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.
{"title":"Mitochondrial Dysfunction in Aging: Future Therapies and Precision Medicine Approaches","authors":"Lanlan Jia, Ziyu Wei, Jinyuan Luoqian, Xi Wang, Chao Huang","doi":"10.1002/mef2.70026","DOIUrl":"https://doi.org/10.1002/mef2.70026","url":null,"abstract":"<p>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.</p>","PeriodicalId":74135,"journal":{"name":"MedComm - Future medicine","volume":"4 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/mef2.70026","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144647436","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}
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.
{"title":"Recent Progress in Gene Delivery Systems Based on Gemini-Surfactant","authors":"Peng Qian, Yuxin Chen, Yangchen Xing, Kexin Wu, Qianyu Zhang, Huali Chen","doi":"10.1002/mef2.70027","DOIUrl":"https://doi.org/10.1002/mef2.70027","url":null,"abstract":"<p>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.</p>","PeriodicalId":74135,"journal":{"name":"MedComm - Future medicine","volume":"4 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/mef2.70027","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144647437","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}
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.
{"title":"ImmunoCheckDB: A Comprehensive Platform for Evaluating Cancer Immunotherapy Biomarkers Through Meta-Analyses and Multiomic Profiling","authors":"Chongxuan Lu, Mingxiao Li, Hong Yang, Zaoqu Liu, Jian Zhang, Quan Cheng, Anqi Lin, Shixiang Wang, Peng Luo","doi":"10.1002/mef2.70025","DOIUrl":"https://doi.org/10.1002/mef2.70025","url":null,"abstract":"<p>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.</p>","PeriodicalId":74135,"journal":{"name":"MedComm - Future medicine","volume":"4 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/mef2.70025","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144323498","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}
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
{"title":"Transsulfuration Reprogramming: A Metabolic Driver of BRAF-V600E Resistance in Melanoma","authors":"Juntong Chen, Guoqing Ding, Jie Zhang","doi":"10.1002/mef2.70024","DOIUrl":"https://doi.org/10.1002/mef2.70024","url":null,"abstract":"<p>Recently, a study by Péter Nagy's team [<span>1</span>] published in <i>Cell Metabolism</i> 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 <span>d</span>,<span>l</span>-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.</p><p>Malignant melanoma is a highly aggressive tumor originating from melanocytes, with approximately 50% of patients harboring the BRAF V600E mutation [<span>1</span>]. 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 [<span>2</span>]. 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 [<span>3</span>].</p><p>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 [<span>4</span>]. 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","PeriodicalId":74135,"journal":{"name":"MedComm - Future medicine","volume":"4 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-06-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/mef2.70024","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144245018","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}
<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
{"title":"MALT1: The Dual Domains Drive Resistance to Immune Checkpoint Inhibitors","authors":"Haoze Xie, Jie Zhang, Yicheng Chen","doi":"10.1002/mef2.70023","DOIUrl":"https://doi.org/10.1002/mef2.70023","url":null,"abstract":"<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 ","PeriodicalId":74135,"journal":{"name":"MedComm - Future medicine","volume":"4 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/mef2.70023","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144214168","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}
<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, Shuo Zhang, Cenglin Xu","doi":"10.1002/mef2.70022","DOIUrl":"https://doi.org/10.1002/mef2.70022","url":null,"abstract":"<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","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}
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.
{"title":"Critical Role of Skin in Pathogenesis: Bidirectional Crosstalk Between Skin and Multiple Organs","authors":"Wende Deng, Junyi Liu, Changheng Tang, Zhenghao Li, Ying Qiu, Han Zhou, Lanxuan Yang, 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}
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.
{"title":"Large Language Models for Transforming Healthcare: A Perspective on DeepSeek-R1","authors":"Jinsong Zhou, Yuhan Cheng, Sixu He, Yingcong Chen, Hao Chen","doi":"10.1002/mef2.70021","DOIUrl":"https://doi.org/10.1002/mef2.70021","url":null,"abstract":"<p>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.</p>","PeriodicalId":74135,"journal":{"name":"MedComm - Future medicine","volume":"4 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-05-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/mef2.70021","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143939395","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}
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.
{"title":"The Use of Large Language Models and Their Association With Enhanced Impact in Biomedical Research and Beyond","authors":"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","doi":"10.1002/mef2.70019","DOIUrl":"https://doi.org/10.1002/mef2.70019","url":null,"abstract":"<p>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.</p>","PeriodicalId":74135,"journal":{"name":"MedComm - Future medicine","volume":"4 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-04-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/mef2.70019","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143880030","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}
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.
{"title":"Artificial Intelligence in Medical Education: A Practical Guide for Educators","authors":"Nivritti Gajanan Patil, Nga Lok Kou, Daniel T. Baptista-Hon, Olivia Monteiro","doi":"10.1002/mef2.70018","DOIUrl":"https://doi.org/10.1002/mef2.70018","url":null,"abstract":"<p>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.</p>","PeriodicalId":74135,"journal":{"name":"MedComm - Future medicine","volume":"4 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-04-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/mef2.70018","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143749650","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}