详细内容（前10条）

1. ⭐ GSE318234 肿瘤相关感光细胞特征统一了不同的中枢神经系统恶性肿瘤 [ATAC-seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：tumor、nervous、ATAC-seq
• 📝 描述：Contributor : Paul NorthcottSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusPineoblastoma is a clinically aggressive childhood brain tumor composed of distinct molecular subgroups with divergent driver genes, demographics, and clinical outcomes. To identify developmental origins and mechanisms governing disease pathogenesis, we derive single-cell transcriptomes from pineal parenchymal tumors, aligning malignant cells with developmental counterparts to retrace cellular origins. Integrative computational analyses map pineoblastoma origins to transient, cycling pinealocyte progenitors during development. Lineage-specific perturbation of suspected drivers in the early pineal gland yields preclinical models representative of consensus molecular subgroups. Multi-omic characterization of patient tumors and these models uncovers a tumor-associated photoreceptor signature (TAPS) common to pineoblastoma, retinoblastoma, and Group 3 medulloblastoma. Transcriptional activity of this signature within respective cellular origins establishes a developmental basis for molecular similarities between entities. Photoreceptor signature constituents are selective dependencies across these anatomically distinct central nervous system malignancies, motivating future studies evaluating developmentally encoded programs of malignancy as potential therapeutic liabilities.
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2. ⭐ GSE312950 肿瘤相关感光细胞特征统一了不同的中枢神经系统恶性肿瘤 [甲基化阵列]

• ✍️ 作者：未知作者
• 🏷️ 关键词：tumor、nervous、methylation
• 📝 描述：Contributors : Brian Gudenas ; Paul A NorthcottSeries Type : Methylation profiling by genome tiling arrayOrganism : Mus musculusMouse tumor methylation profiling by MouseMethylation Beadchips (MM285) platform
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3. ⭐ GSE273440 肿瘤相关感光细胞特征统一了不同的中枢神经系统恶性肿瘤 [scRNA-seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：tumor、nervous、scRNA
• 📝 描述：Contributors : Brian Gudenas ; Paul A NorthcottSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusPineoblastoma is a clinically aggressive childhood brain tumor that segregates into molecularly distinct subgroups. Mechanisms governing pineoblastoma pathogenesis, including developmental origins, remain poorly defined. Herein, we resolved the cellular composition of pineoblastoma and other pineal parenchymal tumors at single-cell resolution, aligning malignant cells with pineal gland development to retrace cellular origins. Integrative computational analyses mapped divergent pineoblastoma subgroups to cycling progenitors of the pinealocyte lineage. Lineage-specific perturbation of suspected drivers provoked the generation of genetically accurate preclinical models representing distinct molecular subgroups, while uncovering an oncogenic photoreceptor program conserved across pineoblastoma, retinoblastoma, and Group 3 medulloblastoma. Transcriptional activity of this program was acquired from cellular origin, incriminating photoreceptor identity as a common developmental vulnerability, substantiated as a strong dependency. Illuminated through multidisciplinary analysis of an uncommon, heterogeneous pediatric brain tumor, these advances motivate future studies evaluating developmentally encoded transcriptional programs of malignancy as potential therapeutic liabilities in clinically challenging entities.
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4. ⭐ GSE289259 整合转录组学和代谢组学分析揭示苯丙素代谢调控蒙古葱复杂的耐盐碱特性

• ✍️ 作者：未知作者
• 🏷️ 关键词：metabolism、metabolomics、transcriptomics
• 📝 描述：Series Type : Expression profiling by high throughput sequencingOrganism : Allium mongolicumAllium mongolicum, a xerophytic industrial plant native to the Mongolian Plateau, demonstrates notable stress resistance, though its salt-alkali tolerance mechanisms remain poorly understood. This study integrates physiological assessments, transcriptomics, metabolomics, and full-length transcriptome analyses to uncover its adaptive mechanisms under salt-alkali stress.A comprehensive full-length transcriptome was constructed under these conditions, comprising 30,117 non-redundant genes, alongside significant trends observed in the activities of antioxidant enzymes and key enzymes in the phenylpropanoid pathway. Combined transcriptomic and metabolomic analyses identified key genes and metabolites in the phenylpropanoid pathway as central to salt-alkali tolerance. WGCNA further highlighted critical genes, such as AmCOMT1, AmHSP18, and AmPPL7, with functional validation of AmCOMT1 and AmHSP18 confirming transcriptome reliability. The salt tolerance function of AmCOMT1 has been validated through overexpression in plants, and the binding interaction with AmERF4 has also been confirmed.A proposed model suggests A. mongolicum mitigates salt-alkali stress via reactive oxygen species scavenging, osmotic regulation, and structural support, providing valuable insights for breeding salt-tolerant crops and enhancing its agricultural applications.
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5. GSE311943 通过肿瘤纯度校正的DNA甲基化对肺腺癌亚型进行多组学评估

• ✍️ 作者：未知作者
• 🏷️ 关键词：tumor、methylation
• 📝 描述：Contributors : Johan Staaf ; Deborah F NacerSeries Type : Methylation profiling by genome tiling arrayOrganism : Homo sapiensMolecular subtypes of lung adenocarcinoma (LUAD) with varying prognosis and characteristics have been proposed based on one or two-dimensional studies but are not yet implemented into clinical routine. Epigenetic modifications in cancer cells are independent of sequence variants, directly linked to gene and genome regulation, and thus provide important information to guide subclassification efforts. We performed in-depth epigenomic profiling of 95 primary LUAD samples from a Swedish discovery cohort with comprehensive clinicopathological, epigenomic, genomic, transcriptomic, proteomic, and metabolomic data. Not all samples have all omics data, and data have been deposited at different timepoints. Here we include DNA methylation values for 13 LUAD samples. In this project, we subdivided the 95 samples into four epigenetic subtypes, or epitypes, reflecting distinct tumor cell methylation states. Resulting epitypes were contrasted based on clinicopathological and molecular features, and our main findings were validated in two additional primary tumor cohorts totaling over 700 samples.
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6. GSE275307 肿瘤相关感光细胞特征统一了不同的中枢神经系统恶性肿瘤

• ✍️ 作者：未知作者
• 🏷️ 关键词：tumor、nervous
• 📝 描述：Series Type : Expression profiling by high throughput sequencing ; Methylation profiling by genome tiling array ; Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusThis SuperSeries is composed of the SubSeries listed below.
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7. GSE275306 肿瘤相关感光细胞特征统一了不同的中枢神经系统恶性肿瘤 [bulkRNA-seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：tumor、nervous
• 📝 描述：Contributors : Brian Gudenas ; Paul A NorthcottSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusPineoblastoma is a clinically aggressive childhood brain tumor that segregates into molecularly distinct subgroups. Mechanisms governing pineoblastoma pathogenesis, including developmental origins, remain poorly defined. Herein, we resolved the cellular composition of pineoblastoma and other pineal parenchymal tumors at single-cell resolution, aligning malignant cells with pineal gland development to retrace cellular origins. Integrative computational analyses mapped divergent pineoblastoma subgroups to cycling progenitors of the pinealocyte lineage. Lineage-specific perturbation of suspected drivers provoked the generation of genetically accurate preclinical models representing distinct molecular subgroups, while uncovering an oncogenic photoreceptor program conserved across pineoblastoma, retinoblastoma, and Group 3 medulloblastoma. Transcriptional activity of this program was acquired from cellular origin, incriminating photoreceptor identity as a common developmental vulnerability, substantiated as a strong dependency. Illuminated through multidisciplinary analysis of an uncommon, heterogeneous pediatric brain tumor, these advances motivate future studies evaluating developmentally encoded transcriptional programs of malignancy as potential therapeutic liabilities in clinically challenging entities.
• 🔗 查看原文

8. GSE316228 肺特异性地逃避血管内转移性乳腺癌细胞对细胞毒性T细胞的杀伤作用

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、T cell
• 📝 描述：Contributors : Marina Kizner ; Nehora Levi ; Carmel Sochen ; Julia Ryvkin ; Ofer Regev ; Alexander Zarbock ; Lea Eisenbach ; Moshe Biton ; Ronen AlonSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusThe lungs are a major organ of cancer metastasis. Despite advances in the usage of tumor-specific cytotoxic T cells (CTLs) with potent killing activity (i.e., tumor infiltrating T cells, TILs) for killing of primary tumors, how these T cells encounter and kill metastatic lesions at remote organs is still poorly understood. In the present study we compared the ability of potent neoantigen specific CTLs to kill two types of cancer cells that share the same neoantigen and generate distinct metastatic lesions in the lungs of immunocompetent recipient mice. We have used ovalbumin (OVA) as a neoantigen model and found that the OVA-specific OT-I transgenic CD8 CTLs, when intravenously introduced, readily eliminated primary tumors of OVA-expressing breast cancer E0771 cells. Nevertheless, similar OT-I CTLs failed to clear OVA-expressing breast cancer E0771 cells that colonized the lungs. In contrast, similar intravenously introduced OT-I CTLs efficiently eliminated lung metastatic OVA-expressing B16 melanoma cells, ruling out that the intravenous CTLs were exhausted upon entering the lungs. Three-dimensional (3D) imaging of whole lungs revealed that in both experimental and spontaneous metastasis models, the OVA E0771 cells survived inside lung blood vessels but did not recruit circulating OT-I CTLs to their vicinity. Furthermore, canonical vascular adhesion molecules recognized by the CTLs like ICAM-1 and VCAM-1 were not upregulated nearby the lung-residing intravascular E0771 cells as a potential means to recruit lung circulating CTLs to the vicinity of the intravascular tumor cells. Strikingly, the lung residing OVA-expressing E0771 cells lost expression of their OT-I specific OVA-derived SIINFEKL-H-2Kb pMHC complexes while retaining MHC-I expression. This loss was accompanied by a lung-specific transcriptional reduction of key regulators of MHC-I presentation. A temporal loading of OVA-derived SIINFEKL-H-2Kb pMHC complexes on E0771 cells did not result, however, in cancer cell killing inside the lungs. Nevertheless, direct and stable SIINFEKL peptide presentation on these cells overcame their lung specific escape from OT-I mediated killing. Our study is a first indication that subsets of cancer cells that reside in the lungs rap…
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9. GSE294705 高频复发指数预测非肌层浸润性膀胱癌多次复发（验证队列）

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer
• 📝 描述：Contributors : Seung-Woo Baek ; Young-Joon ByunSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensNon-muscle invasive bladder cancer (NMIBC) has a recurrence rate of more than 50% after transurethral resection (TUR) and Calmette-Guérin (BCG) treatment. This study aimed to develop a high-frequency recurrence index (HfRI) to predict multiple recurrences in NMIBC patients and guide personalized treatment strategies. In this study, we analyzed transcriptome data (Discovery cohort) of 45 high-risk NMIBC patients who received intravesical BCG treatment, including patients with >=2 recurrences, to identify genes significantly associated with high-frequency recurrence and construct a signature. In addition, we validated the predictive performance using transcriptome data of 94 patients (Validation cohort).
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10. GSE294703 高频复发指数预测非肌层浸润性膀胱癌的多次复发（发现队列）

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer
• 📝 描述：Contributors : Seung-Woo Baek ; Young-Joon ByunSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensNon-muscle invasive bladder cancer (NMIBC) has a recurrence rate of more than 50% after transurethral resection (TUR) and Calmette-Guérin (BCG) treatment. This study aimed to develop a high-frequency recurrence index (HfRI) to predict multiple recurrences in NMIBC patients and guide personalized treatment strategies. In this study, we analyzed transcriptome data (Discovery cohort) of 45 high-risk NMIBC patients who received intravesical BCG treatment, including patients with >=2 recurrences, to identify genes significantly associated with high-frequency recurrence and construct a signature. In addition, we validated the predictive performance using transcriptome data of 94 patients (Discovery cohort).
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1. 科学家发现了一种有助于保护肝脏的肠道化合物。

• ✍️ 作者：未知作者
• 🏷️ 关键词：gut、regex:gut(-?microbiome)?
• 📝 描述：What a mother eats during pregnancy may quietly shape her child’s liver health years down the road—but new research suggests there may be a way to tip the odds back in a healthier direction. Scientists found that a natural compound made by healthy gut bacteria dramatically reduced fatty liver disease in the offspring of mice whose mothers ate a high-fat, high-sugar diet. The compound, called indole, appeared to protect the liver, improve blood sugar, limit weight gain, and even reshape the gut microbiome in lasting ways.
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• GSE310657 群体感应调节因子 LsrR 通过干扰禽致病性大肠杆菌的硫酸盐同化作用来调节其对氧化应激的抵抗力
• GSE306468 8 周龄 AR-97Q 和 AR-24Q 小鼠的单核 RNA 测序结果。
• GSE286003 RNA-seq 分析了 P7 时 WT、AR-24Q、AR-97Q、睾酮处理的 AR-97Q 小鼠、Scramble-ASO 处理的 AR-97Q 小鼠和 Rest4-ASO #3 处理的 AR-97Q 小鼠脊髓的 RNA。
• GSE261519 RNA-seq 测序数据来自出生后7天和13周龄的AR-97Q和WT小鼠脊髓。
• GSE255505 阿霉素II诱导的人类PSC衍生心肌细胞转录组变化
• GSE225346 9.5日龄NTDs胎鼠脑和脊髓的RNA测序