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Computational frameworks for modelling cancer across scales 跨尺度模拟癌症的计算框架
IF 1.9 Pub Date : 2025-11-03 DOI: 10.1002/ctd2.70093
Celine Desoyer, Daniel Loibner, Dagmar Brislinger, Christian Baumgartner
<div> <section> <p><b>Purpose</b>: Cancer progression is a non-linear, multiscale process driven by the interaction of molecular, cellular and tissue systems, which ultimately leads to tumour growth, invasion and metastasis. Understanding and predicting these dynamics is essential for improving diagnostics and personalising therapy. Mathematical and computational modelling has become central to this effort, enabling in silico simulations of progression and treatment response.</p> <p><b>Methods</b>: This survey outlines computational frameworks for modelling cancer across biological scales, incorporating mathematical formalisms and algorithmic paradigms. These frameworks include: ordinary and partial differential equation models of growth, angiogenesis and invasion; agent-based and hybrid multiscale approaches that capture heterogeneity and microenvironmental feedback; emerging digital twin platforms that integrate mechanistic and data-driven modelling for patient-specific predictions. Recent advances in artificial intelligence (AI), such as graph neural networks, transformer-based architectures and multimodal data fusion, enhance these frameworks by combining interpretability with predictive power through mechanistic learning pipelines.</p> <p><b>Results</b>: Based on these advances, the survey presents a conceptual roadmap for multiscale cancer modelling. This roadmap offers a structured workflow that begins with defining the biological question and modelling scale and continues through selecting appropriate paradigms, calibrating and validating models with experimental or clinical data and integrating multimodal information into individualised simulations. The long-term goal is to develop digital twins of cancer that can personalise and optimise therapy and ultimately guide clinical decisions. These models will capture processes ranging from single-cell dynamics and cancer progression to angiogenesis, tumour evolution and treatment response. To achieve this vision, we need advances in parameter calibration, multimodal dataset integration and cross-scale model validation.</p> <p><b>Conclusion</b>: Computational oncology bridges the gap between biological mechanisms and predictive modelling, offering a framework for reproducible, data-driven precision medicine. The convergence of mechanistic modelling, AI-assisted inference and digital twin technologies establishes a continuum for translating research into real-time, patient-specific decision support in oncology.</p> </section> <section> <h3> Highlights</h3> <div> <ul> <li>Provides an integrative overview of computational frameworks for modelling cancer across biological scales
目的:肿瘤的进展是一个非线性的、多尺度的过程,由分子、细胞和组织系统相互作用驱动,最终导致肿瘤的生长、侵袭和转移。了解和预测这些动态对于改进诊断和个性化治疗至关重要。数学和计算建模已成为这项工作的核心,使计算机模拟进展和治疗反应成为可能。方法:本调查概述了跨生物尺度建模癌症的计算框架,包括数学形式和算法范式。这些框架包括:生长、血管生成和侵袭的常微分方程和偏微分方程模型;捕获异质性和微环境反馈的基于agent和混合多尺度方法;新兴的数字孪生平台,集成了机制和数据驱动的模型,用于特定患者的预测。人工智能(AI)的最新进展,如图神经网络、基于变压器的架构和多模态数据融合,通过机械学习管道将可解释性与预测能力相结合,增强了这些框架。结果:基于这些进展,调查提出了多尺度癌症建模的概念路线图。该路线图提供了一个结构化的工作流程,从定义生物学问题和建模规模开始,继续通过选择适当的范例,用实验或临床数据校准和验证模型,并将多模式信息集成到个性化模拟中。长期目标是开发癌症的数字双胞胎,可以个性化和优化治疗,并最终指导临床决策。这些模型将捕捉从单细胞动力学和癌症进展到血管生成、肿瘤进化和治疗反应的过程。为了实现这一愿景,我们需要在参数校准、多模态数据集集成和跨尺度模型验证方面取得进展。结论:计算肿瘤学弥补了生物学机制和预测模型之间的差距,为可重复的、数据驱动的精准医学提供了一个框架。机制建模、人工智能辅助推理和数字孪生技术的融合建立了一个连续体,将研究转化为肿瘤学中实时的、针对患者的决策支持。重点介绍了跨生物尺度对癌症建模的计算框架的综合概述。阐述了ODE/PDE、基于代理、混合多尺度和综合转化模型的特点、优点和局限性。强调这些范式是如何共同地将机制理解与临床翻译联系起来的。提出了将建模方法与精确肿瘤学应用相联系的概念路线图。
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引用次数: 0
From immune architecture to clinical decision: Insights into the TLS-based RNA model for metastatic risk in nasopharyngeal carcinoma 从免疫结构到临床决策:鼻咽癌转移风险的基于tls的RNA模型的见解
IF 1.9 Pub Date : 2025-11-02 DOI: 10.1002/ctd2.70097
Ciming Sun, Biao Jiang, Kang Ning

Nasopharyngeal carcinoma (NPC) treatment failure is driven primarily by distant metastasis, and increasing evidence indicates that metastasis risk and clinical outcome are more closely linked to the tumour's immune architecture than to anatomical staging alone.1-3 Although NPC is typically an “immune-hot” tumour, many tumours fail to form an effective antitumor immune microenvironment.4 When tertiary lymphoid structures (TLSs) are immature or insufficient, cooperation between B cells and T cells is impaired, plasma-cell generation is reduced, and systemic control of micrometastases is consequently lost; conversely, mature TLSs, representing coordinated humoral and cellular immunity, are usually associated with tumour control and better responses to PD-1 inhibitors.5, 6 Therefore, the integrity of local immune architecture is mechanistically consistent with the tendency for distant metastasis, providing a biological basis for risk stratification and individualized therapy beyond TNM staging.

In this context, the study by Hou et al. provides an important breakthrough.7 The researchers constructed a TLS-related five-gene RNA score to predict the risk of distant metastasis in NPC, used cross-cohort Pareto optimization to select five key genes—RANBP17, TRIM9, ITGAM, ELOVL2, and KCNJ10—and achieved good predictive performance in an independent validation cohort (AUC = 0.74). When this score was integrated with clinical indicators (EBV DNA, BMI, TNM stage), the nomogram AUC increased to 0.90, outperforming clinical models alone (Figure 1). The researchers also found that high-risk patients showed downregulation of B-cell and Th17 pathways, restricted plasma-cell differentiation, and impaired TLS maturation, suggesting that disruption of the local humoral immune architecture is a key biological basis for distant metastasis in NPC and providing a reasonable mechanism for the phenomenon of being “immune-hot yet prone to metastasis.”

This study bridges tumour immunobiology to clinical practice, aligning risk prediction more closely with the biological reality of the immune landscape. However, beyond solving the question of “whether risk can be predicted,” the more important implication is “whether it can guide therapeutic intervention.” The true value of the TLS-RNA model lies in whether it can guide individualized therapy and immunologic decision-making. As the authors noted, the score can be assessed before first-line treatment to assist treatment selection.7 On this basis, we offer the following suggestions to deepen the research: For example, a clinical translation pathway from prediction to decision could be established. The TLS-RNA model could be used in prospective stratification trials to test whether patients with TLS-deficient, immune-cold tumours benefit from adding immunotherapy to chemoradiotherapy, while those

鼻咽癌(NPC)治疗失败主要是由远处转移引起的,越来越多的证据表明,转移风险和临床结果与肿瘤的免疫结构密切相关,而不仅仅是解剖分期。虽然鼻咽癌是典型的“免疫热”肿瘤,但许多肿瘤不能形成有效的抗肿瘤免疫微环境当三级淋巴结构(TLSs)不成熟或不足时,B细胞和T细胞之间的合作受损,浆细胞产生减少,从而失去对微转移的全身控制;相反,成熟的TLSs,代表协调的体液和细胞免疫,通常与肿瘤控制和对PD-1抑制剂的更好反应有关。5,6因此,局部免疫结构的完整性在机制上与远处转移的倾向是一致的,为TNM分期之外的风险分层和个体化治疗提供了生物学基础。在此背景下,Hou等人的研究提供了一个重要的突破研究人员构建了一个tls相关的五基因RNA评分来预测鼻鼻癌远处转移的风险,并采用跨队列Pareto优化选择了五个关键基因——ranbp17、TRIM9、ITGAM、ELOVL2和kcnj10,在独立验证队列中获得了良好的预测效果(AUC = 0.74)。当该评分与临床指标(EBV DNA、BMI、TNM分期)相结合时,nomogram AUC增加到0.90,优于单独的临床模型(图1)。研究人员还发现,高危患者表现出b细胞和Th17通路下调,浆细胞分化受限,TLS成熟受损,提示局部体液免疫结构的破坏是鼻咽癌远处转移的关键生物学基础,为“免疫热但易转移”现象提供了合理的机制。这项研究将肿瘤免疫生物学与临床实践联系起来,将风险预测与免疫景观的生物学现实更紧密地结合起来。然而,除了解决“风险是否可以预测”的问题之外,更重要的含义是“它是否可以指导治疗干预”。TLS-RNA模型的真正价值在于能否指导个体化治疗和免疫决策。正如作者所指出的,该评分可以在一线治疗前进行评估,以辅助治疗方案的选择在此基础上,我们提出以下深化研究的建议:例如,建立从预测到决策的临床翻译路径。TLS-RNA模型可用于前瞻性分层试验,以测试在放化疗中加入免疫治疗是否对tls缺陷、免疫冷肿瘤患者有益,而那些免疫结构完整、远处转移风险较低的患者可考虑适度去强化,从而真正将该模型转变为治疗导航工具。此外,肿瘤免疫微环境不是静态的,TLS活性可能随着治疗而动态变化。如果能够在诱导化疗或免疫治疗前后进行连续检测,TLS信号的早期变化可以作为疗效预测和复发监测的指标,使TLS- rna评分成为实时免疫监测图表,而不是一次性指标。此外,TLS- rna可以与EBV DNA和TNM联合应用:低TLS加高EBV DNA可能需要免疫治疗强化;高TLS加上低EBV DNA可能允许去强化;中间组可以使用TLS动态轨迹进行调整。通过这些进一步的研究,TLS将不再仅仅是一个静态的预后信号,而将成为一个可操作的临床工具。总之,Hou等人的研究提供了一个预测模型,并提出了一个免疫结构决定转移风险的概念框架。tls相关的五基因标记提高了预后准确性,并突出了关键的免疫生物学过程。这些见解支持免疫知情干预,从高危患者的先发制人强化到利用TLS状态进行个性化免疫治疗,并保证在NPC和更广泛的癌症研究中进行前瞻性验证。蒋彪和孙慈铭负责文章的撰写、修改和引用。康宁负责文章的设计和校对,并提供修改建议。所有作者都阅读并批准了最终的手稿。作者声明无利益冲突。不适用。
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引用次数: 0
Targeting CD70 in cancer: Mechanisms of immune escape and translational opportunities 靶向CD70在癌症中的作用:免疫逃逸机制和转化机会
IF 1.9 Pub Date : 2025-10-30 DOI: 10.1002/ctd2.70095
Akash Sabarwal, Saba Tabasum, Laxminarayan Rawat, Soumitro Pal

CD70, a tightly regulated immune co-stimulatory ligand under physiological conditions, becomes aberrantly and persistently overexpressed in a wide spectrum of malignancies, including renal cell carcinoma (RCC), glioblastoma and acute myeloid leukaemia. This tumour-restricted expression pattern, coupled with its potent immunomodulatory effects, positions CD70 as a uniquely actionable target in modern oncology. Unlike classical immune checkpoints, CD70 contributes to immune escape by chronically engaging CD27, leading to T cell exhaustion, regulatory T cell (Treg) expansion and myeloid-derived suppressor cell activation, collectively shaping a profoundly immunosuppressive tumour microenvironment. Mechanistically, CD70 expression is amplified by convergent oncogenic, inflammatory and hypoxic signals, most notably HIF-2α stabilization in VHL-deficient RCC, linking it to aggressive disease biology and poor prognosis. Notably, CD70 expression in tumours often coexists with dysregulation of receptor tyrosine kinase (RTK) pathways (e.g. MET, AXL) and immune checkpoint circuits (e.g. PD-1/PD-L1), supporting rationale combination therapies aimed at overcoming resistance and enhancing anti-tumour immunity. A diverse array of CD70-directed therapies, including antibody-drug conjugates, CAR-T and CAR-NK cells, monoclonal antibodies and radiotheranostic agents, are advancing through preclinical and early clinical pipelines. Beyond therapeutic applications, CD70 also holds promise as a biomarker for tumour detection, patient stratification and response monitoring. This mini-review synthesizes emerging insights into CD70-driven immune evasion, highlights evolving therapeutic strategies and discusses the integration of CD70 targeting into next-generation immunotherapy and precision oncology platforms. This review is novel in linking CD70-mediated immune escape to oncogenic RTK signalling and in foregrounding recent translational advances and rational combination strategies that have not been comprehensively covered in prior reviews.

CD70是一种在生理条件下受到严格调控的免疫共刺激配体,在包括肾细胞癌(RCC)、胶质母细胞瘤和急性髓系白血病在内的多种恶性肿瘤中异常和持续过表达。这种肿瘤限制性表达模式,加上其强大的免疫调节作用,使CD70成为现代肿瘤学中唯一可行的靶点。与经典的免疫检查点不同,CD70通过长期参与CD27来促进免疫逃逸,导致T细胞衰竭、调节性T细胞(Treg)扩增和髓源性抑制细胞激活,共同形成一个深刻的免疫抑制肿瘤微环境。在机制上,CD70的表达被趋同的致癌、炎症和缺氧信号放大,最显著的是在vhl缺陷的RCC中HIF-2α的稳定,将其与侵袭性疾病生物学和不良预后联系起来。值得注意的是,CD70在肿瘤中的表达通常与受体酪氨酸激酶(RTK)通路(如MET、AXL)和免疫检查点回路(如PD-1/PD-L1)的失调共存,这支持了旨在克服耐药性和增强抗肿瘤免疫的基本原理联合治疗。多种cd70导向疗法,包括抗体-药物偶联物、CAR-T和CAR-NK细胞、单克隆抗体和放射治疗药物,正在通过临床前和早期临床管道推进。除了治疗应用之外,CD70还有望作为肿瘤检测、患者分层和反应监测的生物标志物。这篇小型综述综合了CD70驱动的免疫逃避的新见解,强调了不断发展的治疗策略,并讨论了CD70靶向与下一代免疫治疗和精确肿瘤平台的整合。这篇综述在将cd70介导的免疫逃逸与致癌RTK信号联系起来方面是新颖的,并且展望了最近的翻译进展和合理的联合策略,这些在以前的综述中没有全面覆盖。
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引用次数: 0
Metagenomic next-generation sequencing provides a rapid and accurate diagnosis of pathogens in patients undergoing immunosuppressive therapy 新一代宏基因组测序为接受免疫抑制治疗的患者提供了快速准确的病原体诊断
IF 1.9 Pub Date : 2025-10-26 DOI: 10.1002/ctd2.70090
Lei Yue, Mengjiao Yuan, Chang Li, Miaomiao Zhang, Mengjia Qian, Qi Shen, Lingyan Wang, Yanxia Zhan, Bijun Zhu, Yujie Zhou, Hao Chen, Guoming Shi, Yunfeng Cheng

Background

Patients receiving immunosuppressive regimens are at increased risk of life-threatening infections from microorganisms. The comprehensive analysis of the types and composition of pathogenic microorganisms in clinical specimens from immunosuppressed patients is of great importance for prognosis and diagnosis.

Methods

Three hundred and sixty clinical samples from 199 patients were enrolled in this study. The results of metagenomics next-generation sequencing (mNGS) detection were analysed, and diagnostic performance was compared with that of conventional methods (CMs). Differences in microbiological detection were analysed between immunosuppressant monotherapy and combination therapy. The differences in microflora between blood samples and non-blood samples were also examined.

Results

The positive rate of the mNGS results was higher than that of the CMs results in all types of samples, and the number of pathogens detected by mNGS was also greater than that of CMs. The percentage of co-infection detected by mNGS was 45.56% which was higher than that of CMs (6.67%, 24 out of 360). In the immunosuppressant single-drug group, 58.1% of the samples were mixed infections, while in the two-drug combination group, single infections accounted for 56% of the samples. Multiple pathogen infection (63.8%) was the most common type of infection in non-blood samples, of which 28.4% were viral and bacterial co-infections. A single pathogen accounted for 53.8% of the infections detected in blood samples, of which 35.9% were individual viruses. Non-blood samples have a higher negative predictive value (88.9% vs. 77.5%) and accuracy (100% vs. 92%) than blood samples.

Conclusions

mNGS is superior to CMs for the diagnosis of infections in patients treated with immunosuppressants. The immunosuppressive medication regimen needs to be adjusted when the patients have serious infections. Blood samples could be used for rapid diagnosis of suspected viral infection, and samples from infectious sites have significant advantages in detecting bacterial and viral co-infection.

背景:接受免疫抑制治疗的患者受到微生物感染威胁生命的风险增加。综合分析免疫抑制患者临床标本中病原微生物的种类和组成,对预后和诊断具有重要意义。方法选取199例患者共360份临床标本进行研究。分析元基因组新一代测序(mNGS)检测结果,并与常规方法(CMs)的诊断性能进行比较。分析免疫抑制剂单药与联合治疗在微生物检测方面的差异。血液样本和非血液样本之间的微生物群差异也进行了检查。结果各类型标本mNGS检测结果的阳性率均高于CMs检测结果,且mNGS检测出的病原菌数量也大于CMs。mNGS共感染检出率为45.56%,高于CMs(6.67%, 24 / 360)。在免疫抑制剂单药组中,58.1%的样本为混合感染,而在两药联合组中,单一感染占56%。非血液标本中多病原菌感染最为常见(63.8%),其中病毒与细菌共感染占28.4%。血液样本中检测到的感染中,单一病原体占53.8%,其中单个病毒占35.9%。非血液样本的阴性预测值(88.9%对77.5%)和准确率(100%对92%)高于血液样本。结论mNGS对免疫抑制剂患者感染的诊断优于CMs。当患者出现严重感染时,需要调整免疫抑制药物治疗方案。血液样本可用于疑似病毒感染的快速诊断,感染部位样本在检测细菌和病毒共感染方面具有显著优势。
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引用次数: 0
The rise of one-pot nucleic acid detection using CRISPR CRISPR一锅核酸检测的兴起
IF 1.9 Pub Date : 2025-10-23 DOI: 10.1002/ctd2.70091
Shuobo Shi, Qingqing Shang, Wenzhe Si, Jinyu Fu, Yaru Li
<p>Nucleic acid detection is a cornerstone of modern molecular diagnostics, underpinning applications from disease diagnosis and pathogen surveillance to food safety and environmental monitoring. CRISPR-Cas technology has transformed nucleic acid detection by enabling highly precise, rapid and cost-effective diagnostic solutions. Systems such as SHERLOCK (Cas13-based) and DETECTR/HOLMES (Cas12-based) integrate the programmability and precision of CRISPR-Cas with the collateral cleavage activity of Cas proteins toward reporter molecules (e.g., fluorescently quenched ssDNA or RNA), yielding unprecedented levels of specificity and sensitivity for target detection.<span><sup>1</sup></span> However, in molecular diagnostics, target nucleic acids can be present at attomolar levels, revealing a sensitivity bottleneck for direct CRISPR-based detection. Combining isothermal amplification techniques with CRISPR-based detection offers a promising solution: this integration preserves the high specificity of CRISPR while boosting sensitivity through amplification.</p><p>In current CRISPR-based detection workflows, isothermal amplification and Cas-based target recognition usually remain two separate steps, requiring transfer of amplification products to a Cas-based recognition system (Figure 1A). This is operationally cumbersome and risks cross-contamination between samples.<span><sup>1, 2</sup></span> To address these limitations, the field has increasingly shifted toward integrated “one-pot” detection systems—a paradigm that combines two or more key workflow steps (e.g., sample lysis, target amplification, and target detection) within a single, closed reaction vessel. By eliminating manual sample transfer, one-pot systems minimize cross-contamination risks, reduce hands-on time, lessen reliance on specialized equipment, and enable decentralized testing, all of which are critical for expanding global access to high-quality nucleic acid detection.</p><p>To advance the performance, robustness, and practical applicability of one-pot CRISPR-based detection systems, extensive research has focused on resolving the key technical challenge of integrating amplification and Cas-based target recognition. These efforts can be broadly categorized into three complementary strategies (Figure 1B):</p><p>1. Physical separation of the amplification and nuclease steps: Physical compartmentalization isolates isothermal amplification from Cas nuclease reactions to prevent premature cross-reactivity and eliminate manual sample transfer, enabling sequential activation (amplification first, then Cas recognition). A simple approach uses a single tube with amplification reagents at the bottom and Cas reagents on the lid or inner wall. After amplification, gentle mixing initiates Cas detection. For example, opvCRISPR places RT-LAMP reagents at the bottom and Cas12a reagents on the lid, yielding a visible fluorescence readout after mixing.<span><sup>3</sup></span> On the other hand, eng
核酸检测是现代分子诊断的基石,是疾病诊断、病原体监测、食品安全和环境监测等应用的基础。CRISPR-Cas技术通过实现高精度、快速和具有成本效益的诊断解决方案,改变了核酸检测。SHERLOCK(基于cas13)和DETECTR/HOLMES(基于cas12)等系统将CRISPR-Cas的可编程性和精确性与Cas蛋白对报告分子(例如,荧光猝灭的ssDNA或RNA)的侧切活性结合起来,为目标检测提供了前所未有的特异性和敏感性1然而,在分子诊断中,靶核酸可以存在于原子摩尔水平,这揭示了直接基于crispr的检测的灵敏度瓶颈。将等温扩增技术与基于CRISPR的检测相结合提供了一个有希望的解决方案:这种整合保留了CRISPR的高特异性,同时通过扩增提高了灵敏度。在目前基于crispr的检测工作流程中,等温扩增和基于cas的目标识别通常是两个独立的步骤,需要将扩增产物转移到基于cas的识别系统中(图1A)。这在操作上很麻烦,而且有样品间交叉污染的风险。1,2为了解决这些限制,该领域越来越多地转向集成的“一锅”检测系统-一种将两个或多个关键工作流程步骤(例如,样品裂解,目标扩增和目标检测)结合在单个封闭反应容器中的范例。通过消除人工样品转移,一锅系统最大限度地减少了交叉污染风险,减少了动手时间,减少了对专用设备的依赖,并实现了分散检测,所有这些对于扩大全球获得高质量核酸检测至关重要。为了提高基于crispr的单锅检测系统的性能、鲁棒性和实用性,广泛的研究集中在解决整合扩增和基于cas的目标识别的关键技术挑战上。这些努力可以大致分为三种互补策略(图1B):扩增和核酸酶步骤的物理分离:物理分隔将等温扩增从Cas核酸酶反应中分离出来,以防止过早的交叉反应,并消除人工样品转移,实现顺序激活(首先扩增,然后Cas识别)。一种简单的方法是使用一根管,底部装有扩增试剂,盖子或内壁装有Cas试剂。放大后,温和混合启动Cas检测。例如,opvCRISPR将RT-LAMP试剂放在底部,Cas12a试剂放在盖子上,混合后产生可见的荧光读数另一方面,工程微流控芯片或定制设备允许更强大的分离,实现自动化,顺序激活。例如,在空间上分离扩增和Cas13a的离心微流体系统4,以及随着扩增的进行将两步连接起来的植物启发吸力方法,实现了空间分离和时间控制5然而,物理分离的方法将扩增试剂和CRISPR试剂在单个管(例如,在帽中或使用巢状管)或微流控芯片上进行空间分离是有效的,但通常需要人工干预(例如,摇晃,离心)或复杂,昂贵的芯片制造,损害了真正的“样品-输入-输出”的简单性并增加了成本。反应组分优化:一锅式CRISPR核酸检测的关键策略是反应组分优化,通过解决分子不相容,实现等温扩增(如RPA、LAMP)和Cas系统(如Cas12a、Cas13a)的直接共孵化。与物理分离不同,它解决了分子水平上的冲突。研究人员已经调整了缓冲液的组成、酶的比例和辅助因子添加剂,以创建一个与等温扩增和Cas蛋白活性兼容的通用反应环境。例如,在最近的一项研究中,实验统计设计(DoE),特别是明确的筛选设计,用于优化基于CRISPR/ cas12a - rpa的单锅方法,6确定了关键的性能增强因子,如逆转录缓冲液和RNase抑制剂。同时,先进的工程技术进一步提高了性能:模板保护性Cas设计仅针对扩增子,7个短暂失活的Cas蛋白在扩增过程中保持失活,8和次优的PAM位点选择将Cas活性限制在高浓度的扩增子上一个说明性的例子涉及通过PAM选择调整CRISPR-Cas12a切割:次优PAM通常会降低Cas12a活性。Fu等人。 结果表明,为次优PAMs设计的crrna可以大大提高一锅检测的效率和速度此外,通过优化样品裂解缓冲液,该方法实现了一种无提取的一锅检测临床样品的方法。通过在分子水平上解决试剂不相容性,组分优化消除了复杂的物理划分的需要。这简化了一锅系统的设计,降低了制造成本,并提高了分析的可重复性。基于相分离的顺序激活:基于相分离的顺序激活通过在单个容器内空间隔离不相容的反应(例如扩增和cas介导的识别),利用多组分系统的自发脱混,实现了一锅CRISPR检测。驱动这种方法的两个核心策略:(1)粘度和密度调节剂(如甘油和琼脂糖)减缓生物分子的扩散,以防止过早的交叉反应,然后逐渐均质;(2)刺激响应界面(如热响应蜡)产生可逆屏障,可被破坏(例如通过加热)以混合组分。例如,用甘油优化的一锅CRISPR检测系统就证明了这一原理甘油与Cas裂解组分预混合,其增强粘度的特性保持了与RPA(重组酶聚合酶扩增)试剂的空间分离。随着反应的进行,组分在粘度梯度上逐渐扩散,最终形成均匀的混合物,使cas介导的扩增产物检测成为可能。同样,热反应蜡也被用来调节病原体检测的顺序反应在这个设计中,固体蜡最初将RPA试剂和CRISPR组件分隔成独立的隔间。加热后,蜡经历了固-液相转变,允许扩增的RPA产物与Cas蛋白混合并启动目标识别,所有这些都在一个封闭的容器中进行。虽然基于相分离的策略为一锅集成提供了简单和高效的方法,但其可重复性对实验条件具有固有的敏感性。温度梯度、试剂浓度比和相变动力学等因素会导致相分离动力学的变化,从而可能影响分析的一致性。现在,基于crispr的诊断有望实现快速、无污染的一锅核酸检测,但主要障碍仍然存在。一个关键的限制是许多一锅平台不集成样本处理,需要传统的提取,阻碍了真正的样本到答案的POCT。未来的工作应该追求集成的、无提取的工作流程,将样品处理与CRISPR读数结合在一个容器中。此外,通过创新的纳米材料和生物分子推进一锅生物传感器的小型化和便携性,可以增强信号输出和鲁棒性,从而产生具有广泛POCT适用性的紧凑,用户友好的设备。标准化的协议对于可重复性也是必不可少的。解决这些挑战对于实现基于crispr的一锅检测并扩大其在核酸诊断中的影响至关重要。史硕博和李雅茹对这份手稿的构思和设计做出了贡献。史硕博、司文哲、李雅茹收集相关研究纳入,并负责稿件准备。尚青青创作了这些人物。史硕博和付金玉编辑、审读和修改了手稿。所有作者都对文章做出了贡献,并批准了提交的版本。作者声明无利益冲突。不适用。这项工作得到了国防工业技术发展计划(国防工业技术发展计划)的支持。JCKY2021602B009)。
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引用次数: 0
Alveolar IL1β+ neutrophils: Emerging biomarkers and therapeutic targets in CARDS progression 肺泡il - 1β+中性粒细胞:CARDS进展中的新兴生物标志物和治疗靶点
IF 1.9 Pub Date : 2025-10-22 DOI: 10.1002/ctd2.70092
Lu Jia, Ying Tang, Jianfeng Xie
<p>Coronavirus disease 2019 (COVID-19) has presented an unprecedented challenge to intensive care medicine, largely because of its frequent complication with acute respiratory distress syndrome (ARDS), termed coronavirus-associated ARDS (CARDS). Despite advances in supportive care, prognosis for patients with severe CARDS remains poor, and mechanisms of disease progression are still poorly understood. A central theme in CARDS research is the role of dysregulated host immune responses, particularly the excessive activation of innate immune cells that drive hyperinflammation and tissue damage.<span><sup>1</sup></span></p><p>Neutrophils, the most abundant leukocytes in blood, have long been recognized as double-edged swords in pulmonary defence. They are indispensable for antimicrobial responses and promote lung injury through excessive degranulation, oxidative burst, and release of neutrophil extracellular traps in CARDS.<span><sup>2</sup></span> Recent bronchoalveolar lavage (BAL) studies in CARDS demonstrated a complex inflammatory milieu, markedly increased neutrophil proportions, elevated IL-1β and IL-9, and reduced interferon-γ expression. Moreover, studies also show that other pro-inflammatory markers, such as CXCL2, CXCL8, and S100A8, were significantly more pronounced in non-survivors of CARDS.<span><sup>3, 4</sup></span> Importantly, BAL neutrophilia emerged as independent predictors of poor outcomes, highlighting the relevance of neutrophil-driven inflammation in CARDS.<span><sup>5</sup></span></p><p>In this context, the recent study entitled “Multitemporal Single-cell Profiling Uncovers Alveolar interleukin-1β (IL1β) <sup>+</sup> Neutrophils: A Significant Indicator of CARDS Progression” provides important mechanistic insights. Using longitudinal single-cell profiling, the authors identified a distinct alveolar IL1β⁺ neutrophil subset whose abundance correlated with hypoxemia and radiographic severity. The key finding is the emergence of a functionally distinct subset of alveolar IL1β⁺ neutrophils during CARDS progression, which serves as a major source of IL1β. Notably, these cells underwent metabolic reprogramming, shifting from glycolysis toward fatty acid oxidation, accompanied by upregulation of ACSL1, a pivotal driver of inflammasome activation and cytokine release. In parallel, macrophages amplified neutrophil hyperinflammation through IL-6 signalling, while PD-L1–dependent suppression linked neutrophil hyperactivation to systemic immunosuppression. Collectively, these findings illustrate the interplay among metabolic rewiring, inflammatory amplification and immune suppression in driving CARDS pathogenesis (see Figure 1).</p><p>These findings carry translational implications. First, alveolar IL1β⁺ neutrophils may serve as a biomarker of disease trajectory, potentially aiding early risk stratification. Second, clinical trials using antagonists of the IL-1 receptor or the NET-IL1β loop, such as anakinra, canakinumab and rilonacept,
除了CARDS, IL-1β驱动的中性粒细胞炎症也与其他气道疾病有关,在慢性鼻窦炎伴鼻息肉小鼠模型中,药物阻断IL-1β信号可显著减少中性粒细胞浸润和炎症最后,针对IL-1通路的治疗试验应考虑按中性粒细胞表型分层,因为这可能确定可能受益的亚群。总之,肺泡IL1β +中性粒细胞的发现是理解CARDS免疫发病机制的关键一步,将先天免疫过度激活、代谢重编程和全身免疫抑制联系起来。虽然需要进一步的验证和功能研究,但这些发现扩展了中性粒细胞异质性的概念,并为生物标志物的开发和靶向治疗开辟了新的途径。陆佳构思并撰写了手稿。谢剑锋和唐颖提供了重要的修订和全面的指导。不适用。江苏省自然科学基金项目(BK20240210 -唐颖)、国家科技部科技重大专项项目(2023ZD0506506 -谢剑锋)、国家自然科学基金项目(82272210 -谢剑锋)、东南大学智山学者计划项目(2242025RCB0035 -唐颖)资助。
{"title":"Alveolar IL1β+ neutrophils: Emerging biomarkers and therapeutic targets in CARDS progression","authors":"Lu Jia,&nbsp;Ying Tang,&nbsp;Jianfeng Xie","doi":"10.1002/ctd2.70092","DOIUrl":"https://doi.org/10.1002/ctd2.70092","url":null,"abstract":"&lt;p&gt;Coronavirus disease 2019 (COVID-19) has presented an unprecedented challenge to intensive care medicine, largely because of its frequent complication with acute respiratory distress syndrome (ARDS), termed coronavirus-associated ARDS (CARDS). Despite advances in supportive care, prognosis for patients with severe CARDS remains poor, and mechanisms of disease progression are still poorly understood. A central theme in CARDS research is the role of dysregulated host immune responses, particularly the excessive activation of innate immune cells that drive hyperinflammation and tissue damage.&lt;span&gt;&lt;sup&gt;1&lt;/sup&gt;&lt;/span&gt;&lt;/p&gt;&lt;p&gt;Neutrophils, the most abundant leukocytes in blood, have long been recognized as double-edged swords in pulmonary defence. They are indispensable for antimicrobial responses and promote lung injury through excessive degranulation, oxidative burst, and release of neutrophil extracellular traps in CARDS.&lt;span&gt;&lt;sup&gt;2&lt;/sup&gt;&lt;/span&gt; Recent bronchoalveolar lavage (BAL) studies in CARDS demonstrated a complex inflammatory milieu, markedly increased neutrophil proportions, elevated IL-1β and IL-9, and reduced interferon-γ expression. Moreover, studies also show that other pro-inflammatory markers, such as CXCL2, CXCL8, and S100A8, were significantly more pronounced in non-survivors of CARDS.&lt;span&gt;&lt;sup&gt;3, 4&lt;/sup&gt;&lt;/span&gt; Importantly, BAL neutrophilia emerged as independent predictors of poor outcomes, highlighting the relevance of neutrophil-driven inflammation in CARDS.&lt;span&gt;&lt;sup&gt;5&lt;/sup&gt;&lt;/span&gt;&lt;/p&gt;&lt;p&gt;In this context, the recent study entitled “Multitemporal Single-cell Profiling Uncovers Alveolar interleukin-1β (IL1β) &lt;sup&gt;+&lt;/sup&gt; Neutrophils: A Significant Indicator of CARDS Progression” provides important mechanistic insights. Using longitudinal single-cell profiling, the authors identified a distinct alveolar IL1β⁺ neutrophil subset whose abundance correlated with hypoxemia and radiographic severity. The key finding is the emergence of a functionally distinct subset of alveolar IL1β⁺ neutrophils during CARDS progression, which serves as a major source of IL1β. Notably, these cells underwent metabolic reprogramming, shifting from glycolysis toward fatty acid oxidation, accompanied by upregulation of ACSL1, a pivotal driver of inflammasome activation and cytokine release. In parallel, macrophages amplified neutrophil hyperinflammation through IL-6 signalling, while PD-L1–dependent suppression linked neutrophil hyperactivation to systemic immunosuppression. Collectively, these findings illustrate the interplay among metabolic rewiring, inflammatory amplification and immune suppression in driving CARDS pathogenesis (see Figure 1).&lt;/p&gt;&lt;p&gt;These findings carry translational implications. First, alveolar IL1β⁺ neutrophils may serve as a biomarker of disease trajectory, potentially aiding early risk stratification. Second, clinical trials using antagonists of the IL-1 receptor or the NET-IL1β loop, such as anakinra, canakinumab and rilonacept, ","PeriodicalId":72605,"journal":{"name":"Clinical and translational discovery","volume":"5 5","pages":""},"PeriodicalIF":1.9,"publicationDate":"2025-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/ctd2.70092","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145366654","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
A novel mechanism for maintaining spindle normality in mammalian oocytes 维持哺乳动物卵母细胞纺锤体正常的新机制
IF 1.9 Pub Date : 2025-10-08 DOI: 10.1002/ctd2.70089
Zhi-Xia Yang, Zi-Fu Wang, Dong Zhang

Mammalian oocyte meiosis holds distinct features from mitosis in many aspects. For example, the organisation of the spindle poles, the separation processes of the chromosomes, the way microtubules (MTs) are nucleated and so forth.1 Many issues about oocyte meiosis are still to be addressed. Moreover, in the past decade, researchers found that oocyte meiosis in primates, including humans, employed some specific proteins or structures, making the mechanical study of mammalian oocyte meiosis more complicated.2-4 Among these primate-specific proteins, TUBB8 is the most conspicuous since the Tubb8 mutation in humans accounts for about 30% or more of abnormal clinical cases in MI arrest, fertilisation failure, and early embryo development arrest.5, 6 However, there are still many unaddressed questions about TUBB8. For example, what's the exact mechanism by which TUBB8 function to organise and stabilise spindle MTs? Are there effective and easy strategies to rescue all sorts of spindle defects caused by different TUBB8 mutations? Recently, a work by Hui Luo et al has made significant progress on both questions.7

For the first question, through a combination of multiple cell biological & molecular biology, and biochemistry techniques, they found that TUBB8-D417N expression significantly disrupted its interaction with EB1, a fundamental MT nucleator and polymerizer, and thereby dis-localised EB1; meanwhile, the EB1 protein level didn't change, suggesting that TUBB8 help the correct localisation of EB1. EB1 mislocalisation in turn seriously disrupted the distribution of several other MT nucleators, including CKAP5 and TACC, but didn't affect their protein levels (Figure 1). In addition, TUBB8-D417N expression also broke up the localisation of several critical MT polymerisers and stabilisers, including TPX2, Ran-GTP and KIF11. All these suggest that TUBB8 is fundamentally important for MT nucleation & polymerisation and the maintenance of spindle bipolarity.

Nonetheless, it's this study that incites the upper issues, and many others. Therefore, it is a very important and enlightening work. It would be exciting to expect further related investigations. Figure 1

Zhi-Xia Yang wrote the manuscript and made the graphic abstract image. Dong Zhang and Zi-Fu Wang proofread and gave advice. All authors read and approved the final manuscript.

The authors declare no conflict of interest.

Not applicable.

哺乳动物卵母细胞减数分裂在许多方面具有与有丝分裂不同的特征。例如,纺锤极的组织,染色体的分离过程,微管(mt)的成核方式等等关于卵母细胞减数分裂的许多问题仍有待解决。此外,在过去的十年中,研究人员发现,包括人类在内的灵长类动物的卵母细胞减数分裂使用了一些特定的蛋白质或结构,使得哺乳动物卵母细胞减数分裂的机械研究更加复杂。2-4在这些灵长类动物特异性蛋白中,TUBB8是最显著的,因为人类的TUBB8突变约占心肌梗死停搏、受精失败和早期胚胎发育停止的临床异常病例的30%或更多。然而,关于TUBB8仍有许多未解决的问题。例如,TUBB8组织和稳定纺锤体mt的确切机制是什么?是否有有效和简单的策略来挽救由不同的TUBB8突变引起的各种纺锤体缺陷?最近,罗辉等人的一项工作在这两个问题上都取得了重大进展。对于第一个问题,通过多细胞生物学和分子生物学以及生物化学技术的结合,他们发现TUBB8-D417N的表达显著地破坏了其与EB1(一种基本的MT成核剂和聚合剂)的相互作用,从而使EB1失位;同时,EB1蛋白水平没有变化,说明TUBB8有助于EB1的正确定位。EB1错位反过来严重破坏了其他几种MT核子的分布,包括CKAP5和TACC,但不影响它们的蛋白水平(图1)。此外,TUBB8-D417N的表达还破坏了几种关键MT聚合物和稳定剂的定位,包括TPX2、Ran-GTP和KIF11。所有这些都表明,TUBB8对MT成核、聚合和维持纺锤体双极性至关重要。尽管如此,正是这项研究引发了更高层次的问题,以及许多其他问题。因此,这是一项非常重要和具有启发性的工作。期待进一步的相关调查将是令人兴奋的。图1杨志霞撰写稿件,制作图形抽象形象。张东、王子甫校对并出主意。所有作者都阅读并批准了最终的手稿。作者声明无利益冲突。不适用。
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引用次数: 0
Advances in epilepsy associated with 16p11.2 microdeletion syndrome 癫痫与16p11.2微缺失综合征相关的研究进展
IF 1.9 Pub Date : 2025-09-25 DOI: 10.1002/ctd2.70088
Qikai Zhao, Shuqi Liang, Xiao Wu, Xiaohui Min, Nooraynee Bibi Needah Ginowree, Gang Zhang

Background

16p11.2 microdeletion syndrome is a genetic disorder with a population prevalence of approximately 2.84.3 per 100,000 individuals. Epilepsy is one of its core symptoms, significantly impacting neurodevelopment and quality of life. Current treatment strategies are shifting from empirical antiepileptic drug use toward mechanism-based precision therapy. Epilepsy in this syndrome typically presents in infancy, with focal seizures as the most common type.

Methods

Electroencephalogram findings often include focal or multifocal epileptiform discharges. Genomic deletions affecting key genes such as PRRT2, KCTD13, TAOK2, QPRT, and SEZ6L2 contribute to neurodevelopmental abnormalities, synaptic dysfunction, and excitatory-inhibitory imbalance through dysregulated molecular pathways including RhoA signaling, microtubule dynamics, and quinolinic acid metabolism.

Conclusions

Clinically, levetiracetam shows limited efficacy in PRRT2-related epilepsy, whereas valproate, oxcarbazepine, and topiramate are often effective. Emerging therapeutic strategies target specific molecular mechanisms, such as RhoA inhibition or modulation of the kynurenine pathway. The integration of genetic diagnosis with pathway-specific interventions offers promising avenues for improving seizure control and neurodevelopmental outcomes in patients with 16p11.2 microdeletion syndrome. In this article, we review the clinical features.molecular mechanisms and therapeutic strategies of 16p11.2 microdeletion.associated epilepsy to provide a theoretical basis for precision diagnosis and treatment.

16p11.2微缺失综合征是一种遗传疾病,人群患病率约为每10万人2.84.3例。癫痫是其核心症状之一,严重影响神经发育和生活质量。目前的治疗策略正在从经验性抗癫痫药物使用转向基于机制的精确治疗。这种综合征的癫痫通常出现在婴儿期,局灶性癫痫是最常见的类型。方法脑电图常表现为局灶性或多灶性癫痫样放电。影响关键基因如PRRT2、KCTD13、TAOK2、QPRT和SEZ6L2的基因组缺失通过包括RhoA信号、微管动力学和喹啉酸代谢在内的分子通路失调,导致神经发育异常、突触功能障碍和兴奋-抑制失衡。结论在临床上,左乙拉西坦对prrt2相关性癫痫的疗效有限,而丙戊酸盐、奥卡西平和托吡酯通常有效。新兴的治疗策略针对特定的分子机制,如RhoA抑制或调节犬尿氨酸途径。基因诊断与通路特异性干预的整合为改善16p11.2微缺失综合征患者的癫痫控制和神经发育结果提供了有希望的途径。本文就其临床特点作一综述。16p11.2微缺失的分子机制和治疗策略。为关联癫痫的精准诊断和治疗提供理论依据。
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引用次数: 0
A comprehensive atlas of pediatric immune checkpoint inhibitors-related adverse events: From real-world pharmacovigilance data to mechanistic insights 儿童免疫检查点抑制剂相关不良事件的综合图谱:从现实世界的药物警戒数据到机制见解
IF 1.9 Pub Date : 2025-09-25 DOI: 10.1002/ctd2.70086
Anqi Lin, Junyi Shen, Zhenyu Xie, Quan Cheng, Jian Zhang, Peng Luo

Background

Immune checkpoint inhibitors (ICIs) are widely used in childhood cancer, posing challenges with associated ICIs-related adverse events (irAEs). This study focuses on pediatric irAEs and explores underlying mechanisms.

Methods

Data on ICI-related adverse reactions were gathered from two sources: VigiBase database (1967–2023) and the FDA Adverse Event Reporting System (FAERS) database (2013–2022). Disproportionality analysis (Reporting odds ratio, proportional reporting ratio, information component) compared pediatric and adult cancer patients using ICIs. Integration with the Gene Expression Omnibus (GEO) database explored potential biological mechanisms.

Results

We identified four categories of pediatric irAEs in the VigiBase and FAERS databases, including cytokine release syndrome (RORVigiBase = 17.05; RORFAERS = 14.17), acute respiratory distress syndrome (RORVigiBase = 10.26; RORFAERS = 12.39), seizure (RORVigiBase = 7.18; RORFAERS = 10.63), and febrile neutropenia (FN) (RORVigiBase = 3.01; RORFAERS = 4.84). The development of irAEs in pediatric patients potentially involves various pathways: immune activation, inflammatory imbalance, pathogen recognition systems, decreased inhibitory synapses, altered E/I ratios, and CNS abnormalities.

Conclusions

This study explores pediatric irAEs, revealing potential mechanisms and stressing tailored prevention for young cancer patients on ICIs, providing theoretical insights for better management.

免疫检查点抑制剂(ICIs)广泛应用于儿童癌症,但存在与ICIs相关的不良事件(irAEs)。本研究的重点是儿童irAEs,并探讨其潜在机制。方法从VigiBase数据库(1967-2023)和FDA不良事件报告系统(FAERS)数据库(2013-2022)两个来源收集ici相关不良反应数据。歧化分析(报告优势比、比例报告比、信息成分)比较了儿童和成人使用ICIs的癌症患者。与Gene Expression Omnibus (GEO)数据库的整合探索了潜在的生物学机制。结果:我们在VigiBase和FAERS数据库中确定了四类儿童irae,包括细胞因子释放综合征(RORVigiBase = 17.05; RORFAERS = 14.17)、急性呼吸窘迫综合征(RORVigiBase = 10.26; RORFAERS = 12.39)、癫痫发作(RORVigiBase = 7.18; RORFAERS = 10.63)和发热性中性粒细胞减少症(RORVigiBase = 3.01; RORFAERS = 4.84)。儿童患者irae的发展可能涉及多种途径:免疫激活、炎症失衡、病原体识别系统、抑制性突触减少、E/I比率改变和中枢神经系统异常。结论本研究探讨了儿童脑梗死,揭示了潜在的机制,强调了针对年轻癌症患者的针对性预防,为更好地管理脑梗死提供了理论见解。
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引用次数: 0
Intravital microscopy contribution to cancer: From preclinical to human studies 活体显微镜对癌症的贡献:从临床前到人体研究
IF 1.9 Pub Date : 2025-09-22 DOI: 10.1002/ctd2.70051
Diogo Moniz-Garcia, Wan-Hsin Lin, Loizos Michaelides, Anthony Quagliano, Emmanuel Gabriel, Alfredo Quinones-Hinojosa

Intravital microscopy enables dynamic and real-time visualisation of microscopic structures in living tissues without the need for fixation, with real-life applicability being illustrated by several first-in-human studies in different cancers. Its use in preclinical models has yielded important observations of the microvasculature of both healthy and diseased tissues. It has further enabled the observation of the interactions between important components of the tissue microenvironment such as immune cells and neighbouring microvessels. Important recent technological advances, however, have enabled the translation of this technology to human use. Here, we review the main advances in intravital microscopy and some of the most recent uses in different human disease settings.

活体显微术可以实现活体组织微观结构的动态实时可视化,而无需固定,在不同癌症的几项首次人体研究中证明了其现实适用性。它在临床前模型中的应用已经对健康和病变组织的微血管系统进行了重要观察。它进一步使观察组织微环境的重要组成部分(如免疫细胞和邻近微血管)之间的相互作用成为可能。然而,最近重要的技术进步使这项技术能够转化为人类使用。在这里,我们回顾了活体显微镜的主要进展和一些最新的应用在不同的人类疾病设置。
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引用次数: 0
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Clinical and translational discovery
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