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Sharma V, Khokhar M, Panigrahi P, Gadwal A, Setia P, Purohit P. Advancements, Challenges, and clinical implications of integration of metabolomics technologies in diabetic nephropathy. Clin Chim Acta 2024; 561:119842. [PMID: 38969086 DOI: 10.1016/j.cca.2024.119842] [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: 03/30/2024] [Revised: 06/25/2024] [Accepted: 06/29/2024] [Indexed: 07/07/2024]
Abstract
BACKGROUND Diabetic nephropathy (DN), a severe complication of diabetes, involves a range of renal abnormalities driven by metabolic derangements. Metabolomics, revealing dynamic metabolic shifts in diseases like DN and offering insights into personalized treatment strategies, emerges as a promising tool for improved diagnostics and therapies. METHODS We conducted an extensive literature review to examine how metabolomics contributes to the study of DN and the challenges associated with its implementation in clinical practice. We identified and assessed relevant studies that utilized metabolomics methods, including nuclear magnetic resonance (NMR) spectroscopy and mass spectrometry (MS) to assess their efficacy in diagnosing DN. RESULTS Metabolomics unveils key pathways in DN progression, highlighting glucose metabolism, dyslipidemia, and mitochondrial dysfunction. Biomarkers like glycated albumin and free fatty acids offer insights into DN nuances, guiding potential treatments. Metabolomics detects small-molecule metabolites, revealing disease-specific patterns for personalized care. CONCLUSION Metabolomics offers valuable insights into the molecular mechanisms underlying DN progression and holds promise for personalized medicine approaches. Further research in this field is warranted to elucidate additional metabolic pathways and identify novel biomarkers for early detection and targeted therapeutic interventions in DN.
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Affiliation(s)
- V Sharma
- Department of Biochemistry, All India Institute of Medical Sciences, Jodhpur, Rajasthan 342005, India
| | - M Khokhar
- Department of Biochemistry, All India Institute of Medical Sciences, Jodhpur, Rajasthan 342005, India
| | - P Panigrahi
- Department of Biochemistry, All India Institute of Medical Sciences, Jodhpur, Rajasthan 342005, India
| | - A Gadwal
- Department of Biochemistry, All India Institute of Medical Sciences, Jodhpur, Rajasthan 342005, India
| | - P Setia
- Department of Forensic Medicine and Toxicology, All India Institute of Medical Sciences, Jodhpur, Rajasthan 342005, India
| | - P Purohit
- Department of Biochemistry, All India Institute of Medical Sciences, Jodhpur, Rajasthan 342005, India.
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Kurgan N, Kjærgaard Larsen J, Deshmukh AS. Harnessing the power of proteomics in precision diabetes medicine. Diabetologia 2024; 67:783-797. [PMID: 38345659 DOI: 10.1007/s00125-024-06097-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 12/20/2023] [Indexed: 03/21/2024]
Abstract
Precision diabetes medicine (PDM) aims to reduce errors in prevention programmes, diagnosis thresholds, prognosis prediction and treatment strategies. However, its advancement and implementation are difficult due to the heterogeneity of complex molecular processes and environmental exposures that influence an individual's disease trajectory. To address this challenge, it is imperative to develop robust screening methods for all areas of PDM. Innovative proteomic technologies, alongside genomics, have proven effective in precision cancer medicine and are showing promise in diabetes research for potential translation. This narrative review highlights how proteomics is well-positioned to help improve PDM. Specifically, a critical assessment of widely adopted affinity-based proteomic technologies in large-scale clinical studies and evidence of the benefits and feasibility of using MS-based plasma proteomics is presented. We also present a case for the use of proteomics to identify predictive protein panels for type 2 diabetes subtyping and the development of clinical prediction models for prevention, diagnosis, prognosis and treatment strategies. Lastly, we discuss the importance of plasma and tissue proteomics and its integration with genomics (proteogenomics) for identifying unique type 2 diabetes intra- and inter-subtype aetiology. We conclude with a call for action formed on advancing proteomics technologies, benchmarking their performance and standardisation across sites, with an emphasis on data sharing and the inclusion of diverse ancestries in large cohort studies. These efforts should foster collaboration with key stakeholders and align with ongoing academic programmes such as the Precision Medicine in Diabetes Initiative consortium.
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Affiliation(s)
- Nigel Kurgan
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Jeppe Kjærgaard Larsen
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Atul S Deshmukh
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark.
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Ma Y, Chu Y, Xu Z, Xie C, Ma X, Zhang L, Hu J, Zou B, Wu H, Zhou G. Ultrafast and Highly Specific Detection of One-Base Mutated Cell-Free DNA at a Very Low Abundance. Anal Chem 2024; 96:117-126. [PMID: 38114445 DOI: 10.1021/acs.analchem.3c03326] [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: 12/21/2023]
Abstract
Liquid biopsy as well as genotyping plays important roles in guiding the use of tumor-targeted drugs and monitoring the generation of drug resistance. However, current methods, such as next-generation sequencing (NGS) and pyrosequencing, require long analysis time and complicated steps. To achieve ultrafast and highly specific detection of cell-free DNA (cfDNA) from blood, we improved our recently developed FEN1-aided RPA (FARPA), which combined flap endonuclease 1 (FEN1)-catalyzed invasive reactions with recombinase polymerase amplification (RPA) by inactivating the RPA enzymes before invasive reactions, designing short RPA primers, and changing invasive reaction conditions. Using the L858R and T790M mutations as examples, FARPA was sensitive to detect 5 copies of targeted mutants, specific to sense the mutants with an abundance as low as 0.01% from blood, and ultrafast to get results within 40 min. The method was readily expended to genotyping, and 15 min was enough to report the allele species directly from oral swab samples by coupling quick DNA extraction reagents. Validation was carried out by detecting clinical samples, including 20 cfDNA from patients with non-small cell lung cancer (NSCLC) for liquid biopsy and 43 human genomic DNA (gDNA) purified from blood (33) or lysed from oral swabs (10) for genotyping, giving 100% agreement with NGS and pyrosequencing, respectively. Furthermore, a portable battery-driven device with dual-channel fluorescence detection was successfully constructed to facilitate point-of-care testing (POCT) of liquid biopsy and genotyping, providing doctors with a potential tool to achieve genotyping- or mutant-guided personalized medicine at emergency or source-limited regions.
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Affiliation(s)
- Yi Ma
- Department of Clinical Pharmacy, State Key Laboratory of Analytical Chemistry for Life Science and Jiangsu Key Laboratory of Molecular Medicine, Nanjing Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210002, China
| | - Yanan Chu
- Department of Clinical Pharmacy, State Key Laboratory of Analytical Chemistry for Life Science and Jiangsu Key Laboratory of Molecular Medicine, Nanjing Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210002, China
| | - Zhaoluo Xu
- Department of Clinical Pharmacy, State Key Laboratory of Analytical Chemistry for Life Science and Jiangsu Key Laboratory of Molecular Medicine, Nanjing Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210002, China
| | - Chunmei Xie
- Department of Clinical Pharmacy, State Key Laboratory of Analytical Chemistry for Life Science and Jiangsu Key Laboratory of Molecular Medicine, Nanjing Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210002, China
| | - Xueping Ma
- Department of Clinical Pharmacy, State Key Laboratory of Analytical Chemistry for Life Science and Jiangsu Key Laboratory of Molecular Medicine, Nanjing Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210002, China
| | - Likun Zhang
- Department of Clinical Pharmacy, State Key Laboratory of Analytical Chemistry for Life Science and Jiangsu Key Laboratory of Molecular Medicine, Nanjing Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210002, China
| | - Jingjing Hu
- Department of Clinical Pharmacy, State Key Laboratory of Analytical Chemistry for Life Science and Jiangsu Key Laboratory of Molecular Medicine, Nanjing Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210002, China
| | - Bingjie Zou
- Key Laboratory of Drug Quality Control and Pharmacovigilance of Ministry of Education, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Haiping Wu
- Department of Clinical Pharmacy, State Key Laboratory of Analytical Chemistry for Life Science and Jiangsu Key Laboratory of Molecular Medicine, Nanjing Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210002, China
- Department of Clinical Pharmacy, Nanjing Jinling Hospital, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Guohua Zhou
- Department of Clinical Pharmacy, State Key Laboratory of Analytical Chemistry for Life Science and Jiangsu Key Laboratory of Molecular Medicine, Nanjing Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210002, China
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Tahir F, Farhan M. Exploring the progress of artificial intelligence in managing type 2 diabetes mellitus: a comprehensive review of present innovations and anticipated challenges ahead. FRONTIERS IN CLINICAL DIABETES AND HEALTHCARE 2023; 4:1316111. [PMID: 38161783 PMCID: PMC10757318 DOI: 10.3389/fcdhc.2023.1316111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 11/24/2023] [Indexed: 01/03/2024]
Abstract
A significant worldwide health issue, Type 2 Diabetes Mellitus (T2DM) calls for creative solutions. This in-depth review examines the growing severity of T2DM and the requirement for individualized management approaches. It explores the use of artificial intelligence (AI) in the treatment of diabetes, highlighting its potential for diagnosis, customized treatment plans, and patient self-management. The paper highlights the roles played by AI applications such as expert systems, machine learning algorithms, and deep learning approaches in the identification of retinopathy, the interpretation of clinical guidelines, and prediction models. Examined are difficulties with individualized diabetes treatment, including complex technological issues and patient involvement. The review highlights the revolutionary potential of AI in the management of diabetes and calls for a balanced strategy in which AI supports clinical knowledge. It is crucial to pay attention to ethical issues, data privacy, and joint research initiatives.
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Affiliation(s)
- Farwa Tahir
- Department of Pharmacy, Rashid Latif Medical Complex, Lahore, Pakistan
| | - Muhammad Farhan
- Department of Pharmacy, University of Lahore, Islamabad, Pakistan
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Sadee W, Wang D, Hartmann K, Toland AE. Pharmacogenomics: Driving Personalized Medicine. Pharmacol Rev 2023; 75:789-814. [PMID: 36927888 PMCID: PMC10289244 DOI: 10.1124/pharmrev.122.000810] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 03/09/2023] [Accepted: 03/10/2023] [Indexed: 03/18/2023] Open
Abstract
Personalized medicine tailors therapies, disease prevention, and health maintenance to the individual, with pharmacogenomics serving as a key tool to improve outcomes and prevent adverse effects. Advances in genomics have transformed pharmacogenetics, traditionally focused on single gene-drug pairs, into pharmacogenomics, encompassing all "-omics" fields (e.g., proteomics, transcriptomics, metabolomics, and metagenomics). This review summarizes basic genomics principles relevant to translation into therapies, assessing pharmacogenomics' central role in converging diverse elements of personalized medicine. We discuss genetic variations in pharmacogenes (drug-metabolizing enzymes, drug transporters, and receptors), their clinical relevance as biomarkers, and the legacy of decades of research in pharmacogenetics. All types of therapies, including proteins, nucleic acids, viruses, cells, genes, and irradiation, can benefit from genomics, expanding the role of pharmacogenomics across medicine. Food and Drug Administration approvals of personalized therapeutics involving biomarkers increase rapidly, demonstrating the growing impact of pharmacogenomics. A beacon for all therapeutic approaches, molecularly targeted cancer therapies highlight trends in drug discovery and clinical applications. To account for human complexity, multicomponent biomarker panels encompassing genetic, personal, and environmental factors can guide diagnosis and therapies, increasingly involving artificial intelligence to cope with extreme data complexities. However, clinical application encounters substantial hurdles, such as unknown validity across ethnic groups, underlying bias in health care, and real-world validation. This review address the underlying science and technologies germane to pharmacogenomics and personalized medicine, integrated with economic, ethical, and regulatory issues, providing insights into the current status and future direction of health care. SIGNIFICANCE STATEMENT: Personalized medicine aims to optimize health care for the individual patients with use of predictive biomarkers to improve outcomes and prevent adverse effects. Pharmacogenomics drives biomarker discovery and guides the development of targeted therapeutics. This review addresses basic principles and current trends in pharmacogenomics, with large-scale data repositories accelerating medical advances. The impact of pharmacogenomics is discussed, along with hurdles impeding broad clinical implementation, in the context of clinical care, ethics, economics, and regulatory affairs.
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Affiliation(s)
- Wolfgang Sadee
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, Columbus Ohio (W.S., A.E.T.); Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Gainesville, Florida (D.W.); Department of Radiology, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania (K.H.); Department of Bioengineering and Therapeutic Sciences, Schools of Pharmacy and Medicine, University of California San Francisco, San Francisco, California (W.S.); and Aether Therapeutics, Austin, Texas (W.S.)
| | - Danxin Wang
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, Columbus Ohio (W.S., A.E.T.); Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Gainesville, Florida (D.W.); Department of Radiology, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania (K.H.); Department of Bioengineering and Therapeutic Sciences, Schools of Pharmacy and Medicine, University of California San Francisco, San Francisco, California (W.S.); and Aether Therapeutics, Austin, Texas (W.S.)
| | - Katherine Hartmann
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, Columbus Ohio (W.S., A.E.T.); Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Gainesville, Florida (D.W.); Department of Radiology, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania (K.H.); Department of Bioengineering and Therapeutic Sciences, Schools of Pharmacy and Medicine, University of California San Francisco, San Francisco, California (W.S.); and Aether Therapeutics, Austin, Texas (W.S.)
| | - Amanda Ewart Toland
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, Columbus Ohio (W.S., A.E.T.); Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Gainesville, Florida (D.W.); Department of Radiology, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania (K.H.); Department of Bioengineering and Therapeutic Sciences, Schools of Pharmacy and Medicine, University of California San Francisco, San Francisco, California (W.S.); and Aether Therapeutics, Austin, Texas (W.S.)
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Abdelhalim H, Berber A, Lodi M, Jain R, Nair A, Pappu A, Patel K, Venkat V, Venkatesan C, Wable R, Dinatale M, Fu A, Iyer V, Kalove I, Kleyman M, Koutsoutis J, Menna D, Paliwal M, Patel N, Patel T, Rafique Z, Samadi R, Varadhan R, Bolla S, Vadapalli S, Ahmed Z. Artificial Intelligence, Healthcare, Clinical Genomics, and Pharmacogenomics Approaches in Precision Medicine. Front Genet 2022; 13:929736. [PMID: 35873469 PMCID: PMC9299079 DOI: 10.3389/fgene.2022.929736] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 05/25/2022] [Indexed: 12/13/2022] Open
Abstract
Precision medicine has greatly aided in improving health outcomes using earlier diagnosis and better prognosis for chronic diseases. It makes use of clinical data associated with the patient as well as their multi-omics/genomic data to reach a conclusion regarding how a physician should proceed with a specific treatment. Compared to the symptom-driven approach in medicine, precision medicine considers the critical fact that all patients do not react to the same treatment or medication in the same way. When considering the intersection of traditionally distinct arenas of medicine, that is, artificial intelligence, healthcare, clinical genomics, and pharmacogenomics—what ties them together is their impact on the development of precision medicine as a field and how they each contribute to patient-specific, rather than symptom-specific patient outcomes. This study discusses the impact and integration of these different fields in the scope of precision medicine and how they can be used in preventing and predicting acute or chronic diseases. Additionally, this study also discusses the advantages as well as the current challenges associated with artificial intelligence, healthcare, clinical genomics, and pharmacogenomics.
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Affiliation(s)
- Habiba Abdelhalim
- Rutgers Institute for Health, Health Care Policy and Aging Research, Rutgers University, New Brunswick, NJ, United States
| | - Asude Berber
- Rutgers Institute for Health, Health Care Policy and Aging Research, Rutgers University, New Brunswick, NJ, United States
| | - Mudassir Lodi
- Rutgers Institute for Health, Health Care Policy and Aging Research, Rutgers University, New Brunswick, NJ, United States
| | - Rihi Jain
- Rutgers Institute for Health, Health Care Policy and Aging Research, Rutgers University, New Brunswick, NJ, United States
| | - Achuth Nair
- Rutgers Institute for Health, Health Care Policy and Aging Research, Rutgers University, New Brunswick, NJ, United States
| | - Anirudh Pappu
- Rutgers Institute for Health, Health Care Policy and Aging Research, Rutgers University, New Brunswick, NJ, United States
| | - Kush Patel
- Rutgers Institute for Health, Health Care Policy and Aging Research, Rutgers University, New Brunswick, NJ, United States
| | - Vignesh Venkat
- Rutgers Institute for Health, Health Care Policy and Aging Research, Rutgers University, New Brunswick, NJ, United States
| | - Cynthia Venkatesan
- Rutgers Institute for Health, Health Care Policy and Aging Research, Rutgers University, New Brunswick, NJ, United States
| | - Raghu Wable
- Rutgers Institute for Health, Health Care Policy and Aging Research, Rutgers University, New Brunswick, NJ, United States
| | - Matthew Dinatale
- Rutgers Institute for Health, Health Care Policy and Aging Research, Rutgers University, New Brunswick, NJ, United States
| | - Allyson Fu
- Rutgers Institute for Health, Health Care Policy and Aging Research, Rutgers University, New Brunswick, NJ, United States
| | - Vikram Iyer
- Rutgers Institute for Health, Health Care Policy and Aging Research, Rutgers University, New Brunswick, NJ, United States
| | - Ishan Kalove
- Rutgers Institute for Health, Health Care Policy and Aging Research, Rutgers University, New Brunswick, NJ, United States
| | - Marc Kleyman
- Rutgers Institute for Health, Health Care Policy and Aging Research, Rutgers University, New Brunswick, NJ, United States
| | - Joseph Koutsoutis
- Rutgers Institute for Health, Health Care Policy and Aging Research, Rutgers University, New Brunswick, NJ, United States
| | - David Menna
- Rutgers Institute for Health, Health Care Policy and Aging Research, Rutgers University, New Brunswick, NJ, United States
| | - Mayank Paliwal
- Rutgers Institute for Health, Health Care Policy and Aging Research, Rutgers University, New Brunswick, NJ, United States
| | - Nishi Patel
- Rutgers Institute for Health, Health Care Policy and Aging Research, Rutgers University, New Brunswick, NJ, United States
| | - Thirth Patel
- Rutgers Institute for Health, Health Care Policy and Aging Research, Rutgers University, New Brunswick, NJ, United States
| | - Zara Rafique
- Rutgers Institute for Health, Health Care Policy and Aging Research, Rutgers University, New Brunswick, NJ, United States
| | - Rothela Samadi
- Rutgers Institute for Health, Health Care Policy and Aging Research, Rutgers University, New Brunswick, NJ, United States
| | - Roshan Varadhan
- Rutgers Institute for Health, Health Care Policy and Aging Research, Rutgers University, New Brunswick, NJ, United States
| | - Shreyas Bolla
- Rutgers Institute for Health, Health Care Policy and Aging Research, Rutgers University, New Brunswick, NJ, United States
| | - Sreya Vadapalli
- Rutgers Institute for Health, Health Care Policy and Aging Research, Rutgers University, New Brunswick, NJ, United States
| | - Zeeshan Ahmed
- Rutgers Institute for Health, Health Care Policy and Aging Research, Rutgers University, New Brunswick, NJ, United States.,Department of Medicine, Rutgers Robert Wood Johnson Medical School, Rutgers Biomedical and Health Sciences, New Brunswick, NJ, United States
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Glucagon-like Peptide-1 Receptor Agonists in the Management of Type 2 Diabetes Mellitus and Obesity: The Impact of Pharmacological Properties and Genetic Factors. Int J Mol Sci 2022; 23:ijms23073451. [PMID: 35408810 PMCID: PMC8998939 DOI: 10.3390/ijms23073451] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/19/2022] [Accepted: 03/21/2022] [Indexed: 02/06/2023] Open
Abstract
Glucagon-like peptide-1 (GLP-1) receptor agonists are a new class of antihyperglycemic drugs that enhance appropriate pancreatic β-cell secretion, pancreatic α-cell (glucagon) suppression, decrease liver glucose production, increase satiety through their action on the central nervous system, slow gastric emptying time, and increase insulin action on peripheral tissue. They are effective in the management of type 2 diabetes mellitus and have a favorable effect on weight loss. Their cardiovascular and renal safety has been extensively investigated and confirmed in many clinical trials. Recently, evidence has shown that in addition to the existing approaches for the treatment of obesity, semaglutide in higher doses promotes weight loss and can be used as a drug to treat obesity. However, some T2DM and obese patients do not achieve a desired therapeutic effect of GLP-1 receptor agonists. This could be due to the multifactorial etiologies of T2DM and obesity, but genetic variability in the GLP-1 receptor or signaling pathways also needs to be considered in non-responders to GLP-1 receptor agonists. This review focuses on the pharmacological, clinical, and genetic factors that may influence the response to GLP-1 receptor agonists in the treatment of type 2 diabetes mellitus and obesity.
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