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SynPull: An advanced method for studying neurodegeneration-related aggregates in synaptosomes using super-resolution microscopy
IF 8.6 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-01-24 DOI: 10.1016/j.chembiol.2025.01.001
Shekhar Kedia, Emre Fertan, Yunzhao Wu, Yu P. Zhang, Georg Meisl, Jeff Y.L. Lam, Frances K. Wiseman, William A. McEwan, Annelies Quaegebeur, Maria Grazia Spillantini, John S.H. Danial, David Klenerman
Synaptic dysfunction is a primary hallmark of both Alzheimer’s and Parkinson’s disease, leading to cognitive and behavioral decline. While alpha-synuclein, beta-amyloid, and tau are involved in the physiological functioning of synapses, their pathological aggregation has been linked to synaptopathology. The methodology for studying the small-soluble protein aggregates formed by these proteins is limited. Here we describe SynPull, a method combining single-molecule pull-down, super-resolution microscopy, and advanced computational analyses to characterize the protein aggregates in human and mouse synaptosomes. We show that AT8-positive tau aggregates are the predominant aggregate type in synaptosomes from postmortem Alzheimer’s disease brain, although the aggregate size does not change in disease. Meanwhile, the relatively smaller amount of alpha-synuclein and beta-amyloid aggregates found in the synapses are larger than the extra-synaptic ones. Collectively, these results show the utility of SynPull to study pathological aggregates in neurodegeneration, elucidating the disease mechanisms causing synaptic dysfunction.
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引用次数: 0
New opportunities in mechanistic and functional microbiome studies 机制和功能微生物组研究的新机遇
IF 8.6 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-01-16 DOI: 10.1016/j.chembiol.2024.12.012
Judith Behnsen, Kerwyn Casey Huang, Matthew T. Sorbara, Meng C. Wang, Jun Yu, Melody Y. Zeng
The field of microbiome research has experienced remarkable growth, leading to unprecedented discoveries of the molecular mechanisms that dictate host-microbiota interactions and their crucial roles in human health. In this “chemical biology of the microbiome” focus issue from Cell Chemical Biology, this Voices piece asks researchers from a range of backgrounds to share their insights on the most exciting recent developments in the microbiome field.
微生物组研究领域取得了令人瞩目的发展,人们前所未有地发现了决定宿主与微生物组相互作用的分子机制及其在人类健康中的关键作用。在《细胞化学生物学》的这期 "微生物组的化学生物学 "特刊中,本期《声音》杂志邀请不同背景的研究人员分享他们对微生物组领域最令人兴奋的最新进展的见解。
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引用次数: 0
Meet the authors: Katerina Jones, Camila Bernardo de Brito, and Mariana Xavier Byndloss 认识一下作者:卡特琳娜·琼斯、卡米拉·贝尔纳多·德·布里托和玛丽安娜·泽维尔·拜德罗斯
IF 8.6 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-01-16 DOI: 10.1016/j.chembiol.2024.12.009
Katerina Jones, Camila Bernardo de Brito, Mariana Xavier Byndloss
In an interview with Samantha Nelson, a scientific editor of Cell Chemical Biology, the authors of the review entitled “Metabolic tug-o-war: Microbial metabolism shapes colonization resistance against enteric pathogens” share their perspectives on the field and their lives as scientists.
在接受《细胞化学生物学》(Cell Chemical Biology)科学编辑萨曼莎-尼尔森(Samantha Nelson)的采访时,题为《新陈代谢拉锯战:微生物新陈代谢塑造了对肠道病原体的定植抗性》的综述作者分享了他们对这一领域的看法以及作为科学家的生活:微生物新陈代谢决定了对肠道病原体的定植抵抗力 "的评论文章的作者分享了他们对这一领域的看法以及他们作为科学家的生活。
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引用次数: 0
Human AKR1C3 binds agonists of GPR84 and participates in an expanded polyamine pathway. 人类 AKR1C3 与 GPR84 的激动剂结合,并参与扩展的多胺途径。
IF 6.6 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-01-16 Epub Date: 2024-08-19 DOI: 10.1016/j.chembiol.2024.07.011
Natavan Dudkina, Hyun Bong Park, Deguang Song, Abhishek Jain, Sajid A Khan, Richard A Flavell, Caroline H Johnson, Noah W Palm, Jason M Crawford

Altered human aldo-keto reductase family 1 member C3 (AKR1C3) expression has been associated with poor prognosis in diverse cancers, ferroptosis resistance, and metabolic diseases. Despite its clinical significance, the endogenous biochemical roles of AKR1C3 remain incompletely defined. Using untargeted metabolomics, we identified a major transformation mediated by AKR1C3, in which a spermine oxidation product "sperminal" is reduced to "sperminol." Sperminal causes DNA damage and activates the DNA double-strand break response, whereas sperminol induces autophagy in vitro. AKR1C3 also pulls down acyl-pyrones and pyrone-211 inhibits AKR1C3 activity. Through G protein-coupled receptor ligand screening, we determined that pyrone-211 is also a potent agonist of the semi-orphan receptor GPR84. Strikingly, mammalian fatty acid synthase produces acyl-pyrones in vitro, and this production is modulated by NADPH. Taken together, our studies support a regulatory role of AKR1C3 in an expanded polyamine pathway and a model linking fatty acid synthesis and NADPH levels to GPR84 signaling.

人类醛酮还原酶家族 1 成员 C3(AKR1C3)表达的改变与多种癌症的不良预后、铁中毒抵抗和代谢性疾病有关。尽管AKR1C3具有重要的临床意义,但其内源生化作用仍未完全明确。利用非靶向代谢组学,我们发现了 AKR1C3 介导的一种主要转化,其中精胺氧化产物 "精胺 "被还原为 "精胺醇"。精胺会导致DNA损伤并激活DNA双链断裂反应,而精胺醇则会在体外诱导自噬。AKR1C3 还能拉低酰基吡喃酮,而吡喃酮-211 能抑制 AKR1C3 的活性。通过 G 蛋白偶联受体配体筛选,我们确定 pyrone-211 也是半orphan 受体 GPR84 的强效激动剂。令人吃惊的是,哺乳动物脂肪酸合成酶在体外产生酰基吡咯酮,而这种产生受 NADPH 的调节。综上所述,我们的研究支持 AKR1C3 在扩展的多胺通路中的调控作用,以及将脂肪酸合成和 NADPH 水平与 GPR84 信号联系起来的模型。
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引用次数: 0
Emerging biochemical, microbial and immunological evidence in the search for why HLA-B27 confers risk for spondyloarthritis. 寻找 HLA-B∗27 为何会导致脊柱关节炎风险的生化、微生物和免疫学证据。
IF 6.6 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-01-16 Epub Date: 2024-08-20 DOI: 10.1016/j.chembiol.2024.07.012
Eric M Brown, Phuong N U Nguyen, Ramnik J Xavier

The strong association of the human leukocyte antigen B27 alleles (HLA-B27) with spondyloarthritis and related rheumatic conditions has long fascinated researchers, yet the precise mechanisms underlying its pathogenicity remain elusive. Here, we review how interplay between the microbiome, the immune system, and the enigmatic HLA-B27 could trigger spondyloarthritis, with a focus on whether HLA-B27 presents an arthritogenic peptide. We propose mechanisms by which the unique biochemical characteristics of the HLA-B27 protein structure, particularly its peptide binding groove, could dictate its propensity to induce pathological T cell responses. We further provide new insights into how TRBV9+ CD8+ T cells are implicated in the disease process, as well as how the immunometabolism of T cells modulates tissue-specific inflammatory responses in spondyloarthritis. Finally, we present testable models and suggest approaches to this problem in future studies given recent advances in computational biology, chemical biology, structural biology, and small-molecule therapeutics.

人类白细胞抗原B∗27等位基因(HLA-B∗27)与脊柱关节炎及相关风湿病的密切关系一直令研究人员着迷,但其致病的确切机制却仍然难以捉摸。在这里,我们回顾了微生物组、免疫系统和神秘的 HLA-B∗27 之间的相互作用是如何诱发脊柱关节炎的,重点是 HLA-B∗27 是否会产生致关节炎肽。我们提出了 HLA-B∗27 蛋白结构的独特生化特性(尤其是其肽结合槽)可能决定其诱导病理 T 细胞反应倾向的机制。我们进一步提供了关于 TRBV9+ CD8+ T 细胞如何参与疾病过程以及 T 细胞的免疫代谢如何调节脊柱关节炎组织特异性炎症反应的新见解。最后,鉴于计算生物学、化学生物学、结构生物学和小分子疗法的最新进展,我们提出了可检验的模型,并建议在未来研究中解决这一问题的方法。
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引用次数: 0
Metabolic tug-of-war: Microbial metabolism shapes colonization resistance against enteric pathogens 代谢拔河:微生物代谢形成对肠道病原体的定植抗性
IF 8.6 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-01-16 DOI: 10.1016/j.chembiol.2024.12.005
Katerina Jones, Camila Bernardo de Brito, Mariana Xavier Byndloss
A widely recognized benefit of gut microbiota is that it provides colonization resistance against enteric pathogens. The gut microbiota and their products can protect the host from invading microbes directly via microbe-pathogen interactions and indirectly by host-microbiota interactions, which regulate immune system function. In contrast, enteric pathogens have evolved mechanisms to utilize microbiota-derived metabolites to overcome colonization resistance and increase their pathogenic potential. This review will focus on recent studies of metabolism-mediated mechanisms of colonization resistance and virulence strategies enteric pathogens use to overcome them, along with how induction of inflammation by pathogenic bacteria changes the landscape of the gut and enables alternative metabolic pathways. We will focus on how intestinal pathogens counteract the protective effects of microbiota-derived metabolites to illustrate the growing appreciation of how metabolic factors may serve as crucial virulence determinants and overcome colonization resistance.
肠道微生物群的一个公认益处是,它能提供对肠道病原体的定植抵抗力。肠道微生物群及其产物可通过微生物与病原体之间的相互作用直接保护宿主免受入侵微生物的侵害,也可通过宿主与微生物群之间的相互作用间接保护宿主免受入侵微生物的侵害,从而调节免疫系统的功能。相比之下,肠道病原体已经进化出利用微生物群衍生代谢物的机制,以克服定植阻力并增加其致病潜力。本综述将重点介绍最近对代谢介导的定植阻力机制和肠道病原体用来克服这些阻力的毒力策略的研究,以及致病菌诱导炎症如何改变肠道景观并启用替代代谢途径。我们将重点关注肠道病原体如何抵消微生物群衍生代谢物的保护作用,以说明人们对代谢因素如何作为关键的毒力决定因素并克服定植阻力的认识不断提高。
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引用次数: 0
Commensal-derived tryptophan metabolites fortify the skin barrier: Insights from a 50-species gnotobiotic model of human skin microbiome 评论衍生色氨酸代谢物强化皮肤屏障:来自人类皮肤微生物组的50种非生物模型的见解
IF 8.6 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-01-16 DOI: 10.1016/j.chembiol.2024.12.007
Aayushi Uberoi, Sofía M. Murga-Garrido, Preeti Bhanap, Amy E. Campbell, Simon A.B. Knight, Monica Wei, Anya Chan, Taylor Senay, Saba Tegegne, Ellen K. White, Carrie Hayes Sutter, Clementina Mesaros, Thomas R. Sutter, Elizabeth A. Grice
The epidermal barrier defends the body against dehydration and harmful substances. The commensal microbiota is essential for proper differentiation and repair of the epidermal barrier, an effect mediated by the aryl hydrocarbon receptor (AHR). However, the microbial mechanisms of AHR activation in skin are less understood. Tryptophan metabolites are AHR ligands that can be products of microbial metabolism. To identify microbially regulated tryptophan metabolites in vivo, we established a gnotobiotic model colonized with fifty human skin commensals and performed targeted mass spectrometry on murine skin. Indole-related metabolites were enriched in colonized skin compared to germ-free skin. In reconstructed human epidermis and in murine models of atopic-like barrier damage, these metabolites improved barrier repair and function individually and as a cocktail. These results provide a framework for the identification of microbial metabolites that mediate specific host functions, which can guide the development of microbe-based therapies for skin disorders.
表皮屏障保护人体免受脱水和有害物质的伤害。共生微生物群对表皮屏障的正常分化和修复至关重要,这种作用由芳基烃受体(AHR)介导。然而,人们对皮肤中激活 AHR 的微生物机制了解较少。色氨酸代谢物是 AHR 配体,可能是微生物代谢的产物。为了鉴定体内受微生物调控的色氨酸代谢物,我们建立了一个由 50 种人类皮肤共生菌定植的非生物模型,并对鼠皮肤进行了靶向质谱分析。与无菌皮肤相比,定植皮肤中富含吲哚相关代谢物。在重建的人类表皮和类似特应性屏障损伤的小鼠模型中,这些代谢物可单独或作为鸡尾酒改善屏障修复和功能。这些结果为鉴定介导特定宿主功能的微生物代谢物提供了一个框架,可为开发基于微生物的皮肤病疗法提供指导。
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引用次数: 0
Yeast paves the way for cancer immunotherapy 酵母为癌症免疫治疗铺平了道路
IF 8.6 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-01-16 DOI: 10.1016/j.chembiol.2024.12.011
Dingjiacheng Jia, Shujie Chen
In this issue of Cell Chemical Biology, Rebeck et al.1 construct a system that enables Saccharomyces cerevisiae var. boulardii (Sb) to secrete immune checkpoint inhibitors, reducing intestinal tumor load. This safe and effective delivery platform using engineered yeast demonstrates potential for enhancing the efficacy of biologics.
在这一期的Cell Chemical Biology上,Rebeck et al.1构建了一个系统,使酿酒酵母(Saccharomyces cerevisiae var. boulardii, Sb)分泌免疫检查点抑制剂,减少肠道肿瘤负荷。这种安全有效的工程酵母传递平台显示了增强生物制剂功效的潜力。
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引用次数: 0
Chemical interplay between gut microbiota and epigenetics: Implications in circadian biology. 肠道微生物群与表观遗传学之间的化学相互作用:对昼夜节律生物学的影响
IF 6.6 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-01-16 Epub Date: 2024-05-21 DOI: 10.1016/j.chembiol.2024.04.016
Samskrathi Aravinda Sharma, Sarah Olanrewaju Oladejo, Zheng Kuang

Circadian rhythms are intrinsic molecular mechanisms that synchronize biological functions with the day/night cycle. The mammalian gut is colonized by a myriad of microbes, collectively named the gut microbiota. The microbiota impacts host physiology via metabolites and structural components. A key mechanism is the modulation of host epigenetic pathways, especially histone modifications. An increasing number of studies indicate the role of the microbiota in regulating host circadian rhythms. However, the mechanisms remain largely unknown. Here, we summarize studies on microbial regulation of host circadian rhythms and epigenetic pathways, highlight recent findings on how the microbiota employs host epigenetic machinery to regulate circadian rhythms, and discuss its impacts on host physiology, particularly immune and metabolic functions. We further describe current challenges and resources that could facilitate research on microbiota-epigenetic-circadian rhythm interactions to advance our knowledge of circadian disorders and possible therapeutic avenues.

昼夜节律是使生物功能与昼夜周期同步的内在分子机制。哺乳动物肠道内有大量微生物,统称为肠道微生物群。微生物群通过代谢物和结构成分影响宿主的生理机能。其中一个关键机制是调节宿主的表观遗传途径,尤其是组蛋白修饰。越来越多的研究表明,微生物群在调节宿主昼夜节律方面发挥作用。然而,其中的机制在很大程度上仍不为人所知。在此,我们总结了有关微生物调控宿主昼夜节律和表观遗传途径的研究,重点介绍了有关微生物群如何利用宿主表观遗传机制调控昼夜节律的最新发现,并讨论了其对宿主生理,尤其是免疫和代谢功能的影响。我们进一步介绍了当前的挑战和资源,这些挑战和资源可促进微生物群-表观遗传-昼夜节律相互作用的研究,从而增进我们对昼夜节律紊乱的了解和可能的治疗途径。
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引用次数: 0
Meet the authors: Aayushi Uberoi and Elizabeth A. Grice 来认识一下这篇文章的作者:银井青史和伊丽莎白·a·格赖斯
IF 8.6 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-01-16 DOI: 10.1016/j.chembiol.2024.12.010
Aayushi Uberoi, Elizabeth A. Grice
In an interview with Samantha Nelson, a scientific editor of Cell Chemical Biology, the authors of the research article entitled “Commensal-derived tryptophan metabolites fortify the skin barrier: Insights from a 50-species gnotobiotic model of human skin microbiome” share insights about their paper, field, and lives as scientists.
在与《细胞化学生物学》科学编辑萨曼莎-尼尔森(Samantha Nelson)的一次访谈中,题为《共生菌衍生的色氨酸代谢物可强化皮肤屏障》(Commensal-derived tryptophan metabolites fortify the skin barrier:从 50 种人类皮肤微生物组的非生物模型中获得的启示 "一文的作者分享了他们对论文、研究领域和科学家生活的见解。
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引用次数: 0
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Cell Chemical Biology
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