Fei Yuan, JingXin Ren, HuiPing Liao, Wei Guo, Lei Chen, KaiYan Feng, Tao Huang, Yu-Dong Cai
Background: Different severities of coronavirus disease 2019 (COVID-19) cause different levels of respiratory symptoms and systemic inflammation. DNA methylation, a heritable epigenetic process, also shows differential changes in different severities of COVID-19. DNA methylation is involved in regulating the activity of various immune cells and influences immune pathways associated with viral infections. It may also be involved in regulating the expression of genes associated with the progression of COVID-19. Methods: In this study, a sophisticated machine-learning workflow was designed to analyze whole-blood DNA methylation data from COVID-19 patients with different severities versus healthy controls. We aimed to understand the role of DNA methylation in the development of COVID-19. The sample set contained 101 negative controls, 360 mildly infected individuals, and 113 severely infected individuals. Each sample involved 768,067 methylation sites. Three feature-ranking algorithms (least absolute shrinkage and selection operator (LASSO), light gradient-boosting machine (LightGBM), and Monte Carlo feature selection (MCFS)) were used to rank and filter out sites highly correlated with COVID-19. Based on the obtained ranking results, a high-performance classification model was constructed by combining the feature incremental approach with four classification algorithms (decision tree (DT), k-nearest neighbor (kNN), random forest (RF), and support vector machine (SVM)). Results: Some essential methylation sites and decision rules were obtained. Conclusions: The genes (IGSF6, CD38, and TLR2) of some essential methylation sites were confirmed to play important roles in the immune system.
{"title":"Identification of Whole-Blood DNA Methylation Signatures and Rules Associated with COVID-19 Severity","authors":"Fei Yuan, JingXin Ren, HuiPing Liao, Wei Guo, Lei Chen, KaiYan Feng, Tao Huang, Yu-Dong Cai","doi":"10.31083/j.fbl2811284","DOIUrl":"https://doi.org/10.31083/j.fbl2811284","url":null,"abstract":"Background: Different severities of coronavirus disease 2019 (COVID-19) cause different levels of respiratory symptoms and systemic inflammation. DNA methylation, a heritable epigenetic process, also shows differential changes in different severities of COVID-19. DNA methylation is involved in regulating the activity of various immune cells and influences immune pathways associated with viral infections. It may also be involved in regulating the expression of genes associated with the progression of COVID-19. Methods: In this study, a sophisticated machine-learning workflow was designed to analyze whole-blood DNA methylation data from COVID-19 patients with different severities versus healthy controls. We aimed to understand the role of DNA methylation in the development of COVID-19. The sample set contained 101 negative controls, 360 mildly infected individuals, and 113 severely infected individuals. Each sample involved 768,067 methylation sites. Three feature-ranking algorithms (least absolute shrinkage and selection operator (LASSO), light gradient-boosting machine (LightGBM), and Monte Carlo feature selection (MCFS)) were used to rank and filter out sites highly correlated with COVID-19. Based on the obtained ranking results, a high-performance classification model was constructed by combining the feature incremental approach with four classification algorithms (decision tree (DT), k-nearest neighbor (kNN), random forest (RF), and support vector machine (SVM)). Results: Some essential methylation sites and decision rules were obtained. Conclusions: The genes (IGSF6, CD38, and TLR2) of some essential methylation sites were confirmed to play important roles in the immune system.","PeriodicalId":12366,"journal":{"name":"Frontiers in bioscience","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135393038","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Oxidative stress (OS) is linked to hepatocellular carcinoma (HCC) progression. HCC may develop as a result of genetic changes, including oxidative injury to both nuclear and mitochondrial DNA. Signaling pathways regulated by OS, such as Wnt/β-catenin and Notch pathways, are vital regulators in developing HCC. OS-mediated activation of transcription factors, including nuclear factor-κB and p53, among others, is capable of regulating the redox state of HCC cells. OS also affects the tumor microenvironment, which, in turn, regulates HCC progression. In HCC, reactive oxygen species (ROS) can potentially enhance tumor cell proliferation, metastasis, and resistance to treatment. However, elevated ROS levels can cause cytotoxicity and trigger apoptosis in HCC cells. This review highlights and explores potential oxidative stress-related treatment targets in HCC, offering novel insights for clinical therapies.
{"title":"Insights into the Role of Oxidative Stress in Hepatocellular Carcinoma Development","authors":"Yuanyuan Li, Yang Yu, Lei Yang, Rui Wang","doi":"10.31083/j.fbl2811286","DOIUrl":"https://doi.org/10.31083/j.fbl2811286","url":null,"abstract":"Oxidative stress (OS) is linked to hepatocellular carcinoma (HCC) progression. HCC may develop as a result of genetic changes, including oxidative injury to both nuclear and mitochondrial DNA. Signaling pathways regulated by OS, such as Wnt/β-catenin and Notch pathways, are vital regulators in developing HCC. OS-mediated activation of transcription factors, including nuclear factor-κB and p53, among others, is capable of regulating the redox state of HCC cells. OS also affects the tumor microenvironment, which, in turn, regulates HCC progression. In HCC, reactive oxygen species (ROS) can potentially enhance tumor cell proliferation, metastasis, and resistance to treatment. However, elevated ROS levels can cause cytotoxicity and trigger apoptosis in HCC cells. This review highlights and explores potential oxidative stress-related treatment targets in HCC, offering novel insights for clinical therapies.","PeriodicalId":12366,"journal":{"name":"Frontiers in bioscience","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135430490","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Background: Obesity is a significant health problem with an increasing incidence, causing a low-grade systemic inflammatory state and being implicated in various chronic diseases. Moreover, obesity has been shown to cause mitochondrial dysfunction through oxidative stress and inflammation, eventually affecting energy metabolism. However, high-intensity interval training (HIIT) can improve mitochondrial efficiency through exercise-induced mitochondrial adaptations. This systematic review and meta-analysis aims to examine the potential effects of HIIT on mitochondrial-associated indices in obese and overweight adults. Methods: PubMed, Scopus, and Web of Science databases were searched. Results: Twenty-eight eligible studies were included, involving 530 participants. HIIT was found to significantly improve the activity of citrate synthase (CS), cytochrome C (COX-IV), beta-hydroxyacyl CoA-dehydrogenase (β-HAD), Complexes I-V as well as VO2max in overweight and obese individuals, whereas no significant changes were shown in PGC-1α and SIRT1. Interestingly, subgroup analyses revealed that CS, COX-IV, β-HAD, and Complexes I-V activity exhibited a significant improvement only in the healthy subgroup. Conclusions: Overall, HIIT can be utilized to enhance mitochondrial-associated indices in overweight and obese individuals. However, this improvement may be health status dependent.
背景:肥胖是一个发病率不断上升的重要健康问题，可引起低度全身炎症状态，并与多种慢性疾病有关。此外，肥胖已被证明会通过氧化应激和炎症导致线粒体功能障碍，最终影响能量代谢。然而，高强度间歇训练(HIIT)可以通过运动诱导的线粒体适应来提高线粒体效率。本系统综述和荟萃分析旨在研究HIIT对肥胖和超重成人线粒体相关指标的潜在影响。方法:检索PubMed、Scopus、Web of Science数据库。结果:纳入28项符合条件的研究，涉及530名受试者。研究发现，HIIT可显著改善超重和肥胖个体的柠檬酸合成酶(CS)、细胞色素C (COX-IV)、β-羟酰基辅酶a-脱氢酶(β-HAD)、复合物I-V和VO2max的活性，而PGC-1α和SIRT1无显著变化。有趣的是，亚组分析显示，CS、COX-IV、β-HAD和复合物I-V活性仅在健康亚组中有显著改善。结论:总体而言，HIIT可用于提高超重和肥胖个体的线粒体相关指标。然而，这种改善可能取决于健康状况。
{"title":"The Effect of High-Intensity Interval Training on Mitochondrial-Associated Indices in Overweight and Obese Adults: A Systematic Review and Meta-Analysis","authors":"Spyridon Hadjispyrou, Petros C Dinas, Spyridon Marios Delitheos, Ioannis-Alexios Koumprentziotis, Costas Chryssanthopoulos, Anastassios Philippou","doi":"10.31083/j.fbl2811281","DOIUrl":"https://doi.org/10.31083/j.fbl2811281","url":null,"abstract":"Background: Obesity is a significant health problem with an increasing incidence, causing a low-grade systemic inflammatory state and being implicated in various chronic diseases. Moreover, obesity has been shown to cause mitochondrial dysfunction through oxidative stress and inflammation, eventually affecting energy metabolism. However, high-intensity interval training (HIIT) can improve mitochondrial efficiency through exercise-induced mitochondrial adaptations. This systematic review and meta-analysis aims to examine the potential effects of HIIT on mitochondrial-associated indices in obese and overweight adults. Methods: PubMed, Scopus, and Web of Science databases were searched. Results: Twenty-eight eligible studies were included, involving 530 participants. HIIT was found to significantly improve the activity of citrate synthase (CS), cytochrome C (COX-IV), beta-hydroxyacyl CoA-dehydrogenase (β-HAD), Complexes I-V as well as VO2max in overweight and obese individuals, whereas no significant changes were shown in PGC-1α and SIRT1. Interestingly, subgroup analyses revealed that CS, COX-IV, β-HAD, and Complexes I-V activity exhibited a significant improvement only in the healthy subgroup. Conclusions: Overall, HIIT can be utilized to enhance mitochondrial-associated indices in overweight and obese individuals. However, this improvement may be health status dependent.","PeriodicalId":12366,"journal":{"name":"Frontiers in bioscience","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135430369","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Anna Sendera, Barbara Pikuła, Agnieszka Banaś-Ząbczyk
Mesenchymal stem cells (MSCs) offer great potential for use in stem cell-based therapies due to their unique regenerative potential via reconstructive and paracrine capacities. These therapies offer new hope for patients suffering from conditions that have no cure. Currently, mesenchymal stem cells (from adipose tissues, bone marrow, and umbilical cords) are most interesting for application in those therapies. Nevertheless, the development of MSC-based medical products requires thorough research and standardization that maximizes the therapeutic effect while minimizing side effects. One of the interesting novel approaches to achieving this goal is combining MSC therapy with an electromagnetic field (EMF). Many studies have shown that EMF can enhance the regenerative properties of MSCs by influencing stem cell fate through modulating differentiation, proliferation, cell cycle regulation, metabolism, and cytokine and growth factor secretions. Combination therapy of EMF-MSCs is a promising perspective; however, it is important to select appropriate EMF parameters to obtain beneficial therapeutic effects. Therefore, understanding the mechanisms involved in the EMF impact on MSCs is crucial. In this study, we provide an overview of the effects of EMF on the biological response and “fate” of MSCs, paying attention to the gaps in research that remain unfilled and discuss the clinical application of this approach.
{"title":"Preconditioning of Mesenchymal Stem Cells with Electromagnetic Fields and Its Impact on Biological Responses and “Fate”—Potential Use in Therapeutic Applications","authors":"Anna Sendera, Barbara Pikuła, Agnieszka Banaś-Ząbczyk","doi":"10.31083/j.fbl2811285","DOIUrl":"https://doi.org/10.31083/j.fbl2811285","url":null,"abstract":"Mesenchymal stem cells (MSCs) offer great potential for use in stem cell-based therapies due to their unique regenerative potential via reconstructive and paracrine capacities. These therapies offer new hope for patients suffering from conditions that have no cure. Currently, mesenchymal stem cells (from adipose tissues, bone marrow, and umbilical cords) are most interesting for application in those therapies. Nevertheless, the development of MSC-based medical products requires thorough research and standardization that maximizes the therapeutic effect while minimizing side effects. One of the interesting novel approaches to achieving this goal is combining MSC therapy with an electromagnetic field (EMF). Many studies have shown that EMF can enhance the regenerative properties of MSCs by influencing stem cell fate through modulating differentiation, proliferation, cell cycle regulation, metabolism, and cytokine and growth factor secretions. Combination therapy of EMF-MSCs is a promising perspective; however, it is important to select appropriate EMF parameters to obtain beneficial therapeutic effects. Therefore, understanding the mechanisms involved in the EMF impact on MSCs is crucial. In this study, we provide an overview of the effects of EMF on the biological response and “fate” of MSCs, paying attention to the gaps in research that remain unfilled and discuss the clinical application of this approach.","PeriodicalId":12366,"journal":{"name":"Frontiers in bioscience","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135430215","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Background: Kidney clear cell carcinoma (KIRC) is the most common type of kidney cancer, accounting for approximately 60–85% of all the kidney cancers. However, there are few options available for early treatment. Therefore, it is extremely important to identify biomarkers and study therapeutic targets for KIRC. Methods: Since there are few studies on KIRC, we used a data-driven approach to identify differential genes. Here, we used miRNA gene expression profile data from the TCGA database species of KIRC and proposed a machine learning-based approach to quantify the importance score of each gene. Then, an ensemble method was utilized to find the optimal subset of genes used to predict KIRC by clustering. The most genetic subset was then used to classify and predict KIRC. Results: Differential genes were screened by several traditional differential analysis methods, and the selected gene subset showed a better performance. Independent testing sets from the GEO database were used to verify the effectiveness of the optimal subset of genes. Besides, cross-validation was made to verify the effectiveness of the approach. Conclusions: Finally, important genes, such as miR-140 and miR-210, were found to be involved in the biochemical processes of KIRC, which also proved the effectiveness of our approach.
{"title":"Differential Expression Analysis Based on Ensemble Strategy on miRNA Profiles of Kidney Clear Cell Carcinoma","authors":"Enyang Zhao, Ziqi Xi, Qiong Wu","doi":"10.31083/j.fbl2811283","DOIUrl":"https://doi.org/10.31083/j.fbl2811283","url":null,"abstract":"Background: Kidney clear cell carcinoma (KIRC) is the most common type of kidney cancer, accounting for approximately 60–85% of all the kidney cancers. However, there are few options available for early treatment. Therefore, it is extremely important to identify biomarkers and study therapeutic targets for KIRC. Methods: Since there are few studies on KIRC, we used a data-driven approach to identify differential genes. Here, we used miRNA gene expression profile data from the TCGA database species of KIRC and proposed a machine learning-based approach to quantify the importance score of each gene. Then, an ensemble method was utilized to find the optimal subset of genes used to predict KIRC by clustering. The most genetic subset was then used to classify and predict KIRC. Results: Differential genes were screened by several traditional differential analysis methods, and the selected gene subset showed a better performance. Independent testing sets from the GEO database were used to verify the effectiveness of the optimal subset of genes. Besides, cross-validation was made to verify the effectiveness of the approach. Conclusions: Finally, important genes, such as miR-140 and miR-210, were found to be involved in the biochemical processes of KIRC, which also proved the effectiveness of our approach.","PeriodicalId":12366,"journal":{"name":"Frontiers in bioscience","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135392359","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Background: Cervical cancer has high morbidity and intratumor heterogeneity. Anoikis, a form of programmed cell death preventing detached cancer cells from readhering, may serve as a potential prognostic signature for cervical cancer. This study aimed to assess the predictive performance of anoikis patterns in cervical cancer prognosis. Methods: Differentially expressed anoikis-related genes (DEARGs) were identified between normal and cancer samples using data from the Gene Expression Omnibus database with the elucidation of mutation status and bio-function. Novel anoikis molecular subtypes were defined in The Cancer Genome Atlas (TCGA) cohort with consensus clustering analysis. A multigene prognostic signature was constructed through least absolute shrinkage and selection operator (LASSO) Cox analysis with internal and external validation. The nomogram-based survival probability of cervical cancer over 3 and 5 years was predicted and assessed with calibration, receiver operating characteristic, decision curve analysis, and Kaplan-Meier curves. Additionally, mutation, function, and immune analysis were conducted among different risk groups. Results: We identified 77 DEARGs between normal and cervical cancer tissues and explored their mutation status and functions. The TCGA cohort could be categorized into two subtypes based on these genes. Furthermore, seven prognostic signature genes were constructed, and the nomogram involving DEARGs and clinicopathological characteristics showed satisfactory predictive performance. Functional analysis indicated that immune-related genes were enriched, and immune status, as well as sensitivity of chemotherapies and targeting drugs, were correlated with the risk model. Conclusions: Anoikis patterns play important roles in tumor immunity and can be used to predict the prognosis of cervical cancers.
{"title":"Anoikis Patterns in Cervical Cancer: Identification of Subgroups and Construction of a Novel Risk Model for Predicting Prognosis and Immune Response","authors":"Xuesong Xiang, Jingxin Ding","doi":"10.31083/j.fbl2811287","DOIUrl":"https://doi.org/10.31083/j.fbl2811287","url":null,"abstract":"Background: Cervical cancer has high morbidity and intratumor heterogeneity. Anoikis, a form of programmed cell death preventing detached cancer cells from readhering, may serve as a potential prognostic signature for cervical cancer. This study aimed to assess the predictive performance of anoikis patterns in cervical cancer prognosis. Methods: Differentially expressed anoikis-related genes (DEARGs) were identified between normal and cancer samples using data from the Gene Expression Omnibus database with the elucidation of mutation status and bio-function. Novel anoikis molecular subtypes were defined in The Cancer Genome Atlas (TCGA) cohort with consensus clustering analysis. A multigene prognostic signature was constructed through least absolute shrinkage and selection operator (LASSO) Cox analysis with internal and external validation. The nomogram-based survival probability of cervical cancer over 3 and 5 years was predicted and assessed with calibration, receiver operating characteristic, decision curve analysis, and Kaplan-Meier curves. Additionally, mutation, function, and immune analysis were conducted among different risk groups. Results: We identified 77 DEARGs between normal and cervical cancer tissues and explored their mutation status and functions. The TCGA cohort could be categorized into two subtypes based on these genes. Furthermore, seven prognostic signature genes were constructed, and the nomogram involving DEARGs and clinicopathological characteristics showed satisfactory predictive performance. Functional analysis indicated that immune-related genes were enriched, and immune status, as well as sensitivity of chemotherapies and targeting drugs, were correlated with the risk model. Conclusions: Anoikis patterns play important roles in tumor immunity and can be used to predict the prognosis of cervical cancers.","PeriodicalId":12366,"journal":{"name":"Frontiers in bioscience","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135392413","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Wu Xiong, Xue Bai, Xi Zhang, Huajuan Lei, Hui Xiao, Luyao Zhang, Yuting Xiao, Qianpei Yang, Xiaoling Zou
Objective: We explore the effects of endothelial progenitor cell (EPC)-derived exosomes (EPCexos) and of astragaloside IV (ASIV)-stimulated EPCexos (ASIV-EPCexos) on type I diabetic-wound healing, and determine the basic molecular mechanisms of action. Methods: EPCs were exposed to different concentrations of ASIV to generate ASIV-EPCexos. A chronic-wound healing model involving streptozotocin-stimulated diabetic rats was established. These rats were treated with EPCexos, ASIV-EPCexos, rapamycin, and wortmannin. Wound healing was evaluated by direct photographic observation, hematoxylin and eosin staining, and Masson’s trichrome staining. Results: ASIV treatment increased the abilities of EPCs (e.g., proliferation), as well as exosome secretion. EPCexo showed a “cup holder” like structure. Treatment with ASIV-EPCexos increased the wound-healing rate, collagen-deposition area, bromodeoxyuridine uptake, VEGF expression, and the number of CD31- and αSMA- positive cells, whereas decreased epidermal thickness and CD45 expression. The expression of the PI3K/AKT/mTOR pathway increased, whereas the expression of inflammatory factor decreased. However, rapamycin and wortmannin reversed these changes. Conclusions: ASIV-EPCexos may accelerate type I diabetic-wound healing via the PI3K/AKT/mTOR pathway. This study may lay the foundation for new clinical treatment options for patients with type I diabetic wounds.
{"title":"Endothelial Progenitor-Cell-Derived Exosomes Induced by Astragaloside IV Accelerate Type I Diabetic-wound Healing via the PI3K/AKT/mTOR Pathway in Rats","authors":"Wu Xiong, Xue Bai, Xi Zhang, Huajuan Lei, Hui Xiao, Luyao Zhang, Yuting Xiao, Qianpei Yang, Xiaoling Zou","doi":"10.31083/j.fbl2811282","DOIUrl":"https://doi.org/10.31083/j.fbl2811282","url":null,"abstract":"Objective: We explore the effects of endothelial progenitor cell (EPC)-derived exosomes (EPCexos) and of astragaloside IV (ASIV)-stimulated EPCexos (ASIV-EPCexos) on type I diabetic-wound healing, and determine the basic molecular mechanisms of action. Methods: EPCs were exposed to different concentrations of ASIV to generate ASIV-EPCexos. A chronic-wound healing model involving streptozotocin-stimulated diabetic rats was established. These rats were treated with EPCexos, ASIV-EPCexos, rapamycin, and wortmannin. Wound healing was evaluated by direct photographic observation, hematoxylin and eosin staining, and Masson’s trichrome staining. Results: ASIV treatment increased the abilities of EPCs (e.g., proliferation), as well as exosome secretion. EPCexo showed a “cup holder” like structure. Treatment with ASIV-EPCexos increased the wound-healing rate, collagen-deposition area, bromodeoxyuridine uptake, VEGF expression, and the number of CD31- and αSMA- positive cells, whereas decreased epidermal thickness and CD45 expression. The expression of the PI3K/AKT/mTOR pathway increased, whereas the expression of inflammatory factor decreased. However, rapamycin and wortmannin reversed these changes. Conclusions: ASIV-EPCexos may accelerate type I diabetic-wound healing via the PI3K/AKT/mTOR pathway. This study may lay the foundation for new clinical treatment options for patients with type I diabetic wounds.","PeriodicalId":12366,"journal":{"name":"Frontiers in bioscience","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135392411","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Hafsa Boulenouar, Nadia Bouchoutrouch, Youssef Amar, Moulay El Abbes Faouzi, Yahia Cherrah, Hassan Sefrioui, Hassan Ait Benhassou
Background: Trastuzumab (Herceptin®) is currently the main treatment option for breast cancer patients that overexpress the human epidermal growth factor receptor 2 (HER2). This antibody binds specifically to HER2, blocks cancer cell growth, and promotes effective cell death. In the present study, we sought to develop a robust and efficient process for the development of a stable Chinese hamster ovary (CHO) cell line with high trastuzumab expression and production. Methods: We adapted a process that combines transposon system-based vector construction, suspension cell culture, and a high selection process. The latter, involved enhanced green fluorescent protein (eGFP) expression, fluorescence-activated cell sorting (FACS), and semi-solid methylcellulose media. Results: The construction of trastuzumab as a humanized monoclonal antibody was achieved by subcloning the synthesized light and heavy chain sequences into a suitable piggyBac expression vector. The optimized piggyBac vector used for the expression of trastuzumab in CHO cells resulted in the production of trastuzumab and reached 4.24 g/L in the T1A7 clone after a 7-day batch culture. The T1A7 clone was selected after screening over 1500 clones. Conclusions: The current simple workflow ensures strict monoclonality and relatively high production of trastuzumab. This workflow could potentially be implemented in Research and Development (R&D) laboratories, including in developing countries for the production of recombinant monoclonal antibodies in a cost-effective manner.
{"title":"Strategy for Developing a Stable CHO Cell Line that Produces Large Titers of Trastuzumab Antibody","authors":"Hafsa Boulenouar, Nadia Bouchoutrouch, Youssef Amar, Moulay El Abbes Faouzi, Yahia Cherrah, Hassan Sefrioui, Hassan Ait Benhassou","doi":"10.31083/j.fbe1504024","DOIUrl":"https://doi.org/10.31083/j.fbe1504024","url":null,"abstract":"Background: Trastuzumab (Herceptin®) is currently the main treatment option for breast cancer patients that overexpress the human epidermal growth factor receptor 2 (HER2). This antibody binds specifically to HER2, blocks cancer cell growth, and promotes effective cell death. In the present study, we sought to develop a robust and efficient process for the development of a stable Chinese hamster ovary (CHO) cell line with high trastuzumab expression and production. Methods: We adapted a process that combines transposon system-based vector construction, suspension cell culture, and a high selection process. The latter, involved enhanced green fluorescent protein (eGFP) expression, fluorescence-activated cell sorting (FACS), and semi-solid methylcellulose media. Results: The construction of trastuzumab as a humanized monoclonal antibody was achieved by subcloning the synthesized light and heavy chain sequences into a suitable piggyBac expression vector. The optimized piggyBac vector used for the expression of trastuzumab in CHO cells resulted in the production of trastuzumab and reached 4.24 g/L in the T1A7 clone after a 7-day batch culture. The T1A7 clone was selected after screening over 1500 clones. Conclusions: The current simple workflow ensures strict monoclonality and relatively high production of trastuzumab. This workflow could potentially be implemented in Research and Development (R&D) laboratories, including in developing countries for the production of recombinant monoclonal antibodies in a cost-effective manner.","PeriodicalId":12366,"journal":{"name":"Frontiers in bioscience","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-11-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135541289","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Shidi Zhao, Huan Chen, Yan Zhou, Quanfang Wang, Xiao Liang, Na Yang, Li Yan, Jin Yang
Background: Six transmembrane epithelial antigen 1 (STEAP1) is aberrantly expressed in cancers and could therefore be a potential biomarker. This study examined the connection between STEAP1 expression and clinical features/prognosis in cancer patients. Methods: Several databases were comprehensively searched for related published studies. The combination of hazard ratios (HRs), odd ratios (ORs), and 95% confidence intervals (95% CIs) was used to assess the role of STEAP1. The Cancer Genome Atlas (TCGA) dataset was used to estimate the prognostic value of STEAP1 in multiple cancer types, and several biological behaviors related to STEAP1 were evaluated by CancerSEA. Results: Searches of electronic databases revealed 7 relevant trials with 765 patients. A significant connection was found between high STEAP1 expression and worse overall survival amongst cancer patients (HR = 1.87, 95% CI: 1.49–2.34, p < 0.001). In addition, a strong correlation was found between high STEAP1 expression and the occurrence of lymph node metastases (OR = 3.19, 95% CI: 1.26–8.09, p < 0.001). Analysis of TCGA datasets verified that a higher level of STEAP1 expression is linked with reduced survival in many kinds of cancer. At the single cell level, STEAP1 expression was correlated with some tumor biological behaviors, such as angiogenesis, quiescence, and stemness. Conclusions: STEAP1 could regulate various biological functions in tumors and predict prognosis as a novel biomarker in a number of cancer types.
背景:6跨膜上皮抗原1 (STEAP1)在癌症中异常表达，因此可能是一种潜在的生物标志物。本研究探讨了STEAP1表达与癌症患者临床特征/预后之间的关系。方法:综合检索多个数据库中已发表的相关研究。采用风险比(hr)、奇比(ORs)和95%置信区间(95% ci)的组合来评估STEAP1的作用。使用癌症基因组图谱(TCGA)数据集估计STEAP1在多种癌症类型中的预后价值，并通过CancerSEA评估与STEAP1相关的几种生物学行为。结果:检索到7项相关试验，765例患者。在癌症患者中，STEAP1高表达与较差的总生存率之间存在显著关联(HR = 1.87, 95% CI: 1.49-2.34, p <0.001)。此外，STEAP1高表达与淋巴结转移的发生有很强的相关性(OR = 3.19, 95% CI: 1.26-8.09, p <0.001)。TCGA数据集的分析证实，在许多癌症中，较高水平的STEAP1表达与生存率降低有关。在单细胞水平上，STEAP1的表达与肿瘤的一些生物学行为有关，如血管生成、静止和干性。结论:STEAP1作为一种新型的生物标志物，在多种肿瘤中具有调节多种生物学功能和预测预后的作用。
{"title":"Six Transmembrane Epithelial Antigen 1 as a Prognostic Biomarker in Carcinomas: A Meta-Analysis","authors":"Shidi Zhao, Huan Chen, Yan Zhou, Quanfang Wang, Xiao Liang, Na Yang, Li Yan, Jin Yang","doi":"10.31083/j.fbl2811280","DOIUrl":"https://doi.org/10.31083/j.fbl2811280","url":null,"abstract":"Background: Six transmembrane epithelial antigen 1 (STEAP1) is aberrantly expressed in cancers and could therefore be a potential biomarker. This study examined the connection between STEAP1 expression and clinical features/prognosis in cancer patients. Methods: Several databases were comprehensively searched for related published studies. The combination of hazard ratios (HRs), odd ratios (ORs), and 95% confidence intervals (95% CIs) was used to assess the role of STEAP1. The Cancer Genome Atlas (TCGA) dataset was used to estimate the prognostic value of STEAP1 in multiple cancer types, and several biological behaviors related to STEAP1 were evaluated by CancerSEA. Results: Searches of electronic databases revealed 7 relevant trials with 765 patients. A significant connection was found between high STEAP1 expression and worse overall survival amongst cancer patients (HR = 1.87, 95% CI: 1.49–2.34, p < 0.001). In addition, a strong correlation was found between high STEAP1 expression and the occurrence of lymph node metastases (OR = 3.19, 95% CI: 1.26–8.09, p < 0.001). Analysis of TCGA datasets verified that a higher level of STEAP1 expression is linked with reduced survival in many kinds of cancer. At the single cell level, STEAP1 expression was correlated with some tumor biological behaviors, such as angiogenesis, quiescence, and stemness. Conclusions: STEAP1 could regulate various biological functions in tumors and predict prognosis as a novel biomarker in a number of cancer types.","PeriodicalId":12366,"journal":{"name":"Frontiers in bioscience","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135685216","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Background: Drosophila melanogaster is a well-studied and highly tractable genetic model system for deciphering the molecular mechanisms underlying various biological processes. Although being one of the most critical post-translational modifications of proteins, the understanding of glycosylation in Drosophila is still lagging behind compared with that of other model organisms. Methods: In this study, we systematically investigated the site-specific N-glycan profile of Drosophila melanogaster using intact glycopeptide analysis technique. This approach identified the glycans, proteins, and their glycosites in Drosophila, as well as information on site-specific glycosylation, which allowed us to know which glycans are attached to which glycosylation sites. Results: The results showed that the majority of N-glycans in Drosophila were high-mannose type (69.3%), consistent with reports in other insects. Meanwhile, fucosylated N-glycans were also highly abundant (22.7%), and the majority of them were mono-fucosylated. In addition, 24 different sialylated glycans attached with 16 glycoproteins were identified, and these proteins were mainly associated with developmental processes. Gene ontology analysis showed that N-glycosylated proteins in Drosophila were involved in multiple biological processes, such as axon guidance, N-linked glycosylation, cell migration, cell spreading, and tissue development. Interestingly, we found that seven glycosyltransferases and four glycosidases were N-glycosylated, which suggested that N-glycans may play a regulatory role in the synthesis and degradation of N-glycans and glycoproteins. Conclusions: To our knowledge, this work represents the first comprehensive analysis of site-specific N-glycosylation in Drosophila, thereby providing new perspectives for the understanding of biological functions of glycosylation in insects.
{"title":"Site-Specific Profiling of N-Glycans in Drosophila melanogaster","authors":"Fei Zhao, Chenyu Jia, Fangyu He, Meiting Hu, Xingyu Guo, Jiaxin Zhang, Xuesong Feng","doi":"10.31083/j.fbl2811278","DOIUrl":"https://doi.org/10.31083/j.fbl2811278","url":null,"abstract":"Background: Drosophila melanogaster is a well-studied and highly tractable genetic model system for deciphering the molecular mechanisms underlying various biological processes. Although being one of the most critical post-translational modifications of proteins, the understanding of glycosylation in Drosophila is still lagging behind compared with that of other model organisms. Methods: In this study, we systematically investigated the site-specific N-glycan profile of Drosophila melanogaster using intact glycopeptide analysis technique. This approach identified the glycans, proteins, and their glycosites in Drosophila, as well as information on site-specific glycosylation, which allowed us to know which glycans are attached to which glycosylation sites. Results: The results showed that the majority of N-glycans in Drosophila were high-mannose type (69.3%), consistent with reports in other insects. Meanwhile, fucosylated N-glycans were also highly abundant (22.7%), and the majority of them were mono-fucosylated. In addition, 24 different sialylated glycans attached with 16 glycoproteins were identified, and these proteins were mainly associated with developmental processes. Gene ontology analysis showed that N-glycosylated proteins in Drosophila were involved in multiple biological processes, such as axon guidance, N-linked glycosylation, cell migration, cell spreading, and tissue development. Interestingly, we found that seven glycosyltransferases and four glycosidases were N-glycosylated, which suggested that N-glycans may play a regulatory role in the synthesis and degradation of N-glycans and glycoproteins. Conclusions: To our knowledge, this work represents the first comprehensive analysis of site-specific N-glycosylation in Drosophila, thereby providing new perspectives for the understanding of biological functions of glycosylation in insects.","PeriodicalId":12366,"journal":{"name":"Frontiers in bioscience","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135685206","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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