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1. ⭐ GSE305875 新生儿过度喂养通过终身肠道黏膜和微生物群编程加速与年龄相关的肌肉减少症和代谢紊乱

• ✍️ 作者：未知作者
• 🏷️ 关键词：metabolic、gut、regex:gut(-?microbiome)?
• 📝 描述：Contributors : Yeyu Song ; Jingyi Xu ; Yameng Liu ; Jian-Gao Fan ; Cen XieSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusEarly-life nutrition shapes lifelong health, yet the long-term consequences of childhood overnutrition, particularly on musculoskeletal aging, remain unclear. To address this gap, we employed an established neonatal overfeeding model by reducing litter size, assigning litters to either 4 pups per dam (Overfed group) or 8 pups per dam (Normal-fed control group). To directly examine whether microbiota alterations mediate neonatal overnutrition-induced acceleration of sarcopenia, we performed fecal microbiota transplantation (FMT) experiments. We transplanted microbiota from either aged normal-fed or overfed donor mice into adult recipients (rNormal and rOver groups) maintained on a high-fat diet (HFD) for 20 weeks to accelerate the onset of metabolic and muscular dysfunction. These findings reveal a developmental origin of age-related sarcopenia and define a gut-muscle axis linking childhood overnutrition to muscle aging.
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2. GSE298899 对缺血再灌注损伤小鼠肾脏的空间转录组分析揭示了特定微环境的代谢功能障碍

• ✍️ 作者：未知作者
• 🏷️ 关键词：metabolic、spatial
• 📝 描述：Contributors : Rosalie Rietjens ; Benedetta Manzato ; Ahmed Mahfouz ; Sébastien Dumas ; Gangqi Wang ; Ton RabelinkSeries Type : OtherOrganism : Mus musculusThis study presents spatial transcriptomic data from mouse kidneys subjected to ischemia-reperfusion injury to investigate the molecular underpinnings of localized tissue responses. Using high-resolution Stereo-seq spatial transcriptomics, we profiled gene expression across healthy and injured renal microenvironments, focusing on areas surrounding failed repair proximal tubule (FR-PT) cells. Transcriptomic analysis revealed distinct niches characterized by downregulation of oxidative phosphorylation and fatty acid β-oxidation pathways, even in proximal tubule cells considered heatlhy.
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3. GSE328445 Adm 和 Ackr3 调控斑马鱼心脏发育和再生过程中的心脏淋巴管形成

• ✍️ 作者：未知作者
• 🏷️ 关键词：regex:lymph(o|atic)?、cardiac
• 📝 描述：Contributors : Sun Yuhan ; Feng Xidi ; Lien Ching-LingSeries Type : Expression profiling by high throughput sequencingOrganism : Danio rerioIt is well established that lymphatic vessels regulate interstitial fluid homeostasis and facilitate the transport of macromolecules and immune cells. However, the molecular mechanisms underlying cardiac lymphatic vessel formation during heart development and regeneration remain unclear. Single-cell RNA sequencing revealed that, during heart regeneration, ackr3a mutants exhibit altered LEC subcluster compositions and differential expression of several candidate downstream genes. Our findings uncover the heterogeneity of cardiac LECs and demonstrate that the Adm–Ackr3 decoy receptor axis regulates cardiac lymphatic vessel formation during zebrafish heart development and regeneration.
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4. GSE325755 空间膜脂质重塑编码人类结肠癌上皮细胞谱系和状态

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、spatial
• 📝 描述：Contributors : Ramon M Rodriguez ; Karim Perez-Romero ; Albert Maimo-Barcelo ; Teresa Ximelis ; Cristina Huergo-Baños ; Marcos A Martinez ; J J Segura-Sampedro ; R Morales-Soriano ; Alvaro Garcia-Granero ; Sebastian Jeri ; Ana M Aransay ; José-Andrés Fernández ; Gwendolyn Barceló-CoblijnSeries Type : OtherOrganism : Homo sapiensCancer progression is driven by profound intratumoral heterogeneity that is spatially organized within tissues, yet remains difficult to resolve at the molecular level. While transcriptomic spatial approaches have advanced rapidly, the spatial organization and functional relevance of tumor lipid metabolism remain poorly understood. Here, we present an integrative spatial multi-omic strategy that anchors high-resolution lipid imaging to transcriptome-defined cellular states. Applying this approach to human primary and metastatic colon cancer specimens, we jointly profiled spatial lipid distributions and gene expression across tumor epithelial compartments. This approach revealed specific, spatially restricted epithelial lipid phenotypes defined by membrane phospholipid composition. These lipid phenotypes were tightly associated with transcriptional programs reflecting epithelial lineage, differentiation state, and proliferative activity. In addition, we observed that secretory-associated epithelial states were enriched in metastatic lesions and were associated with increased levels of DHA-containing phospholipids and transcriptional activation of peroxisomal lipid metabolic pathways. Together, these findings demonstrate that membrane phospholipid composition encodes biologically meaningful epithelial cell states within human tumors. More broadly, this work establishes a generalizable strategy for interpreting spatial lipidomic data through biologically informed integration with spatial transcriptomics, enabling cell-state–resolved metabolic phenotyping in cancer.
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5. GSE343381 二氮烯二醇盐信号 valdiazen 是植物伯克霍尔德氏菌毒力和次级代谢的全局调控因子

• ✍️ 作者：未知作者
• 🏷️ 关键词：metabolism
• 📝 描述：Contributors : María Rodríguez-García ; Simon Sieber ; Paula Bellés-Sancho ; Yi-Chi Chen ; Gabriella Pessi ; Anugraha Mathew ; Karl Gademann ; Leo EberlSeries Type : Expression profiling by high throughput sequencingOrganism : Burkholderia plantariiThe diazeniumdiolate signal family, first identified in Burkholderia cenocepacia H111, now includes a newly discovered member in the rice pathogen Burkholderia plantarii PG1. Here, we show that the ham gene cluster directs the biosynthesis of the diazeniumdiolate signal valdiazen and is required for both antifungal activity and virulence. Transcriptome analysis identified a valdiazen regulon comprising 390 genes, including genes within and flanking the ham cluster, indicating roles in signal modulation, transport and autoregulation. Valdiazen also globally controls genes involved in secondary metabolism and the expression of several bioactive metabolites, including those required for tropolone biosynthesis and the type III secretion system. We further identify tropolone as the major antifungal metabolite of B. plantarii and demonstrate that its antifungal activity is mediated through iron chelation. An AraC family transcriptional regulator located upstream of the ham cluster regulates valdiazen biosynthesis and the downstream regulatory network. Together, these results establish valdiazen as a global signaling molecule that coordinates diverse aspects of bacterial physiology and integrates with the three classical homoserine lactone-based quorum-sensing systems.
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6. GSE341347 平衡脂质合成和氧化可促进实体器官移植受者对疫苗接种的B细胞反应

• ✍️ 作者：未知作者
• 🏷️ 关键词：B cell
• 📝 描述：Contributors : Elizabeth Thompson ; Nicole Skinner ; Andrea Cox ; Justin BaileySeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensPharmacologic immunosuppression is essential for preventing organ rejection and controlling autoimmunity, but profoundly impairs humoral immunity, increasing the risk of vaccine failure and infection. The mechanisms by which immunosuppressive therapies disrupt human B cell responses remain poorly defined. Here, we identified dysregulated lipid metabolism as a central determinant of impaired vaccine response in solid organ transplant recipients (SOTRs). We performed 10x genomics single cell RNA sequencing on isolated B cells from SOTRs and healthy controls before and after a third COVID-19 vaccine dose. The widely used immunosuppressive agent, mycophenolic acid (MPA) was strongly associated with vaccine non-response and induced excessive lipid synthesis, lipid accumulation, and mitochondrial stress in B cells.
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7. GSE319406 接种减毒活流感疫苗后，终末分化的流感特异性效应记忆 B 细胞循环 [scRNA-Seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：scRNA
• 📝 描述：Contributors : Anoma Nellore ; Christopher F Fucile ; Christopher Scharer ; Jack T Geer ; Jacey Lemonds ; Betty Mousseau ; Fen Zhou ; Esther Zumaquero ; Jobaida Akhter ; Paul A Goepfert ; Ralf Duerr ; Ramin S Herati ; Alexander Rosenberg ; Frances E Lund ; Troy RandallSeries Type : Expression profiling by high throughput sequencing ; OtherOrganism : Homo sapiensLive attenuated influenza vaccination (LAIV) is the only FDA approved mucosal vaccine. Easily assayed, circulating correlates of protection after LAIV are lacking. Using fluorochrome labeled hemagglutinin (HA) antigen, we previously identified a subset of HA-specific (HA+) IgDneg memory B cells that circulate after inactivated intramuscular vaccination (IIV), express the master transcriptional regulator, T-bet, as well as effector memory genes and predict durable antibody (Ab) responses to IIV. Here we profile the circulating HA+ IgDneg memory B cell response in a cohort of immunized patients who seroconvert after LAIV to identify which, if any, circulating HA+ B cells predict antibody responses after LAIV. Although we report LAIV elicits circulating T-bet+ HA+ IgDneg B cells that are phenotypically similar to those we described after IIV, we find no correlation between the magnitude of these cells and systemic HA-IgG responses after LAIV. Supervised and unsupervised analyses demonstrate that unlike IIV, LAIV preferentially elicits circulating HA+ IgDneg B cells that co-express TBX21 and the terminal effector cell gene, Zeb2. Consistent with their terminal differentiation status, LAIV-elicited T-bet+ cells cannot be recalled as short-lived antibody-secreting cells (ASCs) after systemic or mucosal antigen re-challenge. We conclude that the transcriptional profiles and functions of HA+ IgDneg B cells vary by influenza vaccine platform.
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8. GSE296098 TRAF6 缺陷患者全血细胞的 Bluk RNAseq 分析。

• ✍️ 作者：未知作者
• 🏷️ 关键词：RNAseq
• 📝 描述：Contributors : Yuwei Hao ; Cindy Lee ; Zhi-Ping Feng ; Matthew CookSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensBulk RNAseq was performed for whole blood cells from a TRAF6-/- patient and an age-matched healthy control. The TRAF6-/- patient with lymphoproliferation showed increased T cell transcripts and an enrichment of CD4+ T cell-related markers.
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9. GSE344584 奥拉帕尼联合曲美木单抗治疗携带生殖系 BRCA1 或 BRCA2 突变的复发性卵巢癌女性患者：一项 I/II 期研究

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer
• 📝 描述：Contributors : Sarah F Adams ; Phyllis A Gimotty ; Teresa L Rutledge ; David M O’Malley ; Kari Ring ; Robert M Wenham ; Karen Finkelstein ; Elizabeth Lokich ; Daniel M Falcon ; Allyson Yeckes ; Olufunmilola M Oyebamiji ; Kathryn J Brayer ; Eleanor Paskus ; Nadja K Falk ; Ryland Richards ; Ji-Hyun Lee ; Steven C Eberhardt ; Dennis McCance ; Xavier Paliard ; Sean Boyle ; Richard Chen ; Huining Kang ; Jose R Conejo-Garcia ; Olivier Rixe ; Carolyn Y MullerSeries Type : OtherOrganism : Homo sapiensResponse rates to immune checkpoint blockade (ICB) in ovarian cancer are low. In preclinical studies, poly(ADP-ribose) polymerase (PARP) inhibition synergized with CTLA4 ICB to achieve long-term survival in Brca1-deficient ovarian cancer models. Here, we evaluated the safety and efficacy of combined treatment with the PARP inhibitor olaparib and the CTLA4 ICB tremelimumab for recurrent epithelial ovarian cancer in a multi-site single-arm phase I/II study enrolling 50 women with a germline BRCA1 or BRCA2 mutation (NCT0257125). Grade 3 or 4 non-hematologic toxicity was reported in 57% of subjects, with tremelimumab discontinuation in 34.7%. The overall response rate was 32.7% (95% CI 19.5-45.8%), with a disease control rate of 47.7% (95% CI 33.0-62.5%). In exploratory biomarker analyses, low VSTM5 or IFIT1B expression was associated with treatment benefit and progression-free survival (p<0.001). Although this trial did not meet its prespecified efficacy endpoint, durable responses in some subjects in this heavily pre-treated cohort highlight the need for predictive biomarkers to select combinatorial regimens for patients with recurrent ovarian cancer.
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10. GSE325828 皮质丘脑组装体重现了人类胎儿脑形态并增强了神经元复杂性

• ✍️ 作者：未知作者
• 🏷️ 关键词：Neuronal
• 📝 描述：Contributors : A S Antunes ; M C Athié ; A C Silveira ; J Renner ; E V Dias ; J V dos Santos ; B Hrvoj-Mihic ; C Canateli ; J Meidanis ; A R Muotri ; A S Vieira ; A A Rasia-Filho ; S H AvansiniSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensNeuronal morphology governs how neurons connect, integrate, and process information, offering critical insights into the functional architecture of the brain. Characterizing the three-dimensional (3D) morphology of individual neurons is key not only for mapping circuit connectivity but also for understanding the cellular diversity that emerges during development. Neural organoids are valuable models of human brain development and disease, yet their morphological complexity remains poorly characterized despite advances in single-cell transcriptomics. Here, we use 3D confocal imaging and manual reconstruction of 735 neurons to analyze forebrain (dorsal and ventral) and thalamic (dorsal and ventral) organoids, as well as forebrain, thalamic, and corticothalamic assembloids. We find that organoids and assembloids exhibit distinct morphologies resembling fetal brain neurons, including immature pyramidal-like, double-bouquet, and bushy-like neurons. Interregional assembloids show greater neuronal morphological complexity than individual organoids, with more extensive dendritic branching, longer projections, and diverse soma shapes. Corticothalamic assembloids further display features of emerging connectivity. Complementary transcriptomic profiling supports regional identity and reveals expression of genes involved in projection guidance. We observe dendritic spines with excitatory and inhibitory profiles and varicosities, indicative of maturing synaptic architecture. Together, our work makes an initial effort in describing the diversity of neuronal morphology in human neural organoids and assembloids. It further establishes structural phenotyping as a critical dimension for validating human neural models and underscores their value for modeling morphofunctional disorders.
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1. ⭐ ARCADIA结合了RNA测序和空间蛋白质组学，揭示了组织位置如何影响细胞行为。

• ✍️ 作者：未知作者
• 🏷️ 关键词：sequencing、spatial、proteomics
• 📝 描述：ARCADIA integrates single-cell RNA sequencing with spatial proteomics to reveal how tissue neighborhoods influence B-cell maturation, T-cell activation, and other transcriptional programs…
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2. 单细胞数据中超快速且无需参考序列的序列发现

• ✍️ 作者：未知作者
• 🏷️ 关键词：single-cell
• 📝 描述：Malva enables ultrafast, reference-free searches across massive single-cell RNA sequencing datasets for mutations, splice junctions, pathogens, transcripts, and other sequence-level features…
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3. 智能纳米粒子可照亮脑癌细胞并摧毁手术遗漏的组织。

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer
• 📝 描述：Scientists created smart nanoparticles that can both illuminate hidden glioblastoma cells during surgery and destroy microscopic cancer left behind afterward. In mice, the treatment prevented recurrence and led to 100% survival at 60 days, though it has not yet been tested in humans.
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4. 多吃超加工食品可能会使前列腺癌风险增加30%。

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer
• 📝 描述：Ultra-processed foods make up a huge share of the American diet, and new research suggests they may carry another serious health risk for men. In a nationally representative study of more than 17,000 U.S. men, those who ate more ultra-processed foods, including soft drinks, packaged snacks, cereals, and processed meats, had roughly 24% to 31% higher risks of prostate cancer after accounting for factors such as age, smoking, race and ethnicity, and poverty status.
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• GSE330811 野生型 (WT) 和 Gα12 敲除小鼠 (Gα12 KO) 喂食正常饲料 (NCD) 或高脂饲料 (HFD) 的小鼠性腺白色脂肪组织 (gWAT) 的转录组分析
• GSE328466 SETD6介导的PPARγ甲基化建立了一个转录反馈回路，促进肝源性细胞中的脂质积累。
• GSE315876 GSEC编码的多肽GESP通过NPM1-c-Myc介导的NDRG1抑制驱动结直肠癌的肿瘤发生
• GSE305870 对野生型 (WT)、脂肪细胞特异性 Gα13 敲除 (Gα13 AKO) 和 Gα12/13 双敲除 (Gα12/13 DKO；Gα13 AKO 与全身性 Gα12 缺失相结合) 小鼠的性腺白色脂肪组织 (gWAT) 进行深度测序
• GSE305406 IL17D 过表达和对照 H460 细胞的 ATAC-seq 数据
• GSE156518 MHV-68 对易感细胞进行从头感染的批量细胞 RNA-seq 分析。