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Lin C, Tian Q, Guo S, Xie D, Cai Y, Wang Z, Chu H, Qiu S, Tang S, Zhang A. Metabolomics for Clinical Biomarker Discovery and Therapeutic Target Identification. Molecules 2024; 29:2198. [PMID: 38792060 PMCID: PMC11124072 DOI: 10.3390/molecules29102198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 04/10/2024] [Accepted: 04/25/2024] [Indexed: 05/26/2024] Open
Abstract
As links between genotype and phenotype, small-molecule metabolites are attractive biomarkers for disease diagnosis, prognosis, classification, drug screening and treatment, insight into understanding disease pathology and identifying potential targets. Metabolomics technology is crucial for discovering targets of small-molecule metabolites involved in disease phenotype. Mass spectrometry-based metabolomics has implemented in applications in various fields including target discovery, explanation of disease mechanisms and compound screening. It is used to analyze the physiological or pathological states of the organism by investigating the changes in endogenous small-molecule metabolites and associated metabolism from complex metabolic pathways in biological samples. The present review provides a critical update of high-throughput functional metabolomics techniques and diverse applications, and recommends the use of mass spectrometry-based metabolomics for discovering small-molecule metabolite signatures that provide valuable insights into metabolic targets. We also recommend using mass spectrometry-based metabolomics as a powerful tool for identifying and understanding metabolic patterns, metabolic targets and for efficacy evaluation of herbal medicine.
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Affiliation(s)
- Chunsheng Lin
- Graduate School and Second Affiliated Hospital, Heilongjiang University of Chinese Medicine, Harbin 150040, China; (C.L.); (S.G.); (Y.C.); (Z.W.)
| | - Qianqian Tian
- Faculty of Social Sciences, The University of Hong Kong, Hong Kong 999077, China;
| | - Sifan Guo
- Graduate School and Second Affiliated Hospital, Heilongjiang University of Chinese Medicine, Harbin 150040, China; (C.L.); (S.G.); (Y.C.); (Z.W.)
- International Advanced Functional Omics Platform, Scientific Experiment Center, International Joint Research Center on Traditional Chinese and Modern Medicine, Hainan Engineering Research Center for Biological Sample Resources of Major Diseases (First Affiliated Hospital of Hainan Medical University), Key Laboratory of Tropical Cardiovascular Diseases Research of Hainan Province, Hainan Medical University, Xueyuan Road 3, Haikou 571199, China; (D.X.); (S.Q.); (S.T.)
| | - Dandan Xie
- International Advanced Functional Omics Platform, Scientific Experiment Center, International Joint Research Center on Traditional Chinese and Modern Medicine, Hainan Engineering Research Center for Biological Sample Resources of Major Diseases (First Affiliated Hospital of Hainan Medical University), Key Laboratory of Tropical Cardiovascular Diseases Research of Hainan Province, Hainan Medical University, Xueyuan Road 3, Haikou 571199, China; (D.X.); (S.Q.); (S.T.)
| | - Ying Cai
- Graduate School and Second Affiliated Hospital, Heilongjiang University of Chinese Medicine, Harbin 150040, China; (C.L.); (S.G.); (Y.C.); (Z.W.)
- International Advanced Functional Omics Platform, Scientific Experiment Center, International Joint Research Center on Traditional Chinese and Modern Medicine, Hainan Engineering Research Center for Biological Sample Resources of Major Diseases (First Affiliated Hospital of Hainan Medical University), Key Laboratory of Tropical Cardiovascular Diseases Research of Hainan Province, Hainan Medical University, Xueyuan Road 3, Haikou 571199, China; (D.X.); (S.Q.); (S.T.)
| | - Zhibo Wang
- Graduate School and Second Affiliated Hospital, Heilongjiang University of Chinese Medicine, Harbin 150040, China; (C.L.); (S.G.); (Y.C.); (Z.W.)
- International Advanced Functional Omics Platform, Scientific Experiment Center, International Joint Research Center on Traditional Chinese and Modern Medicine, Hainan Engineering Research Center for Biological Sample Resources of Major Diseases (First Affiliated Hospital of Hainan Medical University), Key Laboratory of Tropical Cardiovascular Diseases Research of Hainan Province, Hainan Medical University, Xueyuan Road 3, Haikou 571199, China; (D.X.); (S.Q.); (S.T.)
| | - Hang Chu
- Department of Biomedical Sciences, Beijing City University, Beijing 100193, China;
| | - Shi Qiu
- International Advanced Functional Omics Platform, Scientific Experiment Center, International Joint Research Center on Traditional Chinese and Modern Medicine, Hainan Engineering Research Center for Biological Sample Resources of Major Diseases (First Affiliated Hospital of Hainan Medical University), Key Laboratory of Tropical Cardiovascular Diseases Research of Hainan Province, Hainan Medical University, Xueyuan Road 3, Haikou 571199, China; (D.X.); (S.Q.); (S.T.)
| | - Songqi Tang
- International Advanced Functional Omics Platform, Scientific Experiment Center, International Joint Research Center on Traditional Chinese and Modern Medicine, Hainan Engineering Research Center for Biological Sample Resources of Major Diseases (First Affiliated Hospital of Hainan Medical University), Key Laboratory of Tropical Cardiovascular Diseases Research of Hainan Province, Hainan Medical University, Xueyuan Road 3, Haikou 571199, China; (D.X.); (S.Q.); (S.T.)
| | - Aihua Zhang
- Graduate School and Second Affiliated Hospital, Heilongjiang University of Chinese Medicine, Harbin 150040, China; (C.L.); (S.G.); (Y.C.); (Z.W.)
- International Advanced Functional Omics Platform, Scientific Experiment Center, International Joint Research Center on Traditional Chinese and Modern Medicine, Hainan Engineering Research Center for Biological Sample Resources of Major Diseases (First Affiliated Hospital of Hainan Medical University), Key Laboratory of Tropical Cardiovascular Diseases Research of Hainan Province, Hainan Medical University, Xueyuan Road 3, Haikou 571199, China; (D.X.); (S.Q.); (S.T.)
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Sheikh E, Agrawal K, Roy S, Burk D, Donnarumma F, Ko YH, Guttula PK, Biswal NC, Shukla HD, Gartia MR. Multimodal Imaging of Pancreatic Cancer Microenvironment in Response to an Antiglycolytic Drug. Adv Healthc Mater 2023; 12:e2301815. [PMID: 37706285 PMCID: PMC10842640 DOI: 10.1002/adhm.202301815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Indexed: 09/15/2023]
Abstract
Lipid metabolism and glycolysis play crucial roles in the progression and metastasis of cancer, and the use of 3-bromopyruvate (3-BP) as an antiglycolytic agent has shown promise in killing pancreatic cancer cells. However, developing an effective strategy to avoid chemoresistance requires the ability to probe the interaction of cancer drugs with complex tumor-associated microenvironments (TAMs). Unfortunately, no robust and multiplexed molecular imaging technology is currently available to analyze TAMs. In this study, the simultaneous profiling of three protein biomarkers using SERS nanotags and antibody-functionalized nanoparticles in a syngeneic mouse model of pancreatic cancer (PC) is demonstrated. This allows for comprehensive information about biomarkers and TAM alterations before and after treatment. These multimodal imaging techniques include surface-enhanced Raman spectroscopy (SERS), immunohistochemistry (IHC), polarized light microscopy, second harmonic generation (SHG) microscopy, fluorescence lifetime imaging microscopy (FLIM), and untargeted liquid chromatography and mass spectrometry (LC-MS) analysis. The study reveals the efficacy of 3-BP in treating pancreatic cancer and identifies drug treatment-induced lipid species remodeling and associated pathways through bioinformatics analysis.
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Affiliation(s)
- Elnaz Sheikh
- Department of Mechanical and Industrial Engineering, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Kirti Agrawal
- Department of Mechanical and Industrial Engineering, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Sanjit Roy
- Department of Radiation Oncology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - David Burk
- Department of Cell Biology and Bioimaging, Pennington Biomedical Research Center, Baton Rouge, LA, 70808, USA
| | - Fabrizio Donnarumma
- Department of Chemistry, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Young H Ko
- NewG Lab Pharma, 701 East Pratt Street, Columbus Center, Baltimore, MD, 21202, USA
| | - Praveen Kumar Guttula
- Sprott Center for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON, K1H 8L6, Canada
- Department of Biochemistry, Microbiology, and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, K1H 8M5, Canada
| | - Nrusingh C Biswal
- Department of Radiation Oncology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Hem D Shukla
- Department of Radiation Oncology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Manas Ranjan Gartia
- Department of Mechanical and Industrial Engineering, Louisiana State University, Baton Rouge, LA, 70803, USA
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Alfaro GF, Palombo V, D'Andrea M, Cao W, Zhang Y, Beever J, Muntifering RB, Pacheco WJ, Rodning SP, Wang X, Moisá SJ. Hepatic transcript profiling in beef cattle: Effects of rumen-protected niacin supplementation. PLoS One 2023; 18:e0289409. [PMID: 37535643 PMCID: PMC10399858 DOI: 10.1371/journal.pone.0289409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 07/18/2023] [Indexed: 08/05/2023] Open
Abstract
The objective of our study was to assess the effect of rumen-protected niacin supplementation on the transcriptome of liver tissue in growing Angus × Simmental steers and heifers through RNA-seq analysis. Consequently, we wanted to assess the known role of niacin in the physiological processes of vasodilation, detoxification, and immune function in beef hepatic tissue. Normal weaned calves (~8 months old) were provided either a control diet or a diet supplemented with rumen-protected niacin (6 g/hd/d) for a 30-day period, followed by a liver biopsy. We observed a significant list of changes at the transcriptome level due to rumen-protected niacin supplementation. Several metabolic pathways revealed potential positive effects to the animal's liver metabolism due to administration of rumen-protected niacin; for example, a decrease in lipolysis, apoptosis, inflammatory responses, atherosclerosis, oxidative stress, fibrosis, and vasodilation-related pathways. Therefore, results from our study showed that the liver transcriptional machinery switched several metabolic pathways to a condition that could potentially benefit the health status of animals supplemented with rumen-protected niacin. In conclusion, based on the results of our study, we can suggest the utilization of rumen-protected niacin supplementation as a nutritional strategy could improve the health status of growing beef cattle in different beef production stages, such as backgrounding operations or new arrivals to a feedlot.
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Affiliation(s)
- Gastón F Alfaro
- Department of Animal Sciences, Auburn University, Auburn, AL, United States of America
| | - Valentino Palombo
- Department of Agricultural, Environmental and Food Sciences, Università degli Studi del Molise, Campobasso, Italy
| | - Mariasilvia D'Andrea
- Department of Agricultural, Environmental and Food Sciences, Università degli Studi del Molise, Campobasso, Italy
| | - Wenqi Cao
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL, United States of America
| | - Yue Zhang
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL, United States of America
| | - Jonathan Beever
- Department of Animal Sciences, University of Tennessee, Knoxville, TN, United States of America
| | - Russell B Muntifering
- Department of Animal Sciences, Auburn University, Auburn, AL, United States of America
- Cooperative Extension Service, University of Kentucky, Kentucky, Lexington, United States of America
| | - Wilmer J Pacheco
- Department of Poultry Sciences, Auburn University, Auburn, AL, United States of America
| | - Soren P Rodning
- Department of Animal Sciences, Auburn University, Auburn, AL, United States of America
| | - Xu Wang
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL, United States of America
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States of America
| | - Sonia J Moisá
- Department of Animal Sciences, University of Tennessee, Knoxville, TN, United States of America
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Guo Y, Wu Z, Cen K, Bai Y, Dai Y, Mai Y, Hong K, Qu L. Establishment and validation of a ubiquitination-related gene signature associated with prognosis in pancreatic duct adenocarcinoma. Front Immunol 2023; 14:1171811. [PMID: 37359528 PMCID: PMC10289160 DOI: 10.3389/fimmu.2023.1171811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 05/26/2023] [Indexed: 06/28/2023] Open
Abstract
Background Patients with pancreatic duct adenocarcinoma (PDAC) have varied prognoses that depend on numerous variables. However, additional research is required to uncover the latent impact of ubiquitination-related genes (URGs) on determining PDAC patients' prognoses. Methods The URGs clusters were discovered via consensus clustering, and the prognostic differentially expressed genes (DEGs) across clusters were utilized to develop a signature using a least absolute shrinkage and selection operator (LASSO) regression analysis of data from TCGA-PAAD. Verification analyses were conducted across TCGA-PAAD, GSE57495 and ICGC-PACA-AU to show the robustness of the signature. RT-qPCR was used to verify the expression of risk genes. Lastly, we formulated a nomogram to improve the clinical efficacy of our predictive tool. Results The URGs signature, comprised of three genes, was developed and was shown to be highly correlated with the prognoses of PAAD patients. The nomogram was established by combining the URGs signature with clinicopathological characteristics. We discovered that the URGs signature was remarkably superior than other individual predictors (age, grade, T stage, et al). Also, the immune microenvironment analysis indicated that ESTIMATEscore, ImmuneScores, and StromalScores were elevated in the low-risk group. The immune cells that infiltrated the tissues were different between the two groups, as did the expression of immune-related genes. Conclusion The URGs signature could act as the biomarker of prognosis and selecting appropriate therapeutic drugs for PDAC patients.
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Affiliation(s)
- Yangyang Guo
- Department of General Surgery, The First Affiliated Hospital of Ningbo University, Ningbo, China
- Department of Emergency, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Taizhou, Zhejiang, China
| | - Zhixuan Wu
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Kenan Cen
- Department of General Surgery, The First Affiliated Hospital of Ningbo University, Ningbo, China
| | - Yongheng Bai
- National Key Clinical Specialty (General Surgery), The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Ying Dai
- Department of General Surgery, The First Affiliated Hospital of Ningbo University, Ningbo, China
| | - Yifeng Mai
- Department of General Surgery, The First Affiliated Hospital of Ningbo University, Ningbo, China
| | - Kai Hong
- Department of General Surgery, The First Affiliated Hospital of Ningbo University, Ningbo, China
| | - Liangchen Qu
- Department of Emergency, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Taizhou, Zhejiang, China
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Zhou X, Liang R, Shi Y, Xu Q, Qian L. Metabolic variation and oxidative stress response of blue mussels (Mytilus sp.) perturbed by norfloxacin exposure. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023:10.1007/s11356-023-27599-6. [PMID: 37247149 DOI: 10.1007/s11356-023-27599-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Accepted: 05/09/2023] [Indexed: 05/30/2023]
Abstract
Antibiotics are currently widely applied in agricultural cultivation, animal husbandry, and medical treatment, but the effects and ecological risks of antibiotics need to be further investigated. Norfloxacin is one of the most widely applied fluoroquinolone antibiotics and is commonly detected in aquatic ecosystems. In this study, the activities of catalase (CAT) and glutathione S-transferase (GST) in blue mussels (Mytilus sp.) exposed to norfloxacin (from 25 to 200 mg/L) for 2 d of acute exposure and 7 d of subacute exposure were measured. 1H nuclear magnetic resonance (1H-NMR)-based metabolomics was applied to identify the metabolites and to investigate the physiological metabolism of blue mussels (Mytilus sp.) under different concentrations of norfloxacin. The activity of the CAT enzyme was induced in acute exposure, while the activity of GST was inhibited in subacute exposure when the concentration of norfloxacin reached 200 mg/L. Orthogonal partial least squares discriminant analysis (OPLS-DA) revealed that the increased concentrations of norfloxacin might cause greater metabolic differences between the treatment and control groups and cause greater metabolic variation within the same treatment group. The contents of taurine in the 150 mg/L acute exposure group were 5.17 times higher than those in the control group. The pathway analysis indicated that exposure to high concentrations of norfloxacin disturbed different pathways involved in energy metabolism, amino acid metabolism, neuroregulation, and the regulation of osmotic pressure. These results may provide a molecular and metabolic view of the effects of norfloxacin and the regulatory mechanism of blue mussels when exposed to extremely high doses of antibiotics.
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Affiliation(s)
- Xuan Zhou
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ruoyu Liang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yajuan Shi
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Qiuyun Xu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Li Qian
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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Gu X, Jiang C, Zhao J, Qiao Q, Wu M, Cai B. Identification of lipid metabolism-associated genes as prognostic biomarkers based on the immune microenvironment in hepatocellular carcinoma. Front Cell Dev Biol 2022; 10:883059. [PMID: 36330335 PMCID: PMC9622944 DOI: 10.3389/fcell.2022.883059] [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: 02/24/2022] [Accepted: 09/02/2022] [Indexed: 02/05/2023] Open
Abstract
Lipid metabolism has been associated with progression of various cancers. However, the underlying mechanisms of the impact of lipid metabolism-associated genes (LMAGs) on the tumor immune microenvironment have not been well-elucidated. This study aimed to determine the effects of lipid metabolism on the progression and development of hepatocellular carcinoma (HCC). Expression profiles and clinical data of 371 and 231 patients with HCC were obtained from the TCGA and Internal Cancer Genome Consortium (ICGC) databases, respectively. Using Cox regression and LASSO regression analyses, a prognostic risk model was constructed based on the LMAG data. The tumor mutation burden (TMB), immune cell infiltration levels, and immune response checkpoints of the identified risk groups were determined and compared. A total of two clusters were identified based on the LMAG expression, showing significant differences in tumor stage and immune cell infiltration. A prognostic risk model based on four LMAGs was constructed and proven to have a significant prognostic value. The 1-, 3-, and 5-year survival rates in the high-risk group were 62.2%, 20.5%, and 8.1%, respectively, whereas those in the low-risk group were 78.9%, 28.1%, and 13.5%, respectively. The survival differences between the two risk groups were likely associated with TP53 mutation status, TMB score, degree of immunocyte infiltration, and immune checkpoint level. Likewise, the expression level of every LMAG included in the model had the same effect on the overall survival and immune cell infiltration levels. More importantly, the prognostic value of the signature was verified in an independent ICGC cohort. Thus, the expression levels of LMAGs are closely related to the tumor microenvironment in HCC and may serve as promising biological indicators for prognosis and immune therapy in patients with HCC.
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Affiliation(s)
| | | | | | | | - Mingyu Wu
- *Correspondence: Mingyu Wu, ; Bing Cai,
| | - Bing Cai
- *Correspondence: Mingyu Wu, ; Bing Cai,
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