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Underlining the Molecular Mechanism of Nonalcoholic Fatty Liver Disease and Coronary Artery Disease in Lipid Metabolism by Combining Multiple Sets of Data Sets 结合多组数据揭示非酒精性脂肪性肝病和冠状动脉疾病在脂质代谢中的分子机制
IF 3.2 3区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-07-09 DOI: 10.1002/iub.70040
Wei Zheng, Shouhao Wang, Huafang Wang, Chengan Xu, Qiaoqiao Yin, Hua Di

Nonalcoholic fatty liver disease (NAFLD) is closely associated with coronary artery disease (CAD); however, their shared genetic traits and molecular mechanisms in lipid metabolism remain unclear. In this study, we identified that the differentially expressed genes in NAFLD and CAD intersected with lipid metabolism genes to obtain three key genes—GPD1, MVK, and PIK3R2. Data from the GeneCards database indicated a significant correlation between NAFLD-related regulatory genes and the expression levels of these key genes. Notably, GPD1 showed a significant positive correlation with PNPLA3 (r = 0.715), while PIK3R2 exhibited a significant negative correlation with MIR21 (r = −0.691). Similarly, CAD regulatory genes were significantly correlated with the expression levels of these key genes; GPD1 showed a significant positive correlation with APOA1 (r = 0.751), and PIK3R2 had a significant negative correlation with LPA (r = −0.362). Additionally, single-cell sequencing analysis of NAFLD showed that GPD1, MVK, and PIK3R2 had higher activity in cells with a high expression of bile acid metabolism genes in the immune pathway. In CAD, GPD1 showed higher activity in cells with high oxidative phosphorylation in the immune pathway. Finally, we found that one drug interacted with MVK, while 38 drugs interacted with PIK3R2. This study highlights GPD1, MVK, and PIK3R2 as key genes involved in NAFLD, CAD, and lipid metabolism, suggesting potential targets for further mechanistic studies and novel therapeutic approaches for patients with NAFLD and CAD.

非酒精性脂肪肝(NAFLD)与冠状动脉疾病(CAD)密切相关;然而,它们在脂质代谢中的共同遗传特征和分子机制尚不清楚。在本研究中,我们发现NAFLD和CAD的差异表达基因与脂质代谢基因相交,得到三个关键基因——gpd1、MVK和PIK3R2。来自GeneCards数据库的数据表明,nafld相关调控基因与这些关键基因的表达水平之间存在显著相关性。值得注意的是,GPD1与PNPLA3呈显著正相关(r = 0.715), PIK3R2与MIR21呈显著负相关(r = - 0.691)。同样,CAD调节基因与这些关键基因的表达水平显著相关;GPD1与APOA1呈显著正相关(r = 0.751), PIK3R2与LPA呈显著负相关(r = - 0.362)。此外,NAFLD的单细胞测序分析显示,GPD1、MVK和PIK3R2在免疫通路中胆汁酸代谢基因高表达的细胞中具有更高的活性。在CAD中,GPD1在免疫通路中具有高氧化磷酸化的细胞中表现出更高的活性。最后,我们发现一种药物与MVK相互作用,而38种药物与PIK3R2相互作用。本研究强调GPD1, MVK和PIK3R2是参与NAFLD, CAD和脂质代谢的关键基因,为NAFLD和CAD患者的进一步机制研究和新的治疗方法提供了潜在的靶点。
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引用次数: 0
SPP1 Regulates SASP via the p53 Signaling Pathway to Affect ALI Progression SPP1通过p53信号通路调控SASP影响ALI进展
IF 3.2 3区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-06-29 DOI: 10.1002/iub.70038
Congcong Yuan, Shilong Zhao, Wentao Ma, Hongjun Na, Qiuyue Tan, Jing Gao

Acute lung injury (ALI) is a condition with acute respiratory failure caused by various factors, characterized by severe hypoxemia and diffuse alveolar damage, involving multiple cytokines and signaling pathways. This study investigates the role of secreted phosphoprotein 1 (SPP1) in ALI and explores its underlying mechanisms through a series of in vitro and in vivo experiments. Our results demonstrate that SPP1 expression is significantly upregulated in ALI animal models, correlating with increased oxidative stress and inflammatory responses. In LPS-induced lung injury models, elevated levels of malondialdehyde (MDA) and IL1β, along with decreased superoxide dismutase (SOD) levels, were observed, further confirming the active state of SPP1 in ALI. In vitro experiments using BEAS-2B cells revealed that LPS treatment increased IL1β and reactive oxygen species (ROS) levels while decreasing SOD levels, with concomitant upregulation of SPP1. SPP1 knockdown significantly inhibited these changes, directly confirming its regulatory role in ALI progression. We further explored the regulatory mechanisms of SPP1 on the senescence-associated secretory phenotype (SASP), a key pathological process in ALI. SA-β-GAL staining and γ-H2AX results indicated elevated cellular senescence in LPS-treated cells and ALI models. SPP1 knockdown reduced senescence markers, enhanced cell viability, decreased apoptosis, and improved cell proliferation capacity, suggesting that SPP1 promotes ALI via the SASP phenotype. Mechanistically, we found that SPP1 regulates ALI via the p53 signaling pathway. LPS treatment increased p-p53 levels, whereas SPP1 knockdown reduced p53 activation. The use of a p53 inhibitor further suppressed SASP and improved ALI-related indicators. Animal model validation corroborated these findings, showing that SPP1 knockdown and p53 inhibitor treatment reduced lung tissue damage and improved ALI-related indicators. Collectively, our study reveals a novel mechanism by which SPP1 regulates ALI progression via the p53 signaling pathway and SASP. This discovery not only enriches our understanding of ALI pathogenesis but also provides a new therapeutic target and potential intervention strategies for ALI treatment.

急性肺损伤(Acute lung injury, ALI)是由多种因素引起的急性呼吸衰竭,以严重低氧血症和弥漫性肺泡损伤为特征,涉及多种细胞因子和信号通路。本研究通过一系列体外和体内实验探讨了分泌磷酸化蛋白1 (SPP1)在ALI中的作用,并探讨了其潜在的机制。我们的研究结果表明,SPP1的表达在ALI动物模型中显著上调,与氧化应激和炎症反应的增加有关。在lps诱导的肺损伤模型中,观察到丙二醛(MDA)和il - 1β水平升高,超氧化物歧化酶(SOD)水平下降,进一步证实了ALI中SPP1的活性状态。BEAS-2B细胞的体外实验显示,LPS处理增加了il - 1β和活性氧(ROS)水平,降低了SOD水平,同时上调了SPP1。SPP1敲低显著抑制了这些变化,直接证实了其在ALI进展中的调节作用。我们进一步探讨了SPP1对衰老相关分泌表型(SASP)的调控机制,SASP是ALI的一个关键病理过程。SA-β-GAL染色和γ-H2AX结果显示lps处理的细胞和ALI模型的细胞衰老程度升高。SPP1敲低可降低衰老标志物,增强细胞活力,减少细胞凋亡,提高细胞增殖能力,表明SPP1通过SASP表型促进ALI。在机制上,我们发现SPP1通过p53信号通路调节ALI。LPS处理增加了p-p53水平,而SPP1敲低则降低了p53的激活。使用p53抑制剂进一步抑制SASP并改善ali相关指标。动物模型验证证实了这些发现,表明SPP1敲除和p53抑制剂治疗减轻了肺组织损伤,改善了ali相关指标。总之,我们的研究揭示了SPP1通过p53信号通路和SASP调控ALI进展的新机制。这一发现不仅丰富了我们对ALI发病机制的认识,而且为ALI的治疗提供了新的治疗靶点和潜在的干预策略。
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引用次数: 0
Fungi and Myxomycetes of the Tehuacán-Cuicatlán Biosphere Reserve, Mexico: A Comprehensive Review and Future Perspectives 墨西哥Tehuacán-Cuicatlán生物圈保护区的真菌和黏菌:综合回顾和未来展望
IF 3.2 3区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-06-20 DOI: 10.1002/iub.70034
Julio Mena-Portales, Yordanis Pérez-Llano, Marco Antonio Vásquez-Dávila, Taimy Cantillo, Gladys Isabel Manzanero-Medina, María del Rayo Sánchez-Carbente, Ramón Alberto Batista-García

The Tehuacán-Cuicatlán Biosphere Reserve in Mexico, spanning approximately 10,000 km2, is crucial for conserving arid and semi-arid ecosystems, as it hosts unique endemic species and complex ecological interactions. Despite their environmental significance, fungi and myxomycetes in this region have been understudied, particularly those adapted to extreme conditions. These organisms are vital for nutrient cycling, soil stability, and plant health, making them excellent bioindicators for monitoring ecosystem health and detecting environmental changes. However, challenges such as limited historical data, remote fieldwork, and advanced identification techniques complicate their study. Based on a review of mycological literature and various biodiversity databases, the first inventory of fungi and myxomycetes of the Tehuacán-Cuicatlán Biosphere Reserve (Tehuacán Desert) was prepared in this work. This inventory lists 436 taxa of organisms traditionally identified as fungi, belonging to 254 different genera. Of these, 266 taxa belong to 214 genera of fungi sensu stricto, and 170 taxa from 40 genera of myxomycetes. Fungal and myxomycete communities must be documented, and their inherent variability understood through baseline research. Research on fungal adaptation to shifting environments in the Tehuacán Valley may reveal resilience mechanisms in desert ecosystems. Fungi and myxomycetes are useful bioindicators for assessing ecosystem health and ecological alterations under global climate stress, due to their rapid environmental response. Understanding these adaptive strategies helps preserve the environment, produce new drugs, and foster agricultural resilience. Polyextremotolerant and extremophilic fungi are studied in the reserve to understand the boundaries of life and survival processes. To use fungi to protect sensitive ecosystems and mitigate climate change in the Tehuacán-Cuicatlán Biosphere Reserve, interdisciplinary collaboration and innovative methods are needed. The Tehuacán Desert can be considered a natural laboratory for studying polyextremotolerant and extremophilic fungi.

墨西哥的Tehuacán-Cuicatlán生物圈保护区占地约1万平方公里,因其拥有独特的特有物种和复杂的生态相互作用,对保护干旱和半干旱生态系统至关重要。尽管真菌和黏菌具有重要的环境意义,但对该地区的真菌和黏菌,特别是那些适应极端条件的真菌和黏菌的研究还不够充分。这些生物对养分循环、土壤稳定和植物健康至关重要,是监测生态系统健康和检测环境变化的优秀生物指标。然而,有限的历史数据、远程现场工作和先进的识别技术等挑战使他们的研究复杂化。本文在查阅真菌学文献和各种生物多样性数据库的基础上,编制了Tehuacán-Cuicatlán生物圈保护区(Tehuacán Desert)真菌和黏菌的第一次清查。该目录列出了436个传统上被确定为真菌的生物分类群,属于254个不同的属。其中,严格感真菌214属266个分类群,黏菌40属170个分类群。必须记录真菌和黏菌群落,并通过基线研究了解其固有的可变性。研究真菌对Tehuacán山谷变化环境的适应可能揭示沙漠生态系统的恢复机制。真菌和黏菌因其快速的环境响应而成为评估全球气候胁迫下生态系统健康和生态变化的有用生物指标。了解这些适应性策略有助于保护环境、生产新药和促进农业恢复力。在保护区研究了多极端耐受性和嗜极性真菌,以了解生命和生存过程的边界。利用真菌保护Tehuacán-Cuicatlán生物圈保护区的敏感生态系统和减缓气候变化,需要跨学科合作和创新方法。Tehuacán沙漠可以被认为是研究多极端耐受性和嗜极端真菌的天然实验室。
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引用次数: 0
Single-Cell Profiling of the Microenvironment in High-Risk Neuroblastoma 高危神经母细胞瘤微环境的单细胞分析
IF 3.2 3区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-06-19 DOI: 10.1002/iub.70029
Yuxuan Xu, Jinsheng Ding, Zhenyu Shi, Li Bao

Although tumor biology and treatment of neuroblastoma (NB) have substantially advanced, the clinical outcomes of patients with high-risk NB (HR-NB) still remain unsatisfactory. Increasing evidence suggests that targeting the tumor microenvironment (TME) is an effective strategy for the treatment of patients with HR-NB, highlighting the necessity to deepen the understanding of the complex TME in HR-NB. We analyzed the single-cell RNA sequencing data of 16 NB samples from 11 patients with HR-NB and 5 patients with intermediate-/low-risk NB. We found that proliferating CD8+ TUBA1B+ T cells, H2AFZ+ macrophages, and proliferating HMGB2+ B cells were particularly enriched in HR-NB samples and played an immunosuppressive role. LAG3 and HAVCR2 could serve as potential immunotherapeutic targets for HR-NB. SCENIC analysis innovatively revealed that proliferating HMGB2+ B cells had a special differentiation process compared with that of plasma cells. H2AFZ+ macrophages evolved from monocytes and M1-like macrophages and exhibited an M2-like phenotype. HR-NB-enriched cancer-associated fibroblasts and endothelial cells were related to tumor migration and progression. An immune-related risk model based on five genes (BIRC5, UBE2C, CDKN3, TK1, and PTTG1) was constructed in the training set and applied to the validation set. Both sets showed a promising clinical prediction value. In sum, this study preliminarily revealed the landscape of the TME in HR-NB at a single-cell level; several TME cell clusters that could inhibit immune activities or promote tumor progression in HR-NB were determined, thereby providing novel immunotherapeutic targets and an immune-related prognostic signature for HR-NB and promoting the development of immunotherapy of HR-NB.

尽管肿瘤生物学和神经母细胞瘤(NB)的治疗有了长足的进步,但高危NB (HR-NB)患者的临床结果仍然令人不满意。越来越多的证据表明,靶向肿瘤微环境(tumor microenvironment, TME)是治疗HR-NB患者的有效策略,这凸显了对HR-NB中复杂TME的深入了解的必要性。我们分析了来自11例HR-NB患者和5例中/低危NB患者的16份NB样本的单细胞RNA测序数据。我们发现增殖的CD8+ TUBA1B+ T细胞、H2AFZ+巨噬细胞和HMGB2+ B细胞在HR-NB样品中特别富集,并发挥免疫抑制作用。LAG3和HAVCR2可作为HR-NB的潜在免疫治疗靶点。SCENIC分析创新性地揭示了增殖的HMGB2+ B细胞与浆细胞相比具有特殊的分化过程。H2AFZ+巨噬细胞由单核细胞和m1样巨噬细胞进化而来,表现出m2样表型。富含hr - nb的癌相关成纤维细胞和内皮细胞与肿瘤的迁移和进展有关。在训练集中构建基于BIRC5、UBE2C、CDKN3、TK1、PTTG1 5个基因的免疫相关风险模型,并应用于验证集中。两组均具有良好的临床预测价值。综上所述,本研究初步揭示了HR-NB在单细胞水平上的TME格局;确定了几个可抑制HR-NB免疫活性或促进肿瘤进展的TME细胞簇,从而为HR-NB提供了新的免疫治疗靶点和免疫相关预后标志,促进了HR-NB免疫治疗的发展。
{"title":"Single-Cell Profiling of the Microenvironment in High-Risk Neuroblastoma","authors":"Yuxuan Xu,&nbsp;Jinsheng Ding,&nbsp;Zhenyu Shi,&nbsp;Li Bao","doi":"10.1002/iub.70029","DOIUrl":"10.1002/iub.70029","url":null,"abstract":"<div>\u0000 \u0000 <p>Although tumor biology and treatment of neuroblastoma (NB) have substantially advanced, the clinical outcomes of patients with high-risk NB (HR-NB) still remain unsatisfactory. Increasing evidence suggests that targeting the tumor microenvironment (TME) is an effective strategy for the treatment of patients with HR-NB, highlighting the necessity to deepen the understanding of the complex TME in HR-NB. We analyzed the single-cell RNA sequencing data of 16 NB samples from 11 patients with HR-NB and 5 patients with intermediate-/low-risk NB. We found that proliferating CD8+ <i>TUBA1B</i>+ T cells, <i>H2AFZ</i>+ macrophages, and proliferating <i>HMGB2</i>+ B cells were particularly enriched in HR-NB samples and played an immunosuppressive role. <i>LAG3</i> and <i>HAVCR2</i> could serve as potential immunotherapeutic targets for HR-NB. SCENIC analysis innovatively revealed that proliferating <i>HMGB2</i>+ B cells had a special differentiation process compared with that of plasma cells. <i>H2AFZ</i>+ macrophages evolved from monocytes and M1-like macrophages and exhibited an M2-like phenotype. HR-NB-enriched cancer-associated fibroblasts and endothelial cells were related to tumor migration and progression. An immune-related risk model based on five genes (<i>BIRC5</i>, <i>UBE2C</i>, <i>CDKN3</i>, <i>TK1</i>, and <i>PTTG1</i>) was constructed in the training set and applied to the validation set. Both sets showed a promising clinical prediction value. In sum, this study preliminarily revealed the landscape of the TME in HR-NB at a single-cell level; several TME cell clusters that could inhibit immune activities or promote tumor progression in HR-NB were determined, thereby providing novel immunotherapeutic targets and an immune-related prognostic signature for HR-NB and promoting the development of immunotherapy of HR-NB.</p>\u0000 </div>","PeriodicalId":14728,"journal":{"name":"IUBMB Life","volume":"77 6","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144315048","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
Modulation of PPAR-α and PPAR-γ Influences Cardiomyocyte Growth and Cardiac Remodeling PPAR-α和PPAR-γ调控心肌细胞生长和心脏重构
IF 3.2 3区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-06-19 DOI: 10.1002/iub.70035
Qinkao Xuan, Jin Li, Zexiong Feng, Li Zhu, Tingbo Jiang, Hongxia Li, Ming Liu, Xiaodong Qian, Xiao Ma

Peroxisome proliferator–activated receptors (PPARs), particularly PPAR-α and PPAR-γ, are key regulators of cardiac energy metabolism and have been implicated in cardiac remodeling. However, their roles in cardiomyocyte proliferation and hypertrophy remain incompletely understood. In this study, we investigated the effects of PPAR-α and PPAR-γ modulation on neonatal rat cardiomyocytes (NRCMs) using pharmacological agonists (WY-14643 for PPAR-α and pioglitazone for PPAR-γ) and inhibitors (MK-886 for PPAR-α and GW9662 for PPAR-γ), as well as siRNA-mediated knockdown approaches. Cardiomyocyte proliferation and hypertrophy were assessed by immunofluorescence, cell size measurements, and proliferation assays. Our findings demonstrate that PPAR-α activation significantly promotes cardiomyocyte proliferation and reduces hypertrophy, whereas PPAR-α inhibition induces hypertrophic changes and suppresses proliferation. Similarly, PPAR-γ activation enhances both proliferation and hypertrophy of cardiomyocytes, suggesting its involvement in physiological hypertrophy and a potential protective role in pathological remodeling. In contrast, pharmacological activation or genetic inhibition of PPAR-δ showed no significant effects on cardiomyocyte proliferation or hypertrophy, highlighting its distinct role in metabolic homeostasis rather than structural remodeling. PPAR-α and PPAR-γ play distinct but complementary roles in regulating cardiomyocyte proliferation and hypertrophy. These results suggest that targeting PPAR-α and PPAR-γ may represent promising therapeutic strategies for cardiac hypertrophy and heart failure. Further in vivo studies are warranted to clarify their molecular mechanisms and potential clinical applications.

过氧化物酶体增殖物激活受体(PPAR),特别是PPAR-α和PPAR-γ,是心脏能量代谢的关键调节因子,并与心脏重塑有关。然而,它们在心肌细胞增殖和肥厚中的作用仍不完全清楚。在这项研究中,我们使用药理学激动剂(PPAR-α的y -14643和PPAR-γ的吡格列酮)和抑制剂(PPAR-α的MK-886和PPAR-γ的GW9662)以及sirna介导的敲低方法研究了PPAR-α和PPAR-γ调节对新生大鼠心肌细胞(NRCMs)的影响。通过免疫荧光、细胞大小测量和增殖试验评估心肌细胞增殖和肥厚。我们的研究结果表明,PPAR-α激活可显著促进心肌细胞增殖并减少肥厚,而PPAR-α抑制可诱导肥厚变化并抑制增殖。同样,PPAR-γ激活可增强心肌细胞的增殖和肥厚,提示其参与生理性肥厚并在病理性重构中发挥潜在的保护作用。相比之下,药理激活或基因抑制PPAR-δ对心肌细胞增殖或肥厚没有显著影响,这表明PPAR-δ在代谢稳态而非结构重塑中发挥着独特的作用。PPAR-α和PPAR-γ在调节心肌细胞增殖和肥厚中发挥着不同但互补的作用。这些结果表明,靶向PPAR-α和PPAR-γ可能是治疗心脏肥厚和心力衰竭的有希望的治疗策略。需要进一步的体内研究来阐明其分子机制和潜在的临床应用。
{"title":"Modulation of PPAR-α and PPAR-γ Influences Cardiomyocyte Growth and Cardiac Remodeling","authors":"Qinkao Xuan,&nbsp;Jin Li,&nbsp;Zexiong Feng,&nbsp;Li Zhu,&nbsp;Tingbo Jiang,&nbsp;Hongxia Li,&nbsp;Ming Liu,&nbsp;Xiaodong Qian,&nbsp;Xiao Ma","doi":"10.1002/iub.70035","DOIUrl":"10.1002/iub.70035","url":null,"abstract":"<div>\u0000 \u0000 <p>Peroxisome proliferator–activated receptors (PPARs), particularly PPAR-α and PPAR-γ, are key regulators of cardiac energy metabolism and have been implicated in cardiac remodeling. However, their roles in cardiomyocyte proliferation and hypertrophy remain incompletely understood. In this study, we investigated the effects of PPAR-α and PPAR-γ modulation on neonatal rat cardiomyocytes (NRCMs) using pharmacological agonists (WY-14643 for PPAR-α and pioglitazone for PPAR-γ) and inhibitors (MK-886 for PPAR-α and GW9662 for PPAR-γ), as well as siRNA-mediated knockdown approaches. Cardiomyocyte proliferation and hypertrophy were assessed by immunofluorescence, cell size measurements, and proliferation assays. Our findings demonstrate that PPAR-α activation significantly promotes cardiomyocyte proliferation and reduces hypertrophy, whereas PPAR-α inhibition induces hypertrophic changes and suppresses proliferation. Similarly, PPAR-γ activation enhances both proliferation and hypertrophy of cardiomyocytes, suggesting its involvement in physiological hypertrophy and a potential protective role in pathological remodeling. In contrast, pharmacological activation or genetic inhibition of PPAR-δ showed no significant effects on cardiomyocyte proliferation or hypertrophy, highlighting its distinct role in metabolic homeostasis rather than structural remodeling. PPAR-α and PPAR-γ play distinct but complementary roles in regulating cardiomyocyte proliferation and hypertrophy. These results suggest that targeting PPAR-α and PPAR-γ may represent promising therapeutic strategies for cardiac hypertrophy and heart failure. Further in vivo studies are warranted to clarify their molecular mechanisms and potential clinical applications.</p>\u0000 </div>","PeriodicalId":14728,"journal":{"name":"IUBMB Life","volume":"77 6","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144315047","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
Euryhaline Black Yeasts From the Arabian Gulf: Descriptions of Salinomyces qatarensis sp. nov. and Hortaea werneckii Genotypic Variations 来自阿拉伯海湾的广盐黑酵母:卡塔仑盐菌sp. 11 .和Hortaea werneckii基因型变异的描述
IF 3.2 3区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-06-18 DOI: 10.1002/iub.70026
Rashmi Fotedar, Polona Zalar, Amina Al Malaki, Aisha Al Zeyara, Ridhima Kaul, Anna Kolecka, Jack W. Fell, Teun Boekhout, Nina Gunde-Cimerman

The Arabian Gulf surrounding Qatar is an oligotrophic marine environment characterized by extreme conditions, such as increased water temperatures and high salinity compared to other semi-enclosed seas, such as the Mediterranean Sea. Thirty-six black yeast-like isolates were obtained from marine waters surrounding Qatar, representing 4% of all isolated yeasts. DNA sequence analysis of the internal transcribed spacers (ITS1, ITS2), the 5.8S rRNA gene, and the D1/D2 domains of the LSU rDNA identified 20 isolates as Hortaea werneckii, and 15 (75%) of them represent previously unknown genotypes with a wide NaCl tolerance at 37°C. In addition, 16 meristematic black yeast-like cultures were isolated that grew as multi-cellular bodies and reproduced by endoconidiation. Phylogenetic analysis based on the D1/D2 domains of LSU rDNA, partial sequences of the second largest subunit of RNA polymerase II (RPB2) and translation elongation factor 1-alpha (TEF) of selected representative strains of Dothideomycetes and of morphologically similar taxa, Pseudotaeniolina globosa and Trimmatostroma salinum, supported the proposal of meristematic black yeast-like cultures as a new species, Salinomyces qatarensis sp. nov., within Teratosphaeriaceae, Mycosphaerellales. The holotype is designated as CBS 150510, with ex-type strains EXF-15246 and QCC/Y38/18, and the species is registered in Mycobank as MB#848869. In addition, based on the above molecular analysis, a new combination was proposed for an euryhaline fungus from Mediterranean salterns, Trimmatostroma salinum, into the genus Verrucocladosporium as V. salinum, MB#856063. This study increases our knowledge of the distribution and genetic diversity of Hortaea werneckii, the etiological agent of tinea nigra. In addition, the description of S. qatarensis and the combination of euryhaline T. salinum to Verrucocladosporium provides support for halotolerance as one of the traits in Dothideomycetes.

卡塔尔周围的阿拉伯湾是一个贫营养的海洋环境,其特点是极端的条件,如水温升高和高盐度,与其他半封闭的海洋相比,如地中海。从卡塔尔周围的海水中获得了36个黑色酵母样分离株,占所有分离酵母的4%。对20株Hortaea werneckii的内部转录间隔区(ITS1、ITS2)、5.8S rRNA基因和LSU rDNA的D1/D2结构域进行DNA序列分析,鉴定为Hortaea werneckii,其中15株(75%)为以前未知的基因型,在37°C下具有较宽的耐盐性。此外,还分离出16个分生的黑色酵母样培养物,它们以多细胞体的形式生长,并通过内分生繁殖。对Dothideomycetes代表菌株和形态相似的分类群Pseudotaeniolina globosa和Trimmatostroma salinum的LSU rDNA D1/D2结构域、RNA聚合酶II第二大亚基(RPB2)和翻译伸长因子1- α (TEF)的部分序列进行系统发育分析,支持分生黑色酵母样培养物Salinomyces qatarensis sp. nov.作为teratosphaeriiaceae Mycosphaerellales中的新种的建议。该菌株全型编号为CBS 150510,前型菌株为EXF-15246和QCC/Y38/18,菌种在Mycobank注册编号为mb# 848869。此外,在上述分子分析的基础上,提出了地中海盐碱菌Trimmatostroma salinum的新组合,将其纳入Verrucocladosporium属,称为V. salinum, MB#856063。本研究增加了我们对黑癣病原Hortaea werneckii的分布和遗传多样性的认识。此外,对qatarensis的描述以及对Verrucocladosporium的广盐T. salinum的组合也支持了嗜盐性是dothideomycates的性状之一。
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引用次数: 0
Squalene: A High-Value Compound for COVID-19 Vaccine Adjuvants and Beyond Pathways, Production Strategies, and Market Potential 角鲨烯:一种用于COVID-19疫苗佐剂的高价值化合物及其途径、生产策略和市场潜力
IF 3.2 3区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-06-18 DOI: 10.1002/iub.70032
Dileep Dasari, Reeta Rani Singhania, Shashi Kant Bhatia, Cheng-Di Dong, Anil Kumar Patel

Squalene, a naturally occurring triterpene, has gained significant attention due to its critical role as an adjuvant in COVID-19 vaccines and its broad applications in pharmaceuticals, cosmetics, and nutraceuticals. This review explores the potential of squalene production, prompting a shift toward sustainable and innovative approaches. Key biosynthetic pathways across various organisms, including plants, fungi, and microalgae, are analyzed to identify efficient production systems as compared to fast-growing heterotrophic thraustochytrids. Advanced strategies to enhance squalene yields are explored, including the use of chemical enhancers (methyl jasmonate), antioxidants (alpha-tocopherol), cofactor recycling, and squalene epoxidase inhibitors (terbinafine). Additionally, the global market potential of squalene is assessed, highlighting its economic importance and growing demand in the healthcare and cosmetic industries. The challenges of large-scale squalene production are addressed with a focus on sustainable alternatives to shark-derived sources as a high ethical concern. By aligning with Sustainable Development Goals (SDG-3: Good Health and Well-Being), squalene production supports advancements in vaccine development and biotechnological innovations. Future opportunities are highlighted, including novel applications in cancer therapy, functional foods, and anti-aging products, offering pathways to harness its full potential while contributing to a sustainable bioeconomy.

角鲨烯是一种天然存在的三萜,由于其在COVID-19疫苗中作为佐剂的关键作用以及在药品、化妆品和营养保健品中的广泛应用,引起了极大的关注。这篇综述探讨了角鲨烯生产的潜力,促使转向可持续和创新的方法。通过分析包括植物、真菌和微藻在内的各种生物的关键生物合成途径,以确定与快速生长的异养水蚤相比有效的生产系统。探讨了提高角鲨烯产量的先进策略,包括化学增强剂(茉莉酸甲酯)、抗氧化剂(α -生育酚)、辅助因子回收和角鲨烯环氧化酶抑制剂(特比萘芬)的使用。此外,评估了角鲨烯的全球市场潜力,强调了其经济重要性和医疗保健和化妆品行业日益增长的需求。大规模角鲨烯生产的挑战是通过关注鲨鱼来源的可持续替代品来解决的,这是一个高度的道德问题。通过与可持续发展目标(可持续发展目标3:良好健康和福祉)保持一致,角鲨烯生产支持疫苗开发和生物技术创新的进步。强调了未来的机会,包括在癌症治疗,功能食品和抗衰老产品中的新应用,提供了充分利用其潜力的途径,同时为可持续的生物经济做出贡献。
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引用次数: 0
Nonsense Mutations in Rare and Ultra-Rare Human Disorders: An Overview 罕见和超罕见人类疾病的无义突变:综述
IF 3.2 3区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-06-06 DOI: 10.1002/iub.70031
Emanuele Vitale, Davide Ricci, Federica Corrao, Ignazio Fiduccia, Ilenia Cruciata, Pietro Salvatore Carollo, Alessio Branchini, Laura Lentini, Ivana Pibiri

Over 7000 rare diseases have been described, collectively affecting 350 million people worldwide. Most of these conditions result from nonsense mutations, representing approximately 10% of all genetic mutations associated with human inherited diseases. Nonsense mutations convert a sense codon into a premature termination codon (PTC), leading to premature translation termination and the production of truncated, nonfunctional proteins. This results in a loss-of-function phenotype in many genetic disorders, contributing to the disease's severity and progression. The molecular mechanisms of PTC formation involve various genetic alterations, including single-nucleotide changes, frameshifts, and splicing mutations. The nonsense-mediated mRNA decay (NMD) pathway degrades mRNAs containing premature termination codons (PTCs). In contrast, 25% of PTC mRNAs, depending on the PTC position and cellular context, can evade NMD, resulting in the synthesis of truncated proteins. A termination codon during translation is essential for proper protein synthesis, and translational readthrough—a process in which the ribosome bypasses the PTC and reaches the natural stop codon—may restore some level of protein function. The effectiveness of readthrough depends on the surrounding genetic context and the type of amino acid incorporated at the PTC position. This review aims to explore the molecular characteristics of nonsense-related diseases (NRDs), including cystic fibrosis, hemophilia, Fabry disease, choroideremia, Usher syndrome, Shwachman-Diamond syndrome, and certain hereditary neuropathies and cancers.

目前已发现7000多种罕见疾病,影响到全世界3.5亿人。这些疾病大多由无义突变引起,约占与人类遗传疾病相关的所有基因突变的10%。无义突变将一个有义密码子转化为一个过早终止密码子(PTC),导致翻译过早终止和产生截断的无功能蛋白质。这导致许多遗传疾病的功能丧失表型,导致疾病的严重程度和进展。PTC形成的分子机制涉及多种遗传改变,包括单核苷酸改变、帧移位和剪接突变。无义介导的mRNA衰变(NMD)途径降解含有过早终止密码子(ptc)的mRNA。相比之下,25%的PTC mrna,取决于PTC的位置和细胞环境,可以逃避NMD,导致截断蛋白的合成。翻译过程中的终止密码子对于正确的蛋白质合成是必不可少的,而翻译读透-核糖体绕过PTC并到达自然终止密码子的过程-可能会恢复某种程度的蛋白质功能。读透的有效性取决于周围的遗传环境和在PTC位置结合的氨基酸类型。本文旨在探讨无意义相关疾病(nrd)的分子特征,包括囊性纤维化、血友病、Fabry病、脉络膜血症、Usher综合征、Shwachman-Diamond综合征以及某些遗传性神经病变和癌症。
{"title":"Nonsense Mutations in Rare and Ultra-Rare Human Disorders: An Overview","authors":"Emanuele Vitale,&nbsp;Davide Ricci,&nbsp;Federica Corrao,&nbsp;Ignazio Fiduccia,&nbsp;Ilenia Cruciata,&nbsp;Pietro Salvatore Carollo,&nbsp;Alessio Branchini,&nbsp;Laura Lentini,&nbsp;Ivana Pibiri","doi":"10.1002/iub.70031","DOIUrl":"10.1002/iub.70031","url":null,"abstract":"<p>Over 7000 rare diseases have been described, collectively affecting 350 million people worldwide. Most of these conditions result from nonsense mutations, representing approximately 10% of all genetic mutations associated with human inherited diseases. Nonsense mutations convert a sense codon into a premature termination codon (PTC), leading to premature translation termination and the production of truncated, nonfunctional proteins. This results in a loss-of-function phenotype in many genetic disorders, contributing to the disease's severity and progression. The molecular mechanisms of PTC formation involve various genetic alterations, including single-nucleotide changes, frameshifts, and splicing mutations. The nonsense-mediated mRNA decay (NMD) pathway degrades mRNAs containing premature termination codons (PTCs). In contrast, 25% of PTC mRNAs, depending on the PTC position and cellular context, can evade NMD, resulting in the synthesis of truncated proteins. A termination codon during translation is essential for proper protein synthesis, and translational readthrough—a process in which the ribosome bypasses the PTC and reaches the natural stop codon—may restore some level of protein function. The effectiveness of readthrough depends on the surrounding genetic context and the type of amino acid incorporated at the PTC position. This review aims to explore the molecular characteristics of nonsense-related diseases (NRDs), including cystic fibrosis, hemophilia, Fabry disease, choroideremia, Usher syndrome, Shwachman-Diamond syndrome, and certain hereditary neuropathies and cancers.</p>","PeriodicalId":14728,"journal":{"name":"IUBMB Life","volume":"77 6","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/iub.70031","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144219913","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Tyrosine and Phenylalanine Activate Neuronal DNA Repair but Exhibit Opposing Effects on Global Transcription and Adult Female Mice Are Resilient to TyrRS/YARS1 Depletion 酪氨酸和苯丙氨酸激活神经元DNA修复,但在全球转录中表现出相反的作用,成年雌性小鼠对TyrRS/YARS1缺失具有弹性
IF 3.2 3区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-06-06 DOI: 10.1002/iub.70030
Megha Jhanji, Ashita Bhan, Colin Arrowood, Dina W. Yakout, Ankit Shroff, Danielle McManus, Henrietta Gifford, Janay Vacharasin, Sofia B. Lizarraga, Taras Y. Nazarko, Angela M. Mabb, Mathew Sajish

Serum tyrosine and phenylalanine levels increase during aging and age-associated disorders. We previously showed that tyrosyl-tRNA synthetase (TyrRS/YARS1) is reduced in Alzheimer's Disease (AD) brains, and tyrosine and phenylalanine decrease TyrRS in neurons. Here, we found that tau is a negative regulator, whereas estrogen and leucine act as positive regulators of TyrRS. Young female mice exhibit increased TyrRS in the cortex compared to male mice. Notably, young Tau knockout male, but not female mice showed increased cortical TyrRS. Tau accumulation in middle-aged female mice did not decrease cortical TyrRS compared to males, suggesting that middle-aged females are resilient to tau-mediated TyrRS depletion. Tyrosine and phenylalanine treatment decreased tubulin tyrosination, activated DNA repair pathways, and protected against etoposide (ETO) and camptothecin (CPT)-induced toxicity, respectively, in neurons. While tyrosine facilitated topoisomerase 1 (TOP1) recruitment to chromatin and inhibited global transcription, in contrast, phenylalanine recruited topoisomerase 2 beta (TOP2β) to chromatin and stimulated global transcription. Furthermore, tyrosine decreased the presence of DNA fragments in a comet assay whereas phenylalanine increased them. Addition of cis-resveratrol (cis-RSV) protected against tyrosine-induced transcription inhibition by facilitating the recruitment of both TOP1 and TOP2β to chromatin and increasing tubulin tyrosination. Moreover, cis-RSV decreased both total and phosphorylated tau and protected neurons against amyloid beta (Aβ)-induced neurite degeneration and DNA damage. Gene expression profiling using human embryonic stem cell (hESC)-derived neurons demonstrated that cis-RSV is a broad-spectrum neuroprotective and anti-viral agent. In contrast, trans-RSV mimics phenylalanine-induced gene expression, including downregulation of long genes and induction of an AD-like gene expression signature. This work suggests that age and disease-associated increases in serum tyrosine and phenylalanine levels would activate neuronal DNA repair while inhibiting transcription and tubulin tyrosination. cis-RSV protects against their toxicity by restoring tubulin tyrosination, TOP1 and TOP2β-mediated transcription, and decreasing tau in primary neurons.

血清酪氨酸和苯丙氨酸水平在衰老和与年龄相关的疾病中增加。我们之前的研究表明,酪氨酸- trna合成酶(TyrRS/YARS1)在阿尔茨海默病(AD)大脑中减少,酪氨酸和苯丙氨酸减少神经元中的TyrRS。在这里,我们发现tau是一个负调节因子,而雌激素和亮氨酸是TyrRS的正调节因子。与雄性小鼠相比,年轻雌性小鼠的皮层中TyrRS增加。值得注意的是,年轻的Tau基因敲除的雄性小鼠皮质TyrRS增加,而雌性小鼠则没有。与雄性小鼠相比,中年雌性小鼠的Tau积累并没有减少皮质TyrRS,这表明中年雌性小鼠对Tau介导的TyrRS耗竭具有弹性。酪氨酸和苯丙氨酸处理降低了微管蛋白酪氨酸化,激活了DNA修复途径,并分别保护神经元免受依托opo苷(ETO)和喜树碱(CPT)诱导的毒性。酪氨酸促进拓扑异构酶1 (TOP1)聚集到染色质上并抑制全局转录,而苯丙氨酸则促进拓扑异构酶2β (TOP2β)聚集到染色质上并刺激全局转录。此外,酪氨酸减少了彗星试验中DNA片段的存在,而苯丙氨酸增加了它们。顺式白藜芦醇(cis-resveratrol, cis-RSV)的加入通过促进染色质上TOP1和TOP2β的募集和增加微管蛋白酪氨酸化来保护酪氨酸诱导的转录抑制。此外,顺式rsv减少总tau蛋白和磷酸化tau蛋白,保护神经元免受β淀粉样蛋白(Aβ)诱导的神经突变性和DNA损伤。利用人胚胎干细胞(hESC)来源的神经元进行基因表达分析表明,顺式rsv是一种广谱神经保护和抗病毒药物。相反,反式rsv模拟苯丙氨酸诱导的基因表达,包括下调长基因和诱导ad样基因表达特征。这项工作表明,年龄和疾病相关的血清酪氨酸和苯丙氨酸水平的增加会激活神经元DNA修复,同时抑制转录和微管蛋白酪氨酸化。顺式rsv通过恢复微管蛋白酪氨酸化、TOP1和top2 β介导的转录以及减少原代神经元中的tau蛋白来保护它们免受毒性。
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引用次数: 0
Advancing Therapeutic Strategies for Nonsense-Related Diseases: From Small Molecules to Nucleic Acid-Based Innovations 推进无意义相关疾病的治疗策略:从小分子到基于核酸的创新
IF 3.2 3区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-05-27 DOI: 10.1002/iub.70027
Davide Ricci, Ilenia Cruciata, Ignazio Fiduccia, Emanuele Vitale, Federica Corrao, Alessio Branchini, Pietro Salvatore Carollo, Ivana Pibiri, Laura Lentini

Nonsense mutations in gene coding regions introduce an in-frame premature termination codon (PTC) in the mRNA transcript, resulting in the early termination of translation and the production of a truncated, nonfunctional protein. The absence of protein expression and the consequent loss of essential cellular functions are responsible for the severe phenotypes in the so-called genetic nonsense-related diseases (NRDs), such as cystic fibrosis, hemophilia, Duchenne muscular dystrophy, Fabry disease, Choroideremia, Usher syndrome, Shwachman–Diamond syndrome, and even certain types of cancer. Nonsense mutations pose a significant challenge in the treatment of NRDs, as a specific approach directly addressing this genetic defect is currently unavailable. Developing new therapeutic strategies for nonsense suppression is a crucial goal of precision medicine. This review describes some of the most promising therapeutic approaches and emerging strategies for treating NRDs. It considered both the use of small molecules to interfere with molecular mechanisms related to nonsense mutations, such as translational readthrough-inducing drugs (TRIDs) or inhibitors of the nonsense-mediated decay (NMD) pathway, and also innovative approaches involving nucleic acids, such as gene editing, anticodon engineered-tRNA (ACE-tRNA), or mRNA-based therapy. Future research should focus on refining these approaches and exploring integrated and personalized treatments to enhance therapeutic outcomes and ensure continuous improvement in the quality of care.

基因编码区的无义突变在mRNA转录物中引入帧内过早终止密码子(PTC),导致翻译的早期终止和产生截断的无功能蛋白质。蛋白质表达的缺失和随之而来的基本细胞功能的丧失是导致所谓的遗传性无意义相关疾病(NRDs)的严重表型的原因,如囊性纤维化、血友病、杜氏肌营养不良症、法布里病、脉膜血症、Usher综合征、Shwachman-Diamond综合征,甚至某些类型的癌症。无义突变对NRDs的治疗提出了重大挑战,因为目前还没有直接解决这种遗传缺陷的具体方法。开发新的无意义抑制治疗策略是精准医学的一个重要目标。本文综述了一些最有前途的治疗方法和新兴的NRDs治疗策略。它既考虑了使用小分子来干扰与无义突变相关的分子机制,如翻译读透诱导药物(TRIDs)或无义介导的衰变(NMD)途径的抑制剂,也考虑了涉及核酸的创新方法,如基因编辑、抗密码子工程trna (ACE-tRNA)或基于mrna的治疗。未来的研究应侧重于完善这些方法,探索综合和个性化的治疗方法,以提高治疗效果,确保护理质量的持续改善。
{"title":"Advancing Therapeutic Strategies for Nonsense-Related Diseases: From Small Molecules to Nucleic Acid-Based Innovations","authors":"Davide Ricci,&nbsp;Ilenia Cruciata,&nbsp;Ignazio Fiduccia,&nbsp;Emanuele Vitale,&nbsp;Federica Corrao,&nbsp;Alessio Branchini,&nbsp;Pietro Salvatore Carollo,&nbsp;Ivana Pibiri,&nbsp;Laura Lentini","doi":"10.1002/iub.70027","DOIUrl":"10.1002/iub.70027","url":null,"abstract":"<p>Nonsense mutations in gene coding regions introduce an in-frame premature termination codon (PTC) in the mRNA transcript, resulting in the early termination of translation and the production of a truncated, nonfunctional protein. The absence of protein expression and the consequent loss of essential cellular functions are responsible for the severe phenotypes in the so-called genetic nonsense-related diseases (NRDs), such as cystic fibrosis, hemophilia, Duchenne muscular dystrophy, Fabry disease, Choroideremia, Usher syndrome, Shwachman–Diamond syndrome, and even certain types of cancer. Nonsense mutations pose a significant challenge in the treatment of NRDs, as a specific approach directly addressing this genetic defect is currently unavailable. Developing new therapeutic strategies for nonsense suppression is a crucial goal of precision medicine. This review describes some of the most promising therapeutic approaches and emerging strategies for treating NRDs. It considered both the use of small molecules to interfere with molecular mechanisms related to nonsense mutations, such as translational readthrough-inducing drugs (TRIDs) or inhibitors of the nonsense-mediated decay (NMD) pathway, and also innovative approaches involving nucleic acids, such as gene editing, anticodon engineered-tRNA (ACE-tRNA), or mRNA-based therapy. Future research should focus on refining these approaches and exploring integrated and personalized treatments to enhance therapeutic outcomes and ensure continuous improvement in the quality of care.</p>","PeriodicalId":14728,"journal":{"name":"IUBMB Life","volume":"77 5","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-05-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/iub.70027","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144140486","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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