详细内容（前10条）

1. GSE333956 鉴定对雌激素受体α结合及其对子宫内膜癌基因表达的影响具有独特影响的基因组特征 [ATAC-seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、ATAC-seq
• 📝 描述：Contributors : Alexandra Richey ; Noel Kitchen ; Jason GertzSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensEstrogen receptor alpha (ER) is an established oncogenic transcription factor in breast and endometrial cancer; however, more is known about the mechanisms controlling ER behavior in breast cancer, and therapies targeting ER have been much more successful in breast cancer. To address this disparity, we seek to identify genomic features that control ER in endometrial cancer and determine to what extent these factors differ from those in breast cancer. We focus on the locations of estrogen response elements (EREs), ER’s preferred DNA binding motif, throughout the human genome. To identify factors that predict ER genomic binding and effects on target gene expression, we apply machine learning to genomic data for each ERE in Ishikawa cells (ER+ endometrial cancer) and T-47D cells (ER+ breast cancer). Many of these factors, such as chromatin accessibility and histone modifications, are predictive of ER activity in both cell lines. However, the transcription factors that predict ER activity are found to be cell type-specific, including FOXA1 and GATA3 in T-47D cells, and ETV4 and SOX17 in Ishikawa cells. In addition, the features that predict ER binding and effects on gene expression differ, with transcription at EREs in the absence of estrogen being predictive of regulatory activity. To verify our findings in the Ishikawa cells, we perform a CRISPR knockout screen, which confirms the discovery that SOX17 controls ER activity in endometrial cancer cells. These results identify important genomic features of ER binding and regulatory activity and how these features differ between endometrial cancer and breast cancer cells.
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2. GSE333530 CD40激动剂在肾细胞癌中通过髓系细胞增强免疫检查点活性

• ✍️ 作者：未知作者
• 🏷️ 关键词：carcinoma、immune
• 📝 描述：Contributor : Dijana DjureinovicSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusImmune checkpoint blockade (ICB) has improved survival for patients with metastatic renal cell carcinoma (RCC) but there remains a need to overcome resistance mechanisms. CD40 agonists increase anti-tumoral immunity, but limited data are available on their activity in RCC. We evaluated CD40 agonism in combination with ICB in preclinical RCC models. Adding CD40 agonism to anti-CTLA-4, but not anti-PD1, improved survival in Renca-bearing mice. CD40 agonism and anti-CTLA-4 upregulated CCL2, increased intra-tumoral macrophages and type 1 conventional dendritic cells (cDC1), whereas polymorphonuclear myeloid-derived suppressor cells (PMN-MDSCs) decreased compared to control. Neutralizing CCL2 with CD40 agonism and CTLA-4 blockade partially abrogated the anti-tumoral effect and led to less increase of cDC1 and less decrease of PMN-MDSCs populations. Our studies suggest that CCL2 at least partially mediates the anti-tumoral effects of CD40 agonism, and more importantly, that the addition of CD40 agonism to ICB, particularly anti-CTLA-4, might be beneficial in RCC.
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3. GSE291053 一项前瞻性观察研究对全基因组 DNA 甲基化进行了分析，发现 ESRD 患者在肾脏替代治疗期间存在多个表观遗传失调基因。

• ✍️ 作者：未知作者
• 🏷️ 关键词：genome、methylation
• 📝 描述：Contributors : García Testal Alicia ; Riffo-Campos Ángela L. ; Sandoval del Amor Juan ; López-Rodas GerardoSeries Type : Methylation profiling by genome tiling arrayOrganism : Homo sapiensRenal replacement therapy (RRT) can be initiated in the end-stage renal disease (ESRD). Over four million people worldwide receive RRT. Haemodialysis (HD) is the most frequently employed treatment, followed by peritoneal dialysis (PD), while conservative treatment (CT) is selected more frequently for elderly individuals, particularly women. The molecular mechanisms of ESRD-RRT, and its possible impact on cellular processes, are not yet fully understood, although recent evidence suggests a correlation between epigenetic regulation of chromatin dynamics, mainly DNA methylation, and control of gene transcription in this pathology. This investigation represents the first prospective study of epigenomic alterations during HD, PD and CT treatments in ESRD. Advanced Infinium EPIC array technology, capable of measuring levels of DNA methylation of over 850,000 CpG sites in the genome, was used in peripheral blood mononuclear cells. The results show an inverse relationship between the methylation levels of certain CpGs of significant genes and changes in gene expression during the different ESRD treatments. Namely, the genes FBXWD7, TMEM229B and MZF1 in CT group, NELL1, CBLN1 and EEF1D in HD group and COX11, TMCO and RSPO3 in PD group. These genes are linked to inflammation, oxidative stress, immune response, mitochondrial disorders, pericardial oedema, vascular congestion or metabolic diseases. The findings suggest that these genes may contribute to the differing prognoses observed between the different treatment groups. The epigenomic alterations identified could contribute to the pathophysiology and prognosis of ESRD and may represent important therapeutic targets for the improvement of future treatment options.
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4. GSE294385 结直肠癌大转移和微转移的空间多组学图谱

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、spatial
• 📝 描述：Contributor : Yang LiuSeries Type : OtherOrganism : Homo sapiensColorectal cancer (CRC) metastases often recur due to minimal residual disease (MRD) and micrometastases that persist after therapy. Here, we analyzed 341,328 spatially resolved spots from 37 tumors, including liver (CLiM) and lung (CLuM) metastases, and primary CRC from 11 patients. Phylogenetic analysis of copy number variations revealed heterogeneous tumor evolution, with early dissemination and quiescence in liver micrometastases (CLiMi). Spatial analysis identified 10 conserved and 7 distinct metaprograms, highlighting stromal interactions in CLiM and CLuM, with macrophages enriched in CLiM and lymphocytes in CLuM. Micrometastases showed strong immunosuppressive signature and increased T cell exhaustion. Notably, we identified a CLiMi-specific six-gene signature associated with MRD status, disease-free survival, and chemotherapy resistance across multiple independent cohorts. These findings elucidate the spatial evolutionary landscape of CRC metastases and provide tissue-based spatially validated biomarkers for surveillance and therapeutic targeting.
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5. GSE237963 清迈-PM2.5刺激下人类单核细胞的代谢和先天免疫记忆改变

• ✍️ 作者：未知作者
• 🏷️ 关键词：immune、metabolic
• 📝 描述：Contributors : Naunpun Sangphech ; Tanapat Palaga ; Tassanee Prueksasit ; Jomkhwan MeerakSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensThe rise of PM2.5 in air pollution correlates with increased disease exacerbation, especially in asthma. This study aims to examine how Chiang-Mai, Thailand PM2.5 (CM-PM2.5) affects innate immune responses in primary human monocytes. A transcriptomic profile was obtained from cells that were stimulated with low and high doses of CM-PM2.5 (5 and 20 μg/ml) for 24 hr. The data indicated that primary human monocytes respond to CM-PM2.5 in a dose-dependent manner. The pyrimidine ribonucleotide metabolism was predominant in both datasets, but the suppression of glycolytic rate was found in high doses of CM-PM2.5 stimulation. The upregulation of the key metabolic genes was unable to compensate for the suppression. Moreover, CM-PM2.5 priming induced immune tolerance during subsequent LPS stimulation in primary human monocytes from asthma.
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6. GSE334100 鉴定对雌激素受体α结合及其对子宫内膜癌基因表达的影响具有独特影响的基因组特征 [RNA-seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、RNA-seq
• 📝 描述：Contributors : Alexandra Richey ; Noel Kitchen ; Jason GertzSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensEstrogen receptor alpha (ER) is an established oncogenic transcription factor in breast and endometrial cancer; however, more is known about the mechanisms controlling ER behavior in breast cancer, and therapies targeting ER have been much more successful in breast cancer. To address this disparity, we seek to identify genomic features that control ER in endometrial cancer and determine to what extent these factors differ from those in breast cancer. We focus on the locations of estrogen response elements (EREs), ER’s preferred DNA binding motif, throughout the human genome. To identify factors that predict ER genomic binding and effects on target gene expression, we apply machine learning to genomic data for each ERE in Ishikawa cells (ER+ endometrial cancer) and T-47D cells (ER+ breast cancer). Many of these factors, such as chromatin accessibility and histone modifications, are predictive of ER activity in both cell lines. However, the transcription factors that predict ER activity are found to be cell type-specific, including FOXA1 and GATA3 in T-47D cells, and ETV4 and SOX17 in Ishikawa cells. In addition, the features that predict ER binding and effects on gene expression differ, with transcription at EREs in the absence of estrogen being predictive of regulatory activity. To verify our findings in the Ishikawa cells, we perform a CRISPR knockout screen, which confirms the discovery that SOX17 controls ER activity in endometrial cancer cells. These results identify important genomic features of ER binding and regulatory activity and how these features differ between endometrial cancer and breast cancer cells.
• 🔗 查看原文

7. GSE334097 鉴定对雌激素受体α结合及其对子宫内膜癌基因表达的影响具有独特影响的基因组特征 [ChIP-seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、ChIP-seq
• 📝 描述：Contributors : Alexandra Richey ; Noel Kitchen ; Craig Rush ; Jason GertzSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensEstrogen receptor alpha (ER) is an established oncogenic transcription factor in breast and endometrial cancer; however, more is known about the mechanisms controlling ER behavior in breast cancer, and therapies targeting ER have been much more successful in breast cancer. To address this disparity, we seek to identify genomic features that control ER in endometrial cancer and determine to what extent these factors differ from those in breast cancer. We focus on the locations of estrogen response elements (EREs), ER’s preferred DNA binding motif, throughout the human genome. To identify factors that predict ER genomic binding and effects on target gene expression, we apply machine learning to genomic data for each ERE in Ishikawa cells (ER+ endometrial cancer) and T-47D cells (ER+ breast cancer). Many of these factors, such as chromatin accessibility and histone modifications, are predictive of ER activity in both cell lines. However, the transcription factors that predict ER activity are found to be cell type-specific, including FOXA1 and GATA3 in T-47D cells, and ETV4 and SOX17 in Ishikawa cells. In addition, the features that predict ER binding and effects on gene expression differ, with transcription at EREs in the absence of estrogen being predictive of regulatory activity. To verify our findings in the Ishikawa cells, we perform a CRISPR knockout screen, which confirms the discovery that SOX17 controls ER activity in endometrial cancer cells. These results identify important genomic features of ER binding and regulatory activity and how these features differ between endometrial cancer and breast cancer cells.
• 🔗 查看原文

8. GSE333537 一项针对免疫疗法难治性头颈部转移性鳞状细胞癌患者的静脉注射VCN-01溶瘤腺病毒联合度伐利尤单抗的I期临床试验

• ✍️ 作者：未知作者
• 🏷️ 关键词：carcinoma、regex:immuno(logy|therapy|suppression)
• 📝 描述：Contributors : Maria Jove ; Ricard Mesía ; Francisco X Real ; Jaime. Martínez de VillarrealSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensVCN-01 is a hyaluronidase-expressing oncolytic adenovirus that increases immune checkpoint antibody tumor uptake in mice. VCN-01 was evaluated with durvalumab in recurrent/metastatic head and neck squamous cell carcinoma (R/M HNSCC) patients refractory to anti-PD-(L)1
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9. GSE333514 全基因组 CRISPR 筛选发现 AMBRA1 是口腔鳞状细胞癌对铂类疗法反应的潜在生物标志物 [RNA-Seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：RNA-seq、genome
• 📝 描述：Contributors : Ana Sastre-Perona ; Lucía Acero-RiaguasSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensOral Squamous Cell Carcinomas (OSCC) are among the most frequent and lethal cancers worldwide. Advanced stage tumors are still treated with standard chemotherapy, however, most of the patients develop chemotherapy resistance. To uncover new functional biomarkers of cisplatin response, we performed a synthetic lethality genome wide CRISPR/Cas9 screen in an oral squamous cell carcinoma cell line. This led to the discovery of AMBRA1, as a regulator of cisplatin sensitivity. In all tested OSCC cell lines and oral primary cultures, AMBRA1 knockout cells showed increased sensitivity to cisplatin treatment. Mechanistically, we demonstrated a new function of AMBRA1, where loss of AMBRA1 led to higher S phase, higher expression of genome instability markers, and higher DNA damage in basal conditions, thereby predisposing cancer cells to an increased sensitivity to cisplatin as well as to other platinum drugs. In summary, we uncovered AMBRA1 as a potential biomarker of response to platinum-based therapies in oral squamous cell carcinomas.
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10. GSE307415 小鼠和人类狼疮中与年龄相关的B细胞的单细胞RNA和BCR测序

• ✍️ 作者：未知作者
• 🏷️ 关键词：sequencing、single-cell
• 📝 描述：Contributors : Taiichiro Shirai ; Kentaro Kuzuya ; Yu-Chen Liu ; Daisuke Motooka ; Daisuke Okuzaki ; Kazuhiro SuzukiSeries Type : Expression profiling by high throughput sequencing ; OtherOrganism : Homo sapiens ; Mus musculusTo characterize age-associated B cells (ABCs), we performed single-cell RNA and BCR sequencing on splenic B-lineage cells from a murine lupus model induced by Toll-like receptor 7 (TLR7) stimulation and on peripheral blood B-lineage cells from a treatment-naïve patient with systemic lupus erythematosus (SLE). We identified a population of ABCs with features of plasmablast precursors (pre-PB ABCs). In the TLR7-induced lupus model, B cell-specific Commd3 deletion reduced the frequency of pre-PB ABCs and was associated with increased apoptosis in this population.
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1. ⭐ 科学家发现肠道细菌可能有助于预防自闭症和多动症

• ✍️ 作者：未知作者
• 🏷️ 关键词：bacteria、regex:bacter(ia|ial|ium)、gut、regex:gut(-?microbiome)?
• 📝 描述：A major study suggests that some of the groundwork for brain development may be shaped before birth through a surprising partnership between a baby’s genes and gut microbes. Researchers found that epigenetic changes present at birth can influence how the gut microbiome develops during the first year of life, and certain combinations were linked to early signs of autism and ADHD by age three.
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2. ⭐ scMVAF——一种用于单细胞RNA测序数据的多视图自适应融合聚类方法

• ✍️ 作者：未知作者
• 🏷️ 关键词：sequencing、single-cell、clustering
• 📝 描述：A new multi-view learning framework improves clustering of single-cell RNA sequencing data by integrating multiple cellular perspectives to better identify biologically meaningful cell populations… The post scMVAF – a multi-view adaptive fusion clustering approach for single-cell RNA-sequencing data appeared first on RNA-Seq Blog.
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3. 长读长RNA测序揭示了可变剪接如何影响免疫反应

• ✍️ 作者：未知作者
• 🏷️ 关键词：immune、sequencing
• 📝 描述：Long-read RNA sequencing revealed extensive alternative splicing changes in activated human monocytes, uncovering functional isoforms that enhance immune protein production during inflammatory responses… The post Long-read RNA sequencing reveals how alternative splicing shapes immune responses appeared first on RNA-Seq Blog.
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4. 一种单一蛋白质可能阻碍了CAR-T细胞癌症疗法的发展。

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer
• 📝 描述：A newly identified protein may be one of the biggest obstacles holding CAR T-cell therapy back. Researchers found that NFIL3 causes these engineered immune cells to become exhausted and lose their cancer-fighting power over time. When NFIL3 was disabled, the cells remained stronger for longer and controlled tumors more effectively in animal models.
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5. 一种脂肪促进了胰腺癌的生长，而另一种脂肪则使这种疾病减少了一半。

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer
• 📝 描述：A surprising new study suggests that when it comes to pancreatic cancer, the kind of fat you eat may matter more than how much. Researchers found that oleic acid—the main fat in olive oil and several other common foods—sped up tumor growth in mice predisposed to pancreatic cancer, while omega-3-rich fats from fish oil dramatically slowed disease development.
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• GSE286404 B 细胞 CD19 在免疫细胞间广泛转移 [M]
• GSE286403 B 细胞 CD19 在免疫细胞 [CD11b+] 之间广泛转移
• GSE334093 生酮饮食通过脂质而非酮体介导肠道肿瘤发生
• GSE334038 抗癌头孢噻肟和高红霉素生物碱生物合成酶表征的原始 RNA-seq 数据
• GSE299923 先锋因子 Ascl1/E12a 与核小体之间的独特相互作用驱动细胞命运转变 [ATAC-seq]
• GSE332906 鉴定预测单细胞中最佳T细胞受体功能的基因
• GSE312618 内质网相关脂肪分解调节肝脏脂肪合成和周转 [RNA-seq]
• GSE334086 BAF155 的精氨酸甲基化调控与 RNA 加工机制的相互作用 [RNA-seq]
• GSE334085 BAF155 的精氨酸甲基化调控与 RNA 加工机制的相互作用 [TT-seq]
• GSE334083 BAF155 的精氨酸甲基化调控与 RNA 加工机制的相互作用 [ATAC-seq]
• GSE333513 全基因组 CRISPR 筛选发现 AMBRA1 是口腔鳞状细胞癌对铂类疗法反应的潜在生物标志物 [CRISPR 筛选]
• GSE298288 转录组学揭示大麻（Cannabis sativa L.）中外源腐胺介导的冷适应机制 [RNA-Seq]
• GSE278712 MbovP475 对 BoMac 细胞基因表达的影响 [ChIP-seq]
• GSE301365 利用三相Wnt调控结合动态生物反应器生成的人类iPSC衍生中脑类器官的单细胞分析
• GSE291239 神经胶质细胞特异性和可诱导的全身C3缺乏症不影响AppNL−G−F阿尔茨海默病小鼠模型中的淀粉样蛋白病理
• GSE235313 HSD 和 HFD 对果蝇心脏功能的影响