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de la Lastra JMP, Wardell SJT, Pal T, de la Fuente-Nunez C, Pletzer D. From Data to Decisions: Leveraging Artificial Intelligence and Machine Learning in Combating Antimicrobial Resistance - a Comprehensive Review. J Med Syst 2024; 48:71. [PMID: 39088151 PMCID: PMC11294375 DOI: 10.1007/s10916-024-02089-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Accepted: 07/12/2024] [Indexed: 08/02/2024]
Abstract
The emergence of drug-resistant bacteria poses a significant challenge to modern medicine. In response, Artificial Intelligence (AI) and Machine Learning (ML) algorithms have emerged as powerful tools for combating antimicrobial resistance (AMR). This review aims to explore the role of AI/ML in AMR management, with a focus on identifying pathogens, understanding resistance patterns, predicting treatment outcomes, and discovering new antibiotic agents. Recent advancements in AI/ML have enabled the efficient analysis of large datasets, facilitating the reliable prediction of AMR trends and treatment responses with minimal human intervention. ML algorithms can analyze genomic data to identify genetic markers associated with antibiotic resistance, enabling the development of targeted treatment strategies. Additionally, AI/ML techniques show promise in optimizing drug administration and developing alternatives to traditional antibiotics. By analyzing patient data and clinical outcomes, these technologies can assist healthcare providers in diagnosing infections, evaluating their severity, and selecting appropriate antimicrobial therapies. While integration of AI/ML in clinical settings is still in its infancy, advancements in data quality and algorithm development suggest that widespread clinical adoption is forthcoming. In conclusion, AI/ML holds significant promise for improving AMR management and treatment outcome.
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Affiliation(s)
- José M Pérez de la Lastra
- Biotechnology of Macromolecules, Instituto de Productos Naturales y Agrobiología, IPNA (CSIC), Avda. Astrofísico Francisco Sánchez, 3, 38206, San Cristóbal de la Laguna, (Santa Cruz de Tenerife), Spain.
| | - Samuel J T Wardell
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, 9054, Dunedin, New Zealand
| | - Tarun Pal
- School of Bioengineering and Food Technology, Faculty of Applied Sciences and Biotechnology, Shoolini University, Solan, 173229, Himachal Pradesh, India
| | - Cesar de la Fuente-Nunez
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, USA
- Department of Chemistry, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, USA
- Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, PA, USA
| | - Daniel Pletzer
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, 9054, Dunedin, New Zealand.
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Zhang P, Li B, Chen H, Ge Z, Shang Q, Liang D, Yu X, Ren H, Jiang X, Cui J. RNA sequencing-based approaches to identifying disulfidptosis-related diagnostic clusters and immune landscapes in osteoporosis. Aging (Albany NY) 2024; 16:8198-8216. [PMID: 38738994 PMCID: PMC11131997 DOI: 10.18632/aging.205813] [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: 10/09/2023] [Accepted: 04/08/2024] [Indexed: 05/14/2024]
Abstract
Disulfidptosis, a newly recognized cell death triggered by disulfide stress, has garnered attention for its potential role in osteoporosis (OP) pathogenesis. Although sulfide-related proteins are reported to regulate the balance of bone metabolism in OP, the precise involvement of disulfidptosis regulators remains elusive. Herein, leveraging the GSE56815 dataset, we conducted an analysis to delineate disulfidptosis-associated diagnostic clusters and immune landscapes in OP. Subsequently, vertebral bone tissues obtained from OP patients and controls were subjected to RNA sequencing (RNA-seq) for the validation of key disulfidptosis gene expression. Our analysis unveiled seven significant disulfidptosis regulators, including FLNA, ACTB, PRDX1, SLC7A11, NUBPL, OXSM, and RAC1, distinguishing OP samples from controls. Furthermore, employing a random forest model, we identified four diagnostic disulfidptosis regulators including FLNA, SLC7A11, NUBPL, and RAC1 potentially predictive of OP risk. A nomogram model integrating these four regulators was constructed and validated using the GSE35956 dataset, demonstrating promising utility in clinical decision-making, as affirmed by decision curve analysis. Subsequent consensus clustering analysis stratified OP samples into two different disulfidptosis subgroups (clusters A and B) using significant disulfidptosis regulators, with cluster B exhibiting higher disulfidptosis scores and implicating monocyte immunity, closely linked to osteoclastogenesis. Notably, RNA-seq analysis corroborated the expression patterns of two disulfidptosis modulators, PRDX1 and OXSM, consistent with bioinformatics predictions. Collectively, our study sheds light on disulfidptosis patterns, offering potential markers and immunotherapeutic avenues for future OP management.
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Affiliation(s)
- Peng Zhang
- Guangzhou University of Chinese Medicine, Guangzhou 510405, China
| | - Bing Li
- The First Affiliated Hospital of Guangxi University of Chinese Medicine, Nanning 530023, China
| | - Honglin Chen
- Guangzhou University of Chinese Medicine, Guangzhou 510405, China
| | - Zhilin Ge
- Guangzhou University of Chinese Medicine, Guangzhou 510405, China
| | - Qi Shang
- Guangzhou University of Chinese Medicine, Guangzhou 510405, China
| | - De Liang
- The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510405, China
| | - Xiang Yu
- The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510405, China
| | - Hui Ren
- The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
| | - Xiaobing Jiang
- The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
| | - Jianchao Cui
- The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510405, China
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Pan C, Zhang C, Lin Z, Liang Z, Cui Y, Shang Z, Wei Y, Chen F. Disulfidptosis-related Protein RPN1 may be a Novel Anti-osteoporosis Target of Kaempferol. Comb Chem High Throughput Screen 2024; 27:1611-1628. [PMID: 38213143 DOI: 10.2174/0113862073273655231213070619] [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: 07/23/2023] [Revised: 10/07/2023] [Accepted: 10/13/2023] [Indexed: 01/13/2024]
Abstract
BACKGROUND Osteoporosis (OP) is an age-related skeletal disease. Kaempferol can regulate bone mesenchymal stem cells (BMSCs) osteogenesis to improve OP, but its mechanism related to disulfidptosis, a newly discovered cell death mechanism, remains unclear. OBJECTIVE The study aimed to investigate the biological function and immune mechanism of disulfidptosis- related ribophorin I (RPN1) in OP and to experimentally confirm that RPN1 is the target for the treatment of OP with kaempferol. METHODS Differential expression analysis was conducted on disulfide-related genes extracted from the GSE56815 and GSE7158 datasets. Four machine learning algorithms identified disease signature genes, with RPN1 identified as a significant risk factor for OP through the nomogram. Validation of RPN1 differential expression in OP patients was performed using the GSE56116 dataset. The impact of RPN1 on immune alterations and biological processes was explored. Predictive ceRNA regulatory networks associated with RPN1 were generated via miRanda, miRDB, and TargetScan databases. Molecular docking estimated the binding model between kaempferol and RPN1. The targeting mechanism of kaempferol on RPN1 was confirmed through pathological HE staining and immunohistochemistry in ovariectomized (OVX) rats. RESULTS RPN1 was abnormally overexpressed in the OP cohort, associated with TNF signaling, hematopoietic cell lineage, and NF-kappa B pathway. Immune infiltration analysis showed a positive correlation between RPN1 expression and CD8+ T cells and resting NK cells, while a negative correlation with CD4+ naive T cells, macrophage M1, T cell gamma delta, T cell follicular helper cells, activated mast cells, NK cells, and dendritic cells, was found. Four miRNAs and 17 lncRNAs associated with RPN1 were identified. Kaempferol exhibited high binding affinity (-7.2 kcal/mol) and good stability towards the RPN1. The experimental results verified that kaempferol could improve bone microstructure destruction and reverse the abnormally high expression of RPN1 in the femur of ovariectomized rats. CONCLUSION RPN1 may be a new diagnostic biomarker in patients with OP, and may serve as a new target for kaempferol to improve OP.
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Affiliation(s)
- Chengzhen Pan
- Ruikang Hospital Affiliated with Guangxi University of Chinese Medicine, Nanning, Guangxi, China
| | - Chi Zhang
- Ruikang Hospital Affiliated with Guangxi University of Chinese Medicine, Nanning, Guangxi, China
| | - Zonghan Lin
- Ruikang Hospital Affiliated with Guangxi University of Chinese Medicine, Nanning, Guangxi, China
| | - Zhou Liang
- Yulin Orthopedic Hospital of Integrated Traditional Chinese and Western Medicine, Yulin, Guangxi, China
| | - Yinhang Cui
- Ruikang Hospital Affiliated with Guangxi University of Chinese Medicine, Nanning, Guangxi, China
| | - Zhihao Shang
- Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Yuanxun Wei
- Ruikang Hospital Affiliated with Guangxi University of Chinese Medicine, Nanning, Guangxi, China
| | - Feng Chen
- Ruikang Hospital Affiliated with Guangxi University of Chinese Medicine, Nanning, Guangxi, China
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Hu Y, Han J, Ding S, Liu S, Wang H. Identification of ferroptosis-associated biomarkers for the potential diagnosis and treatment of postmenopausal osteoporosis. Front Endocrinol (Lausanne) 2022; 13:986384. [PMID: 36105394 PMCID: PMC9464919 DOI: 10.3389/fendo.2022.986384] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 08/05/2022] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVE Postmenopausal osteoporosis (PMOP) is one of the most commonly occurring conditions worldwide and is characterized by estrogen deficiency as well as persistent calcium loss with age. The aim of our study was to identify significant ferroptosis-associated biomarkers for PMOP. METHODS AND MATERIALS We obtained our training dataset from the Gene Expression Omnibus (GEO) database using GSE56815 expression profiling data. Meanwhile, we extracted ferroptosis-associated genes for further analysis. Differentially expressed ferroptosis-associated genes (DEFAGs) between OP patients and normal controls were selected using the "limma" package. We established a ferroptosis-associated gene signature using training models, specifically, random forest (RF) and support vector machine (SVM) models. It was further validated in another dataset (GSE56814) which also showed a high AUC: 0.98, indicating high diagnostic value. Using consensus clustering, the OP patient subtypes were identified. A ferroptosis associated gene (FAG)-Scoring scheme was developed by PCA. The important candidate genes associated with OP were also compared between different ferrclusters and geneclusters. RESULTS There were significant DEFAGs acquired, of which five (HMOX1, HAMP, LPIN1, MAP3K5, FLT3) were selected for establishing a ferroptosis-associated gene signature. Analyzed from the ROC curve, our established RF model had a higher AUC value than the SVM model (RF model AUC:1.00). Considering these results, the established RF model was chosen to be the most appropriate training model. Later, based on the expression levels of the five DEFAGs, a clinical application nomogram was established. The OP patients were divided into two subtypes (ferrcluster A, B and genecluster A, B, respectively) according to the consensus clustering method based on DEFAGs and differentially expressed genes (DEGs). Ferrcluster B and genecluster B had higher ferroptosis score than ferrcluster A and genecluster A, respectively. The expression of COL1A1 gene was significantly higher in ferrcluster B and gencluster B compared with ferrcluster A and gencluster A, respectively, while there is no statistical difference in term of VDR gene, COL1A2 genes, and PTH gene expressions between ferrcluster A and B, together with gencluster A and B. CONCLUSIONS On the basis of five explanatory variables (HMOX1, HAMP, LPIN1, MAP3K5 and FLT3), we developed a diagnostic ferroptosis-associated gene signature and identified two differently categorized OP subtypes that may potentially be applied for the early diagnosis and individualized treatment of PMOP. The ER gene, VDR gene, IL-6 gene, COL1A1 and COL1A2 genes, and PTH gene are important candidate gene of OP, however, more studies are still anticipated to further elucidate the relationship between these genes and ferroptosis in OP.
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Affiliation(s)
- Yunxiang Hu
- Department of Orthopedics, Dalian Municipal Central Hospital Affiliated of Dalian Medical University, Dalian, China
- School of Graduates, Dalian Medical University, Dalian, China
| | - Jun Han
- Department of Orthopedics, Dalian Municipal Central Hospital Affiliated of Dalian Medical University, Dalian, China
- School of Graduates, Dalian Medical University, Dalian, China
- Department of Spine Surgery, the First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Shengqiang Ding
- Department of Spine Surgery, The People’s Hospital of Liuyang City, Changsha, China
| | - Sanmao Liu
- Department of Orthopedics, Dalian Municipal Central Hospital Affiliated of Dalian Medical University, Dalian, China
- School of Graduates, Dalian Medical University, Dalian, China
| | - Hong Wang
- Department of Orthopedics, Dalian Municipal Central Hospital Affiliated of Dalian Medical University, Dalian, China
- School of Graduates, Dalian Medical University, Dalian, China
- *Correspondence: Hong Wang,
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