Thyroid cancer (TC) is the most common malignant tumor of the head and neck. As a common epigenetic modification in mRNAs, N6-methyladenosine (m6A) modification plays critical roles in biological process of cancers. However, m6A methyltransferase methyltransferase-like 14 (METTL14)-mediated m6A modification and its potential regulatory mechanisms in TC are not fully elucidated. In our study, we observed that METTL14 was decreased in TC tissues and cells. And upregulation of METTL14 induced apoptotic cell death and hampered cell proliferation, epithelial mesenchymal transition (EMT) and tumor growth in vitro and in vivo. Mechanistically, METTL14 increased the expression of suppressor of cytokine signaling 3 (SOCS3) through m6A methylation modification, and knockdown of SOCS3 reversed the inhibitory effect of overexpressing METTL14 on TC tumorigenesis. In addition, METTL14-mediated m6A modification of SOCS3 inactivated the janus kinase 2 (JAK2)-signal transducer and activator of transcription 3 (STAT3) pathway, and in the METTL14-overexpressing TC cells, silencing SOCS3-induced upregulation of cell proliferation, EMT and suppression of apoptosis was reversed by JAK2/STAT3 inhibitor AG490 and WP1066. Together, we indicated that METTL14/m6A/SOCS3/JAK2/STAT3 axis play an important role in the progression of TC.
{"title":"METTL14-mediated m6A modification upregulated SOCS3 expression alleviates thyroid cancer progression by regulating the JAK2/STAT3 pathway","authors":"Ming Zhou , Yaqi Zhang , Qiong Zhang , Yanchu Tong","doi":"10.1016/j.mcp.2024.101987","DOIUrl":"10.1016/j.mcp.2024.101987","url":null,"abstract":"<div><div>Thyroid cancer (TC) is the most common malignant tumor of the head and neck. As a common epigenetic modification in mRNAs, N6-methyladenosine (m6A) modification plays critical roles in biological process of cancers. However, m6A methyltransferase methyltransferase-like 14 (METTL14)-mediated m6A modification and its potential regulatory mechanisms in TC are not fully elucidated. In our study, we observed that METTL14 was decreased in TC tissues and cells. And upregulation of METTL14 induced apoptotic cell death and hampered cell proliferation, epithelial mesenchymal transition (EMT) and tumor growth <em>in vitro</em> and <em>in vivo</em>. Mechanistically, METTL14 increased the expression of suppressor of cytokine signaling 3 (SOCS3) through m6A methylation modification, and knockdown of SOCS3 reversed the inhibitory effect of overexpressing METTL14 on TC tumorigenesis. In addition, METTL14-mediated m6A modification of SOCS3 inactivated the janus kinase 2 (JAK2)-signal transducer and activator of transcription 3 (STAT3) pathway, and in the METTL14-overexpressing TC cells, silencing SOCS3-induced upregulation of cell proliferation, EMT and suppression of apoptosis was reversed by JAK2/STAT3 inhibitor AG490 and WP1066. Together, we indicated that METTL14/m6A/SOCS3/JAK2/STAT3 axis play an important role in the progression of TC.</div></div>","PeriodicalId":49799,"journal":{"name":"Molecular and Cellular Probes","volume":"78 ","pages":"Article 101987"},"PeriodicalIF":2.3,"publicationDate":"2024-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142479163","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}
Pub Date : 2024-10-10DOI: 10.1016/j.mcp.2024.101984
Shaosheng Lou , Wang Yang , Qian Zhao , Yunshan Ouyang , Lingling Cao , Chen Lin
Background
The abnormal expression of circRNA may contribute to the progression of cervical cancer by influencing the biological processes.
Aim
This study aimed to identify the differentially expressed circRNAs in cervical cancer and validate the circ_0008193 ceRNA network in cervical cancer cells.
Methods
Using the absolute log2 value of fold change >1 and p-value of <0.05, the differentially expressed circRNAs were obtained from GSE102686 and GSE113696 from cervical cancer tissues and cervical cancer cells with the help of the GEO2R tool. Downstream miRNAs and mRNAs were predicted using relevant informatics databases. The circRNA-miRNA-mRNA interaction network was conducted with the assistance of Cytoscape. Circ_0008193-miR-182-5p-PTEN axis was validated with expression level and cell function using RT-qPCR, a dual-luciferase reporter assay, and cellular experiments.
Results
GSE102686 and GSE113696 databases overlapped 7 differentially expressed circRNAs and five circRNAs have the same expression pattern. Based on the literature and expression pattern, a circRNA-miRNA-mRNA network was conducted. The circ_0008193, miR-182-5p, and PTEN expression patterns were downregulation, upregulation, and downregulation, respectively. Overexpressed circ_0008193 suppressed proliferation, migration, and invasion of cervical cancer cells. MiR-182-5p diminished the inhibitory influence of circ_0008193 on cellular behaviors, while PTEN counteracted the effect of miR-182-5p.
Conclusion
This investigation revealed the existence of a circRNA-miRNA-mRNA network in cervical cancer, and preliminary verified the function of circ_0008193-miR-182-5p-PTEN axis in cervical cancer cells, which offers additional guidance on investigating the molecular mechanisms of cervical cancer.
{"title":"Identification of circRNA-mediated competing endogenous RNA network involved in the development of cervical cancer","authors":"Shaosheng Lou , Wang Yang , Qian Zhao , Yunshan Ouyang , Lingling Cao , Chen Lin","doi":"10.1016/j.mcp.2024.101984","DOIUrl":"10.1016/j.mcp.2024.101984","url":null,"abstract":"<div><h3>Background</h3><div>The abnormal expression of circRNA may contribute to the progression of cervical cancer by influencing the biological processes.</div></div><div><h3>Aim</h3><div>This study aimed to identify the differentially expressed circRNAs in cervical cancer and validate the circ_0008193 ceRNA network in cervical cancer cells.</div></div><div><h3>Methods</h3><div>Using the absolute log2 value of fold change >1 and <em>p</em>-value of <0.05, the differentially expressed circRNAs were obtained from GSE102686 and GSE113696 from cervical cancer tissues and cervical cancer cells with the help of the GEO2R tool. Downstream miRNAs and mRNAs were predicted using relevant informatics databases. The circRNA-miRNA-mRNA interaction network was conducted with the assistance of Cytoscape. Circ_0008193-miR-182-5p-PTEN axis was validated with expression level and cell function using RT-qPCR, a dual-luciferase reporter assay, and cellular experiments.</div></div><div><h3>Results</h3><div>GSE102686 and GSE113696 databases overlapped 7 differentially expressed circRNAs and five circRNAs have the same expression pattern. Based on the literature and expression pattern, a circRNA-miRNA-mRNA network was conducted. The circ_0008193, miR-182-5p, and PTEN expression patterns were downregulation, upregulation, and downregulation, respectively. Overexpressed circ_0008193 suppressed proliferation, migration, and invasion of cervical cancer cells. MiR-182-5p diminished the inhibitory influence of circ_0008193 on cellular behaviors, while PTEN counteracted the effect of miR-182-5p.</div></div><div><h3>Conclusion</h3><div>This investigation revealed the existence of a circRNA-miRNA-mRNA network in cervical cancer, and preliminary verified the function of circ_0008193-miR-182-5p-PTEN axis in cervical cancer cells, which offers additional guidance on investigating the molecular mechanisms of cervical cancer.</div></div>","PeriodicalId":49799,"journal":{"name":"Molecular and Cellular Probes","volume":"78 ","pages":"Article 101984"},"PeriodicalIF":2.3,"publicationDate":"2024-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142299498","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}
Various pieces of evidence suggest an elevation in the levels of EGFR and HER2 in different cancers leading to the proliferation, invasion, and metastasis of cancer cells. In this study, we conducted a comprehensive investigation into the expression alterations of these two receptors in various cancers using in silico data. In addition, we investigated the therapeutic potential of lapatinib as an inhibitor of these receptors in various cancer types.
Methods
RNAseq data for prevalent cancers were downloaded from The Cancer Genome Atlas (TCGA). After initial preprocessing, expression changes of HER2, EGFR, and candidate genes—identified based on their association with EGFR and HER2 signaling pathways—were examined. Human protein atlas data were utilized to assess the protein expression of HER2 and EGFR. GSE129254 was employed to identify molecular pathways and candidate genes associated with lapatinib. The protein-protein interaction network was used to identify lapatinib-influenced hub genes. Clinical data for common cancers were used to investigate the correlation between the expression of candidate genes and patients' mortality rates by Cox regression test.
Results
The findings clearly indicated a significant increase in the expression levels of HER2 and EGFR in cancers such as kidney, lung, breast, bladder, pancreas, head and neck, stomach, and endometrial, both at the mRNA and protein levels (p-value <0.01). Additionally, more than 30 % of samples in some cancers showed a twofold increase in HER2 or EGFR expression. The analysis of GSE129254 data revealed that lapatinib reduces the expression of numerous genes associated with cell proliferation. METTL1, LYAR, LTV1, CCND1, NOP2, and DDX21 were identified as hub genes related to the effect of lapatinib. Our results demonstrated that many hub genes exhibited elevated expression in candidate cancers, and the upregulation of some of them was correlated with poor prognosis.
Conclusion
Our results indicate an upregulation in the expression levels of HER2 and EGFR in certain common cancers, suggesting that lapatinib, in addition to breast cancer, could be considered for the treatment of these cancers. Furthermore, we demonstrated that some genes with increased expression in prevalent cancers and associated with poor prognosis have the potential to be modulated by lapatinib.
{"title":"The Prospective role of lapatinib as an adjuvant therapy in prevalent cancers: Insights from in silico analysis targeting EGFR and HER2","authors":"Behnaz Dolatabadi , Maryam Peymani , Leila Rouhi , Ali Salehzadeh , Kiavash Hushmandi , Mehrdad Hashemi","doi":"10.1016/j.mcp.2024.101985","DOIUrl":"10.1016/j.mcp.2024.101985","url":null,"abstract":"<div><h3>Introduction</h3><div>Various pieces of evidence suggest an elevation in the levels of EGFR and HER2 in different cancers leading to the proliferation, invasion, and metastasis of cancer cells. In this study, we conducted a comprehensive investigation into the expression alterations of these two receptors in various cancers using in silico data. In addition, we investigated the therapeutic potential of lapatinib as an inhibitor of these receptors in various cancer types.</div></div><div><h3>Methods</h3><div>RNAseq data for prevalent cancers were downloaded from The Cancer Genome Atlas (TCGA). After initial preprocessing, expression changes of HER2, EGFR, and candidate genes—identified based on their association with EGFR and HER2 signaling pathways—were examined. Human protein atlas data were utilized to assess the protein expression of HER2 and EGFR. GSE129254 was employed to identify molecular pathways and candidate genes associated with lapatinib. The protein-protein interaction network was used to identify lapatinib-influenced hub genes. Clinical data for common cancers were used to investigate the correlation between the expression of candidate genes and patients' mortality rates by Cox regression test.</div></div><div><h3>Results</h3><div>The findings clearly indicated a significant increase in the expression levels of HER2 and EGFR in cancers such as kidney, lung, breast, bladder, pancreas, head and neck, stomach, and endometrial, both at the mRNA and protein levels (p-value <0.01). Additionally, more than 30 % of samples in some cancers showed a twofold increase in HER2 or EGFR expression. The analysis of GSE129254 data revealed that lapatinib reduces the expression of numerous genes associated with cell proliferation. METTL1, LYAR, LTV1, CCND1, NOP2, and DDX21 were identified as hub genes related to the effect of lapatinib. Our results demonstrated that many hub genes exhibited elevated expression in candidate cancers, and the upregulation of some of them was correlated with poor prognosis.</div></div><div><h3>Conclusion</h3><div>Our results indicate an upregulation in the expression levels of HER2 and EGFR in certain common cancers, suggesting that lapatinib, in addition to breast cancer, could be considered for the treatment of these cancers. Furthermore, we demonstrated that some genes with increased expression in prevalent cancers and associated with poor prognosis have the potential to be modulated by lapatinib.</div></div>","PeriodicalId":49799,"journal":{"name":"Molecular and Cellular Probes","volume":"78 ","pages":"Article 101985"},"PeriodicalIF":2.3,"publicationDate":"2024-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142382179","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}
Pub Date : 2024-09-30DOI: 10.1016/j.mcp.2024.101983
Guoda Han , Xu Liu , Tian Gao , Lei Zhang , Xiaoling Zhang , Xiaonan Wei , Yecheng Lin , Bohong Yin
Aim
In this research, we aimed to develop a model for the accurate prediction of gastric cancer based on H&E findings combined with machine learning pathomics.
Methods
Transcriptome data, pathological images, and clinical data from 443 cases were retrieved from TCGA (The Cancer Genome Atlas Program) for survival analysis. The images were segmented using the Otsu algorithm, and features were extracted using the PyRadiomics package. Subsequently, the cases were randomly divided into a training cohort of 165 cases and a validation cohort of 69 cases. Features selected via minimum Redundancy - Maximum Relevance (mRMR)- recursive feature elimination (RFE) screening were used to train a model using the Gradient Boosting Machine (GBM) algorithm. The model's performance was evaluated using the area under the receiver operating characteristic (ROC) curve (AUC), calibration curves, and decision curves. Additionally, the correlation between the Pathomics score (PS) and immune genes was examined.
Results
In the multivariate analysis, heightened infiltration of activated CD4 memory T cells was strongly associated with improved overall survival (HR = 0.505, 95 % CI = 0.342–0.745, P < 0.001). The pathomic model, exhibiting robust predictive capability, demonstrated impressive AUC values of 0.844 and 0.750 in both study cohorts. The Decision Curve Analysis (DCA) unequivocally underscored the model's exceptional clinical utility. In a subsequent multivariate analysis, heightened infiltration of the PS also emerged as a significant protective factor for overall survival (HR = 0.506, 95 % CI = 0.329–0.777, P = 0.002).
Conclusion
The pathomic model based on H&E slides for predicting the infiltration degree of activated CD4 memory T cells, along with integrated bioinformatics analysis elucidating potential molecular mechanisms, offers novel prognostic indicators for the precise stratification and individualized prognosis of gastric cancer patients.
目的：在这项研究中，我们旨在开发一种基于H&E结果并结合机器学习病理组学的胃癌准确预测模型：方法：我们从 TCGA（癌症基因组图谱计划）中获取了 443 个病例的转录组数据、病理图像和临床数据，用于生存分析。使用Otsu算法对图像进行分割，并使用PyRadiomics软件包提取特征。随后，病例被随机分为 165 例训练队列和 69 例验证队列。通过最小冗余-最大相关性（mRMR）-递归特征剔除（RFE）筛选出的特征被用于使用梯度提升机（GBM）算法训练模型。使用接收者操作特征曲线（ROC）下面积（AUC）、校准曲线和决策曲线对模型的性能进行了评估。此外，还研究了病理组学评分（PS）与免疫基因之间的相关性：在多变量分析中，活化的 CD4 记忆 T 细胞浸润增加与总生存期的改善密切相关（HR = 0.505，95% CI = 0.342-0.745，P <0.001）。病理模型具有强大的预测能力，在两个研究队列中的AUC值分别为0.844和0.750，令人印象深刻。决策曲线分析（DCA）明确强调了该模型卓越的临床实用性。在随后的多变量分析中，PS的高度浸润也成为总生存率的重要保护因素（HR = 0.506，95% CI = 0.329-0.777，P = 0.002）：基于H&E切片预测活化CD4记忆T细胞浸润程度的病理模型，以及阐明潜在分子机制的综合生物信息学分析，为胃癌患者的精确分层和个体化预后提供了新的预后指标。
{"title":"Prognostic prediction of gastric cancer based on H&E findings and machine learning pathomics","authors":"Guoda Han , Xu Liu , Tian Gao , Lei Zhang , Xiaoling Zhang , Xiaonan Wei , Yecheng Lin , Bohong Yin","doi":"10.1016/j.mcp.2024.101983","DOIUrl":"10.1016/j.mcp.2024.101983","url":null,"abstract":"<div><h3>Aim</h3><div>In this research, we aimed to develop a model for the accurate prediction of gastric cancer based on H&E findings combined with machine learning pathomics.</div></div><div><h3>Methods</h3><div>Transcriptome data, pathological images, and clinical data from 443 cases were retrieved from TCGA (The Cancer Genome Atlas Program) for survival analysis. The images were segmented using the Otsu algorithm, and features were extracted using the PyRadiomics package. Subsequently, the cases were randomly divided into a training cohort of 165 cases and a validation cohort of 69 cases. Features selected via minimum Redundancy - Maximum Relevance (mRMR)- recursive feature elimination (RFE) screening were used to train a model using the Gradient Boosting Machine (GBM) algorithm. The model's performance was evaluated using the area under the receiver operating characteristic (ROC) curve (AUC), calibration curves, and decision curves. Additionally, the correlation between the Pathomics score (PS) and immune genes was examined.</div></div><div><h3>Results</h3><div>In the multivariate analysis, heightened infiltration of activated CD4 memory T cells was strongly associated with improved overall survival (HR = 0.505, 95 % CI = 0.342–0.745, P < 0.001). The pathomic model, exhibiting robust predictive capability, demonstrated impressive AUC values of 0.844 and 0.750 in both study cohorts. The Decision Curve Analysis (DCA) unequivocally underscored the model's exceptional clinical utility. In a subsequent multivariate analysis, heightened infiltration of the PS also emerged as a significant protective factor for overall survival (HR = 0.506, 95 % CI = 0.329–0.777, P = 0.002).</div></div><div><h3>Conclusion</h3><div>The pathomic model based on H&E slides for predicting the infiltration degree of activated CD4 memory T cells, along with integrated bioinformatics analysis elucidating potential molecular mechanisms, offers novel prognostic indicators for the precise stratification and individualized prognosis of gastric cancer patients.</div></div>","PeriodicalId":49799,"journal":{"name":"Molecular and Cellular Probes","volume":"78 ","pages":"Article 101983"},"PeriodicalIF":2.3,"publicationDate":"2024-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142299499","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}
Pub Date : 2024-08-31DOI: 10.1016/j.mcp.2024.101981
Yuan-yuan Lu , Yi Li , Zhi-li Chen , Xiang-hua Xiong , Qing-yang Wang , Hao-long Dong , Chen Zhu , Jia-zhen Cui , Ao Hu , Lei Wang , Na Song , Gang Liu , Hui-peng Chen
The clinical treatment of hepatocellular carcinoma (HCC) is still a heavy burden worldwide. Intracellular microRNAs (miRNAs) commonly express abnormally in cancers, thus they are potential therapeutic targets for cancer treatment. miR-21 is upregulated in HCC whereas miR-122 is enriched in normal hepatocyte but downregulated in HCC. In our study, we first generated a reporter genetic switch compromising of miR-21 and miR-122 sponges as sensor, green fluorescent protein (GFP) as reporter gene and L7Ae:K-turn as regulatory element. The reporter expression was turned up in miR-21 enriched environment while turned down in miR-122 enriched environment, indicating that the reporter switch is able to respond distinctly to different miRNA environment. Furthermore, an AAT promoter, which is hepatocyte-specific, is applied to increase the specificity to hepatocyte. A killing switch with AAT promoter and an apoptosis-inducing element, Bax, in addition to miR-21 and miR-122 significantly inhibited cell viability in Huh-7 by 70 % and in HepG2 by 60 %. By contrast, cell viability was not affected in five non-HCC cells. Thus, we provide a novel feasible strategy to improve the safety of miRNA-based therapeutic agent to cancer.
{"title":"Genetic switch selectively kills hepatocellular carcinoma cell based on microRNA and tissue-specific promoter","authors":"Yuan-yuan Lu , Yi Li , Zhi-li Chen , Xiang-hua Xiong , Qing-yang Wang , Hao-long Dong , Chen Zhu , Jia-zhen Cui , Ao Hu , Lei Wang , Na Song , Gang Liu , Hui-peng Chen","doi":"10.1016/j.mcp.2024.101981","DOIUrl":"10.1016/j.mcp.2024.101981","url":null,"abstract":"<div><p>The clinical treatment of hepatocellular carcinoma (HCC) is still a heavy burden worldwide. Intracellular microRNAs (miRNAs) commonly express abnormally in cancers, thus they are potential therapeutic targets for cancer treatment. miR-21 is upregulated in HCC whereas miR-122 is enriched in normal hepatocyte but downregulated in HCC. In our study, we first generated a reporter genetic switch compromising of miR-21 and miR-122 sponges as sensor, green fluorescent protein (GFP) as reporter gene and L7Ae:K-turn as regulatory element. The reporter expression was turned up in miR-21 enriched environment while turned down in miR-122 enriched environment, indicating that the reporter switch is able to respond distinctly to different miRNA environment. Furthermore, an AAT promoter, which is hepatocyte-specific, is applied to increase the specificity to hepatocyte. A killing switch with AAT promoter and an apoptosis-inducing element, Bax, in addition to miR-21 and miR-122 significantly inhibited cell viability in Huh-7 by 70 % and in HepG2 by 60 %. By contrast, cell viability was not affected in five non-HCC cells. Thus, we provide a novel feasible strategy to improve the safety of miRNA-based therapeutic agent to cancer.</p></div>","PeriodicalId":49799,"journal":{"name":"Molecular and Cellular Probes","volume":"77 ","pages":"Article 101981"},"PeriodicalIF":2.3,"publicationDate":"2024-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0890850824000331/pdfft?md5=f411ef273941f5ad14203bbffa219364&pid=1-s2.0-S0890850824000331-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142094104","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}
Pub Date : 2024-08-14DOI: 10.1016/j.mcp.2024.101979
Sha Lu, Cong'e Tan, Xue Xiao
Backgroud
Cellular senescence is closely related to human aging and multiple aging-related diseases, and impaired mitochondrial energy metabolism is an important mechanism of cellular senescence. Notably, microRNA-125b-1-3p (miR-125b-1-3p) is a microRNA (miR, miRNA) that may be associated with mitochondrial energy metabolism. Ubiquinol-cytochrome c reductase binding protein (UQCRB) gene, predicted by bioinformatics tools to be targeted by miR-125b-1-3p, could serve as a novel diagnostic indicator and therapeutic target for cellular senescence-associated diseases, as well as a new idea for delaying aging.
Methods
First, the dual-luciferase reporter gene assay was used to identify UQCRB as a target gene of miR-125b-1-3p. Next, miRNA interference technology was conducted to verify that miR-125b-1-3p could negatively regulate the expression of UQCRB. Subsequently, the influence of miR-125b-1-3p on mitochondrial energy metabolism function was explored by observing the internal substances and ultrastructure of mitochondria. Further, an in vitro model of cellular senescence was established in rat renal tubular epithelial cells, which was characterized by detecting senescence-related proteins p16 and p21 and beta-galactosidase (β-gal) activity. Finally, the mitochondrial energy metabolism function of hydrogen peroxide (H2O2)-incubated cells was explored.
Results
The experimental results revealed that miR-125b-1-3p affected the mitochondrial energy metabolism function by inhibiting the target gene UQCRB. Meanwhile, the level of mitochondrial energy metabolism function in H2O2-incubated senescent cells was lower than that in normal cells.
Conclusion
In this study, we identified the target gene, UQCRB, of miR-125b-1-3p, and demonstrated its role in the pathway of mitochondrial energy metabolism, as well as its possible effect on cellular senescence through this pathway. The ameliorative effects on cellular senescence can be further explored in subsequent studies to provide additional options for delaying aging or treating aging-related diseases.
{"title":"MiR-125b-1-3p-mediated UQCRB inhibition facilitates mitochondrial metabolism disorders in a rat cellular senescencemodel","authors":"Sha Lu, Cong'e Tan, Xue Xiao","doi":"10.1016/j.mcp.2024.101979","DOIUrl":"10.1016/j.mcp.2024.101979","url":null,"abstract":"<div><h3>Backgroud</h3><p>Cellular senescence is closely related to human aging and multiple aging-related diseases, and impaired mitochondrial energy metabolism is an important mechanism of cellular senescence. Notably, microRNA-125b-1-3p (miR-125b-1-3p) is a microRNA (miR, miRNA) that may be associated with mitochondrial energy metabolism. Ubiquinol-cytochrome c reductase binding protein (<em>UQCRB</em>) gene, predicted by bioinformatics tools to be targeted by miR-125b-1-3p, could serve as a novel diagnostic indicator and therapeutic target for cellular senescence-associated diseases, as well as a new idea for delaying aging.</p></div><div><h3>Methods</h3><p>First, the dual-luciferase reporter gene assay was used to identify <em>UQCRB</em> as a target gene of miR-125b-1-3p. Next, miRNA interference technology was conducted to verify that miR-125b-1-3p could negatively regulate the expression of <em>UQCRB</em>. Subsequently, the influence of miR-125b-1-3p on mitochondrial energy metabolism function was explored by observing the internal substances and ultrastructure of mitochondria. Further, an <em>in vitro</em> model of cellular senescence was established in rat renal tubular epithelial cells, which was characterized by detecting senescence-related proteins p16 and p21 and beta-galactosidase (β-gal) activity. Finally, the mitochondrial energy metabolism function of hydrogen peroxide (H<sub>2</sub>O<sub>2</sub>)-incubated cells was explored.</p></div><div><h3>Results</h3><p>The experimental results revealed that miR-125b-1-3p affected the mitochondrial energy metabolism function by inhibiting the target gene <em>UQCRB.</em> Meanwhile, the level of mitochondrial energy metabolism function in H<sub>2</sub>O<sub>2</sub>-incubated senescent cells was lower than that in normal cells.</p></div><div><h3>Conclusion</h3><p>In this study, we identified the target gene, <em>UQCRB</em>, of miR-125b-1-3p, and demonstrated its role in the pathway of mitochondrial energy metabolism, as well as its possible effect on cellular senescence through this pathway. The ameliorative effects on cellular senescence can be further explored in subsequent studies to provide additional options for delaying aging or treating aging-related diseases.</p></div>","PeriodicalId":49799,"journal":{"name":"Molecular and Cellular Probes","volume":"77 ","pages":"Article 101979"},"PeriodicalIF":2.3,"publicationDate":"2024-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0890850824000318/pdfft?md5=2f164a8a41a33e01fed76a3bd1c7f0e6&pid=1-s2.0-S0890850824000318-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141908126","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}
Pub Date : 2024-08-12DOI: 10.1016/j.mcp.2024.101975
Mei Yang , Yongzhen Mo , Daixi Ren , Yan Hu , Yiting Tian , Zhaoyang Zeng , Wei Xiong
Recently, it has been discovered surprisingly that tRNA can be cleaved into specific small fragments under certain conditions. Most importantly, these tRNA-derived fragments (tRFs) participate in the regulation of gene expression, playing pivotal roles in various physiological and pathological processes and thus attracting widespread attention. Detecting tRF expression in tissues and cells often involves using tRF-specific stem-loop primers for reverse transcription. However, the high specificity offered by this method limits it to transcribing only one specific tRF sequence per reaction, necessitating separate reverse transcription and qPCR steps for multiple tRFs, leading to substantially increased time and resource consumption. This becomes especially challenging in precious samples with limited RNA availability. To address these issues, there is an urgent need for a universal and cost-effective tRF identification method. This study introduces a versatile tRF detection approach based on the uniform polyadenylation of all tRFs, allowing reverse transcription with a universal oligo(dT) primer. This method enables simultaneous reverse transcription of all target tRFs in one reaction, greatly facilitating subsequent qPCR analysis. Furthermore, it demonstrates exceptional sensitivity and specificity, offering significant value in tRF-related research.
{"title":"A versatile and efficient method for detecting tRNA-derived fragments","authors":"Mei Yang , Yongzhen Mo , Daixi Ren , Yan Hu , Yiting Tian , Zhaoyang Zeng , Wei Xiong","doi":"10.1016/j.mcp.2024.101975","DOIUrl":"10.1016/j.mcp.2024.101975","url":null,"abstract":"<div><p>Recently, it has been discovered surprisingly that tRNA can be cleaved into specific small fragments under certain conditions. Most importantly, these tRNA-derived fragments (tRFs) participate in the regulation of gene expression, playing pivotal roles in various physiological and pathological processes and thus attracting widespread attention. Detecting tRF expression in tissues and cells often involves using tRF-specific stem-loop primers for reverse transcription. However, the high specificity offered by this method limits it to transcribing only one specific tRF sequence per reaction, necessitating separate reverse transcription and qPCR steps for multiple tRFs, leading to substantially increased time and resource consumption. This becomes especially challenging in precious samples with limited RNA availability. To address these issues, there is an urgent need for a universal and cost-effective tRF identification method. This study introduces a versatile tRF detection approach based on the uniform polyadenylation of all tRFs, allowing reverse transcription with a universal oligo(dT) primer. This method enables simultaneous reverse transcription of all target tRFs in one reaction, greatly facilitating subsequent qPCR analysis. Furthermore, it demonstrates exceptional sensitivity and specificity, offering significant value in tRF-related research.</p></div>","PeriodicalId":49799,"journal":{"name":"Molecular and Cellular Probes","volume":"77 ","pages":"Article 101975"},"PeriodicalIF":2.3,"publicationDate":"2024-08-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0890850824000276/pdfft?md5=3915668f148fff980843d3d63acb916c&pid=1-s2.0-S0890850824000276-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141903412","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}
Pub Date : 2024-08-12DOI: 10.1016/j.mcp.2024.101980
Janghyun Kim , Jee-hye Kang , Myung-Giun Noh , Bora Lee , Yoo-Duk Choi , Ok Joon Kim , Young Kim
Verrucous carcinoma (VC) is a rare subtype of squamous cell carcinoma (SCC) characterized by its histological presentation as a low-grade tumor with no potential for metastasis, setting it apart from invasive SCC. However, distinguishing VC from its benign counterpart, verrucous hyperplasia (VH), is challenging due to their clinical and morphological similarities. Despite the importance of accurate diagnosis for determining treatment strategies, diagnosis for of VH and VC relied only on lesion recurrence after resection. To address this challenge, we generated RNA profiling data from tissue samples of VH and VC patients to identify novel diagnostic markers. We analyzed differentially expressed (DE) mRNA and long non-coding RNA (lncRNA) in tissue samples from VH and VC patients. Additionally, ChIP-X Enrichment Analysis 3 (ChEA3) was conducted to identify the top five transcription factors potentially regulating the expression of DE mRNAs in VH and VC. Our analysis of mRNA and lncRNA expression profiles in VH and VC provides insights into the underlying molecular characteristics of these diseases and offers potential new diagnostic markers. The identification of specific DE genes and lncRNAs may enable clinicians to more accurately differentiate between VH and VC, leading to better treatment choices.
{"title":"New potential diagnostic markers for verrucous hyperplasia and verrucous carcinoma based on RNA-sequencing data","authors":"Janghyun Kim , Jee-hye Kang , Myung-Giun Noh , Bora Lee , Yoo-Duk Choi , Ok Joon Kim , Young Kim","doi":"10.1016/j.mcp.2024.101980","DOIUrl":"10.1016/j.mcp.2024.101980","url":null,"abstract":"<div><p>Verrucous carcinoma (VC) is a rare subtype of squamous cell carcinoma (SCC) characterized by its histological presentation as a low-grade tumor with no potential for metastasis, setting it apart from invasive SCC. However, distinguishing VC from its benign counterpart, verrucous hyperplasia (VH), is challenging due to their clinical and morphological similarities. Despite the importance of accurate diagnosis for determining treatment strategies, diagnosis for of VH and VC relied only on lesion recurrence after resection. To address this challenge, we generated RNA profiling data from tissue samples of VH and VC patients to identify novel diagnostic markers. We analyzed differentially expressed (DE) mRNA and long non-coding RNA (lncRNA) in tissue samples from VH and VC patients. Additionally, ChIP-X Enrichment Analysis 3 (ChEA3) was conducted to identify the top five transcription factors potentially regulating the expression of DE mRNAs in VH and VC. Our analysis of mRNA and lncRNA expression profiles in VH and VC provides insights into the underlying molecular characteristics of these diseases and offers potential new diagnostic markers. The identification of specific DE genes and lncRNAs may enable clinicians to more accurately differentiate between VH and VC, leading to better treatment choices.</p></div>","PeriodicalId":49799,"journal":{"name":"Molecular and Cellular Probes","volume":"77 ","pages":"Article 101980"},"PeriodicalIF":2.3,"publicationDate":"2024-08-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S089085082400032X/pdfft?md5=6ce56ca8e894161482b951df26676cb7&pid=1-s2.0-S089085082400032X-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141914376","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}
Pub Date : 2024-08-07DOI: 10.1016/j.mcp.2024.101977
Wan Zhong , Chun Wang , Ye Sun
Objective
Utilizing transcriptome analysis to investigate the mechanisms and therapeutic approaches for cisplatin resistance in non-small cell lung cancer (NSCLC).
Methods
Firstly, the biological characters of A549 cells and A549/DDP cells were detected by RNA sequencing, CCK-8 and hippocampal energy analyzer. Then, the differential Genes were functionally enriched by GO and KEGG and the competitive endogenous RNA network map was constructed. Finally, the effects of the predicted biogenesis pathway on the biological functions of A549/DDP cells were verified by in vitro and in vivo experiments.
Result
The differentially transcribed genes of A549 and A549/DDP cells were analyzed by enrichment analysis and cell biological characteristics detection. The results showed that A549/DDP cells showed significantly increased resistance to cisplatin, glucose metabolism signaling pathway and glycolysis levels compared with A549 cells. Among glycolysis-related transcription genes, PKM had the most significant difference Fold Change is 8. LncRNA PCIF1 is a new marker of A549/DDP cells and can be used as a molecular sponge to regulate the expression of PKM. LncRNA PCIF1 targets miR-326 to induce PKM expression, promote glycolysis level, and enhance the resistance of A549/DDP cells to cisplatin.
Conclusion
LncRNA PCIF1 as biomarkers of A549/DDP cells, higher expression can induce the PKM, promote cell glycolysis, lead to the occurrence of cisplatin resistance. LncRNA PCIF1 can be considered as a potential target for treating cisplatin-resistant NSCLC.
{"title":"LncRNA PCIF1 promotes aerobic glycolysis in A549/DDP cells by competitively binding miR-326 to regulate PKM expression","authors":"Wan Zhong , Chun Wang , Ye Sun","doi":"10.1016/j.mcp.2024.101977","DOIUrl":"10.1016/j.mcp.2024.101977","url":null,"abstract":"<div><h3>Objective</h3><p>Utilizing transcriptome analysis to investigate the mechanisms and therapeutic approaches for cisplatin resistance in non-small cell lung cancer (NSCLC).</p></div><div><h3>Methods</h3><p>Firstly, the biological characters of A549 cells and A549/DDP cells were detected by RNA sequencing, CCK-8 and hippocampal energy analyzer. Then, the differential Genes were functionally enriched by GO and KEGG and the competitive endogenous RNA network map was constructed. Finally, the effects of the predicted biogenesis pathway on the biological functions of A549/DDP cells were verified by in vitro and in vivo experiments.</p></div><div><h3>Result</h3><p>The differentially transcribed genes of A549 and A549/DDP cells were analyzed by enrichment analysis and cell biological characteristics detection. The results showed that A549/DDP cells showed significantly increased resistance to cisplatin, glucose metabolism signaling pathway and glycolysis levels compared with A549 cells. Among glycolysis-related transcription genes, PKM had the most significant difference Fold Change is 8. LncRNA PCIF1 is a new marker of A549/DDP cells and can be used as a molecular sponge to regulate the expression of PKM. LncRNA PCIF1 targets miR-326 to induce PKM expression, promote glycolysis level, and enhance the resistance of A549/DDP cells to cisplatin.</p></div><div><h3>Conclusion</h3><p>LncRNA PCIF1 as biomarkers of A549/DDP cells, higher expression can induce the PKM, promote cell glycolysis, lead to the occurrence of cisplatin resistance. LncRNA PCIF1 can be considered as a potential target for treating cisplatin-resistant NSCLC.</p></div>","PeriodicalId":49799,"journal":{"name":"Molecular and Cellular Probes","volume":"77 ","pages":"Article 101977"},"PeriodicalIF":2.3,"publicationDate":"2024-08-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S089085082400029X/pdfft?md5=f5d1e132c9ded44bf4ac17a2e707db00&pid=1-s2.0-S089085082400029X-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141793890","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}
Pub Date : 2024-08-03DOI: 10.1016/j.mcp.2024.101978
Jiao Zhao, Jingru Zhang, Xiaojing Tong, Lili Zhao, Rong Cao
Ovarian cancer (OC) is the fifth most common cause of death in women worldwide. Chemoresistance is a key reason for treatment failure, causing high mortality. As a member of the tripartite motif-containing (TRIM) protein family, tripartite motif 47 (TRIM47) plays a vital role in the carcinogenesis and drug resistance of various cancers. This study investigated the impact and mechanisms of TRIM47 on cisplatin (DDP) chemosensitivity and apoptosis in OC. OC cell viability was assessed with a cell counting kit-8 assay and OC cell apoptosis was assessed using flow cytometry, caspase-3 and caspase-9 activity, and Bax and Bcl-2 expression assays while gene and protein expression were assessed using qRT–PCR and Western blot assays. The expression of TRIM47 was significantly increased in both DDP-resistant tissues from patients with OC tissues and in cancer cell lines compared with that in normal tissue or parental cell lines. The increased level of TRIM47 correlated with poor prognosis in patients with OC. Functional assays demonstrated that TRIM47 promoted DDP resistance both in vitro and in vivo. The increased viability and reduced apoptosis of OC cells induced by TRIM47 can be rescued by the endoplasmic reticulum (ER) stress–inducer tunicamycin, suggesting that TRIM47 inhibits OC cell apoptosis by suppressing ER stress. Therefore, TRIM47 may be targeted as a therapeutic strategy for DDP resistance in OC.
{"title":"TRIM47 inhibits cisplatin chemosensitivity and endoplasmic reticulum stress-induced apoptosis of ovarian cancer cells","authors":"Jiao Zhao, Jingru Zhang, Xiaojing Tong, Lili Zhao, Rong Cao","doi":"10.1016/j.mcp.2024.101978","DOIUrl":"10.1016/j.mcp.2024.101978","url":null,"abstract":"<div><p>Ovarian cancer (OC) is the fifth most common cause of death in women worldwide. Chemoresistance is a key reason for treatment failure, causing high mortality. As a member of the tripartite motif-containing (TRIM) protein family, tripartite motif 47 (TRIM47) plays a vital role in the carcinogenesis and drug resistance of various cancers. This study investigated the impact and mechanisms of TRIM47 on cisplatin (DDP) chemosensitivity and apoptosis in OC. OC cell viability was assessed with a cell counting kit-8 assay and OC cell apoptosis was assessed using flow cytometry, caspase-3 and caspase-9 activity, and Bax and Bcl-2 expression assays while gene and protein expression were assessed using qRT–PCR and Western blot assays. The expression of TRIM47 was significantly increased in both DDP-resistant tissues from patients with OC tissues and in cancer cell lines compared with that in normal tissue or parental cell lines. The increased level of TRIM47 correlated with poor prognosis in patients with OC. Functional assays demonstrated that TRIM47 promoted DDP resistance both in vitro and in vivo. The increased viability and reduced apoptosis of OC cells induced by TRIM47 can be rescued by the endoplasmic reticulum (ER) stress–inducer tunicamycin, suggesting that TRIM47 inhibits OC cell apoptosis by suppressing ER stress. Therefore, TRIM47 may be targeted as a therapeutic strategy for DDP resistance in OC.</p></div>","PeriodicalId":49799,"journal":{"name":"Molecular and Cellular Probes","volume":"77 ","pages":"Article 101978"},"PeriodicalIF":2.3,"publicationDate":"2024-08-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0890850824000306/pdfft?md5=e2e2a5f7397a5e10237b67c8397fdd1b&pid=1-s2.0-S0890850824000306-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141890711","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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