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Unlocking lignin valorization and harnessing lignin-based raw materials for bio-manufacturing. 解锁木质素增值和利用木质素为基础的原料生物制造。
IF 8 2区 生物学 Q1 BIOLOGY Pub Date : 2025-04-01 Epub Date: 2024-12-18 DOI: 10.1007/s11427-024-2792-x
Le Gao, Fangting Jiang, Zhaokun Zhang, Tongtong Bao, Daochen Zhu, Xin Wu

Lignin, an energy-rich and adaptable polymer comprising phenylpropanoid monomers utilized by plants for structural reinforcement, water conveyance, and defense mechanisms, ranks as the planet's second most prevalent biopolymer, after cellulose. Despite its prevalence, lignin is frequently underused in the process of converting biomass into fuels and chemicals. Instead, it is commonly incinerated for industrial heat due to its intricate composition and resistance to decomposition, presenting obstacles for targeted valorization. In contrast to chemical catalysts, biological enzymes show promise not only in selectively converting lignin components but also in seamlessly integrating into cellular structures, offering biocatalysis as a potentially efficient pathway for lignin enhancement. This review comprehensively summarizes cutting-edge biostrategies, ligninolytic enzymes, metabolic pathways, and lignin-degrading strains or consortia involved in lignin degradation, while critically evaluating the underlying mechanisms. Metabolic and genetic engineering play crucial roles in redirecting lignin and its derivatives towards metabolic pathways like the tricarboxylic acid cycle, opening up novel avenues for its valorization. Recent advancements in lignin valorization are scrutinized, highlighting key challenges and promising solutions. Furthermore, the review underscores the importance of innovative approaches, such as leveraging digital systems and synthetic biology, to unlock the commercial potential of lignin-derived raw materials as sustainable feedstocks. Artificial intelligence-driven technologies offer promise in overcoming current challenges and driving widespread adoption of lignin valorization, presenting an alternative to sugar-based feedstocks for bio-based manufacturing in the future. The utilization of available lignin residue for synthesis of high-value chemicals or energy, even alternative food, addresses various crises looming in the food-energy-water nexus.

木质素是一种能量丰富、适应性强的聚合物,由苯丙类单体组成,被植物用于结构加固、输水和防御机制,是地球上第二大最普遍的生物聚合物,仅次于纤维素。尽管木质素普遍存在,但在将生物质转化为燃料和化学品的过程中,木质素经常未得到充分利用。相反,由于其复杂的成分和抗分解性,它通常被焚烧作为工业热,这给目标定价带来了障碍。与化学催化剂相比,生物酶不仅可以选择性地转化木质素成分,而且可以无缝地整合到细胞结构中,从而为木质素增强提供了一种潜在的有效途径。本文综述了木质素降解的最新生物策略、木质素降解酶、代谢途径和木质素降解菌株或菌群,并对木质素降解的潜在机制进行了批判性评价。代谢和基因工程在将木质素及其衍生物转向三羧酸循环等代谢途径方面发挥着至关重要的作用,为其增值开辟了新的途径。木质素增值的最新进展进行了审查,突出了关键的挑战和有前途的解决方案。此外,该审查强调了创新方法的重要性,例如利用数字系统和合成生物学,以释放木质素衍生原料作为可持续原料的商业潜力。人工智能驱动的技术有望克服当前的挑战,推动木质素增值的广泛采用,为未来的生物基制造提供糖基原料的替代方案。利用可利用的木质素渣来合成高价值的化学品或能源,甚至替代食品,解决了食物-能源-水关系中迫在眉睫的各种危机。
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引用次数: 0
Genetic advancements and future directions in ruminant livestock breeding: from reference genomes to multiomics innovations. 反刍家畜育种的遗传进展和未来方向:从参考基因组到多组学创新。
IF 8 2区 生物学 Q1 BIOLOGY Pub Date : 2025-04-01 Epub Date: 2024-11-26 DOI: 10.1007/s11427-024-2744-4
Songsong Xu, Zhanerke Akhatayeva, Jiaxin Liu, Xueyan Feng, Yi Yu, Bouabid Badaoui, Ali Esmailizadeh, Juha Kantanen, Marcel Amills, Johannes A Lenstra, Anna M Johansson, David W Coltman, George E Liu, Ino Curik, Pablo Orozco-terWengel, Samuel R Paiva, Natalia A Zinovieva, Linwei Zhang, Ji Yang, Zhihong Liu, Yachun Wang, Ying Yu, Menghua Li

Ruminant livestock provide a rich source of products, such as meat, milk, and wool, and play a critical role in global food security and nutrition. Over the past few decades, genomic studies of ruminant livestock have provided valuable insights into their domestication and the genetic basis of economically important traits, facilitating the breeding of elite varieties. In this review, we summarize the main advancements for domestic ruminants in reference genome assemblies, population genomics, and the identification of functional genes or variants for phenotypic traits. These traits include meat and carcass quality, reproduction, milk production, feed efficiency, wool and cashmere yield, horn development, tail type, coat color, environmental adaptation, and disease resistance. Functional genomic research is entering a new era with the advancements of graphical pangenomics and telomere-to-telomere (T2T) gap-free genome assembly. These advancements promise to improve our understanding of domestication and the molecular mechanisms underlying economically important traits in ruminant livestock. Finally, we provide new perspectives and future directions for genomic research on ruminant genomes. We suggest how ever-increasing multiomics datasets will facilitate future studies and molecular breeding in livestock, including the potential to uncover novel genetic mechanisms underlying phenotypic traits, to enable more accurate genomic prediction models, and to accelerate genetic improvement programs.

反刍家畜提供了丰富的产品来源,如肉、奶和羊毛,在全球粮食安全和营养方面发挥着关键作用。在过去的几十年里,对反刍家畜的基因组研究为它们的驯化和重要经济性状的遗传基础提供了有价值的见解,促进了优良品种的培育。本文综述了国内反刍动物在参考基因组组合、群体基因组学、表型性状功能基因或变异鉴定等方面的主要研究进展。这些性状包括肉和胴体质量、繁殖、产奶量、饲料效率、羊毛和羊绒产量、角发育、尾巴类型、被毛颜色、环境适应性和抗病性。随着图形泛基因组学和端粒-端粒(T2T)无间隙基因组组装技术的进步,功能基因组研究正在进入一个新的时代。这些进展有望提高我们对反刍家畜驯化和重要经济性状的分子机制的理解。最后,提出了反刍动物基因组研究的新视角和未来发展方向。我们建议不断增加的多组学数据集将如何促进牲畜的未来研究和分子育种,包括揭示表型性状背后的新遗传机制的潜力,实现更准确的基因组预测模型,并加速遗传改良计划。
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引用次数: 0
Landscapes of gut microbiome and blood metabolomic signatures in relapsing remitting multiple sclerosis. 复发缓解型多发性硬化症中肠道微生物组和血液代谢组特征的景观。
IF 8 2区 生物学 Q1 BIOLOGY Pub Date : 2025-04-01 Epub Date: 2025-01-13 DOI: 10.1007/s11427-024-2653-2
Jinzhou Feng, Shi Tang, Xiaolin Yang, Mengjie Zhang, Zhizhong Li, Shaoru Zhang, Yongliang Han, Yongmei Li, Philippe P Monnier, Gang Yu, Peng Zheng, Cunjin Zhang, Ke Xu, Xinyue Qin

Although disturbances in the gut microbiome have been implicated in multiple sclerosis (MS), little is known about the changes and interactions between the gut microbiome and blood metabolome, and how these changes affect disease-modifying therapy (DMT) in preventing the progression of MS. In this study, the structure and composition of the gut microbiota were evaluated using 16S rRNA gene sequencing and an untargeted metabolomics approach was used to compare the serum metabolite profiles from patients with relapsing-remitting MS (RRMS) and healthy controls (HCs). Results indicated that RRMS was characterized by phase-dependent α-phylogenetic diversity and significant disturbances in serum glycerophospholipid metabolism. Notably, α-phylogenetic diversity was significantly decreased in RRMS patients during the chronic phase (CMS) compared with those in the acute phase (AMS). A distinctive combination of two elevated genera (Slackia, Lactobacillus) and five glycerophospholipid metabolism-associated metabolites (four increased: GPCho(22:5/20:3), PC(18:2(9Z,12Z)/16:0), PE(16:0/18:2(9Z,12Z)), PE(18:1(11Z)/18:2(9Z,12Z)); one decreased: PS(15:0/22:1(13Z))) in RRMS patients when comparing to HCs. Moreover, a biomarker panel consisting of four microbial genera (three decreased: Lysinibacillus, Parabacteroides, UBA1819; one increased: Lachnoanaerobaculum) and two glycerophospholipid metabolism-associated metabolites (one increased: PE(P-16:0/22:6); one decreased: CL(i-12:0/i-16:0/i-17:0/i-12:0)) effectively discriminated CMS patients from AMS patients, which indicate correlation with higher disability. Additionally, DMTs appeared to attenuate MS progression by reducing UBA1819 and upregulating CL(i-12:0/i-16:0/i-17:0/i-12:0). These findings expand our understanding of the microbiome and metabolome roles in RRMS and may contribute to identifying novel diagnostic biomarkers and promising therapeutic targets.

尽管肠道微生物组紊乱与多发性硬化症(MS)有关,但肠道微生物组与血液代谢组之间的变化和相互作用,以及这些变化如何影响疾病修饰治疗(DMT)以预防MS进展,我们对此知之甚少。使用16S rRNA基因测序评估肠道微生物群的结构和组成,并使用非靶向代谢组学方法比较复发-缓解型MS (RRMS)患者和健康对照(hc)的血清代谢物谱。结果表明,RRMS具有相依赖性α-系统发育多样性,血清甘油磷脂代谢明显紊乱。值得注意的是,RRMS患者在慢性期(CMS)与急性期(AMS)相比,α-系统发育多样性明显降低。两个升高的属(Slackia, Lactobacillus)和五个甘油磷脂代谢相关代谢物的独特组合(四个增加:GPCho(22:5/20:3), PC(18:2(9Z,12Z)/16:0), PE(16:0/18:2(9Z,12Z)), PE(18:1(11Z)/18:2(9Z,12Z));与hc患者相比,RRMS患者的PS(15:0/22:1(13Z))降低。此外,一个由四个微生物属组成的生物标志物面板(减少了三个:Lysinibacillus, Parabacteroides, UBA1819;1个增加:厌氧乳酸)和2个甘油磷脂代谢相关代谢物(1个增加:PE(P-16:0/22:6);1降低:CL(i-12:0/i-16:0/i-17:0/i-12:0))能有效区分CMS患者和AMS患者,表明其残疾程度较高。此外,dmt似乎通过降低UBA1819和上调CL(i-12:0/i-16:0/i-17:0/i-12:0)来减缓MS的进展。这些发现扩大了我们对微生物组和代谢组在RRMS中的作用的理解,并可能有助于确定新的诊断生物标志物和有希望的治疗靶点。
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引用次数: 0
Population genomics advances in frontier ethnic minorities in China. 中国边疆少数民族群体基因组学研究进展。
IF 8 2区 生物学 Q1 BIOLOGY Pub Date : 2025-04-01 Epub Date: 2024-12-04 DOI: 10.1007/s11427-024-2659-2
Hao Chen, Shuhua Xu

China, with its large geographic span, possesses rich genetic diversity across vast frontier regions in addition to the Han Chinese majority. Importantly, demographic events and various natural and cultural environments in Chinese frontier regions have shaped the genomic diversity of ethnic minorities via local adaptations. Thus, insights into the genetic diversity and adaptive evolution of these under-represented ethnic groups are crucial for understanding evolutionary scenarios and biomedical implications in East Asian populations. Here, we focus on ethnic minorities in Chinese frontier regions and review research advances regarding genomic diversity, genetic structure, population history, genetic admixture, and local adaptation. We first provide an overview of the extensive genetic diversity across populations in different Chinese frontier regions. Next, we summarize research progress regarding genetic ancestry, demographic history, the adaptive process, and the archaic identification of multiple ethnic minorities in different Chinese frontier regions. Finally, we discuss the gaps and opportunities in genomic studies of Chinese populations and the need for a more comprehensive understanding of genomic diversity and the evolution of populations of East Asian ancestry in the post-genomic era.

中国幅员辽阔,除了汉族人口占多数外,在广阔的边疆地区拥有丰富的遗传多样性。重要的是,中国边疆地区的人口事件和各种自然文化环境通过当地适应塑造了少数民族的基因组多样性。因此,深入了解这些代表性不足的族群的遗传多样性和适应性进化,对于理解东亚人群的进化情景和生物医学意义至关重要。本文以中国边疆少数民族为研究对象,从基因组多样性、遗传结构、种群历史、遗传混合和地方适应等方面综述了研究进展。我们首先概述了中国不同边疆地区人群广泛的遗传多样性。其次,总结了中国边疆地区多民族的遗传祖先、人口历史、适应过程和古籍鉴定等方面的研究进展。最后,我们讨论了中国人群基因组研究的空白和机遇,以及在后基因组时代更全面地了解基因组多样性和东亚祖先群体进化的必要性。
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引用次数: 0
Dietary carbohydrate intake and risk of type 2 diabetes: a 16-year prospective cohort study. 饮食碳水化合物摄入与2型糖尿病风险:一项16年前瞻性队列研究
IF 8 2区 生物学 Q1 BIOLOGY Pub Date : 2025-04-01 Epub Date: 2025-01-13 DOI: 10.1007/s11427-024-2804-0
Lu Gan, Yi Yang, Bin Zhao, Kai Yu, Kehua Guo, Fang Fang, Zhiguang Zhou, Demetrius Albanes, Jiaqi Huang

Despite considerable research underscoring the importance of carbohydrate intake in relation to the risk of type 2 diabetes (T2D), a comprehensive assessment of this relationship is currently lacking. We aimed to examine the associations of various types and food sources of dietary carbohydrate intake with the risk of T2D, to evaluate potential effect modification by other factors, including genetic susceptibility, and to explore the potential mediators for such associations. The present study included 161,872 participants of the UK Biobank who were free of prevalent cancer, cardiovascular disease, or diabetes, and had at least one validated 24-h dietary recall assessment. Multivariable-adjusted age-stratified Cox proportional hazard regression models were applied to estimate hazard ratios (HRs) and 95% confidence intervals (CI) for the associations of various types and food sources of dietary carbohydrate intake with risk of T2D. During a median follow-up of 13.6 years, 4,176 incident cases of T2D were identified. In the multivariable-adjusted models, a greater intake of fiber, carbohydrates from whole grains, and carbohydrates from non-starchy vegetables was significantly associated with a lower risk of T2D (highest vs. lowest quantile, HR [95% CI]=0.70 [0.62-0.79], 0.74 [0.67-0.82], and 0.83 [0.75-0.92], respectively, all P for trend <0.005). In contrast, a higher intake of starch and carbohydrate from starchy vegetables was associated with an increased risk of T2D (highest vs. lowest quantile, HR [95% CI]=1.31 [1.16-1.48] and 1.19 [1.09-1.31], respectively, both P for trend <0.005). Replacing one serving of refined grains or starchy vegetables with an equal amount of whole grains or non-starchy vegetables was associated with 4% to 10% lower risk of T2D (all P values <0.001). The observed associations were generally similar across population subgroups, including individuals with different genetic susceptibility to T2D. Mediation analyses of the inverse association between T2D risk and isocaloric substitution of carbohydrates from refined grains with carbohydrate from whole grains demonstrated that 39.6%, 43.4%, 44.0%, 27.8%, and 34.9% were mediated through body mass index, waist-to-hip ratio, glycosylated hemoglobin, high-density lipoprotein cholesterol, and C-reactive protein, respectively. In addition, the inverse association between the isocaloric substitution of carbohydrates from starchy vegetables with carbohydrates from non-starchy vegetables and T2D was partially mediated through high-density lipoprotein cholesterol (15.9%). These findings underscore the importance of dietary modifications of carbohydrates, particularly considering types and food sources of carbohydrate intake, in the primary prevention of T2D.

尽管大量研究强调了碳水化合物摄入与2型糖尿病(T2D)风险相关的重要性,但目前缺乏对这种关系的全面评估。我们的目的是研究膳食碳水化合物摄入的不同类型和食物来源与T2D风险的关系,评估其他因素(包括遗传易感性)对潜在影响的改变,并探索这种关联的潜在介质。本研究包括来自英国生物银行的161872名参与者,他们没有常见的癌症、心血管疾病或糖尿病,并且至少有一次有效的24小时饮食回忆评估。应用多变量校正的年龄分层Cox比例风险回归模型来估计不同类型和食物来源的碳水化合物摄入与T2D风险的关联的风险比(hr)和95%置信区间(CI)。在中位随访13.6年期间,共发现4176例T2D病例。在多变量调整模型中,摄入更多的纤维、全谷物碳水化合物和非淀粉类蔬菜碳水化合物与较低的T2D风险显著相关(最高分位数vs最低分位数,HR [95% CI]分别=0.70[0.62-0.79]、0.74[0.67-0.82]和0.83[0.75-0.92],均为趋势P
{"title":"Dietary carbohydrate intake and risk of type 2 diabetes: a 16-year prospective cohort study.","authors":"Lu Gan, Yi Yang, Bin Zhao, Kai Yu, Kehua Guo, Fang Fang, Zhiguang Zhou, Demetrius Albanes, Jiaqi Huang","doi":"10.1007/s11427-024-2804-0","DOIUrl":"10.1007/s11427-024-2804-0","url":null,"abstract":"<p><p>Despite considerable research underscoring the importance of carbohydrate intake in relation to the risk of type 2 diabetes (T2D), a comprehensive assessment of this relationship is currently lacking. We aimed to examine the associations of various types and food sources of dietary carbohydrate intake with the risk of T2D, to evaluate potential effect modification by other factors, including genetic susceptibility, and to explore the potential mediators for such associations. The present study included 161,872 participants of the UK Biobank who were free of prevalent cancer, cardiovascular disease, or diabetes, and had at least one validated 24-h dietary recall assessment. Multivariable-adjusted age-stratified Cox proportional hazard regression models were applied to estimate hazard ratios (HRs) and 95% confidence intervals (CI) for the associations of various types and food sources of dietary carbohydrate intake with risk of T2D. During a median follow-up of 13.6 years, 4,176 incident cases of T2D were identified. In the multivariable-adjusted models, a greater intake of fiber, carbohydrates from whole grains, and carbohydrates from non-starchy vegetables was significantly associated with a lower risk of T2D (highest vs. lowest quantile, HR [95% CI]=0.70 [0.62-0.79], 0.74 [0.67-0.82], and 0.83 [0.75-0.92], respectively, all P for trend <0.005). In contrast, a higher intake of starch and carbohydrate from starchy vegetables was associated with an increased risk of T2D (highest vs. lowest quantile, HR [95% CI]=1.31 [1.16-1.48] and 1.19 [1.09-1.31], respectively, both P for trend <0.005). Replacing one serving of refined grains or starchy vegetables with an equal amount of whole grains or non-starchy vegetables was associated with 4% to 10% lower risk of T2D (all P values <0.001). The observed associations were generally similar across population subgroups, including individuals with different genetic susceptibility to T2D. Mediation analyses of the inverse association between T2D risk and isocaloric substitution of carbohydrates from refined grains with carbohydrate from whole grains demonstrated that 39.6%, 43.4%, 44.0%, 27.8%, and 34.9% were mediated through body mass index, waist-to-hip ratio, glycosylated hemoglobin, high-density lipoprotein cholesterol, and C-reactive protein, respectively. In addition, the inverse association between the isocaloric substitution of carbohydrates from starchy vegetables with carbohydrates from non-starchy vegetables and T2D was partially mediated through high-density lipoprotein cholesterol (15.9%). These findings underscore the importance of dietary modifications of carbohydrates, particularly considering types and food sources of carbohydrate intake, in the primary prevention of T2D.</p>","PeriodicalId":21576,"journal":{"name":"Science China Life Sciences","volume":" ","pages":"1149-1157"},"PeriodicalIF":8.0,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143010850","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
BEND6 promotes RNA viruses' replication by inhibiting innate immune responses. BEND6通过抑制先天免疫反应促进RNA病毒复制。
IF 8 2区 生物学 Q1 BIOLOGY Pub Date : 2025-04-01 Epub Date: 2025-01-10 DOI: 10.1007/s11427-024-2698-6
Tong Chen, Ling Ding, Shaoyu Tu, Huimin Sun, Jiahui Zou, Aotian Ouyang, Meijun Jiang, Yi Feng, Meilin Jin, Huanchun Chen, Hongbo Zhou

Innate immunity serves as a crucial defense mechanism against invading pathogens, yet its negative regulatory network remains under explored. In this study, we identify BEN domain-containing protein 6 (BEND6) as a novel negative regulator of innate immunity through a genome-scale CRISPR knockout screen for host factors essential for viral replication. We show that BEND6 exhibits characteristics of an interferon-stimulated gene (ISG), with its mRNA and protein levels upregulated by RNA virus-induced IFN-β. BEND6 targets IRF3 and inhibits its recruitment by TBK1, thus preventing IRF3 phosphorylation and dimerization. Additionally, BEND6 directly binds to ISRE, thereby hindering the DNA binding activity of IRF3 and blocking the subsequent activation of IFN-β transcription. Taken together, our study reveals the mechanism of BEND6 in promoting the replication of various RNA viruses and provides a potential therapeutic target for RNA virus infection.

先天免疫是抵御病原体入侵的重要防御机制,但其负调控网络仍未得到充分研究。在这项研究中,我们通过基因组级CRISPR敲除筛选病毒复制所必需的宿主因子,发现BEN结构域蛋白6 (BEND6)是先天免疫的一种新的负调节因子。我们发现BEND6表现出干扰素刺激基因(ISG)的特征,其mRNA和蛋白水平被RNA病毒诱导的IFN-β上调。BEND6以IRF3为靶点,通过TBK1抑制IRF3的募集,从而阻止IRF3磷酸化和二聚化。此外,BEND6直接与ISRE结合,从而阻碍了IRF3的DNA结合活性,阻断了随后IFN-β转录的激活。综上所述,我们的研究揭示了BEND6促进多种RNA病毒复制的机制,为RNA病毒感染提供了潜在的治疗靶点。
{"title":"BEND6 promotes RNA viruses' replication by inhibiting innate immune responses.","authors":"Tong Chen, Ling Ding, Shaoyu Tu, Huimin Sun, Jiahui Zou, Aotian Ouyang, Meijun Jiang, Yi Feng, Meilin Jin, Huanchun Chen, Hongbo Zhou","doi":"10.1007/s11427-024-2698-6","DOIUrl":"10.1007/s11427-024-2698-6","url":null,"abstract":"<p><p>Innate immunity serves as a crucial defense mechanism against invading pathogens, yet its negative regulatory network remains under explored. In this study, we identify BEN domain-containing protein 6 (BEND6) as a novel negative regulator of innate immunity through a genome-scale CRISPR knockout screen for host factors essential for viral replication. We show that BEND6 exhibits characteristics of an interferon-stimulated gene (ISG), with its mRNA and protein levels upregulated by RNA virus-induced IFN-β. BEND6 targets IRF3 and inhibits its recruitment by TBK1, thus preventing IRF3 phosphorylation and dimerization. Additionally, BEND6 directly binds to ISRE, thereby hindering the DNA binding activity of IRF3 and blocking the subsequent activation of IFN-β transcription. Taken together, our study reveals the mechanism of BEND6 in promoting the replication of various RNA viruses and provides a potential therapeutic target for RNA virus infection.</p>","PeriodicalId":21576,"journal":{"name":"Science China Life Sciences","volume":" ","pages":"1073-1083"},"PeriodicalIF":8.0,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143010866","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Regulation and application of m6A modification in tumor immunity. m6A修饰在肿瘤免疫中的调控及应用。
IF 8 2区 生物学 Q1 BIOLOGY Pub Date : 2025-04-01 Epub Date: 2024-12-06 DOI: 10.1007/s11427-024-2648-0
Qunli Xiong, Yaguang Zhang, Ying Zheng, Qing Zhu

The m6A modification is an RNA modification that impacts various processes of RNA molecules, including transcription, splicing, stability, and translation. Recently, researchers have discovered that the presence of m6A modification can influence the interaction between tumor cells and immune cells and also play a role in regulating the expression of immune response-related genes. Additionally, m6A modification is intricately involved in the regulation of tumor immune evasion and drug resistance. Specifically, certain tumor cells can manipulate the gene expression through m6A modification to evade immune system attacks. Therefore, it might be possible to enhance tumor immune surveillance and improve the effectiveness of immune-based therapies by manipulating m6A modification. This review systematically discusses the role of m6A modification in tumor immunity, specifically highlighting its regulation of immune cells and immune-related genes in tumor cells. Furthermore, we explore the potential of m6A modification inhibitors as anti-cancer therapies and the significance of m6A regulatory factors in predicting the efficacy of tumor immune therapy.

m6A修饰是一种影响RNA分子转录、剪接、稳定性和翻译等多种过程的RNA修饰。最近,研究人员发现m6A修饰的存在可以影响肿瘤细胞与免疫细胞的相互作用,还可以调节免疫反应相关基因的表达。此外,m6A修饰复杂地参与肿瘤免疫逃避和耐药的调控。具体来说,某些肿瘤细胞可以通过m6A修饰来操纵基因表达以逃避免疫系统的攻击。因此,通过操纵m6A修饰来增强肿瘤免疫监测和提高免疫治疗的有效性是可能的。本文系统讨论了m6A修饰在肿瘤免疫中的作用,重点介绍了其对肿瘤细胞免疫细胞和免疫相关基因的调控。此外,我们还探讨了m6A修饰抑制剂作为抗癌药物的潜力,以及m6A调节因子在预测肿瘤免疫治疗疗效中的意义。
{"title":"Regulation and application of m<sup>6</sup>A modification in tumor immunity.","authors":"Qunli Xiong, Yaguang Zhang, Ying Zheng, Qing Zhu","doi":"10.1007/s11427-024-2648-0","DOIUrl":"10.1007/s11427-024-2648-0","url":null,"abstract":"<p><p>The m<sup>6</sup>A modification is an RNA modification that impacts various processes of RNA molecules, including transcription, splicing, stability, and translation. Recently, researchers have discovered that the presence of m<sup>6</sup>A modification can influence the interaction between tumor cells and immune cells and also play a role in regulating the expression of immune response-related genes. Additionally, m<sup>6</sup>A modification is intricately involved in the regulation of tumor immune evasion and drug resistance. Specifically, certain tumor cells can manipulate the gene expression through m<sup>6</sup>A modification to evade immune system attacks. Therefore, it might be possible to enhance tumor immune surveillance and improve the effectiveness of immune-based therapies by manipulating m<sup>6</sup>A modification. This review systematically discusses the role of m<sup>6</sup>A modification in tumor immunity, specifically highlighting its regulation of immune cells and immune-related genes in tumor cells. Furthermore, we explore the potential of m<sup>6</sup>A modification inhibitors as anti-cancer therapies and the significance of m<sup>6</sup>A regulatory factors in predicting the efficacy of tumor immune therapy.</p>","PeriodicalId":21576,"journal":{"name":"Science China Life Sciences","volume":" ","pages":"974-993"},"PeriodicalIF":8.0,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142795106","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Bioactive materials from berberine-treated human bone marrow mesenchymal stem cells accelerate tooth extraction socket healing through the jaw vascular unit. 小檗碱处理的人骨髓间充质干细胞的生物活性物质通过颌骨血管单元加速拔牙槽愈合。
IF 8 2区 生物学 Q1 BIOLOGY Pub Date : 2025-04-01 Epub Date: 2025-01-13 DOI: 10.1007/s11427-024-2745-2
Ruyu Wang, Tianxiao Wang, Ziyu Chen, Jiandong Jiang, Yifei Du, Hua Yuan, Yongchu Pan, Yuli Wang

Delayed tooth extraction socket (TES) healing can cause failure of subsequent oral implantation and increase socioeconomic burden on patients. Excessive amounts of M1 macrophages, apoptotic neutrophils (ANs), and neutrophil extracellular traps (NETs) impair alveolar bone regeneration during TES healing. In the present study, we first discovered that conditioned medium (CM) collected from berberine-treated human bone marrow mesenchymal stem cells (BBR-HB-CM) accelerated TES healing. BBR-HB-CM contained bioactive materials that promoted the polarization of macrophages from M1 to M2, impeded the formation of ANs and NETs, and modulated M2 macrophage efferocytosis in vivo and in vitro. Mechanistically, BBR-HB-CM promoted bone formation by inhibiting macrophage-myofibroblast transition and reprogrammed macrophage polarization through p85/AKT/mTOR pathway-dependent autophagy. The 3-methyladenine abolished the therapeutic effects of BBR-HB-CM. Further studies revealed that BBR-HB-CM accelerated TES healing in rats with type 2 diabetes mellitus. Overall, our results demonstrated that BBR-HB-CM had high potential to promote rapid TES healing.

拔牙槽区(TES)愈合延迟会导致后续种植失败,增加患者的社会经济负担。过量的M1巨噬细胞、凋亡中性粒细胞(ANs)和中性粒细胞细胞外陷阱(NETs)会损害TES愈合过程中的牙槽骨再生。在本研究中,我们首次发现从小檗碱处理的人骨髓间充质干细胞(BBR-HB-CM)中收集的条件培养基(CM)加速TES愈合。BBR-HB-CM所含的生物活性物质能促进巨噬细胞从M1向M2极化,阻碍ANs和NETs的形成,并在体内外调节M2巨噬细胞的efferocysis。从机制上讲,BBR-HB-CM通过p85/AKT/mTOR途径依赖的自噬抑制巨噬细胞-肌成纤维细胞转化和巨噬细胞极化重编程,从而促进骨形成。3-甲基腺嘌呤消除了BBR-HB-CM的治疗效果。进一步研究表明,BBR-HB-CM可加速2型糖尿病大鼠TES愈合。总体而言,我们的结果表明,BBR-HB-CM具有促进TES快速愈合的高潜力。
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引用次数: 0
Pilot work of the 10K Chinese People Genomic Diversity Project along the Silk Road suggests a complex east-west admixture landscape and biological adaptations.
IF 8 2区 生物学 Q1 BIOLOGY Pub Date : 2025-04-01 Epub Date: 2025-01-22 DOI: 10.1007/s11427-024-2748-4
Guanglin He, Hongbing Yao, Shuhan Duan, Lintao Luo, Qiuxia Sun, Renkuan Tang, Jing Chen, Zhiyong Wang, Yuntao Sun, Xiangping Li, Liping Hu, Libing Yun, Junbao Yang, Jiangwei Yan, Shengjie Nie, Yanfeng Zhu, Chuan-Chao Wang, Bing Liu, Lan Hu, Chao Liu, Mengge Wang

Genomic sources from China are underrepresented in the population-specific reference database. We performed whole-genome sequencing or genome-wide genotyping on 1,207 individuals from four linguistically diverse groups (1,081 Sinitic, 56 Mongolic, 40 Turkic, and 30 Tibeto-Burman people) living in North China included in the 10K Chinese People Genomic Diversity Project (10K_CPGDP) to characterize the genetic architecture and adaptative history of ethnic groups in the Silk Road Region of China. We observed a population split between Northwest Chinese minorities (NWCMs) and Han Chinese since the Upper Paleolithic and later Neolithic genetic differentiation within NWCMs. The observed population substructures among ethnically/linguistically diverse NWCMs suggested that differentiated admixture events contributed to the differences in their genomic and phenotypic diversity. We estimated that the Dongxiang, Tibetan, and Yugur people inherited more than 10% of the Western Eurasian ancestry, which is much greater than that of the Salar and Tu people (<7%), while Han neighbors showed less West Eurasian ancestry (∼1%-3%). Male-biased admixture introduced Western Eurasian ancestry in the Dongxiang, Tibetan, and Yugur populations. We found that the eastern-western admixture in NWCMs occurred ∼800-1,100 years ago, coinciding with intensive economic and cultural exchanges during the Tang and Song dynasties. Additionally, we identified the signatures of natural selection associated with cardiovascular system diseases or lipid metabolism and developmental/neurogenetic disorders. Moreover, the EPAS1 gene showed relatively high population branch statistic values in NWCMs. The well-fitted demographical models presented the vast landscape of complex admixture processes of the Silk Road people, and the newly reported functionally important variations suggested the importance of including ethnolinguistically diverse populations in Chinese genetic studies for uncovering the genetic basis of complex traits/diseases.

{"title":"Pilot work of the 10K Chinese People Genomic Diversity Project along the Silk Road suggests a complex east-west admixture landscape and biological adaptations.","authors":"Guanglin He, Hongbing Yao, Shuhan Duan, Lintao Luo, Qiuxia Sun, Renkuan Tang, Jing Chen, Zhiyong Wang, Yuntao Sun, Xiangping Li, Liping Hu, Libing Yun, Junbao Yang, Jiangwei Yan, Shengjie Nie, Yanfeng Zhu, Chuan-Chao Wang, Bing Liu, Lan Hu, Chao Liu, Mengge Wang","doi":"10.1007/s11427-024-2748-4","DOIUrl":"10.1007/s11427-024-2748-4","url":null,"abstract":"<p><p>Genomic sources from China are underrepresented in the population-specific reference database. We performed whole-genome sequencing or genome-wide genotyping on 1,207 individuals from four linguistically diverse groups (1,081 Sinitic, 56 Mongolic, 40 Turkic, and 30 Tibeto-Burman people) living in North China included in the 10K Chinese People Genomic Diversity Project (10K_CPGDP) to characterize the genetic architecture and adaptative history of ethnic groups in the Silk Road Region of China. We observed a population split between Northwest Chinese minorities (NWCMs) and Han Chinese since the Upper Paleolithic and later Neolithic genetic differentiation within NWCMs. The observed population substructures among ethnically/linguistically diverse NWCMs suggested that differentiated admixture events contributed to the differences in their genomic and phenotypic diversity. We estimated that the Dongxiang, Tibetan, and Yugur people inherited more than 10% of the Western Eurasian ancestry, which is much greater than that of the Salar and Tu people (<7%), while Han neighbors showed less West Eurasian ancestry (∼1%-3%). Male-biased admixture introduced Western Eurasian ancestry in the Dongxiang, Tibetan, and Yugur populations. We found that the eastern-western admixture in NWCMs occurred ∼800-1,100 years ago, coinciding with intensive economic and cultural exchanges during the Tang and Song dynasties. Additionally, we identified the signatures of natural selection associated with cardiovascular system diseases or lipid metabolism and developmental/neurogenetic disorders. Moreover, the EPAS1 gene showed relatively high population branch statistic values in NWCMs. The well-fitted demographical models presented the vast landscape of complex admixture processes of the Silk Road people, and the newly reported functionally important variations suggested the importance of including ethnolinguistically diverse populations in Chinese genetic studies for uncovering the genetic basis of complex traits/diseases.</p>","PeriodicalId":21576,"journal":{"name":"Science China Life Sciences","volume":" ","pages":"914-933"},"PeriodicalIF":8.0,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143041557","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
A haplotype-resolved genome assembly of tetraploid Medicago sativa ssp. falcata. 四倍体紫花苜蓿单倍型分离基因组组装。falcata。
IF 8 2区 生物学 Q1 BIOLOGY Pub Date : 2025-04-01 Epub Date: 2024-12-20 DOI: 10.1007/s11427-024-2753-2
Wanying Li, Xuanzhao Li, Wei Li, Haibo Yang, Diandian Guo, Ting Guo, Yingying Meng, Qiang He, Hao Lin, Huilong Du, Lifang Niu
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引用次数: 0
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Science China Life Sciences
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