详细内容（前10条）

1. ⭐ GSE325991 人类肾上腺肿瘤的高分辨率空间转录组学

• ✍️ 作者：未知作者
• 🏷️ 关键词：spatial、spatial transcriptomics、transcriptomics
• 📝 描述：Contributors : Tomohiro Tamura ; Masaki Uchihara ; Kotaro Umamoto ; Akiyo TanabeSeries Type : OtherOrganism : Homo sapiensTo characterize the tumor microenvironment and elucidate mechanisms of immune evasion in malignant adrenal tumors, we performed spatial transcriptomics (Visium HD) on pathological specimens from adrenocortical adenoma (ACA) and pheochromocytoma mixed tumor. Using each cell’s spatial coordinates and gene expression profiles, we inferred tumor cell–immune cell interactions.
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2. GSE282248 移植后间充质细胞的单细胞多组学分析揭示了肺纤维化的分子特征和调控因子（scRNA-seq）

• ✍️ 作者：未知作者
• 🏷️ 关键词：single-cell、scRNA
• 📝 描述：Contributors : Lu Lu ; Aidan P McLinden ; Natalie M Walker ; Ragini Vittal ; Michael P Combs ; Joshua D Welch ; Vibha N LamaSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensChronic lung allograft dysfunction (CLAD) is a critical challenge in lung transplantation. Dysregulated gene expression and epigenomic states in lung mesenchymal cells (MCs) play a key role in these conditions. We performed single-cell multi-omic profiling on MCs isolated from human bronchoalveolar lavage samples of lung transplant recipients with CLAD, compared with time-matched controls. Our results provide deeper insights into the transcriptomic and epigenomic changes in post-transplant MCs, nominating biomarkers and disease-associated factors with implications for future therapeutic efforts.
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3. GSE281481 移植后间充质细胞的单细胞多组学分析揭示了肺纤维化的分子特征和调控因子（RNA-seq）

• ✍️ 作者：未知作者
• 🏷️ 关键词：RNA-seq、single-cell
• 📝 描述：Contributors : Lu Lu ; Aidan P McLinden ; Natalie M Walker ; Ragini Vittal ; Michael P Combs ; Joshua D Welch ; Vibha N LamaSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensChronic lung allograft dysfunction (CLAD) is a critical challenge in lung transplantation. Dysregulated gene expression and epigenomic states in lung mesenchymal cells (MCs) play a key role in these conditions. We performed single-cell multi-omic profiling on MCs isolated from human bronchoalveolar lavage samples of lung transplant recipients with CLAD, compared with time-matched controls. Our results provide deeper insights into the transcriptomic and epigenomic changes in post-transplant MCs, nominating biomarkers and disease-associated factors with implications for future therapeutic efforts.
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4. GSE325983 乳酸驱动的H3K18乳酸化通过HNRNPF-Parkin介导的线粒体自噬促进膀胱癌的顺铂耐药性

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、resistance
• 📝 描述：Contributors : Henghui Zhang ; Dongqing Li ; Mingqiang Su ; Zaosong Zheng ; Wei Chen ; Haiyong ChenSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensCisplatin resistance in bladder cancer (BCa) is driven by metabolic reprogramming that enhances glycolysis and lactate production. Here, we report that lactate-induced histone H3K18 lactylation (H3K18la) drives chemoresistance by activating a novel signaling axis that couples epigenetic regulation with mitochondrial quality control. Through integrative multi-omics analysis, we identified HNRNPF as a key effector downstream of H3K18la, with its promoter being directly enriched by H3K18la in cisplatin-resistant BCa cells. Unexpectedly, HNRNPF, primarily known as an RNA-binding protein, promotes chemoresistance through a non-canonical mechanism: it directly interacts with the core mitophagy protein Parkin. Mechanistically, the RRM2 domain of HNRNPF binds the R0 domain of Parkin, facilitating Parkin’s recruitment to damaged mitochondria. This interaction potentiates Parkin’s E3 ubiquitin ligase activity, leading to enhanced ubiquitination of VDAC1 and robust activation of mitophagy. Collectively, our findings establish the H3K18la-HNRNPF-Parkin axis as a previously unrecognized signaling cascade that bridges epigenetic reprogramming with to mitochondrial quality control in chemoresistance. Targeting this axis, particularly the HNRNPF-Parkin interaction or mitophagy activation, may represent a novel therapeutic strategy to overcome cisplatin resistance in BCa, pending further validation in preclinical models.
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5. GSE323385 非裔美国人前列腺癌转录组和表观基因组DNA甲基化变化的比较和整合分析[贝勒]

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、methylation
• 📝 描述：Contributors : Chad J Creighton ; Flora Zhang ; Yiqun Zhang ; Patricia Castro ; Rong Hu ; Md Islam ; Somiranjan Ghosh ; Michael Ittmann ; Bernard Kwabi-AddoSeries Type : Methylation profiling by genome tiling arrayOrganism : Homo sapiensAfrican American (AA) men have the highest incidence and mortality rate from Prostate cancer (PCa) than any other racial/ethnic group. To date, PCa genomic studies have largely under- represented tumour samples from AA men. We measured genome-wide DNA methylation in benign and tumor prostate tissues from AA men using the Illumina Infunium 850 K EPIC array. mRNA expression database from a subset of the AA biospecimen were used to assess correlation of transcriptome and methylation datasets. Genome-wide methylation analysis identified 11,460 probes that were significant (p < 0.01) and differentially methylated in AA PCa compared to normal prostate tissues and showed significant (p < 0.01) inverse-correlation with mRNA expression. Ingenuity pathway analysis and Gene Ontology analysis in our AA dataset compared with TCGA dataset showed similarities in methylation patterns: top candidate genes with significant hypermethylation and corresponding down-regulated gene expression were associated with biological pathways in hemidesmosome assembly, mammary gland development, epidermis development, hormone biosynthesis, and cell communication. In addition, top candidate genes with significant hypomethylation and corresponding up-regulated gene expression were associated with biological pathways in macrophage differentiation, cAMP-dependent protein kinase activity, protein destabilization, transcription co-repression, and fatty acid biosynthesis. In contrast, differences in genome-wide methylation in our AA dataset compared with TCGA dataset were enriched for genes in steroid signalling, immune signalling, chromatin structure remodelling and RNA processing. Overall, differential methylation of AMIGO3, IER3, UPB1, GRM7, TFAP2C, TOX2, PLSCR2, ZNF292, ESR2, MIXL1, BOLL, and FGF6 were significant and uniquely associated with PCa progression in our AA cohort.
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6. GSE323379 非裔美国男性前列腺腺癌、良性增生、转移性疾病及相关生活方式因素的全基因组DNA甲基化模式[乔治城]

• ✍️ 作者：未知作者
• 🏷️ 关键词：epigenome、methylation
• 📝 描述：Contributors : H Song ; A Duttargi ; C Albanese ; V Apprey ; W F Huang ; B Kwabi-AddoSeries Type : Methylation profiling by genome tiling arrayOrganism : Homo sapiensAfrican American (AA) men have higher prostate cancer (PCa) incidence and mortality rates than any other racial/ethnic group in the USA. Biological differences including aberrant epigenetic DNA methylation changes likely contribute to the PCa disparities. Our study aims to identify differentially methylated CpG sites and genes among histologic localized adenocarcinoma PCa, metastatic PCa (mCRPC), and Benign Prostatic Hyperplasia (BPH) samples. We performed genome-wide DNA methylation profiling in 100 AA prostate tissues using Illumina Methylation EPIC array. Global hypermethylation indicating epigenetic silence was observed in localized adenocarcinoma PCa compared to paired normal and BPH samples. On the other hand, significant hypomethylation suggesting tumor associated activation of oncogenes and chromatin remodeling was observed in mCRPC. Using Shannon entropy as a metric for epigenetic heterogeneity, mCRPC samples exhibited significant elevated entropy, reflecting greater methylation variability than localized adenocarcinoma PCa and BPH. We also identified distinct smoking and alcohol-associated methylation signatures, with specific CpG sites showing significant differential methylation compared to non-exposed patients. Our analysis provides insights into methylation profiles as predictive markers for distinguishing between BPH, PCa and mCRPC that are also influenced by lifestyle factors. More importantly, aberrations in methylation favor PCa aggressiveness to metastasis and genomic instability that implies aging and environmental factors. Overall, the differential methylation patterns suggest potential for patient stratification, biomarker-driven treatment strategies including epigenetic therapeutic strategies for AA PCa.
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7. GSE305094 体内 RNA 代谢标记鉴定再生斑马鱼心脏的哨兵细胞 [scrna-seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：metabolic、scRNA
• 📝 描述：Contributors : Janita Mintcheva ; Tzu-Lun Tseng ; Pinelopi Goumenaki ; Anika Neuschulz ; Anis Senoussi ; Ronny Schäfer ; Sara Lelek ; Daniela Panakova ; Didier Stainier ; Jan Philipp JunkerSeries Type : Expression profiling by high throughput sequencingOrganism : Danio rerioThe adult zebrafish heart has high regenerative capacity. Heart injury triggers a cascade of events including inflammation, fibrosis, revascularization, and proliferation of cardiomyocytes, culminating in full functional recovery of the heart. However, the first events that are induced upon injury and trigger the regenerative cascade remain elusive. Here, we established in vivo single-cell RNA metabolic labeling in the adult heart to systematically identify the cells that first respond to injury, as well as the processes that are induced in these sentinel cells. We found that activation of damage response pathways including Toll-like receptor signaling and expression of pro-inflammatory genes in macrophages are the first response to heart injury. In conjunction with detailed dissection of single-cell transcriptomics atlases, this finding led us to postulate that macrophage-specific inhibition of Toll-like receptor signaling would improve hallmarks of regeneration, a hypothesis we validated in functional experiments. In summary, our work establishes RNA metabolic labeling as a powerful approach for measuring perturbation response in vivo, identifies macrophages as the sentinel cells of the heart, and highlights the importance of fine-tuning the early pro-inflammatory phase for optimal regenerative outcomes.
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8. GSE277255 通过原位多聚腺苷酸化和空间 RNA 测序对微生物组-宿主相互作用进行高分辨率空间映射 [STOmics]

• ✍️ 作者：未知作者
• 🏷️ 关键词：sequencing、spatial
• 📝 描述：Contributors : Ioannis Ntekas ; David W McKellar ; Lena Takayasu ; Iwijn De VlaminckSeries Type : OtherOrganism : Mus musculusInter-microbial and host–microbial interactions are thought to be critical for the functioning of the gut microbiome, but few substantive tools are available to measure these interactions. Here, we report a method for unbiased spatial sampling of microbiome-host interactions in the gut at high spatial resolution. This method combines enzymatic in situ polyadenylation of both bacterial and host transcripts with spatial RNA-sequencing. Application of this method revealed the biogeography of the mouse gut microbiome as function of location in the intestine, short-range intermicrobial interaction, local shaping of the microbiome by the host, and tumor-associated changes in the architecture of the host-microbiome interface. This method is compatible with broadly available commercial platforms for spatial RNA-sequencing, and can therefore be readily adopted to broadly study the role of short-range, bidirectional host-microbe interactions in microbiome health and disease.
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9. GSE272558 “耐受”先天性感染病毒携带者的抗病毒 Tfh 反应驱动抗体介导的病毒载量控制 [scRNA-Seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：antibody、scRNA
• 📝 描述：Contributors : Katrin Martin ; Peter Reuther ; Florian Geier ; Anna-Friederike Marx ; Tiago Abreu-Mota ; Jonas Fixemer ; Anna L Kastner ; Karen Tintignac ; Karsten Stauffer ; Ingrid Wagner ; Doron Merkler ; Daniel D PinschewerSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusCongenital infection can result in viral persistence as commonly observed for hepatitis B virus in humans. The accompanying “neonatal tolerance” state remains immunologically ill-defined and treatment options are unsatisfactory.Studying congenital lymphocytic choriomeningitis virus infection, the prototypic mouse model of neonatal antiviral tolerance, we observe antibody-mediated suppression of viral replication. These responses are driven by canonical antiviral CD4 Tfh responses, whereas CD8 T cells are irrelevant for viral load control. Viral epitope-specific CD4 T cells of congenitally infected animals are less abundant than in adult infection. They exhibit reduced clonal diversity and distinct differences in gene expression patterns. Importantly, exogenous supplementation of T help augments antiviral germinal center B responses of congenitally infected mice.These findings reveal that humoral immune defense is partially exempt from neonatal tolerance and remains effective against congenital infection. Imperfect virus control by limited CD4 Tfh responses may offer opportunities for a functional cure by immunotherapy.
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10. GSE197887 人类前脑类器官（来自典型和自闭症受试者）的单细胞RNA测序

• ✍️ 作者：未知作者
• 🏷️ 关键词：sequencing、single-cell
• 📝 描述：Contributors : Jinyue Liu ; Li Lin ; Wan K ChockSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensThe goal of this experiment is to define cellular phenotypes in human brain organoid models of autism.
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💡 该来源还有 16 条内容，详见 文末

• GSE325993 人类和食蟹猴iPSCs中POU5F1的单细胞CRISPRi扰动
• GSE325763 维甲酸受体转录共调节因子RIP140预测急性髓系白血病预后不良并抑制ATRA反应
• GSE325723 细胞大小依赖性 mRNA 转录驱动蛋白质组重塑 [SLAM-seq]
• GSE325535 染色质重塑因子 Mit1 促进组蛋白修饰 H3K9me 的传播
• GSE320531 神经酰胺破坏TM9SF2-PGK1轴以重定向PD-L1转运并增强抗肿瘤免疫
• GSE314295 低级别浆液性卵巢癌治疗靶点的鉴定 [EM-seq]
• GSE313802 低级别浆液性卵巢癌治疗靶点的鉴定
• GSE305095 体内 RNA 代谢标记鉴定再生斑马鱼心脏的哨兵细胞 [scslam-seq]
• GSE305090 体内 RNA 代谢标记鉴定再生斑马鱼心脏的哨兵细胞 [bulk_slamseq]
• GSE297148 多种癌症类型的癌症类器官模型汇编
• GSE292563 穿心莲内酯通过抑制血管紧张素II处理的小鼠腹主动脉瘤模型中的NF-κB信号通路改善主动脉病变
• GSE272559 先天性病毒感染者“耐受”状态下的抗病毒Tfh反应驱动抗体介导的病毒载量控制
• GSE272557 “耐受”先天性感染病毒携带者的抗病毒 Tfh 反应驱动抗体介导的病毒载量控制 [scTCR-Seq]
• GSE197050 对来自典型受试者和自闭症受试者的人类前脑类器官进行批量 RNA 测序
• GSE312175 HyperTRIBE 揭示了 MEX3A 在结直肠癌 (CRC) 细胞中的 RNA 结合活性
• GSE309791 靶向巨噬细胞的可吸入纳米药物，用于调节肺纤维化治疗中的STING通路