详细内容（前10条）

1. GSE289865 血液中的鞘氨醇 1-磷酸维持血管阻力和心脏功能。

• ✍️ 作者：未知作者
• 🏷️ 关键词：cardiac、resistance
• 📝 描述：Contributors : Ilaria Del Gaudio ; Eric CamererSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusSphingosine 1-phosphate (S1P) circulates in plasma bound to high-density lipoproteins (HDL) and albumin. In mice, isolated deficiency in HDL-S1P and endothelial cell S1P receptor (R)-1 both trigger hypertension, supporting an essential role for HDL-S1P in endothelial function. Physiological roles of albumin-S1P and myocyte S1PRs in the cardiovascular system remain incompletely defined. We report that depletion of all circulating S1P pools induces hypotension and lack of blood pressure increase with age, which contrasts with HDL-S1P deficiency and suggests an essential role for albumin-S1P in cardiovascular homeostasis. Left ventricular contractile function was also reduced but cardiac output preserved in a basal state. Cardiac function and blood pressure was partially or fully normalized by bone marrow transplantation or transfusion of erythrocytes capable of S1P production. Hypotension was accompanied by reduced peripheral resistance, and BSA-S1P, but not S1P complexed to an HDL-like chaperone, dose-dependently increased vascular resistance in isolated perfused kidneys via S1PR2 and S1PR3. Epistatic analysis supported a critical role for S1PR3 in S1P-dependent blood pressure regulation and pointed to a distinct origin of the cardiac phenotype. These observations suggests that albumin-S1P crosses the endothelium in resistance arteries to access contractile receptors, and that myocyte S1PR signaling is essential for vascular resistance and blood pressure maintenance in mice.
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2. 利用 RNA 测序对伊马替尼耐药细胞的 K562/S 和 K562/R、KU812/S 和 KU812/R 进行转录组学分析（GSE314129）。

• ✍️ 作者：未知作者
• 🏷️ 关键词：sequencing、transcriptomics
• 📝 描述：Contributors : Shashi Kumari ; Rukmini Govekar ; Rahul Mojidra ; Mythreyi NarasimhanSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensCML-CP Patients showing resistance to Imatinib, due to Bcr-Abl mechanisms of resistance are treated with 2nd and 3rd generation TKIs but some non-responders shown Bcr-Abl independant mechanism of resistance. We hypothesize that this could be due to activation of novel pathway, or activation of downstream molecules of Bcr-Abl pathway. In this study we have performed Transcriptomics and epigenomics analysis of K562 and KU812 CML-BC cell sensitive and resistant to imatinib, ITGB3 showed high transcript levels, and was also hypomethylated in K562/R cells as compared to sensitive counterparts and showed higher protein levels in both K562 and KU812 resistant cell lines. Previous studies in the lab also showed ITGB1 as a differentiator in proteomic analysis and further on-going studies indicate its role in resistance. ITGB1 was however not modulated at transcriptional level. The protein levels of ITGB3 were significantly increased in resistant cells (K562; KU812: while those of ITGB1 were significantly decreased in resistant cells (K562; KU812. With the known switching of integrins, whether higher expression of ITGB3 had a role in modulating the levels of transcriptionally non-regulated ITGB1 was investigated in K562/S cells with ITGB1 knocked down (KD) protein levels of ITGB3 were upregulated as compared to VC. Similarly, knock down of ITGB3 in K562/R resulted in increased level of ITGB1 protein. These striking results confirmed switching of integrins and explained reduced levels of ITGB1 despite no alteration at genomic or transcriptomic level in resistant cells.
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3. GSE313872 家蚕中肠感染BmCPV的基因组规模DNA甲基化组和转录组分析

• ✍️ 作者：未知作者
• 🏷️ 关键词：genome、transcriptome
• 📝 描述：Contributors : Qunnan Qiu ; Chengliang Gong ; Zhe Liu ; Yuqing Huang ; Huilin Pang ; Liuyang Li ; Min Zhu ; Xiaolong HuSeries Type : Methylation profiling by high throughput sequencingOrganism : Bombyx moriDNA methylation, as well as histone modifications, is an important regulatory mechanism for altered gene expressions. Our previous study has shown that Bombyx mori cytoplasmic polyhedrosis virus (BmCPV) infection could change the level of trimethylation of lysine 9 of histone 3 (H3K9me3) and acetylation of lysine 9 of histone 3 (H3K9ac), thus regulating the mRNAs expressions in the midgut of silkworm, B. mori. However, the correlation between genome-scale DNA methylome and transcriptome remains underexplored. In this study, whole genome bisulfite sequencing (WGBS) was performed on the midgut of BmCPV-infected silkworms at 48 h and 96 h post infection, and corresponding midguts of uninfected silkworms. And intersection genes were screened by correlation analysis between differentially methylated regions (DMR)-associated genes and differentially expressed genes (DEGs). Above analysis will contribute to further understanding how BmCPV regulate gene expression through epigenetic modification at the genome-wide level.
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4. GSE158629 单细胞 RNA 测序揭示人类视网膜色素上皮的异质性

• ✍️ 作者：未知作者
• 🏷️ 关键词：sequencing、single-cell
• 📝 描述：Contributors : Farhad Farjood ; Nicholas Labbe ; Carol J Charniga ; Thomas R Kiehl ; Sally Temple ; Jeffrey H Stern ; Nathan C BolesSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensPurpose: In this work, we performed single-cell RNA sequencing on adult human RPE cells to characterize heterogeneity in human RPE and identify the RPE stem cells.Methods: RPE cells were isolated from four adult human donor eyes. Single-cell RNA sequencing for cells from one donor eye was performed using 10X Genomics pipeline to survey the RPE subpopulations. For RPE cells from the other three donor eyes, the ICELL8 pipeline was used to obtain a broader and more in-depth survey of gene expression. RNA sequencing results were analyzed using the Seurat package for R.Results: Uniform Manifold Approximation and Projection (UMAP) analyses for the 10x data showed 8 different RPE subpopulations. Within the different RPE subpopulations we found a cluster with cones-specific transcripts (ARR3, PDE6H and OPN1MW), clusters with rod RNA (RHO and PDE6A), and a cluster with transcripts involved in vascular endothelial growth factor signaling (TF and SPP1). ICELL8 results revealed a small subpopulation of RPE cells positive for RPE65 that also expressed early retinal developmental genes (VIM, GNL3), and MKI67, a marker of actively cycling cells, making the cells of this cluster strong candidates for being the RPE stem cells. Our immunostaining for potential markers of clusters uncovered in our single-cell RNA-Seq results, further verify the identity of RPE populations.Conclusions: Our single-cell RNA sequencing results show that RPE is a heterogeneous tissue. Of the varied subpopulations, we have identified a small population with the potential to proliferate and expressing stem cell markers, suggesting that they may be the RPE stem cells.
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5. GSE314824 化生性三阴性乳腺癌细胞外基质结构和蛋白质组成的评估

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer
• 📝 描述：Contributors : Elizabeth C Martin ; Jorge A Belgodere ; Matthew E Burow ; Katherine L HebertSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensAlterations in the tumor extracellular environment and matrix stiffness promotes tumor progression. Furthermore, correlational studies have identified enrichment of extracellular matrix (ECM) proteins (glycoproteins, collagens) in breast tumors. Despite these findings, there has yet to be an interdisciplinary analysis of both ECM composition and structural architecture in rare breast tumors, such as metaplastic breast cancer. Here, we explored changes in ECM protein expression and architecture in a triple-negative breast cancer (TNBC) metaplastic tumor through SEM, proteomics, and RNA sequencing. SEM revealed tumor pore size was larger compared to control adipose tissue. Oscillating rheometry demonstrated increased ECM stiffness in the tumor compared to control adipose breast adipose. Proteomic analysis of the metaplastic TNBC tumor showed significant enrichment for ECM proteins, notably glycoproteins compared to control adipose. Interestingly, these samples showed no observed changes in expression for major fibrillar collagens COL1A1 and COL1A2, and a reduced expression of COL3A1. To determine the impact of less characterized ECMs in metaplastic TNBC, we overexpressed MFAP2 in primary metaplastic breast cancer cells and performed RNA sequencing. MFAP2 overexpression was associated with upregulation of epithelial-to-mesenchymal transition related genes . Overall, our results establish an extracellular signature and onco-architecture for the metaplastic triple-negative tumor type.
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6. GSE314697 NAT10 通过 DDIT4 mRNA 的 ac4C 修饰驱动头颈部鳞状细胞癌增殖

• ✍️ 作者：未知作者
• 🏷️ 关键词：carcinoma
• 📝 描述：Contributors : Panpan Song ; Qian Xiao ; Yue Jiang ; Hui Li ; Zheng Liang ; Junguo Wang ; Xiaoyun Qian ; Xia GaoSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensTo investigate the function NAT10 in the regulation of proliferation, we established SAS cell lines in which target gene has been knocked down by siRNA.
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7. GSE282094 PARP7 通过 NAD+ 感知机制介导脂肪生成转录调控 [RNA-Seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：RNA-seq
• 📝 描述：Contributors : MiKayla S Stokes ; Yoon Jung Kim ; Sneh Koul ; Josue Zuniga ; Shu-Ping Chiu ; Tulip Nandu ; Kraus W LeeSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusThe process of differentiating from a preadipocyte into a mature, fat storing, adipocyte (adipogenesis) is a complex and tightly regulated process vital to human health. The molecular mechanisms regulating adipogenesis are incompletely understood, although key facets of the signaling and regulatory pathways have been defined. Here we have identified a mono(ADP-ribosyl)transferase (MART), PARP7, that plays a pivotal role in adipogenesis. ADP-ribosylation – the process whereby specific members of the poly(ADP-ribosyl)polymerase (PARP) family facilitate the covalent transfer of ADP-ribose moieties from NAD+ to substrate proteins – has been shown to control multiple components of the adipogenic regulatory machinery. Herein we have found that PARP7 is required for modulation of the adipogenic transcriptional program during adipogenesis, and that the loss of PARP7 results in a decrease of the adipogenic process. Contrary to previous studies, the ability to modulate the adipogenic transcriptional program is independent of PARP7 catalytic activity. However, the catalytic activity of PARP7 plays a vital role in regulating protein stability, in a time and space specific manner, which is required for modulation of the adipogenic transcriptional program. This study has found a novel pathway which utilizes NAD+ compartmentalization to stabilize PARP7 at a specific time during the adipogenic process allowing for the regulation of adipogenic genes, through modulation of the well-known adipogenic transcription factor C/EBPß, in a time sensitive manner. Therefore, acting as another check and balance to the adipogenic differentiation process.
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8. GSE282093 PARP7 通过 NAD+ 感知机制介导脂肪生成转录调控 [ChIP-Seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：ChIP-seq
• 📝 描述：Contributors : MiKayla S Stokes ; Yoon Jung Kim ; Sneh Koul ; Josue Zuniga ; Shu-Ping Chiu ; Tulip Nandu ; Kraus W LeeSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusThe process of differentiating from a preadipocyte into a mature, fat storing, adipocyte (adipogenesis) is a complex and tightly regulated process vital to human health. The molecular mechanisms regulating adipogenesis are incompletely understood, although key facets of the signaling and regulatory pathways have been defined. Here we have identified a mono(ADP-ribosyl)transferase (MART), PARP7, that plays a pivotal role in adipogenesis. ADP-ribosylation – the process whereby specific members of the poly(ADP-ribosyl)polymerase (PARP) family facilitate the covalent transfer of ADP-ribose moieties from NAD+ to substrate proteins – has been shown to control multiple components of the adipogenic regulatory machinery. Herein we have found that PARP7 is required for modulation of the adipogenic transcriptional program during adipogenesis, and that the loss of PARP7 results in a decrease of the adipogenic process. Contrary to previous studies, the ability to modulate the adipogenic transcriptional program is independent of PARP7 catalytic activity. However, the catalytic activity of PARP7 plays a vital role in regulating protein stability, in a time and space specific manner, which is required for modulation of the adipogenic transcriptional program. This study has found a novel pathway which utilizes NAD+ compartmentalization to stabilize PARP7 at a specific time during the adipogenic process allowing for the regulation of adipogenic genes, through modulation of the well-known adipogenic transcription factor C/EBPß, in a time sensitive manner. Therefore, acting as another check and balance to the adipogenic differentiation process.
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9. GSE282092 PARP7 通过 NAD+ 感知机制介导脂肪生成转录调控 [ATAC-seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：ATAC-seq
• 📝 描述：Contributors : MiKayla S Stokes ; Yoon Jung Kim ; Sneh Koul ; Josue Zuniga ; Shu-Ping Chiu ; Tulip Nandu ; Kraus W LeeSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusThe process of differentiating from a preadipocyte into a mature, fat storing, adipocyte (adipogenesis) is a complex and tightly regulated process vital to human health. The molecular mechanisms regulating adipogenesis are incompletely understood, although key facets of the signaling and regulatory pathways have been defined. Here we have identified a mono(ADP-ribosyl)transferase (MART), PARP7, that plays a pivotal role in adipogenesis. ADP-ribosylation – the process whereby specific members of the poly(ADP-ribosyl)polymerase (PARP) family facilitate the covalent transfer of ADP-ribose moieties from NAD+ to substrate proteins – has been shown to control multiple components of the adipogenic regulatory machinery. Herein we have found that PARP7 is required for modulation of the adipogenic transcriptional program during adipogenesis, and that the loss of PARP7 results in a decrease of the adipogenic process. Contrary to previous studies, the ability to modulate the adipogenic transcriptional program is independent of PARP7 catalytic activity. However, the catalytic activity of PARP7 plays a vital role in regulating protein stability, in a time and space specific manner, which is required for modulation of the adipogenic transcriptional program. This study has found a novel pathway which utilizes NAD+ compartmentalization to stabilize PARP7 at a specific time during the adipogenic process allowing for the regulation of adipogenic genes, through modulation of the well-known adipogenic transcription factor C/EBPß, in a time sensitive manner. Therefore, acting as another check and balance to the adipogenic differentiation process.
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10. GSE301220 RNA-seq 分析揭示了 NPs 处理后 CAFs 中通路失调。

• ✍️ 作者：未知作者
• 🏷️ 关键词：RNA-seq
• 📝 描述：Contributors : Shuren Wang ; Zaozao WangSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensCancer-associated fibroblasts (CAFs) contribute to immunotherapy resistance in colorectal cancer (CRC) by creating physical barriers and fostering an immunosuppressive microenvironment, critically influencing tumor development and metastasis.Nowadays, nanotherapy has been extensively explored in oncology for its dual capabilities in cancer targeted treatment.However, the mechanisms by which nanoparticles (NPs) exert their antitumor effects through targeting and eliminating CAFs remain incompletely understood.In this study,NPs modulated intrinsic signaling pathways in CAFs, leading to altered chemokine secretion profiles. This modification enhanced dendritic cell maturation and promoted CD8+ T cell activation and functionality, ultimately amplifying the anti-tumor immune response to suppress CRC progression.
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1. 科学家逆转小鼠阿尔茨海默病并恢复其记忆力

• ✍️ 作者：未知作者
• 🏷️ 关键词：Alzheimer
• 📝 描述：Alzheimer’s has long been considered irreversible, but new research challenges that assumption. Scientists discovered that severe drops in the brain’s energy supply help drive the disease—and restoring that balance can reverse damage, even in advanced cases. In mouse models, treatment repaired brain pathology, restored cognitive function, and normalized Alzheimer’s biomarkers. The results offer fresh hope that recovery may be possible.
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• GSE314721 PLAG1 KD 和 VC 细胞对伊马替尼耐药的 DNA 甲基化。
• GSE314718 对伊马替尼敏感和耐药的 K562 和 KU812 细胞的 DNA 甲基化。
• GSE314685 Piezo1-ATF3-PPP1r15a轴在低强度聚焦超声作用下将机械应力转化为胶质瘤细胞凋亡
• GSE314496 非病毒 CISH 位点特异性整合 FAPα CAR-T 细胞在胶质母细胞瘤中实现强大的抗肿瘤疗效
• GSE290884 分析局部粘膜免疫失调以指导针对 COVID 长期嗅觉丧失的试点治疗 [TCR-seq]
• GSE290883 分析局部粘膜免疫失调以指导针对 COVID 长期嗅觉丧失的试点治疗 [5’ GEX]
• GSE285487 Themis 通过促进 PD-1 信号传导和调节转录因子 TCF-1 和 TOX 的表达来指导 T 细胞耗竭。
• GSE252078 以单细胞分辨率量化 Stim2 缺失对神经元起源细胞的影响