1
|
He Y, Yu Q, Ma X, Lv D, Wang H, Qiu W, Chen XF, Jiao Y, Liu Y. A metabolomics approach reveals metabolic disturbance of human cholangiocarcinoma cells after parthenolide treatment. JOURNAL OF ETHNOPHARMACOLOGY 2024; 328:118075. [PMID: 38513779 DOI: 10.1016/j.jep.2024.118075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 03/09/2024] [Accepted: 03/18/2024] [Indexed: 03/23/2024]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Tanacetum parthenium (L.) Schultz-Bip, commonly known as feverfew, has been traditionally used to treat fever, migraines, rheumatoid arthritis, and cancer. Parthenolide (PTL), the main bioactive ingredient isolated from the shoots of feverfew, is a sesquiterpene lactone with anti-inflammatory and antitumor properties. Previous studies showed that PTL exerts anticancer activity in various cancers, including hepatoma, cholangiocarcinoma, acute myeloid leukemia, breast, prostate, and colorectal cancer. However, the metabolic mechanism underlying the anticancer effect of PTL remains poorly understood. AIM OF THE STUDY To explore the anticancer activity and underlying mechanism of PTL in human cholangiocarcinoma cells. MATERIAL AND METHODS In this investigation, the effects and mechanisms of PTL on human cholangiocarcinoma cells were investigated via a liquid chromatography/mass spectrometry (LC/MS)-based metabolomics approach. First, cell proliferation and apoptosis were evaluated using cell counting kit-8 (CCK-8), flow cytometry analysis, and western blotting. Then, LC/MS-based metabolic profiling along with orthogonal partial least-squares discriminant analysis (OPLS-DA) has been constructed to distinguish the metabolic changes between the negative control group and the PTL-treated group in TFK1 cells. Next, enzyme-linked immunosorbent assay (ELISA) was applied to investigate the changes of metabolic enzymes associated with significantly alerted metabolites. Finally, the metabolic network related to key metabolic enzymes, metabolites, and metabolic pathways was established using MetaboAnalyst 5.0 and Kyoto Encyclopedia of Genes and Genomes (KEGG) Pathway Database. RESULTS PTL treatment could induce the proliferation inhibition and apoptosis of TFK1 in a concentration-dependent manner. Forty-three potential biomarkers associated with the antitumor effect of PTL were identified, which primarily related to glutamine and glutamate metabolism, alanine, aspartate and glutamate metabolism, phenylalanine, tyrosine and tryptophan biosynthesis, phenylalanine metabolism, arginine biosynthesis, arginine and proline metabolism, glutathione metabolism, nicotinate and nicotinamide metabolism, pyrimidine metabolism, fatty acid metabolism, phospholipid catabolism, and sphingolipid metabolism. Pathway analysis of upstream and downstream metabolites, we found three key metabolic enzymes, including glutaminase (GLS), γ-glutamyl transpeptidase (GGT), and carnitine palmitoyltransferase 1 (CPT1), which mainly involved in glutamine and glutamate metabolism, glutathione metabolism, and fatty acid metabolism. The changes of metabolic enzymes associated with significantly alerted metabolites were consistent with the levels of metabolites, and the metabolic network related to key metabolic enzymes, metabolites, and metabolic pathways was established. PTL may exert its antitumor effect against cholangiocarcinoma by disturbing metabolic pathways. Furthermore, we selected two positive control agents that are considered as first-line chemotherapy standards in cholangiocarcinoma therapy to verify the reliability and accuracy of our metabolomic study on PTL. CONCLUSION This research enhanced our comprehension of the metabolic profiling and mechanism of PTL treatment on cholangiocarcinoma cells, which provided some references for further research into the anti-cancer mechanisms of other drugs.
Collapse
Affiliation(s)
- Yongping He
- School of Pharmacy, Guangxi Medical University, Guangxi, Nanning, 530021, China; School of Pharmacy, Naval Medical University (Second Military Medical University), Shanghai, 200433, China; Department of Pharmacy, The People's Hospital of Chongzuo, Guangxi, Chongzuo, 532200, China
| | - Qianxue Yu
- School of Pharmacy, Naval Medical University (Second Military Medical University), Shanghai, 200433, China
| | - Xiaoyu Ma
- School of Pharmacy, Naval Medical University (Second Military Medical University), Shanghai, 200433, China
| | - Diya Lv
- School of Pharmacy, Naval Medical University (Second Military Medical University), Shanghai, 200433, China
| | - Hui Wang
- School of Pharmacy, Naval Medical University (Second Military Medical University), Shanghai, 200433, China
| | - Weian Qiu
- School of Pharmacy, Guangxi Medical University, Guangxi, Nanning, 530021, China
| | - Xiao Fei Chen
- School of Pharmacy, Naval Medical University (Second Military Medical University), Shanghai, 200433, China; Shanghai Key Laboratory for Pharmaceutical Metabolite Research, Shanghai, 200433, China
| | - Yang Jiao
- School of Pharmacy, Guangxi Medical University, Guangxi, Nanning, 530021, China.
| | - Yue Liu
- School of Pharmacy, Naval Medical University (Second Military Medical University), Shanghai, 200433, China; Shanghai Key Laboratory for Pharmaceutical Metabolite Research, Shanghai, 200433, China.
| |
Collapse
|
2
|
Wei T, Liu J, Ma S, Wang M, Yuan Q, Huang A, Wu Z, Shang D, Yin P. A Nucleotide Metabolism-Related Gene Signature for Risk Stratification and Prognosis Prediction in Hepatocellular Carcinoma Based on an Integrated Transcriptomics and Metabolomics Approach. Metabolites 2023; 13:1116. [PMID: 37999212 PMCID: PMC10673507 DOI: 10.3390/metabo13111116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 09/25/2023] [Accepted: 09/29/2023] [Indexed: 11/25/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is a leading cause of cancer-related mortality worldwide. The in-depth study of genes and metabolites related to nucleotide metabolism will provide new ideas for predicting the prognosis of HCC patients. This study integrated the transcriptome data of different cancer types to explore the characteristics and significance of nucleotide metabolism-related genes (NMGRs) in different cancer types. Then, we constructed a new HCC classifier and prognosis model based on HCC samples from TCGA and GEO, and detected the gene expression level in the model through molecular biology experiments. Finally, nucleotide metabolism-related products in serum of HCC patients were examined using untargeted metabolomics. A total of 97 NMRGs were obtained based on bioinformatics techniques. In addition, a clinical model that could accurately predict the prognostic outcome of HCC was constructed, which contained 11 NMRGs. The results of PCR experiments showed that the expression levels of these genes were basically consistent with the predicted trends. Meanwhile, the results of untargeted metabolomics also proved that there was a significant nucleotide metabolism disorder in the development of HCC. Our results provide a promising insight into nucleotide metabolism in HCC, as well as a tailored prognostic and chemotherapy sensitivity prediction tool for patients.
Collapse
Affiliation(s)
- Tianfu Wei
- Clinical Laboratory of Integrative Medicine, First Affiliated Hospital of Dalian Medical University, Dalian 116000, China; (T.W.)
- Department of General Surgery, First Affiliated Hospital of Dalian Medical University, Dalian 116000, China
| | - Jifeng Liu
- Clinical Laboratory of Integrative Medicine, First Affiliated Hospital of Dalian Medical University, Dalian 116000, China; (T.W.)
- Department of General Surgery, First Affiliated Hospital of Dalian Medical University, Dalian 116000, China
| | - Shurong Ma
- Clinical Laboratory of Integrative Medicine, First Affiliated Hospital of Dalian Medical University, Dalian 116000, China; (T.W.)
- Department of General Surgery, First Affiliated Hospital of Dalian Medical University, Dalian 116000, China
| | - Mimi Wang
- Institute of Integrative Medicine, Dalian Medical University, Dalian 116000, China
| | - Qihang Yuan
- Clinical Laboratory of Integrative Medicine, First Affiliated Hospital of Dalian Medical University, Dalian 116000, China; (T.W.)
- Department of General Surgery, First Affiliated Hospital of Dalian Medical University, Dalian 116000, China
| | - Anliang Huang
- Institute of Integrative Medicine, Dalian Medical University, Dalian 116000, China
| | - Zeming Wu
- iPhenome Biotechnology (Yun Pu Kang) Inc., Dalian 116000, China
| | - Dong Shang
- Clinical Laboratory of Integrative Medicine, First Affiliated Hospital of Dalian Medical University, Dalian 116000, China; (T.W.)
- Department of General Surgery, First Affiliated Hospital of Dalian Medical University, Dalian 116000, China
- Institute of Integrative Medicine, Dalian Medical University, Dalian 116000, China
| | - Peiyuan Yin
- Clinical Laboratory of Integrative Medicine, First Affiliated Hospital of Dalian Medical University, Dalian 116000, China; (T.W.)
- Department of General Surgery, First Affiliated Hospital of Dalian Medical University, Dalian 116000, China
- Institute of Integrative Medicine, Dalian Medical University, Dalian 116000, China
| |
Collapse
|
3
|
Ma G, Sun Y, Cai F, Zhang M, Liang H, Deng J, Zhang R, Zhang L. DEPTOR as a novel prognostic marker inhibits the proliferation via deactivating mTOR signaling pathway in gastric cancer cells. Exp Cell Res 2023; 427:113598. [PMID: 37054772 DOI: 10.1016/j.yexcr.2023.113598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 02/15/2023] [Accepted: 04/09/2023] [Indexed: 04/15/2023]
Abstract
Aberrantly activated mTOR signaling pathway is commonly found in malignancies including gastric cancer (GC). DEPTOR, as a naturally occurred inhibitor of mTOR, functions in the pro- or anti-tumor manner depending on distinct tumor contexts. However, the roles of DEPTOR in GC remain largely unknown. In this study, DEPTOR expression was identified to be significantly decreased in GC tissues compared with matched normal gastric tissues, and reduced DEPTOR level was indicative of poor prognosis in patients. Restored DEPTOR expression inhibited the propagation in AGS and NCI-N87 cells, whose DEPTOR levels are low, via deactivating mTOR signaling pathway. Likewise, cabergoline (CAB) attenuated the proliferation in AGS and NCI-N87 cells via partially rescuing DEPTOR protein level. Targeted metabolomics analysis showed that several key metabolites, such as l-serine, significantly changed in AGS cells with DEPTOR restoration. These results revealed the anti-proliferation function of DEPTOR in GC cells, suggesting that restored DEPTOR expression using CAB may be a potential therapeutic approach for patients with GC.
Collapse
Affiliation(s)
- Gang Ma
- Department of Gastric Surgery, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, China; Key Laboratory of Cancer Prevention and Therapy, Tianjin, China; Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China
| | - Yi Sun
- Department of Anatomy, Histology and Embryology, School of Basic Medical Sciences, Peking University, Beijing, 100191, China
| | - Fenglin Cai
- Department of Gastric Surgery, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, China; Key Laboratory of Cancer Prevention and Therapy, Tianjin, China; Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China
| | - Mengmeng Zhang
- Department of Gastric Surgery, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, China; Key Laboratory of Cancer Prevention and Therapy, Tianjin, China; Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China
| | - Han Liang
- Department of Gastric Surgery, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, China; Key Laboratory of Cancer Prevention and Therapy, Tianjin, China; Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China
| | - Jingyu Deng
- Department of Gastric Surgery, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, China; Key Laboratory of Cancer Prevention and Therapy, Tianjin, China; Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China
| | - Rupeng Zhang
- Department of Gastric Surgery, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, China; Key Laboratory of Cancer Prevention and Therapy, Tianjin, China; Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China
| | - Li Zhang
- Department of Gastric Surgery, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, China; Key Laboratory of Cancer Prevention and Therapy, Tianjin, China; Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China.
| |
Collapse
|
4
|
Crystal Structure of Allantoinase from Escherichia coli BL21: A Molecular Insight into a Role of the Active Site Loops in Catalysis. Molecules 2023; 28:molecules28020827. [PMID: 36677881 PMCID: PMC9863593 DOI: 10.3390/molecules28020827] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 01/10/2023] [Accepted: 01/11/2023] [Indexed: 01/17/2023] Open
Abstract
Allantoinase (ALLase; EC 3.5.2.5) possesses a binuclear metal center in which two metal ions are bridged by a posttranslationally carbamylated lysine. ALLase acts as a key enzyme for the biogenesis and degradation of ureides by catalyzing the conversion of allantoin into allantoate. Biochemically, ALLase belongs to the cyclic amidohydrolase family, which also includes dihydropyrimidinase, dihydroorotase, hydantoinase (HYDase), and imidase. Previously, the crystal structure of ALLase from Escherichia coli K-12 (EcALLase-K12) was reported; however, the two active site loops crucial for substrate binding were not determined. This situation would limit further docking and protein engineering experiments. Here, we solved the crystal structure of E. coli BL21 ALLase (EcALLase-BL21) at a resolution of 2.07 Å (PDB ID 8HFD) to obtain more information for structural analyses. The structure has a classic TIM barrel fold. As compared with the previous work, the two missed active site loops in EcALLase-K12 were clearly determined in our structure of EcALLase-BL21. EcALLase-BL21 shared active site similarity with HYDase, an important biocatalyst for industrial production of semisynthetic penicillin and cephalosporins. Based on this structural comparison, we discussed the functional role of the two active site loops in EcALLase-BL21 to better understand the substrate/inhibitor binding mechanism for further biotechnological and pharmaceutical applications.
Collapse
|
5
|
Bouwknegt J, Vos AM, Ortiz Merino RA, van Cuylenburg DC, Luttik MAH, Pronk JT. Identification of fungal dihydrouracil-oxidase genes by expression in Saccharomyces cerevisiae. Antonie Van Leeuwenhoek 2022; 115:1363-1378. [PMID: 36241945 PMCID: PMC9585004 DOI: 10.1007/s10482-022-01779-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 09/23/2022] [Indexed: 11/29/2022]
Abstract
Analysis of predicted fungal proteomes revealed a large family of sequences that showed similarity to the Saccharomyces cerevisiae Class-I dihydroorotate dehydrogenase Ura1, which supports synthesis of pyrimidines under aerobic and anaerobic conditions. However, expression of codon-optimised representatives of this gene family, from the ascomycete Alternaria alternata and the basidiomycete Schizophyllum commune, only supported growth of an S. cerevisiae ura1Δ mutant when synthetic media were supplemented with dihydrouracil. A hypothesis that these genes encode NAD(P)+-dependent dihydrouracil dehydrogenases (EC 1.3.1.1 or 1.3.1.2) was rejected based on absence of complementation in anaerobic cultures. Uracil- and thymine-dependent oxygen consumption and hydrogen-peroxide production by cell extracts of S. cerevisiae strains expressing the A. alternata and S. commune genes showed that, instead, they encode active dihydrouracil oxidases (DHO, EC1.3.3.7). DHO catalyses the reaction dihydrouracil + O2 → uracil + H2O2 and was only reported in the yeast Rhodotorula glutinis (Owaki in J Ferment Technol 64:205–210, 1986). No structural gene for DHO was previously identified. DHO-expressing strains were highly sensitive to 5-fluorodihydrouracil (5F-dhu) and plasmids bearing expression cassettes for DHO were readily lost during growth on 5F-dhu-containing media. These results show the potential applicability of fungal DHO genes as counter-selectable marker genes for genetic modification of S. cerevisiae and other organisms that lack a native DHO. Further research should explore the physiological significance of this enigmatic and apparently widespread fungal enzyme.
Collapse
Affiliation(s)
- Jonna Bouwknegt
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629, HZ, Delft, The Netherlands
| | - Aurin M Vos
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629, HZ, Delft, The Netherlands
| | - Raúl A Ortiz Merino
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629, HZ, Delft, The Netherlands
| | - Daphne C van Cuylenburg
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629, HZ, Delft, The Netherlands
| | - Marijke A H Luttik
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629, HZ, Delft, The Netherlands
| | - Jack T Pronk
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629, HZ, Delft, The Netherlands.
| |
Collapse
|
6
|
Lin ES, Huang CY. Cytotoxic Activities and the Allantoinase Inhibitory Effect of the Leaf Extract of the Carnivorous Pitcher Plant Nepenthes miranda. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11172265. [PMID: 36079647 PMCID: PMC9460348 DOI: 10.3390/plants11172265] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 08/25/2022] [Accepted: 08/30/2022] [Indexed: 05/14/2023]
Abstract
Nepenthes are carnivorous pitcher plants that have several ethnobotanical uses, such as curing stomachache and fever. Here, we prepared different extracts from the stem, leaf, and pitcher of Nepenthes miranda to further investigate their pharmacological potential. The leaf extract of N. miranda obtained by 100% acetone (N. miranda-leaf-acetone) was used in this study to analyze the cytotoxic activities, antioxidation capacity, antibacterial activity, and allantoinase (ALLase) inhibitory effect of this plant. The cytotoxic effects of N. miranda-leaf-acetone on the survival, apoptosis, and migration of the cancer cell lines PC-9 pulmonary adenocarcinoma, B16F10 melanoma, and 4T1 mammary carcinoma cells were demonstrated. Based on collective data, the cytotoxic activities of N. miranda-leaf-acetone followed the order: B16F10 > 4T1 > PC-9 cells. In addition, the cytotoxic activities of N. miranda-leaf-acetone were synergistically enhanced when co-acting with the clinical anticancer drug 5-fluorouracil. N. miranda-leaf-acetone could also inhibit the activity of ALLase, a key enzyme in the catabolism pathway for purine degradation. Through gas chromatography−mass spectrometry, the 16 most abundant ingredients in N. miranda-leaf-acetone were identified. The top six compounds in N. miranda-leaf-acetone, namely, plumbagin, lupenone, palmitic acid, stigmast-5-en-3-ol, neophytadiene, and citraconic anhydride, were docked to ALLase, and their docking scores were compared. The docking results suggested plumbagin and stigmast-5-en-3-ol as potential inhibitors of ALLase. Overall, these results may indicate the pharmacological potential of N. miranda for further medical applications.
Collapse
Affiliation(s)
- En-Shyh Lin
- Department of Beauty Science, National Taichung University of Science and Technology, Taichung City 403, Taiwan
| | - Cheng-Yang Huang
- Department of Biomedical Sciences, Chung Shan Medical University, Taichung City 402, Taiwan
- Department of Medical Research, Chung Shan Medical University Hospital, Taichung City 402, Taiwan
- Correspondence:
| |
Collapse
|
7
|
Jin S, Zhang W, Xiong Y, Jiang S, Qiao H, Gong Y, Wu Y, Fu H. Identification of Important Genes Involved in the Sex-Differentiation Mechanism of Oriental River Prawn, Macrobrachium nipponense, During the Gonad Differentiation and Development Period. Front Genet 2022; 13:797796. [PMID: 35242165 PMCID: PMC8886218 DOI: 10.3389/fgene.2022.797796] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 01/26/2022] [Indexed: 11/13/2022] Open
Abstract
Identification of important genes, involved in the gonad differentiation and development, plays essential roles in the establishment of the artificial technique to regulate the process of testis development in M. nipponense. In this study, we aimed to determine the sensitive period of gonad differentiation and development through hematoxylin and eosin (HE) staining. The important genes involved in the gonad differentiation and development of M. nipponense were then identified through transcriptome profiling analysis during the sensitive period of gonad differentiation and development. HE staining analysis revealed that the sensitive period of gonad differentiation and development was from the post–larval developmental stages 5 (PL5) to PL25, which was dramatically faster than was for the other identified aquatic animals. The transcriptome profiling analysis predicted that phagosome, lysosome, oxidative phosphorylation, and glycolysis/gluconeogenesis play essential roles in the mechanism of gonad differentiation and development in M. nipponense. A total of 29 genes were further identified as the candidate genes, involved in the process of gonad differentiation and development in M. nipponense, based on the gene annotation and gene expression pattern. The qPCR analysis of Mn-JHEH, Mn-DHP, Mn-ALY, and Mn-SMA6 during the whole developmental process revealed that all of these four genes showed high expression levels during the sensitive period of gonad differentiation and development in M. nipponense. Mn-JHEH, Mn-DHP, and Mn-ALY showed higher expressions at PL25F than at PL25M, while Mn-SMA6 showed a higher expression at PL25M. The RNA interference (RNAi) analysis was further used to investigate the potential functions of SMA6 in male sexual development of M. nipponense. The RNAi analysis revealed that SMA6 positively regulated the testis development in M. nipponense by affecting the expression of Mn-IAG. This study provided valuable evidences for the establishment of the technique to regulate the process of gonad development in M. nipponense.
Collapse
|
8
|
Wu Z, Tan J, Zhuang Y, Zhong M, Xiong Y, Ma J, Yang Y, Gao Z, Zhao J, Ye Z, Zhou H, Zhu Y, Lu H, Hong X. Identification of crucial genes of pyrimidine metabolism as biomarkers for gastric cancer prognosis. Cancer Cell Int 2021; 21:668. [PMID: 34906153 PMCID: PMC8670209 DOI: 10.1186/s12935-021-02385-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 11/30/2021] [Indexed: 11/17/2022] Open
Abstract
Background Metabolic reprogramming has been reported in various kinds of cancers and is related to clinical prognosis, but the prognostic role of pyrimidine metabolism in gastric cancer (GC) remains unclear. Methods Here, we employed DEG analysis to detect the differentially expressed genes (DEGs) in pyrimidine metabolic signaling pathway and used univariate Cox analysis, Lasso-penalizes Cox regression analysis, Kaplan–Meier survival analysis, univariate and multivariate Cox regression analysis to explore their prognostic roles in GC. The DEGs were experimentally validated in GC cells and clinical samples by quantitative real-time PCR. Results Through DEG analysis, we found NT5E, DPYS and UPP1 these three genes are highly expressed in GC. This conclusion has also been verified in GC cells and clinical samples. A prognostic risk model was established according to these three DEGs by Univariate Cox analysis and Lasso-penalizes Cox regression analysis. Kaplan–Meier survival analysis suggested that patient cohorts with high risk score undertook a lower overall survival rate than those with low risk score. Stratified survival analysis, Univariate and multivariate Cox regression analysis of this model confirmed that it is a reliable and independent clinical factor. Therefore, we made nomograms to visually depict the survival rate of GC patients according to some important clinical factors including our risk model. Conclusion In a word, our research found that pyrimidine metabolism is dysregulated in GC and established a prognostic model of GC based on genes differentially expressed in pyrimidine metabolism. Supplementary Information The online version contains supplementary material available at 10.1186/s12935-021-02385-x.
Collapse
Affiliation(s)
- Zhengxin Wu
- School of Medicine, Guangxi University, Nanning, 530004, China
| | - Jinshui Tan
- Department of Hematology, The First Affiliated Hospital of Xiamen University and Institute of Hematology, School of Medicine, Xiamen University, Xiamen, 361003, China
| | - Yifan Zhuang
- Institute of Gastrointestinal Oncology, School of Medicine, Xiamen University, Xiamen, 361000, China.,Department of Gastrointestinal Surgery, Zhongshan Hospital, Xiamen University, No. 201-209 Hubin South Road, Xiamen, 361004, Fujian, China
| | - Mengya Zhong
- Department of Hematology, The First Affiliated Hospital of Xiamen University and Institute of Hematology, School of Medicine, Xiamen University, Xiamen, 361003, China
| | - Yubo Xiong
- Institute of Gastrointestinal Oncology, School of Medicine, Xiamen University, Xiamen, 361000, China.,Department of Gastrointestinal Surgery, Zhongshan Hospital, Xiamen University, No. 201-209 Hubin South Road, Xiamen, 361004, Fujian, China
| | - Jingsong Ma
- Institute of Gastrointestinal Oncology, School of Medicine, Xiamen University, Xiamen, 361000, China.,Department of Gastrointestinal Surgery, Zhongshan Hospital, Xiamen University, No. 201-209 Hubin South Road, Xiamen, 361004, Fujian, China
| | - Yan Yang
- Organ Transplantation Institute of Xiamen University, Fujian Provincial Key Laboratory of Organ and Tissue Regeneration, School of Medicine, Xiamen University, Xiang An South Road, Xiamen, 361102, China
| | - Zhi Gao
- National Center for International Research of Biological Targeting Diagnosis and Therapy, Guangxi Medical University, Nanning, 530000, China
| | - Jiabao Zhao
- Institute of Gastrointestinal Oncology, School of Medicine, Xiamen University, Xiamen, 361000, China.,Department of Gastrointestinal Surgery, Zhongshan Hospital, Xiamen University, No. 201-209 Hubin South Road, Xiamen, 361004, Fujian, China
| | - Zhijian Ye
- Department of Gastrointestinal Surgery, Zhongshan Hospital, Xiamen University, No. 201-209 Hubin South Road, Xiamen, 361004, Fujian, China.,National Center for International Research of Biological Targeting Diagnosis and Therapy, Guangxi Medical University, Nanning, 530000, China
| | - Huiwen Zhou
- Institute of Gastrointestinal Oncology, School of Medicine, Xiamen University, Xiamen, 361000, China.,Department of Gastrointestinal Surgery, Zhongshan Hospital, Xiamen University, No. 201-209 Hubin South Road, Xiamen, 361004, Fujian, China
| | - Yuekun Zhu
- Department of Colorectal Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, 150001, Heilongjiang, China
| | - Haijie Lu
- Department of Radiation Oncology, Affiliated Zhongshan Hospital of Xiamen University, Xiamen, 361102, China
| | - Xuehui Hong
- School of Medicine, Guangxi University, Nanning, 530004, China. .,Institute of Gastrointestinal Oncology, School of Medicine, Xiamen University, Xiamen, 361000, China. .,Department of Gastrointestinal Surgery, Zhongshan Hospital, Xiamen University, No. 201-209 Hubin South Road, Xiamen, 361004, Fujian, China.
| |
Collapse
|
9
|
Liu M, Liu Y, Feng H, Jing Y, Zhao S, Yang S, Zhang N, Jin S, Li Y, Weng M, Xue X, Wang F, Yang Y, Jin X, Kong D. Clinical Significance of Screening Differential Metabolites in Ovarian Cancer Tissue and Ascites by LC/MS. Front Pharmacol 2021; 12:701487. [PMID: 34795577 PMCID: PMC8593816 DOI: 10.3389/fphar.2021.701487] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 10/12/2021] [Indexed: 12/24/2022] Open
Abstract
Tumor cells not only show a vigorous metabolic state, but also reflect the disease progression and prognosis from their metabolites. To judge the progress and prognosis of ovarian cancer is generally based on the formation of ascites, or whether there is ascites recurrence during chemotherapy after ovarian cancer surgery. To explore the relationship between the production of ascites and ovarian cancer tissue, metabolomics was used to screen differential metabolites in this study. The significant markers leading to ascites formation and chemoresistance were screened by analyzing their correlation with the formation of ascites in ovarian cancer and the clinical indicators of patients, and then provided a theoretical basis. The results revealed that nine differential metabolites were screened out from 37 ovarian cancer tissues and their ascites, among which seven differential metabolites were screened from 22 self-paired samples. Sebacic acid and 20-COOH-leukotriene E4 were negatively correlated with the high expression of serum CA125. Carnosine was positively correlated with the high expression of serum uric acid. Hexadecanoic acid was negatively correlated with the high expression of serum γ-GGT and HBDH. 20a,22b-Dihydroxycholesterol was positively correlated with serum alkaline phosphatase and γ-GGT. In the chemotherapy-sensitive and chemotherapy-resistant ovarian cancer tissues, the differential metabolite dihydrothymine was significantly reduced in the chemotherapy-resistant group. In the ascites supernatant of the drug-resistant group, the differential metabolites, 1,25-dihydroxyvitamins D3-26, 23-lactonel and hexadecanoic acid were also significantly reduced. The results indicated that the nine differential metabolites could reflect the prognosis and the extent of liver and kidney damage in patients with ovarian cancer. Three differential metabolites with low expression in the drug-resistant group were proposed as new markers of chemotherapy efficacy in ovarian cancer patients with ascites.
Collapse
Affiliation(s)
- Miao Liu
- Department of Pathology, Harbin Medical University, Harbin, China.,Department of Pathology, Beidahuang Industry Group General Hospital, Harbin, China
| | - Yu Liu
- Department of Pathology, Harbin Medical University, Harbin, China
| | - Hua Feng
- Department of Pathology, Harbin Medical University, Harbin, China
| | - Yixin Jing
- Department of Pathology, Harbin Medical University, Harbin, China
| | - Shuang Zhao
- Department of Gynecology, Tumor Hospital of Harbin Medical University, Harbin, China
| | - Shujia Yang
- Department of Pathology, Harbin Medical University, Harbin, China
| | - Nan Zhang
- Department of Pathology, Harbin Medical University, Harbin, China
| | - Shi Jin
- Department of Pathology, Harbin Medical University, Harbin, China
| | - Yafei Li
- Department of Pathology, Harbin Medical University, Harbin, China
| | - Mingjiao Weng
- Department of Pathology, Harbin Medical University, Harbin, China
| | - Xinzhu Xue
- Department of Pathology, Harbin Medical University, Harbin, China
| | - Fuya Wang
- Department of Gynecology, Tumor Hospital of Harbin Medical University, Harbin, China
| | - Yongheng Yang
- Department of Pathology, Harbin Medical University, Harbin, China
| | - Xiaoming Jin
- Department of Pathology, Harbin Medical University, Harbin, China
| | - Dan Kong
- Department of Gynecology, Tumor Hospital of Harbin Medical University, Harbin, China
| |
Collapse
|
10
|
Poupore N, Chosed R, Arce S, Rainer R, Goodwin RL, Nathaniel TI. Metabolomic Profiles of Men and Women Ischemic Stroke Patients. Diagnostics (Basel) 2021; 11:diagnostics11101786. [PMID: 34679483 PMCID: PMC8534835 DOI: 10.3390/diagnostics11101786] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Revised: 09/20/2021] [Accepted: 09/22/2021] [Indexed: 12/02/2022] Open
Abstract
Background: Stroke is known to affect both men and women; however, incidence and outcomes differ between them. Therefore, the discovery of novel, sex-specific, blood-based biomarkers for acute ischemic stroke (AIS) patients has the potential to enhance the understanding of the etiology of this deadly disease in the content of sex. The objective of this study was to identify serum metabolites associated with male and female AIS patients. Methods: Metabolites were measured with the use of untargeted, reverse-phase ultra-performance liquid chromatography-tandem mass spectrometry quantification from blood specimens collected from AIS patients. Samples were collected from 36 patients comprising each of 18 men and women with matched controls. Metabolic pathway analysis and principal component analysis (PCA) was used to differentiate metabolite profiles for male and female AIS patients from the control, while logistic regression was used to determine differences in metabolites between male and female AIS patients. Results: In female AIS patients, 14 distinct altered metabolic pathways and 49 corresponding metabolites were identified, while 39 metabolites and 5 metabolic pathways were identified in male patients. Metabolites that are predictive of ischemic stroke in female patients were 1-(1-enyl-palmitoyl)-2-arachidonoyl-GPC (P-16:0/20:4) (AUC = 0.914, 0.765–1.000), 1-(1-enyl-palmitoyl)-2-palmitoyl-GPC (P-16:0/16:0) (AUC = 0.840, 0.656–1.000), and 5,6-dihydrouracil (P-16:0/20:2) (AUC = 0.815, 0.601–1.000). Significant metabolites that were predictive of stroke in male patients were 5alpha-androstan-3alpha,17beta-diol disulfate (AUC = 0.951, 0.857–1.000), alpha-hydroxyisocaproate (AUC = 0.938, 0.832–1.000), threonate (AUC = 0.877, 0.716–1.000), and bilirubin (AUC = 0.817, 0.746–1.000). Conclusions: In the current study, the untargeted serum metabolomics platform identified multiple pathways and metabolites associated with male and female AIS patients. Further research is necessary to characterize how these metabolites are associated with the pathophysiology in male and female AIS patients.
Collapse
Affiliation(s)
- Nicolas Poupore
- School of Medicine Greenville, University of South Carolina, Greenville, SC 29605, USA; (N.P.); (R.C.); (S.A.); (R.L.G.)
| | - Renee Chosed
- School of Medicine Greenville, University of South Carolina, Greenville, SC 29605, USA; (N.P.); (R.C.); (S.A.); (R.L.G.)
| | - Sergio Arce
- School of Medicine Greenville, University of South Carolina, Greenville, SC 29605, USA; (N.P.); (R.C.); (S.A.); (R.L.G.)
| | | | - Richard L. Goodwin
- School of Medicine Greenville, University of South Carolina, Greenville, SC 29605, USA; (N.P.); (R.C.); (S.A.); (R.L.G.)
| | - Thomas I. Nathaniel
- School of Medicine Greenville, University of South Carolina, Greenville, SC 29605, USA; (N.P.); (R.C.); (S.A.); (R.L.G.)
- Correspondence: ; Tel.: +1-8644559846; Fax: +1-8644558404
| |
Collapse
|
11
|
Ellison V, Annor GK, Freedman C, Xiao G, Lundine D, Freulich E, Prives C, Bargonetti J. Frame-shift mediated reduction of gain-of-function p53 R273H and deletion of the R273H C-terminus in breast cancer cells result in replication-stress sensitivity. Oncotarget 2021; 12:1128-1146. [PMID: 34136083 PMCID: PMC8202772 DOI: 10.18632/oncotarget.27975] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 05/15/2021] [Indexed: 11/25/2022] Open
Abstract
We recently documented that gain-of-function (GOF) mutant p53 (mtp53) R273H in triple negative breast cancer (TNBC) cells interacts with replicating DNA and PARP1. The missense R273H GOF mtp53 has a mutated central DNA binding domain that renders it unable to bind specifically to DNA, but maintains the capacity to interact tightly with chromatin. Both the C-terminal domain (CTD) and oligomerization domain (OD) of GOF mtp53 proteins are intact and it is unclear whether these regions of mtp53 are responsible for chromatin-based DNA replication activities. We generated MDA-MB-468 cells with CRISPR-Cas9 edited versions of the CTD and OD regions of mtp53 R273H. These included a frame-shift mtp53 R273Hfs387, which depleted mtp53 protein expression; mtp53 R273HΔ381-388, which had a small deletion within the CTD; and mtp53 R273HΔ347-393, which had both the OD and CTD regions truncated. The mtp53 R273HΔ347-393 existed exclusively as monomers and disrupted the chromatin interaction of mtp53 R273H. The CRISPR variants proliferated more slowly than the parental cells and mt53 R273Hfs387 showed the most extreme phenotype. We uncovered that after thymidine-induced G1/S synchronization, but not hydroxyurea or aphidicholin, R273Hfs387 cells displayed impairment of S-phase progression while both R273HΔ347-393 and R273HΔ381-388 displayed only moderate impairment. Moreover, reduced chromatin interaction of MCM2 and PCNA in mtp53 depleted R273Hfs387 cells post thymidine-synchronization revealed delayed kinetics of replisome assembly underscoring the slow S-phase progression. Taken together our findings show that the CTD and OD domains of mtp53 R273H play critical roles in mutant p53 GOF that pertain to processes associated with DNA replication.
Collapse
Affiliation(s)
- Viola Ellison
- The Department of Biological Sciences, Hunter College, City University of New York, New York, NY, USA
| | - George K. Annor
- The Department of Biological Sciences, Hunter College, City University of New York, New York, NY, USA
- The Graduate Center Biology and Biochemistry Programs, City University of New York, New York, NY, USA
| | - Clara Freedman
- The Department of Biological Sciences, Hunter College, City University of New York, New York, NY, USA
| | - Gu Xiao
- The Department of Biological Sciences, Hunter College, City University of New York, New York, NY, USA
| | - Devon Lundine
- The Department of Biological Sciences, Hunter College, City University of New York, New York, NY, USA
- The Graduate Center Biology and Biochemistry Programs, City University of New York, New York, NY, USA
| | - Elzbieta Freulich
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Carol Prives
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Jill Bargonetti
- The Department of Biological Sciences, Hunter College, City University of New York, New York, NY, USA
- The Graduate Center Biology and Biochemistry Programs, City University of New York, New York, NY, USA
- Department of Cell and Developmental Biology, Weill Cornell Medical College, New York, NY, USA
| |
Collapse
|
12
|
Interplay between Cellular Metabolism and the DNA Damage Response in Cancer. Cancers (Basel) 2020; 12:cancers12082051. [PMID: 32722390 PMCID: PMC7463900 DOI: 10.3390/cancers12082051] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 07/20/2020] [Accepted: 07/23/2020] [Indexed: 12/15/2022] Open
Abstract
Metabolism is a fundamental cellular process that can become harmful for cells by leading to DNA damage, for instance by an increase in oxidative stress or through the generation of toxic byproducts. To deal with such insults, cells have evolved sophisticated DNA damage response (DDR) pathways that allow for the maintenance of genome integrity. Recent years have seen remarkable progress in our understanding of the diverse DDR mechanisms, and, through such work, it has emerged that cellular metabolic regulation not only generates DNA damage but also impacts on DNA repair. Cancer cells show an alteration of the DDR coupled with modifications in cellular metabolism, further emphasizing links between these two fundamental processes. Taken together, these compelling findings indicate that metabolic enzymes and metabolites represent a key group of factors within the DDR. Here, we will compile the current knowledge on the dynamic interplay between metabolic factors and the DDR, with a specific focus on cancer. We will also discuss how recently developed high-throughput technologies allow for the identification of novel crosstalk between the DDR and metabolism, which is of crucial importance to better design efficient cancer treatments.
Collapse
|
13
|
Huang CY. Structure, catalytic mechanism, posttranslational lysine carbamylation, and inhibition of dihydropyrimidinases. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2020; 122:63-96. [PMID: 32951816 DOI: 10.1016/bs.apcsb.2020.05.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Dihydropyrimidinase catalyzes the reversible hydrolytic ring opening of dihydrouracil and dihydrothymine to N-carbamoyl-β-alanine and N-carbamyl-β-aminoisobutyrate, respectively. Dihydropyrimidinase from microorganisms is normally known as hydantoinase because of its role as a biocatalyst in the synthesis of d- and l-amino acids for the industrial production of antibiotic precursors and its broad substrate specificity. Dihydropyrimidinase belongs to the cyclic amidohydrolase family, which also includes imidase, allantoinase, and dihydroorotase. Although these metal-dependent enzymes share low levels of amino acid sequence homology, they possess similar active site architectures and may use a similar mechanism for catalysis. By contrast, the five human dihydropyrimidinase-related proteins possess high amino acid sequence identity and are structurally homologous to dihydropyrimidinase, but they are neuronal proteins with no dihydropyrimidinase activity. In this chapter, we summarize and discuss current knowledge and the recent advances on the structure, catalytic mechanism, and inhibition of dihydropyrimidinase.
Collapse
Affiliation(s)
- Cheng-Yang Huang
- School of Biomedical Sciences, Chung Shan Medical University, Taichung City, Taiwan; Department of Medical Research, Chung Shan Medical University Hospital, Taichung City, Taiwan
| |
Collapse
|