{"title":"AI tool adjusts for ancestral bias in genetic data","authors":"Iris Marchal","doi":"10.1038/s41587-025-02651-7","DOIUrl":"https://doi.org/10.1038/s41587-025-02651-7","url":null,"abstract":"<p>Human ancestry has a considerable impact on gene expression, but genomic datasets for disease analysis severely underrepresent non-European populations, thereby limiting the advancement of precision medicine. In a paper in <i>Nature Communications</i>, Smith et al. introduce a machine learning tool to mitigate the effects of ancestral bias in transcriptomic data.</p><p>The tool, called PhyloFrame, creates ancestry-aware signatures of disease by integrating population genomics data with smaller, disease-relevant training datasets. PhyloFrame uses a logistic regression model with LASSO penalty to obtain an initial set of disease-relevant genes. It then uses population genomics data to help compensate for data distribution shifts caused by human ancestry differences. In short, PhyloFrame projects the initial disease signature onto a functional interaction network, extending the network to include the first and second neighbors of each signature gene. This new set is then filtered by a statistic defined as enhanced allele frequency (EAF) — which captures population-specific allelic enrichment in healthy tissue — to identify ancestrally diverse genes that interact with the original signature. From each ancestry, a selected subset of genes with high EAF and gene expression variability in the training data are added to the PhyloFrame signature. Retraining the model with the forced inclusion of these equitable genes results in a signature of disease that generalizes to all populations, even if not represented in the training data.</p>","PeriodicalId":19084,"journal":{"name":"Nature biotechnology","volume":"7 1","pages":""},"PeriodicalIF":46.9,"publicationDate":"2025-04-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143831851","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"People","authors":"","doi":"10.1038/s41587-025-02637-5","DOIUrl":"https://doi.org/10.1038/s41587-025-02637-5","url":null,"abstract":"Recent moves of note in and around the biotech and pharma industries.","PeriodicalId":19084,"journal":{"name":"Nature biotechnology","volume":"183 1","pages":""},"PeriodicalIF":46.9,"publicationDate":"2025-04-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143831825","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Not just obesity: GLP-1 receptor agonists advance on addiction","authors":"","doi":"10.1038/s41587-025-02644-6","DOIUrl":"https://doi.org/10.1038/s41587-025-02644-6","url":null,"abstract":"GLP-1 agonists may lessen alcohol, smoking and possibly drug addictions. Evidence from clinical trials remains sparse, but that is about to change.","PeriodicalId":19084,"journal":{"name":"Nature biotechnology","volume":"38 1","pages":""},"PeriodicalIF":46.9,"publicationDate":"2025-04-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143831831","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Turn cold tumors hot by reprogramming the tumor microenvironment","authors":"Xiangliang Yuan, Yi Xiao, Dihua Yu","doi":"10.1038/s41587-025-02597-w","DOIUrl":"https://doi.org/10.1038/s41587-025-02597-w","url":null,"abstract":"The identification of novel targets together with technological advances is transforming our ability to effectively modulate the tumor microenvironment.","PeriodicalId":19084,"journal":{"name":"Nature biotechnology","volume":"40 1","pages":""},"PeriodicalIF":46.9,"publicationDate":"2025-04-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143831524","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Five questions with Jie Sun","authors":"Michael Francisco","doi":"10.1038/s41587-025-02631-x","DOIUrl":"https://doi.org/10.1038/s41587-025-02631-x","url":null,"abstract":"This developer of cancer immunotherapies discusses her early fascination with cellular behavior, perseverance and deep desire to directly impact patient care.","PeriodicalId":19084,"journal":{"name":"Nature biotechnology","volume":"40 1","pages":""},"PeriodicalIF":46.9,"publicationDate":"2025-04-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143831828","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Spotlight on cancer immunotherapies","authors":"","doi":"10.1038/s41587-025-02645-5","DOIUrl":"https://doi.org/10.1038/s41587-025-02645-5","url":null,"abstract":"Advances in cancer immunotherapy have shown promising results for treatment of tumors, yet challenges related to therapeutic efficacy and manufacturing processes need to be overcome.","PeriodicalId":19084,"journal":{"name":"Nature biotechnology","volume":"74 1","pages":""},"PeriodicalIF":46.9,"publicationDate":"2025-04-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143831853","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Wildflowers soak up nickel from toxic soil","authors":"","doi":"10.1038/s41587-025-02647-3","DOIUrl":"https://doi.org/10.1038/s41587-025-02647-3","url":null,"abstract":"<p>Some plants from the family Asteraceae, which includes daisies, belong to an unusual group known as hyperaccumulators. These species soak up metals from their roots and store them at exceptionally high concentrations in their tissues, a capacity that probably evolved as a defense mechanism against herbivores and pathogens. Of the 750 known hyperaccumulator species, most can thrive in fields with otherwise toxic levels of copper, cobalt, lithium, nickel and rare earth elements. The plants store the metals in vacuoles in the leaf cells. To ramp up their phytomining capacity, GenoMines boosted the plant’s height and the size of its leaves. The biotech also developed a targeted soil microbiome to enhance nickel absorption.</p><p>The GenoMines team grows the hyperaccumulator plants in nickel-rich fields and harvests them after six months. The company then recovers the metal from the biomass by a combination of techniques that include bioleaching, extracting up to 2.5 tonnes of nickel per hectare per year. Not only does this process yield nickel, but by extracting the metal, the plants also remediate the land.</p>","PeriodicalId":19084,"journal":{"name":"Nature biotechnology","volume":"26 1","pages":""},"PeriodicalIF":46.9,"publicationDate":"2025-04-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143831826","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"USDA conditionally approves H5N1 poultry vaccine","authors":"","doi":"10.1038/s41587-025-02658-0","DOIUrl":"https://doi.org/10.1038/s41587-025-02658-0","url":null,"abstract":"<p>The US Department of Agriculture (USDA) has given a conditional approval to animal healthcare company Zoetis for an updated vaccine to protect poultry against the H5N1 bird flu strain. The Zoetis vaccine contains a killed version of an H5N2 variant that the company designed to work against currently circulating variants of the H5N1 virus.</p><p>The avian influenza has been spreading in dairy cow and poultry farms in the United States, causing at least several dozen infections in humans and one death. Although vaccination can help control the virus spread, the US government has long resisted its use, unlike those of China, Mexico, Egypt and France, where poultry are vaccinated against avian flu. So far, highly pathogenic influenza viruses have been eliminated from affected flocks by euthanasia. But this strategy has failed to eradicate the H5N1 viruses of the clade 2.3.4.4b that has been circulating in the country since February 2022.</p>","PeriodicalId":19084,"journal":{"name":"Nature biotechnology","volume":"60 1","pages":""},"PeriodicalIF":46.9,"publicationDate":"2025-04-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143831823","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Ting-Fang Lo, Yi-Chih Huang, Nai-Yu Cho, Yufeng Jane Tseng
{"title":"SPARK Taiwan: a decade of insights in adapting US translational medicine and commercialization methods","authors":"Ting-Fang Lo, Yi-Chih Huang, Nai-Yu Cho, Yufeng Jane Tseng","doi":"10.1038/s41587-025-02630-y","DOIUrl":"https://doi.org/10.1038/s41587-025-02630-y","url":null,"abstract":"SPARK Taiwan has strengthened the country’s biotech sector, encouraged scientists to start businesses and fostered cross-disciplinary collaboration.","PeriodicalId":19084,"journal":{"name":"Nature biotechnology","volume":"90 1","pages":""},"PeriodicalIF":46.9,"publicationDate":"2025-04-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143831832","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Engineered E. coli creates biodegradable plastics","authors":"Iris Marchal","doi":"10.1038/s41587-025-02653-5","DOIUrl":"https://doi.org/10.1038/s41587-025-02653-5","url":null,"abstract":"<p>Replacing fossil-fuel-based plastics with bio-based polymers is crucial in tackling the environmental issues caused by our heavy reliance on these materials. Microorganisms can synthesize numerous biopolymers but have not yet been reported to produce one of the most promising polymers, known as polyester amides (PEAs). In a study published in <i>Nature Chemical Biology</i>, Chae et al. engineer a new-to-nature metabolic pathway in <i>Escherichia coli</i> to biosynthesize PEAs, which might one day be used in various industrial applications.</p><p>The production of PEAs in <i>E. coli</i> was accomplished through a two-step synthetic pathway. First, the authors selected the broad-activity β-alanine coenzyme A (CoA) transferase from <i>Clostridium propionicum</i> to activate amino acids to amino acyl-CoA. This step was followed by polymerization of amino acyl-CoA by a mutant PHA synthase from <i>Pseudomonas</i> species, which accepts various monomers as substrates. Metabolic flux optimization resulted in the biosynthesis of two PEAs from glucose as the sole carbon source. Further engineering and optimization of the culture medium was performed to enhance production titers and amino acid fractions. The engineered bacteria converted more than 50% of dry cell weight into polymers.</p>","PeriodicalId":19084,"journal":{"name":"Nature biotechnology","volume":"122 1","pages":""},"PeriodicalIF":46.9,"publicationDate":"2025-04-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143831824","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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