/3 inhibitor entinostat promotes CD8⁺ T-cell activation, cytotoxicity, and the recruitment of CD8+CD103⁺ tissue-resident memory (TRM) T cells. Mechanistically, these immune-boosting effects are triggered by a Hippo pathway switch, in which Yes-associated protein 1 (YAP1) is suppressed and vestigial-like family member 3 (VGLL3) is induced, thereby rewiring transcription. Furthermore, we identified that VGLL3/CD103 signatures predict a response to anti-PD-1 treatment in sarcoma patients, and that combining H3K27ac induction with anti-PD-1 further augments T cell-mediated killing in ex vivo autologous patient-derived spheroid models. Our findings reveal an epigenetic-Hippo-immunomodulatory axis in osteosarcoma that also extends to other sarcomas, providing a rationale for incorporating epigenetic preconditioning with immunotherapy to improve patient outcomes and pointing towards novel biomarkers for treatment guidance.
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2. ⭐ GSE297632 抗PD-1抗体耐受性LLC细胞的单细胞RNA测序数据

• ✍️ 作者：未知作者
• 🏷️ 关键词：antibody、sequencing、single-cell
• 📝 描述：Contributors : M Sumii ; T MasudaSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusEven after anti-PD-1 antibody is administrated to subcutaneous model mouse using LLC cells, there are a few cells which survive, and these tolerant cells are considered to be the source of later recurrence. We performed single-cell analysis to explore the mechanism behind the tolerance to anti-PD-1 antibody in LLC cells
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3. ⭐ GSE297015 LncRNA NEAT1 通过在内质网应激下通过外泌体维持 CAFs 中 SEMA3A 的 m6A 甲基化来促进胃癌的免疫抑制 [SGC7901]

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、regex:immuno(logy|therapy|suppression)、methylation
• 📝 描述：Contributors : Youqin Xu ; Rui Xu ; Zixin Chen ; Hangyu Zhou ; Jiaqi Liao ; Kaiyuan Ji ; Shengnan Yang ; Xuxian Zhong ; Yuanyuan Li ; Qianbing Zhang ; Linping Zhao ; Qiang ZuoSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensIn order to find out the impact of endoplasmic reticulum stress (ERS) to the tumor microenvironment (TME) of gastric cancer. Transcriptome sequence of exosomes between ERS-GC group and normal GC group. 192 lncRNAs were found to be highly expressed in the exosomes of gastric cancer cells under ERS state.
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4. ⭐ GSE290384 lncRNA NEAT1 通过在内质网应激下通过外泌体维持 CAFs 中 SEMA3A 的 m6A 甲基化，从而促进胃癌的免疫抑制。

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、regex:immuno(logy|therapy|suppression)、methylation
• 📝 描述：Contributors : Youqin Xu ; Rui Xu ; Zixin Chen ; Hangyu Zhou ; Jiaqi Liao ; Kaiyuan Ji ; Shengnan Yang ; Xuxian Zhong ; Yuanyuan Li ; Qianbing Zhang ; Linping Zhao ; Qiang ZuoSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensEndoplasmic reticulum stress (ERS) regulates the function of immune cells in the tumor microenvironment and suppresses the antitumor immune response. In order to formulate the TME of ERS-GC, we cocultured the human CAFs with the supernatant of human gastric cancer cells stimulated by TM. Mass spectrometry sequencing revealed that ERS state regulated the overexpression of 58 proteins and downregulation of the expression of 56 proteins in CAFs, including m6A-modified proteins and SEMA3A, an immunosuppression-related protein.
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5. ⭐ GSE285362 通过单细胞和空间转录组学鉴定人类卵巢皮质中的冷冻敏感微环境和可靶向的FOS/AP-1程序

• ✍️ 作者：未知作者
• 🏷️ 关键词：spatial、spatial transcriptomics、transcriptomics
• 📝 描述：Contributors : Fanghao Guo ; Di Sun ; Wen LiSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensOvary is a vital and dynamic reproductive organ. Ovarian tissue cryopreservation (OTC) plays vital role in female fertility preservation, especially for adolescent female cancer patients. Yet, the sensitive cell populations and cryoinjury molecular mechanisms underlying cryopreservation remain elusive. This study employs single-cell RNA sequencing and spatial transcriptomics to dissect the impacts of temperature stress and cryoprotectant toxicity on the human ovarian cortex. The spatiotemporal molecular characteristics of eight ovarian cell types following vitrification-thawing had been comprehensively characterized. Granulosa, perivascular and stromal cells are identified as most sensitive cell types to OTC procedure. Further analysis using Smart-seq2 on oocytes highlights alterations in “cell cycle” and “DNA methylation” pathways. Notably, the FOS/AP-1 pathway emerges as a crucial response factor to stress and toxicity during cryopreservation. Inhibition of this pathway with T-5224 mitigates vascular damage and reduces apoptosis in vitrification-thawed ovaries. These findings provide insight into the spatiotemporal dynamics during ovarian vitrification and thawing, aiding in prioritizing therapeutic strategies for pre- and post-cryopreservation interventions.
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6. ⭐ GSE244508 ITGB1 是一种 TNBC 肿瘤微环境依赖性免疫调节剂

• ✍️ 作者：未知作者
• 🏷️ 关键词：tumor、immune、tumor microenvironment
• 📝 描述：Contributors : Nuozi Song ; Siqi Chen ; Mingye FengSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensTumorigenesis and metastasis, as well as insufficient response and the emergence of resistance to immunotherapy, are frequently attributed to the intricate interplay between cancer cells and tumor microenvironment (TME). Cancer cells significantly contribute to the recruitment of tumor-infiltrating leukocytes, which, in turn, directly regulate cancer cell proliferation and viability. Comprehending the mechanism and key regulators of the crosstalk between cancer cells and immune components in the TME is imperative for developing efficacious immunotherapeutic interventions. Here, through an in vivo CRISPR screen targeting cell surface genes, we identify ITGB1 as a central arbiter dictating the tumorigenicity of triple-negative breast cancer (TNBC). ITGB1 mediates the establishment of pro-tumorigenic TME by orchestrating tumor-associated myeloid populations and impeding T cell infiltration, while transducing pro-survival signaling from the tumor-favorable milieu into TNBC cells, to bolster tumor development.
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7. ⭐ GSE327731 一项社区机器学习挑战，旨在预测基因扰动对癌症免疫疗法中T细胞分化的影响

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、T cell、regex:immuno(logy|therapy|suppression)
• 📝 描述：Contributors : Jiaqi Zhang ; Marc A Schwartz ; Mohammed Mutaher ; Oluwatomisin Olajide ; Yuri Pritkyin ; Orr Ashenbrg ; Nir Hacohen ; Caroline UhlerSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusPerturbations of genes with functional importance in T cells could be used to change the distribution of CD8 T cell states to enhance anti-tumor functions for cancer immunotherapies. We launched a world-wide computational challenge to predict the effects of gene perturbations and to devise objective functions for prioritizing gene perturbations that lead to desired T-cell state distributions. We supported the challenge by generating a single-cell Perturb-seq dataset profiling the effect of knocking out 73 individual expert-defined genes in T cells transferred into a mouse melanoma model. We compared the top algorithms developed by participants, and found that performance was primarily determined by the prior data used for gene feature representation, with perturbational data derived features, proving most effective. Experimental validation of the top 61 genes nominated by the algorithms revealed that perturbation of Ndufv2 and Dimt1 reached the defined objective and biased differentiation toward desired states.
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8. ⭐ GSE328176 单细胞 RNA 测序揭示益气化郁解毒方通过调节巨噬细胞趋化性缓解急性呼吸窘迫综合征

• ✍️ 作者：未知作者
• 🏷️ 关键词：macrophage、sequencing、single-cell
• 📝 描述：Contributor : Boyue WangSeries Type : Expression profiling by high throughput sequencingOrganism : Rattus norvegicusIntegrated network pharmacology, single-cell RNA sequencing, and experimental analyses revealed that Yiqi Huayu Jiedu Formula (YQHYJDF) protects lung tissue by inhibiting macrophage chemotaxis and neutrophil recruitment through suppression of proinflammatory cytokines IL-6, IL-1β, and TNF-α, PI3K/AKT, MAPK, and NF-κB signaling, and downregulation of chemokines CCL2, CCL7, and CCL12.
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9. GSE325631 T调节细胞中TET功能的丧失导致前Treg细胞偏向于T滤泡辅助细胞，并通过自身抗体的产生引发自身免疫性疾病——脾脏和外周淋巴结

• ✍️ 作者：未知作者
• 🏷️ 关键词：lymph、regex:lymph(o|atic)?
• 📝 描述：Contributors : Kazumasa Suzuki ; Leo J Arteaga-Vazquez ; Bruno Villalobos Reveles ; Lot Hernández-Espinosa ; Isaac F López-Moyado ; Atsushi Odonera ; Daniela Samaniego-Castruita ; Ferhat Ay ; Arlet Lara-Custodio ; Patrick G Hogan ; Hugo Sepulveda ; Anjana RaoSeries Type : OtherOrganism : Mus musculusT regulatory cells (Treg cells) express the transcription factor FOXP3 and maintain immune homeostasis by attenuating effector responses. Treg cells are prone to lose FOXP3 and convert to pathological ‘ex-Treg’ cells under conditions of strong or chronic inflammation. One mechanism for loss of FOXP3 expression involves increased DNA methylation of intronic enhancers CNS1 and CNS2 in the Foxp3 locus; these enhancers are maintained in a demethylated state by TET enzymes, 5-methylcytosine (5mC) dioxygenases that generate 5-hydroxymethylcytosine (5hmC) and other oxidized methylcytosines that are essential intermediates in all pathways of DNA demethylation. We previously showed that FOXP3+ Treg cells from Tet2/3-deficient (Tet2/3 DKO) mice displayed increased methylation of CNS1 and CNS2 and converted to FOXP3-negative ex-Treg cells considerably more efficiently than WT Treg cells. Here we extend our previous analysis of Foxp3-Cre Tet2/3fl/fl mice. We classified the mice as DKO-moderate or DKO-severe based on the total number of leukocytes in the spleen and peripheral lymph nodes and investigated the phenotypic and molecular basis for the progressive inflammation occurring in these mice. RNA-seq as well as histological and immunocytochemical analyses showed a striking expansion of T follicular helper (Tfh) cells and plasma cells in Tet2/3 DKO-severe mice. And single-cell (sc) RNA-seq analyses suggested that this was due to skewed differentiation of both Tet2/3 DKO FOXP3+ Treg cells and Tet2/3 DKO FOXP3– ex-Treg cells into Tfh-like cells. Base-resolution “6-base” sequencing showed the expected loss of 5hmC and increased 5mC in Tfh cells purified from Tet2/3 DKO-severe mice, and suggested that the observed bias in gene expression patterns could arise either from a direct increase in methylation of essential enhancers due to TET deficiency, or from interference with binding of methylation-sensitive transcriptional repressors including CTCF.
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10. GSE319803 CENPF 过表达通过 MYC 通路促进肝细胞癌细胞的 G1/S 细胞周期转换

• ✍️ 作者：未知作者
• 🏷️ 关键词：carcinoma、pathway
• 📝 描述：Contributors : Saiping Qi ; Donghu Zhou ; Sisi Chen ; Liying Sun ; Jian HuangSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensCentromere protein F (CENPF), a mitosis-related protein, is overexpressed in hepatocellular carcinoma (HCC) and has emerged as a promising biomarker for early HCC. However, with ultra-large molecular weight of 358kDa of CENPF, no study has directly explored its carcinogenicity with an overexpression model. In the present study, a CRISPR/dCas9 system was applied to construct the CENPF overexpression model. CENPF was upregulated and downregulated to analyze its functions in vitro. CENPF knockdown cell models showed inhibition of HCC proliferation. Notably, as a cell cycle protein with high constitutive expression in G2/M phase, CENPF overexpression cell models also showed inhibitory effects, probably due to the toxic effect of excessive CENPF expression on G2/M transition. However, in both CENPF downregulation and overexpression models, cell cycle assays showed CENPF promoted G1/S transition in HCC cells. RNA-seq showed that CENPF overexpression activated the MYC pathway, thereby promoting G1/S transition. The rescue experiment indicated that the MYC pathway inhibitor 10058-F4 counteracted the G1/S transition induced by CENPF overexpression in HCCLM3 cells. CENPF overexpression might facilitate HCC cells G1/S cell cycle transition via the MYC pathway.
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详细内容（全部2条）

1. 一种新的RNA测序方法揭示了耐药肺癌细胞中隐藏的多样性

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、sequencing
• 📝 描述：RNA sequencing with sc-rDSeq captures diverse RNA types, revealing hidden tumor heterogeneity and drug-resistant cell populations in lung cancer…
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2. 人工智能可识别皮肤癌的早期风险模式

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer
• 📝 描述：A massive Swedish study shows that AI can spot people at higher risk of melanoma using routine health data. Advanced models significantly outperformed basic methods, identifying high-risk groups with striking accuracy. Some individuals flagged by the system had up to a 33% chance of developing melanoma within five years. This approach could pave the way for smarter, more targeted screening.
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• GSE317568 整合素β3缺乏通过CD40-CD40L轴促进B细胞过度活化，从而引发自发性肺部炎症
• GSE315511 中和抗体对VEGFA和/或ANG-2的抑制作用可减弱氧诱导的新血管生成和炎症
• GSE313263 MIZ-1（c-Myc 相互作用锌指蛋白-1，ZBTB17）是有效 B 细胞受体信号传导所必需的 [RNA-seq]
• GSE313262 MIZ-1（c-Myc 相互作用锌指蛋白-1，ZBTB17）是有效 B 细胞受体信号传导所必需的 [ChIP-seq]
• GSE311231 SBNO1 和 TAF4 的染色质免疫沉淀测序 (ChIP-seq)
• GSE304937 小鼠鼻部形态发生的单细胞分辨率连续时间图谱 [scRNA-seq]
• GSE287988 通过RNA测序鉴定了肝癌中COP1基因敲低后的基因变化
• GSE234192：愈伤组织在愈伤组织诱导培养基上培养7天和12天后收获的愈伤组织的单细胞RNA测序
• GSE328096 单细胞 RNA 测序揭示 Epac1 缺失可减弱缺血性视网膜病变中 Müller 胶质细胞的病理激活
• GSE305395 PGC-1α通路失调破坏脊髓延髓肌萎缩症小鼠模型中的肌纤维分化[AR113Q RNA-Seq]
• GSE305394 PGC-1α通路失调破坏SBMA​​小鼠模型中的肌纤维分化[ChIP-Seq]
• GSE320375 按需表达GLUT3可增强CAR-T细胞的代谢适应性和抗肿瘤疗效，同时预防胶质母细胞瘤的毒性
• GSE270548 细胞表面免疫受体对群体感应信号的感知增强植物抗病性
• GSE319951 胰腺肿瘤间质液对PDAC细胞转录反应的影响
• GSE318865 胎盘基因特征与新生儿高脂肪含量相关：免疫细胞激活的作用
• GSE318662 ATP合成酶体有助于恶性乳腺癌中高效的能量流动
• GSE315825 非洲绿松石鳉雄性肝脏衰老标志物的鉴定
• GSE314154 STAG2 缺失增强 EWS-FLI1 驱动的微卫星增强子活性，促进尤文氏肉瘤的侵袭性 [RNA-Seq]
• GSE314152 STAG2 缺失增强 EWS-FLI1 驱动的微卫星增强子活性，促进尤文氏肉瘤的侵袭性 [ChIP-Seq]
• GSE314150 STAG2 缺失增强 EWS-FLI1 驱动的微卫星增强子活性，促进尤文氏肉瘤的侵袭性 [ATAC-seq]
• GSE313768 人类反应性星形胶质细胞的时间调控揭示了其抗原呈递能力
• GSE312836 代谢应激揭示广泛存在的未甲基化帽mRNA
• GSE311638 心肌细胞来源的TGFB3可减轻心力衰竭中的心肌纤维化并保护心脏功能
• GSE311232 利用RNA测序分析在HCC细胞系Hep3B中敲低SBNO1后的基因表达
• GSE311155 小鼠脓毒症后髓系来源抑制细胞中年龄和性别驱动的转录和代谢多样性
• GSE307577 人类中枢神经系统活性T细胞的分离方案
• GSE306297 黏连蛋白介导的环挤出和增强子相关因子对 Sox2 与其远端增强子的环化有累加贡献 [ATAC-seq]
• GSE305558 单细胞分析揭示老年人骨髓中存在 RAB13+ 内皮细胞和促纤维化间充质细胞
• GSE304339 小鼠鼻部形态发生的单细胞分辨率连续时间图谱
• GSE298758 DCPS 通过 P 小体调控调节 TDP-43 介导的神经退行性变 [RNA-seq]
• GSE297631 抗PD-1抗体耐受的KLN205细胞的表达数据
• GSE297630 对照或抗PD-1抗体耐受的LLC细胞的表达数据
• GSE297106 脂质代谢缺陷是Diamond-Blackfan贫血综合征的潜在致病因素
• GSE296604 芬太尼诱导的快速皮质损伤和心肺骤停与小鼠模型中细胞凋亡和免疫反应的非典型动态有关 [miRNA]
• GSE296051 芬太尼诱导的小鼠模型快速皮质损伤和心肺骤停与细胞凋亡和免疫反应的非典型动态相关
• GSE286360 血管生成素-2 通过促进血脑屏障破坏和神经炎症加剧阿尔茨海默病。
• GSE277244 SBNO1 在肝癌细胞系 HLF 中的敲低
• GSE276017 红细胞 ACKR1 缺乏症加重免疫介导的肾脏疾病
• GSE270112 Gpnmb 是斑马鱼心脏再生过程中免疫反应和纤维化反应所必需的
• GSE267211 Ogg1Tg 小鼠白色脂肪组织、腓肠肌和肝脏组织的转录组学分析。
• GSE252138 RNA-seq 三组小鼠海马体。
• GSE234191 对在愈伤组织诱导培养基上培养7天和12天后收获的愈伤组织进行批量RNA测序
• GSE327968 肥胖驱动的PTPN11突变白血病中GLP1R-IL17A轴的基因表达谱分析
• GSE325861 巨噬细胞信号传导与儿童原发性硬化性胆管炎中胆管周围成纤维细胞的纤维化程序激活相关。
• GSE312816 犬粪便宏基因组学特征与寿命变异：来自犬衰老项目的研究结果
• GSE310256 绘制自关联染色质枢纽图谱，揭示 Id 蛋白是耗竭 T 细胞命运的关键决定因素
• GSE305396 PGC-1α通路失调破坏SBMA​​小鼠模型中的肌纤维分化[snRNA-Seq]
• GSE303271 儿童自身免疫性肝病患者肝脏活检的 RNA 测序
• GSE274219 非倍体选择乳腺癌驱动基因的获得
• GSE328076 LHX2驱动TP53/RB1缺陷型前列腺癌的神经内分泌转化
• GSE327761 对暴露于敌草快（1/5 LC50）72 小时的白纹伊蚊幼虫进行 mRNA 测序分析
• GSE310639 葡萄糖处理和RabGTPase沉默的人类永生化足细胞来源的细胞外囊泡的小RNA测序