详细内容（前10条）

1. ⭐ GSE275418 断奶驱动的肠道微生物群塑造肠道干细胞表观遗传学以训练免疫记忆（RNA-seq）

• ✍️ 作者：未知作者
• 🏷️ 关键词：RNA-seq、gut、regex:gut(-?microbiome)?、regex:intestin(e|al)
• 📝 描述：Contributors : Li Yang ; Lanlan ShenSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusDuring weaning, the transition to solid food diversifies the gut microbiome, triggering a programmed immune response critical for long-lasting mucosal immunity. Previous work showed that the gut microbiome mediates epigenetic development in intestinal stem cells (ISCs) during suckling, but what happens during weaning is unclear. Here, using genome-wide methylation profiling revealed that weaning-driven microbiome changes shape the DNA methylome and transcriptome of murine ISCs in an IFN-g dependent manner. Specifically, we observe demethylation of enhancer elements essential for MHC class II genes, which result in a transcriptional memory that persists through differentiation into adulthood. IFN-g blockade, or low-dose penicillin to target Gram-positive bacteria, in early life impaired microbiome-mediated epigenetic control and mucosal immunity, and exacerbated colitis. Murine organoids primed with IFN-g showed rapid, amplified transcriptional responses upon secondary stimulations. These findings reveal that early-life events alter the gut microbiome and these changes reprogram ISC epigenetic memory to shape mucosal immunity.
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2. ⭐ GSE316301 肿瘤基质蛋白聚糖的积累和加工改变了寡转移性结直肠癌中T细胞的效应功能和对免疫疗法的反应

• ✍️ 作者：未知作者
• 🏷️ 关键词：tumor、cancer、T cell、regex:immuno(logy|therapy|suppression)
• 📝 描述：Contributors : Dustin Deming ; Sean Krau ; Joshua Brand ; Katherine Johnson ; Daniel Abbott ; Jeremy Kratz ; Anita Turk ; Philip Emmeric ; Evie Carchman ; Sam Lubner ; Noelle LoConte ; Anita Turk ; Nataliya Uboha ; Somak Chaudhuri ; Ruchi Shah ; Anna Field ; Elizabeth Field ; Cheri Pasch ; David Kim ; Sharon Weber ; Charles Heise ; Elise Lawson ; Cristina Sanger ; Kristina Matkowskyj ; Fotis Asimakopoulos ; Jens Eickhoff ; Huy Dinh ; Michael BassettiSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensVersican (VCAN) is an immunoregulatory extracellular matrix proteoglycan that when cleaved by ADAMTS proteases releases an immunostimulatory fragment, versikine. Here, we confirm that VCAN accumulates within colorectal cancers (CRCs) and inhibits T cell trafficking/effector function. VCAN is heavily proteolyzed in a subset of CRCs (VCAN proteolytic predominant (VPP)), leading to enhanced T cell infiltration. This phenotype was found to be more common in oligometastatic CRCs. A phase 1b clinical trial examined the safety/efficacy of the sequential combination of stereotactic body radiotherapy and pembrolizumab in patients undergoing resection of their microsatellite stable oligometastatic CRCs. The primary endpoint was met with a 1-year recurrence free survival (RFS) of 60%. Of those enrolled, 40% of cancers had the VPP phenotype, which was associated with improved RFS and overall survival. The VPP phenotype was associated with improved circulating T cell effector function, which was enhanced with study treatment. Clinical trial information: NCT02837263.
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3. ⭐ GSE280079 放射疗法与基于 AAV 的免疫疗法协同作用，可诱导局部和全身抗肿瘤免疫 [RNA-Seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：immunity、regex:immuno(logy|therapy|suppression)、RNA-seq
• 📝 描述：Contributors : Juan Dubrot ; Jesús Prieto ; Elizabeth Guruceaga ; Sonia MarcoSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusRadiotherapy (RT) primes the immune system against cancer antigens but fails to trigger effective antitumor responses due to concomitant induction of immunosuppressive factors. To expand the benefits of RT, we combine local radiation with immuno-gene therapy by harnessing the ability of ionizing radiation to enhance AAV-mediated tumor transduction. To successfully deliver AAV-based local immunotherapy and restrict transgene expression within tumors, we designed a recombinant AAV that expresses IL-12 through an interferon (IFN)-inducible promoter (AAV-iIL12). Local administration of AAV-iIL12 upon RT results in marked and durable elevation of intratumor IL-12 with minor and transient systemic release. This strategy generates a highly immunostimulatory tumor microenvironment (TME) leading to strong antitumor responses in an IFNg-dependent manner. Moreover, local treatment with RT and AAV-iIL12 elicits systemic antitumor immunity with marked CD8+ T cell infiltration and regression of distant tumors. Our work shows that radiation coupled with AAV-based immuno-gene delivery is a novel, efficient and safe approach that can be exploited as cancer therapy.
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4. ⭐ GSE280078 放射疗法与基于 AAV 的免疫疗法协同作用，可诱导局部和全身抗肿瘤免疫 [scRNA-Seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：immunity、regex:immuno(logy|therapy|suppression)、scRNA
• 📝 描述：Contributors : Juan Dubrot ; Jesús Prieto ; Elizabeth Guruceaga ; Seth Anderson ; Sonia MarcoSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusRadiotherapy (RT) primes the immune system against cancer antigens but fails to trigger effective antitumor responses due to concomitant induction of immunosuppressive factors. To expand the benefits of RT, we combine local radiation with immuno-gene therapy by harnessing the ability of ionizing radiation to enhance AAV-mediated tumor transduction. To successfully deliver AAV-based local immunotherapy and restrict transgene expression within tumors, we designed a recombinant AAV that expresses IL-12 through an interferon (IFN)-inducible promoter (AAV-iIL12). Local administration of AAV-iIL12 upon RT results in marked and durable elevation of intratumor IL-12 with minor and transient systemic release. This strategy generates a highly immunostimulatory tumor microenvironment (TME) leading to strong antitumor responses in an IFNg-dependent manner. Moreover, local treatment with RT and AAV-iIL12 elicits systemic antitumor immunity with marked CD8+ T cell infiltration and regression of distant tumors. Our work shows that radiation coupled with AAV-based immuno-gene delivery is a novel, efficient and safe approach that can be exploited as cancer therapy.
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5. ⭐ GSE279313 TGF-β 控制 IFN 抗病毒训练免疫的表观遗传重编程并损害 SIV 感染恒河猴的病毒控制 [bulk RNA-seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：immunity、RNA-seq、epigenetic
• 📝 描述：Contributors : Felipe ten-Caten ; Khader Ghneim ; Mirko Paiardini ; Susan P Ribeiro ; Rafick P SekalySeries Type : Expression profiling by high throughput sequencingOrganism : Macaca mulattaCurrent immunotherapeutic approaches to eliminate latently HIV-infected cells have focused on targeting the adaptive arm of the immune system using vaccines and passive transfer of broadly neutralizing antibodies (bNAbs). Epigenetic reprogramming of innate myeloid cells triggered by adjuvants was recently shown to promote a state of interferon (IFN)-induced antiviral immunity and resistance to heterologous viral infections. Herein, flow cytometry, bulk and single-cell RNA-Seq/ATAC-Seq were performed on samples from a cohort of SIV-infected, virologically suppressed rhesus macaques (RMs) treated with anti-IL-10 and anti-PD-1 monoclonal antibodies (combo treatment) prior to analytical treatment interruption (ATI). These experiments revealed that combo treatment led to selective changes in chromatin accessibility, expression of IRF7/3 and STAT1, and expression of IFN-stimulated antiviral genes in myeloid cells and CD4+ T cells. These RMs showed a stringent and prolonged control of SIV viral rebound following ATI and a decay in levels of cell-associated viral DNA (CA-vDNA) in lymph nodes. These RMs showed reduced chromatin accessibility for the SMAD2/SMAD3, AP-1, and NFKB1 loci and lower expression of TGF-b and SMADs target genes. This signature is consistent with that observed in HIV elite controllers, who maintain undetectable levels of virus in the absence of ART and whose HIV reservoir size is small. These results highlight the critical role of the interplay between TGF-b and IFN in epigenetically regulated innate antiviral immune responses that can impact the viral reservoir.
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6. ⭐ GSE314342 人类原代 CD4+ T 细胞的基因组规模扰动测序揭示了调控 T 细胞程序和人类免疫特征的基因。

• ✍️ 作者：未知作者
• 🏷️ 关键词：immune、T cell、genome
• 📝 描述：Contributors : Ronghui Zhu ; Emma Dann ; Jun Yan ; Justine Reyes Retana ; Ryunosuke Goto ; Reese C Guitche ; Lillian K Petersen ; Mineto Ota ; Brian R Shy ; Jonathan K Pritchard ; Alexander MarsonSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensCD4+ T cells orchestrate immune responses against infection and cancer, yet a comprehensive map of their gene regulatory networks has been lacking. Perturb-seq enables systematic mapping of such networks, but large-scale application in primary human T cells has been challenging. Here, we developed a scalable, probe-based Perturb-seq platform and performed genome-scale perturbations of all expressed genes across 22 million primary CD4+ T cells from four donors under three stimulation conditions. We demonstrate the utility of this dataset in three ways. First, we identify previously unrecognized regulators of the two important immune cytokines, IL-10 and IL-21. Second, we show that ex vivo perturbation signatures can model T cell states observed in population-scale atlases, revealing regulators of helper T cell polarization and T cell aging. Third, we leverage regulatory relationships to mechanistically explain gene–trait associations in immune-related diseases, nominating genes for uncharacterized immune functions. Thus genome-scale perturb-seq in primary human T cells provides a foundational resource for decoding immune variation in humans and reprogramming T cell states for next-generation precision therapies.
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7. ⭐ GSE310995 断奶驱动的肠道微生物群塑造肠道干细胞表观遗传学以训练免疫记忆（全基因组测序）

• ✍️ 作者：未知作者
• 🏷️ 关键词：gut、regex:gut(-?microbiome)?、regex:intestin(e|al)
• 📝 描述：Contributors : Li Yang ; Lanlan ShenSeries Type : OtherOrganism : Mus musculusDuring weaning, the shift from milk to solid food is accompanied by a rapid expansion and diversification of the gut microbiome. This triggers the weaning reaction, a programmed immune response important for long-lasting mucosal immunity that is poorly understood. Here, we characterize the impact of the gut microbiome on the DNA methylome and transcriptome of intestinal stem cells (ISCs) from weaning to young adulthood in mice. We identify a weaning- IFN-g-TET3 axis that reprograms epithelial MHC-II signaling via enhancer demethylation in ISCs, establishing a lasting transcriptional memory into adulthood. Disruption of this axis by IFN-g blockade or low-dose penicillin attenuates the microbiota-mediated epigenetic control of epithelial MHC-II signaling, leading to impaired mucosal immunity. By engaging immune crosstalk and metabolite production, the weaning microbiome drives epigenetic reprogramming, thereby establishing a microbiome-induced regulatory pathway that couples developmental cues to lifelong epithelial immune resilience.
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8. ⭐ GSE275219 断奶驱动的肠道微生物群塑造肠道干细胞表观遗传学以训练免疫记忆 (WGBS)

• ✍️ 作者：未知作者
• 🏷️ 关键词：gut、regex:gut(-?microbiome)?、regex:intestin(e|al)
• 📝 描述：Contributors : Li Yang ; Lanlan ShenSeries Type : Methylation profiling by high throughput sequencingOrganism : Mus musculusDuring weaning, the transition from milk to solid food rapidly expands and diversifies the gut microbiome, triggering the weaning reaction, a programmed immune response critical for long-lasting mucosal immunity. We characterized how these microbiome changes from weaning through young adulthood in mice shape the DNA methylome and transcriptome of intestinal stem cells (ISCs). We identified a weaning-induced IFN-g–TET3 axis as a key driver of MHC class II enhancer-linked epigenetic reprogramming, creating a transcriptional memory that persists through differentiation into adulthood. Early-life disruption of this axis, via IFN-g blockade or low-dose penicillin, impaired microbiota-mediated epigenetic control and mucosal immunity. Weaning-associated microbiome shifts enriched metabolites such as α-ketoglutarate, Fe2+, and methionine g-lyase, promoting TET-dependent DNA demethylation. These findings reveal how early-life events imprint lifelong epigenetic regulation of mucosal immunity, highlighting epithelial cells as innate immune sentinels that acquire trained transcriptional memory in response to microbial cues.
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9. ⭐ GSE318371 新诊断的NK/T细胞淋巴瘤患者外周血单核细胞单细胞图谱

• ✍️ 作者：未知作者
• 🏷️ 关键词：lymphoma、T cell、single-cell
• 📝 描述：Contributors : Xiaozhen Liang ; Rong Tao ; Ran Jia ; Chuanxu LiuSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensNatural killer/T cell lymphoma (NKTCL) is a rare and aggressive form of non-Hodgkin’s lymphoma associated with Epstein-Barr Virus (EBV) infection.The recent advancement of multi-omics technologies has significantly enhanced our understanding of NKTCL disease biology, including genetics, transcription landscape, variations of EBV strain, and microenvironments. Emerging evidence suggests that immunoprofiling of peripheral blood mononuclear cells (PBMCs) is associated with the treatment response of cancer patients and can be used to guide clinical trials and therapy. In this study, we utilized single-cell RNA sequencing (scRNA-seq) to comprehensively characterize the phenotypic landscape of PBMCs in newly diagnosed patients with NKTCL. This research offers a valuable peripheral blood-based signature for newly diagnosed NKTCL, which could be a crucial resource for further investigations into the pathogenesis of NKTCL and the optimization of therapeutic regimens.
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10. ⭐ GSE317297 卵巢炎症衰老的多细胞起源 [空间转录组学]

• ✍️ 作者：未知作者
• 🏷️ 关键词：spatial、spatial transcriptomics、transcriptomics
• 📝 描述：Contributors : Anna Galligos ; Joseph Varberg ; Wei-Ting Yueh ; Aubrey Converse ; Seth Malloy ; Fatimah Aljubran ; Francesca E Duncan ; Jennifer L GertonSeries Type : OtherOrganism : Mus musculusAge-dependent reproductive decline has become a significant global health concern as the average maternal age at first birth increases. Fertility loss associated with reproductive aging is driven in part by alterations to ovarian composition and function, dysregulation of folliculogenesis and increased inflammatory signaling. Our understanding of the molecular changes underlying ovarian aging has been expanded by single cell and spatial transcriptomic studies, which identified infiltration of immune cells as a feature of ovarian aging. However, the function of these age-associated immune cells and their potential contributions to the inflammaging phenotype remains unclear. In this study we integrate single cell and spatial transcriptomics to define changes in the composition and intercellular signaling in the aging mouse ovary. We identify specific macrophage and T cell subpopulations that increase with age and are key sources of pro-inflammatory signaling in old ovaries. Further, we predict bidirectional signaling between these pro-inflammatory cells and granulosa cell populations that may impair follicular growth and development while promoting immune cell recruitment. These findings provide new insights into the mechanisms that drive ovarian inflammaging.
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详细内容（全部3条）

1. 一种免疫变量可以预测不同肿瘤类型和物种的不良预后。

• ✍️ 作者：未知作者
• 🏷️ 关键词：tumor、immune
• 📝 描述：Using RNA sequencing, researchers identify a conserved pro-tumor neutrophil state marked by CCL3 expression, revealing how specific immune cell programs support cancer growth across tumor types…
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2. 为什么结直肠癌会打破免疫系统的规则

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer、immune
• 📝 描述：Colorectal cancer has long baffled scientists because, unlike most tumors, patients often do better when their cancers are packed with immune-suppressing regulatory T cells. New research finally explains why. Scientists discovered that these T cells aren’t all the same: one subtype actually helps keep tumors in check, while another shields cancer from immune attack. The balance between these “good” and “bad” cells can determine whether a tumor grows or shrinks.
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3. 利用纳米孔测序直接读取RNA修饰

• ✍️ 作者：未知作者
• 🏷️ 关键词：sequencing
• 📝 描述：New RNA sequencing tools enable direct detection of multiple RNA modifications from nanopore data, simplifying epitranscriptome analysis with a single modification-aware basecalling model…
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• GSE318384 整合多组学分析揭示 METTL3 过表达在 A549 肺癌细胞中引起的抑癌表型及相关转录组重塑
• GSE298505 蛋白激酶 CK2α’ 作为 Tau 蛋白病中免疫信号传导和突触功能障碍的双重调节因子
• GSE294115 单细胞多模态分析揭示糖尿病小鼠尽管血糖控制良好，主动脉平滑肌细胞仍持续发生变化 [scATAC-seq]
• GSE294114 单细胞多模态分析揭示糖尿病小鼠尽管血糖控制良好，主动脉平滑肌细胞仍持续发生变化 [scRNA-seq]
• GSE282071 拟南芥 ROS1 在调节染色质可及性和 DNA 甲基化中的多种作用 [ChIP-seq]
• GSE280080 放射疗法与基于AAV的免疫疗法协同作用，可诱导局部和全身抗肿瘤免疫反应。
• GSE279314 TGF-β 控制 IFN 抗病毒训练免疫的表观遗传重编程，并损害 SIV 感染恒河猴的病毒控制 [scMultiome]
• GSE318611 果蝇黑腹果蝇嗅觉投射神经元在蛹形成后 12 小时 (h APF) 的单细胞转录组谱
• GSE302760 抑制LSD1可解锁类视黄醇AP-1程序，从而激活上皮免疫和皮肤肿瘤抑制
• GSE302485 抑制 LSD1 可解锁类视黄醇 AP-1 编程，从而激活上皮免疫和皮肤肿瘤抑制 [RNAseq_LSD1iRARi]
• GSE302483 抑制 LSD1 可解锁类视黄醇 AP-1 编程，从而激活上皮免疫和皮肤肿瘤抑制 [CutRun_LSD1i48h]
• GSE302480 抑制 LSD1 可解锁类视黄醇 AP-1 编程，从而激活上皮免疫和皮肤肿瘤抑制 [CreERTRNAseq]
• GSE302477 抑制 LSD1 可解锁类视黄醇 AP-1 编程，从而激活上皮免疫和皮肤肿瘤抑制 [CreERTCutRun]
• GSE302474 抑制 LSD1 可解锁类视黄醇 AP-1 编程，从而激活上皮免疫和皮肤肿瘤抑制 [Xenium CreERT]
• GSE302473 抑制 LSD1 可解锁类视黄醇 AP-1 编程，从而激活上皮免疫和皮肤肿瘤抑制 [Xenium 肿瘤]
• GSE302470 抑制 LSD1 可解锁类视黄醇 AP-1 编程，从而激活上皮免疫和皮肤肿瘤抑制 [Xenium 胚胎]
• GSE299107 炎症性 epiCaspase-1 通过远程偏向骨髓造血来抑制免疫原性细胞死亡，从而驱动以中性粒细胞为主的全身性炎症 [T24 RNAseq]
• GSE317789 单细胞和空间分析揭示了皮肤和黏膜扁平苔藓中 cDC2A-CXCL13+ CD8+ T 上皮细胞通过 TNFRSF9 进行串扰和细胞毒性
• GSE318649 载体和谷氨酸硼酸处理小鼠脾脏免疫细胞的单细胞RNA测序数据[重复实验]
• GSE289185 新辅助放疗和免疫疗法治疗食管鳞状细胞癌的安全性和有效性
• GSE294237 单细胞多模态分析揭示糖尿病小鼠尽管血糖控制良好，主动脉平滑肌细胞仍持续发生改变
• GSE291420 解读小鼠各器官衰老的转录组特征
• GSE289338 RNA-Seq 分析人足细胞中 ATOH8 敲低
• GSE282075 ROS1：拟南芥中可及染色质的关键标记和调节因子 [RNA-Seq]
• GSE282073 拟南芥 ROS1 在调节染色质可及性和 DNA 甲基化中的多种作用 [亚硫酸氢盐测序]
• GSE282072 ROS1: Key Marker and Regulator of Accessible Chromatin in Arabidopsis [ATAC-Seq]
• GSE281781 MYC 与新生 RNA 的结合通过 R 环衍生的 RNA-DNA 杂交体抑制先天免疫信号传导
• GSE259427 miR-203 控制植入前胚胎发生过程中的发育时序和早期命运限制（scRNA-Seq）
• GSE259426 miR-203 控制植入前胚胎发生过程中的发育时序和早期命运限制（RNA-Seq）
• GSE317412 膳食谷氨酰胺补充剂通过限制 H3K27me3 来缓解与年龄相关的心脏衰退
• GSE313923 靶向淋巴管可通过增强小鼠截肢模型中的破骨细胞活性来促进骨再生
• GSE307297 类风湿性关节炎相关间质性肺疾病的单细胞RNA测序
• GSE305629 肌层浸润性膀胱癌 (MIBC) 中的中性粒细胞和 CD8+ T 细胞
• GSE304377 营养基因组学揭示维生素 B3 疗法可治愈 NAXD 疾病
• GSE303721 肾癌中SOCS3–JAK1–STAT3轴介导的HIF-2α增强子调控
• GSE298565 使用 PATTY 校正批量和单细胞 CUT&Tag 数据中的开放染色质偏倚 [CUT&Tag]
• GSE298319 炎症性表观Caspase-1通过远程调控骨髓造血，驱动以中性粒细胞为主的全身性炎症，从而抑制免疫原性细胞死亡
• GSE314609 酮体β-羟基丁酸通过非代谢依赖性机制恢复Tau蛋白稳态
• GSE311934 应激诱导的 ADGRL4 通过 Gαs-YAP1 信号通路和血管生成调控肿瘤休眠和复发
• GSE299422 对共培养的癌细胞-宿主细胞进行转录组分析，发现缺氧是骨骼肌细胞抑制癌细胞增殖作用的驱动因素。
• GSE296363：对单个卵母细胞进行小RNA和长RNA的整合测序揭示了人类卵子发生过程中piRNA介导的转座子抑制。
• GSE289182 表观转录组分析揭示了两种西瓜感染的RNA病毒中不存在m6A修饰
• GSE318449 Wnt7a-Hoxa13通路在子宫形态发生过程中促进体中线苗勒氏管融合
• GSE318448 药理学方法提高乳酸水平可通过组蛋白乳化诱导的IL-10产生缓解脓毒症
• GSE289127 金头鲷肠道的实时定量PCR分析
• GSE286304 乙酸盐可促进红酵母菌（Rhodotorula toruloides）的木糖代谢
• GSE268657 Isl1CKO小鼠模型内分泌胰腺谱系的单细胞RNA测序
• GSE252636 小鼠脾脏来源的幼稚T细胞、中央记忆T细胞和效应记忆T细胞的RNA测序
• GSE224872 ATAC-seq 数据来自在 OVA257-264 刺激下与载体或 TAMos 共培养的 OT-I 细胞。
• GSE224871 RNA-seq 分析了在 OVA257-264 刺激下，与载体、TANs 或 TAMos 共培养的 OT-I 细胞。