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Bridging viral hepatitis and liver cancer: Emerging concepts in pathogenesis and therapeutic innovation 桥接病毒性肝炎和肝癌:发病机制和治疗创新的新概念
Pub Date : 2025-06-23 DOI: 10.1002/ctd2.70063
Keyin Zheng, Aimin Jiang, Zhengrui Li, Li Chen, Kailai Li, Junyi Shen, Hank Z. H. Wong, Quan Cheng, Jian Zhang, Anqi Lin, Peng Luo
<div> <section> <h3> Background</h3> <p>Viral hepatitis, particularly hepatitis B virus (HBV) and hepatitis C virus (HCV) infections, represent the predominant etiological factors for hepatocellular carcinoma (HCC) worldwide. HBV and HCV drive hepatocellular malignant transformation through complex molecular mechanisms that are both distinct and overlapping. Comprehensive elucidation of these mechanisms, particularly the role of viral-mediated remodeling of the tumor microenvironment, is crucial for developing novel preventive and diagnostic strategies as well as personalized therapeutic approaches.</p> </section> <section> <h3> Aim</h3> <p>This review aims to systematically elucidate the key molecular mechanisms underlying HBV- and HCV-related HCC development and progression (including virus-specific pathways and common pathways), to explore the translational potential of these mechanisms in clinical medicine, and to provide perspectives on future research frontiers.</p> </section> <section> <h3> Results</h3> <p>This review systematically elucidates the pathogenic mechanisms of HBV- and HCV-related HCC and provides comprehensive analysis of the common molecular mechanisms underlying viral hepatitis-to-HCC transformation. For HBV-related HCC, we focus on analyzing the following oncogenic mechanisms: genomic instability caused by HBV DNA integration, oncogenic effects of HBV proteins, and the impact of virus infection-mediated tumor microenvironment remodeling on immune responses. For HCV-related HCC, we focus on exploring the following oncogenic mechanisms: oncogenic mechanisms of viral proteins, virus infection-mediated metabolic disorders, functional dysregulation of immune cells in the microenvironment, and virus-induced hepatic fibrosis. Furthermore, we thoroughly investigated the common mechanisms underlying viral hepatitis-to-HCC transformation, including the construction of pro-inflammatory factor networks in chronic inflammatory microenvironments, virus-induced epigenetic alterations, and genomic instability. Based on current research, we further discuss future research directions and perspectives in this field.</p> </section> <section> <h3> Conclusion</h3> <p>This review systematically elucidates the pathogenic mechanisms of HBV- and HCV-related HCC and provides comprehensive analysis of the common molecular mechanisms underlying viral hepatitis-to-HCC transformation, with particular emphasis on the remodeling effects of viral infection on the HCC microenvironment, which hold significant clinical implications for developing novel preventiv
病毒性肝炎,特别是乙型肝炎病毒(HBV)和丙型肝炎病毒(HCV)感染,是世界范围内肝细胞癌(HCC)的主要病因。HBV和HCV通过复杂的分子机制驱动肝细胞恶性转化,这些机制既不同又重叠。全面阐明这些机制,特别是病毒介导的肿瘤微环境重塑的作用,对于开发新的预防和诊断策略以及个性化治疗方法至关重要。本综述旨在系统阐明HBV和hcv相关HCC发生发展的关键分子机制(包括病毒特异性途径和共同途径),探讨这些机制在临床医学中的转化潜力,并为未来的研究前沿提供展望。结果系统阐述了HBV和hcv相关HCC的发病机制,全面分析了病毒性肝炎向HCC转化的常见分子机制。对于HBV相关的HCC,我们重点分析了以下致癌机制:HBV DNA整合引起的基因组不稳定,HBV蛋白的致癌作用,以及病毒感染介导的肿瘤微环境重塑对免疫反应的影响。对于hcv相关的HCC,我们重点探索以下致瘤机制:病毒蛋白的致瘤机制、病毒感染介导的代谢紊乱、微环境中免疫细胞功能失调以及病毒诱导的肝纤维化。此外,我们深入研究了病毒性肝炎向hcc转化的共同机制,包括慢性炎症微环境中促炎因子网络的构建、病毒诱导的表观遗传改变和基因组不稳定性。在现有研究的基础上,进一步探讨了该领域未来的研究方向和前景。本综述系统阐述了HBV和hcv相关HCC的致病机制,全面分析了病毒性肝炎向HCC转化的常见分子机制,重点研究了病毒感染对HCC微环境的重塑作用,这对制定新的预防策略、诊断生物标志物、以及个性化的治疗方法。通过系统分析病毒感染诱导的表观遗传重编程在HCC发生发展中的长期影响,结合多组学数据构建HCC风险预测模型,为制定早期筛查和精准治疗策略提供科学依据。同时,研究病毒整合模式与HCC预后的关系,开发新的分子分类方法,将有助于为患者设计更个性化、更精准的治疗方案。此外,利用尖端的人工智能技术和开发创新的研究方法,如病毒性肝炎相关的肝类器官模型,也将为降低病毒性肝炎相关的HCC的发病率和死亡率提供新的见解和方法。
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引用次数: 0
Molecular mechanisms of ageing in cancer development and therapeutic response: Translational implications for precision oncology 衰老在癌症发展和治疗反应中的分子机制:对精确肿瘤学的转化意义
Pub Date : 2025-06-23 DOI: 10.1002/ctd2.70065
Laiba Husain

Background

The intricate relationship between cellular ageing processes and cancer development represents one of the most significant challenges in contemporary oncology. As populations worldwide experience unprecedented demographic shifts towards advanced age, understanding the molecular mechanisms that link ageing to cancer initiation, progression, and therapeutic response has become essential for developing effective precision medicine approaches.

Main body

This review examines the fundamental molecular pathways through which ageing influences cancer biology, including telomere dysfunction, cellular senescence, DNA damage accumulation, and epigenetic alterations. These age-related changes create a permissive environment for oncogenesis while simultaneously affecting therapeutic efficacy and treatment tolerance. Key ageing-associated molecular signatures include p16^INK4a^ upregulation, shortened telomeres, increased DNA damage response activation, and altered chromatin structure. The accumulation of senescent cells with age contributes to chronic inflammation and tissue dysfunction that promotes tumour development. Additionally, age-related changes in drug metabolism, DNA repair capacity, and immune function significantly impact therapeutic outcomes. Recent advances in molecular ageing biomarkers, including transcriptomic ageing clocks and protein-based signatures, offer promising approaches for personalizing cancer treatment strategies. The integration of ageing biology into precision oncology frameworks presents opportunities for developing age-informed therapeutic protocols that optimize efficacy while minimizing toxicity. Emerging technologies, including artificial intelligence-driven molecular analysis and advanced imaging techniques, enable more precise characterization of ageing-cancer interactions at the cellular and tissue levels.

Conclusion

The molecular mechanisms underlying ageing-cancer relationships provide critical insights for advancing precision oncology approaches. Understanding these pathways enables the development of targeted interventions that account for age-related biological changes, ultimately improving therapeutic outcomes for older cancer patients. Future research must focus on translating molecular ageing discoveries into clinically actionable tools that enhance treatment personalization and optimize care delivery across the cancer continuum.

细胞老化过程与癌症发展之间的复杂关系是当代肿瘤学中最重大的挑战之一。随着全球人口经历前所未有的高龄人口转变,了解衰老与癌症发生、发展和治疗反应之间的分子机制对于开发有效的精准医学方法至关重要。本文综述了衰老影响癌症生物学的基本分子途径,包括端粒功能障碍、细胞衰老、DNA损伤积累和表观遗传改变。这些与年龄相关的变化为肿瘤的发生创造了一个宽松的环境,同时影响了治疗效果和治疗耐受性。衰老相关的关键分子特征包括p16^INK4a^上调、端粒缩短、DNA损伤反应激活增加和染色质结构改变。随着年龄的增长,衰老细胞的积累会导致慢性炎症和组织功能障碍,从而促进肿瘤的发展。此外,年龄相关的药物代谢、DNA修复能力和免疫功能的变化显著影响治疗结果。分子老化生物标志物的最新进展,包括转录组老化时钟和基于蛋白质的特征,为个性化癌症治疗策略提供了有希望的方法。将衰老生物学整合到精确肿瘤学框架中,为开发年龄知情的治疗方案提供了机会,这些治疗方案可以优化疗效,同时将毒性降到最低。新兴技术,包括人工智能驱动的分子分析和先进的成像技术,可以在细胞和组织水平上更精确地表征衰老与癌症的相互作用。结论衰老与癌症关系的分子机制为推进精准肿瘤学方法提供了重要见解。了解这些途径有助于开发有针对性的干预措施,以解释与年龄相关的生物学变化,最终改善老年癌症患者的治疗效果。未来的研究必须专注于将分子衰老的发现转化为临床可操作的工具,以增强治疗个性化并优化整个癌症连续体的护理交付。
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引用次数: 0
Therapeutic potential of the annexin A family in atherosclerosis 膜联蛋白A家族在动脉粥样硬化中的治疗潜力
Pub Date : 2025-06-22 DOI: 10.1002/ctd2.70064
Suha Jarad, Da-wei Zhang

Atherosclerotic cardiovascular disease (ASCVD) is the leading cause of mortality and morbidity worldwide despite advancements in therapeutic options for the management of atherosclerosis (AS). Treatments that lower low-density lipoprotein (LDL) cholesterol levels, such as statins or proprotein convertase subtilisin/kexin type 9 inhibitors, have effectively reduced ASCVD risk. However, residual CVD risk remains high, highlighting the need for additional effective therapies. Recently, colchicine has been approved for managing AS, introducing new avenues for targeting inflammation, a key process in AS.

Various factors contribute to AS progression, such as endothelial dysfunction, leukocyte transmigration, vascular smooth muscle cell migration and phenotype-switching, increased lipid retention, production of pro-inflammatory cytokines and regulated cell death processes such as apoptosis. The annexin A (AnxA) family of proteins is well-known for their ability to bind Ca2+ and phospholipids, and they play diverse roles in inflammation, cell proliferation, migration, differentiation and signalling. Several AnxA proteins have been implicated in essential processes involved in AS development, including endothelial dysfunction, leukocyte transmigration and apoptosis.

In this mini-review, we highlight the roles of AnxA1, AnxA2, AnxA5, AnxA6, AnxA7 and AnxA8 in AS development and progression and their therapeutic potential in AS management.

动脉粥样硬化性心血管疾病(ASCVD)是世界范围内死亡率和发病率的主要原因,尽管动脉粥样硬化(AS)的治疗选择取得了进展。降低低密度脂蛋白(LDL)胆固醇水平的治疗,如他汀类药物或蛋白转化酶枯草杆菌素/ keexin 9型抑制剂,有效降低了ASCVD的风险。然而,残留的心血管疾病风险仍然很高,强调需要额外的有效治疗。最近,秋水仙碱被批准用于治疗AS,为AS的关键过程炎症的靶向治疗提供了新的途径。多种因素促进AS的进展,如内皮功能障碍、白细胞转运、血管平滑肌细胞迁移和表型转换、脂质保留增加、促炎细胞因子的产生和细胞凋亡等细胞死亡过程的调节。膜联蛋白A (AnxA)家族因其结合Ca2+和磷脂的能力而闻名,它们在炎症、细胞增殖、迁移、分化和信号传导中发挥着多种作用。一些AnxA蛋白参与了AS发展的基本过程,包括内皮功能障碍、白细胞转运和细胞凋亡。在这篇小型综述中,我们重点介绍了AnxA1、AnxA2、AnxA5、AnxA6、AnxA7和AnxA8在AS发生和进展中的作用及其在AS治疗中的潜力。
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引用次数: 0
Endothelial single-cell sequencing: A new way to understand endothelial biomedicine 内皮单细胞测序:了解内皮生物医学的新途径
Pub Date : 2025-06-02 DOI: 10.1002/ctd2.70062
Zehua Shao, Hao Tang, Wanxin Duan, Hongwei Guo
<p>Vascular endothelial cells (ECs) are critical guardians of vascular homeostasis, regulating angiogenesis, inflammation, and barrier integrity. However, their phenotypic and functional heterogeneity across vascular beds has posed challenges to traditional bulk analysis methods. Single-cell RNA sequencing (scRNA-seq) has emerged as a transformative tool, offering unparalleled resolution at the individual cell level. This technology has revolutionized our ability to dissect endothelial diversity and function and unveiled novel endothelial subtypes, unexpected signaling pathways, and dynamic responses to environmental stimuli (Figure 1). scRNA-seq now stands at the forefront of endothelial biology research, providing insights into both physiological and pathological processes.</p><p>In vascular inflammation, scRNA-seq has transformed our ability to dissect endothelial plasticity and pathological transitions. For instance, McQueen et al. demonstrated how scRNA-seq in atherosclerotic lesions identified distinct endothelial subsets specializing in lipid handling, oxidative stress response, and leukocyte recruitment.<span><sup>1</sup></span> Bondareva and Sheikh further highlighted that scRNA-seq platforms uncover vascular zonation patterns and region-specific endothelial responses to inflammation, thereby redefining our understanding of vascular homeostasis.<span><sup>2</sup></span> In human heart failure, Rao et al. mapped fibrotic and non-fibrotic myocardial tissues, revealing that fibrotic-region ECs could upregulate adhesion molecules and foster leukocyte infiltration.<span><sup>3</sup></span> Notably, tools for single-cell trajectory inference allowed dynamic modeling of endothelial activation, illustrating a continuum from quiescence to inflammation rather than discrete states.</p><p>In oncology, scRNA-seq has improved the concept of tumour-associated ECs (TECs). Shiau et al. performed single-nucleus RNA-seq on pancreatic ductal adenocarcinoma samples and identified a “reactive EndMT” program enriched in hypoxia-driven signaling and mesenchymal traits, which correlates with poor outcomes.<span><sup>4</sup></span> Yang et al. integrated scRNA-seq-derived TEC markers into a liver cancer prognostic model and then linked endothelial gene signatures to immune infiltration and therapy response.<span><sup>5</sup></span> In gastric cancer, Chen et al. used longitudinal scRNA-seq to reveal endothelial expansion and pro-angiogenic activation following neoadjuvant chemotherapy,<span><sup>6</sup></span> suggesting that endothelial remodeling is highly dynamic and therapy-responsive.</p><p>Recent studies further highlight the critical role of vascular ECs in cancer progression. Using single-cell RNA sequencing, Zhang et al. characterized endothelial heterogeneity in colorectal cancer liver metastases and identified specific subpopulations that actively engage with immune cells.<span><sup>7</sup></span> In gastric cancer, Yang et al. demonstrated that chemot
血管内皮细胞(ECs)是血管稳态的关键守护者,调节血管生成、炎症和屏障完整性。然而,它们在血管床上的表型和功能异质性给传统的批量分析方法带来了挑战。单细胞RNA测序(scRNA-seq)已经成为一种变革性的工具,在单个细胞水平上提供无与伦比的分辨率。这项技术彻底改变了我们解剖内皮多样性和功能的能力,揭示了新的内皮亚型、意想不到的信号通路和对环境刺激的动态反应(图1)。scRNA-seq现在站在内皮生物学研究的前沿,为生理和病理过程提供了见解。在血管炎症中,scRNA-seq改变了我们解剖内皮可塑性和病理转变的能力。例如,McQueen等人证明了scRNA-seq在动脉粥样硬化病变中如何识别出不同的内皮亚群,这些亚群专门负责脂质处理、氧化应激反应和白细胞招募Bondareva和Sheikh进一步强调,scRNA-seq平台揭示了血管分区模式和区域特异性内皮对炎症的反应,从而重新定义了我们对血管稳态的理解在人类心力衰竭中,Rao等绘制了纤维化和非纤维化心肌组织,揭示了纤维化区ECs可以上调粘附分子并促进白细胞浸润值得注意的是,单细胞轨迹推断工具允许内皮细胞激活的动态建模,说明了从静止到炎症的连续体,而不是离散状态。在肿瘤学领域,scRNA-seq改进了肿瘤相关ECs (TECs)的概念。Shiau等人对胰腺导管腺癌样本进行了单核rna测序,发现了一个富含缺氧驱动信号和间质特征的“反应性EndMT”程序,这与预后不良有关Yang等人将scrna -seq衍生的TEC标志物整合到肝癌预后模型中,然后将内皮基因特征与免疫浸润和治疗反应联系起来在胃癌中,Chen等人使用纵向scRNA-seq揭示了新辅助化疗后内皮扩张和促血管生成激活,6表明内皮重塑是高度动态和治疗反应性的。最近的研究进一步强调了血管内皮细胞在癌症进展中的关键作用。Zhang等人利用单细胞RNA测序研究了结直肠癌肝转移的内皮异质性,并确定了与免疫细胞积极结合的特定亚群在胃癌中,Yang等人证明化疗可以动态改变肿瘤微环境中的内皮-免疫串扰总之,这些发现表明内皮细胞是肿瘤血管结构和免疫调节的关键调节因子。除了疾病状态,单细胞图谱加深了我们对组织特异性内皮特化的理解。在人类皮肤中,He等人发现了六种不同的血管内皮亚型,每种亚型都表现出代谢和免疫调节的特殊模式Li等人通过表明皮肤中的毛细血管内皮细胞表现出强烈的HLA-II表达谱来扩展这一结果,表明积极参与免疫监视这些真皮血管图强化了内皮身份是由环境线索和局部组织需求形成的概念。在系统水平上,Augustin和Koh建议重新思考血管内皮作为一个广泛分布的器官,积极地塑造器官的功能,而不仅仅是作为一个被动的屏障这一新观点越来越多地得到单细胞研究的支持,这些研究表明内皮细胞可以分泌调节信号,调节其代谢,并在应激反应中重塑其局部组织环境。展望未来,血管研究将越来越依赖于整合的单细胞多组学方法,包括转录组学、染色质可及性、蛋白质组学和空间定位,以充分捕捉健康和疾病中内皮生物学的复杂性。正如Shiau等人所总结并由Bondareva和Sheikh进一步扩展的那样,ECs具有固有的可塑性,能够迅速适应机械应力、代谢变化、炎症提示和治疗干预。2,4 scRNA-seq的预测能力,特别是与轨迹分析和细胞间通讯分析相结合时,使其成为精准血管医学的基石。除了对静态细胞类型进行分类外,单细胞技术还在向内皮细胞转变的动态分析方向发展。 纵向单细胞分析有可能追踪ECs在疾病发生、进展和治疗反应期间的变化,将我们的理解从孤立的快照转移到连续的生物学叙述。整合互补技术,如单细胞ATAC-seq探测染色质景观,空间转录组学保存组织结构,单细胞蛋白质组学功能验证,将进一步加强对内皮调节的机制见解。为了充分发挥这一潜力,开发包括儿童、老年人和不同种族人群在内的不同人群的综合单细胞图谱,对于揭示血管适应的环境依赖性至关重要。将大规模单细胞数据集与机器学习相结合,可以预测内皮状态、疾病轨迹和治疗脆弱性。最终,单细胞技术不仅有望以前所未有的分辨率重新定义血管生物学,而且还为针对广泛疾病的内皮功能障碍的精确干预铺平了道路。作者声明无利益冲突。
{"title":"Endothelial single-cell sequencing: A new way to understand endothelial biomedicine","authors":"Zehua Shao,&nbsp;Hao Tang,&nbsp;Wanxin Duan,&nbsp;Hongwei Guo","doi":"10.1002/ctd2.70062","DOIUrl":"https://doi.org/10.1002/ctd2.70062","url":null,"abstract":"&lt;p&gt;Vascular endothelial cells (ECs) are critical guardians of vascular homeostasis, regulating angiogenesis, inflammation, and barrier integrity. However, their phenotypic and functional heterogeneity across vascular beds has posed challenges to traditional bulk analysis methods. Single-cell RNA sequencing (scRNA-seq) has emerged as a transformative tool, offering unparalleled resolution at the individual cell level. This technology has revolutionized our ability to dissect endothelial diversity and function and unveiled novel endothelial subtypes, unexpected signaling pathways, and dynamic responses to environmental stimuli (Figure 1). scRNA-seq now stands at the forefront of endothelial biology research, providing insights into both physiological and pathological processes.&lt;/p&gt;&lt;p&gt;In vascular inflammation, scRNA-seq has transformed our ability to dissect endothelial plasticity and pathological transitions. For instance, McQueen et al. demonstrated how scRNA-seq in atherosclerotic lesions identified distinct endothelial subsets specializing in lipid handling, oxidative stress response, and leukocyte recruitment.&lt;span&gt;&lt;sup&gt;1&lt;/sup&gt;&lt;/span&gt; Bondareva and Sheikh further highlighted that scRNA-seq platforms uncover vascular zonation patterns and region-specific endothelial responses to inflammation, thereby redefining our understanding of vascular homeostasis.&lt;span&gt;&lt;sup&gt;2&lt;/sup&gt;&lt;/span&gt; In human heart failure, Rao et al. mapped fibrotic and non-fibrotic myocardial tissues, revealing that fibrotic-region ECs could upregulate adhesion molecules and foster leukocyte infiltration.&lt;span&gt;&lt;sup&gt;3&lt;/sup&gt;&lt;/span&gt; Notably, tools for single-cell trajectory inference allowed dynamic modeling of endothelial activation, illustrating a continuum from quiescence to inflammation rather than discrete states.&lt;/p&gt;&lt;p&gt;In oncology, scRNA-seq has improved the concept of tumour-associated ECs (TECs). Shiau et al. performed single-nucleus RNA-seq on pancreatic ductal adenocarcinoma samples and identified a “reactive EndMT” program enriched in hypoxia-driven signaling and mesenchymal traits, which correlates with poor outcomes.&lt;span&gt;&lt;sup&gt;4&lt;/sup&gt;&lt;/span&gt; Yang et al. integrated scRNA-seq-derived TEC markers into a liver cancer prognostic model and then linked endothelial gene signatures to immune infiltration and therapy response.&lt;span&gt;&lt;sup&gt;5&lt;/sup&gt;&lt;/span&gt; In gastric cancer, Chen et al. used longitudinal scRNA-seq to reveal endothelial expansion and pro-angiogenic activation following neoadjuvant chemotherapy,&lt;span&gt;&lt;sup&gt;6&lt;/sup&gt;&lt;/span&gt; suggesting that endothelial remodeling is highly dynamic and therapy-responsive.&lt;/p&gt;&lt;p&gt;Recent studies further highlight the critical role of vascular ECs in cancer progression. Using single-cell RNA sequencing, Zhang et al. characterized endothelial heterogeneity in colorectal cancer liver metastases and identified specific subpopulations that actively engage with immune cells.&lt;span&gt;&lt;sup&gt;7&lt;/sup&gt;&lt;/span&gt; In gastric cancer, Yang et al. demonstrated that chemot","PeriodicalId":72605,"journal":{"name":"Clinical and translational discovery","volume":"5 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-06-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/ctd2.70062","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144197527","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Current advances in the role of classical non-homologous end joining in hematologic malignancies 经典非同源末端连接在血液恶性肿瘤中的作用的最新进展
Pub Date : 2025-05-29 DOI: 10.1002/ctd2.70053
Pengcheng Liu, Zizhen Xu

Background

Double-strand breaks (DSBs) are universally acknowledged as the most detrimental type of DNA damage, and their effective repair primarily depends on the non-homologous end joining (NHEJ) pathway. Such DSBs, which require NHEJ for resolution, can arise from intrinsic and extrinsic DNA-damaging factors or emerge naturally during essential biological processes like V(D)J recombination and antibody class switch recombination.

Main Body

Failure to properly repair DSBs may lead to genomic instability, disruption of cellular functions, and immunodeficiency, thereby promoting the development of hematologic malignancies. Conversely, overexpression of NHEJ-related genes can enhance resistance to DNA-damaging therapies in these cancers. Analyzing mutations in key classical NHEJ (cNHEJ) components and understanding their mechanisms could provide valuable biomarkers for predicting therapeutic outcomes and guiding treatment decisions. Consequently, defects in cNHEJ may offer insights into the development of novel drugs targeting DNA repair pathways.

Conclusion

We focus on genetic changes and alterations in gene regulation, while also providing an overview of cNHEJ.

双链断裂(DSBs)是公认的最有害的DNA损伤类型,其有效修复主要依赖于非同源末端连接(NHEJ)途径。这类dsb需要NHEJ来解决,可能是由内在和外在的dna损伤因素引起的,也可能是在V(D)J重组和抗体类开关重组等基本生物过程中自然产生的。不能正确修复dsb可能导致基因组不稳定、细胞功能破坏和免疫缺陷,从而促进血液恶性肿瘤的发展。相反,nhej相关基因的过表达可以增强这些癌症对dna损伤疗法的抵抗力。分析关键经典NHEJ (cNHEJ)组分的突变并了解其机制可以为预测治疗结果和指导治疗决策提供有价值的生物标志物。因此,cNHEJ中的缺陷可能为开发靶向DNA修复途径的新型药物提供见解。结论本研究重点关注基因调控中的遗传变化和改变,同时对cNHEJ进行了概述。
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引用次数: 0
A snapshot of the role of estrogen-regulated divergent non-coding transcripts 雌激素调控的发散性非编码转录物的作用快照
Pub Date : 2025-05-25 DOI: 10.1002/ctd2.70055
Barbara Yang, Melina J. Sedano, Kimberly Diwa, Johnathan Dominguez, Gabriela Boisselier, Alana L. Harrison, Victoria A. Reid, Enrique I. Ramos, Maria V. Jimenez, Laura A. Sanchez-Michael, Shreya Kolli, Jai Patel, Debra Lee, Mahalakshmi Vijayaraghavan, Jessica Chacon, Subramanian Dhandayuthapani, Shrikanth S. Gadad

Recent high-throughput sequencing technologies have discovered various polymerase II transcribed transcripts. The majority of them are non-protein-coding, understudied and poorly conserved. Non-coding transcripts are categorised based on their location in the genome and the direction in which they are transcribed; these categories classify a non-coding transcript as either antisense, intergenic or divergent. The RNAs belonging to divergent classes consist of two transcripts, transcribed in sense and antisense direction, generated from the same promoter or locus. Multiple environmental and genetic cues can determine the regulation of these transcripts. One of the well-known signalling molecules, estrogen, has been shown to play a vital role in the activation and regulation of divergent transcripts by mediating effects through the estrogen receptors. Emerging studies have shown a strong causative effect between estrogen-regulated divergent transcripts and diseases such as cancer. However, few, viz., lncRNA67, CUPID1 and CUPID2, show a causal relationship with estrogen-dependent biology. This mini-review summarises their role in estrogen-dependent processes that may drive the research to identify novel estrogen-signalling regulators.

最近的高通量测序技术已经发现了多种聚合酶II转录物。它们中的大多数是非蛋白质编码的,研究不足,保守性差。非编码转录物根据其在基因组中的位置和转录方向进行分类;这些分类将非编码转录物分为反义、基因间或分化。属于不同类别的rna由两个转录本组成,分别在正义和反义方向转录,由相同的启动子或位点产生。多种环境和遗传线索可以决定这些转录本的调控。众所周知的信号分子之一,雌激素,已被证明通过雌激素受体介导作用,在激活和调节分化转录本中起着至关重要的作用。新兴的研究表明,雌激素调控的分化转录物与癌症等疾病之间存在很强的因果关系。然而,lncRNA67、CUPID1和CUPID2等少数基因显示出与雌激素依赖生物学的因果关系。这篇迷你综述总结了它们在雌激素依赖过程中的作用,这些过程可能会推动研究确定新的雌激素信号调节因子。
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引用次数: 0
Friend or foe: The paradoxical roles of cancer-associated fibroblasts in tumour immunotherapy 朋友还是敌人:肿瘤免疫治疗中癌症相关成纤维细胞的矛盾作用
Pub Date : 2025-05-19 DOI: 10.1002/ctd2.70056
Minying Xiong, Aimin Jiang, Zhengrui Li, Hank Z. H. Wong, Jian Zhang, Anqi Lin, Suyin Feng, Peng Luo

Cancer-associated fibroblasts (CAFs) represent critical cellular components of the tumor microenvironment and have garnered widespread attention in the field of tumor immunology. However, given the pronounced heterogeneity of CAFs, research investigating their impact on tumor immunity has yielded diverse and often contradictory results. Therefore, in this review, we have systematically summarized previous studies to comprehensively elucidate the role of CAFs in the tumor immune microenvironment and have explored the bidirectional regulatory effects of CAFs on immune cells and immune molecules within this complex niche. We highlight the multifaceted role of CAFs in cancer immunotherapy, focusing on their impact on immunotherapeutic efficacy, as well as the synergistic effects between CAF-targeted therapies and immunotherapies in anti-cancer treatment. Addressing the heterogeneity of CAFs, we also critically analyze controversies surrounding these cells in the field of tumor immunology and propose strategic directions for future investigations targeting this cell population. Our comprehensive analysis provides a strategic framework for future research directions and clinical translation of CAF-targeted strategies, ultimately facilitating the development of more effective and personalized cancer immunotherapeutic approaches.

癌症相关成纤维细胞(Cancer-associated fibroblasts, CAFs)是肿瘤微环境的关键细胞成分,在肿瘤免疫学领域引起了广泛关注。然而,由于caf具有明显的异质性,研究其对肿瘤免疫的影响的研究产生了多种多样且往往相互矛盾的结果。因此,在本文中,我们系统地总结了以往的研究,全面阐明了CAFs在肿瘤免疫微环境中的作用,并探讨了在这个复杂的生态位中,CAFs对免疫细胞和免疫分子的双向调节作用。我们强调了CAFs在癌症免疫治疗中的多方面作用,重点关注其对免疫治疗效果的影响,以及CAFs靶向治疗与免疫治疗在抗癌治疗中的协同作用。为了解决CAFs的异质性,我们还批判性地分析了围绕这些细胞在肿瘤免疫学领域的争议,并提出了针对该细胞群的未来研究的战略方向。我们的综合分析为未来的研究方向和针对caf的策略的临床转化提供了战略框架,最终促进了更有效和个性化的癌症免疫治疗方法的发展。
{"title":"Friend or foe: The paradoxical roles of cancer-associated fibroblasts in tumour immunotherapy","authors":"Minying Xiong,&nbsp;Aimin Jiang,&nbsp;Zhengrui Li,&nbsp;Hank Z. H. Wong,&nbsp;Jian Zhang,&nbsp;Anqi Lin,&nbsp;Suyin Feng,&nbsp;Peng Luo","doi":"10.1002/ctd2.70056","DOIUrl":"https://doi.org/10.1002/ctd2.70056","url":null,"abstract":"<p>Cancer-associated fibroblasts (CAFs) represent critical cellular components of the tumor microenvironment and have garnered widespread attention in the field of tumor immunology. However, given the pronounced heterogeneity of CAFs, research investigating their impact on tumor immunity has yielded diverse and often contradictory results. Therefore, in this review, we have systematically summarized previous studies to comprehensively elucidate the role of CAFs in the tumor immune microenvironment and have explored the bidirectional regulatory effects of CAFs on immune cells and immune molecules within this complex niche. We highlight the multifaceted role of CAFs in cancer immunotherapy, focusing on their impact on immunotherapeutic efficacy, as well as the synergistic effects between CAF-targeted therapies and immunotherapies in anti-cancer treatment. Addressing the heterogeneity of CAFs, we also critically analyze controversies surrounding these cells in the field of tumor immunology and propose strategic directions for future investigations targeting this cell population. Our comprehensive analysis provides a strategic framework for future research directions and clinical translation of CAF-targeted strategies, ultimately facilitating the development of more effective and personalized cancer immunotherapeutic approaches.</p>","PeriodicalId":72605,"journal":{"name":"Clinical and translational discovery","volume":"5 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/ctd2.70056","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144085040","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Senescence as a pathogenic driver in chronic kidney disease: From cellular fate to clinical stratification 衰老作为慢性肾脏疾病的致病驱动因素:从细胞命运到临床分层
Pub Date : 2025-05-19 DOI: 10.1002/ctd2.70059
Samuel Chauvin, Ariane Coutrot, Camille Cohen
<p>Chronic kidney disease (CKD) is increasingly viewed through the lens of premature ageing.<span><sup>1</sup></span> Among the many cellular processes implicated in CKD progression, senescence—defined as a stable cell cycle arrest in metabolically active cells—has gained prominence in recent years.<span><sup>2</sup></span> Initially studied in the context of ageing, senescence has now been implicated in a range of chronic conditions, including cardiovascular disease, pulmonary fibrosis, and more recently, renal pathology.<span><sup>3</sup></span></p><p>Within the kidney, senescence has been observed both in aging and in disease states across species, including human and murine models.<span><sup>4, 5</sup></span> While the full spectrum of mechanisms driving lesion development remains unclear, growing evidence suggests that the senescence-associated secretory phenotype (SASP)—a complex network of pro-inflammatory cytokines, chemokines and proteases—plays a key role. The SASP may mediate its effects locally (cell-autonomous) or by influencing the surrounding microenvironment (non-autonomous), promoting inflammation, fibrosis and tubular atrophy.<span><sup>6</sup></span></p><p>Experimental studies have demonstrated that SASP components can drive tissue damage in both the tubulo-interstitial compartment<span><sup>4, 7</sup></span> and the glomerulus.<span><sup>5</sup></span> However, SASP molecules are not exclusive to senescent cells; they can also be produced by other cell types in response to injury. As such, establishing the direct contribution of senescence to kidney damage remains a challenge.</p><p>The advent of omics technologies, coupled with the availability of large-scale public datasets, has opened new avenues to study SASP in the context of human disease. Proteomic profiling and transcriptomic analyses now enable us to identify signatures of senescence beyond histology, and potentially, without the need for invasive tissue sampling.</p><p>The recent article by McLarnon et al. represents a significant advance in this field.<span><sup>8</sup></span> Leveraging multi-omic approaches, including plasma proteomics, kidney biopsy transcriptomics and injury-induced kidney organoid models, the authors propose a novel stratification method for CKD patients based on senescence profiles.</p><p>Using proximity extension assays, they identified a 16-protein panel enriched in senescence-associated markers, which could reliably cluster CKD patients into two major groups—or <b>‘</b>sendotypes<b>’</b>—corresponding to disease severity. These sendotypes correlated with current and future measures of renal function, such as estimated Glomerular Filtration Rate (eGFR) and serum creatinine, validating their potential as prognostic indicators.</p><p>Among the most differentially expressed proteins were TNFR1, EFNA4, N2DL2 and TNFRSF14, all implicated in inflammatory signalling and previously linked to senescence. Importantly, transcriptomic analyses from huma
慢性肾脏疾病(CKD)越来越多地从早衰的角度来看待在与CKD进展相关的许多细胞过程中,衰老——被定义为代谢活跃细胞的稳定细胞周期停滞——近年来得到了重视衰老最初是在衰老的背景下研究的,现在已经涉及到一系列慢性疾病,包括心血管疾病、肺纤维化,以及最近的肾脏病理。在肾脏中,衰老在不同物种(包括人类和小鼠模型)的衰老和疾病状态中都被观察到。虽然驱动病变发展的完整机制尚不清楚,但越来越多的证据表明,衰老相关分泌表型(SASP) -一个由促炎细胞因子、趋化因子和蛋白酶组成的复杂网络-起着关键作用。SASP可能在局部(细胞自主)或通过影响周围微环境(非自主)介导其作用,促进炎症、纤维化和小管萎缩。实验研究表明,SASP成分可导致小管间质室和肾小球的组织损伤然而,SASP分子并非衰老细胞所独有;它们也可以由其他类型的细胞对损伤做出反应而产生。因此,确定衰老对肾脏损害的直接贡献仍然是一个挑战。组学技术的出现,加上大规模公共数据集的可用性,为在人类疾病背景下研究SASP开辟了新的途径。蛋白质组学分析和转录组学分析现在使我们能够识别超越组织学的衰老特征,并且可能不需要侵入性组织采样。麦克拉农等人最近发表的一篇文章在这一领域取得了重大进展利用多组学方法,包括血浆蛋白质组学、肾活检转录组学和损伤诱导的肾类器官模型,作者提出了一种基于衰老谱的CKD患者分层新方法。通过邻近扩展试验,他们发现了一个富含衰老相关标记的16蛋白组,它可以可靠地将CKD患者分为两大组-或“sendotypes”-与疾病严重程度相对应。这些sendotypes与当前和未来的肾功能测量相关,如肾小球滤过率(eGFR)和血清肌酐,验证了它们作为预后指标的潜力。其中差异表达最多的蛋白是TNFR1、EFNA4、N2DL2和TNFRSF14,它们都与炎症信号传导有关,以前与衰老有关。重要的是,来自人肾活检和TNF-α(肿瘤坏死因子α)处理的类器官的转录组学分析证实,在sendotype阳性患者中,NF-κB(核因子κB)、TNF(肿瘤坏死因子)、MAPK(丝裂原活化蛋白激酶)和凋亡途径富集,这些途径已知与衰老和CKD进展相关。检测血浆中衰老相关模式的能力具有深远的意义。在临床肾脏病学中,除非诊断或治疗有必要,否则通常避免肾活检。因此,识别血液中的SASP特征可以实现无创检测衰老活动,促进早期识别高危患者。然而,谨慎是必要的。SASP蛋白缺乏细胞类型特异性,全身性炎症或合并症可能会混淆它们的解释。在更大的、表型多样化的CKD队列中进行严格的验证将是至关重要的。此外,sendotype是否反映了原发致病过程或仅仅是晚期疾病的替代标志物还有待澄清。衰老分析也为治疗干预打开了大门。抗衰老药物——一种选择性消除衰老细胞的药物——已经在临床前肾损伤模型中显示出前景,并且正在积极地进行人体研究。识别具有显性衰老特征的患者可以指导精确治疗,与肾脏病学和老年科学的新兴框架保持一致。另一个有趣的途径是剖析单个SASP组件的功能相关性。SASP网络中有限的一组分子驱动组织损伤是合理的,而其他分子可能发挥稳态或代偿作用。精确定位这些效应物可以产生新的药物靶点,理想情况下保留SASP的有益方面。最后,对CKD病因(糖尿病肾病、免疫球蛋白A肾病和高血压肾硬化)中衰老类型的更深入表征可能有助于阐明衰老是一种常见的最终途径,还是在特定情况下是一种独特的疾病调节剂。在CKD的背景下定义sendotypes对我们理解CKD病理生理学是一个及时和重要的贡献。 通过整合临床数据、分子谱和系统生物学,作者证明衰老不仅仅是衰老的细胞标志,而且是CKD进展中潜在的可操作轴。他们对“衰老型”的识别为患者分层引入了一个新的框架,并为肾脏病学中的衰老靶向治疗铺平了道路(见图1)。持续的努力应该集中在将这些发现扩展到更大的队列,探索sasp相关损伤的机制基础,并开发用于衰老检测的临床级工具。随着老年病学已经进入临床领域,肾脏病学可能很快就会加入准备从衰老导向的精准医学中受益的专业行列。作者声明无利益冲突。
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引用次数: 0
Complex, cell-type-specific role of EEPD1: Bridging TNF-α, inflammation and apoptosis in endothelial cells EEPD1复杂的细胞特异性作用:在内皮细胞中架起TNF-α、炎症和凋亡的桥梁
Pub Date : 2025-05-15 DOI: 10.1002/ctd2.70057
Rong Li, Cindy Xinyu Zhang, Gaohui Zhu, Da-Wei Zhang
<p>Atherosclerotic cardiovascular disease (ASCVD) is one of the leading causes of mortality and morbidity worldwide. Plasma low-density lipoprotein (LDL) cholesterol levels are positively correlated with the risk of ASCVD. Current lipid-lowering medications, such as statins and PCSK9 inhibitors, can effectively reduce plasma LDL cholesterol levels and lower ASCVD risk.<span><sup>1-3</sup></span> However, the residual risk remains high.<span><sup>4</sup></span> Therefore, there is an urgent need to develop alternative therapeutic strategies for patients who do not respond to existing treatments.</p><p>Atherosclerosis is the hardening and narrowing of arteries, accompanied by chronic inflammation. The development and progression of atherosclerosis involve the dysfunction and activation of multiple cell types and signalling pathways within the arteries. Emerging evidence demonstrates that vascular endothelial cells play a critical role in this process, highlighting their potential as a therapeutic target for preventing and treating ASCVD.</p><p>Endothelial cells line the inner surface of blood vessels and are essential for regulating vascular tone and structure. They control the permeability of blood vessels, preventing the entry of lipoproteins and leukocytes and thereby reducing the development of atherosclerosis. Additionally, endothelial cells have antiplatelet, anticoagulant and fibrinolytic functions. However, when endothelial cells become activated and dysfunctional, they promote atherosclerosis progression and contribute to cardiovascular events, such as plaque erosion. Activated endothelial cells express adhesive molecules and inflammatory mediators, which stimulate inflammation. Dysfunctional endothelial cells compromise vascular integrity and increase the permeability of lipoprotein particles, leading to lipid accumulation in the intima.<span><sup>5</sup></span> Therefore, targeting endothelial cells presents a promising therapeutic approach for the treatment of ASCVD. However, achieving this requires a comprehensive understanding of the pathophysiology and underlying mechanisms of endothelial cells in atherogenesis, areas that remain elusive.</p><p>In a recent publication in <i>Clinical and Translational Medicine</i>, Yu et al. reported that Endonuclease/Exonuclease/Phosphatase Family Domain Containing 1 (EEPD1) is a crucial regulator of inflammation and apoptosis in endothelial cells during atherogenesis, acting through the Kruppel-like factor 4 (KLF4)–EEPD1–extracellular signal-regulated kinase (ERK) signalling axis (Figure 1).<span><sup>6</sup></span> EEPD1, an endonuclease, plays a vital role in DNA repair and maintaining genome stability.<span><sup>7</sup></span> The authors reported that EEPD1 expression was elevated in both human and murine atherosclerotic plaques. They demonstrated that knockout of <i>Eepd1</i> in <i>ApoE</i>-deficient mice provided significant vascular protection, reducing macrophage infiltration, endothelial ce
动脉粥样硬化性心血管疾病(ASCVD)是世界范围内死亡率和发病率的主要原因之一。血浆低密度脂蛋白(LDL)胆固醇水平与ASCVD风险呈正相关。目前的降脂药物,如他汀类药物和PCSK9抑制剂,可以有效降低血浆LDL胆固醇水平,降低ASCVD风险。1-3但是,剩余风险仍然很高因此,迫切需要为那些对现有治疗没有反应的患者制定替代治疗策略。动脉粥样硬化是动脉硬化和狭窄,伴有慢性炎症。动脉粥样硬化的发生和发展涉及动脉内多种细胞类型和信号通路的功能障碍和激活。新出现的证据表明,血管内皮细胞在这一过程中起着关键作用,突出了它们作为预防和治疗ASCVD的治疗靶点的潜力。内皮细胞排列在血管的内表面,对调节血管张力和结构至关重要。它们控制血管的渗透性,阻止脂蛋白和白细胞的进入,从而减少动脉粥样硬化的发展。此外,内皮细胞具有抗血小板、抗凝血和纤溶功能。然而,当内皮细胞被激活和功能失调时,它们会促进动脉粥样硬化的进展,并导致斑块侵蚀等心血管事件。活化的内皮细胞表达黏附分子和炎症介质,刺激炎症。功能失调的内皮细胞损害血管完整性,增加脂蛋白颗粒的渗透性,导致内膜内脂质积聚因此,靶向内皮细胞是治疗ASCVD的一种很有前景的治疗方法。然而,实现这一目标需要对动脉粥样硬化中内皮细胞的病理生理和潜在机制有全面的了解,这些领域仍然难以捉摸。在最近发表于《临床与转化医学》的一篇文章中,Yu等人报道了内切酶/外切酶/磷酸酶家族结构域1 (EEPD1)是动脉粥样硬化过程中内皮细胞炎症和凋亡的关键调节剂,通过kruppel样因子4 (KLF4) - EEPD1 -细胞外信号调节激酶(ERK)信号轴起作用(图1)6EEPD1是一种内切酶,在DNA修复和维持基因组稳定中起着至关重要的作用作者报道了EEPD1在人和小鼠动脉粥样硬化斑块中的表达升高。他们证明,敲除apoe缺陷小鼠的Eepd1可提供显著的血管保护,减少巨噬细胞浸润、内皮细胞凋亡、炎症和斑块大小。相反,过表达EEPD1加剧了动脉粥样硬化的进展。在机制上,他们的研究发现,EEPD1促进ERK磷酸化,导致BCL2(凋亡抑制剂)的表达降低,血管细胞粘附分子1(VCAM-1)和细胞间粘附分子1(ICAM-1)以及单核细胞化学引诱蛋白1(MCP-1)的表达增加。这些变化增强了内皮细胞的炎症和凋亡,加重了动脉粥样硬化。此外,作者发现KLF4抑制EEPD1表达,抑制KLF4消除了与EEPD1缺乏相关的动脉粥样硬化保护作用。这些发现强调了抑制内皮细胞EEPD1在ASCVD中的治疗潜力。有趣的是,据报道,EEPD1可被肝脏X受体上调,从而增强巨噬细胞中的胆固醇外排考虑到巨噬细胞胆固醇外排在逆向胆固醇运输中的关键作用,人们可能会认为巨噬细胞EEPD1的缺失会加重动脉粥样硬化。然而,van Wouw的一项研究表明,与移植野生型骨髓的小鼠相比,将缺乏Eepd1的骨髓移植到Ldlr−/−敲除小鼠体内并不会影响动脉粥样硬化的发展,尽管缺乏Eepd1的骨髓源性巨噬细胞在LXR激活后显示胆固醇流出减少(图1)研究EEPD1是否也促进巨噬细胞的炎症和凋亡,潜在地抵消其增强胆固醇外排的保护作用将是有趣的。EEPD1在脂肪细胞中也高表达。Eepd1 (Eepd1−/−)的全身敲除对喂食常规食物长达4个月的小鼠体重增加没有显著影响。然而,当喂食高脂肪或西式饮食时,Eepd1 - / -小鼠的体重增加。 9敲除脂肪细胞Eepd1也没有显著影响正常饮食4个月的小鼠体重增加,但敲除脂肪细胞Eepd1的小鼠在8-10个月后体重明显增加,表明中年肥胖。与此一致的是,肥胖个体的EEPD1表达降低,恢复EEPD1通过促进脂肪脂解和生热有效减轻肥胖因此,增强而不是抑制脂肪细胞EEPD1可能有利于解决肥胖问题。同样,在肝细胞中,促进EEPD1降解会加剧代谢功能障碍相关脂肪性肝炎(MASH)的进展,而抑制其降解则会缓解这一问题这些发现揭示了EEPD1复杂的、依赖于细胞类型的作用,并强调了对EEPD1活性进行精确的、细胞类型特异性调节以避免治疗中的脱靶效应的必要性(图1)。总之,通过利用包括遗传模型、高通量转录组学、组织学分析和机制分析在内的综合体内和体外方法,作者提出了令人信服的证据,揭示了EEPD1在心血管病理中的新作用。值得注意的是,虽然EEPD1因其在DNA损伤修复和肿瘤发生中的功能而闻名,但本研究发现它是动脉粥样硬化背景下内皮炎症和细胞凋亡的重要介质。它在肿瘤发生和血管炎症中的双重作用为癌症和心血管疾病患者带来了巨大的希望。鉴于EEPD1的作用和表达模式的复杂性,未来的研究应该使用细胞类型特异性的EEPD1敲除小鼠来准确描述其功能。
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引用次数: 0
scICB: A pan-cancer database of human temporal immune checkpoint blockade therapy at single-cell transcriptomic resolution scICB:在单细胞转录组分辨率下人类时间免疫检查点阻断治疗的泛癌症数据库
Pub Date : 2025-04-28 DOI: 10.1002/ctd2.70044
Fansen Ji, Weitong Bi, Jiawei Zhang, Bingjun Tang, Ying Xiao, Huan Li, Hao Liu, Boyang Wu, Fei Yu, Shizhong Yang, Gang Xu, Jiahong Dong
<p>Dear Editor,</p><p>We developed a pan-cancer scRNA-seq database under the treatment of Immune checkpoint blockade (ICB): scICB. The detailed biopsy timepoint relative to the ICB and clinical efficacy assessment information after the treatment have been identified to help clinicians to analyse different aspects of immunotherapy responsive biomarkers (Figure 1). The database is freely accessible at http://www.scimmnue.com/.</p><p>Herein, we collected scRNA-seq datasets related to ICB treatment and corresponding clinical information from multiple sources (Table 1). scICB includes 807 samples from 338 patients treated by ICB or ICB combination therapy across 13 cancer types (Figure 2a, Tables S1–S3). A total of 3 686 385 single cells covering NSCLC, CRC, RCC, HNSCC, BLCA, BCC, SCC, HCC, BRCA, SKCM, ESCC, GC and UCEC. For response status level, there are 174 patients defined as responders (R) while 170 patients labelled as nonresponders (NR) (Figure 2b). For biopsy timepoint level, a total of 23 patients only has pre ICB treatment scRNA-seq data, while a total of 68 patients only has post ICB treatment data and a total of 247 patients has matched pre and post treatment scRNA-seq data (Figure 2c), which facilitate us to trace the dynamic TME changes during the intervention of ICB. After annotating the major cell type and removing mitochondrial or ribosome genes enriched cells, we have annotated the cell types for each cell (Figure 2d). BRCA, HNSCC, CRC, SKCM and NSCLC rank top 5 both in terms of both patient and sample number in scICB, implying the high level of clinical translational research activity for ICB in these cancer types over the past few years.</p><p>scICB provides mainly four functionalities for users. In Browse module, users can browse information like Cancer Type, Dataset ID, Tissue Type, Patient ID, Sample ID, Cell Type, Timepoint, Response and ICB Drug. Besides, the logFC value expression table for each cell type, TNSE, UMAP, marker gene heatmap plots, cell type annotation and relative proportion for each patient, patient/response status/biopsy timepoint/tissue type can also be browsed (Figure S1). In Pre VS Post module, users could select an interested cancer type and dataset to see the dynamic changes before and after the ICB for a certain tissue type and cell type and the relevant volcano plot, differential genes and enrichment analysis will be returned (Figure S2). In R VS NR module, users can compare the DEGs between R and NR for a certain cell type after selecting a certain cancer type and dataset ID, helping to uncover the underlying mechanisms or biomarkers of immune response to ICB (Figure S3). In GeneSet module, we provide functionality for users to upload custom gene sets or specific signalling pathway genes for analysis using our curated datasets. After selecting the cancer type, dataset, tissue type, and cell type, and uploading their gene sets, users will receive a boxplot illustrating gene set activity across differen
我们在免疫检查点阻断(Immune checkpoint blockade, ICB)治疗下建立了一个泛癌症scRNA-seq数据库:scICB。已经确定了与ICB相关的详细活检时间点和治疗后的临床疗效评估信息,以帮助临床医生分析免疫治疗反应性生物标志物的不同方面(图1)。该数据库可免费访问http://www.scimmnue.com/.Herein。我们从多个来源收集了与ICB治疗相关的scRNA-seq数据集和相应的临床信息(表1)。scICB包括13种癌症类型中接受ICB或ICB联合治疗的338例患者的807个样本(图2a,表S1-S3)。共3 686 385个单细胞,涵盖NSCLC、CRC、RCC、HNSCC、BLCA、BCC、SCC、HCC、BRCA、SKCM、ESCC、GC和UCEC。对于反应状态水平,174例患者被定义为反应者(R), 170例患者被标记为无反应者(NR)(图2b)。在活检时间点水平上,共有23例患者只有ICB治疗前的scRNA-seq数据,而共有68例患者只有ICB治疗后的scRNA-seq数据,共有247例患者有匹配的治疗前后的scRNA-seq数据(图2c),这有助于我们追踪ICB干预过程中TME的动态变化。在注释了主要细胞类型并去除线粒体或核糖体基因富集的细胞后,我们对每个细胞的细胞类型进行了注释(图2d)。BRCA、HNSCC、CRC、SKCM和NSCLC在scICB中患者和样本数均排在前5位,这表明近年来这些癌症类型的ICB在临床转化研究中的活跃程度很高。scICB主要为用户提供四种功能。在浏览模块中,用户可以浏览癌症类型、数据集ID、组织类型、患者ID、样本ID、细胞类型、时间点、反应、ICB药物等信息。此外,还可以浏览各细胞类型的logFC值表达表、TNSE、UMAP、标记基因热图图、细胞类型注释以及每个患者、患者/反应状态/活检时间点/组织类型的相对比例(图S1)。在Pre VS Post模块中,用户可以选择感兴趣的癌症类型和数据集,查看ICB前后某一组织类型和细胞类型的动态变化,并返回相应的火山图、差异基因和富集分析(图S2)。在R VS NR模块中,用户可以在选择某种癌症类型和数据集ID后,比较特定细胞类型的R和NR之间的deg,有助于揭示免疫应答ICB的潜在机制或生物标志物(图S3)。在GeneSet模块中,我们为用户提供上传自定义基因集或特定信号通路基因的功能,以便使用我们的精选数据集进行分析。在选择癌症类型、数据集、组织类型和细胞类型并上传他们的基因集后,用户将收到一个显示不同时间点-反应组合的基因集活性的箱线图(图S4)。在我们的泛癌症水平综合分析中,我们首先研究了不同细胞类型的deg对ICB治疗的反应。在比较ICB治疗前后,以及反应者(R)与无反应者(NR)时,我们观察到不同细胞类型的deg数量存在相当大的差异(图3a和S5),反映了数据集的内在异质性。然后,我们使用Ro/e方法对包含不同组织类型的数据集进行了细胞类型富集分析在肿瘤组织中,我们发现内皮细胞、肥大细胞、CD8耗竭T细胞、浆细胞和巨噬细胞显著富集,表明肿瘤组织中血管生成、抗原呈递、T细胞毒性和体液免疫等生物过程上调。2-4成纤维细胞和上皮细胞不仅在肿瘤组织中丰富,而且在正常组织中也丰富,表明它们参与了恶性和非恶性环境在外周血单核细胞(PBMCs)中,单核细胞、双阴性T细胞(DNT)、CD8效应T细胞和γδ T细胞主要富集,表明它们在癌症免疫应答中的循环性质。6-8另一方面,B细胞作为淋巴结的主要组成部分,在肿瘤引流淋巴结(tdln,图3b)中富集,这与先前的研究一致,即B细胞可以在tdln中形成生发中心,并可能作为免疫应答的一种抗原提呈细胞这些结果突出了不同组织类型的不同免疫微环境。鉴于CD8效应T细胞(Teff)在抗肿瘤免疫中的关键作用,我们分析了这种细胞类型中R和NR之间的deg,特别是在ICB治疗后的肿瘤组织中(Post)。在28个数据集中的25个中鉴定出CD8效应T细胞。 我们根据差异表达的数据集数量对基因进行排序,并选择在10多个数据集中发现的基因,并将这些基因称为T细胞应答基因集(TRS)(图3c)。在TRS中,CXCL13在28个数据集中的18个中上调。应答者中其他高表达基因包括VCAM1(14/28数据集)、CD8A(12/28数据集)和ENTPD1(12/28数据集)。免疫检查点分子在应答者中也显著上调。TIGIT(12/28数据集)、HAVCR2(11/28数据集,也称为TIM-3)和PDCD1(11/28数据集,编码PD-1)是排名前三位的免疫检查点基因。这些抑制分子的上调可能被ICB靶向并激活T细胞的细胞毒性。进一步对10多个数据集中差异表达的deg进行基因本体(GO)富集分析,发现与T细胞活化、分化和抗原呈递相关的过程显著富集(图3d)。总之,我们的结果强调了免疫细胞类型和基因表达模式在决定患者对ICB治疗的反应中的复杂相互作用。关键deg的鉴定和丰富的生物过程为癌症免疫治疗中驱动成功免疫反应的机制提供了有价值的见解。综上所述,我们在ICB治疗下建立了scRNA-seq数据库的泛癌数据库scICB。以T细胞在scICB中的应用为例,我们分析了预测ICB疗效的T细胞应答性生物标志物,这有助于临床医生和研究人员探索自己感兴趣的生物标志物。更多信息可以在补充说明中看到。季凡森:数据整理,方法论,验证,形式分析,调查,写作-原稿。毕维桐:形式分析,方法论。张佳伟:数据管理,调查。唐炳军:资源。应晓:资源。李欢:资源。刘浩:资源。吴伯阳:资源。费宇:资源。杨世忠:概念化、写作-评论&编辑、监制、项目管理。徐刚:概念、方法论、写作评论编辑。董佳红:概念、资源、写作评论&编辑、监督、项目管理、资金获取。所有作者都阅读并批准了最终稿件。作者声明没有利益冲突。国家自然科学基金(批准号:82090052、82090050、82090053)和清华大学“精准医学”科研计划项目(2022ZLA007)资助。本研究不涉及内部人类参与者、动物实验或需要伦理批准的临床数据。
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