详细内容（前10条）

1. ⭐ GSE273166 肠道微生物组特征与基于DNA甲基化的生物衰老相关

• ✍️ 作者：未知作者
• 🏷️ 关键词：aging、methylation、gut、regex:gut(-?microbiome)?
• 📝 描述：Contributors : Alika Maunakea ; Braden KunihiroSeries Type : Methylation profiling by genome tiling arrayOrganism : Homo sapiensRecent advances in machine learning have applied novel tools to aging research, yet the relationship between the gut microbiome and epigenetic aging remains underexplored. This proof-of-concept study investigates whether gut microbial composition is associated with biological aging pace independent of chronological age. Using paired 16S rRNA gene sequencing and DNA methylation data from 123 monocyte-enriched samples in a cohort enriched for Native Hawaiian and Pacific Islander participants, we developed “EpiBiome” models to predict epigenetic age acceleration residuals and DunedinPACE, a DNA methylation biomarker that estimates the instantaneous pace of biological aging. Models predicting residuals of traditional clocks (Horvath, Levine, GrimAge2) showed no predictive signal at either taxonomic rank. By contrast, the EpiBiome-Accel model for DunedinPACE reached statistical significance at both the species level (R² = 0.152, Spearman ρ = 0.408, p = 0.012; permutation p < 0.001) and the genus level (R² = 0.099, permutation p = 0.036). Adding chronological age as a feature did not improve performance (ΔR² = −0.046 at species level), indicating age-independence. SHAP analysis of the species-level ElasticNet model identified Bifidobacterium adolescentis as the dominant contributor and the strongest predictor of decelerated aging, with Succinivibrio dextrinosolvens showing the strongest association with accelerated aging. These findings nominate specific gut taxa as hypothesis-generating candidates for mechanistic follow-up, rather than as individual-level diagnostic markers.Recent advances in machine learning have applied novel tools to aging research, yet the relationship between the gut microbiome and epigenetic aging remains underexplored. This proof-of-concept study investigates whether gut microbial features are associated with biological aging rates independent of chronological time. Using paired 16S rRNA gene sequencing and DNA methylation data from 123 monocyte-enriched samples, we developed “EpiBiome” models to predict epigenetic age acceleration residuals and DunedinPACE, a DNA methylation biomarker that estimates the instantaneous pace of biological aging. While models predicting residuals of traditional clocks (Horvath, Levine, GrimAge2) showed minimal signal, the EpiBiome-Accel model for DunedinPACE showed a modest associa…
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2. ⭐ GSE319969 空间和批量转录组分析定义了皮肤鳞状细胞癌的分子演变，并揭示了具有临床意义的阶段特异性生物标志物 [RNA-Seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：carcinoma、RNA-seq、spatial
• 📝 描述：Contributors : Sergio Oterino-Sogo ; Fatima Naji ; Jean-Philippe Guegan ; Marie Beylot-Barry ; Léa Dousset ; Macha Nikolski ; Hamid-Reza RedvaniSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensBackground: Cutaneous squamous cell carcinoma (cSCC) is among the most common skin cancers and can be associated with poor prognosis in aggressive cases, with a median overall survival of approximately two years. Despite its well-described stepwise progression from actinic keratosis to invasive disease, robust molecular markers that discriminate disease stages and inform clinical decision-making remain limited. Objectives: This study aimed to delineate progression continuum and stage-related transcriptional programs underlying cSCC evolution, identify candidate biomarkers for risk stratification and invasion, and assess the broader relevance of these molecular signatures across human cancers. Methods: We applied bulk RNA sequencing (HTG EdgeSeq) and spatial transcriptomics (GeoMx DSP) to profile skin biopsies from 8 patients recruited in collaboration with Bordeaux University Hospital. Importantly, each patient simultaneously presented four stages (healthy skin, pre-malignant lesion, tumor core, and invasive front) providing a unique framework to interrogate the full molecular trajectory of cSCC progression within individuals. Results: Spatial transcriptomic analyses identified more than 2,000 differentially expressed genes (adjusted p < 0.01) whose expression in squamous cells changed across disease stages. These genes were organized into 18 coordinated expression programs reflecting progressive biological rewiring during tumor evolution. Pathways related to cellular stress responses, proliferation, extracellular matrix remodeling, and inflammation were progressively upregulated, whereas differentiation programs and lipid and amino acid metabolism were consistently downregulated. In contrast, peritumoral macrophages showed increased expression of genes involved in purine metabolism, glycolysis, and pyruvate metabolism across progression. To assess the broader clinical relevance of the progression-associated gene programs, we developed a Snakemake-based pipeline to systematically screen 32 solid and hematological malignancies from The Cancer Genome Atlas. This workflow is designed to be fully reproducible and readily extensible, enabling other researchers to perform similar progression and survival analyses across cancer types. N…
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3. ⭐ GSE319536 肌层浸润性膀胱癌的空间图谱揭示谱系特异性脆弱性和免疫结构

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、immune、spatial
• 📝 描述：Contributors : Yu Kai ; Wang Linghua ; Gao Jianjun ; Chen JianfengSeries Type : OtherOrganism : Homo sapiensMuscle-invasive bladder cancer (MIBC) is clinically heterogeneous, current molecular subtyping lacks spatial context and therapeutic relevance. Here, we construct the first spatial atlas of MIBC by integrating spatial transcriptomics from 22 tumors with matched bulk RNA sequencing and whole-exome sequencing. We identify a continuous, spatially organized luminal-to-basal differentiation axis within each individual tumor, driven by progressive copy number alterations and transcriptional plasticity. This axis delineates tumor compartments with opposing therapeutic vulnerabilities. Luminal tumor cores are enriched for FGFR3 and NECTIN4 expression, and heightened sensitivity to NECTIN4-directed antibody–drug conjugates. In contrast, basal-like tumor states localize to invasive margins, elevated EGFR signaling, epithelial–mesenchymal transition, genomic instability, immune infiltration, and increased chemosensitivity. Spatial analyses further reveal lineage- and proximity-dependent tertiary lymphoid structure states.
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4. ⭐ GSE314446 人类 GPR15 缺陷揭示肠道炎症中 CD8+ T 调节细胞与巨噬细胞的相互作用

• ✍️ 作者：未知作者
• 🏷️ 关键词：macrophage、inflammation、regex:intestin(e|al)
• 📝 描述：Contributors : Jing Cui ; Can Liu ; Chuan Wu ; Michael LenardoSeries Type : Expression profiling by high throughput sequencing ; OtherOrganism : Homo sapiens ; Mus musculusWe employed a CITE-seq combined with single-cell sequencing approach using 10x Genomics scRNA-seq to analyze peripheral and intestinal lymphocytes from Gpr15⁻/⁻ mice and from patients carrying deleterious GPR15 mutations. We show that GPR15, a G protein–coupled receptor (GPCR) expressed in immune cells and previously described as an entry co-factor for human and simian immunodeficiency viruses, serves as a crucial marker and homing receptor for a unique subset of intramucosal GPR15-guided regulatory CD8⁺ T lymphocytes (CD8⁺ TIGR cells). Our results demonstrate that deleterious GPR15 variants in humans impair the homing of CD8⁺ TIGR cells, leading to severe early-onset inflammatory bowel disease (IBD). In mice, GPR15 deficiency disrupts the colonic recruitment of CD8⁺ TIGR cells, causing an accumulation of inflammatory macrophages and heightened susceptibility to colitis. Together, our findings identify CD8⁺ TIGR cells as a previously unrecognized component of organ-specific immune regulation and reveal potential therapeutic avenues for the treatment of IBD.
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5. ⭐ GSE232419 LINC01770 介导鼻咽癌的放射抗性并使肿瘤细胞易受铁死亡的影响

• ✍️ 作者：未知作者
• 🏷️ 关键词：tumor、cancer、resistance
• 📝 描述：Contributors : Qing Q Xu ; Xin Wen ; Xuan Li ; Lei ChenSeries Type : Expression profiling by high throughput sequencing ; Non-coding RNA profiling by high throughput sequencingOrganism : Homo sapiensLong noncoding RNAs (lncRNAs) participate in regulation of various essential biological processes including cell proliferation, differentiation, apoptosis, migration, and invasion. However, the clinical significances of lncRNAs and their functions and mechanisms in nasopharyngeal carcinoma (NPC) involved in malignant progression need to be further investigated. We find that the LINC01770-TEAD1 signal axis leads to radiotherapy resistance of NPC and causes NPC cells to be in a fragile oxidative stress equilibrium. Meanwhile radioresistant cells are more sensitive to ferroptosis inducers. LINC01770 stabilizes TEAD1 by competitive binding with microRNA 615-5p and microRNA -1293. Radiation resistant cell is in a delicate balance of lipid peroxidation and more vulnerable to ferroptosis. In conclusion, our research suggest that LINC01770 serves as an independent prognostic factor in NPC. During the malignant progression of NPC caused by high expression of LINC01770, ferroptosis can be induced to effectively kill cancer cells and reverse RT resistance of NPC cells, providing evidence for the clinical application of ferroptosis in the treatment of recurrent and refractory NPC.
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6. GSE318085 鞘氨醇激酶-2 抑制增加乙酰辅酶A羧化酶活性和磷脂酰胆碱水平，从而调控髓系来源抑制细胞的免疫原性 [RNA-seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：kinase、RNA-seq
• 📝 描述：Contributors : Paramita Chakraborty ; Shikhar MehrotraSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusMyeloid-derived suppressor cells (MDSCs) in the tumor microenvironment (TME) are a major barrier to adoptive T cell therapy, underscoring the need to enhance T cell efficacy by overcoming immunosuppression. Here, we investigated how sphingosine-1-phosphate (S1P), an abundant signaling lipid in the TME, regulates the programming and function of MDSCs. We show that inhibition of sphingosine kinase-2 (SphK2), which generates S1P in MDSCs, reduces their suppressive activity and enhances antigen presentation. Pharmacological inhibition of SphK2 improved the response to anti-PD1 therapy in preclinical models of checkpoint-resistant breast, bladder, and melanoma cancers by mitigating MDSC- mediated suppression, thereby limiting tumor progression. Mechanistically, S1P directly interacts with Acetyl-CoA Carboxylase 1 (ACC1) to inhibit its activity, altering fatty acid and glycolytic pathways. Lowering intracellular S1P restores ACC activity and promotes phosphatidylcholine synthesis, reducing the immunosuppressive phenotype of MDSCs. These findings highlight the SphK2/ACC/phospholipid axis as a promising therapeutic target in cancer immunotherapy.
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7. GSE306852 利用TRV探针进行自身免疫性肾病中T细胞克隆性的空间分析

• ✍️ 作者：未知作者
• 🏷️ 关键词：T cell、spatial
• 📝 描述：Contributors : Cedric Ly ; Darius P Schaub ; Robin Khatri ; Zeba Sultana ; Annika Boxnick ; Zheng Song ; Tobias Huber ; Thorsten Wiech ; Eva Tolosa ; Ulf Panze ; Stefan Bonn ; Christian Krebs ; Immo PrinzSeries Type : OtherOrganism : Homo sapiensHypothesizing that the localization of T cell clones correlates with immune function, our goal was to develop an unbiased method to study the spatial distribution of T cells in tissues. We created an in situ hybridization panel with 248 probes that identify immune and tissue cell types, and 132 probes for all variable TRAV, TRBV, TRGV, and TRDV gene segments. Applying this approach to analyze renal biopsies from patients with autoimmune kidney disease, combinations of TRV segments reliably provided spatial information about T cell clonality. Confined clusters of clonally related αβ T cells were found in proximity to increased numbers of antigen-presenting cells, B cells, and other T cells, reflecting local immune cell interactions. γδ T cells were more frequently located outside or at their periphery of T cell infiltration areas. In conclusion, integrating spatial information with TCR clonotype analysis provided new insights into the organization of immune responses at the tissue level.
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8. GSE326226 一项基于Xenium的肌层浸润性膀胱癌空间图谱揭示了谱系特异性脆弱性

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、spatial
• 📝 描述：Contributors : Yu Kai ; Gao Jianjun ; Wang Linghua ; Chen JianfengSeries Type : OtherOrganism : Homo sapiensXenium-based spatial transcriptomics was performed to characterize cellular heterogeneity and spatial organization in muscle-invasive bladder cancer (MIBC). Xenium enabled high-resolution in situ mapping of selected gene expression at single-cell resolution in formalin-fixed paraffin-embedded (FFPE) tissue sections. Together, these data provide complementary insights into tumor cell states, lineage programs, and their spatial relationships with the tumor microenvironment, including immune and stromal components. This dataset enables investigation of tumor heterogeneity, lineage plasticity, and spatially resolved cell–cell interactions in MIBC.
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9. GSE326225 肌层浸润性膀胱癌的单细胞图谱揭示了谱系特异性脆弱性

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、single-cell
• 📝 描述：Contributors : Yu Kai ; Wang Linghua ; Gao Jianjun ; Chen JianfengSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensSingle-cell RNA sequencing (scRNA-seq) was performed to characterize cellular heterogeneity and spatial organization in muscle-invasive bladder cancer (MIBC). scRNA-seq was used to define tumor and microenvironmental cell populations and transcriptional states.
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10. GSE325108 RFX5 介导高级结构以调控癌症进展相关基因 [ATAC-seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、ATAC-seq
• 📝 描述：Contributors : Ge Xiao ; Zhang Yijun ; Wang YongmingSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensRFX5 is a DNA binding protein known to regulate MHC genes expressions with little studies on its role in maintaining 3D genome architecture. Recent studies have shown its potential in mediating long-range interactions in specific regions, though the underlying mechanism remains poorly understood. Here, using genes related to cancer progression as a paradigm, we studied the role of RFX5 and found that it specifically regulates these genes. It mediates interactions between gene promoters and their distal enhancers, which can be several hundreds of kilobases apart. We also found that RFX5 regulates higher-order structures of TADs and compartments, which become unstable upon loss of RFX5. Our findings elucidate the fundamental role of RFX5 in maintaining proper chromosome architecture and shed light on the relationship between chromatin loops and gene expression.
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1. 通过囊泡输出进行非破坏性转录组学分析

• ✍️ 作者：未知作者
• 🏷️ 关键词：transcriptomics
• 📝 描述：RNA sequencing with NTVE enables repeated monitoring of gene expression in living cells, supporting time-course analysis of differentiation, perturbation responses, and cellular dynamics…
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2. 利用纳米孔直接RNA测序对多种RNA修饰进行系统评估

• ✍️ 作者：未知作者
• 🏷️ 关键词：sequencing
• 📝 描述：RNA sequencing with nanopore technology reveals how diverse therapeutic RNA modifications affect signal detection, helping define current capabilities and limitations for modification analysis…
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3. 科学家表示，旅行可以延缓衰老，增进健康。

• ✍️ 作者：未知作者
• 🏷️ 关键词：aging
• 📝 描述：A new study suggests travel could be a surprisingly powerful anti-aging tool. By viewing tourism through the lens of entropy, researchers found that positive travel experiences may help the body stay balanced and resilient. Activities like exploring new places, staying active, and connecting with others can boost immunity, metabolism, and stress recovery. However, stressful or unsafe travel could reverse these benefits.
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4. 结肠癌突破性进展使患者近3年内无癌生存

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer
• 📝 描述：A short burst of immunotherapy before surgery is delivering surprisingly powerful results for a specific type of colorectal cancer. Patients in a UK-led trial who received just nine weeks of pembrolizumab prior to surgery have remained cancer-free nearly three years later—an outcome that challenges the standard approach of surgery followed by months of chemotherapy.
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• GSE319968 空间和批量转录组分析定义了皮肤鳞状细胞癌的分子演变，并揭示了具有临床意义的阶段特异性生物标志物 [GeoMx]
• GSE315531 RNA测序分析卵巢癌HGSOC上皮细胞中KLK5的过表达
• GSE311189 整合转录组学和功能分析揭示肉桂精油对宫颈癌细胞的选择性细胞毒性和癌基因抑制作用
• GSE306431 RFX5 介导高级结构以调控癌症进展相关基因 [Hi-C]
• GSE305794 RFX5 介导高级结构以调控癌症进展相关基因 [ChIP-Seq]
• GSE305793 RFX5 介导高级结构以调控癌症进展相关基因 [RNA-Seq]
• GSE297687 Ephrin-A4 配体通过 PI3K/AKT 信号通路促进胃癌细胞上皮-间质转化
• GSE287987 生物合成可塑性使 CD8+ T 细胞在营养胁迫下具有功能恢复力 [多聚核糖体 RNA 测序]
• GSE287894 生物合成可塑性使 CD8+ T 细胞在营养胁迫下具有功能恢复力 [Atf4 & Cebpg KO RNA-seq]
• GSE296448 甘油-3-磷酸脱氢酶1样蛋白通过ATF3介导的铁死亡在结直肠癌中发挥抑癌作用
• GSE329912 小鼠银屑病样炎症模型脾脏组织的转录组分析
• GSE329833 血浆胆固醇升高通过促进肝脏代谢重编程改善脓毒症预后
• GSE326142 Notch驱动的不对称性通过命运特异性激酶决定毛细胞行为
• GSE324380 可诱导 Cdh11 报告基因小鼠成纤维细胞的单细胞 RNA 测序
• GSE324353 全氟壬酸 (PFNA) 暴露后斑马鱼 (Danio rerio) 幼鱼的转录组和行为评估
• GSE311541 RNA-seq 分析了心肌细胞特异性 Pkn2 敲除小鼠和对照小鼠胚胎第 10.5 天心脏的 RNA 测序结果
• GSE305795 RFX5 作为空间染色质接触和基因表达的调节因子
• GSE305790 RFX5 介导高级结构以调控癌症进展相关基因 [4C-Seq]
• GSE299628 转移的 WT 或 Mek1/2-tKO CD45.2+OT-II T 细胞的基因组结合/占有率分析。
• GSE298870 药物抑制硬骨蛋白可保护骨骼免受B细胞急性淋巴细胞白血病介导的破坏
• GSE296920 急性 3 倍气管内注射博来霉素诱导肺纤维化小鼠模型中分选的肺细胞的单细胞 RNA 测序数据
• GSE296918 单细胞RNA测序评估了在纤维化肺疾病模型中，DPT表达成纤维细胞中Tgfbr2缺失的影响
• GSE296916 单细胞 RNA 测序数据来自肺纤维化疾病小鼠模型不同时间点的 PDPN+ 成纤维细胞。
• GSE296912 正常肺和 COPD 肺的单细胞 RNA 测序
• GSE329822 斑马鱼3日龄、5日龄和7日龄pMN神经祖细胞的单细胞RNA测序分析
• GSE329743 神经元分化过程中醚脂重塑可预防铁死亡
• GSE329526 克隆谱系追踪揭示三阴性乳腺癌中不同的侵袭性亚群
• GSE329430 阿尔茨海默病中的骨髓造血功能障碍
• GSE317763 通过自然杀伤细胞活性调节黄斑变性的免疫反应
• GSE293759 人类脾脏固有淋巴细胞的空间和功能特化 [Xenium]
• GSE293758 人类脾脏固有淋巴细胞的空间和功能特化（CITE-seq）
• GSE329468 SEC13 在 NMD 通路中发挥作用，并与核心 NMD 因子共同调节未折叠蛋白反应。
• GSE310296 Polycomb 反应元件的环路特异性需要 GAF 和环路因子的组合代码 [Hi-C]