1
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Lee GB, Mazli WNAB, Hao L. Multiomics Evaluation of Human iPSCs and iPSC-Derived Neurons. J Proteome Res 2024. [PMID: 38415376 DOI: 10.1021/acs.jproteome.3c00790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/29/2024]
Abstract
Human induced pluripotent stem cells (iPSCs) can be differentiated into neurons, providing living human neurons to model brain diseases. However, it is unclear how different types of molecules work together to regulate stem cell and neuron biology in healthy and disease states. In this study, we conducted integrated proteomics, lipidomics, and metabolomics analyses with confident identification, accurate quantification, and reproducible measurements to compare the molecular profiles of human iPSCs and iPSC-derived neurons. Proteins, lipids, and metabolites related to mitosis, DNA replication, pluripotency, glycosphingolipids, and energy metabolism were highly enriched in iPSCs, whereas synaptic proteins, neurotransmitters, polyunsaturated fatty acids, cardiolipins, and axon guidance pathways were highly enriched in neurons. Mutations in the GRN gene lead to the deficiency of the progranulin (PGRN) protein, which has been associated with various neurodegenerative diseases. Using this multiomics platform, we evaluated the impact of PGRN deficiency on iPSCs and neurons at the whole-cell level. Proteomics, lipidomics, and metabolomics analyses implicated PGRN's roles in neuroinflammation, purine metabolism, and neurite outgrowth, revealing commonly altered pathways related to neuron projection, synaptic dysfunction, and brain metabolism. Multiomics data sets also pointed toward the same hypothesis that neurons seem to be more susceptible to PGRN loss compared to iPSCs, consistent with the neurological symptoms and cognitive impairment from patients carrying inherited GRN mutations.
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Affiliation(s)
- Gwang Bin Lee
- Department of Chemistry, The George Washington University, 800 22nd St. NW, Washington, D.C. 20052, United States
| | - Wan Nur Atiqah Binti Mazli
- Department of Chemistry, The George Washington University, 800 22nd St. NW, Washington, D.C. 20052, United States
| | - Ling Hao
- Department of Chemistry, The George Washington University, 800 22nd St. NW, Washington, D.C. 20052, United States
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2
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Liu J, Li L, Xiong Z, Robert CAM, Li B, He S, Chen W, Bi J, Zhai G, Guo S, Zhang H, Li J, Zhou S, Zhang X, Song CP. Trade-offs between the accumulation of cuticular wax and jasmonic acid-mediated herbivory resistance in maize. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:143-159. [PMID: 37975264 DOI: 10.1111/jipb.13586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 11/14/2023] [Indexed: 11/19/2023]
Abstract
Plants have evolved complex physical and chemical defense systems that allow them to withstand herbivory infestation. Composed of a complex mixture of very-long-chain fatty acids (VLCFAs) and their derivatives, cuticular wax constitutes the first physical line of defense against herbivores. Here, we report the function of Glossy 8 (ZmGL8), which encodes a 3-ketoacyl reductase belonging to the fatty acid elongase complex, in orchestrating wax production and jasmonic acid (JA)-mediated defenses against herbivores in maize (Zea mays). The mutation of GL8 enhanced chemical defenses by activating the JA-dependent pathway. We observed a trade-off between wax accumulation and JA levels across maize glossy mutants and 24 globally collected maize inbred lines. In addition, we demonstrated that mutants defective in cuticular wax biosynthesis in Arabidopsis thaliana and maize exhibit enhanced chemical defenses. Comprehensive transcriptomic and lipidomic analyses indicated that the gl8 mutant confers chemical resistance to herbivores by remodeling VLCFA-related lipid metabolism and subsequent JA biosynthesis and signaling. These results suggest that VLCFA-related lipid metabolism has a critical role in regulating the trade-offs between cuticular wax and JA-mediated chemical defenses.
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Affiliation(s)
- Jiong Liu
- School of Life Sciences, Henan University, Kaifeng, 475004, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan University, Kaifeng, 475004, China
| | - Lu Li
- School of Life Sciences, Henan University, Kaifeng, 475004, China
- State Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Henan University, Kaifeng, 475004, China
| | - Zhilong Xiong
- School of Life Sciences, Henan University, Kaifeng, 475004, China
- State Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Henan University, Kaifeng, 475004, China
- Sanya Institute of Henan University, Sanya, 572025, China
| | | | - Baozhu Li
- School of Life Sciences, Henan University, Kaifeng, 475004, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan University, Kaifeng, 475004, China
- Sanya Institute of Henan University, Sanya, 572025, China
| | - Shan He
- School of Life Sciences, Henan University, Kaifeng, 475004, China
- State Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Henan University, Kaifeng, 475004, China
| | - Wenjie Chen
- School of Life Sciences, Henan University, Kaifeng, 475004, China
- State Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Henan University, Kaifeng, 475004, China
| | - Jiasheng Bi
- School of Life Sciences, Henan University, Kaifeng, 475004, China
- State Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Henan University, Kaifeng, 475004, China
| | - Guanqing Zhai
- School of Life Sciences, Henan University, Kaifeng, 475004, China
- State Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Henan University, Kaifeng, 475004, China
- Sanya Institute of Henan University, Sanya, 572025, China
| | - Siyi Guo
- School of Life Sciences, Henan University, Kaifeng, 475004, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan University, Kaifeng, 475004, China
- Sanya Institute of Henan University, Sanya, 572025, China
| | - Hui Zhang
- School of Life Sciences, Henan University, Kaifeng, 475004, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan University, Kaifeng, 475004, China
| | - Jieping Li
- School of Life Sciences, Henan University, Kaifeng, 475004, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan University, Kaifeng, 475004, China
| | - Shutang Zhou
- School of Life Sciences, Henan University, Kaifeng, 475004, China
- State Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Henan University, Kaifeng, 475004, China
- Sanya Institute of Henan University, Sanya, 572025, China
| | - Xi Zhang
- School of Life Sciences, Henan University, Kaifeng, 475004, China
- State Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Henan University, Kaifeng, 475004, China
- Sanya Institute of Henan University, Sanya, 572025, China
| | - Chun-Peng Song
- School of Life Sciences, Henan University, Kaifeng, 475004, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan University, Kaifeng, 475004, China
- Sanya Institute of Henan University, Sanya, 572025, China
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3
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Shi J, Zhao J, Zhang Y, Wang Y, Tan CP, Xu YJ, Liu Y. Windows Scanning Multiomics: Integrated Metabolomics and Proteomics. Anal Chem 2023; 95:18793-18802. [PMID: 38095040 DOI: 10.1021/acs.analchem.3c03785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2023]
Abstract
Metabolomics and proteomics offer significant advantages in understanding biological mechanisms at two hierarchical levels. However, conventional single omics analysis faces challenges due to the high demand for specimens and the complexity of intrinsic associations. To obtain comprehensive and accurate system biological information, we developed a multiomics analytical method called Windows Scanning Multiomics (WSM). In this method, we performed simultaneous extraction of metabolites and proteins from the same sample, resulting in a 10% increase in the coverage of the identified biomolecules. Both metabolomics and proteomics analyses were conducted by using ultrahigh-performance liquid chromatography mass spectrometry (UPLC-MS), eliminating the need for instrument conversions. Additionally, we designed an R-based program (WSM.R) to integrate mathematical and biological correlations between metabolites and proteins into a correlation network. The network created from simultaneously extracted biomolecules was more focused and comprehensive compared to those from separate extractions. Notably, we excluded six pairs of false-positive relationships between metabolites and proteins in the network established using simultaneously extracted biomolecules. In conclusion, this study introduces a novel approach for multiomics analysis and data processing that greatly aids in bioinformation mining from multiomics results. This method is poised to play an indispensable role in systems biology research.
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Affiliation(s)
- Jiachen Shi
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Research Center for Functional Food, National Engineering Laboratory for Cereal Fermentation Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, People's Republic of China
| | - Jialiang Zhao
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Research Center for Functional Food, National Engineering Laboratory for Cereal Fermentation Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, People's Republic of China
| | - Yu Zhang
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Research Center for Functional Food, National Engineering Laboratory for Cereal Fermentation Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, People's Republic of China
| | - Yanan Wang
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Research Center for Functional Food, National Engineering Laboratory for Cereal Fermentation Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, People's Republic of China
| | - Chin Ping Tan
- Department of Food Technology, Faculty of Food Science and Technology, Universiti Putra Malaysia, Serdang, Selangor 43400, Malaysia
| | - Yong-Jiang Xu
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Research Center for Functional Food, National Engineering Laboratory for Cereal Fermentation Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, People's Republic of China
| | - Yuanfa Liu
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Research Center for Functional Food, National Engineering Laboratory for Cereal Fermentation Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, People's Republic of China
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4
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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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5
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Zhang Y, Dong T, Wang M. Lipidomic landscape of lipokines in adipose tissue derived extracellular vesicles. Front Mol Biosci 2023; 10:1281244. [PMID: 38028559 PMCID: PMC10644713 DOI: 10.3389/fmolb.2023.1281244] [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: 08/22/2023] [Accepted: 10/17/2023] [Indexed: 12/01/2023] Open
Abstract
Introduction: Adipose tissue-derived extracellular vesicles (EVs-AT) are recognized as critical mediators of metabolic alterations in obesity-related diseases. However, few studies have focused on the role of lipids within EVs-AT in the development of obesity-related diseases. Methods: In this study, we performed a targeted lipidomic analysis to compare the lipidome of EVs secreted by inguinal white adipose tissue (EVs-iWAT), epididymal white adipose tissue (EVs-eWAT), and interscapular brown adipose tissue (EVs-BAT) in lean and obese mice. Results: We uncovered a comprehensive lipidomic map, revealing the diversity and specific lipid sorting in EVs-iWAT, EVs-eWAT, and EVs-BAT in obesity. Biological function analyses suggested that lipids encapsulated within EVs-AT of obese individuals might correlate with metabolism, pro-inflammatory response, and insulin resistance. These effects were particularly pronounced in EVs-eWAT and EVs-BAT. Conclusion: Our findings indicated that EVs-AT serves as novel carriers for lipokines, thereby mediating the biological functions of EVs-AT. This study holds promise for the identification of new biomarkers for obesity-related diseases and the development of new strategies to combat metabolic diseases.
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Affiliation(s)
- Yan Zhang
- Department of Oral and Maxillofacial Surgery, Tianjin Stomatological Hospital, School of Medicine, Nankai University, Tianjin, China
- Key Laboratory of Bioactive Materials (Ministry of Education), State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin, China
- Tianjin Key Laboratory of Oral and Maxillofacial Function Reconstruction, Tianjin, China
| | - Tingyan Dong
- Key Laboratory of Bioactive Materials (Ministry of Education), State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin, China
- Tianjin Key Laboratory of Oral and Maxillofacial Function Reconstruction, Tianjin, China
| | - Muyao Wang
- Department of Oral and Maxillofacial Surgery, Tianjin Stomatological Hospital, School of Medicine, Nankai University, Tianjin, China
- Key Laboratory of Bioactive Materials (Ministry of Education), State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin, China
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6
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Guo X, Zhu Y, Guo L, Qi Y, Liu X, Wang J, Zhang J, Cui L, Shi Y, Wang Q, Liu C, Lu G, Liu Y, Li T, Hong S, Qin Y, Xiong X, Wu H, Huang L, Huang H, Gu C, Li B, Li J. BCAA insufficiency leads to premature ovarian insufficiency via ceramide-induced elevation of ROS. EMBO Mol Med 2023; 15:e17450. [PMID: 36847712 PMCID: PMC10086587 DOI: 10.15252/emmm.202317450] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 01/31/2023] [Accepted: 01/31/2023] [Indexed: 03/01/2023] Open
Abstract
Premature ovarian insufficiency (POI) is a disease featured by early menopause before 40 years of age, accompanied by an elevation of follicle-stimulating hormone. Though POI affects many aspects of women's health, its major causes remain unknown. Many clinical studies have shown that POI patients are generally underweight, indicating a potential correlation between POI and metabolic disorders. To understand the pathogenesis of POI, we performed metabolomics analysis on serum and identified branch-chain amino acid (BCAA) insufficiency-related metabolic disorders in two independent cohorts from two clinics. A low BCAA diet phenotypically reproduced the metabolic, endocrine, ovarian, and reproductive changes of POI in young C57BL/6J mice. A mechanism study revealed that the BCAA insufficiency-induced POI is associated with abnormal activation of the ceramide-reactive oxygen species (ROS) axis and consequent impairment of ovarian granulosa cell function. Significantly, the dietary supplement of BCAA prevented the development of ROS-induced POI in female mice. The results of this pathogenic study will lead to the development of specific therapies for POI.
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Affiliation(s)
- Xiao Guo
- Obstetrics and Gynecology Hospital, State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital and Institute of Metabolism and Integrative Biology, Fudan University, Shanghai, China
| | - Yuemeng Zhu
- Obstetrics and Gynecology Hospital, State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital and Institute of Metabolism and Integrative Biology, Fudan University, Shanghai, China.,Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Shanghai, China
| | - Lu Guo
- Obstetrics and Gynecology Hospital, State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital and Institute of Metabolism and Integrative Biology, Fudan University, Shanghai, China.,Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Shanghai, China
| | - Yiwen Qi
- Obstetrics and Gynecology Hospital, State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital and Institute of Metabolism and Integrative Biology, Fudan University, Shanghai, China.,Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Shanghai, China.,Shanghai First Maternity and Infant Hospital, Shanghai, China
| | - Xiaocheng Liu
- Obstetrics and Gynecology Hospital, State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital and Institute of Metabolism and Integrative Biology, Fudan University, Shanghai, China.,Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Shanghai, China
| | - Jinhui Wang
- Obstetrics and Gynecology Hospital, State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital and Institute of Metabolism and Integrative Biology, Fudan University, Shanghai, China
| | - Jiangtao Zhang
- Center for Reproductive Medicine, Cheeloo College of Medicine, Shandong University, Jinan, China.,Key Laboratory of Reproductive Endocrinology of Ministry of Education, National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Jinan, China
| | - Linlin Cui
- Center for Reproductive Medicine, Cheeloo College of Medicine, Shandong University, Jinan, China.,Key Laboratory of Reproductive Endocrinology of Ministry of Education, National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Jinan, China
| | - Yueyang Shi
- Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Qichu Wang
- Obstetrics and Gynecology Hospital, State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital and Institute of Metabolism and Integrative Biology, Fudan University, Shanghai, China
| | - Cenxi Liu
- Obstetrics and Gynecology Hospital, State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital and Institute of Metabolism and Integrative Biology, Fudan University, Shanghai, China
| | - Guangxing Lu
- Obstetrics and Gynecology Hospital, State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital and Institute of Metabolism and Integrative Biology, Fudan University, Shanghai, China
| | - Yilian Liu
- Obstetrics and Gynecology Hospital, State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital and Institute of Metabolism and Integrative Biology, Fudan University, Shanghai, China
| | - Tao Li
- Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Shangyu Hong
- Obstetrics and Gynecology Hospital, State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital and Institute of Metabolism and Integrative Biology, Fudan University, Shanghai, China
| | - Yingying Qin
- Shanghai First Maternity and Infant Hospital, Shanghai, China.,Center for Reproductive Medicine, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Xuelian Xiong
- Obstetrics and Gynecology Hospital, State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital and Institute of Metabolism and Integrative Biology, Fudan University, Shanghai, China
| | - Hao Wu
- Obstetrics and Gynecology Hospital, State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital and Institute of Metabolism and Integrative Biology, Fudan University, Shanghai, China
| | - Lin Huang
- Obstetrics and Gynecology Hospital, State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital and Institute of Metabolism and Integrative Biology, Fudan University, Shanghai, China
| | - He Huang
- Obstetrics and Gynecology Hospital, State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital and Institute of Metabolism and Integrative Biology, Fudan University, Shanghai, China
| | - Chao Gu
- Obstetrics and Gynecology Hospital, State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital and Institute of Metabolism and Integrative Biology, Fudan University, Shanghai, China.,Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Shanghai, China
| | - Bin Li
- Obstetrics and Gynecology Hospital, State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital and Institute of Metabolism and Integrative Biology, Fudan University, Shanghai, China.,Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Shanghai, China
| | - Jin Li
- Obstetrics and Gynecology Hospital, State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital and Institute of Metabolism and Integrative Biology, Fudan University, Shanghai, China
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7
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Lipidomics and Transcriptomics Differ Liposarcoma Differentiation Characteristics That Can Be Altered by Pentose Phosphate Pathway Intervention. Metabolites 2022; 12:metabo12121227. [PMID: 36557266 PMCID: PMC9783184 DOI: 10.3390/metabo12121227] [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: 10/14/2022] [Revised: 11/10/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022] Open
Abstract
Liposarcoma (LPS) is a rare and heterogeneous malignancy of adipocytic origin. Well-differentiated liposarcoma (WDLPS) and dedifferentiated liposarcoma (DDLPS) are two of the most common subtypes, showing similar genetic characterizations but distinct biological behaviors and clinical prognosis. Compared to WDLPS, DDLPS is more aggressive and has the potential of metastasis, as the malignant adipocytic tumor's metabolic changes may have taken place during the tumorigenesis of LPSs. Therefore, to investigate the lipid alterations between the two subtypes, high-resolution liquid chromatography tandem mass spectrometry (LC-MS/MS) based untargeted lipidomic analysis was performed onto LPS tissues from 6 WDLPS and 7 DDLPS patients. The lipidomic analysis showed the upregulated phosphatidylcholines and phosphoethanolamines in DDLPS, and the upregulated triglycerides and diglycerides in WDLPS, which might be due to the uncompleted adipocytic dedifferentiation leading to such tumorigenesis. Such a finding was also confirmed by the similarity comparison of two LPS subtypes to the transcriptome of stromal vascular fraction at different differentiation stages. Transcriptomic analysis also demonstrated that metabolic pathways including the pentose phosphate pathway (PPP) were upregulated in WDLPS compared to DDLPS. Therefore, the cell line LPS853 was treated with the PPP inhibitor 6-aminonicotinamide ex vivo and the proliferation and invasion of LPS853 was significantly promoted by PPP inhibition, suggesting the potential role of PPP in the development and differentiation of LPS. In conclusion, this study described the altered lipid profiles of WDLPS and DDLPS for the first time, revealing the different differentiation stages of the two subtypes and providing a potential metabolic target for LPS treatment.
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8
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Wang R, Miao X. Lipid turnover and SQUAMOSA promoter-binding proteins mediate variation in fatty acid desaturation under early nitrogen deprivation revealed by lipidomic and transcriptomic analyses in Chlorella pyrenoidosa. FRONTIERS IN PLANT SCIENCE 2022; 13:987354. [PMID: 36247620 PMCID: PMC9558234 DOI: 10.3389/fpls.2022.987354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 09/06/2022] [Indexed: 06/16/2023]
Abstract
Nitrogen deprivation induces variations in fatty acid desaturation in microalgae, which determines the performance of biodiesel and the nutritional value of bioproducts. However, the detailed scenario and the underlying regulatory mechanism remain unclear. In this study, we attempt to outline these scenario and mechanisms by performing biochemical, lipidomic, and transcriptomic analyses in Chlorella pyrenoidosa and functional characterization of transcription factors in Yarrowia lipolytica. We found that early nitrogen deprivation dramatically reduced fatty acid desaturation without increasing lipid content. The contents of palmitic acid (16:0) and oleic acid (18:1) dramatically increased to 2.14 and 2.87 times that of nitrogen repletion on the second day, respectively. Lipidomic analysis showed the transfer of polyunsaturated fatty acids from phospholipids and glycolipids to triacylglycerols, and an increase in lipid species with 16:0 or 18:1 under nitrogen deprivation conditions. Upregulated stearoyl-ACP desaturase and oleyl-ACP thioesterase promoted the synthesis of 18:1, but restricted acetyl-CoA supply revealed that it was the intensive lipid turnover instead of an attenuated Kennedy pathway that played an important role in the variation in fatty acid composition under early nitrogen deprivation. Finally, two differentially expressed SQUAMOSA promoter-binding proteins (SBPs) were heterologously expressed in Y. lipolytica, demonstrating their role in promoting the accumulation of total fatty acid and the reduction in fatty acid desaturation. These results revealed the crucial role of lipid turnover and SBPs in determining fatty acid desaturation under early nitrogen deprivation, opening new avenues for the metabolic engineering of fatty acid desaturation in microalgae.
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Affiliation(s)
- Rui Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, Shanghai, China
- Biomass Energy Research Center, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaoling Miao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, Shanghai, China
- Biomass Energy Research Center, Shanghai Jiao Tong University, Shanghai, China
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9
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Xie P, Zhang H, Wu P, Chen Y, Cai Z. Three-Dimensional Mass Spectrometry Imaging Reveals Distributions of Lipids and the Drug Metabolite Associated with the Enhanced Growth of Colon Cancer Cell Spheroids Treated with Triclosan. Anal Chem 2022; 94:13667-13675. [PMID: 36170179 PMCID: PMC9558077 DOI: 10.1021/acs.analchem.2c00768] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The application of mass spectrometry imaging (MSI) to explore the responses of cancer cell spheroids (CCS) after treatment of exogenous molecules has attracted growing attention. Increasing studies have utilized MSI to image the two-dimensional distributions of exogenous and endogenous molecules in planar CCS sections. However, because CCS are volumetric and heterogenous, maintaining their three-dimensional (3D) information is essential for acquiring a better understanding of the tumor microenvironment and mechanisms of action of exogenous molecules. Here, an established method of 3D MSI was applied to distinguish the distributions of triclosan sulfate and endogenous lipids in three microregions of colon CCS with an enhanced growth induced by the treatment of triclosan, a common antimicrobial agent. The results of 3D MSI showed that triclosan sulfate gradually accumulated from the periphery to the entire structure of CCS and finally localized in the core region. Spatial lipidomics analysis revealed that the upregulated phosphatidylethanolamine (fold change (FD) = 1.26, p = 0.0021), phosphatidylinositol (FD = 1.17, p = 0.0180), and phosphatidylcholine (FD = 1.22, p = 0.0178) species mainly distributed in the outer proliferative region, while the upregulated sphingomyelin (FD = 1.18, p = 0.024) species tended to distribute in the inner necrotic region. Our results suggest that a competitive mechanism between inhibiting and promoting CCS growth might be responsible for the proliferation of CCS treated with triclosan.
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Affiliation(s)
- Peisi Xie
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Kowloon 999077, Hong Kong SAR, China
| | - Hongna Zhang
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Kowloon 999077, Hong Kong SAR, China
| | - Pengfei Wu
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Kowloon 999077, Hong Kong SAR, China
| | - Yanyan Chen
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Kowloon 999077, Hong Kong SAR, China
| | - Zongwei Cai
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Kowloon 999077, Hong Kong SAR, China
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10
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Tian H, Ni Z, Lam SM, Jiang W, Li F, Du J, Wang Y, Shui G. Precise Metabolomics Reveals a Diversity of Aging-Associated Metabolic Features. SMALL METHODS 2022; 6:e2200130. [PMID: 35527334 DOI: 10.1002/smtd.202200130] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 04/24/2022] [Indexed: 06/14/2023]
Abstract
Mass spectrometry-based metabolomics has emerged as a powerful technique for biomedical research, although technical issues with its analytical precision and structural characterization remain. Herein, a robust non-targeted strategy for accurate quantitation and precise profiling of metabolomes is developed and applied to investigate plasma metabolic features associated with human aging. A comprehensive set of isotope-labeled standards (ISs) covering major metabolic pathways is incorporated to quantify polar metabolites. Matching rules to select ISs for calibration follow a primary criterion of minimal coefficients of variations (COVs). If minimal COVs between specific ISs for a particular metabolite fall within 5% window, a further selection of ISs is conducted based on structural similarities and proximity in retention time. The introduction and refined selection of appropriate ISs for quantitation reduces the COVs of 480 identified metabolites in quality control samples from 14.3% to 9.8% and facilitates identification of additional metabolite. Finally, the precise metabolomics approach reveals perturbations in a diverse array of metabolic pathways across aging that principally implicate steroid metabolism, amino acid metabolism, lipid metabolism, and purine metabolism, which allows the authors to draw correlates to the pathology of various age-related diseases. These findings provide clues for the prevention and treatment of these age-related diseases.
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Affiliation(s)
- He Tian
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zhen Ni
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Sin Man Lam
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- LipidALL Technologies Company Limited, Changzhou, Jiangsu Province, 213022, China
| | - Wenxi Jiang
- Beijing Institute of Heart, Lung, and Blood Vessel Diseases, Beijing Anzhen Hospital, Capital Medical University, Beijing, 100029, China
| | - Fengjuan Li
- Beijing Institute of Heart, Lung, and Blood Vessel Diseases, Beijing Anzhen Hospital, Capital Medical University, Beijing, 100029, China
| | - Jie Du
- Beijing Institute of Heart, Lung, and Blood Vessel Diseases, Beijing Anzhen Hospital, Capital Medical University, Beijing, 100029, China
| | - Yuan Wang
- Beijing Institute of Heart, Lung, and Blood Vessel Diseases, Beijing Anzhen Hospital, Capital Medical University, Beijing, 100029, China
| | - Guanghou Shui
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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11
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The Storage Conditions of High-Fat Diet Are the Key Factors for Diet-Induced Obesity and Liver Damage. Nutrients 2022; 14:nu14112222. [PMID: 35684023 PMCID: PMC9182774 DOI: 10.3390/nu14112222] [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: 04/27/2022] [Revised: 05/24/2022] [Accepted: 05/24/2022] [Indexed: 11/21/2022] Open
Abstract
The diet-induced obesity (DIO) mouse model has been widely used for obesity studies. The effects of storage conditions on the composition of nutrients in high-fat diets (HFDs) and their impact on metabolic homeostasis have not been systemically investigated. In the current study, we tested the effects of HFDs stored under different conditions and found that mice fed a HFD stored in the fridge (HFDfri) gained less weight than those fed HFDs stored in the freezer (HFDfre). Further analysis revealed that changes in the relative abundance of medium-chain triglyceride (MCT) in the HFDfri, which have much lower intestinal absorption rates, contributed to the body weight differences. In contrast, exacerbated liver damage and elevated levels of unfolded protein response (UPR) was observed in the mice fed by HFDfri. Depletion of the UPR-regulated gene Nnmt alleviated liver damage via the inhibition of the integrated stress response (ISR). Our study, for the first time, provides evidence that HFD storage conditions can have a significant impact on both body weight changes and liver damage in the DIO model.
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