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1. ⭐ GSE344576 淋巴结收缩与中年时期性别偏向的幼稚 CD8 T 细胞减少和抗原识别受损有关 [TCR-Seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：lymph、T cell、antigen、regex:lymph(o|atic)?
• 📝 描述：Contributors : Lutz Menzel ; Timothy P PaderaSeries Type : OtherOrganism : Mus musculusThe numerical abundance of diverse naive CD8 T cell clones is essential to provide broad protection against infection and cancer. Here, we uncover a sex-biased mechanism of immune aging in which an early, male-biased depletion of naive CD8 T cells driven by accelerated, antigen-agnostic differentiation into virtual memory cells is combined with age-related thymic involution that limits naive CD8 T cell replenishment. These mechanisms lead to contraction of lymph nodes and reduced local naive T cell clone availability, limiting antigen recognition capacity. Therapeutic thymus regeneration via androgen ablation repopulates naive CD8 T cells in lymph nodes, which reinvigorates tumor-specific T cell responses and enhances responsiveness to immune checkpoint blockade. These findings reveal the crucial impact of sex and age on naive T cell clone abundance in lymph nodes and suggest strategies to restore immune competence in middle age males.
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2. ⭐ GSE344535 利用 10x Genomics Flex 固定 RNA 分析技术，在 hTERT RPE-1 细胞中对富集的病毒微蛋白库进行单细胞 ORF 扰动筛选

• ✍️ 作者：未知作者
• 🏷️ 关键词：single-cell、10x、genomics
• 📝 描述：Contributors : Yi H Chen-Neumann ; Jonathan S WeissmanSeries Type : Other ; Expression profiling by high throughput sequencingOrganism : Homo sapiensViral genomes encode large numbers of short open reading frames whose products (microproteins) remain largely uncharacterized. To assay their cellular consequences at scale, we assembled an enriched viral microprotein ORF library in the doxycycline-inducible pANDORA lentiviral vector and delivered it to hTERT RPE-1 cells expressing the pINDUCER20 at low multiplicity of infection (<30% infection rate). The library was split into two sublibraries by insert length (“300mer” and “400mer”). Transduced cells were induced with doxycycline and collected at two time points (24 h and 48 h post-induction), then fixed and profiled by single-cell transcriptomics using the 10x Genomics Single Cell Gene Expression Flex (fixed RNA profiling) assay with 16-plex probe barcoding. ORF identity was read out per cell from a custom probe panel targeting the library inserts, amplified into a dedicated ORF feature library. This dataset comprises paired whole-transcriptome and ORF-assignment measurements for individual cells, enabling the transcriptional consequence of each viral microprotein to be resolved against isogenic controls in the same pool.
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3. ⭐ GSE314273 肿瘤内递送 EpCAM-CD3-Fc 双特异性抗体与 IL-12 和 GM-CSF mRNA-脂质纳米颗粒 (LNP) 可阻断局部和远端肿瘤生长 [RNA-Seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：tumor、antibody、RNA-seq
• 📝 描述：Contributors : Vita Golubovskaya ; Liang Hu ; Shiming Zhang ; John Sienkiewicz ; Hua Zhou ; Michael Li ; Robert Berahovich ; Jinying Sun ; Walter Bodmer ; Lijun WuSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusIntratumoral delivery of mRNA–lipid nanoparticles (LNPs)–encoded bispecific antibodies and immunomodulatory proteins is a promising strategy for tumor eradication, offering potent local activity with limited toxicity and minimal systemic exposure. In this study, we evaluated two combinations of four immunostimulatory mRNAs and found that intratumoral administration of IL-2 and GM-CSF mRNA–LNPs together with EpCAM-CD3-Fc mRNA–LNP in OVCAR-5 and PC3 xenograft models significantly blocked the growth of not only local, treated tumors but also distant, untreated lesions. In PC3 tumors, enhanced local and systemic antitumor activity of the combination treatment was associated with activation of T-cell–related pathways, as revealed by RNA-seq analysis. Key effector genes—including perforin (PRF1), granzyme H (GZMH), CD3E, CD3D, HLA-DPA1, among others—were upregulated following treatment with the bispecific antibody plus immunomodulator mRNA–LNPs, providing mechanistic support for the observed efficacy in both local and distant tumors. Collectively, these data demonstrate that intratumoral delivery of EpCAM-CD3-Fc together with IL-2 and GM-CSF mRNA–LNPs represents a promising approach for future clinical investigation.
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4. ⭐ GSE306151 单细胞测序揭示 BTP-NPs 靶向 TGFβ1 和 PD-L1 在 M109 肺癌模型中的抗肿瘤机制

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、sequencing、single-cell
• 📝 描述：Contributors : Zewen Song ; Yongxuan Du ; Hualing Li ; Guoyin Li ; Zheng Zhu ; Lu ZhangSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusTo investigate the effects of BTP-NPs (targeting TGFβ1 and PD-L1) on the tumor microenvironment in an M109 lung cancer model established in C57BL/6 mice, compared to CBTP-NPs or PBS treatment, using single-cell sequencing
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5. GSE328034 Δ-9-四氢大麻酚 (THC) 通过调节 LPS 诱导的小鼠炎症模式下的免疫反应来缓解炎症

• ✍️ 作者：未知作者
• 🏷️ 关键词：immune、inflammation
• 📝 描述：Contributors : Shallu Tomer ; Jeffrey Harding ; Nandita Kedia ; Ye Zhang ; Anjie ZhenSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensWhile Δ⁹-Tetrahydrocannabinol (THC), is known for its psychoactive effects, its role in modulating complex innate immune cascades remains poorly defined. In this study, we integrated transcriptomic, cellular, and in vivo approaches to investigate how THC regulates lipopolysaccharide (LPS) induced inflammation. Using human THP-1 monocytic cells, we found that THC independently induces a stress-adaptive transcriptional program upregulating genes associated with the unfolded protein response (UPR) and autophagy pathways while robustly suppressing LPS-induced Type-I interferon stimulated genes (ISGs) and pro-inflammatory cytokines such as IL-1β and TNF-α. These results were corroborated in primary human monocytes, where THC significantly reduced the expression of activation markers CD80, CD83, and CD209. In a murine model of systemic inflammation, chronic THC exposure attenuated the activation of splenic myeloid and T cells. Notably, RNA-seq analysis of brain tissue revealed that THC dampened neuroinflammatory gene expression while promoting pathways linked to neurogenesis and synaptic plasticity. Our findings suggest that THC reprograms innate immune cells toward a metabolically adaptive phenotype that limits excessive activation in both the periphery and the central nervous system. This dual action provides a mechanistic framework for the therapeutic potential of cannabinoids in treating chronic inflammatory and neuroimmune disorders.
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6. GSE318529 IL-15 信号在 NK 细胞发育的关键窗口期抑制其成熟和 KIR 获得 [RNA-Seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：NK cell、RNA-seq
• 📝 描述：Contributors : Michael A Ruesch ; Aharon G FreudSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensNatural killer (NK) cells are key mediators of immune surveillance following hematopoietic stem cell transplantation (HSCT). However, despite the known post-conditioning spike in interleukin-15 (IL-15), NK cell maturation is frequently delayed following HSCT. We found that during in vitro NK cell development from CD34+ hematopoietic progenitor cells (HPCs), early exposure to IL-15 drove aberrant mTOR activation, resulting in epigenetic and transcriptional dysregulation and suppressed maturation and KIR acquisition. In contrast, transiently withholding IL-15 or blocking mTOR with rapamycin produced NK cell developmental intermediates intrinsically poised to mature into highly functional, KIR-expressing NK cells. Single-cell analysis of HSCT patients at early time points post-transplant revealed a similar aberrant transcriptional signature of IL-15/mTOR overactivation in circulating donor-derived NK cells. These findings define a developmental window during which IL-15 signaling can paradoxically subvert NK cell maturation and KIR acquisition, suggesting that temporally regulated cytokine signaling could accelerate immune reconstitution and improve therapeutic efficacy.
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7. GSE318453 IL-15 信号在 NK 细胞发育的关键窗口期抑制其成熟和 KIR 获得 [甲基化芯片]

• ✍️ 作者：未知作者
• 🏷️ 关键词：NK cell、methylation
• 📝 描述：Contributors : Michael A Ruesch ; Aharon G Freud ; Christopher C Oakes ; Yue-Zhong WuSeries Type : Methylation profiling by genome tiling arrayOrganism : Homo sapiensNatural killer (NK) cells are key mediators of immune surveillance following hematopoietic stem cell transplantation (HSCT). However, despite the known post-conditioning spike in interleukin-15 (IL-15), NK cell maturation is frequently delayed following HSCT. We found that during in vitro NK cell development from CD34+ hematopoietic progenitor cells (HPCs), early exposure to IL-15 drove aberrant mTOR activation, resulting in epigenetic and transcriptional dysregulation and suppressed maturation and KIR acquisition. In contrast, transiently withholding IL-15 or blocking mTOR with rapamycin produced NK cell developmental intermediates intrinsically poised to mature into highly functional, KIR-expressing NK cells. Single-cell analysis of HSCT patients at early time points post-transplant revealed a similar aberrant transcriptional signature of IL-15/mTOR overactivation in circulating donor-derived NK cells. These findings define a developmental window during which IL-15 signaling can paradoxically subvert NK cell maturation and KIR acquisition, suggesting that temporally regulated cytokine signaling could accelerate immune reconstitution and improve therapeutic efficacy.
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8. GSE312815 肿瘤内递送EpCAM-CD3-Fc双特异性抗体联合IL-12和GM-CSF mRNA-脂质纳米颗粒（LNP）可阻断局部和远端肿瘤生长

• ✍️ 作者：未知作者
• 🏷️ 关键词：tumor、antibody
• 📝 描述：Contributors : Vita Golubovskaya ; Liang Hu ; Shiming Zhang ; John Sienkiewicz ; Hua Zhou ; Michael Li ; Robert Berahovich ; Jinying Sun ; Walter Bodmer ; Lijun WuSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusIntratumoral delivery of mRNA–lipid nanoparticles (LNPs)–encoded bispecific antibodies and immunomodulatory proteins is a promising strategy for tumor eradication, offering potent local activity with limited toxicity and minimal systemic exposure. In this study, we evaluated two combinations of four immunostimulatory mRNAs and found that intratumoral administration of IL-2 and GM-CSF mRNA–LNPs together with EpCAM-CD3 mRNA–LNPs in OVCAR-5 and PC3 xenograft models significantly reduced not only treated tumors but also distant, untreated lesions. In PC3 tumors, enhanced local and systemic antitumor activity of the three-mRNA–LNP combination was associated with activation of T-cell–related pathways, as revealed by RNA-seq analysis. Key effector genes—including perforin (PRF1), granzyme H (GZMH), CD3E, CD3D, HLA-DPA1, among others—were upregulated following treatment with the bispecific antibody plus immunomodulator mRNA–LNPs, providing mechanistic support for the observed efficacy in both local and distant tumors. Collectively, these data demonstrate that intratumoral delivery of EpCAM-CD3 together with IL-2 and GM-CSF mRNA–LNPs represents a promising approach for future clinical investigation.
• 🔗 查看原文

9. GSE344050 评估牙周炎和糖尿病与阿尔茨海默病在小鼠模型中的关联性 [RNA-seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：Alzheimer、RNA-seq
• 📝 描述：Contributors : Momoko Nakahara ; Kota Kataoka ; Takayuki Maruyama ; Daisuke EkuniSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusThe purpose of this study was to investigate the association of periodontitis and diabetes mellitus (DM) with Alzheimer’s disease (AD)-related changes through microRNA (miRNA) using AD model mice. Twenty-four male knock-in mice (B6-AppNL-G-F/NL-G-F/J) were divided into four groups: control (C), DM, periodontitis (P), and DM plus periodontitis (DM+P). After an 8-week experimental period, memory performance was assessed using the Y-maze test, and brain samples were analyzed by next-generation sequencing. miRNA and mRNA expression profiles were evaluated by comparing the DM+P and C groups, and integrated miRNA–mRNA analysis was performed to identify candidate regulatory relationships. Neurod1 protein expression in the hippocampus was also assessed. The DM+P group showed significantly lower memory performance than the C group. Integrated analysis identified seven candidate miRNA–mRNA pairs, among which Neurod1 showed the greatest decrease in mRNA expression and was predicted to be regulated by miR-693-3p. Neurod1 protein expression in the hippocampus was significantly lower in the DM+P group than in the C group. These findings suggest that combined exposure to periodontitis and DM was associated with AD-like pathological changes and alterations in miRNA–mRNA regulatory relationships, with the miR-693-3p/Neurod1 pair identified as a candidate regulatory axis.
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10. GSE336080 伤害感受器神经元抑制乳腺癌的抗肿瘤免疫

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、immunity
• 📝 描述：Contributors : Sebastien Talbot ; Maryam Ahmadi ; Amin Reza NikpoorSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusPeripheral nerves are emerging regulators of the tumor microenvironment, but how sensory innervation shapes breastcancer immunity remains poorly defined. Here we show that triple-negative breast cancers (TNBCs) co-opt nociceptorneurons to suppress antitumor immunity and promote disease progression. Across orthotopic TNBC models, we foundthat primary tumors and tumor-draining lymph nodes were densely innervated by CGRP⁺ sensory fibers. Tumor-derivedcues directly activated dorsal root ganglion neurons, increased calcium responsiveness, induced Ngfr and Atf3, andtriggered release of CGRP and substance P. Mechanistically, a tumor-derived proNGF-NGFR axis reprogrammednociceptors and promoted neuropeptide secretion. Soluble mediators from activated nociceptors suppressed CD8⁺ Tcell-mediated tumor-cell killing, whereas sensory-neuron silencing or ablation curtailed tumor growth and remodeled theimmune microenvironment toward dendritic-cell activation, myeloid reprogramming, and enhanced CD8⁺ T cell and NK-cell effector states. Subset-specific analysis revealed nonredundant sensory control of immune states, with MrgD⁺neurons selectively shaping macrophage-centered programs. Finally, blockade of CGRP signaling through RAMP1 reduced tumor growth and markedly enhanced PD-1 blockade, nearly eliminating primary tumor burden and lungmetastasis in vivo. T cell-specific Ramp1 deletion similarly restrained tumor growth, and RAMP1⁺ CD8⁺ T cells in humanTNBC displayed an exhaustion-associated phenotype. Together, these findings define a tumor-promoting proNGF-nociceptor-CGRP-RAMP1 axis and identify neuroimmune signaling as a therapeuticall
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1. BiocJobs：在 Bioconductor 包中声明可调度作业

• ✍️ 作者：未知作者
• 🏷️ 关键词：Bioconductor
• 📝 描述：The gap Much of what Bioconductor packages do is interactive and exploratory, and rightly belongs in an R session. But some of it is batch-shaped: a well-defined analysis with file inputs, file outputs, and a handful of parameters. Differential… Continue reading: BiocJobs: declaring dispatchable jobs inside Bioconductor packages
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1. ⭐ 科学家发现肠道细菌如何“训练”肠道对抗炎症

• ✍️ 作者：未知作者
• 🏷️ 关键词：bacteria、inflammation、regex:bacter(ia|ial|ium)、gut、regex:gut(-?microbiome)?、regex:intestin(e|al)
• 📝 描述：A compound made when gut bacteria break down dietary fiber may do more than briefly calm inflammation—it could leave a lasting protective “memory” in the gut. Northwestern Medicine researchers found that butyrate can reprogram intestinal lining cells so they continue encouraging anti-inflammatory immune responses even after the compound is gone. In mice, this effect boosted production of the immune-calming molecule IL-10 and reduced the severity of colitis-like disease.
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2. 人工智能或许在你接种疫苗之前就能知道你会对疫苗作何反应。

• ✍️ 作者：未知作者
• 🏷️ 关键词：vaccine
• 📝 描述：AI may be able to predict how strongly someone will respond to a vaccine before they receive it. By analyzing antibody patterns in more than 4,000 people, researchers found signs of “immune readiness” that helped distinguish strong responders from weak ones. Surprisingly, even some healthy people responded poorly, while some immunosuppressed people mounted strong responses.
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3. 一种简单的居家检测方法可以将结直肠癌死亡风险降低43%。

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer
• 📝 描述：People who participated in colorectal cancer screening had a 43% lower risk of dying from the disease, according to long-term data from more than 376,000 people in Sweden. The findings suggest that completing a simple at-home screening test could make a major difference in survival.
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• GSE344470 重建胶质母细胞瘤侵袭的单细胞时空动态
• GSE343577 Raji B 细胞的 RNA 测序
• GSE341625 MAIT细胞通过减少肝内调节性T细胞的数量加剧肝纤维化。
• GSE327194 利用多能干细胞模拟B细胞发育
• GSE319103转录组分析揭示了氮素利用效率（NUE）不同的小麦基因型在应对氮素缺乏时的关键基因差异
• GSE314343 干扰 PADI1 和 PADI3 通过促进非溶解性细胞凋亡，使 KRAS 突变型 PDAC 和 CRC 对 KRAS ON/OFF 抑制剂重新敏感
• GSE311821 PVN–DMV–肝脏通路在抑郁症合并症背景下驱动肝细胞癌进展
• GSE310055 人类视网膜类器官来源的具有增强轴突动力学的红/绿锥细胞前体细胞的鉴定和富集
• GSE303612 RNA测序：胫前肌损伤后7天FACS分离的卫星细胞
• GSE280925 ZCCHC10 促进 RBM39 降解以抑制急性髓系白血病中 RBM39 介导的错误剪接
• GSE344632 纳米二氧化钛缓解草莓微塑料胁迫：生理、根系转录组和根际微生物群落响应的综合分析
• GSE342202 nf_xpatial：用于 Xenium 数据标准化预处理和聚类的可复现框架
• GSE333707 人类脑类器官记录多年时间的流逝 [scRNA-seq]
• GSE318454 IL-15信号在NK细胞发育的关键窗口期抑制其成熟和KIR获得
• GSE318250 IL-15 信号在 NK 细胞发育的关键窗口期抑制其成熟和 KIR 获得 [CITE-seq]
• GSE344057 RNA-seq 对照组和 ALDH3A2 敲低 A549 细胞
• GSE344051 评估牙周炎和糖尿病与阿尔茨海默病在小鼠模型中的关联性 [miRNA-seq]
• GSE342534 长读长单细胞转录组学揭示发育中人类视网膜的亚型偏好性
• GSE337240 GDP驱动的嘌呤代谢重编程促进CD4⁺ T细胞向Th17样极化，并揭示了RANBP1相关的核代谢程序