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Mitochondrial Dysfunction in Aging: Future Therapies and Precision Medicine Approaches 衰老中的线粒体功能障碍:未来的治疗方法和精准医学方法
Pub Date : 2025-07-17 DOI: 10.1002/mef2.70026
Lanlan Jia, Ziyu Wei, Jinyuan Luoqian, Xi Wang, Chao Huang

Mitochondria are the primary energy hubs of cells and are critical for maintaining cellular functions. However, aging leads to a decline in mitochondrial efficiency. This decline is marked by increased reactive oxygen species, accumulation of mitochondrial DNA mutations, impaired oxidative phosphorylation, and breakdown of mitochondrial quality control systems. Such changes are associated with the development of neurodegenerative, cardiovascular, and metabolic diseases. Although much research has been done, the precise connection between mitochondrial dysfunction and aging remains unclear. Furthermore, current literature exhibits a lack of systematic organization regarding the mitochondria-targeted therapeutic interventions. This review systematically explores the mechanisms underlying mitochondrial deterioration during aging. Key focuses include impaired biogenesis, disrupted dynamics, dysregulated stress responses, and defective clearance of damaged mitochondria. Additionally, this review explores innovative therapeutic strategies for these mitochondrial problems, including a combination of nanodelivery systems, artificially intelligent drug-screening techniques, and cutting-edge tools, such as CRISPR/Cas9 gene editing. By integrating recent advances in mitochondrial biology, this review provides a comprehensive framework that bridges basic mechanisms with clinical applications. The insights presented here underscore the potential of precision mitochondrial medicine as a novel approach to combating age-related disorders, enhancing our capacity to address age-related diseases, and foster healthy aging.

线粒体是细胞的主要能量中枢,对维持细胞功能至关重要。然而,衰老会导致线粒体效率下降。这种下降的标志是活性氧增加,线粒体DNA突变积累,氧化磷酸化受损,线粒体质量控制系统崩溃。这种变化与神经退行性疾病、心血管疾病和代谢性疾病的发生有关。尽管已经做了很多研究,但线粒体功能障碍和衰老之间的确切联系仍不清楚。此外,目前的文献显示缺乏关于线粒体靶向治疗干预的系统组织。这篇综述系统地探讨了衰老过程中线粒体退化的机制。关键的焦点包括受损的生物发生,破坏动力学,失调的应激反应,以及受损线粒体的缺陷清除。此外,本文还探讨了针对这些线粒体问题的创新治疗策略,包括纳米递送系统、人工智能药物筛选技术和尖端工具(如CRISPR/Cas9基因编辑)的组合。通过整合线粒体生物学的最新进展,本综述提供了一个全面的框架,桥梁的基本机制与临床应用。这里提出的见解强调了精确线粒体医学作为对抗年龄相关疾病的新方法的潜力,增强了我们解决年龄相关疾病的能力,并促进健康老龄化。
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引用次数: 0
Recent Progress in Gene Delivery Systems Based on Gemini-Surfactant 基于双表面活性剂的基因传递系统研究进展
Pub Date : 2025-07-17 DOI: 10.1002/mef2.70027
Peng Qian, Yuxin Chen, Yangchen Xing, Kexin Wu, Qianyu Zhang, Huali Chen

Gemini surfactants (GSs) are two single-chain surfactant molecules covalently linked to their hydrophilic head groups via a spacer, resulting in a distinct structure with two hydrophilic heads and two hydrophobic tails. The GSs with cationic head groups have the potential for gene delivery by forming aggregates with negatively charged nucleic acids under the action of positive charge and self-assembly ability. Therefore, they have attracted increasing attention in the field of gene delivery. However, there remains a lack of systematic reviews summarizing various optimization strategies for GSs as gene delivery vectors in recent years. To address this gap, this review summarizes strategies for enhancing the transfection efficiency and biocompatibility of Gemini surfactant vectors, explores the relationship between their molecular structure and gene delivery performance, along with their delivery mechanism, highlights their applications in various gene delivery contexts, and discusses future development strategies and key challenges. This review provides a foundation for the further development of superior GSs, offering additional viable approaches for effective gene delivery and gene therapy of diseases.

Gemini表面活性剂(GSs)是两个单链表面活性剂分子,通过间隔基团共价连接到它们的亲水性头基团上,从而形成具有两个亲水性头和两个疏水性尾的独特结构。具有阳离子头基的GSs在正电荷和自组装能力的作用下与带负电荷的核酸形成聚集体,具有基因传递的潜力。因此,它们在基因传递领域受到越来越多的关注。然而,近年来对GSs作为基因传递载体的各种优化策略还缺乏系统的综述。为了解决这一问题,本文综述了提高Gemini表面活性剂载体转染效率和生物相容性的策略,探讨了其分子结构与基因传递性能的关系及其传递机制,重点介绍了其在各种基因传递环境中的应用,并讨论了未来的发展策略和主要挑战。本文的研究为进一步开发优质GSs奠定了基础,为有效的基因传递和疾病的基因治疗提供了新的可行途径。
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引用次数: 0
ImmunoCheckDB: A Comprehensive Platform for Evaluating Cancer Immunotherapy Biomarkers Through Meta-Analyses and Multiomic Profiling ImmunoCheckDB:通过荟萃分析和多组学分析评估癌症免疫治疗生物标志物的综合平台
Pub Date : 2025-06-19 DOI: 10.1002/mef2.70025
Chongxuan Lu, Mingxiao Li, Hong Yang, Zaoqu Liu, Jian Zhang, Quan Cheng, Anqi Lin, Shixiang Wang, Peng Luo

Immune checkpoint inhibitors (ICIs) have transformed cancer immunotherapy, but their clinical efficacy varies significantly due to tumor heterogeneity and patient-specific factors. Existing databases lack comprehensive integration of ICI efficacy data and fail to explore biomarkers across pan-cancer contexts, limiting their utility in precision oncology. To address this gap, we developed ImmunoCheckDB, a systematic platform that curates 173 studies on cancer ICI treatment, integrating survival outcomes for traditional and network meta-analyses with multiomic data sets from public repositories, including over 93,000+ individuals across 18 cancer types and 30 ICI regimens to provide a robust resource for pan-cancer biomarker discovery. Equipped with online tools for meta-analysis, network meta-analysis, and multiomic profiling, ImmunoCheckDB enables researchers to investigate correlations between ICI efficacy and molecular biomarkers, featuring key functionalities such as real-time visualization of forest plots, funnel plots, and network diagrams, as well as association analyses linking multiomic data to clinical outcomes. Uniquely combining meta-analytical with multiomic exploration, our platform offers insights into optimal patient populations for ICI therapy, thereby bridging the gap between clinical data and molecular research to empower researchers in advancing precision immunotherapy, with access available at https://smuonco.shinyapps.io/ImmunoCheckDB/ to democratize data-driven insights for personalized cancer treatment.

免疫检查点抑制剂(ICIs)已经改变了癌症的免疫治疗,但由于肿瘤的异质性和患者特异性因素,其临床疗效差异很大。现有数据库缺乏ICI疗效数据的全面整合,无法在泛癌症背景下探索生物标志物,限制了它们在精确肿瘤学中的应用。为了解决这一差距,我们开发了ImmunoCheckDB,这是一个系统化的平台,汇集了173项关于癌症ICI治疗的研究,将传统和网络荟萃分析的生存结果与来自公共存储库的多组数据集相结合,包括18种癌症类型和30种ICI方案的93,000多名个体,为泛癌症生物标志物的发现提供了强大的资源。ImmunoCheckDB配备了用于荟萃分析、网络荟萃分析和多组学分析的在线工具,使研究人员能够调查ICI疗效与分子生物标志物之间的相关性,具有诸如森林图、漏斗图和网络图的实时可视化等关键功能,以及将多组学数据与临床结果联系起来的关联分析。我们的平台独特地结合了荟萃分析和多组学探索,为ICI治疗的最佳患者群体提供了见解,从而弥合了临床数据和分子研究之间的差距,使研究人员能够推进精确免疫治疗,并可访问https://smuonco.shinyapps.io/ImmunoCheckDB/,使数据驱动的见解民主化,以实现个性化癌症治疗。
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引用次数: 0
Transsulfuration Reprogramming: A Metabolic Driver of BRAF-V600E Resistance in Melanoma 转硫重编程:黑色素瘤BRAF-V600E耐药的代谢驱动因素
Pub Date : 2025-06-09 DOI: 10.1002/mef2.70024
Juntong Chen, Guoqing Ding, Jie Zhang

Recently, a study by Péter Nagy's team [1] published in Cell Metabolism identified that the upregulation of cystathionine γ-lyase (CSE) and the inhibition of cystathionine β-synthase (CBS) are key factors contributing to the development of resistance to B-Raf proto-oncogene, serine/threonine kinase (BRAF) inhibitors (BRAFi) in treatment. Coadministration of the CSE inhibitor d,l-propargylglycine (PAG) with BRAFi significantly improved therapeutic efficacy and delayed the onset of resistance, offering a novel therapeutic strategy for patients with BRAF V600E-mutant (a valine-to-glutamic acid substitution at position 600 in the BRAF protein) melanoma.

Malignant melanoma is a highly aggressive tumor originating from melanocytes, with approximately 50% of patients harboring the BRAF V600E mutation [1]. This mutation leads to the activation of the downstream mitogen-activated protein kinase kinase/extracellular-signal-regulated kinase (MEK/ERK) signaling pathway, which in turn results in an increase in aerobic glycolysis, thereby supporting the proliferation of melanoma cells [2]. BRAF V600E inhibitors, such as vemurafenib (V) and dabrafenib (D), have been approved by the Food and Drug Administration (FDA) for the treatment of melanoma. However, resistance to these therapies often develops. Even when combining dabrafenib with the MEK inhibitor trametinib, resistance remains an inevitable challenge [3].

Existing research has indicated that treatment with dabrafenib-trametinib (DT) inhibits the BRAF/MEK/ERK pathway, leading to a shift in melanoma cell metabolism from aerobic glycolysis to mitochondrial respiration, which is unfavorable for melanoma cell proliferation [4]. Concurrently, the increased mitochondrial oxidative phosphorylation and electron transport chain (ETC) pathways result in enhanced reactive oxygen species (ROS) production. Excessive ROS production can disrupt the cellular redox balance and trigger oxidative stress responses. Building on this, the study discovered significant expression of cytochrome P (CYP)450 enzymes in dabrafenib- and trametinib-treated cells (DTC), with upregulation of CYP1B1 and CYP2F1 in dabrafenib- and trametinib-double resistant cells (DTR). These enzymes contribute to ROS production. To counteract the effects of ROS accumulation, antioxidant enzymes, such as superoxide dismutase 2 (SOD2), thioredoxin reductase 1 (TrxR1), catalase, 14-kDa human thioredoxin (Trx)-related protein (TRP14), glucose-6-phosphate dehydrogenase (G6PD), and glutathione (GSH) peroxidase 1 and 4 (GPX1, 4), are upregulated in DTC. However, this antioxidant response is limited, and the cells become more sensitive to exogenous oxidants, making them more susceptible to oxidative stress-induced damage. To support the function of antioxidant enzymes, DTC increasingly rely on the pentose phosphate pathway (PPP) to generate more nicoti

CySSCy可以通过CSE或CBS的作用转化为Cys- ssh,也可以通过Trx途径加工生成Cys,随后产生H₂S等RSS。研究人员通过细胞内氨基酸代谢分析和同位素标记进一步验证了这一途径,证实了这一途径对DTC存活至关重要。基因敲除实验也证实了CSE是DTC耐药获得的关键因素。在接受DT治疗的黑色素瘤患者中,CSE的表达升高进一步支持了这一假设,并表明靶向CSE联合DT作为黑色素瘤治疗策略的潜力。研究小组利用PAG抑制CSE活性,并结合DT处理。实验表明,PAG和DT联合使用可显著延缓耐药的发生。在黑色素瘤小鼠模型中,联合治疗显着延长了无进展生存期并抑制了肿瘤生长。这表明联合CSE抑制剂可能是提高BRAF V600E靶向治疗疗效的关键策略。然而,值得注意的是,这种组合并不适用于DTR。CSE在耐药细胞中下调,表明一旦出现耐药性,PAG治疗可能无效。因此,未来的研究需要评估CSE抑制的时机和情境特异性应用,并探讨早期干预是否可以最大限度地提高治疗效果,同时避免耐药性。总之,该研究表明,在DT联合治疗下,黑色素瘤细胞经历了广泛的代谢重编程。DT处理诱导DTC氧化应激,促使PPP活性增加,从而提高细胞氧化还原系统的活性。同时,DTC增加CySSCy的摄取,并通过CSE生成cysssh, cysssh在保护DTC免受氧化应激损伤和耐药发展中起关键作用。该研究揭示了DT治疗耐药的新机制,并为开发更有效的联合治疗策略提供了新的见解。图1总结了DTC的耐药机理。然而,这项研究也有一些局限性。xCT活性对DTC存活至关重要,这表明进一步抑制xCT与PAG和DT联合可能会提高治疗效果。鉴于这些发现,值得考虑的是DTR是否仍然保留可靶向的代谢脆弱性。虽然CSE的下调可能会使PAG治疗无效,但未来的研究可能会探索进一步调节转硫途径是否会使耐药细胞对治疗重新敏感。这些策略可能有助于扩大治疗窗口,提高黑色素瘤靶向治疗的疗效。此外,新的联合疗法仍处于临床前阶段,需要进行临床试验以确认该方法在人体中的可行性。总的来说,该研究拓宽了黑色素瘤治疗策略的视角,值得进一步研究。军统陈:概念化、写初稿。丁国庆:资金获取、监管、资源。张杰:经费筹措、写作审编、监督、资源。所有作者已阅读并认可最终文章。作者没有什么可报告的。作者声明无利益冲突。
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引用次数: 0
MALT1: The Dual Domains Drive Resistance to Immune Checkpoint Inhibitors MALT1:双结构域驱动免疫检查点抑制剂的耐药性
Pub Date : 2025-06-04 DOI: 10.1002/mef2.70023
Haoze Xie, Jie Zhang, Yicheng Chen
<p>A recent research article published by Tao et al. [<span>1</span>] in <i>Nature Cancer</i> pointed out that two domains of Mucosa-Associated Lymphoid Tissue Lymphoma Translocation Protein 1 (MALT1) can promote tumor immune evasion, and that MALT1-targeting antisense oligonucleotides (ASOs) can effectively overcome resistance to immune checkpoint inhibitor (ICI), which are immunotherapy drugs that work by blocking inhibitory immune pathways like PD-1/PD-L1 or CTLA-4 to restore antitumor immunity. These results reveal an innovative method to overcome ICI resistance, offering fresh perspectives for developing cancer immunotherapies.</p><p>Cancer immunotherapy refers to therapeutic approaches that harness or enhance the body's immune system to recognize and eliminate tumor cells. With the discovery and characterization of tumor antigens, cancer immunotherapy has gained increasing attention, with research focus evolving from immune cells to tumor cells themselves and their immune microenvironment [<span>2</span>]. Current mainstream immunotherapies, including ICIs, CAR-T cell therapy, and cancer vaccines, have demonstrated promising clinical potential in oncology. Specifically, ICIs block immune checkpoint molecules such as PD-1/PD-L1 and CTLA-4, thereby blocking the suppression of immune cells by tumors and restoring the killing power of immune cells against tumors. Despite their efficacy, ICIs suffer from high rates of primary nonresponse and secondary resistance [<span>3</span>], restricting their widespread use. Studies have identified that the primary mechanisms underlying treatment failure and resistance involve both intrinsic tumor cell drug resistance pathways and the immunosuppressive properties of the tumor microenvironment (TME). Notably, tumor-associated macrophages (TAMs) have attracted much attention due to their unique plasticity and powerful immune regulatory function [<span>4</span>]. By polarizing into M2-type macrophages, TAMs secrete immunosuppressive molecules that inhibit T-cell function, thereby facilitating tumor immune escape.</p><p>Originally identified through its chromosomal translocation in MALT lymphoma, MALT1 not only drives lymphomagenesis but also plays broad immunoregulatory roles. As the central component of the CARD11-BCL10-MALT1 (CBM) signaling complex [<span>5</span>], MALT1 orchestrates T/B cell activation and signal transduction through its functional domains. Given its dual roles in promoting tumor immune evasion and lymphocyte dysfunction, MALT1 represents a promising target for overcoming immunotherapy resistance. Using CRISPR screening, Tao et al. created a focused library covering 810 genes in ten core oncogenic pathways. Through CD8<sup>+</sup> T cell-mediated tumor killing experiments and mouse tumor cell line screening, they found that overexpression of MALT1 in tumor cells significantly enhanced their resistance to CD8<sup>+</sup> T cell killing. MALT1 regulates the expression level of PD-L1 through
近期Tao等人在Nature Cancer杂志上发表的一篇研究文章指出,粘膜相关淋巴组织淋巴瘤易位蛋白1 (MALT1)的两个结构域可促进肿瘤免疫逃避,而MALT1靶向的反义寡核苷酸(ASOs)可有效克服对免疫检查点抑制剂(ICI)的耐药性,ICI是一种通过阻断PD-1/PD-L1或CTLA-4等抑制免疫通路来恢复抗肿瘤免疫的免疫治疗药物。这些结果揭示了一种克服ICI耐药性的创新方法,为开发癌症免疫疗法提供了新的视角。癌症免疫疗法是指利用或增强人体免疫系统来识别和消除肿瘤细胞的治疗方法。随着肿瘤抗原的发现和表征,肿瘤免疫治疗越来越受到重视,研究重点从免疫细胞发展到肿瘤细胞本身及其免疫微环境[2]。目前的主流免疫疗法,包括ICIs、CAR-T细胞疗法和癌症疫苗,已经在肿瘤学领域显示出了良好的临床潜力。具体来说,ICIs阻断PD-1/PD-L1和CTLA-4等免疫检查点分子,从而阻断肿瘤对免疫细胞的抑制,恢复免疫细胞对肿瘤的杀伤能力。尽管其疗效显著,但ICIs的原发性无反应和继发性耐药率很高,限制了其广泛应用。研究发现,治疗失败和耐药的主要机制涉及肿瘤细胞固有的耐药途径和肿瘤微环境(TME)的免疫抑制特性。肿瘤相关巨噬细胞(tumor associated macrophages, tam)因其独特的可塑性和强大的免疫调节功能[4]而备受关注。tam通过极化进入m2型巨噬细胞,分泌抑制t细胞功能的免疫抑制分子,促进肿瘤免疫逃逸。MALT1最初是通过MALT淋巴瘤的染色体易位发现的,它不仅驱动淋巴瘤的发生,还具有广泛的免疫调节作用。作为CARD11-BCL10-MALT1 (CBM)信号复合体[5]的核心成分,MALT1通过其功能域协调T/B细胞的激活和信号转导。鉴于其促进肿瘤免疫逃避和淋巴细胞功能障碍的双重作用,MALT1是克服免疫治疗耐药性的一个有希望的靶点。Tao等人利用CRISPR筛选技术,建立了一个涵盖10个核心致癌途径810个基因的重点文库。通过CD8+ T细胞介导的肿瘤杀伤实验和小鼠肿瘤细胞系筛选,他们发现肿瘤细胞中MALT1的过表达显著增强了肿瘤细胞对CD8+ T细胞杀伤的抵抗力。MALT1通过其caspase样活性调节PD-L1的表达水平,导致肿瘤细胞从CD8+ T细胞免疫逃逸。在利用RNA免疫沉淀实验确认了ROQUIN1/2蛋白与Cd274 mRNA之间的相互作用后,研究小组进一步证明,MALT1通过蛋白水解失活ROQUIN1/2来稳定Cd274 mRNA,这两个关键的RNA结合蛋白负责其降解。同时,MALT1的死亡结构域与BCL10结合,从而激活NF-κB信号通路。该级联可促进多种免疫抑制因子的分泌,包括集落刺激因子1 (CSF1)、前列腺素E2 (PGE2)和趋化因子C-X-C基序配体1 (CXCL1)。这些因素在驱动tam的增殖及其向M2表型的极化中起着至关重要的作用。众所周知,m2极化tam具有免疫抑制功能,包括分泌抗炎细胞因子和抑制T细胞活化。这一过程最终会抑制CD8+ T细胞的功能,而CD8+ T细胞是抗肿瘤免疫的关键角色。通过抑制CD8+ T细胞的细胞毒活性,肿瘤微环境变得更具免疫抑制性,从而促进对ICIs的抵抗。这突出了MALT1在形成免疫抑制肿瘤微环境和促进ICI耐药性中的关键作用(图1)。针对这一机制,Tao等人开发了ASO24,一种旨在抑制MALT1的反义寡核苷酸。实验结果表明,ASO24可显著降低肿瘤细胞中MALT1和PD-L1的表达水平,增强CD8+ T细胞的杀伤肿瘤能力,同时抑制tam的增殖,促进其向m1型巨噬细胞分化,具有抗肿瘤活性。值得注意的是,尽管MALT1在CD8+ T细胞、CD4+ T细胞和调节性T细胞(Tregs)中表达,ASO治疗并没有显著改变这些免疫细胞的激活标记物。 这一发现提示全身给药ASO对免疫细胞功能没有明显的负面影响,为其临床应用提供了重要的安全性依据。综上所述,本研究发现,针对MALT1的ASOs在多种实验模型中均表现出显著的抗肿瘤活性,尤其是在增强ICIs的疗效方面。这不仅为解决ICI耐药性提供了新的治疗途径,也为肿瘤免疫治疗领域开辟了新的研究方向。这对促进肿瘤免疫治疗的临床转化具有重要的理论和实践意义。然而,值得注意的是,这项研究的临床样本量相对较小,而且只关注结直肠癌和乳腺癌。由于MALT1的作用可能在不同类型的癌症中有所不同,因此需要涉及多种癌症类型的更大规模的验证研究。MALT1在包括T细胞和B细胞在内的正常免疫细胞中起关键作用。MALT1的全身性抑制可能导致免疫相关的不良反应,如自身免疫反应或感染的风险增加。虽然在研究中没有观察到明显的毒性,但长期安全性需要进一步评估。研究表明,靶向MALT1可以克服ICI耐药性,但一些肿瘤可能通过其他旁路途径(如替代免疫检查点或细胞因子信号)逃避治疗。未来,需要探索结合其他目标的战略。谢浩泽:构思,写作-原稿。张杰:经费筹措、写作审编、监督、资源。陈一诚:资金获取、监管、资源。所有作者都阅读并认可了文章。作者没有什么可报告的。作者声明无利益冲突。
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引用次数: 0
TabPFN: Shedding a New Light for Biomedicine With a Small Data Prediction Model TabPFN:用小数据预测模型为生物医学提供新思路
Pub Date : 2025-05-27 DOI: 10.1002/mef2.70022
Menghan Li, Shuo Zhang, Cenglin Xu
<p>In a recent study published in <i>Nature</i>, the Transformer-based Tabular Prior-data Fitted Network (TabPFN) model was introduced. The important finding is that it outperforms traditional methods on small-to-medium data sets, mainly because of its in-context learning mechanism and synthetic data generation [<span>1</span>]. This has significant translational implications for biomedicine and can efficiently analyze tabular data and make reliable predictions in resource-constrained scenarios.</p><p>The TabPFN model capitalizes on the in-context learning (ICL) mechanism, commencing with a methodology for generating diverse tabular datasets. And the target values of a subset of samples are masked to mimic supervised prediction scenarios. Then a transformer-based neural network (PFN) is trained to predict these masked targets, acquiring a generalized learning algorithm. TabPFN fundamentally differs from conventional supervised deep learning through three innovations. First, it employs cross-dataset training that exposes the model to diverse datasets, enabling universal pattern recognition beyond single-task limitations. Second, it performs whole-dataset inference by processing complete datasets simultaneously during prediction rather than individual samples. Third, its two-way attention mechanism operates bidirectionally: horizontally through intra-sample attention (analyzing feature interactions within each row) and vertically through inter-sample attention (identifying feature distribution patterns across columns). This architecture achieves inherent invariance to permutations in both sample and feature ordering while allowing efficient scaling to datasets exceeding the training size, effectively balancing model generalization with computational practicality. Additionally, it generates synthetic data using structural causal models (SCMs), sampling high-level parameters to fabricate a directed acyclic graph with a predefined causal structure, propagating random noise through root nodes, applying computational mappings (e.g., small neural networks, discretization, decision trees), and using post-processing techniques (e.g., Kumaraswamy distribution warping and quantization) to enhance realism and complexity. During inference, the model separates training and test samples. It performs ICL on the training set once, then reuses the learned state for multiple test set inferences, significantly enhancing inference speed. Memory optimization techniques (e.g., half-precision layer norms, flash attention, activation checkpointing, sequential state computation) reduce memory usage to under 1000 bytes per cell, enabling processing of data sets up to 50 million cells on a single H100 GPU. In performance, TabPFN surpasses traditional machine learning methods with three key advantages. Compared with CatBoost, XGBoost, and random forest, in the end-to-end process (training and inference), TabPFN is 5140 times faster than CatBoost (2.8 s vs. 4 h of hyperparamet
在最近发表在《自然》杂志上的一项研究中,介绍了基于变压器的表格先验数据拟合网络(TabPFN)模型。重要的发现是,它在中小型数据集上优于传统方法,主要是因为它的上下文学习机制和合成数据生成[1]。这对生物医学具有重要的转化意义,可以有效地分析表格数据并在资源受限的情况下做出可靠的预测。TabPFN模型利用了上下文学习(ICL)机制,从生成各种表格数据集的方法开始。样本子集的目标值被屏蔽以模拟监督预测场景。然后训练基于变压器的神经网络(PFN)来预测这些被屏蔽的目标,获得广义学习算法。TabPFN通过三个创新从根本上区别于传统的监督式深度学习。首先,它采用跨数据集训练,使模型暴露于不同的数据集,从而实现超越单一任务限制的通用模式识别。其次,它通过在预测过程中同时处理完整的数据集而不是单个样本来进行整个数据集推理。其三,其双向注意机制是双向的:横向通过样本内注意(分析每行内特征的相互作用),纵向通过样本间注意(识别跨列特征的分布模式)。该架构在样本和特征排序中实现了对排列的固有不变性,同时允许对超过训练规模的数据集进行有效缩放,有效地平衡了模型泛化和计算实用性。此外,它使用结构因果模型(scm)生成合成数据,采样高级参数以制造具有预定义因果结构的有向无环图,通过根节点传播随机噪声,应用计算映射(例如,小型神经网络,离散化,决策树),并使用后处理技术(例如,Kumaraswamy分布扭曲和量化)来增强真实感和复杂性。在推理过程中,模型将训练样本和测试样本分离。它对训练集执行一次ICL,然后重用学习到的状态进行多个测试集的推理,显著提高了推理速度。内存优化技术(例如,半精度层规范、闪光注意、激活检查点、顺序状态计算)将每个单元的内存使用减少到1000字节以下,使单个H100 GPU能够处理多达5000万个单元的数据集。在性能方面,TabPFN超越了传统的机器学习方法,具有三个关键优势。与CatBoost、XGBoost和随机森林相比,在端到端过程(训练和推理)中,由于其ICL机制不需要超参数调优,TabPFN比CatBoost (2.8 s vs. 4 h超参数调优)快5140倍。此外,TabPFN的速度比XGBoost或random forest分别快约3200倍和640倍。在预测精度方面,在默认设置下,其ROC AUC领先0.187-0.221单位(0.939 vs. 0.752/0.741/0.718)。即使与调整后的模型相比,仍然保持着0.13-0.16的显著优势(0.952 vs. 0.822/0.807/0.791)。特别是在样本稀缺的生物医学场景中,TabPFN通过预训练的先验知识降低了过拟合的风险,突出了其在小数据高噪声环境中的领先性能。这些功能支持各种生物医学应用。在药物发现中,TabPFN可以分析包含化合物化学性质、生物活性和结构特征的小规模数据集。它预测化合物的疗效/毒性,以加速药物筛选,同时减少时间/资源投资。例如,在配体-蛋白质相互作用预测[2]中,该模型集成了蛋白质结构、配体性质和历史结合亲和力数据,识别结合模式/亲和力,以简化药物设计。这个功能加速了虚拟筛选工作流程并最小化了实验验证周期(图1)。在疾病预测[3]中,TabPFN将多维临床、组学和环境数据结构化为表格格式。它是一种表格优化的基础模型,无需人工进行特征工程或架构选择,直接预测疾病风险,辅助诊断或预后,推进个性化医疗。在遗传病研究中,TabPFN分析基因表型关系以实现早期诊断和靶向治疗,而其小样本能力支持罕见病分析和早期临床试验。 在生物多样性特征预测方面,该模型以表格形式处理基因序列、生物样本和环境变量,以预测性状和揭示生态模式。它执行降维和特征提取,促进生态系统动力学的理解[4]。该框架在进化分析和代谢途径探索中也证明了其价值。TabPFN的创新之处在于突破了传统机器学习“单一任务”的训练范式。通过元学习、因果推理机制和全局关注,构建了一个适用于表格数据的通用智能系统。它在低数据表格场景下的优势本质上是传统模型的优势(统计归纳能力)和深度学习的优势(结构建模能力)的深度融合。目前,TabPFN模型在小数据集的生物医学任务中表现出色,但在处理非表格数据(如医学成像[MRI/DICOM],这需要像卷积网络这样的专门架构)和大规模应用方面面临挑战。将其功能扩展到多模态融合和时间序列分析仍然是一个关键的研究前沿。李梦涵:构思、调查、形式分析、撰写原稿。张硕:资源,验证。徐增林:概念、资金获取、资源、监督、验证、写作-评审和编辑。所有作者都阅读并批准了最终稿件。作者没有什么可报告的。作者声明无利益冲突。
{"title":"TabPFN: Shedding a New Light for Biomedicine With a Small Data Prediction Model","authors":"Menghan Li,&nbsp;Shuo Zhang,&nbsp;Cenglin Xu","doi":"10.1002/mef2.70022","DOIUrl":"https://doi.org/10.1002/mef2.70022","url":null,"abstract":"&lt;p&gt;In a recent study published in &lt;i&gt;Nature&lt;/i&gt;, the Transformer-based Tabular Prior-data Fitted Network (TabPFN) model was introduced. The important finding is that it outperforms traditional methods on small-to-medium data sets, mainly because of its in-context learning mechanism and synthetic data generation [&lt;span&gt;1&lt;/span&gt;]. This has significant translational implications for biomedicine and can efficiently analyze tabular data and make reliable predictions in resource-constrained scenarios.&lt;/p&gt;&lt;p&gt;The TabPFN model capitalizes on the in-context learning (ICL) mechanism, commencing with a methodology for generating diverse tabular datasets. And the target values of a subset of samples are masked to mimic supervised prediction scenarios. Then a transformer-based neural network (PFN) is trained to predict these masked targets, acquiring a generalized learning algorithm. TabPFN fundamentally differs from conventional supervised deep learning through three innovations. First, it employs cross-dataset training that exposes the model to diverse datasets, enabling universal pattern recognition beyond single-task limitations. Second, it performs whole-dataset inference by processing complete datasets simultaneously during prediction rather than individual samples. Third, its two-way attention mechanism operates bidirectionally: horizontally through intra-sample attention (analyzing feature interactions within each row) and vertically through inter-sample attention (identifying feature distribution patterns across columns). This architecture achieves inherent invariance to permutations in both sample and feature ordering while allowing efficient scaling to datasets exceeding the training size, effectively balancing model generalization with computational practicality. Additionally, it generates synthetic data using structural causal models (SCMs), sampling high-level parameters to fabricate a directed acyclic graph with a predefined causal structure, propagating random noise through root nodes, applying computational mappings (e.g., small neural networks, discretization, decision trees), and using post-processing techniques (e.g., Kumaraswamy distribution warping and quantization) to enhance realism and complexity. During inference, the model separates training and test samples. It performs ICL on the training set once, then reuses the learned state for multiple test set inferences, significantly enhancing inference speed. Memory optimization techniques (e.g., half-precision layer norms, flash attention, activation checkpointing, sequential state computation) reduce memory usage to under 1000 bytes per cell, enabling processing of data sets up to 50 million cells on a single H100 GPU. In performance, TabPFN surpasses traditional machine learning methods with three key advantages. Compared with CatBoost, XGBoost, and random forest, in the end-to-end process (training and inference), TabPFN is 5140 times faster than CatBoost (2.8 s vs. 4 h of hyperparamet","PeriodicalId":74135,"journal":{"name":"MedComm - Future medicine","volume":"4 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-05-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/mef2.70022","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144148553","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
Critical Role of Skin in Pathogenesis: Bidirectional Crosstalk Between Skin and Multiple Organs 皮肤在发病中的关键作用:皮肤与多器官的双向串扰
Pub Date : 2025-05-25 DOI: 10.1002/mef2.70020
Wende Deng, Junyi Liu, Changheng Tang, Zhenghao Li, Ying Qiu, Han Zhou, Lanxuan Yang, Ting Li

The skin, the largest organ in the human body, serves both as a mechanical barrier and an autonomous lymphoid organ, protecting against various environmental threats while maintaining the balance and functionality of multiple bodily systems. This relationship extends beyond the skin itself, involving other organs closely linked to skin homeostasis and related diseases. However, systematic reviews in this area are still lacking. This review seeks to explore this bidirectional communication, with a particular focus on the critical role of the immune system. We present a comprehensive review of the latest evidence, highlighting the fundamental roles of immune cells and cytokines within the skin–organ axis, particularly IL-17A, which appears to interact with nearly all organs, illustrating their interplay and impact on skin health. Additionally, we discuss the implications of these interactions for the design and application of skin-on-a-chip and organ-on-a-chip technologies, emphasizing the importance of understanding these relationships for developing physiologically relevant in vitro models. By providing a comprehensive analysis of these complex interactions, this review establishes a solid theoretical foundation for the prevention, diagnosis, and treatment of diseases associated with the skin–organ axis, particularly regarding immune cells, cytokines, microorganisms, and their metabolites, ultimately aiming to advance research in related fields and offer new insights for clinical applications.

皮肤是人体最大的器官,既是一个机械屏障,又是一个自主的淋巴器官,在保护人体免受各种环境威胁的同时,维持人体多个系统的平衡和功能。这种关系超出了皮肤本身,涉及与皮肤稳态和相关疾病密切相关的其他器官。然而,这方面的系统综述仍然缺乏。这篇综述试图探索这种双向交流,特别关注免疫系统的关键作用。我们对最新证据进行了全面的回顾,强调了免疫细胞和细胞因子在皮肤器官轴中的基本作用,特别是IL-17A,它似乎与几乎所有器官相互作用,说明了它们的相互作用和对皮肤健康的影响。此外,我们讨论了这些相互作用对皮肤芯片和器官芯片技术的设计和应用的影响,强调了理解这些关系对于开发生理相关的体外模型的重要性。通过对这些复杂相互作用的全面分析,本综述为皮肤器官轴相关疾病的预防、诊断和治疗,特别是免疫细胞、细胞因子、微生物及其代谢物的预防、诊断和治疗奠定了坚实的理论基础,最终旨在推进相关领域的研究,并为临床应用提供新的见解。
{"title":"Critical Role of Skin in Pathogenesis: Bidirectional Crosstalk Between Skin and Multiple Organs","authors":"Wende Deng,&nbsp;Junyi Liu,&nbsp;Changheng Tang,&nbsp;Zhenghao Li,&nbsp;Ying Qiu,&nbsp;Han Zhou,&nbsp;Lanxuan Yang,&nbsp;Ting Li","doi":"10.1002/mef2.70020","DOIUrl":"https://doi.org/10.1002/mef2.70020","url":null,"abstract":"<p>The skin, the largest organ in the human body, serves both as a mechanical barrier and an autonomous lymphoid organ, protecting against various environmental threats while maintaining the balance and functionality of multiple bodily systems. This relationship extends beyond the skin itself, involving other organs closely linked to skin homeostasis and related diseases. However, systematic reviews in this area are still lacking. This review seeks to explore this bidirectional communication, with a particular focus on the critical role of the immune system. We present a comprehensive review of the latest evidence, highlighting the fundamental roles of immune cells and cytokines within the skin–organ axis, particularly IL-17A, which appears to interact with nearly all organs, illustrating their interplay and impact on skin health. Additionally, we discuss the implications of these interactions for the design and application of skin-on-a-chip and organ-on-a-chip technologies, emphasizing the importance of understanding these relationships for developing physiologically relevant in vitro models. By providing a comprehensive analysis of these complex interactions, this review establishes a solid theoretical foundation for the prevention, diagnosis, and treatment of diseases associated with the skin–organ axis, particularly regarding immune cells, cytokines, microorganisms, and their metabolites, ultimately aiming to advance research in related fields and offer new insights for clinical applications.</p>","PeriodicalId":74135,"journal":{"name":"MedComm - Future medicine","volume":"4 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-05-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/mef2.70020","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144135789","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
Large Language Models for Transforming Healthcare: A Perspective on DeepSeek-R1 面向医疗保健转型的大型语言模型:基于DeepSeek-R1的视角
Pub Date : 2025-05-12 DOI: 10.1002/mef2.70021
Jinsong Zhou, Yuhan Cheng, Sixu He, Yingcong Chen, Hao Chen

DeepSeek-R1 is an open-source Large Language Model (LLM) with advanced reasoning capabilities. It has gained significant attention for its impressive advantages including low costs and visualized reasoning steps. Recent advancements in reasoning LLMs like ChatGPT-o1 have significantly exhibited their considerable reasoning potential, but the closed-source nature of existing models limits customization and transparency, presenting substantial barriers to their integration into healthcare systems. This gap motivates the exploration of DeepSeek-R1 in the medical field. Thus, we comprehensively review the transformative potential, applications, and challenges of DeepSeek-R1 in healthcare. Specifically, we investigate how DeepSeek-R1 can enhance clinical decision support, patient engagement, and medical education to help for clinic, outpatient and medical research. Furthermore, we critically evaluate challenges including modality limitations (text-only), hallucination risks, and ethical issues, particularly related to patient autonomy and safety-focused recommendations. By assessing DeepSeek-R1′s integration potential, this perspective highlights promising opportunities for advancing medical AI while emphasizing necessary improvements to maximize clinical reliability and ethical compliance. This paper provides valuable guidance for future research directions and elucidates practical application scenarios for DeepSeek-R1′s successful integration into healthcare settings.

DeepSeek-R1是一个开源的大型语言模型(LLM),具有先进的推理能力。它以其令人印象深刻的优势获得了极大的关注,包括低成本和可视化的推理步骤。最近在推理法学硕士(如chatgpt - 01)方面取得的进展显著地展示了其相当大的推理潜力,但现有模型的闭源性限制了定制和透明度,为其集成到医疗保健系统中带来了实质性障碍。这一差距促使DeepSeek-R1在医学领域进行探索。因此,我们全面回顾了DeepSeek-R1在医疗保健领域的变革潜力、应用和挑战。具体而言,我们研究了DeepSeek-R1如何增强临床决策支持、患者参与和医学教育,以帮助临床、门诊和医学研究。此外,我们批判性地评估了包括模式限制(纯文本)、幻觉风险和伦理问题在内的挑战,特别是与患者自主和以安全为重点的建议相关的挑战。通过评估DeepSeek-R1的整合潜力,该观点强调了推进医疗人工智能的有希望的机会,同时强调了最大化临床可靠性和道德合规的必要改进。本文为未来的研究方向提供了有价值的指导,并阐明了DeepSeek-R1成功集成到医疗保健环境中的实际应用场景。
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引用次数: 0
The Use of Large Language Models and Their Association With Enhanced Impact in Biomedical Research and Beyond 大型语言模型的使用及其与生物医学研究及其他领域的增强影响的关联
Pub Date : 2025-04-27 DOI: 10.1002/mef2.70019
Huzi Cheng, Wen Shi, Bin Sheng, Aaron Y. Lee, Josip Car, Varun Chaudhary, Atanas G. Atanasov, Nan Liu, Yue Qiu, Qingyu Chen, Tien Yin Wong, Yih-Chung Tham, Ying-Feng Zheng

The release of ChatGPT in 2022 has catalyzed the adoption of large language models (LLMs) across diverse writing domains, including academic writing. However, this technological shift has raised critical questions regarding the prevalence of LLM usage in academic writing and its potential influence on the quality and impact of research articles. Here, we address these questions by analyzing preprint articles from arXiv, bioRxiv, and medRxiv between 2022 and 2024, employing a novel LLM usage detection tool. Our study reveals that LLMs have been widely adopted in biomedical and other types of academic writing since late 2022. Notably, we noticed that LLM usage is linked to an enhanced impact of research articles after examining their correlation, as measured by citation numbers. Furthermore, we observe that LLMs influence specific content types in academic writing, including hypothesis formulation, conclusion summarization, description of phenomena, and suggestions for future work. Collectively, our findings underscore the potential benefits of LLMs in scientific communication, suggesting that they may not only streamline the writing process but also enhance the dissemination and impact of research findings across disciplines.

ChatGPT于2022年发布,促进了大型语言模型(llm)在不同写作领域的采用,包括学术写作。然而,这种技术转变提出了一些关键问题,如法学硕士在学术写作中的普遍使用,以及它对研究文章的质量和影响的潜在影响。在这里,我们通过分析arXiv, bioRxiv和medRxiv在2022年至2024年间的预印本文章来解决这些问题,采用了一种新的法学硕士使用检测工具。我们的研究表明,自2022年底以来,法学硕士已被广泛应用于生物医学和其他类型的学术写作。值得注意的是,我们注意到法学硕士的使用与研究文章的影响力增强有关,这是通过引用数量来衡量的。此外,我们观察到法学硕士对学术写作的具体内容类型有影响,包括假设提出、结论总结、现象描述和对未来工作的建议。总的来说,我们的研究结果强调了法学硕士在科学传播方面的潜在好处,表明它们不仅可以简化写作过程,还可以增强跨学科研究成果的传播和影响。
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引用次数: 0
Artificial Intelligence in Medical Education: A Practical Guide for Educators 医学教育中的人工智能:教育工作者的实用指南
Pub Date : 2025-04-02 DOI: 10.1002/mef2.70018
Nivritti Gajanan Patil, Nga Lok Kou, Daniel T. Baptista-Hon, Olivia Monteiro

Artificial intelligence (AI)-driven learning is transforming education, requiring educators to quickly develop the skills to integrate AI tools effectively so they complement rather than replace traditional teaching practices. The fast pace of generative AI development poses challenges, particularly for less tech-savvy teachers or those who delay learning about these tools, leaving them at risk of falling behind. This is further compounded by students' quick adaptation to widely available models such as ChatGPT-3.5 and Deepseek R1, which they increasingly use for learning, assignments, and assessments. Despite existing discussions on AI in education, there is a lack of practical guidance on how medical educators can effectively and responsibly implement AI tools in teaching. This perspective provides a practical guide for medical educators to effectively incorporate AI tools to complement their teaching strategies, generate student assessments and to adapt assignments suitable for the AI era. We address challenges such as data bias, accuracy, and ethics, ensuring AI enhances rather than undermines medical training when aligned with sound pedagogical principles. This review provides a practical, structured approach for educators, offering clear recommendations to help bridge the gap between AI advancements and effective teaching methodologies in medical education.

人工智能(AI)驱动的学习正在改变教育,这要求教育工作者快速发展有效整合人工智能工具的技能,以便它们补充而不是取代传统的教学实践。生成式人工智能的快速发展带来了挑战,特别是对于那些不太懂技术的教师或那些推迟学习这些工具的人来说,这使他们有落后的风险。这进一步加剧了学生对ChatGPT-3.5和Deepseek R1等广泛可用的模型的快速适应,他们越来越多地使用这些模型进行学习、作业和评估。尽管现有关于教育中的人工智能的讨论,但缺乏关于医学教育工作者如何有效和负责任地在教学中使用人工智能工具的实际指导。这一观点为医学教育工作者提供了实用指南,可以有效地将人工智能工具纳入其教学策略,生成学生评估并调整适合人工智能时代的作业。我们应对数据偏差、准确性和道德等挑战,确保人工智能在符合合理的教学原则的情况下增强而不是破坏医学培训。这篇综述为教育工作者提供了一个实用的、结构化的方法,提供了明确的建议,以帮助弥合医学教育中人工智能进步与有效教学方法之间的差距。
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引用次数: 0
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