Pub Date : 2024-09-10DOI: 10.3389/fmolb.2024.1388476
Fuqiang Wang, Xiaoli Mei, Yunhao Yang, Hanlu Zhang, Zhiyang Li, Lei Zhu, Senyi Deng, Yun Wang
Myasthenia Gravis (MG) is a chronic autoimmune disease that primarily affects the neuromuscular junction, leading to muscle weakness in patients with this condition. Previous studies have identified several dysfunctions in thymus and peripheral blood mononuclear cells (PBMCs), such as the formation of ectopic germinal centers in the thymus and an imbalance of peripheral T helper cells and regulatory T cells, that contribute to the initiation and development of MG. Recent evidences suggest that noncoding RNA, including miRNA, lncRNA and circRNA may play a significant role in MG progression. Additionally, the network between these noncoding RNAs, such as the competing endogenous RNA regulatory network, has been found to be involved in MG progression. In this review, we summarized the roles of miRNA, lncRNA, and circRNA, highlighted their potential application as biomarkers in diagnosing MG, and discussed their potential regulatory networks in the abnormal thymus and PBMCs during MG development.
{"title":"Non-coding RNA and its network in the pathogenesis of Myasthenia Gravis","authors":"Fuqiang Wang, Xiaoli Mei, Yunhao Yang, Hanlu Zhang, Zhiyang Li, Lei Zhu, Senyi Deng, Yun Wang","doi":"10.3389/fmolb.2024.1388476","DOIUrl":"https://doi.org/10.3389/fmolb.2024.1388476","url":null,"abstract":"Myasthenia Gravis (MG) is a chronic autoimmune disease that primarily affects the neuromuscular junction, leading to muscle weakness in patients with this condition. Previous studies have identified several dysfunctions in thymus and peripheral blood mononuclear cells (PBMCs), such as the formation of ectopic germinal centers in the thymus and an imbalance of peripheral T helper cells and regulatory T cells, that contribute to the initiation and development of MG. Recent evidences suggest that noncoding RNA, including miRNA, lncRNA and circRNA may play a significant role in MG progression. Additionally, the network between these noncoding RNAs, such as the competing endogenous RNA regulatory network, has been found to be involved in MG progression. In this review, we summarized the roles of miRNA, lncRNA, and circRNA, highlighted their potential application as biomarkers in diagnosing MG, and discussed their potential regulatory networks in the abnormal thymus and PBMCs during MG development.","PeriodicalId":12465,"journal":{"name":"Frontiers in Molecular Biosciences","volume":null,"pages":null},"PeriodicalIF":5.0,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142220154","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}
Pub Date : 2024-09-10DOI: 10.3389/fmolb.2024.1421699
Connor N. Brown, Babar Shahzad, Mukhtiar Zaman, Xiaobei Pan, Brian D. Green, Nicola M. Lowe, Imre Lengyel
BackgroundBiofortified Zinc Flour to Eliminate Deficiency in Pakistan (BiZiFED) is a nutritional research program that evaluates the impact of consuming zinc biofortified wheat flour on zinc status and associated health outcomes of vulnerable communities in northwest Pakistan. Measuring zinc status from blood samples is fraught with problems. This feasibility study evaluated whether metabolite changes in tear biofluids could be used to understand zinc status.MethodsZinc deficiency is particularly prevalent amongst the female population in Pakistan. Therefore, a crossover trial was developed in which 25 women of reproductive age received standard, wheat flour, and another 25 received zinc-biofortified wheat flour for 8 weeks. At the end of this period, the nutritional intervention was switched between the groups for another 8 weeks. Tear biofluid was collected using Schirmer strips at baseline and after 8 and 16 weeks. Metabolomic analysis was conducted using the MxP® Quant 500 kit on the tear biofluid from a subset of the study participants.ResultsTwo metabolites had a significantly negative correlation with plasma zinc concentration: tiglylcarnitine and valine. Compared to baseline metabolite concentrations, acetylcarnitine, glutamine, two lysophosphatidylcholines (lysoPC a C16:0 and lysoPC a C18:1), and four sphingomyelins (SM (OH) C16:1, SM C16:0, SM C16:1, and SM C24:0) were all significantly decreased post-zinc intervention, whilst a ceramide (Cer(d18:1/18:0) was significantly increased.ConclusionThese results highlight the potential of using tear biofluids as an alternative source for metabolomic biomarkers, both for the assessment of the zinc status of individuals enrolled in nutritional studies and for indicating physiological changes that arise from nutritional supplementation.
背景巴基斯坦消除锌缺乏症生物强化面粉（BiZiFED）是一项营养研究计划，旨在评估食用锌生物强化面粉对巴基斯坦西北部脆弱社区锌状况及相关健康结果的影响。通过血液样本测量锌含量存在很多问题。这项可行性研究评估了能否利用泪液生物液体中代谢物的变化来了解锌的状况。因此，我们开展了一项交叉试验，让 25 名育龄妇女食用标准小麦粉，让另外 25 名育龄妇女食用锌生物强化小麦粉，为期 8 周。试验结束后，两组之间再进行为期 8 周的营养干预。在基线期以及 8 周和 16 周后，使用施尔默试纸收集泪液生物流体。结果有两种代谢物与血浆锌浓度呈显著负相关：替甘利肉碱和缬氨酸。与基线代谢物浓度相比，锌干预后乙酰肉碱、谷氨酰胺、两种溶血磷脂酰胆碱（溶血磷脂酰胆碱 a C16:0 和溶血磷脂酰胆碱 a C18:1）和四种鞘磷脂（SM (OH) C16:1、SM C16:0、SM C16:1 和 SM C24:0）的浓度均明显下降，而一种神经酰胺（Cer(d18:1/18:0）的浓度则明显上升。结论：这些结果凸显了利用泪液生物流体作为代谢组生物标志物替代来源的潜力，既可用于评估营养研究中参与个体的锌状况，也可用于显示营养补充引起的生理变化。
{"title":"Metabolomic changes in tear fluid following zinc biofortification in the BiZiFED nutritional study: a feasibility study","authors":"Connor N. Brown, Babar Shahzad, Mukhtiar Zaman, Xiaobei Pan, Brian D. Green, Nicola M. Lowe, Imre Lengyel","doi":"10.3389/fmolb.2024.1421699","DOIUrl":"https://doi.org/10.3389/fmolb.2024.1421699","url":null,"abstract":"BackgroundBiofortified Zinc Flour to Eliminate Deficiency in Pakistan (BiZiFED) is a nutritional research program that evaluates the impact of consuming zinc biofortified wheat flour on zinc status and associated health outcomes of vulnerable communities in northwest Pakistan. Measuring zinc status from blood samples is fraught with problems. This feasibility study evaluated whether metabolite changes in tear biofluids could be used to understand zinc status.MethodsZinc deficiency is particularly prevalent amongst the female population in Pakistan. Therefore, a crossover trial was developed in which 25 women of reproductive age received standard, wheat flour, and another 25 received zinc-biofortified wheat flour for 8 weeks. At the end of this period, the nutritional intervention was switched between the groups for another 8 weeks. Tear biofluid was collected using Schirmer strips at baseline and after 8 and 16 weeks. Metabolomic analysis was conducted using the MxP<jats:sup>®</jats:sup> Quant 500 kit on the tear biofluid from a subset of the study participants.ResultsTwo metabolites had a significantly negative correlation with plasma zinc concentration: tiglylcarnitine and valine. Compared to baseline metabolite concentrations, acetylcarnitine, glutamine, two lysophosphatidylcholines (lysoPC a C16:0 and lysoPC a C18:1), and four sphingomyelins (SM (OH) C16:1, SM C16:0, SM C16:1, and SM C24:0) were all significantly decreased post-zinc intervention, whilst a ceramide (Cer(d18:1/18:0) was significantly increased.ConclusionThese results highlight the potential of using tear biofluids as an alternative source for metabolomic biomarkers, both for the assessment of the zinc status of individuals enrolled in nutritional studies and for indicating physiological changes that arise from nutritional supplementation.","PeriodicalId":12465,"journal":{"name":"Frontiers in Molecular Biosciences","volume":null,"pages":null},"PeriodicalIF":5.0,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142220155","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}
Pub Date : 2024-09-09DOI: 10.3389/fmolb.2024.1429281
Juan José Oropeza-Valdez, Cristian Padron-Manrique, Aarón Vázquez-Jiménez, Xavier Soberon, Osbaldo Resendis-Antonio
The COVID-19 pandemic, caused by SARS-CoV-2, has led to significant challenges worldwide, including diverse clinical outcomes and prolonged post-recovery symptoms known as Long COVID or Post-COVID-19 syndrome. Emerging evidence suggests a crucial role of metabolic reprogramming in the infection’s long-term consequences. This study employs a novel approach utilizing machine learning (ML) and explainable artificial intelligence (XAI) to analyze metabolic alterations in COVID-19 and Post-COVID-19 patients. Samples were taken from a cohort of 142 COVID-19, 48 Post-COVID-19, and 38 control patients, comprising 111 identified metabolites. Traditional analysis methods, like PCA and PLS-DA, were compared with ML techniques, particularly eXtreme Gradient Boosting (XGBoost) enhanced by SHAP (SHapley Additive exPlanations) values for explainability. XGBoost, combined with SHAP, outperformed traditional methods, demonstrating superior predictive performance and providing new insights into the metabolic basis of the disease’s progression and aftermath. The analysis revealed metabolomic subgroups within the COVID-19 and Post-COVID-19 conditions, suggesting heterogeneous metabolic responses to the infection and its long-term impacts. Key metabolic signatures in Post-COVID-19 include taurine, glutamine, alpha-Ketoglutaric acid, and LysoPC a C16:0. This study highlights the potential of integrating ML and XAI for a fine-grained description in metabolomics research, offering a more detailed understanding of metabolic anomalies in COVID-19 and Post-COVID-19 conditions.
{"title":"Exploring metabolic anomalies in COVID-19 and post-COVID-19: a machine learning approach with explainable artificial intelligence","authors":"Juan José Oropeza-Valdez, Cristian Padron-Manrique, Aarón Vázquez-Jiménez, Xavier Soberon, Osbaldo Resendis-Antonio","doi":"10.3389/fmolb.2024.1429281","DOIUrl":"https://doi.org/10.3389/fmolb.2024.1429281","url":null,"abstract":"The COVID-19 pandemic, caused by SARS-CoV-2, has led to significant challenges worldwide, including diverse clinical outcomes and prolonged post-recovery symptoms known as Long COVID or Post-COVID-19 syndrome. Emerging evidence suggests a crucial role of metabolic reprogramming in the infection’s long-term consequences. This study employs a novel approach utilizing machine learning (ML) and explainable artificial intelligence (XAI) to analyze metabolic alterations in COVID-19 and Post-COVID-19 patients. Samples were taken from a cohort of 142 COVID-19, 48 Post-COVID-19, and 38 control patients, comprising 111 identified metabolites. Traditional analysis methods, like PCA and PLS-DA, were compared with ML techniques, particularly eXtreme Gradient Boosting (XGBoost) enhanced by SHAP (SHapley Additive exPlanations) values for explainability. XGBoost, combined with SHAP, outperformed traditional methods, demonstrating superior predictive performance and providing new insights into the metabolic basis of the disease’s progression and aftermath. The analysis revealed metabolomic subgroups within the COVID-19 and Post-COVID-19 conditions, suggesting heterogeneous metabolic responses to the infection and its long-term impacts. Key metabolic signatures in Post-COVID-19 include taurine, glutamine, alpha-Ketoglutaric acid, and LysoPC a C16:0. This study highlights the potential of integrating ML and XAI for a fine-grained description in metabolomics research, offering a more detailed understanding of metabolic anomalies in COVID-19 and Post-COVID-19 conditions.","PeriodicalId":12465,"journal":{"name":"Frontiers in Molecular Biosciences","volume":null,"pages":null},"PeriodicalIF":5.0,"publicationDate":"2024-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142220184","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}
Metabolites represent the end product of gene expression, protein interaction and other regulatory mechanisms. The metabolome reflects a biological system’s response to genetic and environmental changes, providing a more accurate description of plants’ phenotype than the transcriptome or the proteome. Grapevine (Vitis vinifera L.), established for the production of wine grapes, table grapes, and raisins, holds immense agronomical and economic significance not only in the Mediterranean region but worldwide. As all plants, grapevines face the adverse impact of biotic and abiotic stresses that negatively affect multiple stages of grape and wine industry, including plant and berry development pre- and post-harvest, fresh grapes processing and consequently wine quality. In the present review we highlight the applicability of metabolome analysis in the understanding of the mechanisms involved in grapevine response and acclimatization upon the main biotic and abiotic constrains. The metabolome of induced morphogenic processes such as adventitious rooting and somatic embryogenesis is also explored, as it adds knowledge on the physiological and molecular phenomena occurring in the explants used, and on the successfully propagation of grapevines with desired traits. Finally, the microbiome-induced metabolites in grapevine are discussed in view of beneficial applications derived from the plant symbioses.
{"title":"Applicability of metabolomics to improve sustainable grapevine production","authors":"Catarina Estêvão, Lénia Rodrigues, Ana Elisa Rato, Raquel Garcia, Hélia Cardoso, Catarina Campos","doi":"10.3389/fmolb.2024.1395677","DOIUrl":"https://doi.org/10.3389/fmolb.2024.1395677","url":null,"abstract":"Metabolites represent the end product of gene expression, protein interaction and other regulatory mechanisms. The metabolome reflects a biological system’s response to genetic and environmental changes, providing a more accurate description of plants’ phenotype than the transcriptome or the proteome. Grapevine (<jats:italic>Vitis vinifera</jats:italic> L.), established for the production of wine grapes, table grapes, and raisins, holds immense agronomical and economic significance not only in the Mediterranean region but worldwide. As all plants, grapevines face the adverse impact of biotic and abiotic stresses that negatively affect multiple stages of grape and wine industry, including plant and berry development pre- and post-harvest, fresh grapes processing and consequently wine quality. In the present review we highlight the applicability of metabolome analysis in the understanding of the mechanisms involved in grapevine response and acclimatization upon the main biotic and abiotic constrains. The metabolome of induced morphogenic processes such as adventitious rooting and somatic embryogenesis is also explored, as it adds knowledge on the physiological and molecular phenomena occurring in the explants used, and on the successfully propagation of grapevines with desired traits. Finally, the microbiome-induced metabolites in grapevine are discussed in view of beneficial applications derived from the plant symbioses.","PeriodicalId":12465,"journal":{"name":"Frontiers in Molecular Biosciences","volume":null,"pages":null},"PeriodicalIF":5.0,"publicationDate":"2024-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142220189","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}
Pub Date : 2024-09-06DOI: 10.3389/fmolb.2024.1451280
Asma Fatima, Anupriya M. Geethakumari, Wesam S. Ahmed, Kabir H. Biswas
Anti-COVID19 drugs, such as nirmatrelvir, have been developed targeting the SARS-CoV-2 main protease, Mpro, based on the critical requirement of its proteolytic processing of the viral polyproteins into functional proteins essential for viral replication. However, the emergence of SARS-CoV-2 variants with Mpro mutations has raised the possibility of developing resistance against these drugs, likely due to therapeutic targeting of the Mpro catalytic site. An alternative to these drugs is the development of drugs that target an allosteric site distant from the catalytic site in the protein that may reduce the chance of the emergence of resistant mutants. Here, we combine computational analysis with in vitro assay and report the discovery of a potential allosteric site and an allosteric inhibitor of SARS-CoV-2 Mpro. Specifically, we identified an Mpro metastable state with a deformed catalytic site harboring potential allosteric sites, raising the possibility that stabilization of this metastable state through ligand binding can lead to the inhibition of Mpro activity. We then performed a computational screening of a library (∼4.2 million) of drug-like compounds from the ZINC database and identified several candidate molecules with high predicted binding affinity. MD simulations showed stable binding of the three top-ranking compounds to the putative allosteric sites in the protein. Finally, we tested the three compounds in vitro using a BRET-based Mpro biosensor and found that one of the compounds (ZINC4497834) inhibited the Mpro activity. We envisage that the identification of a potential allosteric inhibitor of Mpro will aid in developing improved anti-COVID-19 therapy.
{"title":"A potential allosteric inhibitor of SARS-CoV-2 main protease (Mpro) identified through metastable state analysis","authors":"Asma Fatima, Anupriya M. Geethakumari, Wesam S. Ahmed, Kabir H. Biswas","doi":"10.3389/fmolb.2024.1451280","DOIUrl":"https://doi.org/10.3389/fmolb.2024.1451280","url":null,"abstract":"Anti-COVID19 drugs, such as nirmatrelvir, have been developed targeting the SARS-CoV-2 main protease, M<jats:sup>pro</jats:sup>, based on the critical requirement of its proteolytic processing of the viral polyproteins into functional proteins essential for viral replication. However, the emergence of SARS-CoV-2 variants with M<jats:sup>pro</jats:sup> mutations has raised the possibility of developing resistance against these drugs, likely due to therapeutic targeting of the M<jats:sup>pro</jats:sup> catalytic site. An alternative to these drugs is the development of drugs that target an allosteric site distant from the catalytic site in the protein that may reduce the chance of the emergence of resistant mutants. Here, we combine computational analysis with <jats:italic>in vitro</jats:italic> assay and report the discovery of a potential allosteric site and an allosteric inhibitor of SARS-CoV-2 M<jats:sup>pro</jats:sup>. Specifically, we identified an M<jats:sup>pro</jats:sup> metastable state with a deformed catalytic site harboring potential allosteric sites, raising the possibility that stabilization of this metastable state through ligand binding can lead to the inhibition of M<jats:sup>pro</jats:sup> activity. We then performed a computational screening of a library (∼4.2 million) of drug-like compounds from the ZINC database and identified several candidate molecules with high predicted binding affinity. MD simulations showed stable binding of the three top-ranking compounds to the putative allosteric sites in the protein. Finally, we tested the three compounds <jats:italic>in vitro</jats:italic> using a BRET-based M<jats:sup>pro</jats:sup> biosensor and found that one of the compounds (ZINC4497834) inhibited the M<jats:sup>pro</jats:sup> activity. We envisage that the identification of a potential allosteric inhibitor of M<jats:sup>pro</jats:sup> will aid in developing improved anti-COVID-19 therapy.","PeriodicalId":12465,"journal":{"name":"Frontiers in Molecular Biosciences","volume":null,"pages":null},"PeriodicalIF":5.0,"publicationDate":"2024-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142220146","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}
IntroductionLong non-coding RNAs (lncRNAs) play crucial roles in genetic markers, genome rearrangement, chromatin modifications, and other biological processes. Increasing evidence suggests that lncRNA functions are closely related to their subcellular localization. However, the distribution of lncRNAs in different subcellular localizations is imbalanced. The number of lncRNAs located in the nucleus is more than ten times that in the exosome.MethodsIn this study, we propose a new oversampling method to construct a predictive dataset and develop a predictive model called LncSTPred. This model improves the Adaboost algorithm for subcellular localization prediction using 3-mer, 3-RF sequence, and minimum free energy structure features.Results and DiscussionBy using our improved Adaboost algorithm, better prediction accuracy for lncRNA subcellular localization was obtained. In addition, we evaluated feature importance by using the F-score and analyzed the influence of highly relevant features on lncRNAs. Our study shows that the ANA features may be a key factor for predicting lncRNA subcellular localization, which correlates with the composition of stems and loops in the secondary structure of lncRNAs.
引言 长非编码 RNA（lncRNA）在遗传标记、基因组重排、染色质修饰和其他生物过程中发挥着至关重要的作用。越来越多的证据表明，lncRNA的功能与其亚细胞定位密切相关。然而，lncRNA 在不同亚细胞定位中的分布是不平衡的。在本研究中，我们提出了一种新的超采样方法来构建预测数据集，并开发了一种名为 LncSTPred 的预测模型。该模型利用3-mer、3-RF序列和最小自由能结构特征改进了用于亚细胞定位预测的Adaboost算法。结果与讨论通过使用我们改进的Adaboost算法，获得了更好的lncRNA亚细胞定位预测准确率。此外，我们还利用 F 分数评估了特征的重要性，并分析了高相关性特征对 lncRNA 的影响。我们的研究表明，ANA特征可能是预测lncRNA亚细胞定位的一个关键因素，它与lncRNA二级结构中茎和环的组成相关。
{"title":"LncSTPred: a predictive model of lncRNA subcellular localization and decipherment of the biological determinants influencing localization","authors":"Si-Le Hu, Ying-Li Chen, Lu-Qiang Zhang, Hui Bai, Jia-Hong Yang, Qian-Zhong Li","doi":"10.3389/fmolb.2024.1452142","DOIUrl":"https://doi.org/10.3389/fmolb.2024.1452142","url":null,"abstract":"IntroductionLong non-coding RNAs (lncRNAs) play crucial roles in genetic markers, genome rearrangement, chromatin modifications, and other biological processes. Increasing evidence suggests that lncRNA functions are closely related to their subcellular localization. However, the distribution of lncRNAs in different subcellular localizations is imbalanced. The number of lncRNAs located in the nucleus is more than ten times that in the exosome.MethodsIn this study, we propose a new oversampling method to construct a predictive dataset and develop a predictive model called LncSTPred. This model improves the Adaboost algorithm for subcellular localization prediction using 3-mer, 3-RF sequence, and minimum free energy structure features.Results and DiscussionBy using our improved Adaboost algorithm, better prediction accuracy for lncRNA subcellular localization was obtained. In addition, we evaluated feature importance by using the F-score and analyzed the influence of highly relevant features on lncRNAs. Our study shows that the ANA features may be a key factor for predicting lncRNA subcellular localization, which correlates with the composition of stems and loops in the secondary structure of lncRNAs.","PeriodicalId":12465,"journal":{"name":"Frontiers in Molecular Biosciences","volume":null,"pages":null},"PeriodicalIF":5.0,"publicationDate":"2024-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142220220","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}
Varying from other identified cell death pathways, cuproptosis is a new type of regulated cell death characterized by excess Cu ions, abnormal aggregation of lipoylated proteins in TCA cycle, loss of Fe-S cluster proteins, upregulation of HSP70, leading to proteotoxic and oxidative stress. Cuproptosis is highly concerned by scientific community and as the field of cuproptosis further develops, remarkable progress has been made in the verification and mechanism of cuproptosis, and methods used to detect cuproptosis have been continuously improved. According to the characteristic changes of cuproptosis, techniques based on cell death verification, Cu content, morphology, molecular biology of protein levels of cuproptosis-related molecules and biochemical pathways of cuproptosis-related enzyme activity and metabolites of oxidative stress, lipoic acid, TCA cycle, Fe-S cluster proteins, oxidative phosphorylation, cell respiration intensity have been subject to cuproptosis verification and research. In order to further deepen the understanding of detecting cuproptosis, the principle and application of common cuproptosis detection methods are reviewed and categorized in cellular phenomena and molecular mechanism in terms of cell death, Cu content, morphology, molecular biology, biochemical pathways with a flow chart. All the indicating results have been displayed in response to the markers of cuproptosis, their advantages and limitations are summaried, and comparison of cuproptosis and ferroptosis detection is performed in this study. Our collection of methods for cuproptosis detection will provide a great basis for cuproptosis verification and research in the future.
{"title":"Recent progress of methods for cuproptosis detection","authors":"Ligang Zhang, Ruiting Deng, Raoqing Guo, Yawen Jiang, Yichen Guan, Caiyue Chen, Wudi Zhao, Guobin Huang, Lian Liu, Hongli Du, Dongsheng Tang","doi":"10.3389/fmolb.2024.1460987","DOIUrl":"https://doi.org/10.3389/fmolb.2024.1460987","url":null,"abstract":"Varying from other identified cell death pathways, cuproptosis is a new type of regulated cell death characterized by excess Cu ions, abnormal aggregation of lipoylated proteins in TCA cycle, loss of Fe-S cluster proteins, upregulation of HSP70, leading to proteotoxic and oxidative stress. Cuproptosis is highly concerned by scientific community and as the field of cuproptosis further develops, remarkable progress has been made in the verification and mechanism of cuproptosis, and methods used to detect cuproptosis have been continuously improved. According to the characteristic changes of cuproptosis, techniques based on cell death verification, Cu content, morphology, molecular biology of protein levels of cuproptosis-related molecules and biochemical pathways of cuproptosis-related enzyme activity and metabolites of oxidative stress, lipoic acid, TCA cycle, Fe-S cluster proteins, oxidative phosphorylation, cell respiration intensity have been subject to cuproptosis verification and research. In order to further deepen the understanding of detecting cuproptosis, the principle and application of common cuproptosis detection methods are reviewed and categorized in cellular phenomena and molecular mechanism in terms of cell death, Cu content, morphology, molecular biology, biochemical pathways with a flow chart. All the indicating results have been displayed in response to the markers of cuproptosis, their advantages and limitations are summaried, and comparison of cuproptosis and ferroptosis detection is performed in this study. Our collection of methods for cuproptosis detection will provide a great basis for cuproptosis verification and research in the future.","PeriodicalId":12465,"journal":{"name":"Frontiers in Molecular Biosciences","volume":null,"pages":null},"PeriodicalIF":5.0,"publicationDate":"2024-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142220221","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}
Pub Date : 2024-09-03DOI: 10.3389/fmolb.2024.1457875
Jiaqian Yuan, Kaiqi Yan, Yong Guo, Yan Li
Pancreatic cancer (PC) is a highly malignant disease with high aggressiveness and a dismal prognosis, which is challenging to diagnose clinically early and gains low benefit from standard therapies. MicroRNAs (miRNAs) have become a hot topic in oncology research. Current evidence indicates that miRNAs are regulators involved in the entire process of PC, providing new diagnostic and therapeutic strategies for this fatal disease. Related research has been rapidly updated, making it necessary to review it to propose new directions and ideas and provide guidance for the development of precision medicine for PC. We reviewed the relevant literature through Pubmed, Embase, Web of Science and Medline, showing that abnormally expressed miRNAs in PC patients have the potential to be used as biomarkers for diagnosis and prognosis, highlighting the excellent prospect of combining miRNAs with traditional therapies, and the effective application of these factors for PC, especially miRNA mimics and inhibitors. MiRNAs participate in the entire process of PC and play important roles in diagnosis, treatment and prognosis. They are potential factors in conquering PC in the future.
胰腺癌（PC）是一种高度恶性疾病，具有侵袭性强、预后不良等特点，临床上难以早期诊断，标准疗法的获益率低。微RNA（miRNA）已成为肿瘤学研究的热门话题。目前的证据表明，miRNAs 是参与 PC 整个过程的调控因子，为这种致命疾病提供了新的诊断和治疗策略。相关研究更新很快，因此有必要对其进行回顾，以提出新的方向和思路，为 PC 精准医疗的发展提供指导。我们通过Pubmed、Embase、Web of Science和Medline查阅了相关文献，发现PC患者中异常表达的miRNAs有可能被用作诊断和预后的生物标志物，凸显了miRNAs与传统疗法相结合的良好前景，以及这些因子尤其是miRNA模拟物和抑制剂在PC中的有效应用。miRNA 参与了 PC 的整个过程，在诊断、治疗和预后方面发挥着重要作用。它们是未来攻克 PC 的潜在因素。
{"title":"MicroRNAs: emerging biomarkers and therapeutic targets in pancreatic cancer","authors":"Jiaqian Yuan, Kaiqi Yan, Yong Guo, Yan Li","doi":"10.3389/fmolb.2024.1457875","DOIUrl":"https://doi.org/10.3389/fmolb.2024.1457875","url":null,"abstract":"Pancreatic cancer (PC) is a highly malignant disease with high aggressiveness and a dismal prognosis, which is challenging to diagnose clinically early and gains low benefit from standard therapies. MicroRNAs (miRNAs) have become a hot topic in oncology research. Current evidence indicates that miRNAs are regulators involved in the entire process of PC, providing new diagnostic and therapeutic strategies for this fatal disease. Related research has been rapidly updated, making it necessary to review it to propose new directions and ideas and provide guidance for the development of precision medicine for PC. We reviewed the relevant literature through Pubmed, Embase, Web of Science and Medline, showing that abnormally expressed miRNAs in PC patients have the potential to be used as biomarkers for diagnosis and prognosis, highlighting the excellent prospect of combining miRNAs with traditional therapies, and the effective application of these factors for PC, especially miRNA mimics and inhibitors. MiRNAs participate in the entire process of PC and play important roles in diagnosis, treatment and prognosis. They are potential factors in conquering PC in the future.","PeriodicalId":12465,"journal":{"name":"Frontiers in Molecular Biosciences","volume":null,"pages":null},"PeriodicalIF":5.0,"publicationDate":"2024-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142220186","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}
Pub Date : 2024-09-03DOI: 10.3389/fmolb.2024.1455153
Yenisleidy de las Mercedes Zulueta Diaz, Eva C. Arnspang
Biological membranes are complex, heterogeneous, and dynamic systems that play roles in the compartmentalization and protection of cells from the environment. It is still a challenge to elucidate kinetics and real-time transport routes for molecules through biological membranes in live cells. Currently, by developing and employing super-resolution microscopy; increasing evidence indicates channels and transporter nano-organization and dynamics within membranes play an important role in these regulatory mechanisms. Here we review recent advances and discuss the major advantages and disadvantages of using super-resolution microscopy to investigate protein organization and transport within plasma membranes.
{"title":"Super-resolution microscopy to study membrane nanodomains and transport mechanisms in the plasma membrane","authors":"Yenisleidy de las Mercedes Zulueta Diaz, Eva C. Arnspang","doi":"10.3389/fmolb.2024.1455153","DOIUrl":"https://doi.org/10.3389/fmolb.2024.1455153","url":null,"abstract":"Biological membranes are complex, heterogeneous, and dynamic systems that play roles in the compartmentalization and protection of cells from the environment. It is still a challenge to elucidate kinetics and real-time transport routes for molecules through biological membranes in live cells. Currently, by developing and employing super-resolution microscopy; increasing evidence indicates channels and transporter nano-organization and dynamics within membranes play an important role in these regulatory mechanisms. Here we review recent advances and discuss the major advantages and disadvantages of using super-resolution microscopy to investigate protein organization and transport within plasma membranes.","PeriodicalId":12465,"journal":{"name":"Frontiers in Molecular Biosciences","volume":null,"pages":null},"PeriodicalIF":5.0,"publicationDate":"2024-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142220188","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}
BackgroundMuscle is an important tissue of the human body. Muscle atrophy is common in people of all ages, which will lead to human weakness and decline of motor function, which is one of the important causes of disability. The common methods of genomics research are transcriptome, proteomics and metabolomics, which are important means to explore the molecular pathology of diseases. In recent years, combinatorial research has been carried out on a large scale in the field of muscle atrophy. However, no author in this field has carried out bibliometrics and visual analysis.MethodsIn this study, articles related to the histological study of muscular dystrophy since 2000 were searched from the Web of Science core database (WoSCC). We will retrieve the results through CiteSpace, VosViewer and R for data statistics and visual analysis.ResultsIn this study, a total of 141 publications were collected, and the number of publications increased year by year. These 141 articles came from 1031 co-authors from 361 institutions in 31 countries and were published in 92 journals. A total of 6286 articles from 1383 journals were cited. Authors from American institutions have published the most articles and have been cited the most, and authors from other countries have also made considerable contributions.ConclusionThis is the first bibliometric and visual analysis of published research in the field of muscular dystrophy through systematic data retrieval and combined with a variety of bibliometric analysis tools. Through these data, we summarize the previous studies of scholars, and provide prospects for future research in the field.
{"title":"Sequencing technology in sarcopenia: current research progress and future trends","authors":"Yuxia Yang, Xiangji Meng, Xiaomei Dai, Jian Zhang, Jihang Dai, Jingcheng Wang, Wenyong Fei","doi":"10.3389/fmolb.2024.1309006","DOIUrl":"https://doi.org/10.3389/fmolb.2024.1309006","url":null,"abstract":"BackgroundMuscle is an important tissue of the human body. Muscle atrophy is common in people of all ages, which will lead to human weakness and decline of motor function, which is one of the important causes of disability. The common methods of genomics research are transcriptome, proteomics and metabolomics, which are important means to explore the molecular pathology of diseases. In recent years, combinatorial research has been carried out on a large scale in the field of muscle atrophy. However, no author in this field has carried out bibliometrics and visual analysis.MethodsIn this study, articles related to the histological study of muscular dystrophy since 2000 were searched from the Web of Science core database (WoSCC). We will retrieve the results through CiteSpace, VosViewer and R for data statistics and visual analysis.ResultsIn this study, a total of 141 publications were collected, and the number of publications increased year by year. These 141 articles came from 1031 co-authors from 361 institutions in 31 countries and were published in 92 journals. A total of 6286 articles from 1383 journals were cited. Authors from American institutions have published the most articles and have been cited the most, and authors from other countries have also made considerable contributions.ConclusionThis is the first bibliometric and visual analysis of published research in the field of muscular dystrophy through systematic data retrieval and combined with a variety of bibliometric analysis tools. Through these data, we summarize the previous studies of scholars, and provide prospects for future research in the field.","PeriodicalId":12465,"journal":{"name":"Frontiers in Molecular Biosciences","volume":null,"pages":null},"PeriodicalIF":5.0,"publicationDate":"2024-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142220256","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}
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