详细内容（前10条）

1. ⭐ GSE304458 单细胞 RNA-Seq 分析用于表征接受抗 PD-1 免疫治疗期间补充铁剂的乳腺肿瘤浸润免疫细胞

• ✍️ 作者：未知作者
• 🏷️ 关键词：tumor、immune、regex:immuno(logy|therapy|suppression)、RNA-seq、single-cell
• 📝 描述：Contributors : Qingfei Wang ; Mateusz OpyrchalSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusIn previous study, we demonstrated that iron supplementation augmented the antitumor effect of PD-1 based immunotherapy in triple-negative breast cancer models. To gain a more profound understanding into whether and how iron plus PD-1 antibody combination influences tumor immune microenvironment to exert better therapeutic activity, in this study, we performed single cell RNA-sequencing with PIP-seq to profile and compare tumor infiltrated CD45+ cells derived from control, iron or PD-1 antibody alone, and combination treated E0771 tumors.
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2. ⭐ GSE305350 CD27激动剂增强长效CD4⁺ T细胞疫苗反应，这对2种抗肿瘤免疫至关重要

• ✍️ 作者：未知作者
• 🏷️ 关键词：tumor、immunity、vaccine、T cell
• 📝 描述：Contributors : Zachary C Hartman ; Bin-Jin Hwang ; David T Severson ; Erika J CrosbySeries Type : Expression profiling by high throughput sequencing ; OtherOrganism : Mus musculusPatients with metastatic breast cancer were vaccinated with dendritic cell (DC) vaccine targeting HER2, and all seven survived >18 years. PBMC analysis revealed HER2-specific CD27⁺ memory CD4⁺ and CD8⁺ T cells, suggesting that CD27 signaling supports durable immune memory. We tested this by combining an anti-CD27 agonist antibody (Varlilumab) with a HER2 vaccine, which enhanced HER2-specific responses, particularly long-lived CD4⁺ memory T cells detectable up to 300 days post-vaccination. CD27 agonism improved tumor control (~40% regression) compared to vaccine alone (~6%), and synergy with PD-1 blockade led to complete tumor rejection in ~90% of mice. CD4⁺ T cells were essential for this effect, as shown by depletion and adoptive transfer experiments, while CD8⁺ T cells played a less critical role. We utilized combined scRNA-seq and TCR sequencing to identify expanded clonotypes and increased CD8+ and CD4+ functional subsets with combined CD27 agonism and vaccination as well as vaccination alone. These findings demonstrate that antigen-specific huCD27⁺ CD4⁺ T cells are key effectors of vaccine-induced immunity and support CD27 agonism as a promising strategy to enhance therapeutic cancer vaccination.
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3. ⭐ GSE319155 转化型小细胞肺癌中肿瘤谱系可塑性和免疫微环境的单细胞分析

• ✍️ 作者：未知作者
• 🏷️ 关键词：tumor、cancer、immune、single-cell
• 📝 描述：Contributors : Jie Huang ; Zhenhua Zhang ; Guodi Cai ; Junjian WangSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensBackground The transformation of non-small cell lung cancer (NSCLC) into small cell lung cancer (SCLC) is a recognized treatment resistance mechanism, most often arising from EGFR-mutant lung adenocarcinoma (LUAD). However, the underlying mechanisms of transformation remain poorly understood. Methods Single-cell RNA sequencing was employed to analyze the tumor cell heterogeneity and to map the intratumoral immune cell landscape of 73,195 cells from five LUAD, three transformed small cell lung cancer (T-SCLC) and four SCLC patients. Multiplex immunofluorescence (mIF) staining and in vitro studies were further conducted to validate the stem-like feature of a malignant cell cluster and the enrichment and the function of interferon-stimulated gene-positive (ISG+) lymphocytes in transformation. Results Although increased intratumoral heterogeneity was observed upon SCLC transformation, a stem-like malignant cell subpopulation was identified to recur across subtypes and groups as the pioneering force of lineage plasticity for SCLC transformation. Further mIF staining and transcription factor analysis validated the stem-like feature. Additionally, tumor immune microenvironment (TIME) analysis revealed that ISG+ T cells and B cells were enriched in T-SCLC. Further cell co-culture analyses disclosed that ISG+ lymphocytes promoted neuroendocrine differentiation in LUAD cells via type I interferons (IFN-Is). Deciphering cell-cell interactions revealed that the stem-like malignant cells might activate and attract ISG+ T cells. Finally, we developed an ISG-associated gene signature that significantly correlates with poor prognosis in LUAD. Conclusion Our findings provide a comprehensive understanding of the lineage plasticity and the immune landscape in T-SCLC, highlighting the crucial role of the stem-like cell cluster and ISG+ lymphocytes in LUAD-to-SCLC transformation.
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4. ⭐ GSE301741 单细胞分析突显了恶性细胞 IFN/MHC-II 在头颈部鳞状细胞癌免疫治疗反应中的重要性

• ✍️ 作者：未知作者
• 🏷️ 关键词：carcinoma、MHC、regex:immuno(logy|therapy|suppression)
• 📝 描述：Contributors : Michael Mints ; Reilly A Sample ; Anuraag S Parikh ; Jesse M Zaretsky ; Itay Tirosh ; Sidharth V PuramSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensFor many cancers, including head and neck squamous cell carcinoma (HNSCC), response rates to immunotherapy remain modest, with limited ability to predict responders. Previous studies that characterized cellular changes associated with immunotherapy in HNSCC focused on immune cells, providing limited insight into malignant cell responses. Motivated by this gap, we performed single cell RNA-sequencing on 16 HNSCC patients pre- and post-neoadjuvant pembrolizumab treatment. We identified a malignant-interferon (IFN)/MHC-II program in malignant cells, characterized by expression of MHC-II and interferon response genes, which was associated with tumor response to pembrolizumab. We validated malignant cell MHC-II expression at the protein level and characterized its relationship with surrounding immune subsets via multiplexed immunofluorescence. In a murine HNSCC model, IFN-γ-induced malignant cell MHC-II expression marked tumors with favorable immune microenvironments and sensitivity to immunotherapy. Finally, we confirmed pre-treatment expression of the malignant-IFN/MHC-II program as marker of response through deconvolution of bulk RNA-seq data from an independent cohort of 25 pembrolizumab-treated HNSCC patients. Beyond identifying malignant cell MHC-II expression and the malignant-IFN/MHC-II program as potential biomarkers for immunotherapy response in HNSCC, our work provides additional insights into the specific and important role of malignant cells in immunotherapy.
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5. ⭐ GSE318768 HPV相关DNA甲基化改变在时空上塑造头颈部肿瘤微环境

• ✍️ 作者：未知作者
• 🏷️ 关键词：tumor、tumor microenvironment、methylation
• 📝 描述：Contributors : Sabrina Wurzba ; Mariana MaschiettoSeries Type : Methylation profiling by genome tiling arrayOrganism : Homo sapiensThis study explores DNA methylation profile and their impact on tumor microenvironment (TME) of head and neck cancer (HNC). By integrating advanced high-throughput platforms, including Human Methylation 450K BeadChip microarrays and single-cell imaging mass cytometry (IMC), we identified distinct methylation signatures and immune landscapes in HNC associated with HPV-positive vs. HPV-negative tumors. Differentially methylated sites between HPV-positive and HPV-negative tumors showed enrichment for immune system regulatory pathways, with marked signatures of T lymphocyte regulation. To better understand the relationship between DNA methylation and tumor microenvironment regulation, we sought to evaluate the immunological components from a spatial perspective and observed that in HPV-positive tumors, T lymphocytes appear to activate a self-regulatory mechanism, while in HPV-negative tumors this mechanism is blocked by the action of fibroblasts, which are the cells that interact most with T lymphocytes. The spatial dynamics within the TME regulated by epigenetic mechanisms pave the way for more precise clinical decision-making and personalized therapies for HNC patients.
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6. ⭐ GSE289349 脑膜瘤微环境蕴含丰富的免疫图谱，具有治疗意义（单细胞 RNA 测序部分）

• ✍️ 作者：未知作者
• 🏷️ 关键词：immune、RNA-seq、single-cell
• 📝 描述：Contributors : Wenya Linda Bi ; Xiaopeng Guo ; Joseph DriverSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensEffective therapeutic targets are urgently needed for aggressive meningiomas. Given the pivotal role of immune microenvironment in tumor progression, we developed a comprehensive atlas of the meningioma microenvironment. Using single-cell and bulk techniques, we revealed a rich immune infiltrate in 2,610 meningiomas, among the highest observed across 34 human cancer types. Macrophages predominated in meningioma, contrasting with the lymphoid dominance of peripheral blood, with meninges exhibiting an intermediate immune profile. Cellular states and phenotypes of both immune and tumor cells shift during tumor progression toward an earlier-stage immune-suppressive and proliferative profile in aggressive meningiomas. Using ex vivo patient-derived tumor organoids, we demonstrated inducible responses to STING activation, marked by elevated cytokine release, which were synergistic when combined with PD-1 blockade. Together, these findings provide an extensive resource on the cellular heterogeneity of the meningioma microenvironment and provide a framework for rational therapeutic modeling and strategy development.
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7. GSE301651 膀胱癌患者的单细胞测序

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、sequencing
• 📝 描述：Contributors : Qiuli Liu ; Weihua Lan ; Jun Jiang ; Weiming LuoSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensTo achieve a more profound comprehension of the bladder tumor microenvironment, we have meticulously curated single-cell samples from 11 patients diagnosed with bladder cancer. Our comprehensive analysis not only elucidates the intricate heterogeneity among distinct cellular subpopulations within the tumor but also uncovers the underlying cellular interactions. These findings collectively serve as an invaluable asset, paving the way for the development of innovative and targeted therapeutic strategies for bladder cancer.
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8. GSE301648 前列腺癌对BL-B01D1耐药机制的研究

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、resistance
• 📝 描述：Contributors : Bangwei Fang ; Yao ZhuSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusMetastatic castration-resistant prostate cancer (mCRPC) remains a lethal disease with limited treatment options following resistance to AR signaling inhibitors. Despite the known roles of EGFR and HER3 in prostate cancer progression, prior therapies targeting this pathway have failed clinically. In this study, we evaluate the therapeutic potential of BL-B01D1, a bispecific antibody–drug conjugate (ADC) targeting EGFR and HER3, in prostate cancer models. BL-B01D1 exhibited potent, target-dependent cytotoxicity across prostate cancer cell lines, xenografts, and patient-derived organoids. Mechanistically, we identified ABCG2 upregulation as a driver of acquired resistance, and pharmacological inhibition of ABCG2 restored drug sensitivity. These findings establish BL-B01D1 as a promising therapeutic strategy in mCRPC and nominate ABCG2 as a potential combination target to overcome resistance.
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9. GSE291247 DLEU2 通过 E2F1 的相互正反馈激活促进宫颈鳞状细胞癌的细胞运动和免疫浸润

• ✍️ 作者：未知作者
• 🏷️ 关键词：carcinoma、immune
• 📝 描述：Contributor : Min HeSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensCancer metastasis is the primary cause of high mortality in patients with cervical squamous cell carcinoma (CESC). The invasive ability of cancer cells is enhanced by increased cell motility, which contributes to their distant metastasis. The oncogenic lncRNA DLEU2, implicated in tumor progression and prognosis, remains understudied in CESC. This study investigated how DLEU2 enhances cell motility and regulates immune infiltration in CESC. We found that DLEU2 was upregulated in CESC tissues and correlated with poor prognosis in advanced-stage patients. Functionally, DLEU2 knockdown suppressed cell migration and invasion, while its overexpression enhanced motility. Mechanistically, DLEU2 knockdown altered the expression of downstream genes related to cell motility and adhesion. An interaction between DLEU2 and E2F1 protein was confirmed by RNA pulldown assay. E2F1 expression was downregulated or upregulated after DLEU2 knockdown or overexpression, respectively, while DLEU2 expression was also upregulated after E2F1 overexpression. Therefore, DLEU2 may form a regulatory loop with E2F1 to activate the transcription of downstream genes related to cell motility and adhesion. Additionally, E2F1 expression strongly correlated with immune infiltration levels (e.g., T cells, Tregs, monocytes, mast cells), and DLEU2 exhibited a parallel immune cell abundance pattern, suggesting indirect immunomodulatory effects via E2F1. These findings propose that the DLEU2-E2F1 axis promotes CESC metastasis by dual mechanisms: enhancing tumor cell motility and reshaping the immune microenvironment. The study highlights DLEU2 as a potential therapeutic target to disrupt metastatic pathways and immune evasion in CESC. Further validation is needed to explore clinical applications of targeting this regulatory network.
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10. GSE290273 KLF5 调控表观遗传修饰，驱动人类胰腺导管腺癌转移 [RNA-Seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：RNA-seq、epigenetic
• 📝 描述：Contributors : Masahiro Maeda ; Weqiang Zhou ; Kenna Sherman ; Andrew P FeinbergSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensWe previously showed that distant metastases of human pancreatic ductal adenocarcinoma (PDAC) are driven by epigenetic alterations in the primary tumor rather than by additional mutations1. However, the specific epigenetic driver genes responsible have not been identified. To identify genes modulating these changes, we performed a pooled CRISPR genetic screen and single-cell multiomics analysis using patient-derived xenograft cell lines established from a primary PDAC tumor and a distant metastasis from the same patient. We identified KLF5 as the leading epigenetic modulator regulating progression in distant metastasis. Knockdown of KLF5 selectively reduced the growth of the distant metastasis and caused a large-scale increase in heterochromatin. Single-cell multiome ATAC and gene expression analysis revealed two clusters with high KLF5 expression and increased expression and chromatin accessibility of stem cell markers and genes related to migration and epithelial to mesenchymal transition. Further, we identified two epigenetic modifiers, NCAPD2 and MTHFD1, which are regulated by KLF5 and result in these increases in heterochromatin when knocked down. These data provide a sequence of epigenetic modulators, modifiers and mediators which shape the metastatic landscape of pancreatic cancer.
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1. 当免疫细胞停止对抗癌症并开始帮助它时

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、immune
• 📝 描述：Scientists have uncovered a surprising way tumors turn the immune system to their advantage. Researchers at the University of Geneva found that neutrophils—normally frontline defenders against infection—can be reprogrammed inside tumors to fuel cancer growth instead. Once exposed to the tumor environment, these immune cells begin producing a molecule called CCL3 that actively promotes tumor progression.
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2. 人工智能模型或可改进RNA测序研究

• ✍️ 作者：未知作者
• 🏷️ 关键词：sequencing
• 📝 描述：An AI-powered model improves RNA sequencing accuracy by identifying and removing chimera artifacts in nanopore direct RNA data, strengthening transcript annotation and gene fusion analysis…
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3. 罗格斯大学开发出一种用于分析癌症基因组数据的新工具，有望改善治疗效果。

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer
• 📝 描述：A new computational tool uses RNA sequencing and genomic data to distinguish real tumor-associated microbes from contamination, clarifying how microbes may influence cancer…
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• GSE205797 对 Wt1CreERT2;Srsf3+/+ 和 Wt1CreERT2; Srsf3fl/fl 胚胎心脏的 E13.5 和 E15.5 心外膜及心外膜衍生细胞进行单细胞 RNA 测序
• GSE317012 人类肾脏活检组织的单细胞分析揭示了上皮细胞和免疫细胞对BK多瘤病毒感染的反应
• GSE299894 神经元 SEL1L-HRD1 ERAD 调控一碳代谢，对运动功能和存活至关重要
• GSE274050 局灶性白质病变驱动灰质炎症、神经元功能障碍和突触丢失
• GSE319148 靶向IGF2BP1可逆转CTL富集型胰腺癌的免疫逃逸
• GSE318762 组蛋白调节剂小分子库筛选揭示 Kdm5b 是心肌细胞中细胞周期基因表达的主要表观遗传调节因子
• GSE317224 GCLC抑制剂增强谷胱甘肽代谢途径抑制在SMARCB1缺陷型横纹肌样瘤中的抗肿瘤疗效
• GSE314070 佐剂mRNA疫苗肠外接种可诱导新生小鼠产生针对轮状病毒的保护性黏膜免疫
• GSE296166 淋巴源性神经降压素在压力超负荷诱导的心脏损伤中的作用
• GSE296165：对野生型小鼠横向主动脉缩窄或假手术后20天心脏中获取的非心肌细胞进行单细胞RNA测序
• GSE290805 脑膜瘤微环境蕴含丰富的免疫图谱，具有治疗意义（批量 RNA 测序部分）
• GSE312204 克隆偏倚决定了结肠癌驱动突变转化的可及性
• GSE307289 胎盘DNA甲基化与母亲社会经济地位：SPAH研究
• GSE300187 无义介导的mRNA衰变（NMD）通路保护多能干细胞中的端粒
• GSE290274 KLF5 调控表观遗传修饰，驱动人类胰腺导管腺癌转移 [多组学]
• GSE261054 RNAPII 绕过阻断损伤揭示了 DNA 损伤诱导的新型应激 [RNA-seq]
• GSE261052 RNAPII 绕过阻断损伤揭示了 DNA 损伤诱导的新型应激 [ChIP-seq]
• GSE319121 利用鲑鱼降钙素治疗胶质母细胞瘤：通过激活Hippo通路靶向YAP/TAZ
• GSE318532 靶向肺泡II型细胞中的脂质代谢蛋白FASN和GPAM可减少肺转移
• GSE316139 研究人源化 TLR8 在自发性小鼠抗磷脂抗体诱导妊娠丢失模型中对胎盘微环境免疫细胞动力学的影响
• GSE307707 BET抑制剂靶向致病性间质巨噬细胞，以限制闭塞性细支气管炎慢性GVHD中的抗体介导纤维化。
• GSE300209 对健康和 MASH 小鼠肝脏的单核 RNA 测序分析揭示了 MASH 条件下肝细胞的异质性
• GSE300162：MASH饮食喂养下肝细胞特异性敲除Themis基因的小鼠肝脏单核RNA测序分析
• GSE300143 小鼠肝脏在 MASH 饮食喂养条件下进行 Themis 消融的批量 RNA-seq 分析
• GSE296356 Fli1 在营养应激期间抑制蛋白质稳态，从而限制 NK 细胞在实体瘤中的持久性 [CUT&Tag_H3K27ac_Mouse]
• GSE296355 Fli1 在营养应激期间抑制蛋白质稳态，从而限制 NK 细胞在实体瘤中的持久性 [CUT&Tag_FLI1_Human]
• GSE296354 Fli1 在营养应激期间抑制蛋白质稳态，从而限制 NK 细胞在实体瘤中的持久性 [CUT&Tag_Fli1_Mouse]
• GSE296353 Fli1 在营养应激期间抑制蛋白质稳态，从而限制 NK 细胞在实体瘤中的持久性 [ATAC-Seq_Human]
• GSE296352 Fli1 在营养应激期间抑制蛋白质稳态，从而限制 NK 细胞在实体瘤中的持久性 [ATAC-Seq_Mouse]
• GSE296351 Fli1 在营养应激期间抑制蛋白质稳态，从而限制 NK 细胞在实体瘤中的持久性 [RNA-Seq_Human]
• GSE296350 Fli1 在营养应激期间抑制蛋白质稳态，从而限制 NK 细胞在实体瘤中的持久性 [RNA-Seq_Mouse]
• GSE292046 针对 MGMT 未甲基化胶质母细胞瘤的佐剂个性化多价新抗原 DNA 疫苗接种：一项 I 期试验 [scRNA-seq]
• GSE292045 针对 MGMT 未甲基化胶质母细胞瘤的佐剂个性化多价新抗原 DNA 疫苗接种：一项 I 期试验 [RNA-seq]
• GSE290812 ATEVs 和 EV-DNA 对免疫原性较差的胰腺癌细胞系转录谱的影响
• GSE319161 抑制 MAPK p38a 可克服 FPR1 功能缺失突变引起的癌症免疫监视缺陷
• GSE319015 mtDNA泄漏通过cGAS-STING驱动的神经炎症和丝氨酸代谢重编程促进神经元-胶质细胞串扰诱发癫痫
• GSE318806 P21+TREM2+-衰老巨噬细胞促进炎症衰老和代谢功能障碍相关的脂肪肝疾病。[血液]
• GSE318804 P21+TREM2+衰老巨噬细胞促进炎症衰老和代谢功能障碍相关的脂肪肝疾病。[macro_senescence]
• GSE318802 P21+TREM2+-衰老巨噬细胞促进炎症衰老和代谢功能障碍相关的脂肪肝疾病。[Trem2ko]
• GSE318801 P21+TREM2+-衰老巨噬细胞促进炎症衰老和代谢功能障碍相关的脂肪肝疾病。
• GSE318719 内皮细胞 DNA 损伤通过 ET-1/ETAR 信号传导协调心肾代谢功能障碍。
• GSE318615 硫酸锌刺激的 Siniperca chuatsi MFF-1 细胞的 RNA-seq 分析
• GSE318614 鲻鱼脾脏对ISKNV感染的单细胞转录组分析
• GSE318442 TRIM28 调控 SUMO-泛素相互作用以稳定 PPARG 并促进膀胱癌进展
• GSE318429 剪接因子SF3B6在肝细胞癌中的作用和治疗潜力
• GSE318329 RNA-Seq定量分析伊马替尼耐药细胞来源外泌体对CML细胞转录组的调控
• GSE318280 COL17A1 的谱系特异性致癌重编程在头颈部干细胞中构建促侵袭性和缺氧适应性微环境
• GSE308682 利用单细胞RNA测序技术对K562细胞中的7个转录因子进行CRISPRi筛选并敲低
• GSE302045 未受影响的结肠、结直肠癌和腹膜转移中的固有淋巴细胞
• GSE289388 铁木皂苷AIII通过抑制CAR-Tr​​eg细胞增强CAR-T细胞的效力并预防复发
• GSE224791 P小体中RNA隔离与染色质结构之间的相互作用维持髓系白血病