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Banerjee S, Hatimuria M, Sarkar K, Das J, Pabbathi A, Sil PC. Recent Contributions of Mass Spectrometry-Based "Omics" in the Studies of Breast Cancer. Chem Res Toxicol 2024; 37:137-180. [PMID: 38011513 DOI: 10.1021/acs.chemrestox.3c00223] [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: 11/29/2023]
Abstract
Breast cancer (BC) is one of the most heterogeneous groups of cancer. As every biotype of BC is unique and presents a particular "omic" signature, they are increasingly characterized nowadays with novel mass spectrometry (MS) strategies. BC therapeutic approaches are primarily based on the two features of human epidermal growth factor receptor 2 (HER2) and estrogen receptor (ER) positivity. Various strategic MS implementations are reported in studies of BC also involving data independent acquisitions (DIAs) of MS which report novel differential proteomic, lipidomic, proteogenomic, phosphoproteomic, and metabolomic characterizations associated with the disease and its therapeutics. Recently many "omic" studies have aimed to identify distinct subsidiary biotypes for diagnosis, prognosis, and targets of treatment. Along with these, drug-induced-resistance phenotypes are characterized by "omic" changes. These identifying aspects of the disease may influence treatment outcomes in the near future. Drug quantifications and characterizations are also done regularly and have implications in therapeutic monitoring and in drug efficacy assessments. We report these studies, mentioning their implications toward the understanding of BC. We briefly provide the MS instrumentation principles that are adopted in such studies as an overview with a brief outlook on DIA-MS strategies. In all of these, we have chosen a model cancer for its revelations through MS-based "omics".
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Affiliation(s)
- Subhrajit Banerjee
- Department of Physiology, Surendranath College, University of Calcutta, Kolkata 700009, India
- Department of Microbiology, St. Xavier's College, Kolkata 700016, India
| | - Madushmita Hatimuria
- Department of Industrial Chemistry, School of Physical Sciences, Mizoram University, Aizawl 796004, Mizoram India
| | - Kasturi Sarkar
- Department of Microbiology, St. Xavier's College, Kolkata 700016, India
| | - Joydeep Das
- Department of Chemistry, School of Physical Sciences, Mizoram University, Aizawl 796004, Mizoram, India
| | - Ashok Pabbathi
- Department of Industrial Chemistry, School of Physical Sciences, Mizoram University, Aizawl 796004, Mizoram India
| | - Parames C Sil
- Department of Molecular Medicine Bose Institute, Kolkata 700054, India
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Song Y, Zhang Y, Xie S, Song X. Screening and diagnosis of triple negative breast cancer based on rapid metabolic fingerprinting by conductive polymer spray ionization mass spectrometry and machine learning. Front Cell Dev Biol 2022; 10:1075810. [PMID: 36589750 PMCID: PMC9798417 DOI: 10.3389/fcell.2022.1075810] [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: 10/20/2022] [Accepted: 11/22/2022] [Indexed: 12/23/2022] Open
Abstract
We present the use of conductive spray polymer ionization mass spectrometry (CPSI-MS) combined with machine learning (ML) to rapidly gain the metabolic fingerprint from 1 μl liquid extraction from the biopsied tissue of triple-negative breast cancer (TNBC) in China. The 76 discriminative metabolite markers are verified at the primary carcinoma site and can also be successfully tracked in the serum. The Lasso classifier featured with 15- and 22-metabolites detected by CPSI-MS achieve a sensitivity of 88.8% for rapid serum screening and a specificity of 91.1% for tissue diagnosis, respectively. Finally, the expression levels of their corresponding upstream enzymes and transporters have been initially confirmed. In general, CPSI-MS/ML serves as a cost-effective tool for the rapid screening, diagnosis, and precise characterization for the TNBC metabolism reprogramming in the clinical practice.
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Affiliation(s)
- Yaoyao Song
- Department of General Surgery, The Sixth Medical Center of Chinese PLA General Hospital, Beijing, China,Department of Burn and Plastic Surgery, The Fourth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Yan Zhang
- Department of General Surgery, The Sixth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Songhai Xie
- Department of Chemistry, Fudan University, Shanghai, China
| | - Xiaowei Song
- Department of Chemistry, Fudan University, Shanghai, China,*Correspondence: Xiaowei Song,
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Li H, Zhang H, Yan F, He Y, Ji A, Liu Z, Li M, Ji X, Li C. Kidney and plasma metabolomics provide insights into the molecular mechanisms of urate nephropathy in a mouse model of hyperuricemia. Biochim Biophys Acta Mol Basis Dis 2022; 1868:166374. [PMID: 35276331 DOI: 10.1016/j.bbadis.2022.166374] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 02/04/2022] [Accepted: 03/04/2022] [Indexed: 02/07/2023]
Abstract
Hyperuricemia (HUA) is closely associated with kidney damage and kidney diseases in humans; however, the underlying mechanisms of HUA-induced kidney diseases remain unknown. In the present study, we examined the kidney and plasma metabolic profiles in a HUA mouse model constructed by knocking out (Ko) the urate oxidase (Uox) gene. The Uox-Ko mice were characterized by an increase in uric acid, glycine, 3'-adenosine monophosphate, citrate, N-acetyl-l-glutamate, l-kynurenine, 5-hydroxyindoleacetate, xanthurenic acid, cortisol, and (-)-prostaglandin e2 together with a decrease of inosine in the kidneys. These altered metabolites confirmed disturbances of purine metabolism, amino acid biosynthesis, tryptophan metabolism, and neuroactive ligand-receptor interaction in Uox-Ko mice. Betaine and biotin were related to kidney function and identified as the potential plasma metabolic biomarker for predicting urate nephropathy (UN). Taken together, these results revealed the underlying pathogenic mechanisms of UN. Investigating these pathways might provide novel targets for the therapeutic intervention of UN and can potentially lead to new treatment strategies.
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Affiliation(s)
- Hailong Li
- Institute of Metabolic Diseases, Qingdao University, Qingdao 266003, China; Shandong Provincial Key Laboratory of Metabolic Disease and Qingdao Key Laboratory of Gout, The Affiliated Hospital of Qingdao University, Qingdao 266003, China
| | - Hui Zhang
- Institute of Metabolic Diseases, Qingdao University, Qingdao 266003, China; Shandong Provincial Key Laboratory of Metabolic Disease and Qingdao Key Laboratory of Gout, The Affiliated Hospital of Qingdao University, Qingdao 266003, China
| | - Fei Yan
- Shandong Provincial Key Laboratory of Metabolic Disease and Qingdao Key Laboratory of Gout, The Affiliated Hospital of Qingdao University, Qingdao 266003, China
| | - Yuwei He
- Shandong Provincial Key Laboratory of Metabolic Disease and Qingdao Key Laboratory of Gout, The Affiliated Hospital of Qingdao University, Qingdao 266003, China
| | - Aichang Ji
- Shandong Provincial Key Laboratory of Metabolic Disease and Qingdao Key Laboratory of Gout, The Affiliated Hospital of Qingdao University, Qingdao 266003, China
| | - Zhen Liu
- Shandong Provincial Key Laboratory of Metabolic Disease and Qingdao Key Laboratory of Gout, The Affiliated Hospital of Qingdao University, Qingdao 266003, China
| | - Maichao Li
- Shandong Provincial Key Laboratory of Metabolic Disease and Qingdao Key Laboratory of Gout, The Affiliated Hospital of Qingdao University, Qingdao 266003, China
| | - Xiaopeng Ji
- Shandong Provincial Key Laboratory of Metabolic Disease and Qingdao Key Laboratory of Gout, The Affiliated Hospital of Qingdao University, Qingdao 266003, China
| | - Changgui Li
- Institute of Metabolic Diseases, Qingdao University, Qingdao 266003, China; Shandong Provincial Key Laboratory of Metabolic Disease and Qingdao Key Laboratory of Gout, The Affiliated Hospital of Qingdao University, Qingdao 266003, China.
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Song X, Mofidfar M, Zare RN. Introducing Nafion for In Situ Desalting and Biofluid Profiling in Spray Mass Spectrometry. Front Chem 2022; 9:807244. [PMID: 35145954 PMCID: PMC8821663 DOI: 10.3389/fchem.2021.807244] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 12/21/2021] [Indexed: 12/16/2022] Open
Abstract
We introduce Nafion into the ambient ionization technique of spray mass spectrometry to serve for in situ desalting and direct analysis of biological fluids. Nafion was coated onto the surface of the triangular spray tip as the cation exchange material. Because the sulfonic group from the Nafion membrane effectively exchanges their carried protons with inorganic salt ions (e.g., Na+ and K+), the analyte’s ionization efficiency can be significantly enhanced by reducing ion suppression. The desalting efficiency can reach 90% and the maximum tolerance of the absolute salt amount reaches 100 μmol. The mass spectral profile can also be simplified by removing the multiple adducted ion types from small-molecule drugs and metabolites ([M + Na]+ and [M + K]+), or multiply charged ions formed by proteins ([M + nNa]n+ and [M + nK]n+). Thus, the Nafion coating makes less ambiguous data interpretation collected from spray mass spectrometry for qualitative profiling or quantitative measurement of a target analyte.
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Affiliation(s)
- Xiaowei Song
- Department of Chemistry, Fudan University, Shanghai, China
- Department of Chemistry, Stanford University, Stanford, CA, United States
| | - Mohammad Mofidfar
- Department of Chemistry, Stanford University, Stanford, CA, United States
| | - Richard N. Zare
- Department of Chemistry, Stanford University, Stanford, CA, United States
- *Correspondence: Richard N. Zare,
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Song X, Li J, Mofidfar M, Zare RN. Distinguishing between Isobaric Ions Using Microdroplet Hydrogen-Deuterium Exchange Mass Spectrometry. Metabolites 2021; 11:728. [PMID: 34822386 PMCID: PMC8625015 DOI: 10.3390/metabo11110728] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 10/21/2021] [Accepted: 10/22/2021] [Indexed: 11/16/2022] Open
Abstract
Isobaric ions having the same mass-to-charge ratio cannot be separately identified by mass spectrometry (MS) alone, but this limitation can be overcome by using hydrogen-deuterium exchange (HDX) in microdroplets. Because isobaric ions may contain a varied number of exchangeable sites and different types of functional groups, each one produces a unique MS spectral pattern after droplet spray HDX without the need for MS/MS experiments or introduction of ion mobility measurements. As an example of the power of this approach, isobaric ions in urinary metabolic profiles are identified and used to distinguish between healthy individuals and those having bladder cancer.
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Affiliation(s)
- Xiaowei Song
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA; (X.S.); (M.M.)
- Department of Chemistry, Fudan University, Shanghai 200438, China;
| | - Jia Li
- Department of Chemistry, Fudan University, Shanghai 200438, China;
| | - Mohammad Mofidfar
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA; (X.S.); (M.M.)
| | - Richard N. Zare
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA; (X.S.); (M.M.)
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