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Cobley JN, Margaritelis NV, Chatzinikolaou PN, Nikolaidis MG, Davison GW. Ten "Cheat Codes" for Measuring Oxidative Stress in Humans. Antioxidants (Basel) 2024; 13:877. [PMID: 39061945 PMCID: PMC11273696 DOI: 10.3390/antiox13070877] [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: 05/23/2024] [Revised: 07/17/2024] [Accepted: 07/18/2024] [Indexed: 07/28/2024] Open
Abstract
Formidable and often seemingly insurmountable conceptual, technical, and methodological challenges hamper the measurement of oxidative stress in humans. For instance, fraught and flawed methods, such as the thiobarbituric acid reactive substances assay kits for lipid peroxidation, rate-limit progress. To advance translational redox research, we present ten comprehensive "cheat codes" for measuring oxidative stress in humans. The cheat codes include analytical approaches to assess reactive oxygen species, antioxidants, oxidative damage, and redox regulation. They provide essential conceptual, technical, and methodological information inclusive of curated "do" and "don't" guidelines. Given the biochemical complexity of oxidative stress, we present a research question-grounded decision tree guide for selecting the most appropriate cheat code(s) to implement in a prospective human experiment. Worked examples demonstrate the benefits of the decision tree-based cheat code selection tool. The ten cheat codes define an invaluable resource for measuring oxidative stress in humans.
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Affiliation(s)
- James N. Cobley
- The University of Dundee, Dundee DD1 4HN, UK
- Ulster University, Belfast BT15 1ED, Northern Ireland, UK;
| | - Nikos V. Margaritelis
- Aristotle University of Thessaloniki, 62122 Serres, Greece; (N.V.M.); (P.N.C.); (M.G.N.)
| | | | - Michalis G. Nikolaidis
- Aristotle University of Thessaloniki, 62122 Serres, Greece; (N.V.M.); (P.N.C.); (M.G.N.)
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Mapes JH, Stover J, Stout HD, Folsom TM, Babcock E, Loudwig S, Martin C, Austin MJ, Tu F, Howdieshell CJ, Simpson ZB, Blom T, Weaver D, Winkler D, Vander Velden K, Ossareh PM, Beierle JM, Somekh T, Bardo AM, Anslyn EV, Marcotte EM, Swaminathan J. Robust and scalable single-molecule protein sequencing with fluorosequencing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.15.558007. [PMID: 37745461 PMCID: PMC10516020 DOI: 10.1101/2023.09.15.558007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
The need to accurately survey proteins and their modifications with ever higher sensitivities, particularly in clinical settings with limited samples, is spurring development of new single molecule proteomics technologies. Fluorosequencing is one such highly parallelized single molecule peptide sequencing platform, based on determining the sequence positions of select amino acid types within peptides to enable their identification and quantification from a reference database. Here, we describe substantial improvements to fluorosequencing, including identifying fluorophores compatible with the sequencing chemistry, mitigating dye-dye interactions through the use of extended polyproline linkers, and developing an end-to-end workflow for sample preparation and sequencing. We demonstrate by fluorosequencing peptides in mixtures and identifying a target neoantigen from a database of decoy MHC peptides, highlighting the potential of the technology for high sensitivity clinical applications.
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Affiliation(s)
| | | | - Heather D Stout
- Erisyon, Inc. Austin, TX, 78752
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712
| | | | | | | | - Christopher Martin
- Erisyon, Inc. Austin, TX, 78752
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712
| | | | - Fan Tu
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712
| | | | | | | | | | | | | | | | | | | | - Angela M Bardo
- Erisyon, Inc. Austin, TX, 78752
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712
| | - Eric V Anslyn
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712
| | - Edward M Marcotte
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712
| | - Jagannath Swaminathan
- Erisyon, Inc. Austin, TX, 78752
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712
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He X, Liu X, Zuo F, Shi H, Jing J. Artificial intelligence-based multi-omics analysis fuels cancer precision medicine. Semin Cancer Biol 2023; 88:187-200. [PMID: 36596352 DOI: 10.1016/j.semcancer.2022.12.009] [Citation(s) in RCA: 35] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/16/2022] [Accepted: 12/29/2022] [Indexed: 01/02/2023]
Abstract
With biotechnological advancements, innovative omics technologies are constantly emerging that have enabled researchers to access multi-layer information from the genome, epigenome, transcriptome, proteome, metabolome, and more. A wealth of omics technologies, including bulk and single-cell omics approaches, have empowered to characterize different molecular layers at unprecedented scale and resolution, providing a holistic view of tumor behavior. Multi-omics analysis allows systematic interrogation of various molecular information at each biological layer while posing tricky challenges regarding how to extract valuable insights from the exponentially increasing amount of multi-omics data. Therefore, efficient algorithms are needed to reduce the dimensionality of the data while simultaneously dissecting the mysteries behind the complex biological processes of cancer. Artificial intelligence has demonstrated the ability to analyze complementary multi-modal data streams within the oncology realm. The coincident development of multi-omics technologies and artificial intelligence algorithms has fuelled the development of cancer precision medicine. Here, we present state-of-the-art omics technologies and outline a roadmap of multi-omics integration analysis using an artificial intelligence strategy. The advances made using artificial intelligence-based multi-omics approaches are described, especially concerning early cancer screening, diagnosis, response assessment, and prognosis prediction. Finally, we discuss the challenges faced in multi-omics analysis, along with tentative future trends in this field. With the increasing application of artificial intelligence in multi-omics analysis, we anticipate a shifting paradigm in precision medicine becoming driven by artificial intelligence-based multi-omics technologies.
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Affiliation(s)
- Xiujing He
- Laboratory of Integrative Medicine, Clinical Research Center for Breast, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan, PR China
| | - Xiaowei Liu
- Laboratory of Integrative Medicine, Clinical Research Center for Breast, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan, PR China
| | - Fengli Zuo
- Laboratory of Integrative Medicine, Clinical Research Center for Breast, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan, PR China
| | - Hubing Shi
- Laboratory of Integrative Medicine, Clinical Research Center for Breast, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan, PR China
| | - Jing Jing
- Laboratory of Integrative Medicine, Clinical Research Center for Breast, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan, PR China.
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