详细内容（前10条）

1. ⭐ GSE322883 炎症牙髓与健康牙髓的空间转录组学分析

• ✍️ 作者：未知作者
• 🏷️ 关键词：spatial、spatial transcriptomics、transcriptomics
• 📝 描述：Contributors : Samer Zaky ; Giueseppe Intini ; Charles Sfeir ; Renato Silva ; Dhivyaa RajasundaramSeries Type : OtherOrganism : Homo sapiensDiagnostic protocols in endodontics rely heavily on subjective pain assessments and sensibility testing, which often fail to reflect the true histopathological and molecular state of the pulp. This limitation can result in misdiagnosis of reversible pulpitis as irreversible, leading to unnecessary devitalization of teeth that might otherwise respond to vital pulp therapy (VPT). Improved understanding of pulp biology is essential to refine case selection and enhance VPT outcomes. We aim to investigate the transcriptomic profiles of pulpitis, identify inflammation subtypes, and improve classification beyond the traditional reversible/irreversible framework. Methods: Spatial transcriptomics (Visium-CytAssist-V2) was used to analyze four dental pulp tissues. Cell deconvolution and differential gene expression analyses were performed to characterize transcriptomic signatures of healthy pulp (HL), reversible pulpitis (RP), and irreversible pulpitis (IP), with specific attention to coronal regions adjacent to carious lesions.
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2. ⭐ GSE304653 乳腺癌肿瘤微环境和癌细胞表型的运动雕塑

• ✍️ 作者：未知作者
• 🏷️ 关键词：tumor、cancer、tumor microenvironment
• 📝 描述：Contributors : Graeme J Koelwyn ; Sayyed Hamed Shahoei ; Courtenay Graham ; Claudia Siguenza ; Geoffrey M Nonis ; Seyed Milad Vahedi ; Puneet Sidhu ; Emily J Brown ; Juan Liu ; Elisa De Stanchina ; Kathryn J Moore ; Jason W Locasale ; Erik R Nelson ; Lee W JonesSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusExercise links with improved cancer outcomes following a diagnosis of primary breast cancer but experimental evidence from preclinical studies and molecular mechanistic insights are limited. Here, we show that exercise inhibits breast cancer growth and metastases across multiple syngeneic mouse models compared to sham control. Utilizing the Met1-iRFP model to interrogate tumor microenvironmental (TME) and tumor-specific effects, exercise decreased intratumoral immune cell content, particularly tumor-associated macrophages, and prompted an activated anticancer innate immune response. Cancer cell-intrinsic effects were characterized by broad transcriptomic reprogramming including downregulation of metabolic pathways and upregulation of pathways regulating proliferation and apoptosis. Metabolomic analyses unveiled broad shifts in tumor metabolism including decreased NAD+ and lactate, as well as availability of biosynthetic precursors. Finally, in silico analyses identified TME ligands such as Hmgb2 as drivers of downstream gene expression changes in cancer cells. Collectively, our findings show that exercise suppresses breast cancer progression and does so via broad reprogramming of TME-cancer components and their interaction.
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3. ⭐ GSE329264 肠道丙酸代谢对全身代谢稳态的影响

• ✍️ 作者：未知作者
• 🏷️ 关键词：metabolism、metabolic、regex:intestin(e|al)
• 📝 描述：Contributors : Jasmine Encarnacion ; Michael J WolfgangSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusPropionate is an abundant short-chain fatty acid in mammals, largely derived from gut microbiota production. Due to its abundance, propionate metabolism is essential to maintain systemic homeostasis. Inborn errors of essential metabolic enzymes in this pathway causes severe illness, such as the development of Propionic Acidemia in cases of Propionyl-CoA Carboxylase (PCC) deficiency. We and others have previously developed mouse models deficient in Pcca, encoding the alpha subunit of PCC, to study the systemic and liver-specific mechanisms of propionic acidemia. However, the role of PCC in the intestine, where propionate is primarily absorbed, is understudied. To investigate the gut-specific role of PCC, we developed a mouse knockout of Pcca using Villin-Cre (Pcca Vill) on a floxed Pcca (Pcca ff) background. Here, we demonstrate the phenotypes present in this model provided both a standard (chow) and high fat (HFD) diets.
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4. GSE328391 近期人类结核病家庭接触者的气道免疫保护和疾病进展特征 [批量 RNA 测序]

• ✍️ 作者：未知作者
• 🏷️ 关键词：immune、RNA-seq
• 📝 描述：Contributors : William J Branchett ; Jee-Whang Kim ; Jessica Shields ; Probir Chakravarty ; Anver Kamil ; Jo Lee ; Ismail Novsarka ; Hubert Slawinski ; Katalin A Wilkinson ; Robert J Wilkinson ; Raman Verma ; Pranabashis Haldar ; Anne O’GarraSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensThe local early immune factors dictating whether individuals who have been infected with Mycobacterium tuberculosis remain healthy or progress to active TB have not been defined. We interrogated the airway immune response at single cell resolution in bronchoalveolar lavage (BAL) from PET-CT characterised recent TB household contacts, who either controlled the infection or progressed to TB disease, as well as of active TB patients at diagnosis. Single cell RNA-sequencing revealed type I IFN-dependent and -independent neutrophil signatures in BAL from active TB patients and TB progressors. We report an inverse relationship between airway neutrophils and T cells, with T cells showing signatures of exhaustion, cytotoxicity and cell death in progressors and active TB patients with a neutrophil dominated airway profile. Conversely, we identified T cell signatures of protection in non-progressor contacts dominated by genes related to regulation, quiescence and a stem-like profile. Both the signature of TB progression and the stem-like T cell signature of non-progressors from human airways were recapitulated in scRNA-seq data from non-human primate (NHP) granulomas, associated with disease or immune protection, respectively. Our findings from early human airway responses in TB contacts reveal genes, pathways and cell states that may dictate infection outcome and inform strategies for developing effective host-directed therapies and vaccines.
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5. GSE320248 单细胞测序研究脾细胞和 YFP+ B 细胞，旨在探究 Eif3e cg1cre 敲除小鼠与对照小鼠之间的差异

• ✍️ 作者：未知作者
• 🏷️ 关键词：sequencing、single-cell
• 📝 描述：Contributors : Lianghua Lin ; Chao Huang ; Yunjie ZhangSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusTo gain insights into the cellular mechanisms underlying the lymphoproliferative disorder developed in cKO mice, we performed single cell RNA-seq (scRNA-seq) analysis of YFP+ and total splenocytes from cKO and control mice at the age of 2 months, when lymphocyte activation and proliferation had not yet become obvious.Through our study, we found that Eif3e-deficient B cells are impaired in their development into GCB and PC, becoming blocked at the pre-GCB stage. Additionally, all B cells exhibited high expression of MHC-II. Among CD4+ T cells, the TFH cell population was significantly expanded in cKO mice and showed high expression of IL4. Based on the early-stage phenotype of this mouse model, we hypothesize that Eif3e-deficient B cells promote IL4 expression in CD4+ T cells, which in turn stimulates upregulation of MHC-II on all B cells. The increased MHC-II further enhances CD4+ T cell activation, forming a positive feedback loop.
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6. GSE300232 拟南芥免疫反应的 RNA-seq 和 Ribo-seq 分析

• ✍️ 作者：未知作者
• 🏷️ 关键词：immune、RNA-seq
• 📝 描述：Contributor : Changzhen LiuSeries Type : Other ; Expression profiling by high throughput sequencingOrganism : Arabidopsis thalianaIn land plants, guard cells sense pathogens and close stomata to resist their entry. Pathogen-infected local leaves transmit the danger status to uninfected distal systemic leaves and trigger their stomatal closure as a global defense termed systemic stomatal immunity. However, the corresponding mobile signals remain unknown. Here, we report that an upstream open reading frame (uORF) encodes a long-distance mobile peptide inducing systemic stomatal closure and named uORF-encoded systemic stomatal immune conductor (USIC). In local leaves, USIC expression is upregulated upon pathogen/pattern signals. In systemic leaves, the SIRK1 receptor and KIN7 coreceptor perceives USIC, and induces KIN7 cleavage by MC4. KIN7 translocates to tonoplasts and mediates stomatal closure by associating with H+-ATPases and aquaporins. This study reveals a systemic signaling mechanism whereby an uORF-encoded mobile peptide and its receptor pathway activating systemic stomatal immunity.
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7. GSE254329 人类烧伤患者全血单细胞RNA测序

• ✍️ 作者：未知作者
• 🏷️ 关键词：sequencing、single-cell
• 📝 描述：Contributors : Sarthak Sinha ; Nicole Rosin ; Keerthana Chockalingam ; Vincent Gabriel ; Jeff BiernaskieSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensTo develop effective therapeutic interventions that prevent scar formation and encourage regeneration of healthy skin, we need to better understand the cellular and molecular process that are engaged during the wound healing process in humans. However, our cellular and molecular understanding of how humans heal deep dermal wounds remains limited. Our recent work using different animal models of skin wound healing has identified the acute wound healing immune response as a key determinant of terminal fibrotic outcomes. Here, our goal is to compare the immune response during human wound healing to datasets we have generated from large animal models that are capable of scarless healing, in order to determine how to most appropriately modify the process in humans to improve outcomes (and mitigate scar).
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8. GSE329489 整合转录组和代谢组分析：解析栽培番茄与番茄褐皱果病毒的相互作用

• ✍️ 作者：未知作者
• 🏷️ 关键词：metabolome、transcriptome
• 📝 描述：Contributors : Jun Zhang ; Dianping Di ; Fei Yang ; Aihong ZhangSeries Type : Expression profiling by high throughput sequencingOrganism : Solanum lycopersicumTomato brown rugose fruit virus (ToBRFV) is an emerging and destructive tobamovirus. To elucidate its interaction with tomato (Solanum lycopersicum), we performed an integrated transcriptomic and metabolomic analysis. Compared to mock-inoculated plants, we identified 4,477 differentially expressed genes and 91 differentially accumulated metabolites. Notably, L‑Histidine was significantly upregulated while the flavonol quercetin was downregulated in response to infection. Functional validation via exogenous application revealed that L‑Histidine enhanced the expression of defense-related genes and activated the ethylene signaling pathway, whereas quercetin treatment upregulated genes involved in the MAPK signaling cascade. Collectively, our integrated multi-omics analysis and functional validation reveal that L‑Histidine acts as a positive immune inducer while quercetin contributes to antiviral defense through distinct signaling pathways. These findings provide novel insights into the molecular basis of tomato-ToBRFV interaction and highlight potential targets for antiviral strategies.
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9. GSE328625 PD-1 调控胸腺细胞毒性 CD8+ T 细胞的潜在效应分化 [scRNA-Seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：scRNA
• 📝 描述：Contributors : Zhiming Mao ; Ying Li ; Haidong DongSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusDurable T cell immunity against cancer depends on the continual replenishment of effector CD8⁺ T cells. Thymic output has been associated with favorable prognosis in cancer patients across a range of ages, suggesting that the thymus is an important source for replenishing T cells capable of controlling cancer progression. However, whether CD8⁺ T cells acquire effector potential within the thymus, and how thymic output of effector CD8⁺ T cells contribute to peripheral tumor immunity, remain unclear. In this study, we discover that thymic single-positive (SP) CD8⁺ T cells undergo latent effector differentiation following thymic selection, but this process is subject to PD-1 regulation. We further demonstrate that PD-1 limits the contribution of thymic output of CD8⁺ T cells in shaping the TCR repertoire within the tumor tissues for tumor immunosurveillance. Although PD-1 inhibition facilitates the expansion of effector CD8⁺ T cells in the periphery, these cells gradually lose antitumor activity within tumors due to accelerated exhaustion in the absence of PD-1. Thus, while latent effector differentiation of thymic CD8⁺ T cells enable a rapid response to malignant cells in the periphery, PD-1 restrains this process to prevent overt or terminal effector differentiation, which could compromise balanced and durable peripheral immunity.
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10. GSE326212 近期结核病家庭接触者的气道免疫保护和疾病进展特征

• ✍️ 作者：未知作者
• 🏷️ 关键词：immune
• 📝 描述：Contributors : William J Branchett ; Jee-Whang Kim ; Jessica Shields ; Probir Chakravarty ; Anver Kamil ; Jo Lee ; Ismail Novsarka ; Hubert Slawinski ; Katalin A Wilkinson ; Robert J Wilkinson ; Raman Verma ; Pranabashis Haldar ; Anne O’GarraSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensThe local early immune factors dictating whether individuals who have been infected with Mycobacterium tuberculosis remain healthy or progress to active TB have not been defined. We interrogated the airway immune response at single cell resolution in bronchoalveolar lavage (BAL) from PET-CT characterised recent TB household contacts, who either controlled the infection or progressed to TB disease, as well as of active TB patients at diagnosis. Single cell RNA-sequencing revealed type I IFN-dependent and -independent neutrophil signatures in BAL from active TB patients and TB progressors. We report an inverse relationship between airway neutrophils and T cells, with T cells showing signatures of exhaustion, cytotoxicity and cell death in progressors and active TB patients with a neutrophil dominated airway profile. Conversely, we identified T cell signatures of protection in non-progressor contacts dominated by genes related to regulation, quiescence and a stem-like profile. Both the signature of TB progression and the stem-like T cell signature of non-progressors from human airways were recapitulated in scRNA-seq data from non-human primate (NHP) granulomas, associated with disease or immune protection, respectively. Our findings from early human airway responses in TB contacts reveal genes, pathways and cell states that may dictate infection outcome and inform strategies for developing effective host-directed therapies and vaccines.
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💡 该来源还有 14 条内容，详见 文末

• GSE326003 髓系祖细胞的分化是由协调的基因表达的级联波所影响的，这些基因表达以特征性的顺序重塑细胞生理[RNA-seq]
• GSE320525 Eif3e cg1cre KO小鼠肿瘤的单细胞V(D)J-seq测序
• GSE320249 对 iGCB 第 3 天细胞进行批量 RNA 测序研究，以探究 Eif3e cg1cre 敲除 B 细胞与对照 B 细胞之间的差异
• GSE319353 瞬时表观遗传改变促进皮下脂肪基质血管组分的心肌细胞分化
• GSE307613 持续低雌激素状态下促性腺激素细胞重塑：单细胞转录组分析揭示促性腺激素细胞亚型和干细胞群的激活。
• GSE306869 RNA结合蛋白LIN28A介导神经元分化过程中的染色质动态变化
• GSE322622 肝脏 BRCA1 通过调节 BHMT 产生矛盾的致癌作用
• GSE301063 通过 RNA-seq 分析 WT、CST-KO 和 CST-KO+CST 处理小鼠左心室的转录谱
• GSE329318 干扰素-γ刺激对RANKL/M-CSF诱导的破骨细胞转录组的影响
• GSE329253 增强子调控 OSR2 在下颌切牙缺失易感性中的作用 [RNA-Seq]
• GSE329203 内聚素环挤出在分化早期增强子激活的基因表达中发挥作用（RNA-Seq，CapC）
• GSE329202 内聚素环挤出在分化早期增强子激活基因表达中发挥作用（ChIP-Seq，Rad21 和 Stag2）
• GSE321696 线粒体分裂因子 (MFF) 调节 AgRP 神经元中的线粒体 Ca2+ 内稳态和神经元活动
• GSE292733 妊娠诱导的 TRM 细胞对乳腺癌具有保护作用 [scRNAseq]