Identifying evolutionarily remote antimicrobial peptides (AMPs) is crucial for discovering underexplored clinical candidates to combat antibiotic resistance. Existing experimental and computational methods are limited by their reliance on sequence identity to known AMPs, missing distant homologues. Here we introduce HMD-AMP, a protein language model-based approach for AMP discovery. HMD-AMP outperforms previous methods in identifying evolutionarily distant AMPs and enables the discovery of unknown and highly potent AMPs from metagenomic data. Applied to host and gut microorganism genomes of nine mammals, HMD-AMP revealed over 37 million predicted AMPs. Of 91 high-confidence sequences experimentally validated, 74 showed strong antibacterial activity and 48 were evolutionarily remote from known AMPs. Four of these AMPs exhibited broad-spectrum antibacterial activity at low effective concentrations and showed low toxicity, with the most potent peptide demonstrating therapeutic efficacy in a mouse model of peritoneal Escherichia coli infection. This study introduces an effective strategy to uncover AMPs.
{"title":"Uncovering evolutionarily remote and highly potent antimicrobial peptides with protein language models.","authors":"Qinze Yu,Hongbin Liu,Haimei Shi,Yerzhan Abdrakhmanov,Junbo Shen,Chunhe Zhang,Zhihang Dong,Licheng Zong,Longlong Si,Lei Dai,Yu Li","doi":"10.1038/s41551-026-01630-w","DOIUrl":"https://doi.org/10.1038/s41551-026-01630-w","url":null,"abstract":"Identifying evolutionarily remote antimicrobial peptides (AMPs) is crucial for discovering underexplored clinical candidates to combat antibiotic resistance. Existing experimental and computational methods are limited by their reliance on sequence identity to known AMPs, missing distant homologues. Here we introduce HMD-AMP, a protein language model-based approach for AMP discovery. HMD-AMP outperforms previous methods in identifying evolutionarily distant AMPs and enables the discovery of unknown and highly potent AMPs from metagenomic data. Applied to host and gut microorganism genomes of nine mammals, HMD-AMP revealed over 37 million predicted AMPs. Of 91 high-confidence sequences experimentally validated, 74 showed strong antibacterial activity and 48 were evolutionarily remote from known AMPs. Four of these AMPs exhibited broad-spectrum antibacterial activity at low effective concentrations and showed low toxicity, with the most potent peptide demonstrating therapeutic efficacy in a mouse model of peritoneal Escherichia coli infection. This study introduces an effective strategy to uncover AMPs.","PeriodicalId":19063,"journal":{"name":"Nature Biomedical Engineering","volume":"268 1","pages":""},"PeriodicalIF":28.1,"publicationDate":"2026-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147346266","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-03-02DOI: 10.1038/s41551-026-01617-7
Sasan Jalili, Ryan R Hosn, Wei-Che Ko, Khashayar Afshari, Ashok Kumar Dhinakaran, Namit Chaudhary, Laura Maiorino, Nazgol-Sadat Haddadi, Anusha Nathan, Matthew A Getz, Gaurav D Gaiha, Mehdi Rashighi, John E Harris, Paula T Hammond, Darrell J Irvine
Detecting antigen-specific lymphocytes is crucial for immune monitoring in vaccination, infection, cancer and autoimmunity. However, their low frequency and dispersed distribution make reliable detection challenging. We developed a strategy exploiting the functions of tissue-resident memory T cells (TRMs) to locally concentrate target circulating immune cells in the skin, enabling their non-invasive sampling using a microneedle (MN) skin patch. TRMs were first induced by antigen sensitization and subsequently restimulated by intradermal inoculation of the same antigen to trigger the 'alarm' and immune recruitment functions of these cells, leading to accumulation of antigen-specific T cells from the circulation over several days. In mouse vaccination models, MN patches with optimized hydrogel coatings effectively isolated thousands of live antigen-specific lymphocytes and innate immune cells. In a human participant with allergic contact dermatitis, allergen-induced TRM stimulation followed by MN application recovered diverse lymphocyte populations absent from untreated skin sites. These results establish TRM restimulation coupled with MN sampling as a non-invasive platform to monitor both local and systemic antigen-specific immune responses across disease or vaccination settings.
{"title":"Leveraging tissue-resident memory T cells for non-invasive immune monitoring via microneedle skin patches.","authors":"Sasan Jalili, Ryan R Hosn, Wei-Che Ko, Khashayar Afshari, Ashok Kumar Dhinakaran, Namit Chaudhary, Laura Maiorino, Nazgol-Sadat Haddadi, Anusha Nathan, Matthew A Getz, Gaurav D Gaiha, Mehdi Rashighi, John E Harris, Paula T Hammond, Darrell J Irvine","doi":"10.1038/s41551-026-01617-7","DOIUrl":"10.1038/s41551-026-01617-7","url":null,"abstract":"<p><p>Detecting antigen-specific lymphocytes is crucial for immune monitoring in vaccination, infection, cancer and autoimmunity. However, their low frequency and dispersed distribution make reliable detection challenging. We developed a strategy exploiting the functions of tissue-resident memory T cells (T<sub>RM</sub>s) to locally concentrate target circulating immune cells in the skin, enabling their non-invasive sampling using a microneedle (MN) skin patch. T<sub>RM</sub>s were first induced by antigen sensitization and subsequently restimulated by intradermal inoculation of the same antigen to trigger the 'alarm' and immune recruitment functions of these cells, leading to accumulation of antigen-specific T cells from the circulation over several days. In mouse vaccination models, MN patches with optimized hydrogel coatings effectively isolated thousands of live antigen-specific lymphocytes and innate immune cells. In a human participant with allergic contact dermatitis, allergen-induced T<sub>RM</sub> stimulation followed by MN application recovered diverse lymphocyte populations absent from untreated skin sites. These results establish T<sub>RM</sub> restimulation coupled with MN sampling as a non-invasive platform to monitor both local and systemic antigen-specific immune responses across disease or vaccination settings.</p>","PeriodicalId":19063,"journal":{"name":"Nature Biomedical Engineering","volume":" ","pages":""},"PeriodicalIF":26.8,"publicationDate":"2026-03-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147344771","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-03-02DOI: 10.1038/s41551-026-01616-8
Muhammad Dawood,Kim Branson,Sabine Tejpar,Nasir Rajpoot,Fayyaz Ul Amir Afsar Minhas
Deep learning models that infer clinically relevant biomarker status from tissue images are being explored as rapid and low-cost alternatives to molecular testing. Here we show, through statistical analysis across multiple cancer types, datasets and modelling approaches, that the datasets used to train these models contain strong dependencies between biomarkers and clinicopathological features, which prevent models from isolating the effect of a single biomarker and lead them to learn confounded signals. Consequently, their prediction accuracy varies substantially with the status of codependent biomarkers and clinicopathological variables, and for several biomarkers, the gain over what a pathologist can already infer from routine histopathological features, such as grade, remains modest. These findings indicate that current approaches are not yet suitable as substitutes for molecular testing but can support triage or complementary decision-making with caution. Unconfounded biomarker prediction will require models that learn causal rather than correlational relationships between biomarkers and tissue morphology.
{"title":"Confounding factors and biases abound when predicting molecular biomarkers from histological images.","authors":"Muhammad Dawood,Kim Branson,Sabine Tejpar,Nasir Rajpoot,Fayyaz Ul Amir Afsar Minhas","doi":"10.1038/s41551-026-01616-8","DOIUrl":"https://doi.org/10.1038/s41551-026-01616-8","url":null,"abstract":"Deep learning models that infer clinically relevant biomarker status from tissue images are being explored as rapid and low-cost alternatives to molecular testing. Here we show, through statistical analysis across multiple cancer types, datasets and modelling approaches, that the datasets used to train these models contain strong dependencies between biomarkers and clinicopathological features, which prevent models from isolating the effect of a single biomarker and lead them to learn confounded signals. Consequently, their prediction accuracy varies substantially with the status of codependent biomarkers and clinicopathological variables, and for several biomarkers, the gain over what a pathologist can already infer from routine histopathological features, such as grade, remains modest. These findings indicate that current approaches are not yet suitable as substitutes for molecular testing but can support triage or complementary decision-making with caution. Unconfounded biomarker prediction will require models that learn causal rather than correlational relationships between biomarkers and tissue morphology.","PeriodicalId":19063,"journal":{"name":"Nature Biomedical Engineering","volume":"51 1","pages":""},"PeriodicalIF":28.1,"publicationDate":"2026-03-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147329214","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-03-02DOI: 10.1038/s41551-026-01613-x
Shih-Ying Wu,Abhishek Tyagi,Kerui Wu,Eleanor C Smith,Qianqian Song,Sambad Sharma,Lance D Miller,Wei Zhang,Bo-Syong Pan,Hui-Kuan Lin,Jung-Shun Lee,Ashok Pullikuth,Fei Xing,Ravindra Pramod Deshpande,Dan Zhao,Yin Liu,Jee Won Kim,Michael H Soike,Jimmy Ruiz,Michael Chan,Jeff Chou,Alexandra Parson,Kounosuke Watabe
Metastatic brain disease occurs in up to 30% of patients with lung, melanoma and breast cancers, and the median survival time remains less than a year. Treating these patients is a challenge because surgical approaches are limited and most chemotherapeutic drugs and immunotherapies are ineffective at crossing the blood-brain barrier (BBB). Given the unique abilities of macrophages to cross the BBB and exert their phagocytic function on tumour cells, we genetically engineer macrophages that express a chimaeric antigen receptor (CAR) targeting mesothelin (MSLN). To specifically target metastatic brain tumours, we fused the cells with the immune signalling molecule MyD88. This chimaeric antigen receptor macrophage (CARMA) penetrates the BBB and decreases brain metastasis growth in a humanized mouse model. MSLN-CARMA shows antigen-specific phagocytosis activity against tumour cells and exhibits a bystander effect by releasing TNF to act on surrounding tumour cells lacking the tumour antigen. These features of CARMA represent advantages over other immune therapies and CARMA may serve as a promising therapeutic tool for the treatment of brain metastasis.
{"title":"MyD88-mediated chimaeric antigen receptor macrophages suppress brain metastasis using target-specific phagocytosis.","authors":"Shih-Ying Wu,Abhishek Tyagi,Kerui Wu,Eleanor C Smith,Qianqian Song,Sambad Sharma,Lance D Miller,Wei Zhang,Bo-Syong Pan,Hui-Kuan Lin,Jung-Shun Lee,Ashok Pullikuth,Fei Xing,Ravindra Pramod Deshpande,Dan Zhao,Yin Liu,Jee Won Kim,Michael H Soike,Jimmy Ruiz,Michael Chan,Jeff Chou,Alexandra Parson,Kounosuke Watabe","doi":"10.1038/s41551-026-01613-x","DOIUrl":"https://doi.org/10.1038/s41551-026-01613-x","url":null,"abstract":"Metastatic brain disease occurs in up to 30% of patients with lung, melanoma and breast cancers, and the median survival time remains less than a year. Treating these patients is a challenge because surgical approaches are limited and most chemotherapeutic drugs and immunotherapies are ineffective at crossing the blood-brain barrier (BBB). Given the unique abilities of macrophages to cross the BBB and exert their phagocytic function on tumour cells, we genetically engineer macrophages that express a chimaeric antigen receptor (CAR) targeting mesothelin (MSLN). To specifically target metastatic brain tumours, we fused the cells with the immune signalling molecule MyD88. This chimaeric antigen receptor macrophage (CARMA) penetrates the BBB and decreases brain metastasis growth in a humanized mouse model. MSLN-CARMA shows antigen-specific phagocytosis activity against tumour cells and exhibits a bystander effect by releasing TNF to act on surrounding tumour cells lacking the tumour antigen. These features of CARMA represent advantages over other immune therapies and CARMA may serve as a promising therapeutic tool for the treatment of brain metastasis.","PeriodicalId":19063,"journal":{"name":"Nature Biomedical Engineering","volume":"40 1","pages":""},"PeriodicalIF":28.1,"publicationDate":"2026-03-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147329213","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-03-01DOI: 10.1038/s41551-026-01649-z
{"title":"Beyond conceptual advances in cancer therapies.","authors":"","doi":"10.1038/s41551-026-01649-z","DOIUrl":"https://doi.org/10.1038/s41551-026-01649-z","url":null,"abstract":"","PeriodicalId":19063,"journal":{"name":"Nature Biomedical Engineering","volume":"10 3","pages":"407-408"},"PeriodicalIF":26.8,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147504424","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-03-01DOI: 10.1038/s41551-026-01641-7
Jeffrey Herron, Aura Kullmann, Timothy Denison, Wayne K Goodman, Aysegul Gunduz, Wolf-Julian Neumann, Nicole R Provenza, Maryam M Shanechi, Sameer A Sheth, Philip A Starr, Alik S Widge
{"title":"Author Correction: Challenges and opportunities of acquiring cortical recordings for chronic adaptive deep brain stimulation.","authors":"Jeffrey Herron, Aura Kullmann, Timothy Denison, Wayne K Goodman, Aysegul Gunduz, Wolf-Julian Neumann, Nicole R Provenza, Maryam M Shanechi, Sameer A Sheth, Philip A Starr, Alik S Widge","doi":"10.1038/s41551-026-01641-7","DOIUrl":"10.1038/s41551-026-01641-7","url":null,"abstract":"","PeriodicalId":19063,"journal":{"name":"Nature Biomedical Engineering","volume":" ","pages":"603"},"PeriodicalIF":26.8,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147348738","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-03-01DOI: 10.1038/s41551-026-01646-2
Rita Strack
{"title":"mRNA delivery to the endothelium.","authors":"Rita Strack","doi":"10.1038/s41551-026-01646-2","DOIUrl":"https://doi.org/10.1038/s41551-026-01646-2","url":null,"abstract":"","PeriodicalId":19063,"journal":{"name":"Nature Biomedical Engineering","volume":"10 3","pages":"409"},"PeriodicalIF":26.8,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147504410","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}