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1. ⭐ GSE268015 间质性肺炎引起的肺鳞状细胞癌的空间转录组分析揭示了肿瘤异质性。

• ✍️ 作者：未知作者
• 🏷️ 关键词：tumor、carcinoma、spatial、transcriptome
• 📝 描述：Contributors : Koto Ukon ; Satoshi Nojima ; Eiichi MoriiSeries Type : OtherOrganism : Homo sapiensInterstitial pneumonia (IP) is a refractory disease that causes severe inflammation and fibrosis in the interstitium of the lungs, often resulting in the development of lung cancer (LC) during treatment. Previous studies have demonstrated that the prognosis of LC complicated by IP is inferior to that of LC without IP. It is therefore of the utmost importance to gain a deeper understanding of the heterogeneity of such tumors. In the present study, we conducted spatial transcriptome analysis of squamous cell carcinoma arising from IP. The results suggested involvement of the glucocorticoid receptor pathway in treatment resistance. Immunostaining of squamous cell carcinoma specimens from patients with IP demonstrated that the tumors expressed NR3C1 to varying degrees. Furthermore, higher NR3C1 expression levels were associated with a significantly increased risk of recurrence. Our results point to a novel subtype of lung squamous cell carcinoma. Further analysis of the molecular mechanisms associated with this subtype may facilitate the development of novel diagnostic criteria and therapeutic approaches.
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2. ⭐ GSE310307 免疫抑制性肿瘤微环境 (TME) 响应弥漫性大B细胞淋巴瘤 (DLBCL) 通过淋巴系统扩散至腹股沟淋巴结。

• ✍️ 作者：未知作者
• 🏷️ 关键词：TME、lymph、regex:lymph(o|atic)?
• 📝 描述：Contributors : Kamil Chahine ; Santiago F GonzálezSeries Type : Expression profiling by arrayOrganism : Mus musculusThe cellular components of the tumor microenvironment (TME) in non-Hodgkin B cell lymphoma demonstrate remarkable diversity. TME cells undergo functional changes as a result of gene expression, epigenetic and metabolic rewiring. Thus, these cells are shown to be capable of exerting either tumor supportive or inhibitory activities. Here, we investigated the TME in the LN of murine mouse model of lymphatic dissemination of Eµ-myc lymphoma cells.
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3. ⭐ GSE303270 糖化 DNA 免疫沉淀测序 (GlyDIP-seq) 用于检测糖尿病特有的表观遗传效应 [ATAC-seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：sequencing、ATAC-seq、epigenetic
• 📝 描述：Contributors : Keitaro Ishii ; Yuka Imamura ; Bansal Ankush ; Sakurako Inoue ; Kojiro Terada ; Priscilla PanSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensDNA glycation, a non-enzymatic modification triggered by reactive metabolites such as methylglyoxal (MG), has been implicated in various metabolic and neurological disorders. However, its genome-wide distribution and biological consequences in the developing brain remain largely unexplored. To address this gap, we developed a novel method, GlyDIP-seq, which enables high-resolution profiling of glycation-derived DNA lesions (specifically N²-carboxyethyl-2’-deoxyguanosine, CEdG) across the genome.
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4. GSE330346 c-Myc 的光邻近标记揭示 SLK 是一种癌症特异性共调节因子 [RNA-Seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、RNA-seq
• 📝 描述：Contributors : Ryan R Milione ; Feifei Tong ; Kelsey L Wolfe ; Cameron J Douglas ; Sara B Linker ; Xinmeng Jasmine Mu ; James V Oakley ; Andrew R Nager ; Michalina Janiszewska ; Ciaran P SeathSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensTranscription factors (TFs) have long been aspirational therapeutic targets for the treatment of diseases, as their dysregulation is a common mechanism for altered cell states. Despite this, many TFs implicated in disease havedisordered structures and lack canonical binding pockets, rendering them non-trivial targets for small moleculebased therapies. Directly inhibiting TF function has proven difficult, but indirect inhibition by targeting the effector molecules that modulate TF function is a promising, yet underexplored, alternative approach. Here we report a strategy for capturing cancer-specific protein-protein interactions using context-dependent µMap photoproximity labeling. Using an intein-based method for catalyst conjugation in biochemically intact nuclei, we demonstrate that we can capture unique protein interactomes of c-Myc in healthy and cancerous prostate cell lines, and that these unique interactors can be mined to identify druggable vulnerabilities. We find that a cancerspecific c-Myc interactor, STE20 like kinase (SLK), selectively promotes c-Myc stabilization at the protein level, drives epithelial morphology, and is essential for tumorigenesis, validating it as a viable therapeutic target. Mechanistically, this stabilization is driven by SLK-mediated phosphorylation of c-Myc at serine 329, which antagonizes GSK3β-dependent phosphorylation of the c-Myc phosphodegron and effectively increases the stability of c-Myc. This cancer-selective interaction is enabled by a change in SLK splicing that promotes nuclear localization of the long isoform, rather than changes at the protein or total RNA level. Furthermore, analysis of cancer patient data shows a strong correlation between the SLK long splice isoform and expression of c-Myc targets across multiple tumor types. Importantly, the SLK-c-Myc interaction is validated in cancer cell lines from diverse tissues, suggesting this novel regulatory axis is broadly operative across human cancer.
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5. GSE330345 c-Myc 的光邻近标记揭示 SLK 是癌症特异性共调节因子 [ChIP-Seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、ChIP-seq
• 📝 描述：Contributors : Ryan R Milione ; Feifei Tong ; Kelsey L Wolfe ; Cameron J Douglas ; Sara B Linker ; Xinmeng Jasmine Mu ; James V Oakley ; Andrew R Nager ; Michalina Janiszewska ; Ciaran P SeathSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensTranscription factors (TFs) have long been aspirational therapeutic targets for the treatment of diseases, as their dysregulation is a common mechanism for altered cell states. Despite this, many TFs implicated in disease have disordered structures and lack canonical binding pockets, rendering them non-trivial targets for small molecule-based therapies. Directly inhibiting TF function has proven difficult, but indirect inhibition by targeting the effector molecules that modulate TF function is a promising, yet underexplored, alternative approach. Here we report a strategy for capturing cancer-specific protein-protein interactions using context-dependent µMap photoproximity labeling. Using an intein-based method for catalyst conjugation in biochemically intact nuclei, we demonstrate that we can capture unique protein interactomes of c-Myc in healthy and cancerous prostate cell lines, and that these unique interactors can be mined to identify druggable vulnerabilities. We find that a cancer-specific c-Myc interactor, STE20 like kinase (SLK), selectively promotes c-Myc stabilization at the protein level, drives epithelial morphology, and is essential for tumorigenesis, validating it as a viable therapeutic target. Mechanistically, this stabilization is driven by SLK-mediated phosphorylation of c-Myc at serine 329, which antagonizes GSK3β-dependent phosphorylation of the c-Myc phosphodegron and effectively increases the stability of c-Myc. This cancer-selective interaction is enabled by a change in SLK splicing that promotes nuclear localization of the long isoform, rather than changes at the protein or total RNA level. Furthermore, analysis of cancer patient data shows a strong correlation between the SLK long splice isoform and expression of c-Myc targets across multiple tumor types. Importantly, the SLK-c-Myc interaction is validated in cancer cell lines from diverse tissues, suggesting this novel regulatory axis is broadly operative across human cancer.
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6. GSE298780 糖化 DNA 免疫沉淀测序 (GlyDIP-seq) 用于检测糖尿病特有的表观遗传效应 [DIP-Seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：sequencing、epigenetic
• 📝 描述：Contributors : Keitaro Ishii ; Yuka Imamura ; Bansal Ankush ; Sakurako Inoue ; Kojiro Terada ; Priscilla PanSeries Type : OtherOrganism : Homo sapiensDNA glycation, a non-enzymatic modification triggered by reactive metabolites such as methylglyoxal (MG), has been implicated in various metabolic and neurological disorders. However, its genome-wide distribution and biological consequences in the developing brain remain largely unexplored. To address this gap, we developed a novel method, GlyDIP-seq, which enables high-resolution profiling of glycation-derived DNA lesions (specifically N²-carboxyethyl-2’-deoxyguanosine, CEdG) across the genome.
• 🔗 查看原文

7. GSE297897 RNA-seq 在用 PI3Ki (GDC-0941) 和 EZH2i (GSK126) 处理的 C4.2B 前列腺癌细胞系中。

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、RNA-seq
• 📝 描述：Contributors : Rhea Sahu ; Karen CichowskiSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensMen with advanced prostate cancer are typically treated with androgen deprivation therapy, but most ultimately develop resistance and incurable disease (e.g. castration-resistant prostate cancer (CRPC)). The majority of CRPCs overexpress the epigenetic enzyme EZH2 and harbor alterations in the PI3K pathway, providing two targetable pathways outside of AR. Here we show that EZH2 inhibitors synergize with PI3K, AKT, or mTORC1 inhibitors to kill CRPC in vitro and promote tumor regression in vivo. Strikingly, these agents trigger a catastrophic energy crisis by cooperatively suppressing glycolysis, the TCA cycle, and oxidative phosphorylation prior to cell death. EZH2 and PI3K pathway inhibitors achieve this by respectively inhibiting two key regulators of metabolism, MYC and HIF-1A, while concomitantly derepressing a pro-apoptotic stress sensor. Together, these studies reveal a promising therapeutic strategy for CRPC and demonstrate how metabolic plasticity can be fatally impaired by co-targeting upstream oncogenic nodes that converge on this important process.
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8. GSE297894 RNA-seq 在用 AKTi（ipatasertib）和 EZH2i（tazemetostat）治疗的 C4.2B 前列腺癌细胞系中。

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、RNA-seq
• 📝 描述：Contributors : Rhea Sahu ; Karen CichowskiSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensMen with advanced prostate cancer are typically treated with androgen deprivation therapy, but most ultimately develop resistance and incurable disease (e.g. castration-resistant prostate cancer (CRPC)). The majority of CRPCs overexpress the epigenetic enzyme EZH2 and harbor alterations in the PI3K pathway, providing two targetable pathways outside of AR. Here we show that EZH2 inhibitors synergize with PI3K, AKT, or mTORC1 inhibitors to kill CRPC in vitro and promote tumor regression in vivo. Strikingly, these agents trigger a catastrophic energy crisis by cooperatively suppressing glycolysis, the TCA cycle, and oxidative phosphorylation prior to cell death. EZH2 and PI3K pathway inhibitors achieve this by respectively inhibiting two key regulators of metabolism, MYC and HIF-1A, while concomitantly derepressing a pro-apoptotic stress sensor. Together, these studies reveal a promising therapeutic strategy for CRPC and demonstrate how metabolic plasticity can be fatally impaired by co-targeting upstream oncogenic nodes that converge on this important process.
• 🔗 查看原文

9. GSE296615 糖化DNA免疫沉淀测序（GlyDIP-seq）用于检测糖尿病特有的表观遗传效应

• ✍️ 作者：未知作者
• 🏷️ 关键词：sequencing、epigenetic
• 📝 描述：Contributors : Keitaro Ishii ; Yuka Imamura ; Bansal Ankush ; Sakurako Inoue ; Kojiro Terada ; Priscilla PanSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensDNA glycation, a non-enzymatic modification triggered by reactive metabolites such as methylglyoxal (MG), has been implicated in various metabolic and neurological disorders. However, its genome-wide distribution and biological consequences in the developing brain remain largely unexplored. To address this gap, we developed a novel method, GlyDIP-seq, which enables high-resolution profiling of glycation-derived DNA lesions (specifically N²-carboxyethyl-2’-deoxyguanosine, CEdG) across the genome.
• 🔗 查看原文

10. GSE202816 胎盘稳态炎症对成人心血管疾病和抑郁症具有保护作用

• ✍️ 作者：未知作者
• 🏷️ 关键词：inflammation、cardiovascular
• 📝 描述：Contributors : Nicholas O’Toole ; Eamon Fitzgerald ; Hannah YongSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensPathological placental inflammation is associated with an increased risk of several adult disorders. However, many inflammation related genes are highly expressed in the healthy placenta. Their contribution to adult health outcomes in this context is unknown but may inform mechanisms of risk associated with pathological placental inflammation. We studied this using RNA sequencing and weighted correlation network analysis in 42 healthy, term placental samples from the GUSTO study. We identified a module strongly associated with homeostatic inflammation and highly enriched in Hofbauer cells. By leveraging placental expression quantitative trait loci (eQTLs), we generated a polygenic score (PGS) that specifically predicted expression of this module in GUSTO. Using identical criteria, we created a PGS in the UK Biobank and carried out a phenome wide association study of 1831 traits. This produced 21 associations (FDR<0.05) primarily within the cardiovascular and mental health domains. Further regression and mendelian randomization analyses identified sex-dependent protective effects on cardiovascular and depressive outcomes. We demonstrate that genes differentially regulated by intra-amniotic infection are both highly enriched and highly connected within our module, suggesting severe module disruption during prenatal infection. This suggests prenatal infection, at least partially confers, risk for adult cardiovascular and depressive outcomes through disrupting protective homeostatic inflammatory expression patterns in the placenta. We finally identify Aspirin as a therapeutic target to mitigate these effects.
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1. 科学家利用突破性纳米技术逆转小鼠阿尔茨海默病

• ✍️ 作者：未知作者
• 🏷️ 关键词：Alzheimer
• 📝 描述：A new nanotechnology treatment reversed Alzheimer’s symptoms in mice by restoring the brain’s natural cleanup system. The specially engineered nanoparticles helped clear toxic amyloid proteins from the brain and repair the blood-brain barrier, which normally protects and regulates the brain’s environment. In one striking experiment, elderly mice treated with the therapy later behaved like healthy younger mice.
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• GSE330725 根癌农杆菌中甲基化敏感的GcrA调节因子对基因组复制和细胞分裂的控制
• GSE303487 转录组指导的纤维化逆转化合物的开发通过线粒体解偶联减少皮肤瘢痕并促进再生 [RNA-seq]
• GSE331167 光邻近标记法揭示 c-Myc 的 SLK 是一种癌症特异性共调节因子
• GSE328265 脑脊液疾病相关巨噬细胞特征定义进行性多发性硬化症
• GSE328264 脑脊液疾病相关巨噬细胞特征定义进行性多发性硬化症 [新鲜]
• GSE327243 脑脊液疾病相关巨噬细胞特征定义进行性多发性硬化症 [Frozen]
• GSE330911 弓形虫感染中脾脏和脑T细胞——scRNA测序、CITE测序和TCRab
• GSE330896 胸腺中 abT 细胞（OT-I 和 OT-II）的阳性和阴性选择 1 - scRNA-seq、CITE-seq 和 TCRab
• GSE330865 多器官转录组学和循环细胞外囊泡分析揭示了年龄依赖性的异氟烷麻醉和手术全身易感性
• GSE330855 CGRP受体增强了甲型流感衍生免疫印迹中的焦虑。
• GSE330828 Hutchinson Gilford 早衰症改变了内皮细胞对层流剪切应力的遗传反应 [RNA-Seq]
• GSE327297 核糖体镊子：快速去除核糖体蛋白揭示转录后基因调控的新层面 [RNA-Seq]
• GSE297899 H3K27me3 CUT&TAG 在用 AKTi (ipatasertib) 和 EZH2i (tazemetostat) 治疗的 C4.2B 前列腺癌细胞系中。
• GSE267821 4-1BB 通过隔离泛素修饰酶 A20 导致 CAR-T 细胞死亡
• GSE331007 T 细胞特异性 IL-21 同工型表达对乳腺上皮细胞基因表达的影响。
• GSE315702 E16.5、P1 和 P5 小鼠新皮层中 SST 表达神经元的单细胞水平基因表达谱 [scRNA-seq P5 纹状体]
• GSE315700 E16.5、P1 和 P5 小鼠新皮层中 SST 表达神经元的单细胞水平基因表达谱 [scRNA-seq E16.5]
• GSE303486 转录组指导的纤维化逆转化合物的开发通过线粒体解偶联减少皮肤瘢痕并促进再生 [DRUG-seq2]
• GSE303020 SARS-CoV-2 感染和 MEK1/2 抑制剂 Zapnometinib 治疗后细胞的转录组分析。