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Chi J, Shu J, Li M, Mudappathi R, Jin Y, Lewis F, Boon A, Qin X, Liu L, Gu H. Artificial Intelligence in Metabolomics: A Current Review. Trends Analyt Chem 2024; 178:117852. [PMID: 39071116 PMCID: PMC11271759 DOI: 10.1016/j.trac.2024.117852] [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: 07/30/2024]
Abstract
Metabolomics and artificial intelligence (AI) form a synergistic partnership. Metabolomics generates large datasets comprising hundreds to thousands of metabolites with complex relationships. AI, aiming to mimic human intelligence through computational modeling, possesses extraordinary capabilities for big data analysis. In this review, we provide a recent overview of the methodologies and applications of AI in metabolomics studies in the context of systems biology and human health. We first introduce the AI concept, history, and key algorithms for machine learning and deep learning, summarizing their strengths and weaknesses. We then discuss studies that have successfully used AI across different aspects of metabolomic analysis, including analytical detection, data preprocessing, biomarker discovery, predictive modeling, and multi-omics data integration. Lastly, we discuss the existing challenges and future perspectives in this rapidly evolving field. Despite limitations and challenges, the combination of metabolomics and AI holds great promises for revolutionary advancements in enhancing human health.
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Affiliation(s)
- Jinhua Chi
- College of Health Solutions, Arizona State University, Phoenix, AZ 85004, USA
- Center for Translational Science, Florida International University, Port St. Lucie, FL 34987, USA
| | - Jingmin Shu
- College of Health Solutions, Arizona State University, Phoenix, AZ 85004, USA
- Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ 85281, USA
| | - Ming Li
- Phoenix VA Health Care System, Phoenix, AZ 85012, USA
- University of Arizona College of Medicine, Phoenix, AZ 85004, USA
| | - Rekha Mudappathi
- College of Health Solutions, Arizona State University, Phoenix, AZ 85004, USA
- Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ 85281, USA
| | - Yan Jin
- Center for Translational Science, Florida International University, Port St. Lucie, FL 34987, USA
| | - Freeman Lewis
- Center for Translational Science, Florida International University, Port St. Lucie, FL 34987, USA
| | - Alexandria Boon
- Center for Translational Science, Florida International University, Port St. Lucie, FL 34987, USA
| | - Xiaoyan Qin
- College of Liberal Arts and Sciences, Arizona State University, Tempe, AZ 85281, USA
| | - Li Liu
- College of Health Solutions, Arizona State University, Phoenix, AZ 85004, USA
- Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ 85281, USA
| | - Haiwei Gu
- College of Health Solutions, Arizona State University, Phoenix, AZ 85004, USA
- Center for Translational Science, Florida International University, Port St. Lucie, FL 34987, USA
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Mi X, Kang C, Hou S, Gao Y, Hao L, Gao X. Mining and exploration of appendicitis nursing targets: An observational study. Medicine (Baltimore) 2024; 103:e38667. [PMID: 38941398 DOI: 10.1097/md.0000000000038667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 06/30/2024] Open
Abstract
Appendicitis is an inflammation caused by obstruction of the appendiceal lumen or termination of blood supply leading to appendiceal necrosis followed by secondary bacterial infection. The relationship between TYROBP gene and the nursing of appendicitis remains unclear. The appendicitis dataset GSE9579 profile was downloaded from the gene expression omnibus database generated from GPL571. Differentially expressed genes were screened, followed by weighted gene co-expression network analysis, functional enrichment analysis, gene set enrichment analysis, construction and analysis of protein-protein interaction network, Comparative Toxicogenomics Database analysis, and immune infiltration analysis. Heatmaps of gene expression levels were plotted. A total of 1570 differentially expressed genes were identified. According to gene ontology analysis, they were mainly enriched in organic acid metabolic process, condensed chromosome kinetochore, oxidoreductase activity. In Kyoto Encyclopedia of Gene and Genome analysis, they mainly concentrated in metabolic pathways, P53 signaling pathway, PPAR signaling pathway. The soft threshold power in weighted gene co-expression network analysis was set to 12. Through the construction and analysis of protein-protein interaction network, 5 core genes (FCGR2A, IL1B, ITGAM, TLR2, TYROBP) were obtained. Heatmap of core gene expression levels revealed high expression of TYROBP in appendicitis samples. Comparative Toxicogenomics Database analysis found that core genes (FCGR2A, IL1B, ITGAM, TLR2, TYROBP) were closely related to abdominal pain, gastrointestinal dysfunction, fever, and inflammation occurrence. TYROBP gene is highly expressed in appendicitis, and higher expression of TYROBP gene indicates worse prognosis. TYROBP may serve as a molecular target for appendicitis and its nursing.
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Affiliation(s)
- Xihua Mi
- Gastrointestinal Rehabilitation Center, Beijing Rehabilitation Hospital, Capital Medical University, Beijing, China
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Wei L, Chen S, Deng X, Liu Y, Wang H, Gao X, Huang Y. Metabolomic discoveries for early diagnosis and traditional Chinese medicine efficacy in ischemic stroke. Biomark Res 2024; 12:63. [PMID: 38902829 PMCID: PMC11188286 DOI: 10.1186/s40364-024-00608-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Accepted: 06/11/2024] [Indexed: 06/22/2024] Open
Abstract
Ischemic stroke (IS), a devastating cerebrovascular accident, presents with high mortality and morbidity. Following IS onset, a cascade of pathological changes, including excitotoxicity, inflammatory damage, and blood-brain barrier disruption, significantly impacts prognosis. However, current clinical practices struggle with early diagnosis and identifying these alterations. Metabolomics, a powerful tool in systems biology, offers a promising avenue for uncovering early diagnostic biomarkers for IS. By analyzing dynamic metabolic profiles, metabolomics can not only aid in identifying early IS biomarkers but also evaluate Traditional Chinese Medicine (TCM) efficacy and explore its mechanisms of action in IS treatment. Animal studies demonstrate that TCM interventions modulate specific metabolite levels, potentially reflecting their therapeutic effects. Identifying relevant metabolites in cerebral ischemia patients holds immense potential for early diagnosis and improved outcomes. This review focuses on recent metabolomic discoveries of potential early diagnostic biomarkers for IS. We explore variations in metabolites observed across different ages, genders, disease severity, and stages. Additionally, the review examines how specific TCM extracts influence IS development through metabolic changes, potentially revealing their mechanisms of action. Finally, we emphasize the importance of integrating metabolomics with other omics approaches for a comprehensive understanding of IS pathophysiology and TCM efficacy, paving the way for precision medicine in IS management.
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Affiliation(s)
- Liangzhe Wei
- Department of Neurosurgery, Ningbo Hospital, Zhejiang University School of Medicine, Ningbo, 315010, China
- Ningbo Key Laboratory of Neurological Diseases and Brain Function, Department of Neurosurgery, The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang, 315010, China
| | - Siqi Chen
- Ningbo Key Laboratory of Neurological Diseases and Brain Function, Department of Neurosurgery, The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang, 315010, China
- Key Laboratory of Precision Medicine for Atherosclerotic Diseases of Zhejiang Province, Ningbo, Zhejiang, 315010, China
| | - Xinpeng Deng
- Department of Neurosurgery, Ningbo Hospital, Zhejiang University School of Medicine, Ningbo, 315010, China
- Ningbo Key Laboratory of Neurological Diseases and Brain Function, Department of Neurosurgery, The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang, 315010, China
| | - Yuchun Liu
- Department of Neurosurgery, Ningbo Hospital, Zhejiang University School of Medicine, Ningbo, 315010, China
- Ningbo Key Laboratory of Neurological Diseases and Brain Function, Department of Neurosurgery, The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang, 315010, China
| | - Haifeng Wang
- Department of Neurosurgery, Ningbo Hospital, Zhejiang University School of Medicine, Ningbo, 315010, China
- Ningbo Key Laboratory of Neurological Diseases and Brain Function, Department of Neurosurgery, The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang, 315010, China
| | - Xiang Gao
- Department of Neurosurgery, Ningbo Hospital, Zhejiang University School of Medicine, Ningbo, 315010, China.
- Ningbo Key Laboratory of Neurological Diseases and Brain Function, Department of Neurosurgery, The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang, 315010, China.
- Key Laboratory of Precision Medicine for Atherosclerotic Diseases of Zhejiang Province, Ningbo, Zhejiang, 315010, China.
| | - Yi Huang
- Department of Neurosurgery, Ningbo Hospital, Zhejiang University School of Medicine, Ningbo, 315010, China.
- Ningbo Key Laboratory of Neurological Diseases and Brain Function, Department of Neurosurgery, The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang, 315010, China.
- Key Laboratory of Precision Medicine for Atherosclerotic Diseases of Zhejiang Province, Ningbo, Zhejiang, 315010, China.
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Mateo-Otero Y. Integrating metabolomics into reproduction: Sperm metabolism and fertility enhancement in pigs. Anim Reprod Sci 2024:107539. [PMID: 38926002 DOI: 10.1016/j.anireprosci.2024.107539] [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: 04/02/2024] [Revised: 06/13/2024] [Accepted: 06/14/2024] [Indexed: 06/28/2024]
Abstract
The last decades of research have revealed that many other factors besides gamete genomes are able to determine the reproductive outcomes. Indeed, paternal factors have been observed to be capable of modulating multiple crucial features of the reproductive process, such as sperm physiology, the maternal environment and, even, the offspring health. These recent advances have been encompassed with the emergence of OMICS technologies, as they comprehensively characterise the molecular composition of biological systems. The present narrative review aimed to take a closer look at the potential of these technologies in the field of reproductive biology. This literature revision shows that most studies up to date have followed a non-targeted approach to screen mammalian seminal plasma (SP) and sperm metabolite composition through different metabolome platforms. These studies have proposed metabolites of multiple natures as potential in vivo fertility biomarkers. Yet, targeted approaches can be used to answer specific biological question, and their power is exemplified herein. For instance, metabolomic studies have uncovered not only that glycolysis is the main ATP energy source of pig sperm, but also that sperm metabolism can trigger DNA damage, hence compromise embryo development. In conclusion, this review shows the potential of both non-targeted and targeted metabolomics for the discovery of cell pathways that govern the reproductive process. Understanding these systems could help make progress in different areas, including livestock efficient breeding, the improvement of artificial reproductive technologies, and the development of biomarkers for infertility detection.
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Affiliation(s)
- Yentel Mateo-Otero
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Jeffrey Cheah Biomedical Centre, Cambridge CB2 0AW, UK.
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Xue M, Ma C, Shan H, Hou S, Kang C. SPAG5 and ASPM play important roles in gastric cancer: An observational study. Medicine (Baltimore) 2024; 103:e38499. [PMID: 38875410 PMCID: PMC11175929 DOI: 10.1097/md.0000000000038499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 05/10/2024] [Accepted: 05/16/2024] [Indexed: 06/16/2024] Open
Abstract
Gastric cancer typically originates from the abnormal proliferation of normal cells within the gastric mucosa, eventually forming tumors. The roles of sperm-associated antigen 5 (SPAG5) and abnormal spindle-like microcephaly (ASPM) associated genes in gastric cancer are not yet clear. Gastric cancer datasets GSE51575 and GSE36076 profiles were downloaded from the GPL13607 and GPL570-generated gene expression omnibus database. The analysis included filtering for differentially expressed genes, weighted gene co-expression network analysis, functional enrichment analysis, gene set enrichment analysis, immune infiltration analysis, construction and analysis of the protein-protein interaction network, survival analysis, and Comparative Toxicogenomics Database analysis. Heatmaps of gene expression were also created. A total of 1457 differentially expressed genes were identified. According to gene ontology analysis, they are primarily enriched in the metabolic processes of organic acids, condensed chromosome centromere regions, and oxidoreductase activity. Kyoto Encyclopedia of Gene and Genome analysis showed they are mainly involved in metabolic pathways, P53 signaling pathway, and PPAR signaling pathway. The soft threshold power for weighted gene co-expression network analysis was set to 8. Three core genes (CENPE, SPAG5, and ASPM) were identified. Heatmaps of core gene expression revealed that SPAG5 and ASPM are highly expressed in gastric cancer samples and low in normal samples. Comparative Toxicogenomics Database analysis indicated that the core genes (CENPE, SPAG5, and ASPM) are associated with gastric tumors, gastric diseases, gastritis, gastric ulcers, tumors, inflammation, and necrosis. The SPAG5 and ASPM genes are overexpressed in gastric cancer tissues, and higher expression levels are associated with worse prognosis, may serve as potential prognostic markers.
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Affiliation(s)
- Mei Xue
- Gastrointestinal Rehabilitation Center, Beijing Rehabilitation Hospital Affiliated to Capital Medical University, Beijing, China
| | - Chao Ma
- Gastrointestinal Rehabilitation Center, Beijing Rehabilitation Hospital Affiliated to Capital Medical University, Beijing, China
| | - HaiFeng Shan
- Gastrointestinal Rehabilitation Center, Beijing Rehabilitation Hospital Affiliated to Capital Medical University, Beijing, China
| | - Shiyang Hou
- Gastrointestinal Rehabilitation Center, Beijing Rehabilitation Hospital Affiliated to Capital Medical University, Beijing, China
| | - Chunbo Kang
- Gastrointestinal Rehabilitation Center, Beijing Rehabilitation Hospital Affiliated to Capital Medical University, Beijing, China
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Meng LB, Li Y, Lv T, Lv C, Liu L, Zhang P. Joint effects of CD8A and ICOS in Long QT Syndrome (LQTS) and Beckwith-Wiedemann Syndrome (BWS). J Cardiothorac Surg 2024; 19:321. [PMID: 38845009 PMCID: PMC11155187 DOI: 10.1186/s13019-024-02804-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 05/25/2024] [Indexed: 06/10/2024] Open
Abstract
BACKGROUND Long QT Syndrome (LQTS) and Beckwith-Wiedemann Syndrome (BWS) are complex disorders with unclear origins, underscoring the need for in-depth molecular investigations into their mechanisms. The main aim of this study is to identify the shared key genes between LQTS and BWS, shedding light on potential common molecular pathways underlying these syndromes. METHODS The LQTS and BWS datasets are available for download from the GEO database. Differential expression genes (DEGs) were identified. Weighted gene co-expression network analysis (WGCNA) was used to detect significant modules and central genes. Gene enrichment analysis was performed. CIBERSORT was used for immune cell infiltration analysis. The predictive protein interaction (PPI) network of core genes was constructed using STRING, and miRNAs regulating central genes were screened using TargetScan. RESULTS Five hundred DEGs associated with Long QT Syndrome and Beckwith-Wiedemann Syndrome were identified. GSEA analysis revealed enrichment in pathways such as T cell receptor signaling, MAPK signaling, and adrenergic signaling in cardiac myocytes. Immune cell infiltration indicated higher levels of memory B cells and naive CD4 T cells. Four core genes (CD8A, ICOS, CTLA4, LCK) were identified, with CD8A and ICOS showing low expression in the syndromes and high expression in normal samples, suggesting potential inverse regulatory roles. CONCLUSION The expression of CD8A and ICOS is low in long QT syndrome and Beckwith-Wiedemann syndrome, indicating their potential as key genes in the pathogenesis of these syndromes. The identification of shared key genes between LQTS and BWS provides insights into common molecular mechanisms underlying these disorders, potentially facilitating the development of targeted therapeutic strategies.
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Affiliation(s)
- Ling-Bing Meng
- Department of Cardiology, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, China
| | - Yongchao Li
- Department of Cardiac Surgery, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, China
| | - Tingting Lv
- Department of Cardiology, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, China
| | - Changhua Lv
- Department of Cardiology, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, China
| | - Lianfeng Liu
- Department of Cardiology, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, China
| | - Ping Zhang
- Department of Cardiology, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, China.
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Chen Y, Li S, Guo F. Tsc22d3 promotes morphine tolerance in mice through the GPX4 ferroptosis pathway. Aging (Albany NY) 2024; 16:9859-9875. [PMID: 38843390 PMCID: PMC11210220 DOI: 10.18632/aging.205903] [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: 01/24/2024] [Accepted: 04/18/2024] [Indexed: 06/22/2024]
Abstract
BACKGROUND Morphine tolerance refers to gradual reduction in response to drug with continuous or repeated use of morphine, requiring higher doses to achieve same effect. METHODS The morphine tolerance dataset GSE7762 profiles, obtained from gene expression omnibus (GEO) database, were used to identify differentially expressed genes (DEGs). Weighted Gene Co-expression Network Analysis (WGCNA) was applied to explore core modules of DEGs related to morphine tolerance. Core genes were input into Comparative Toxicogenomics Database (CTD). Animal experiments were performed to validate role of Tsc22d3 in morphine tolerance and its relationship with ferroptosis-related pathway. RESULTS 500 DEGs were identified. DEGs were primarily enriched in negative regulation of brain development, neuronal apoptosis processes, and neurosystem development. Core gene was identified as Tsc22d3. Tsc22d3 gene-associated miRNAs were mmu-miR-196b-5p and mmu-miR-196a-5p. Compared to Non-morphine tolerant group, Tsc22d3 expression was significantly upregulated in Morphine tolerant group. Tsc22d3 expression was upregulated in Morphine tolerant+Tsc22d3_OE, expression of HIF-1alpha, GSH, GPX4 in GPX4 ferroptosis-related pathway showed a more pronounced decrease. As Tsc22d3 expression was downregulated in Morphine tolerant+Tsc22d3_KO, expression of HIF-1alpha, GSH, GPX4 in GPX4 ferroptosis-related pathway exhibited a more pronounced increase. Upregulation of Tsc22d3 in Morphine tolerant+Tsc22d3_OE led to a more pronounced increase in expression of apoptosis proteins (P53, Caspase-3, Bax, SMAC, FAS). The expression of inflammatory factors (IL6, TNF-alpha, CXCL1, CXCL2) showed a more pronounced increase with upregulated Tsc22d3 expression in Morphine tolerant+Tsc22d3_OE. CONCLUSIONS Tsc22d3 is highly expressed in brain tissue of morphine-tolerant mice, activating ferroptosis pathway, enhancing apoptosis, promoting inflammatory responses in brain cells.
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Affiliation(s)
- Yan Chen
- Department of Anesthesiology, Children’s Hospital of Hebei Province, Shijiazhuang 050071, Hebei, P.R. China
| | - Shan Li
- Department of Oncology, Hebei General Hospital, Shijiazhuang 050051, Hebei, P.R. China
| | - Fenghui Guo
- Department of Anesthesiology, Fourth Hospital of Hebei Medical University, Shijiazhuang 050011, Hebei, P.R. China
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Peng Q, Jiang L, Shen Y, Xu Y, Shen X, Zou L, Zhu Y, Shen Y. LC-MS metabolomics analysis of serum metabolites during neoadjuvant chemoradiotherapy in locally advanced rectal cancer. Clin Transl Oncol 2024:10.1007/s12094-024-03537-x. [PMID: 38831193 DOI: 10.1007/s12094-024-03537-x] [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: 04/24/2024] [Accepted: 05/18/2024] [Indexed: 06/05/2024]
Abstract
BACKGROUND This study aimed to investigate the serum metabolite profiles during neoadjuvant chemoradiotherapy (NCRT) in locally advanced rectal cancer (LARC) using liquid chromatography-mass spectrometry (LC-MS) metabolomics analysis. METHODS 60 serum samples were collected from 20 patients with LARC before, during, and after radiotherapy. LC-MS metabolomics analysis was performed to identify the metabolite variations. Functional annotation was applied to discover altered metabolic pathways. The key metabolites were screened and their ability to predict sensitivity to radiotherapy was calculated using random forests and ROC curves. RESULTS The results showed that NCRT led to significant changes in the serum metabolite profiles. The serum metabolic profiles showed an apparent separation between different time points and different sensitivity groups. Moreover, the functional annotation showed that the differential metabolites were associated with a series of important metabolic pathways. Pre-radiotherapy (3Z,6Z)-3,6-Nonadiena and pro-radiotherapy 1-Hydroxyibuprofen showed good predictive performance in discriminating the sensitive and non-sensitive group to NCRT, with an AUC of 0.812 and 0.75, respectively. Importantly, the combination of different metabolites significantly increased the predictive ability. CONCLUSION This study demonstrated the potential of LC-MS metabolomics for revealing the serum metabolite profiles during NCRT in LARC. The identified metabolites may serve as potential biomarkers and therapeutic targets for the management of this disease. Furthermore, the understanding of the affected metabolic pathways may help design more personalized therapeutic strategies for LARC patients.
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Affiliation(s)
- Qiliang Peng
- Department of Radiotherapy and Oncology, The Second Affiliated Hospital of Soochow University, Suzhou, China
- Institute of Radiotherapy & Oncology, Soochow University, Suzhou, China
- State Key Laboratory of Radiation Medicine and Protection, Soochow University, Suzhou, China
| | - Lili Jiang
- Department of Oncology, Nantong Haimen District People's Hospital, Jiangsu, China
| | - Yi Shen
- Department of Radiation Oncology, Suzhou Hospital, Affiliated Hospital of Medical School, Nanjing University, Suzhou, China
| | - Yao Xu
- Department of Radiology, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Xinan Shen
- Department of Radiotherapy and Oncology, The Second Affiliated Hospital of Soochow University, Suzhou, China
- Institute of Radiotherapy & Oncology, Soochow University, Suzhou, China
| | - Li Zou
- Department of Radiotherapy and Oncology, The Second Affiliated Hospital of Soochow University, Suzhou, China
- Institute of Radiotherapy & Oncology, Soochow University, Suzhou, China
| | - Yaqun Zhu
- Department of Radiotherapy and Oncology, The Second Affiliated Hospital of Soochow University, Suzhou, China.
- Institute of Radiotherapy & Oncology, Soochow University, Suzhou, China.
| | - Yuntian Shen
- Department of Radiotherapy and Oncology, The Second Affiliated Hospital of Soochow University, Suzhou, China.
- Institute of Radiotherapy & Oncology, Soochow University, Suzhou, China.
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Zhang J, Teng F, Hu B, Liu W, Huang Y, Wu J, Wang Y, Su H, Yang S, Zhang L, Guo L, Lei Z, Yan M, Xu X, Wang R, Bao Q, Dong Q, Long J, Qian K. Early Diagnosis and Prognosis Prediction of Pancreatic Cancer Using Engineered Hybrid Core-Shells in Laser Desorption/Ionization Mass Spectrometry. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2311431. [PMID: 38241281 DOI: 10.1002/adma.202311431] [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: 10/31/2023] [Revised: 01/11/2024] [Indexed: 01/21/2024]
Abstract
Effective detection of bio-molecules relies on the precise design and preparation of materials, particularly in laser desorption/ionization mass spectrometry (LDI-MS). Despite significant advancements in substrate materials, the performance of single-structured substrates remains suboptimal for LDI-MS analysis of complex systems. Herein, designer Au@SiO2@ZrO2 core-shell substrates are developed for LDI-MS-based early diagnosis and prognosis of pancreatic cancer (PC). Through controlling Au core size and ZrO2 shell crystallization, signal amplification of metabolites up to 3 orders is not only achieved, but also the synergistic mechanism of the LDI process is revealed. The optimized Au@SiO2@ZrO2 enables a direct record of serum metabolic fingerprints (SMFs) by LDI-MS. Subsequently, SMFs are employed to distinguish early PC (stage I/II) from controls, with an accuracy of 92%. Moreover, a prognostic prediction scoring system is established with enhanced efficacy in predicting PC survival compared to CA19-9 (p < 0.05). This work contributes to material-based cancer diagnosis and prognosis.
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Affiliation(s)
- Juxiang Zhang
- State Key Laboratory of Systems Medicine for Cancer, School of Biomedical Engineering, Institute of Medical Robotics and Shanghai Academy of Experimental Medicine, Shanghai Jiao Tong University, Shanghai, 200030, China
- Division of Cardiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Fei Teng
- Department of Gastrointestinal Surgery, Minhang Hospital, Fudan University, Shanghai, 201199, China
- Key Laboratory of Whole-Period Monitoring and Precise Intervention of Digestive Cancer, Shanghai Municipal Health Commission, Minhang Hospital, Fudan University, Shanghai, 201199, China
| | - Beiyuan Hu
- Department of Pancreatic Surgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China
| | - Wanshan Liu
- State Key Laboratory of Systems Medicine for Cancer, School of Biomedical Engineering, Institute of Medical Robotics and Shanghai Academy of Experimental Medicine, Shanghai Jiao Tong University, Shanghai, 200030, China
- Division of Cardiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Yida Huang
- State Key Laboratory of Systems Medicine for Cancer, School of Biomedical Engineering, Institute of Medical Robotics and Shanghai Academy of Experimental Medicine, Shanghai Jiao Tong University, Shanghai, 200030, China
- Division of Cardiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Jiao Wu
- State Key Laboratory of Systems Medicine for Cancer, School of Biomedical Engineering, Institute of Medical Robotics and Shanghai Academy of Experimental Medicine, Shanghai Jiao Tong University, Shanghai, 200030, China
- Division of Cardiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Yuning Wang
- State Key Laboratory of Systems Medicine for Cancer, School of Biomedical Engineering, Institute of Medical Robotics and Shanghai Academy of Experimental Medicine, Shanghai Jiao Tong University, Shanghai, 200030, China
- Division of Cardiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Haiyang Su
- State Key Laboratory of Systems Medicine for Cancer, School of Biomedical Engineering, Institute of Medical Robotics and Shanghai Academy of Experimental Medicine, Shanghai Jiao Tong University, Shanghai, 200030, China
- Division of Cardiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Shouzhi Yang
- State Key Laboratory of Systems Medicine for Cancer, School of Biomedical Engineering, Institute of Medical Robotics and Shanghai Academy of Experimental Medicine, Shanghai Jiao Tong University, Shanghai, 200030, China
- Division of Cardiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Lumin Zhang
- Key Laboratory of Whole-Period Monitoring and Precise Intervention of Digestive Cancer, Shanghai Municipal Health Commission, Minhang Hospital, Fudan University, Shanghai, 201199, China
| | - Lingchuan Guo
- Department of Pathology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, 215006, China
| | - Zhe Lei
- Department of Pathology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, 215006, China
| | - Meng Yan
- Department of Pathology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, 215006, China
| | - Xiaoyu Xu
- State Key Laboratory of Systems Medicine for Cancer, School of Biomedical Engineering, Institute of Medical Robotics and Shanghai Academy of Experimental Medicine, Shanghai Jiao Tong University, Shanghai, 200030, China
- Division of Cardiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Ruimin Wang
- State Key Laboratory of Systems Medicine for Cancer, School of Biomedical Engineering, Institute of Medical Robotics and Shanghai Academy of Experimental Medicine, Shanghai Jiao Tong University, Shanghai, 200030, China
- Division of Cardiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Qingui Bao
- Fosun Diagnostics (Shanghai) Co., Ltd, Shanghai, 200435, China
| | - Qiongzhu Dong
- Key Laboratory of Whole-Period Monitoring and Precise Intervention of Digestive Cancer, Shanghai Municipal Health Commission, Minhang Hospital, Fudan University, Shanghai, 201199, China
| | - Jiang Long
- Department of Pancreatic Surgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China
| | - Kun Qian
- State Key Laboratory of Systems Medicine for Cancer, School of Biomedical Engineering, Institute of Medical Robotics and Shanghai Academy of Experimental Medicine, Shanghai Jiao Tong University, Shanghai, 200030, China
- Division of Cardiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
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Zhang Y, Ni M, Tao Y, Shen M, Xu W, Fan M, Shan J, Cheng H. Multiple-matrix metabolomics analysis for the distinct detection of colorectal cancer and adenoma. Metabolomics 2024; 20:47. [PMID: 38642214 DOI: 10.1007/s11306-024-02114-1] [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: 10/17/2023] [Accepted: 03/31/2024] [Indexed: 04/22/2024]
Abstract
OBJECTIVES Although colorectal cancer (CRC) is the leading cause of cancer-related morbidity and mortality, current diagnostic tests for early-stage CRC and colorectal adenoma (CRA) are suboptimal. Therefore, there is an urgent need to explore less invasive screening procedures for CRC and CRA diagnosis. METHODS Untargeted gas chromatography-mass spectrometry (GC-MS) metabolic profiling approach was applied to identify candidate metabolites. We performed metabolomics profiling on plasma samples from 412 subjects including 200 CRC patients, 160 CRA patients and 52 normal controls (NC). Among these patients, 45 CRC patients, 152 CRA patients and 50 normal controls had their fecal samples tested simultaneously. RESULTS Differential metabolites were screened in the adenoma-carcinoma sequence. Three diagnostic models were further developed to identify cancer group, cancer stage, and cancer microsatellite status using those significant metabolites. The three-metabolite-only classifiers used to distinguish the cancer group always keeps the area under the receiver operating characteristic curve (AUC) greater than 0.7. The AUC performance of the classifiers applied to discriminate CRC stage is generally greater than 0.8, and the classifiers used to distinguish microsatellite status of CRC is greater than 0.9. CONCLUSION This finding highlights potential early-driver metabolites in CRA and early-stage CRC. We also find potential metabolic markers for discriminating the microsatellite state of CRC. Our study and diagnostic model have potential applications for non-invasive CRC and CRA detection.
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Affiliation(s)
- Ye Zhang
- Department of Oncology, Jiangsu Province Hospital of Chinese Medicine, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
- The First Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing, China
- Jiangsu Collaborative Innovation Center of Traditional Chinese Medicine in Prevention and Treatment of Tumor, Nanjing University of Chinese Medicine, Nanjing, China
| | - Mingxin Ni
- The First Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing, China
- Jiangsu Collaborative Innovation Center of Traditional Chinese Medicine in Prevention and Treatment of Tumor, Nanjing University of Chinese Medicine, Nanjing, China
| | - Yuquan Tao
- The First Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing, China
- Jiangsu Collaborative Innovation Center of Traditional Chinese Medicine in Prevention and Treatment of Tumor, Nanjing University of Chinese Medicine, Nanjing, China
| | - Meng Shen
- The First Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing, China
- Jiangsu Collaborative Innovation Center of Traditional Chinese Medicine in Prevention and Treatment of Tumor, Nanjing University of Chinese Medicine, Nanjing, China
| | - Weichen Xu
- Jiangsu Key Laboratory of Pediatric Respiratory Disease, Institute of Pediatrics, Medical Metabolomics Center, Nanjing University of Chinese Medicine, Nanjing, China
| | - Minmin Fan
- The First Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing, China.
- Jiangsu Collaborative Innovation Center of Traditional Chinese Medicine in Prevention and Treatment of Tumor, Nanjing University of Chinese Medicine, Nanjing, China.
| | - Jinjun Shan
- Jiangsu Key Laboratory of Pediatric Respiratory Disease, Institute of Pediatrics, Medical Metabolomics Center, Nanjing University of Chinese Medicine, Nanjing, China.
| | - Haibo Cheng
- Department of Oncology, Jiangsu Province Hospital of Chinese Medicine, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China.
- The First Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing, China.
- Jiangsu Collaborative Innovation Center of Traditional Chinese Medicine in Prevention and Treatment of Tumor, Nanjing University of Chinese Medicine, Nanjing, China.
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Zhang J, Di Y, Zhang B, Li T, Li D, Zhang H. CDK1 and CCNA2 play important roles in oral squamous cell carcinoma. Medicine (Baltimore) 2024; 103:e37831. [PMID: 38640322 PMCID: PMC11029925 DOI: 10.1097/md.0000000000037831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 03/14/2024] [Accepted: 03/15/2024] [Indexed: 04/21/2024] Open
Abstract
Oral squamous cell carcinoma (OSCC) is a malignant tumor that occurs in oral cavity and is dominated by squamous cells. The relationship between CDK1, CCNA2, and OSCC is still unclear. The OSCC datasets GSE74530 and GSE85195 configuration files were downloaded from the Gene Expression Omnibus (GEO) database and were derived from platforms GPL570 and GPL6480. Differentially expressed genes (DEGs) were screened. The weighted gene co-expression network analysis, functional enrichment analysis, gene set enrichment analysis, construction and analysis of protein-protein interaction (PPI) network, Comparative Toxicogenomics Database analysis were performed. Gene expression heatmap was drawn. TargetScan was used to screen miRNAs that regulate central DEGs. A total of 1756 DEGs were identified. According to Gene Ontology (GO) analysis, they were predominantly enriched in processes related to organic acid catabolic metabolism, centromeric, and chromosomal region condensation, and oxidoreductase activity. In Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, the DEGs were mainly concentrated in metabolic pathways, P53 signaling pathway, and PPAR signaling pathway. Weighted gene co-expression network analysis was performed with a soft-thresholding power set at 9, leading to the identification of 6 core genes (BUB1B, CCNB1, KIF20A, CCNA2, CDCA8, CDK1). The gene expression heatmap revealed that core genes (CDK1, CCNA2) were highly expressed in OSCC samples. Comparative Toxicogenomics Database analysis demonstrated associations between the 6 genes (BUB1B, CCNB1, KIF20A, CCNA2, CDCA8, CDK1) and oral tumors, precancerous lesions, inflammation, immune system disorders, and tongue tumors. The associated miRNAs for CDK1 gene were hsa-miR-203a-3p.2, while for CCNA2 gene, they were hsa-miR-6766-3p, hsa-miR-4782-3p, and hsa-miR-219a-5p. CDK1 and CCNA2 are highly expressed in OSCC. The higher the expression of CDK1 and CCNA2, the worse the prognosis.
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Affiliation(s)
- Junbo Zhang
- Department of Stomatology, Tangshan Gongren Hospital, Tangshan City, China
| | - Yongbin Di
- Department of Stomatology, The First Hospital of Hebei Medical University, Shijiazhuang City, China
| | - Bohao Zhang
- Department of Otolaryngology and Head and Neck Surgery, The First Hospital of Hebei Medical University, Shijiazhuang City, China
| | - Tianke Li
- Department of Stomatology, The Fourth Hospital of Hebei Medical University, Shijiazhuang City, China
| | - Dan Li
- Department of Otolaryngology and Head and Neck Surgery, The First Hospital of Hebei Medical University, Shijiazhuang City, China
| | - Haolei Zhang
- Department of Otolaryngology and Head and Neck Surgery, The First Hospital of Hebei Medical University, Shijiazhuang City, China
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Andreozzi F, Mancuso E, Rubino M, Salvatori B, Morettini M, Monea G, Göbl C, Mannino GC, Tura A. Glucagon kinetics assessed by mathematical modelling during oral glucose administration in people spanning from normal glucose tolerance to type 2 diabetes. Front Endocrinol (Lausanne) 2024; 15:1376530. [PMID: 38681771 PMCID: PMC11045965 DOI: 10.3389/fendo.2024.1376530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 03/28/2024] [Indexed: 05/01/2024] Open
Abstract
Background/Objectives Glucagon is important in the maintenance of glucose homeostasis, with also effects on lipids. In this study, we aimed to apply a recently developed model of glucagon kinetics to determine the sensitivity of glucagon variations (especially, glucagon inhibition) to insulin levels ("alpha-cell insulin sensitivity"), during oral glucose administration. Subjects/Methods We studied 50 participants (spanning from normal glucose tolerance to type 2 diabetes) undergoing frequently sampled 5-hr oral glucose tolerance test (OGTT). The alpha-cell insulin sensitivity and the glucagon kinetics were assessed by a mathematical model that we developed previously. Results The alpha-cell insulin sensitivity parameter (named SGLUCA; "GLUCA": "glucagon") was remarkably variable among participants (CV=221%). SGLUCA was found inversely correlated with the mean glycemic values, as well as with 2-hr glycemia of the OGTT. When stratifying participants into two groups (normal glucose tolerance, NGT, N=28, and impaired glucose regulation/type 2 diabetes, IGR_T2D, N=22), we found that SGLUCA was lower in the latter (1.50 ± 0.50·10-2 vs. 0.26 ± 0.14·10-2 ng·L-1 GLUCA/pmol·L-1 INS, in NGT and IGR_T2D, respectively, p=0.009; "INS": "insulin"). Conclusions The alpha-cell insulin sensitivity is highly variable among subjects, and it is different in groups at different glucose tolerance. This may be relevant for defining personalized treatment schemes, in terms of dietary prescriptions but also for treatments with glucagon-related agents.
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Affiliation(s)
- Francesco Andreozzi
- Department of Medical and Surgical Sciences, Magna Graecia University of Catanzaro, Catanzaro, Italy
| | - Elettra Mancuso
- Department of Medical and Surgical Sciences, Magna Graecia University of Catanzaro, Catanzaro, Italy
| | - Mariangela Rubino
- Department of Medical and Surgical Sciences, Magna Graecia University of Catanzaro, Catanzaro, Italy
| | | | - Micaela Morettini
- Department of Information Engineering, Università Politecnica delle Marche, Ancona, Italy
| | - Giuseppe Monea
- Department of Medical and Surgical Sciences, Magna Graecia University of Catanzaro, Catanzaro, Italy
| | - Christian Göbl
- Department of Obstetrics and Gynaecology, Medical University of Vienna, Vienna, Austria
- Department of Obstetrics and Gynaecology, Medical University of Graz, Graz, Austria
| | - Gaia Chiara Mannino
- Department of Medical and Surgical Sciences, Magna Graecia University of Catanzaro, Catanzaro, Italy
| | - Andrea Tura
- CNR Institute of Neuroscience, Padova, Italy
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Shi H, Zhang Z, Yuan X, Liu G, Fan W, Wang W. PROS1 is a crucial gene in the macrophage efferocytosis of diabetic foot ulcers: a concerted analytical approach through the prisms of computer analysis. Aging (Albany NY) 2024; 16:6883-6897. [PMID: 38613800 PMCID: PMC11087110 DOI: 10.18632/aging.205732] [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: 10/26/2023] [Accepted: 03/18/2024] [Indexed: 04/15/2024]
Abstract
BACKGROUND Diabetic foot ulcers (DFUs) pose a serious long-term threat because of elevated mortality and disability risks. Research on its biomarkers is still, however, very limited. In this paper, we have effectively identified biomarkers linked with macrophage excretion in diabetic foot ulcers through the application of bioinformatics and machine learning methodologies. These findings were subsequently validated using external datasets and animal experiments. Such discoveries are anticipated to offer novel insights and approaches for the early diagnosis and treatment of DFU. METHODS In this work, we used the Gene Expression Omnibus (GEO) database's datasets GSE68183 and GSE80178 as the training dataset to build a gene model using machine learning methods. After that, we used the training and validation sets to validate the model (GSE134431). On the model genes, we performed enrichment analysis using both gene set variant analysis (GSVA) and gene set enrichment analysis (GSEA). Additionally, the model genes were subjected to immunological association and immune function analyses. RESULTS In this study, PROS1 was identified as a potential key target associated with macrophage efflux in DFU by machine learning and bioinformatics approaches. Subsequently, the key biomarker status of PROS1 in DFU was also confirmed by external datasets. In addition, PROS1 also plays a key role in macrophage exudation in DFU. This gene may be associated with macrophage M1, CD4 memory T cells, naïve B cells, and macrophage M2, and affects IL-17, Rap1, hedgehog, and JAK-STAT signaling pathways. CONCLUSIONS PROS1 was identified and validated as a biomarker for DFU. This finding has the potential to provide a target for macrophage clearance of DFU.
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Affiliation(s)
- Hongshuo Shi
- Department of Peripheral Vascular Surgery, Institute of Surgery of Traditional Chinese Medicine, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Zhicheng Zhang
- Dongying People’s Hospital (Dongying Hospital of Shandong Provincial Hospital Group), Dongying, Shandong, China
| | - Xin Yuan
- Department of Peripheral Vascular Surgery, Institute of Surgery of Traditional Chinese Medicine, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Guobin Liu
- Department of Peripheral Vascular Surgery, Institute of Surgery of Traditional Chinese Medicine, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Weijing Fan
- Department of Peripheral Vascular Surgery, Institute of Surgery of Traditional Chinese Medicine, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Wenbo Wang
- The Second Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
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Du G, Chen J, Zhu X, Zhu Z. Bioinformatics analysis identifies TGF-β signaling pathway-associated molecular subtypes and gene signature in diabetic foot. iScience 2024; 27:109094. [PMID: 38439964 PMCID: PMC10910239 DOI: 10.1016/j.isci.2024.109094] [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: 11/19/2023] [Revised: 12/08/2023] [Accepted: 01/30/2024] [Indexed: 03/06/2024] Open
Abstract
The role of transforming growth factor β (TGF-β) in inflammation and immune response is established, but the mechanism of TGF-β signaling pathway-related genes (TRGs) in diabetic foot ulcer (DFU) is not fully understood. We aimed to investigate the contribution of TRGs in the identification, molecular categorization, and immune infiltration of DFU through bioinformatics analysis. TGF-β signaling pathway is activated in DFU. 33 TRGs were upregulated. Regression analysis revealed TGFBR1 and TGFB1 as significant differential expression core genes, validated by quantitative real-time PCR. The diagnostic model with core genes had high clinical validity (AUC = 0.909). Core gene expression was associated with immune cell infiltration. A total of 5672 genes showed differential expression in TGF-related patterns, with differences in biological functions and immune infiltration. TGF-β signaling pathway may be critical in DFU development.
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Affiliation(s)
- Guanggang Du
- Department of Burn and Wound Repair, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu 610072, China
- Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Chengdu 610072, China
| | - Jie Chen
- Department of Burn and Wound Repair, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu 610072, China
- Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Chengdu 610072, China
| | - Xuezhu Zhu
- Department of Burn and Wound Repair, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu 610072, China
- Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Chengdu 610072, China
| | - Zongdong Zhu
- Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Chengdu 610072, China
- Department of Orthopaedics, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu 610072, China
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Wang T, Han JG, Dong W, Yu YH. LCN2 and ELANE overexpression induces sepsis. Medicine (Baltimore) 2024; 103:e37255. [PMID: 38363924 PMCID: PMC10869048 DOI: 10.1097/md.0000000000037255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Accepted: 01/23/2024] [Indexed: 02/18/2024] Open
Abstract
Sepsis is a syndrome characterized by a systemic inflammatory response due to the invasion of pathogenic microorganisms. The relationship between Lipocalin-2 (LCN2), elastase, neutrophil expressed (ELANE) and sepsis remains unclear. The sepsis datasets GSE137340 and GSE154918 profiles were downloaded from gene expression omnibus generated from GPL10558. Batch normalization, differentially expressed Genes (DEGs) screening, weighted gene co-expression network analysis (WGCNA), functional enrichment analysis, Gene Set Enrichment Analysis (GSEA), immune infiltration analysis, construction and analysis of protein-protein interaction (PPI) networks, Comparative Toxicogenomics Database (CTD) analysis were performed. Gene expression heatmaps were generated. TargetScan was used to screen miRNAs of DEGs. 328 DEGs were identified. According to Gene Ontology (GO), in the Biological Process analysis, they were mainly enriched in immune response, apoptosis, inflammatory response, and immune response regulation signaling pathways. In cellular component analysis, they were mainly enriched in vesicles, cytoplasmic vesicles, and secretory granules. In Molecular Function analysis, they were mainly concentrated in hemoglobin binding, Toll-like receptor binding, immunoglobulin binding, and RAGE receptor binding. In Kyoto Encyclopedia of Genes and Genomes (KEGG), they were mainly enriched in NOD-like receptor signaling pathway, Toll-like receptor signaling pathway, TNF signaling pathway, P53 signaling pathway, and legionellosis. Seventeen modules were generated. The PPI network identified 4 core genes (MPO, ELANE, CTSG, LCN2). Gene expression heatmaps revealed that core genes (MPO, ELANE, CTSG, LCN2) were highly expressed in sepsis samples. CTD analysis found that MPO, ELANE, CTSG and LCN2 were associated with sepsis, peritonitis, meningitis, pneumonia, infection, and inflammation. LCN2 and ELANE are highly expressed in sepsis and may serve as molecular targets.
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Affiliation(s)
- Tao Wang
- Department of Anesthesiology, Tianjin University Chest Hospital, Jinnan District, Tianjin, China
- Tianjin Key Laboratory of Cardiovascular Emergency and Critical Care, Jinnan District, Tianjin, China
| | - Jian-Ge Han
- Tianjin Key Laboratory of Cardiovascular Emergency and Critical Care, Jinnan District, Tianjin, China
| | - Wei Dong
- Tianjin Key Laboratory of Cardiovascular Emergency and Critical Care, Jinnan District, Tianjin, China
| | - Yong-Hao Yu
- Department of Anesthesiology, Tianjin Medical University General Hospital, Heping District, Tianjin, China
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Alberca-del Arco F, Prieto-Cuadra D, Santos-Perez de la Blanca R, Sáez-Barranquero F, Matas-Rico E, Herrera-Imbroda B. New Perspectives on the Role of Liquid Biopsy in Bladder Cancer: Applicability to Precision Medicine. Cancers (Basel) 2024; 16:803. [PMID: 38398192 PMCID: PMC10886494 DOI: 10.3390/cancers16040803] [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: 01/14/2024] [Revised: 02/02/2024] [Accepted: 02/05/2024] [Indexed: 02/25/2024] Open
Abstract
Bladder cancer (BC) is one of the most common tumors in the world. Cystoscopy and tissue biopsy are the standard methods in screening and early diagnosis of suspicious bladder lesions. However, they are invasive procedures that may cause pain and infectious complications. Considering the limitations of both procedures, and the recurrence and resistance to BC treatment, it is necessary to develop a new non-invasive methodology for early diagnosis and multiple evaluations in patients under follow-up for bladder cancer. In recent years, liquid biopsy has proven to be a very useful diagnostic tool for the detection of tumor biomarkers. This non-invasive technique makes it possible to analyze single tumor components released into the peripheral circulation and to monitor tumor progression. Numerous biomarkers are being studied and interesting clinical applications for these in BC are being presented, with promising results in early diagnosis, detection of microscopic disease, and prediction of recurrence and response to treatment.
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Affiliation(s)
- Fernardo Alberca-del Arco
- Departamento de Urología, Hospital Universitario Virgen de la Victoria (HUVV), 29010 Málaga, Spain; (F.A.-d.A.); (R.S.-P.d.l.B.); (F.S.-B.)
- Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina (IBIMA Plataforma BIONAND), 29590 Málaga, Spain
| | - Daniel Prieto-Cuadra
- Departamento de Anatomía Patológica, Hospital Universitario Virgen de la Victoria (HUVV), 29010 Málaga, Spain;
- Unidad de Gestion Clinica de Anatomia Patologica, IBIMA, Hospital Universitario Virgen de la Victoria, 29010 Málaga, Spain
- SYNLAB Pathology, 29007 Málaga, Spain
| | - Rocio Santos-Perez de la Blanca
- Departamento de Urología, Hospital Universitario Virgen de la Victoria (HUVV), 29010 Málaga, Spain; (F.A.-d.A.); (R.S.-P.d.l.B.); (F.S.-B.)
- Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina (IBIMA Plataforma BIONAND), 29590 Málaga, Spain
- Genitourinary Alliance for Research and Development (GUARD Consortium), 29071 Málaga, Spain
| | - Felipe Sáez-Barranquero
- Departamento de Urología, Hospital Universitario Virgen de la Victoria (HUVV), 29010 Málaga, Spain; (F.A.-d.A.); (R.S.-P.d.l.B.); (F.S.-B.)
- Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina (IBIMA Plataforma BIONAND), 29590 Málaga, Spain
- Genitourinary Alliance for Research and Development (GUARD Consortium), 29071 Málaga, Spain
| | - Elisa Matas-Rico
- Departamento de Urología, Hospital Universitario Virgen de la Victoria (HUVV), 29010 Málaga, Spain; (F.A.-d.A.); (R.S.-P.d.l.B.); (F.S.-B.)
- Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina (IBIMA Plataforma BIONAND), 29590 Málaga, Spain
- Genitourinary Alliance for Research and Development (GUARD Consortium), 29071 Málaga, Spain
- Departamento de Biología Celular, Genética y Fisiología, Universidad de Málaga (UMA), 29071 Málaga, Spain
| | - Bernardo Herrera-Imbroda
- Departamento de Urología, Hospital Universitario Virgen de la Victoria (HUVV), 29010 Málaga, Spain; (F.A.-d.A.); (R.S.-P.d.l.B.); (F.S.-B.)
- Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina (IBIMA Plataforma BIONAND), 29590 Málaga, Spain
- Genitourinary Alliance for Research and Development (GUARD Consortium), 29071 Málaga, Spain
- Departamento de Especialidades Quirúrgicas, Bioquímica e Inmunología, Universidad de Málaga (UMA), 29071 Málaga, Spain
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Ramos MT, Chang G, Wilson C, Gilbertie J, Krieg J, Parvizi J, Chen AF, Otto CM, Schaer TP. Dogs can detect an odor profile associated with Staphylococcus aureus biofilms in cultures and biological samples. FRONTIERS IN ALLERGY 2024; 5:1275397. [PMID: 38414670 PMCID: PMC10896932 DOI: 10.3389/falgy.2024.1275397] [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: 08/09/2023] [Accepted: 01/23/2024] [Indexed: 02/29/2024] Open
Abstract
Introduction The study investigated the utilization of odor detection dogs to identify the odor profile of Staphylococcus aureus (S. aureus) biofilms in pure in vitro samples and in in vivo biosamples from animals and humans with S. aureus periprosthetic joint infection (PJI). Biofilms form when bacterial communities aggregate on orthopedic implants leading to recalcitrant infections that are difficult to treat. Identifying PJI biofilm infections is challenging, and traditional microbiological cultures may yield negative results even in the presence of clinical signs. Methods Dogs were trained on pure in vitro S. aureus biofilms and tested on lacrimal fluid samples from an in vivo animal model (rabbits) and human patients with confirmed S. aureus PJI. Results The results demonstrated that dogs achieved a high degree of sensitivity and specificity in detecting the odor profile associated with S. aureus biofilms in rabbit samples. Preliminary results suggest that dogs can recognize S. aureus volatile organic compounds (VOCs) in human lacrimal fluid samples. Discussion Training odor detection dogs on in vitro S. aureus, may provide an alternative to obtaining clinical samples for training and mitigates biosecurity hazards. The findings hold promise for culture-independent diagnostics, enabling early disease detection, and improved antimicrobial stewardship. In conclusion, this research demonstrates that dogs trained on in vitro S. aureus samples can identify the consistent VOC profile of PJI S. aureus biofilm infections. The study opens avenues for further investigations into a retained VOC profile of S. aureus biofilm infection. These advancements could revolutionize infectious disease diagnosis and treatment, leading to better patient outcomes and addressing the global challenge of antimicrobial resistance.
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Affiliation(s)
- Meghan T Ramos
- Penn Vet Working Dog Center, Clinical Sciences and Advanced Medicine, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Gerard Chang
- Department of Orthopaedics, Geisel School of Medicine at Dartmouth, Lebanon, NH, United States
| | - Clara Wilson
- Penn Vet Working Dog Center, Clinical Sciences and Advanced Medicine, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Jessica Gilbertie
- Center for One Health Research Edward Via College of Osteopathic Medicine, Blacksburg, VA, United States
| | - James Krieg
- Rothman Orthopaedic Institute, Philadelphia, PA, United States
| | - Javad Parvizi
- Rothman Orthopaedic Institute, Philadelphia, PA, United States
| | - Antonia F Chen
- Department of Orthopaedics, Harvard Medical School, Brigham and Women's Hospital, Harvard University, Boston, MA, United States
| | - Cynthia M Otto
- Penn Vet Working Dog Center, Clinical Sciences and Advanced Medicine, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Thomas P Schaer
- Department of Clinical Studies New Bolton Center, School of Veterinary Medicine, University of Pennsylvania, Kennett Square, PA, United States
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Olkowicz M, Ramadan K, Rosales-Solano H, Yu M, Wang A, Cypel M, Pawliszyn J. Mapping the metabolic responses to oxaliplatin-based chemotherapy with in vivo spatiotemporal metabolomics. J Pharm Anal 2024; 14:196-210. [PMID: 38464782 PMCID: PMC10921245 DOI: 10.1016/j.jpha.2023.08.001] [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: 04/15/2023] [Revised: 07/14/2023] [Accepted: 08/07/2023] [Indexed: 03/12/2024] Open
Abstract
Adjuvant chemotherapy improves the survival outlook for patients undergoing operations for lung metastases caused by colorectal cancer (CRC). However, a multidisciplinary approach that evaluates several factors related to patient and tumor characteristics is necessary for managing chemotherapy treatment in metastatic CRC patients with lung disease, as such factors dictate the timing and drug regimen, which may affect treatment response and prognosis. In this study, we explore the potential of spatial metabolomics for evaluating metabolic phenotypes and therapy outcomes during the local delivery of the anticancer drug, oxaliplatin, to the lung. 12 male Yorkshire pigs underwent a 3 h left lung in vivo lung perfusion (IVLP) with various doses of oxaliplatin (7.5, 10, 20, 40, and 80 mg/L), which were administered to the perfusion circuit reservoir as a bolus. Biocompatible solid-phase microextraction (SPME) microprobes were combined with global metabolite profiling to obtain spatiotemporal information about the activity of the drug, determine toxic doses that exceed therapeutic efficacy, and conduct a mechanistic exploration of associated lung injury. Mild and subclinical lung injury was observed at 40 mg/L of oxaliplatin, and significant compromise of the hemodynamic lung function was found at 80 mg/L. This result was associated with massive alterations in metabolic patterns of lung tissue and perfusate, resulting in a total of 139 discriminant compounds. Uncontrolled inflammatory response, abnormalities in energy metabolism, and mitochondrial dysfunction next to accelerated kynurenine and aldosterone production were recognized as distinct features of dysregulated metabolipidome. Spatial pharmacometabolomics may be a promising tool for identifying pathological responses to chemotherapy.
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Affiliation(s)
- Mariola Olkowicz
- Department of Chemistry, University of Waterloo, Waterloo, ON, Canada
- Jagiellonian Centre for Experimental Therapeutics (JCET), Jagiellonian University, Krakow, Poland
| | - Khaled Ramadan
- Latner Thoracic Surgery Research Laboratories, Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada
| | | | - Miao Yu
- The Jackson Laboratory, JAX Genomic Medicine, Farmington, CT, USA
| | - Aizhou Wang
- Latner Thoracic Surgery Research Laboratories, Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada
| | - Marcelo Cypel
- Latner Thoracic Surgery Research Laboratories, Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada
- Division of Thoracic Surgery, Department of Surgery, University Health Network, University of Toronto, Toronto Lung Transplant Program, Toronto, ON, Canada
| | - Janusz Pawliszyn
- Department of Chemistry, University of Waterloo, Waterloo, ON, Canada
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Yan H, Xu G, Bei L, Jiang S, Zhang R. Duck hepatitis A virus type 1 infection induces hepatic metabolite and gut microbiota changes in ducklings. Poult Sci 2024; 103:103265. [PMID: 38042039 PMCID: PMC10711513 DOI: 10.1016/j.psj.2023.103265] [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: 08/30/2023] [Revised: 10/24/2023] [Accepted: 11/02/2023] [Indexed: 12/04/2023] Open
Abstract
Duck hepatitis A virus type 1 (DHAV-1) can cause severe liver damage in infected ducklings and is a fatal and contagious pathogen that endangers the Chinese duck industry. The objective of this study was to explore the correlation mechanism of liver metabolism-gut microbiota in DHAV-1 infection. Briefly, liquid chromatography-mass spectrometry and 16S rDNA sequencing combined with multivariate statistical analysis were used to evaluate the effects of DHAV-1 infection on liver metabolism, gut microbiota regulation, and other potential mechanisms in ducklings. In DHAV-1-infected ducklings at 72 h postinfection, changes were found in metabolites associated with key metabolic pathways such as lipid metabolism, sugar metabolism, and nucleotide metabolism, which participated in signaling networks and ultimately affecting the function of the liver. The abundance and composition of gut microbiota were also changed, and gut microbiota is significantly involved in lipid metabolism in the liver. The evident correlation between gut microbiota and liver metabolites indicates that DHAV-host gut microbiome interactions play important roles in the development of duck viral hepatitis (DVH).
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Affiliation(s)
- Hui Yan
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Shandong Agricultural University, Tai'an 271018, China; Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Tai'an 271018, China; Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Tai'an 271018, China
| | - Guige Xu
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Shandong Agricultural University, Tai'an 271018, China; Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Tai'an 271018, China; Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Tai'an 271018, China
| | - Lei Bei
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Shandong Agricultural University, Tai'an 271018, China; Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Tai'an 271018, China; Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Tai'an 271018, China
| | - Shijin Jiang
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Shandong Agricultural University, Tai'an 271018, China; Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Tai'an 271018, China; Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Tai'an 271018, China
| | - Ruihua Zhang
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Shandong Agricultural University, Tai'an 271018, China; Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Tai'an 271018, China; Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Tai'an 271018, China.
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20
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Zhu Y, Hou S, Kang C. Complementary biomarkers of computed tomography for diagnostic grading of gastric cancer: DSCC1 and GINS1. Aging (Albany NY) 2024; 16:4149-4168. [PMID: 38301047 PMCID: PMC10968684 DOI: 10.18632/aging.205491] [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: 08/16/2023] [Accepted: 12/19/2023] [Indexed: 02/03/2024]
Abstract
OBJECTIVE Computed tomography (CT) is an important tool for grading gastric cancer. Gastric cancer typically originates from epithelial cells of gastric mucosa. However, complementary markers for gastric cancer, relationship between DSCC1, GINS1 and gastric cancer remain unclear. METHODS Gastric cancer data were obtained from gene expression omnibus (GEO). Differentially expressed genes (DEGs) were identified, weighted gene co-expression network analysis (WGCNA) was conducted. Protein-protein interaction (PPI) network was constructed and analyzed. Functional enrichment analysis, gene set enrichment analysis (GSEA), gene expression heatmaps, immune infiltration analysis were performed. The most relevant diseases related to core genes were identified using Comparative Toxicogenomics Database (CTD). TargetScan was used to screen miRNAs. Validation was carried out using Western blotting (WB) and reverse transcription-polymerase chain reaction (RT-PCR). RESULTS 1243 DEGs were identified. Gene ontology (GO) and Kyoto Encyclopedia of Gene and Genome (KEGG) analyses revealed significant enrichment in cell cycle regulation, macrophage migration control, basement membrane, extracellular regions, growth factor binding, protein complex binding, P53 signaling pathway, protein digestion and absorption, metabolic pathways. Immune infiltration analysis indicated that high expression of activated Mast cells and Neutrophils, with a strong positive correlation between them, may influence progression of gastric cancer. CTD analysis revealed associations between DSCC1, GINS1 and gastric tumors, gastrointestinal diseases, tumors, gastritis, inflammation, necrosis. WB and RT-PCR results demonstrated high expression of DSCC1 and GINS1 in gastric cancer. CONCLUSION The expressions of DSCC1 and GINS1 are up-regulated in gastric cancer, which can be used as supplementary markers for CT diagnostic grading of gastric cancer.
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Affiliation(s)
- Yufeng Zhu
- Department of Radiology, The First People’s Hospital of Fuyang, Fuyang, Hangzhou 311400, China
| | - Shiyang Hou
- Department of General Surgery, Beijing Rehabilitation Hospital Affiliated to Capital Medical University, Shijingshan, Beijing 100144, China
| | - Chunbo Kang
- Department of General Surgery, Beijing Rehabilitation Hospital Affiliated to Capital Medical University, Shijingshan, Beijing 100144, China
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21
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Zhao M, Liu A, Wu J, Mo L, Lu F, Wan G. Il1r2 and Tnfrsf12a in transcranial magnetic stimulation effect of ischemic stroke via bioinformatics analysis. Medicine (Baltimore) 2024; 103:e36109. [PMID: 38277520 PMCID: PMC10817048 DOI: 10.1097/md.0000000000036109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 10/23/2023] [Indexed: 01/28/2024] Open
Abstract
Ischemic stroke refers to ischemic necrosis or softening of localized brain tissue. Transcranial magnetic stimulation (TMS) is a painless, noninvasive and green treatment method, which acts on the central nervous system through a pulsed magnetic field to assist in the treatment of central nervous system injury diseases. However, the role of Il1r2 and Tnfrsf12a in this is unknown. The ischemic stroke datasets GSE81302 and TMS datasets GSE230148 were downloaded from Gene Expression Omnibus database. Differentially expressed genes (DEGs) were screened and weighted gene co-expression network analysis (WGCNA) was performed. The construction and analysis of protein-protein interaction (PPI) network and functional enrichment analysis were performed. Draw heat map gene expression. Through the Comparative Toxicogenomics Database (CTD) to find the most relevant and core gene diseases. TargetScan was used to screen miRNAs regulating DEGs. A total of 39 DEGs were identified. According to gene ontology (GO) analysis results, in biological process (BP) analysis, they were mainly enriched in the positive regulation of apoptosis process, inflammatory response, positive regulation of p38MAPK cascade, and regulation of cell cycle. In cellular component (CC) analysis, they were mainly enriched in the cell surface, cytoplasm, and extracellular space. In Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, they were mainly enriched in nf-κB signaling pathway, fluid shear stress and atherosclerosis, P53 signaling pathway, TNF signaling pathway, and apoptosis. Among the enrichment items of metascape, negative regulation of T cell activation, hematopoietic cell lineage, positive regulation of apoptotic process, fluid shear stress and atherosclerosis were observed in GO enrichment items. Five core genes (Socs3, Irf1, Il1r2, Ccr1, and Tnfrsf12a) were obtained, which were highly expressed in ischemic stroke samples. Il1r2 and Tnfrsf12a were lowly expressed in TMS samples. CTD analysis found that the core gene (Socs3, Irf1 and Il1r2, Ccr1, Tnfrsf12a) and ischemic stroke, atherosclerosis, hypertension, hyperlipidemia, thrombosis, stroke, myocardial ischemia, myocardial infarction, and inflammation. Il1r2 and Tnfrsf12a are highly expressed in ischemic stroke, but lowly expressed in TMS samples.
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Affiliation(s)
- Man Zhao
- Neurological Rehabilitation Center, Beijing Rehabilitation Hospital Affiliated to Capital Medical University, Xixiazhuang, Badachu, Shijingshan District, Beijing
| | - Aixian Liu
- Neurological Rehabilitation Center, Beijing Rehabilitation Hospital Affiliated to Capital Medical University, Xixiazhuang, Badachu, Shijingshan District, Beijing
| | - Jiaojiao Wu
- Neurological Rehabilitation Center, Beijing Rehabilitation Hospital Affiliated to Capital Medical University, Xixiazhuang, Badachu, Shijingshan District, Beijing
| | - Linhong Mo
- Neurological Rehabilitation Center, Beijing Rehabilitation Hospital Affiliated to Capital Medical University, Xixiazhuang, Badachu, Shijingshan District, Beijing
| | - Fang Lu
- Neurological Rehabilitation Center, Beijing Rehabilitation Hospital Affiliated to Capital Medical University, Xixiazhuang, Badachu, Shijingshan District, Beijing
| | - Guiling Wan
- Neurological Rehabilitation Center, Beijing Rehabilitation Hospital Affiliated to Capital Medical University, Xixiazhuang, Badachu, Shijingshan District, Beijing
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22
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Jang M, Shin J, Kim YH, Jeong TY, Jo S, Kim SJ, Devaraj V, Kang J, Choi EJ, Lee JE, Oh JW. 3D superstructure based metabolite profiling for glaucoma diagnosis. Biosens Bioelectron 2024; 244:115780. [PMID: 37939415 DOI: 10.1016/j.bios.2023.115780] [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: 06/13/2023] [Revised: 09/05/2023] [Accepted: 10/21/2023] [Indexed: 11/10/2023]
Abstract
Metabolome analysis has gained widespread application in disease diagnosis owing to its ability to provide comprehensive information, including disease phenotypes. In this study, we utilized 3D superstructures fabricated through evaporation-induced microprinting to analyze the metabolome for glaucoma diagnosis. 3D superstructures offer the following advantages: high hotspot density per unit volume of the structure extending from two to three dimensions, excellent signal repeatability due to the reproducibility and defect tolerance of 3D printing, and high thermal stability due to the PVP-enclosed capsule form. Leveraging the superior optical properties of the 3D superstructure, we aimed to classify patients with glaucoma. The signal obtained from the 3D superstructure was employed in a Deep Neural Network (DNN) classification model to accurately classify glaucoma patients. The sensitivity and specificity of the model were determined as 92.05% and 93.51%, respectively. Additionally, the fabrication of 3D superstructures can be performed at any stage, significantly reducing measurement time. Furthermore, their thermal stability allows for the analysis of smaller samples. One notable advantage of 3D superstructures is their versatility in accommodating different target materials. Consequently, they can be utilized for a wide range of metabolic analyses and disease diagnoses.
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Affiliation(s)
- Minsu Jang
- Department of Nano Fusion Technology, Pusan National University, Busan, 46241, Republic of Korea
| | - Jonghoon Shin
- Department of Ophthalmology, College of Medicine, Pusan National University Yangsan Hospital, Republic of Korea; Department of Ophthalmology, Research Institute for Convergence of Biomedical Science and Technology, Busan, Republic of Korea
| | - You Hwan Kim
- Department of Nano Fusion Technology, Pusan National University, Busan, 46241, Republic of Korea
| | - Tae-Young Jeong
- Bio-IT Fusion Technology Research Institute, Pusan National University, Busan, 46241, Republic of Korea
| | - Soojin Jo
- Department of Nano Fusion Technology, Pusan National University, Busan, 46241, Republic of Korea
| | - Sung-Jo Kim
- Bio-IT Fusion Technology Research Institute, Pusan National University, Busan, 46241, Republic of Korea
| | - Vasanthan Devaraj
- Bio-IT Fusion Technology Research Institute, Pusan National University, Busan, 46241, Republic of Korea
| | - Joonhee Kang
- Department of Nano Energy Engineering, Pusan National University, Busan, 46241, Republic of Korea
| | - Eun-Jung Choi
- Bio-IT Fusion Technology Research Institute, Pusan National University, Busan, 46241, Republic of Korea.
| | - Ji Eun Lee
- Department of Ophthalmology, College of Medicine, Pusan National University Yangsan Hospital, Republic of Korea; Department of Ophthalmology, Research Institute for Convergence of Biomedical Science and Technology, Busan, Republic of Korea.
| | - Jin-Woo Oh
- Department of Nano Fusion Technology, Pusan National University, Busan, 46241, Republic of Korea; Bio-IT Fusion Technology Research Institute, Pusan National University, Busan, 46241, Republic of Korea; Department of Nano Energy Engineering, Pusan National University, Busan, 46241, Republic of Korea.
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23
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Fu J, Gao X, Lu Y, Lu F, Wang Y, Chen P, Wang C, Yuan C, Liu S. Integrated proteomics and metabolomics reveals metabolism disorders in the α-syn mice and potential therapeutic effect of Acanthopanax senticosus extracts. JOURNAL OF ETHNOPHARMACOLOGY 2024; 318:116878. [PMID: 37419226 DOI: 10.1016/j.jep.2023.116878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 06/29/2023] [Accepted: 07/03/2023] [Indexed: 07/09/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Acanthopanax senticosus (Rupr.et.Maxim.)Harms(AS) is an extract of Eleutherococcus senticocus Maxim(Rupr.et.Maxim.). In modern medical interpretation, Acanthopanax senticosus can be used to treat Parkinson's disease, and a large number of modern pharmacological and clinical studies also support this application. Our study demonstrated that AS extracts can increase the activity of various antioxidant enzymes and improve the symptoms of Parkinson's disease in mice. AIM OF THE STUDY The current study looked at the protective effect of Acanthopanax senticosus extracts(ASE) in preventing PD. METHODS AND MATERIALS First, the α-syn-overexpressing mice were chosen as suitable models for Parkinson's disease in vivo. HE staining was used to observe the pathological changes in the substantia nigra. Meanwhile, TH expression in substantia nigra was analyzed by immunohistochemistry. Behavioral and biochemical tests evaluated neuroprotective effects of ASE on PD mice. Subsequently, combined with proteomics and metabolomics analysis, the changes in brain proteins and metabolites in mice treated with ASE for PD were studied. Finally, Western blot was used to detect metabolome-related and proteomic proteins in the brain tissue of α-syn mice. RESULTS Forty-nine common differentially expressed proteins were screened by proteomics analysis, among which 28 were significantly up-regulated,and 21 were significantly down-regulated. Metabolomics analysis showed that twenty-five potentially important metabolites were involved in the therapeutic effect of ASE on PD. Most of the different proteins and metabolites were considered to be enriched in a variety of species in metabolic pathways, including glutathione metabolism and alanine aspartate and glutamate metabolism and other pathways, which means that ASE may have molecular mechanisms to ameliorate PD dysfunction. In addition, we found that decreases in glutathione and glutathione disulfide levels may play a critical role in these systemic changes and warrant further investigation. In the glutathione metabolic pathway, ASE also acts on GPX4, GCLC and GCLM. CONCLUSIONS ASE can effectively relieve behavioral symptoms of α-syn mice and relieve oxidative stress in brain tissue. These findings suggest that ASE offers a potential solution to target these pathways for the treatment of PD.
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Affiliation(s)
- Jiaqi Fu
- Institute of Traditional Chinese Medicine, Heilongjiang University of Chinese Medicine, Harbin, Heilongjiang, China
| | - Xin Gao
- Institute of Traditional Chinese Medicine, Heilongjiang University of Chinese Medicine, Harbin, Heilongjiang, China
| | - Yi Lu
- Institute of Traditional Chinese Medicine, Heilongjiang University of Chinese Medicine, Harbin, Heilongjiang, China
| | - Fang Lu
- Institute of Traditional Chinese Medicine, Heilongjiang University of Chinese Medicine, Harbin, Heilongjiang, China
| | - Yu Wang
- Institute of Traditional Chinese Medicine, Heilongjiang University of Chinese Medicine, Harbin, Heilongjiang, China
| | - Pingping Chen
- Institute of Traditional Chinese Medicine, Heilongjiang University of Chinese Medicine, Harbin, Heilongjiang, China
| | - Chongzhi Wang
- Tang Center for Herbal Medicine Research, Department of Anesthesia and Critical Care, University of Chicago, Chicago, IL, 60637, USA
| | - Chunsu Yuan
- Tang Center for Herbal Medicine Research, Department of Anesthesia and Critical Care, University of Chicago, Chicago, IL, 60637, USA
| | - Shumin Liu
- Institute of Traditional Chinese Medicine, Heilongjiang University of Chinese Medicine, Harbin, Heilongjiang, China.
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24
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Yang Z, Li H, Hao J, Mei H, Qiu M, Wang H, Gao M. EPYC functions as a novel prognostic biomarker for pancreatic cancer. Sci Rep 2024; 14:719. [PMID: 38184732 PMCID: PMC10771449 DOI: 10.1038/s41598-024-51478-w] [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: 10/30/2023] [Accepted: 01/05/2024] [Indexed: 01/08/2024] Open
Abstract
Pancreatic cancer (PC) has become a worldwide challenge attributed to its difficult early diagnosis and rapid progression. Treatments continue to be limited besides surgical resection. Hence, we aimed to discover novel biological signatures as clinically effective therapeutic targets for PC via the mining of public tumor databases. We found that epiphycan (EPYC) could function as an independent risk factor to predict the poor prognosis in PC based on integrated bioinformatics analysis. We downloaded associated PC data profiles from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) online websites, then applied the software Rstudio to filter out genes under the strict criteria. After the batch survival analysis using Log-rank test and univariate cox regression, we obtained 39 candidate genes. Subsequently, we narrowed the scope to 8 genes by establishing a Lasso regression model. Eventually, we focused on 2 genes (EPYC and MET) by further building a multivariate cox regression model. Given that the role of EPYC in PC remains obscure, we then performed a series of molecular functional experiments, including RT-qPCR, CCK8, EdU, colony formation, Transwell, western blot, cell live-dead staining, subcutaneous tumor formation, to enhance our insight into its underlying molecular mechanisms. The above results demonstrated that EPYC was highly expressed in PC cell lines and could promote the proliferation of PCs via PI3K-AKT signaling pathway in vivo and in vitro. We arrived at a conclusion that EPYC was expected to be a biological neo-biomarker for PC followed by being a potential therapeutic target.
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Affiliation(s)
- Zhen Yang
- Department of Clinical Laboratory, Tianjin Union Medical Center of Nankai University, Tianjin, China.
- The Institute of Translational Medicine, Tianjin Union Medical Center of Nankai University, Tianjin, China.
| | - Honglin Li
- Department of Clinical Laboratory, Dachuan District People's Hospital, Sichuan, China
| | - Jie Hao
- Department of Thyroid and Breast Surgery, Tianjin Key Laboratory of General Surgery in Construction, Tianjin Union Medical Center of Nankai University, Tianjin, China
| | - Hanwei Mei
- The Institute of Translational Medicine, Tianjin Union Medical Center of Nankai University, Tianjin, China
- Department of Oncology, Tianjin Union Medical Center of Nankai University, Tianjin, China
| | - Minghan Qiu
- The Institute of Translational Medicine, Tianjin Union Medical Center of Nankai University, Tianjin, China
- Department of Oncology, Tianjin Union Medical Center of Nankai University, Tianjin, China
| | - Huaqing Wang
- The Institute of Translational Medicine, Tianjin Union Medical Center of Nankai University, Tianjin, China.
- Department of Oncology, Tianjin Union Medical Center of Nankai University, Tianjin, China.
| | - Ming Gao
- Department of Thyroid and Breast Surgery, Tianjin Key Laboratory of General Surgery in Construction, Tianjin Union Medical Center of Nankai University, Tianjin, China.
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25
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Lv Q, Han Q, Wen Z, Pan Y, Chen J. The association between atherosclerosis and nonalcoholic fatty liver disease. Medicine (Baltimore) 2024; 103:e36815. [PMID: 38181273 PMCID: PMC10766323 DOI: 10.1097/md.0000000000036815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 12/07/2023] [Indexed: 01/07/2024] Open
Abstract
Atherosclerosis (AS) is closely related to nonalcoholic fatty liver disease (NAFLD), which promotes and exacerbates the development of AS. However, it is uncertain how the precise underlying mechanism occurs. Here, we attempted to further explore the association underlying atherosclerosis and nonalcoholic fatty liver disease through integrated bioinformatics analysis. Microarray data for atherosclerosis and nonalcoholic fatty liver disease were retrieved from the Gene Expression Omnibus (GEO) database. Weighted gene co-expression network analysis (WGCNA) was used to identify the genes related to atherosclerosis and nonalcoholic fatty liver disease showing co-expression. Additionally, the common gene targets associated with atherosclerosis and nonalcoholic fatty liver disease were also analyzed and screened using data from 3 public databases [comparative toxicogenomics database (CTD), DISEASES, and GeneCards]. The Gene Ontology (GO) enrichment analysis and the Kyoto encyclopedia of genes and genomes (KEGG) enrichment analysis were performed using Metascape R, respectively. The protein-protein interaction networks (PPI) network was constructed using Cytoscape. According to the results of an analysis of common genes, matrix metalloproteinase 9 (MMP9) is co-expressed up-regulated in AS and NAFLD and is enriched in inflammatory and immune-related collaterals. Consequently, MMP9 may work together through immunity and inflammation to treat AS and NAFLD and may be a potential therapeutic target in the future. The findings of this study provide new insights into the shared association between AS and NAFLD. MMP9 is co-expressed up-regulated in AS and NAFLD, which be able to reveal the presence of co-expressed genes in atherosclerosis and NAFLD.
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Affiliation(s)
- Qing Lv
- The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, China
| | - Qianqian Han
- The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, China
| | - Ziyun Wen
- The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, China
| | - Yunyun Pan
- Clinical Pharmacy Center, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Jisheng Chen
- The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, China
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Batagov A, Dalan R, Wu A, Lai W, Tan CS, Eisenhaber F. Generalized metabolic flux analysis framework provides mechanism-based predictions of ophthalmic complications in type 2 diabetes patients. Health Inf Sci Syst 2023; 11:18. [PMID: 37008895 PMCID: PMC10060506 DOI: 10.1007/s13755-023-00218-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 02/19/2023] [Indexed: 03/31/2023] Open
Abstract
Chronic metabolic diseases arise from changes in metabolic fluxes through biomolecular pathways and gene networks accumulated over the lifetime of an individual. While clinical and biochemical profiles present just real-time snapshots of the patients' health, efficient computation models of the pathological disturbance of biomolecular processes are required to achieve individualized mechanistic insights into disease progression. Here, we describe the Generalized metabolic flux analysis (GMFA) for addressing this gap. Suitably grouping individual metabolites/fluxes into pools simplifies the analysis of the resulting more coarse-grain network. We also map non-metabolic clinical modalities onto the network with additional edges. Instead of using the time coordinate, the system status (metabolite concentrations and fluxes) is quantified as function of a generalized extent variable (a coordinate in the space of generalized metabolites) that represents the system's coordinate along its evolution path and evaluates the degree of change between any two states on that path. We applied GMFA to analyze Type 2 Diabetes Mellitus (T2DM) patients from two cohorts: EVAS (289 patients from Singapore) and NHANES (517) from the USA. Personalized systems biology models (digital twins) were constructed. We deduced disease dynamics from the individually parameterized metabolic network and predicted the evolution path of the metabolic health state. For each patient, we obtained an individual description of disease dynamics and predict an evolution path of the metabolic health state. Our predictive models achieve an ROC-AUC in the range 0.79-0.95 (sensitivity 80-92%, specificity 62-94%) in identifying phenotypes at the baseline and predicting future development of diabetic retinopathy and cataract progression among T2DM patients within 3 years from the baseline. The GMFA method is a step towards realizing the ultimate goal to develop practical predictive computational models for diagnostics based on systems biology. This tool has potential use in chronic disease management in medical practice. Supplementary Information The online version contains supplementary material available at 10.1007/s13755-023-00218-x.
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Affiliation(s)
- Arsen Batagov
- Mesh Bio Pte. Ltd., 10 Anson Rd, #22-02, 079903 Singapore, Singapore
| | - Rinkoo Dalan
- Department of Endocrinology, Tan Tock Seng Hospital, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Andrew Wu
- Mesh Bio Pte. Ltd., 10 Anson Rd, #22-02, 079903 Singapore, Singapore
| | - Wenbin Lai
- Mesh Bio Pte. Ltd., 10 Anson Rd, #22-02, 079903 Singapore, Singapore
| | - Colin S. Tan
- Fundus Image Reading Center, National Healthcare Group Eye Institute, Singapore, Singapore
- Tan Tock Seng Hospital, National Healthcare Group Eye Institute, Singapore, Singapore
- Duke-NUS Medical School, Singapore, Singapore
| | - Frank Eisenhaber
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- School of Biological Science (SBS), Nanyang Technological University, Singapore, Singapore
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27
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Wang T, Qin Y, Qiao J, Liu Y, Wang L, Zhang X. Overexpression of SIRT6 regulates NRF2/HO-1 and NF-κB signaling pathways to alleviate UVA-induced photoaging in skin fibroblasts. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 2023; 249:112801. [PMID: 37897855 DOI: 10.1016/j.jphotobiol.2023.112801] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 10/02/2023] [Accepted: 10/12/2023] [Indexed: 10/30/2023]
Abstract
Skin photoaging, resulting from prolonged exposure to sunlight, especially UVA rays, has been identified as a key contributor to age-related skin degeneration. However, the mechanism by which UVA radiation induces skin cell senescence has not been fully elucidated. In this investigation, bioinformatics technology was employed to identify SIRT6 as the core hub gene involved in the progression of skin photoaging. The study evinced that prolonged exposure of cutaneous fibroblasts to UVA radiation results in a marked reduction in the expression of SIRT6, both in vivo and in vitro. Knockdown of SIRT6 in skin fibroblasts resulted in the upregulation of genes associated with cellular aging, thereby exacerbating the effects of UVA radiation-induced photoaging. Conversely, overexpression of SIRT6 decreased the expression of cell aging-related genes, indicating that SIRT6 plays a role in the regulation of senescence in skin fibroblasts induced by UVA radiation. We proffer substantiation that overexpression of SIRT6 protects skin fibroblasts from UVA-induced oxidative stress by activating the NRF2/HO-1 signaling cascade. Moreover, SIRT6 overexpression also reduced UVA-induced type I collagen degradation by inhibiting NF-κB signaling cascade. In summary, our findings showed that overexpression of SIRT6 inhibits UVA-induced senescence phenotype and type I collagen degradation in skin fibroblasts by modulating the NRF2/HO-1 and NF-κB signaling pathways. And the regulation of these signaling pathways by SIRT6 may be achieved through its deacetylase activity. Therefore, SIRT6 is a novel and promising therapeutic target for skin aging related to age and UV.
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Affiliation(s)
- Tao Wang
- Department of Plastic Surgery, Lanzhou University Second Hospital, Lanzhou City 730000, Gansu Province, China
| | - Yonghong Qin
- Department of Plastic Surgery, Lanzhou University Second Hospital, Lanzhou City 730000, Gansu Province, China
| | - Jianxiong Qiao
- Department of Plastic Surgery, Lanzhou University Second Hospital, Lanzhou City 730000, Gansu Province, China
| | - Yang Liu
- Center of Gastrointestinal and Minimally Invasive Surgery, Department of General Surgery, the Third People's Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University, Chengdu 610000, China
| | - Lerong Wang
- Department of Plastic Surgery, Lanzhou University Second Hospital, Lanzhou City 730000, Gansu Province, China
| | - Xuanfen Zhang
- Department of Plastic Surgery, Lanzhou University Second Hospital, Lanzhou City 730000, Gansu Province, China.
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28
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Ma Y, Guo S. High expression of NADH Ubiquinone Oxidoreductase Subunit B11 induces catheter-associated venous thrombosis on continuous blood purification. Medicine (Baltimore) 2023; 102:e36520. [PMID: 38050233 PMCID: PMC10986910 DOI: 10.1097/md.0000000000036520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 11/16/2023] [Indexed: 12/06/2023] Open
Abstract
Venous thromboembolism (VTE) is a common vascular disease of venous return disorders, including deep venous thrombosis and pulmonary embolism (PE), with high morbidity and high mortality. However, the relationship between oxidative phosphorylation and NDUFB11 and venous thromboembolism is still unclear. The venous thromboembolism datasets GSE48000 and GSE19151 were downloaded, and the differentially expressed Genes (DEGs) were screened. The protein-protein interaction (PPI) network was constructed. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) were used for functional enrichment analysis. The comparative toxicogenomics database (CTD) was used to identify the diseases most associated with the core genes. TargetScan was used to screen miRNA regulating central DEGs. Western blotting (WB) experiment and real-time quantitative PCR (RT-qPCR) experiment were performed. A total of 500 DEGs were identified. GO analysis showed that the DEGs were mainly enriched in ATP synthesis coupled electron transport, respiratory electron transport chain, cytoplasm, enzyme binding, nonalcoholic fatty liver disease, oxidative phosphorylation, and Alzheimer disease. Enrichment items were similar to GO and KEGG enrichment items of DEGs. The result of CTD showed that 12 genes (RPS24, FAU, RPLP0, RPS15A, RPS29, RPL9, RPL31, RPL27, NDUFB11, RPL34, COX7B, RPS27L) were associated with chemical and drug-induced liver injury, inflammation, kidney disease, and congenital pure red cell aplasia. WB and RT-qPCR results showed that the expression levels of 12 genes in venous thromboembolism were higher than normal whole blood tissue samples. NDUFB11 is highly expressed in catheter-related venous thromboembolism during continuous blood purification, which may lead to the formation of venous thrombosis through oxidative phosphorylation pathway.
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Affiliation(s)
- Yanhong Ma
- Department of ICU, The Fourth Hospital of Hebei Medical University. Shijiazhuang, China
| | - Suzhi Guo
- Department of ICU, The Fourth Hospital of Hebei Medical University. Shijiazhuang, China
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Zhang L, Xu L. Fgf2 and Ptpn11 play a role in cerebral injury caused by sevoflurane anesthesia. Medicine (Baltimore) 2023; 102:e36108. [PMID: 37960778 PMCID: PMC10637467 DOI: 10.1097/md.0000000000036108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 10/23/2023] [Indexed: 11/15/2023] Open
Abstract
Sevoflurane is a new inhaled anesthetic, which has better physical properties than the existing inhalational anesthetics, rapid induction, less tissue uptake, and faster recovery. Sevoflurane can directly dilators cerebral blood vessels and increase cerebral blood flow, but it also reduces cerebral oxygen metabolism rate, thereby reducing cerebral blood flow. However, the role of Fgf2 and Ptpn11 in cerebral injury caused by sevoflurane anesthesia remains unclear. The sevoflurane anesthesia brain tissue datasets GSE139220 and GSE141242 were downloaded from gene expression omnibus (GEO). Differentially expressed genes (DEGs) were screened and weighted gene co-expression network analysis (WGCNA) was performed. Construction and analysis of protein-protein interaction (PPI) Network. Gene Ontology (GO) and Kyoto Encyclopedia of Gene and Genome (KEGG), comparative toxicogenomics database (CTD) were performed. A heat map of gene expression was drawn. TargetScan was used to screen miRNAs regulating DEGs. 500 DEGs were identified. According to GO, in Biological Process analysis, they were mainly enriched in response to hypoxia, blood vessel development, inner ear development, neural tube closure, and aging. In Cellular Component (CC), they were mainly enriched in plasma membrane, integral component of membrane, and basal lamina. In Molecular Function (MF), they were mainly associated with protein binding, Wnt-activated receptor activity, and organic anion transmembrane transporter activity. In the KEGG analysis, they were mainly enriched in proteoglycans in cancer, pathways in cancer, transcriptional misregulation in cancer, basal cell carcinoma, thyroid hormone signaling pathway. In the Metascape enrichment analysis, the GO enrichment items revealed upregulated regulation of vascular endothelial cell proliferation, platelet-derived growth factor receptor signaling pathway, inner ear development, and response to hypoxia. A total of 20 modules were generated. Gene Expression Heatmap showed that the core genes (Fgf2, Pdgfra, Ptpn11, Slc2a1) were highly expressed in sevoflurane anesthesia brain tissue samples. CTD Analysis showed that the 4 core genes (Fgf2, Pdgfra, Ptpn11, Slc2a1) were associated with neurodegenerative diseases, brain injuries, memory disorders, cognitive disorders, neurotoxicity, drug-induced abnormalities, neurological disorders, developmental disorders, and intellectual disabilities. Fgf2 and Ptpn11 are highly expressed in brain tissue after sevoflurane anesthesia, higher the expression level of Fgf2 and Ptpn11, worse the prognosis.
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Affiliation(s)
- Lin Zhang
- Department of Anesthesiology, The Third Affiliated Hospital of Beijing University of Chinese Medicine, Beijing, China
| | - Lingyan Xu
- Department of Disease Control and Prevention, The Third Affiliated Hospital of Beijing University of Chinese Medicine, Beijing, China
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30
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Wang Z, Ding S, Zhang C, Zhan H, Li Y, Yan J, Jia Y, Wang X, Wang Y. Revealing the impact of TOX3 on osteoarthritis: insights from bioinformatics. Front Med (Lausanne) 2023; 10:1256654. [PMID: 38020130 PMCID: PMC10663247 DOI: 10.3389/fmed.2023.1256654] [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: 07/11/2023] [Accepted: 10/19/2023] [Indexed: 12/01/2023] Open
Abstract
Osteoarthritis, a prevalent long-term condition of the joints, primarily impacts older individuals, resulting in discomfort, restrictions in mobility, and a decrease in overall well-being. Although Osteoarthritis is widely spread, there is a lack of successful interventions to stop the advancement of the condition. Numerous signaling pathways have been emphasized in recent research on Osteoarthritis, yet the diagnostic significance of numerous genes has not been investigated. To identify genes that were expressed differently in osteoarthritis, we utilized the Gene Expression Omnibus database. To identify marker genes, we built machine learning models including Least Absolute Shrinkage and Selection Operator and Random Forest. We categorized Osteoarthritis samples and performed immune cell infiltration analysis based on the expression patterns of these characteristic genes. Both the Least Absolute Shrinkage and Selection Operator and Random Forest models selected six marker genes (TOX3, ARG1, CST7, RERGL, COL11A1, NCRNA00185) out of a total of 17 differentially expressed genes. The osteoarthritis samples were categorized into two groups, namely a high expression group and a low expression group, based on the median levels of TOX3 expression. Comparative analysis of these groups identified 85 differentially expressed genes, showing notable enrichment in pathways related to lipid metabolism in the group with high expression. Analysis of immune cell infiltration revealed noticeable differences in immune profiles among the two groups. The group with high expression of TOX3 showed a notable increase in Mast cells and Type II IFN Response, whereas B cells, Cytolytic activity, Inflammation-promoting cells, NK cells, pDCs, T cell co-inhibition, Th1 cells, and Th2 cells were significantly decreased. We constructed a ceRNA network for TOX3, revealing 57 lncRNAs and 18 miRNAs involved in 57 lncRNA-miRNA interactions, and 18 miRNA-mRNA interactions with TOX3. Validation of TOX3 expression was confirmed using an external dataset (GSE29746), revealing a notable increase in Osteoarthritis samples. In conclusion, our study presents a comprehensive analysis identifying TOX3 as a potential feature gene in Osteoarthritis. The distinct immune profiles and involvement in fat metabolism pathways associated with TOX3 expression suggest its significance in Osteoarthritis pathogenesis. The study establishes a basis for comprehending the intricate correlation between characteristic genes and Osteoarthritis, as well as for the formulation of individualized therapeutic approaches.
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Affiliation(s)
- Zhengyan Wang
- College of Traditional Chinese Medicine, Changchun University of Chinese Medicine, Changchun, China
| | - Shuang Ding
- Department of Orthopedics, The Affiliated Hospital of Changchun University of Chinese Medicine, Changchun, China
| | | | - Hongsheng Zhan
- Department of Orthopedics, Shuguang Hospital, Shanghai, China
| | - Yunfei Li
- College of Traditional Chinese Medicine, Changchun University of Chinese Medicine, Changchun, China
| | - Jing Yan
- College of Traditional Chinese Medicine, Changchun University of Chinese Medicine, Changchun, China
| | - Yuyan Jia
- Department of Orthopedics, The Affiliated Hospital of Changchun University of Chinese Medicine, Changchun, China
| | - Xukai Wang
- Department of Orthopedics, The Affiliated Hospital of Changchun University of Chinese Medicine, Changchun, China
| | - Ying Wang
- Department of Orthopedics, The Affiliated Hospital of Changchun University of Chinese Medicine, Changchun, China
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31
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Hou S, Zhang J, Chi X, Li X, Zhang Q, Kang C, Shan H. Roles of DSCC1 and GINS1 in gastric cancer. Medicine (Baltimore) 2023; 102:e35681. [PMID: 37904396 PMCID: PMC10615490 DOI: 10.1097/md.0000000000035681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Accepted: 09/26/2023] [Indexed: 11/01/2023] Open
Abstract
Gastric carcinoma is a common malignant tumor originating from gastric mucosal epithelium. However, role of DS-cell cycle-dependent protein 1 (DSCC1) and GINS1 in gastric carcinoma remains unclear. The gastric carcinoma datasets GSE79973 and GSE118916 were downloaded from gene expression omnibus. Multiple datasets were merged and batched. Differentially expressed genes (DEGs) were screened and weighted gene co-expression network analysis was performed. Functional enrichment analysis, gene set enrichment analysis and immune infiltration analysis were performed. Construction and analysis of protein-protein interaction Network. Survival analysis and comparative toxicogenomics database were performed. A heat map of gene expression was drawn. Target Scan screen miRNAs regulating DEGs. Two thousand forty-four DEGs were identified. According to gene ontology analysis, in biological process, they were mainly enriched in cell migration, transforming growth factor β receptor signaling pathway, angiogenesis, and steroid metabolism process. In cellular component, they were mainly enriched in extracellular vesicles, basement membrane, endoplasmic reticulum lumen, and extracellular space. In molecular function, they focused on extracellular matrix structural components, protein binding, platelet-derived growth factor binding, and catalytic activity. In Kyoto encyclopedia of genes and genomes, they were mainly enriched in protein digestion and absorption, metabolic pathways, fatty acid degradation, Glycerophospholipid metabolism, ether lipid metabolism. Gene set enrichment analysis showed that DEGs were mainly enriched in transforming growth factor β receptor signaling pathway, steroid metabolism process, basement membrane, endoplasmic reticulum lumen, structural components of extracellular matrix, platelet-derived growth factor binding, Glycerophospholipid metabolism, ether lipid metabolism. The results of immune infiltration analysis showed that expression of T cell CD4 memory resting was lower in the samples of gastric cancer. The core genes (TRIP13, CHEK1, DSCC1, GINS1) are protective factors, their expression shows a downward trend with increase of risk score. Comparative toxicogenomics database analysis showed that TRIP13, CHEK1, DSCC1, GINS1 were related to gastric tumors, gastric diseases, tumors, inflammation, and necrosis. DSCC1 and GINS1 are highly expressed in gastric cancer. Higher expression levels of DSCC1 and GINS1, worse the prognosis.
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Affiliation(s)
- Shiyang Hou
- Department of General Surgery, Beijing Rehabilitation Hospital Affiliated to Capital Medical University, Xixia Zhuang, Badachu, Shijingshan District, Beijing, China
| | - Jie Zhang
- Department of General Surgery, Beijing Rehabilitation Hospital Affiliated to Capital Medical University, Xixia Zhuang, Badachu, Shijingshan District, Beijing, China
| | - Xiaoqian Chi
- Department of General Surgery, Beijing Rehabilitation Hospital Affiliated to Capital Medical University, Xixia Zhuang, Badachu, Shijingshan District, Beijing, China
| | - Xiaowei Li
- Department of General Surgery, Beijing Rehabilitation Hospital Affiliated to Capital Medical University, Xixia Zhuang, Badachu, Shijingshan District, Beijing, China
| | - Qijun Zhang
- Department of General Surgery, Beijing Rehabilitation Hospital Affiliated to Capital Medical University, Xixia Zhuang, Badachu, Shijingshan District, Beijing, China
| | - Chunbo Kang
- Department of General Surgery, Beijing Rehabilitation Hospital Affiliated to Capital Medical University, Xixia Zhuang, Badachu, Shijingshan District, Beijing, China
| | - Haifeng Shan
- Department of General Surgery, Beijing Rehabilitation Hospital Affiliated to Capital Medical University, Xixia Zhuang, Badachu, Shijingshan District, Beijing, China
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Yang Y, Li JH, Yao BC, Chen QL, Jiang N, Wang LQ, Guo ZG. NDUFB11 and NDUFS3 play a role in atherosclerosis and chronic stress. Aging (Albany NY) 2023; 15:8026-8043. [PMID: 37642954 PMCID: PMC10496984 DOI: 10.18632/aging.204947] [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: 05/11/2023] [Accepted: 07/18/2023] [Indexed: 08/31/2023]
Abstract
OBJECTIVE Atherosclerosis is characterized by the formation of fibrofatty plaques in the intima of arteries, resulting in thickening of the vessel wall and narrowing of the lumen. Chronic stress refers to individuals in a state of long-term chronic stress. However, the relationship between NDUFB11 and NDUFS3 and atherosclerosis and chronic stress is unclear. METHOD The atherosclerosis with chronic stress group data file was used. DEGs were screened and WGCNA was performed. Construction and analysis of PPI Network. Functional enrichment analysis, GSEA, gene expression heatmap, immune infiltration analysis and mRNA analysis were performed. CTD was used to find diseases most related to core genes. WB was performed. TargetScan was used to screen miRNAs of DEGs. RESULTS 1708 DEGs were identified. According to GO analysis, they were mainly enriched in catabolic processes, organic acid metabolism processes, carboxylic acid metabolism processes. KEGG analysis showed that they were mainly enriched in metabolic pathways, fatty acid metabolism, pentose phosphate pathway, glycolysis / gluconeogenesis, fructose and mannose metabolism. Gene expression heatmap showed that the core genes (NDUFB11, NDUFS3) were lowly expressed in samples of those with atherosclerosis accompanied by chronic stress and highly expressed in the normal samples. NDUFB11 and NDUFS3 were associated with necrosis, hyperplasia, inflammation, renal disease, weight loss, memory impairment, and cognitive impairment. WB showed that the expression level of NDUFS3 in atherosclerosis and chronic stress was lower than that in control group. CONCLUSIONS NDUFB11 and NDUFS3 are underexpressed in atherosclerosis and chronic stress; the lower NDUFB11 and NDUFS3 levels, the worse the prognosis.
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Affiliation(s)
- Yin Yang
- Clinical School of Thoracic, Tianjin Medical University, Tianjin Chest Hospital, Jinnan, Tianjin 300222, P.R. China
| | - Jing-Hui Li
- Clinical School of Thoracic, Tianjin Medical University, Tianjin Chest Hospital, Jinnan, Tianjin 300222, P.R. China
| | - Bo-Chen Yao
- Clinical School of Thoracic, Tianjin Medical University, Tianjin Chest Hospital, Jinnan, Tianjin 300222, P.R. China
| | - Qing-Liang Chen
- Clinical School of Thoracic, Tianjin Medical University, Tianjin Chest Hospital, Jinnan, Tianjin 300222, P.R. China
| | - Nan Jiang
- Clinical School of Thoracic, Tianjin Medical University, Tianjin Chest Hospital, Jinnan, Tianjin 300222, P.R. China
| | - Lian-Qun Wang
- Clinical School of Thoracic, Tianjin Medical University, Tianjin Chest Hospital, Jinnan, Tianjin 300222, P.R. China
| | - Zhi-Gang Guo
- Clinical School of Thoracic, Tianjin Medical University, Tianjin Chest Hospital, Jinnan, Tianjin 300222, P.R. China
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Ma S, Wang Z, Li C, Liu Z, Zhang X, Li L, An F, Qiao X. CEACAM1 as a molecular target in oral cancer. Aging (Albany NY) 2023; 15:8137-8154. [PMID: 37589542 PMCID: PMC10497000 DOI: 10.18632/aging.204960] [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: 05/15/2023] [Accepted: 07/24/2023] [Indexed: 08/18/2023]
Abstract
OBJECTIVE The majority of oral cancer is caused by malignant transformation of squamous cells in surface of the oral mucosa. However, the relationship between CEACAM1 and oral cancer is unclear. METHODS GSE23558 and GSE25099 profiles were downloaded from gene expression omnibus (GEO). Differentially expressed genes (DEGs) were screened and weighted gene co-expression network analysis (WGCNA) was performed. Construction and analysis of protein-protein interaction (PPI) Network. Gene Ontology (GO) and Kyoto Encyclopedia of Gene and Genome (KEGG), gene set enrichment analysis (GSEA), gene expression heatmap, immune infiltration analysis, comparative toxicogenomics database (CTD) were performed. TargetScan screened miRNAs that regulated central DEGs. Western blotting (WB) experiment was performed. RESULTS 1269 DEGs were identified. According to GO analysis, they were mainly enriched in same protein binding, signal receptor binding, cell surface, epithelial cell development. KEGG analysis showed that they were mainly enriched in cancer pathways, PI3K Akt signaling pathway, TNF signaling pathway, NF kappa B signaling pathway, TGF beta signaling pathway. PPI network showed that 11 genes (CDCA8, CCNA2, MELK, KIF2C, CDC45, HMMR, TPX2, CENPF, CDK1, CEP55, CEACAM1) were obtained. Gene expression heatmap showed that CEP55 and MELK were highly expressed in oral cancer samples. CEACAM1 was lowly expressed in oral cancer samples. CEACAM1, CEP55 and MELK were involved in tumor, inflammation, necrosis, and proliferation. Western blotting (WB) showed that CEACAM1 in oral cancer samples was lower than that in normal samples, after CEACAM1 knockdown, it was lower than that in oral cancer samples. CONCLUSION CEACAM1 is lowly expressed in oral cancer, the lower CEACAM1, the worse prognosis.
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Affiliation(s)
- Sai Ma
- Department of Stomatology, The First Affiliated Hospital of Hebei North University, Zhangjiakou, Hebei 075000, China
| | - Zhonghua Wang
- Department of Stomatology, The First Affiliated Hospital of Hebei North University, Zhangjiakou, Hebei 075000, China
| | - Chao Li
- Department of Stomatology, The First Affiliated Hospital of Hebei North University, Zhangjiakou, Hebei 075000, China
| | - Zhenli Liu
- Department of Stomatology, The First Affiliated Hospital of Hebei North University, Zhangjiakou, Hebei 075000, China
| | - Xuan Zhang
- Department of Stomatology, The First Affiliated Hospital of Hebei North University, Zhangjiakou, Hebei 075000, China
| | - Liheng Li
- Department of Stomatology, The First Affiliated Hospital of Hebei North University, Zhangjiakou, Hebei 075000, China
| | - Feng An
- Department of Stomatology, The First Affiliated Hospital of Hebei North University, Zhangjiakou, Hebei 075000, China
| | - Xiaoli Qiao
- Department of Central Sterile Supply, The First Affiliated Hospital of Hebei North University, Zhangjiakou, Hebei 075000, China
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Assress H, Ferruzzi MG, Lan RS. Optimization of Mass Spectrometric Parameters in Data Dependent Acquisition for Untargeted Metabolomics on the Basis of Putative Assignments. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:1621-1631. [PMID: 37419493 PMCID: PMC10402710 DOI: 10.1021/jasms.3c00084] [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: 03/02/2023] [Revised: 06/19/2023] [Accepted: 06/21/2023] [Indexed: 07/09/2023]
Abstract
Optimization of mass spectrometric parameters for a data dependent acquisition (DDA) experiment is essential to increase the MS/MS coverage and hence increase metabolite identifications in untargeted metabolomics. We explored the influence of mass spectrometric parameters including mass resolution, radio frequency (RF) level, signal intensity threshold, number of MS/MS events, cycle time, collision energy, maximum ion injection time (MIT), dynamic exclusion, and automatic gain control (AGC) target value on metabolite annotations on an Exploris 480-Orbitrap mass spectrometer. Optimal annotation results were obtained by performing ten data dependent MS/MS scans with a mass isolation window of 2.0 m/z and a minimum signal intensity threshold of 1 × 104 at a mass resolution of 180,000 for MS and 30,000 for MS/MS, while maintaining the RF level at 70%. Furthermore, combining an AGC target value of 5 × 106 and MIT of 100 ms for MS and an AGC target value of 1 × 105 and an MIT of 50 ms for MS/MS scans provided an improved number of annotated metabolites. A 10 s exclusion duration and a two stepped collision energy were optimal for higher spectral quality. These findings confirm that MS parameters do influence metabolomics results, and propose strategies for increasing metabolite coverage in untargeted metabolomics. A limitation of this work is that our parameters were only optimized for one RPLC method on single matrix and may be different for other protocols. Additionally, no metabolites were identified at level 1 confidence. The results presented here are based on metabolite annotations and need to be validated with authentic standards.
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Affiliation(s)
- Hailemariam
Abrha Assress
- Arkansas
Children’s Nutrition Center, Little Rock, Arkansas 72202, United States
- Department
of Pediatrics, University of Arkansas for
Medical Sciences, Little
Rock, Arkansas 72205, United States
| | - Mario G. Ferruzzi
- Arkansas
Children’s Nutrition Center, Little Rock, Arkansas 72202, United States
- Department
of Pediatrics, University of Arkansas for
Medical Sciences, Little
Rock, Arkansas 72205, United States
| | - Renny S. Lan
- Arkansas
Children’s Nutrition Center, Little Rock, Arkansas 72202, United States
- Department
of Pediatrics, University of Arkansas for
Medical Sciences, Little
Rock, Arkansas 72205, United States
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Ozcariz E, Guardiola M, Amigó N, Rojo-Martínez G, Valdés S, Rehues P, Masana L, Ribalta J. NMR-based metabolomic profiling identifies inflammation and muscle-related metabolites as predictors of incident type 2 diabetes mellitus beyond glucose: the Di@bet.es study. Diabetes Res Clin Pract 2023; 202:110772. [PMID: 37301326 DOI: 10.1016/j.diabres.2023.110772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 05/26/2023] [Accepted: 06/03/2023] [Indexed: 06/12/2023]
Abstract
AIMS The aim of this study was to combine nuclear magnetic resonance-based metabolomics and machine learning to find a glucose-independent molecular signature associated with future type 2 diabetes mellitus development in a subgroup of individuals from the Di@bet.es study. METHODS The study group included 145 individuals developing type 2 diabetes mellitus during the 8-year follow-up, 145 individuals matched by age, sex and BMI who did not develop diabetes during the follow-up but had equal glucose concentrations to those who did and 145 controls matched by age and sex. A metabolomic analysis of serum was performed to obtain the lipoprotein and glycoprotein profiles and 15 low molecular weight metabolites. Several machine learning-based models were trained. RESULTS Logistic regression performed the best classification between individuals developing type 2 diabetes during the follow-up and glucose-matched individuals. The area under the curve was 0.628, and its 95% confidence interval was 0.510-0.746. Glycoprotein-related variables, creatinine, creatine, small HDL particles and the Johnson-Neyman intervals of the interaction of Glyc A and Glyc B were statistically significant. CONCLUSIONS The model highlighted a relevant contribution of inflammation (glycosylation pattern and HDL) and muscle (creatinine and creatine) in the development of type 2 diabetes as independent factors of hyperglycemia.
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Affiliation(s)
- Enrique Ozcariz
- Biosfer Teslab, Plaça del Prim 10, 2on 5a, 43201 Reus, Spain.
| | - Montse Guardiola
- CIBER de Diabetes y Enfermedades Metabólicas Asociadas, Instituto de Salud Carlos III, Madrid, Spain; Institut d'Investigació Sanitària Pere Virgili (IISPV), Reus, Spain; Universitat Rovira i Virgili, Departament de Medicina i Cirurgia, Unitat de Recerca en Lípids i Arteriosclerosi, Reus, Spain.
| | - Núria Amigó
- Biosfer Teslab, Plaça del Prim 10, 2on 5a, 43201 Reus, Spain; CIBER de Diabetes y Enfermedades Metabólicas Asociadas, Instituto de Salud Carlos III, Madrid, Spain; Institut d'Investigació Sanitària Pere Virgili (IISPV), Reus, Spain; Universitat Rovira i Virgili, Departament de Ciències Mèdiques Bàsiques, Reus, Spain; Universitat Rovira i Virgili, Metabolomics Platform, Reus Spain.
| | - Gemma Rojo-Martínez
- CIBER de Diabetes y Enfermedades Metabólicas Asociadas, Instituto de Salud Carlos III, Madrid, Spain; UGC Endocrinología y Nutrición. Hospital Regional Universitario de Málaga, Málaga, Spain; Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina-IBIMA Plataforma BIONAND, Málaga, Spain.
| | - Sergio Valdés
- CIBER de Diabetes y Enfermedades Metabólicas Asociadas, Instituto de Salud Carlos III, Madrid, Spain; UGC Endocrinología y Nutrición. Hospital Regional Universitario de Málaga, Málaga, Spain; Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina-IBIMA Plataforma BIONAND, Málaga, Spain.
| | - Pere Rehues
- CIBER de Diabetes y Enfermedades Metabólicas Asociadas, Instituto de Salud Carlos III, Madrid, Spain; Institut d'Investigació Sanitària Pere Virgili (IISPV), Reus, Spain; Universitat Rovira i Virgili, Departament de Medicina i Cirurgia, Unitat de Recerca en Lípids i Arteriosclerosi, Reus, Spain.
| | - Lluís Masana
- CIBER de Diabetes y Enfermedades Metabólicas Asociadas, Instituto de Salud Carlos III, Madrid, Spain; Institut d'Investigació Sanitària Pere Virgili (IISPV), Reus, Spain; Universitat Rovira i Virgili, Departament de Medicina i Cirurgia, Unitat de Recerca en Lípids i Arteriosclerosi, Reus, Spain.
| | - Josep Ribalta
- CIBER de Diabetes y Enfermedades Metabólicas Asociadas, Instituto de Salud Carlos III, Madrid, Spain; Institut d'Investigació Sanitària Pere Virgili (IISPV), Reus, Spain; Universitat Rovira i Virgili, Departament de Medicina i Cirurgia, Unitat de Recerca en Lípids i Arteriosclerosi, Reus, Spain.
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Mu C, Zhao Q, Zhao Q, Yang L, Pang X, Liu T, Li X, Wang B, Fung SY, Cao H. Multi-omics in Crohn's disease: New insights from inside. Comput Struct Biotechnol J 2023; 21:3054-3072. [PMID: 37273853 PMCID: PMC10238466 DOI: 10.1016/j.csbj.2023.05.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 05/10/2023] [Accepted: 05/11/2023] [Indexed: 06/06/2023] Open
Abstract
Crohn's disease (CD) is an inflammatory bowel disease (IBD) with complex clinical manifestations such as chronic diarrhea, weight loss and hematochezia. Despite the increasing incidence worldwide, cure of CD remains extremely difficult. The rapid development of high-throughput sequencing technology with integrated-omics analyses in recent years has provided a new means for exploring the pathogenesis, mining the biomarkers and designing targeted personalized therapeutics of CD. Host genomics and epigenomics unveil heredity-related mechanisms of susceptible individuals, while microbiome and metabolomics map host-microbe interactions in CD patients. Proteomics shows great potential in searching for promising biomarkers. Nonetheless, single omics technology cannot holistically connect the mechanisms with heterogeneity of pathological behavior in CD. The rise of multi-omics analysis integrates genetic/epigenetic profiles with protein/microbial metabolite functionality, providing new hope for comprehensive and in-depth exploration of CD. Herein, we emphasized the different omics features and applications of CD and discussed the current research and limitations of multi-omics in CD. This review will update and deepen our understanding of CD from integration of broad omics spectra and will provide new evidence for targeted individualized therapeutics.
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Affiliation(s)
- Chenlu Mu
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Qianjing Zhao
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Qing Zhao
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Lijiao Yang
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Xiaoqi Pang
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Tianyu Liu
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Xiaomeng Li
- Department of Immunology, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Science, Tianjin Medical University, Tianjin, China
| | - Bangmao Wang
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Shan-Yu Fung
- Department of Immunology, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Science, Tianjin Medical University, Tianjin, China
| | - Hailong Cao
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
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Zhang J, Fang XY, Leng R, Chen HF, Qian TT, Cai YY, Zhang XH, Wang YY, Mu M, Tao XR, Leng RX, Ye DQ. Metabolic signature of healthy lifestyle and risk of rheumatoid arthritis: observational and Mendelian randomization study. Am J Clin Nutr 2023:S0002-9165(23)48892-2. [PMID: 37127109 DOI: 10.1016/j.ajcnut.2023.04.034] [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: 02/05/2023] [Revised: 04/10/2023] [Accepted: 04/26/2023] [Indexed: 05/03/2023] Open
Abstract
BACKGROUND While substantial evidence reveals that healthy lifestyle behaviors are associated with a lower risk of rheumatoid arthritis (RA), the underlying metabolic mechanisms remain unclear. OBJECTIVES This study aimed to identify the metabolic signature reflecting a healthy lifestyle and investigate its observational and genetic linkage with RA risk. METHODS This study included 87,258 UK Biobank participants (557 cases of incident RA) aged 37 to 73 years with complete lifestyle, genotyping and nuclear magnetic resonance (NMR) metabolomics data. A healthy lifestyle was assessed based on five factors: healthy diet, regular exercise, not smoking, moderate alcohol consumption, and normal body mass index. The metabolic signature was developed by summing selected metabolites' concentrations weighted by the coefficients using elastic net regression. We used multivariate Cox model to assess the associations between metabolic signatures and RA risk, and examined the mediating role of the metabolic signature in the impact of a healthy lifestyle on RA. We performed genome-wide association analysis (GWAS) to obtain genetic variants associated with the metabolic signature, then conducted Mendelian randomization (MR) analyses to detect causality. RESULTS The metabolic signature comprised of 81 metabolites, robustly correlated with healthy lifestyle ( r = 0.45, P = 4.2 × 10-15). The metabolic signature was inversely associated with RA risk (HR per SD increment: 0.76, 95% CI: 0.70-0.83), and largely explained protective effects of healthy lifestyle on RA with 64% (95%CI: 50.4-83.3) mediation proportion. One and two-sample MR analyses also consistently showed the associations of genetically inferred per SD increment in metabolic signature with a reduction in RA risk (HR: 0.84, 95% CI: 0.75-0.94, P = 0.002 and OR: 0.84, 95% CI: 0.73-0.97, P = 0.02 respectively). CONCLUSION Our findings implicate the metabolic signature reflecting healthy lifestyle as a potential causal mediator in the development of RA, highlighting the importance of early lifestyle intervention and metabolic tracking for precise prevention of RA.
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Affiliation(s)
- Jie Zhang
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, 230032, China; Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui, 230032, China
| | - Xin-Yu Fang
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, 230032, China; Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui, 230032, China
| | - Rui Leng
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, 230032, China; Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui, 230032, China
| | - Hai-Feng Chen
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, 230032, China; Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui, 230032, China
| | - Ting-Ting Qian
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, 230032, China; Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui, 230032, China
| | - Yu-Yu Cai
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, 230032, China; Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui, 230032, China
| | - Xin-Hong Zhang
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, 230032, China; Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui, 230032, China
| | - Yi-Yu Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, 230032, China; Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui, 230032, China
| | - Min Mu
- School of Public Health, Anhui University of Science and Technology, Huainan, Anhui, 232001, China
| | - Xin-Rong Tao
- School of Public Health, Anhui University of Science and Technology, Huainan, Anhui, 232001, China
| | - Rui-Xue Leng
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, 230032, China; Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui, 230032, China.
| | - Dong-Qing Ye
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, 230032, China; Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui, 230032, China; School of Public Health, Anhui University of Science and Technology, Huainan, Anhui, 232001, China.
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Qiu S, Cai Y, Yao H, Lin C, Xie Y, Tang S, Zhang A. Small molecule metabolites: discovery of biomarkers and therapeutic targets. Signal Transduct Target Ther 2023; 8:132. [PMID: 36941259 PMCID: PMC10026263 DOI: 10.1038/s41392-023-01399-3] [Citation(s) in RCA: 104] [Impact Index Per Article: 104.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 03/01/2023] [Accepted: 03/03/2023] [Indexed: 03/22/2023] Open
Abstract
Metabolic abnormalities lead to the dysfunction of metabolic pathways and metabolite accumulation or deficiency which is well-recognized hallmarks of diseases. Metabolite signatures that have close proximity to subject's phenotypic informative dimension, are useful for predicting diagnosis and prognosis of diseases as well as monitoring treatments. The lack of early biomarkers could lead to poor diagnosis and serious outcomes. Therefore, noninvasive diagnosis and monitoring methods with high specificity and selectivity are desperately needed. Small molecule metabolites-based metabolomics has become a specialized tool for metabolic biomarker and pathway analysis, for revealing possible mechanisms of human various diseases and deciphering therapeutic potentials. It could help identify functional biomarkers related to phenotypic variation and delineate biochemical pathways changes as early indicators of pathological dysfunction and damage prior to disease development. Recently, scientists have established a large number of metabolic profiles to reveal the underlying mechanisms and metabolic networks for therapeutic target exploration in biomedicine. This review summarized the metabolic analysis on the potential value of small-molecule candidate metabolites as biomarkers with clinical events, which may lead to better diagnosis, prognosis, drug screening and treatment. We also discuss challenges that need to be addressed to fuel the next wave of breakthroughs.
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Affiliation(s)
- Shi Qiu
- International Advanced Functional Omics Platform, Scientific Experiment Center, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), College of Chinese Medicine, Hainan Medical University, Xueyuan Road 3, Haikou, 571199, China
| | - Ying Cai
- Graduate School, Heilongjiang University of Chinese Medicine, Harbin, 150040, China
| | - Hong Yao
- First Affiliated Hospital, Harbin Medical University, Harbin, 150081, China
| | - Chunsheng Lin
- Second Affiliated Hospital, Heilongjiang University of Chinese Medicine, Harbin, 150001, China
| | - Yiqiang Xie
- International Advanced Functional Omics Platform, Scientific Experiment Center, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), College of Chinese Medicine, Hainan Medical University, Xueyuan Road 3, Haikou, 571199, China.
| | - Songqi Tang
- International Advanced Functional Omics Platform, Scientific Experiment Center, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), College of Chinese Medicine, Hainan Medical University, Xueyuan Road 3, Haikou, 571199, China.
| | - Aihua Zhang
- International Advanced Functional Omics Platform, Scientific Experiment Center, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), College of Chinese Medicine, Hainan Medical University, Xueyuan Road 3, Haikou, 571199, China.
- Graduate School, Heilongjiang University of Chinese Medicine, Harbin, 150040, China.
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Fu J, Zhu F, Xu CJ, Li Y. Metabolomics meets systems immunology. EMBO Rep 2023; 24:e55747. [PMID: 36916532 PMCID: PMC10074123 DOI: 10.15252/embr.202255747] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 12/24/2022] [Accepted: 02/24/2023] [Indexed: 03/16/2023] Open
Abstract
Metabolic processes play a critical role in immune regulation. Metabolomics is the systematic analysis of small molecules (metabolites) in organisms or biological samples, providing an opportunity to comprehensively study interactions between metabolism and immunity in physiology and disease. Integrating metabolomics into systems immunology allows the exploration of the interactions of multilayered features in the biological system and the molecular regulatory mechanism of these features. Here, we provide an overview on recent technological developments of metabolomic applications in immunological research. To begin, two widely used metabolomics approaches are compared: targeted and untargeted metabolomics. Then, we provide a comprehensive overview of the analysis workflow and the computational tools available, including sample preparation, raw spectra data preprocessing, data processing, statistical analysis, and interpretation. Third, we describe how to integrate metabolomics with other omics approaches in immunological studies using available tools. Finally, we discuss new developments in metabolomics and its prospects for immunology research. This review provides guidance to researchers using metabolomics and multiomics in immunity research, thus facilitating the application of systems immunology to disease research.
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Affiliation(s)
- Jianbo Fu
- Centre for Individualised Infection Medicine (CiiM), a joint venture between the Helmholtz Centre for Infection Research (HZI) and Hannover Medical School (MHH), Hannover, Germany.,TWINCORE Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany.,College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Feng Zhu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Cheng-Jian Xu
- Centre for Individualised Infection Medicine (CiiM), a joint venture between the Helmholtz Centre for Infection Research (HZI) and Hannover Medical School (MHH), Hannover, Germany.,TWINCORE Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany.,Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Yang Li
- Centre for Individualised Infection Medicine (CiiM), a joint venture between the Helmholtz Centre for Infection Research (HZI) and Hannover Medical School (MHH), Hannover, Germany.,TWINCORE Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany.,Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
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Wang H, Li T, Shi H, Su M, Liu Z, Zhang Y, Ma Y. Analyses of widely targeted metabolic profiling reveals mechanisms of metabolomic variations during Tibetan sheep (Ovis aries) testis development. Theriogenology 2023; 197:116-126. [PMID: 36502589 DOI: 10.1016/j.theriogenology.2022.11.041] [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: 05/31/2022] [Revised: 11/25/2022] [Accepted: 11/25/2022] [Indexed: 11/29/2022]
Abstract
In mammals, the testis is the organ with the highest transcriptional activity. After gene transcription, translation, and post-translational protein modification, the transcriptional results are finally presented at the metabolic level. Metabolites not only essential for cell signaling and energy transfer, but also directly influenced by the physiological and pathological changes in tissues and accurately reflect the physiological changes. The fact that the testes are oxygen-deprived organs can explain why Sertoli cells and germ cells may use distinctive metabolic pathways to obtain energy in their different stages of development. Therefore, studying metabolic changes during testis development can better elucidate metabolic profile of the testis, which is essential to revealing characteristic metabolic pathways. The present study applied a widely targeted UPLC-MS/MS-based metabolomics approach with large-scale detection, identification and quantification to investigate the widespread metabolic changes during Tibetan sheep testis development. Firstly, a total of 847 metabolites were detected in the sheep testis, and their changes along with the three testis-development stages were further investigated. The results indicated that those metabolites were clustered into amino acids and their derivatives, carbohydrates and their derivatives, organic acids and their derivatives, benzene and substituted derivatives, alcohols and amines, lipids, nucleotides and their derivatives, bile acids, coenzymes and vitamins, hormones and hormone-related compounds, etc. Among them, the most abundant metabolites in the testis were amino acids and lipid metabolites. The results showed that most of the lipids, carbohydrates with their derivatives, as well as alcohol and amines metabolites were high in sexually immature sheep while organic acids, amino acids and nucleotides showed a continuously increasing trend along with testis development stages. Among them, the content of metabolites with antioxidant effects increased along with testis development, while those related with energy synthesis was downregulated with age. Further correlation analyses of each metabolite-metabolite pair emphasized the cross talk between differential metabolisms across testis development, suggesting a significant correlation between lipids and other metabolites. Finally, based on KEGG pathway analysis, we found that the metabolic pathways in Tibetan sheep testis development were mainly clustered into energy metabolism, gonadal development, and anti-oxidative stress. Reactive oxygen species (ROS) are by-products of normal cellular metabolism and are inevitable during testicular energy metabolism. Thus, the anti-oxidative stress function is a key process in maintaining the normal physiological function of testis. These results contributed to a broader view of the testis metabolome and a comprehensive analysis on metabolomic variation among different testis-development stages, providing a theoretical basis for us to understand the sheep testis metabolic mechanism.
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Affiliation(s)
- Huihui Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Taotao Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Huibin Shi
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Manchun Su
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Zilong Liu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Yong Zhang
- Gansu Key Laboratory of Animal Generational Physiology and Reproductive Regulation, Lanzhou, 730070, China; College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, 730070, China
| | - Youji Ma
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China; Gansu Key Laboratory of Animal Generational Physiology and Reproductive Regulation, Lanzhou, 730070, China.
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Li B, Li H, Zhang L, Ren T, Meng J. Expression analysis of human glioma susceptibility gene and P53 in human glioma and its clinical significance based on bioinformatics. ANNALS OF TRANSLATIONAL MEDICINE 2023; 11:53. [PMID: 36819578 PMCID: PMC9929792 DOI: 10.21037/atm-22-5646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 12/07/2022] [Indexed: 01/18/2023]
Abstract
Background The exact mechanism of glioblastoma multiforme (GBM) remains unclear. This study was to clarify the expression of P53 in glioma and its molecular mechanism, and to explore the possibility of P53 as a potential therapeutic target of glioma and its clinical application value, so as to provide a new theoretical basis for the treatment of glioma. Methods Firstly, a dataset was established to analyze the expression of P53 in different stages of glioma and its relationship with prognosis by using The Cancer Genome Atlas (TCGA) database, RNA-seq data, and survival data of glioma and normal control samples in gene expression profiling and interactive analysis (GEPIA). The genes co-expressed with P53 were screened out, their differential expression between glioma and normal control group was analyzed, and their functions were analyzed by enrichment analysis. The TGGA database was used for data verification and analysis. The correlation between P53 expression and clinicopathological parameters was analyzed. Kaplan-Meier survival analysis was used to analyze the relationship between P53 expression and overall survival (OS) and progression-free survival (PFS) of glioma patients, and Cox regression analysis was used to analyze the independent factors affecting OS and PFS of glioma patients. Results The results of TCGA data analysis were as follows: The expression level of P53 was different from that of different stages of glioma, namely, the expression level of P53 between grade II and grade III, grade III and grade IV, and grade II and grade IV were significantly different (P<0.05). The results of P53 gene-related survival analysis showed that KNL1 high expression and low expression were significantly different in OS, and the high expression group was associated with poor prognosis (P<0.05). Conclusions The P53 expression can be an effective biological indicator of poor prognosis of glioma.
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Affiliation(s)
- Baiyu Li
- Department of Neurology Care Ward, Gansu Provincial Hospital, Lanzhou, China
| | - Hang Li
- Department of Geriatrics, Chengdu Eighth People's Hospital (Geriatric Hospital of Chengdu Medical College), Chengdu, China
| | - Linghui Zhang
- Department of Internal Medicine, Department of Clinical Medicine, Shijiazhuang Medical College, Shijiazhuang, China
| | - Taowen Ren
- Department of Neurology Care Ward, Gansu Provincial Hospital, Lanzhou, China
| | - Jie Meng
- Department of Psychiatry, The Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
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Jenkins CL, Bean HD. Current Limitations of Staph Infection Diagnostics, and the Role for VOCs in Achieving Culture-Independent Detection. Pathogens 2023; 12:pathogens12020181. [PMID: 36839453 PMCID: PMC9963134 DOI: 10.3390/pathogens12020181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 01/19/2023] [Accepted: 01/20/2023] [Indexed: 01/26/2023] Open
Abstract
Staphylococci are broadly adaptable and their ability to grow in unique environments has been widely established, but the most common and clinically relevant staphylococcal niche is the skin and mucous membranes of mammals and birds. S. aureus causes severe infections in mammalian tissues and organs, with high morbidities, mortalities, and treatment costs. S. epidermidis is an important human commensal but is also capable of deadly infections. Gold-standard diagnostic methods for staph infections currently rely upon retrieval and characterization of the infectious agent through various culture-based methods. Yet, obtaining a viable bacterial sample for in vitro identification of infection etiology remains a significant barrier in clinical diagnostics. The development of volatile organic compound (VOC) profiles for the detection and identification of pathogens is an area of intensive research, with significant efforts toward establishing breath tests for infections. This review describes the limitations of existing infection diagnostics, reviews the principles and advantages of VOC-based diagnostics, summarizes the analytical tools for VOC discovery and clinical detection, and highlights examples of how VOC biomarkers have been applied to diagnosing human and animal staph infections.
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Affiliation(s)
- Carrie L. Jenkins
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ 85287, USA
| | - Heather D. Bean
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
- Center for Fundamental and Applied Microbiomics, The Biodesign Institute, Tempe, AZ 85287, USA
- Correspondence:
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Hristova J, Svinarov D. Enhancing precision medicine through clinical mass spectrometry platform. BIOTECHNOL BIOTEC EQ 2022. [DOI: 10.1080/13102818.2022.2053342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Affiliation(s)
- Julieta Hristova
- Alexander University Hospital, Faculty of Medicine, Medical University of Sofia, Sofia, Bulgaria
| | - Dobrin Svinarov
- Alexander University Hospital, Faculty of Medicine, Medical University of Sofia, Sofia, Bulgaria
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Liu ZM, Bao Y, Li TK, Di YB, Song WJ. MKI67 an potential oncogene of oral squamous cell carcinoma via the high throughput technology. Medicine (Baltimore) 2022; 101:e32595. [PMID: 36596059 PMCID: PMC9803484 DOI: 10.1097/md.0000000000032595] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Oral squamous cell carcinoma is a malignant tumor that occurs in the oral cavity, with poor prognosis and easy recurrence. However, the relationship between MKI67 and oral squamous cell carcinoma remains unclear. The oral squamous cell carcinoma datasets GSE138206, GSE146483 and GSE184616 were downloaded from the gene expression omnibus database, and the differentially expressed genes (DEGs) were screened. The protein-protein interaction network was constructed and analyzed by search tool for the retrieval of interacting genes database and Cytoscape software. Gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) were used for functional enrichment analysis. GO and KEGG analyses were performed on the whole genome, as formulated by gene set enrichment analysis. comparative toxicogenomics database was used to identify the diseases most associated with the core genes. TargetScan was used to screen miRNA regulating central DEGs. A total of 1472 DEGs were identified. GO analysis showed that the differentially expressed genes were mainly enriched in the tissues of extracellular matrix, type i interferon signaling pathway, human papillomavirus infection, adhesion spot, hepatitis C and ECM-receptor interaction. Enrichment items were similar to GO and KEGG enrichment items of differentially expressed genes. 10 core genes were obtained, and their expression was different between oral squamous cell carcinoma and normal tissue samples. MKI67 is highly expressed in oral squamous cell carcinoma and may be an oncogene in oral squamous cell carcinoma.
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Affiliation(s)
- Zhe-Min Liu
- Department of Stomatology, Shijiazhuang Xingye Shengrui Stomatological Hospital, Shijlazhuang, Hebei Province, PR China
| | - Yang Bao
- Department of Stomatology, The Fourth Hospital of Hebei Medical University, Shijlazhuang,Hebei Province, PR China
- * Correspondence: Yang Bao, Department of Stomatology, The Fourth Hospital of Hebei Medical University, Changan District Health Road 12, Shijlazhuang, Hebei Province 050011, PR China (e-mail: )
| | - Tian-Ke Li
- Department of Stomatology, The Fourth Hospital of Hebei Medical University, Shijlazhuang,Hebei Province, PR China
| | - Yong-Bin Di
- Department of Stomatology, The First Hospital of Hebei Medical University, Shijlazhuang,Hebei Province, PR China
| | - Wei-Jing Song
- Department of Stomatology, The Fourth Hospital of Hebei Medical University, Shijlazhuang,Hebei Province, PR China
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Ding J, Feng YQ. Mass spectrometry-based metabolomics for clinical study: Recent progresses and applications. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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A Study of the Metabolic Pathways Affected by Gestational Diabetes Mellitus: Comparison with Type 2 Diabetes. Diagnostics (Basel) 2022; 12:diagnostics12112881. [PMID: 36428943 PMCID: PMC9689375 DOI: 10.3390/diagnostics12112881] [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: 10/24/2022] [Revised: 11/15/2022] [Accepted: 11/17/2022] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Gestational diabetes mellitus (GDM) remains incompletely understood and increases the risk of developing Diabetes mellitus type 2 (DM2). Metabolomics provides insights etiology and pathogenesis of disease and discovery biomarkers for accurate detection. Nuclear magnetic resonance (NMR) spectroscopy is a key platform defining metabolic signatures in intact serum/plasma. In the present study, we used NMR-based analysis of macromolecules free-serum to accurately characterize the altered metabolic pathways of GDM and assessing their similarities to DM2. Our findings could contribute to the understanding of the pathophysiology of GDM and help in the identification of metabolomic markers of the disease. METHODS Sixty-two women with GDM matched with seventy-seven women without GDM (control group). 1H NMR serum spectra were acquired on an 11.7 T Bruker Avance DRX NMR spectrometer. RESULTS We identified 55 metabolites in both groups, 25 of which were significantly altered in the GDM group. GDM group showed elevated levels of ketone bodies, 2-hydroxybutyrate and of some metabolic intermediates of branched-chain amino acids (BCAAs) and significantly lower levels of metabolites of one-carbon metabolism, energy production, purine metabolism, certain amino acids, 3-methyl-2-oxovalerate, ornithine, 2-aminobutyrate, taurine and trimethylamine N-oxide. CONCLUSION Metabolic pathways affected in GDM were beta-oxidation, ketone bodies metabolism, one-carbon metabolism, arginine and ornithine metabolism likewise in DM2, whereas BCAAs catabolism and aromatic amino acids metabolism were affected, but otherwise than in DM2.
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Feng J, Wu S, Yang H, Ai C, Qiao J, Xu J, Guo F. Microbe-bridged disease-metabolite associations identification by heterogeneous graph fusion. Brief Bioinform 2022; 23:6720417. [PMID: 36168719 DOI: 10.1093/bib/bbac423] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/22/2022] [Accepted: 08/31/2022] [Indexed: 12/14/2022] Open
Abstract
MOTIVATION Metabolomics has developed rapidly in recent years, and metabolism-related databases are also gradually constructed. Nowadays, more and more studies are being carried out on diverse microbes, metabolites and diseases. However, the logics of various associations among microbes, metabolites and diseases are limited understanding in the biomedicine of gut microbial system. The collection and analysis of relevant microbial bioinformation play an important role in the revelation of microbe-metabolite-disease associations. Therefore, the dataset that integrates multiple relationships and the method based on complex heterogeneous graphs need to be developed. RESULTS In this study, we integrated some databases and extracted a variety of associations data among microbes, metabolites and diseases. After obtaining the three interconnected bilateral association data (microbe-metabolite, metabolite-disease and disease-microbe), we considered building a heterogeneous graph to describe the association data. In our model, microbes were used as a bridge between diseases and metabolites. In order to fuse the information of disease-microbe-metabolite graph, we used the bipartite graph attention network on the disease-microbe and metabolite-microbe bipartite graph. The experimental results show that our model has good performance in the prediction of various disease-metabolite associations. Through the case study of type 2 diabetes mellitus, Parkinson's disease, inflammatory bowel disease and liver cirrhosis, it is noted that our proposed methodology are valuable for the mining of other associations and the prediction of biomarkers for different human diseases.Availability and implementation: https://github.com/Selenefreeze/DiMiMe.git.
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Affiliation(s)
- Jitong Feng
- College of Intelligence and Computing, Tianjin University, Tianjin, China
| | - Shengbo Wu
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Zhejiang Shaoxing Research Institute of Tianjin University, Shaoxing, China
| | - Hongpeng Yang
- School of Computational Science and Engineering, University of South Carolina, Columbia, U.S
| | - Chengwei Ai
- College of Intelligence and Computing, Tianjin University, Tianjin, China
| | - Jianjun Qiao
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Zhejiang Shaoxing Research Institute of Tianjin University, Shaoxing, China
| | - Junhai Xu
- College of Intelligence and Computing, Tianjin University, Tianjin, China
| | - Fei Guo
- School of Computer Science and Engineering, Central South University, Changsha, China
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Zhang R, Meng J, Wang X, Pu L, Zhao T, Huang Y, Han L. Metabolomics of ischemic stroke: insights into risk prediction and mechanisms. Metab Brain Dis 2022; 37:2163-2180. [PMID: 35612695 DOI: 10.1007/s11011-022-01011-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 05/16/2022] [Indexed: 10/18/2022]
Abstract
Ischemic stroke (IS) is the most prevalent type of stroke. The early diagnosis and prognosis of IS are crucial for successful therapy and early intervention. Metabolomics, a tool in systems biology based on several innovative technologies, can be used to identify disease biomarkers and unveil underlying pathophysiological processes. Accordingly, in recent years, an increasing number of studies have identified metabolites from cerebral ischemia patients and animal models that could improve the diagnosis of IS and prediction of its outcome. In this paper, metabolomic research is comprehensively reviewed with a focus on describing the metabolic changes and related pathways associated with IS. Most clinical studies use biofluids (e.g., blood or plasma) because their collection is minimally invasive and they are ideal for analyzing changes in metabolites in patients of IS. We review the application of animal models in metabolomic analyses aimed at investigating potential mechanisms of IS and developing novel therapeutic approaches. In addition, this review presents the strengths and limitations of current metabolomic studies on IS, providing a reference for future related studies.
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Affiliation(s)
- Ruijie Zhang
- Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, 315010, Zhejiang, China
- Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo, 315010, Zhejiang, China
| | - Jiajia Meng
- Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, 315010, Zhejiang, China
- Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo, 315010, Zhejiang, China
- Xihu District Center for Disease Control and Prevention, Hangzhou, 310013, Zhejiang, China
| | - Xiaojie Wang
- Department of Neurology, Shenzhen Qianhai Shekou Free Trade Zone Hospital, Shenzhen, 518067, Guangdong, China
| | - Liyuan Pu
- Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, 315010, Zhejiang, China
- Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo, 315010, Zhejiang, China
| | - Tian Zhao
- Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, 315010, Zhejiang, China
- Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo, 315010, Zhejiang, China
| | - Yi Huang
- Department of Neurosurgery, Ningbo First Hospital, Ningbo, 315010, Zhejiang, China.
- Key Laboratory of Precision Medicine for Atherosclerotic Diseases of Zhejiang Province, Ningbo, 315010, Zhejiang, China.
- Medical Research Center, Ningbo First Hospital, Ningbo, 315010, Zhejiang, China.
| | - Liyuan Han
- Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, 315010, Zhejiang, China.
- Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo, 315010, Zhejiang, China.
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Deep Learning-Based Medical Data Association Rules to Explore the Connectivity and Regulation Mechanism of miRNA-mRNA Network in Myocarditis. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2022; 2022:9272709. [PMID: 36193199 PMCID: PMC9525760 DOI: 10.1155/2022/9272709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 09/01/2022] [Accepted: 09/06/2022] [Indexed: 12/02/2022]
Abstract
Acute, chronic myocarditis as myocardial localized or diffuse inflammation lesions is usually involving cardiac function in patients with severe adverse outcomes such as heart failure, sudden death, and no unified, but its pathogenesis clinical is mainly composed of a number of factors including infection and autoimmune defects, such as physical and chemical factors; therefore, it is of great significance to explore the regulation mechanism of myocarditis-related miRNA network connectivity and temperament for in-depth understanding of the pathogenesis of myocarditis and the direction of targeted therapy. Based on this, this study explored the miRNA network related to the pathogenesis of myocarditis through deep learning medical data association rules and analyzed its specific mechanism. The results showed that 39 upregulated miRNAs, 88 downregulated miRNAs, 109 upregulated differentially expressed miRNAs, and 589 downregulated mRNAs were obtained by data association through GSE126677 and GSE4172 databases. GO enrichment and KRGG enrichment analysis showed that the differentially expressed mRNAs were involved in the regulation of a variety of biological processes, cellular components, and molecular functions. At the same time, the miRNA with differentially expressed miRNAs and their corresponding mRNAs were connected to further clarify the specific molecular mechanism of the pathological changes of myocarditis by constructing miRNA-mRNA network. It provides effective potential molecular targets for subsequent treatment and diagnosis.
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Olkowicz M, Rosales-Solano H, Ramadan K, Wang A, Cypel M, Pawliszyn J. The metabolic fate of oxaliplatin in the biological milieu investigated during in vivo lung perfusion using a unique miniaturized sampling approach based on solid-phase microextraction coupled with liquid chromatography-mass spectrometry. Front Cell Dev Biol 2022; 10:928152. [PMID: 36092704 PMCID: PMC9453651 DOI: 10.3389/fcell.2022.928152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 07/04/2022] [Indexed: 11/13/2022] Open
Abstract
Adjuvant chemotherapy after pulmonary metastasectomy for colorectal cancer may reduce recurrence and improve survival rates; however, the benefits of this treatment are limited by the significant side effects that accompany it. The development of a novel in vivo lung perfusion (IVLP) platform would permit the localized delivery of high doses of chemotherapeutic drugs to target residual micrometastatic disease. Nonetheless, it is critical to continuously monitor the levels of such drugs during IVLP administration, as lung injury can occur if tissue concentrations are not maintained within the therapeutic window. This paper presents a simple chemical-biopsy approach based on sampling with a small nitinol wire coated with a sorbent of biocompatible morphology and evaluates its applicability for the near-real-time in vivo determination of oxaliplatin (OxPt) in a 72-h porcine IVLP survival model. To this end, the pigs underwent a 3-h left lung IVLP with 3 doses of the tested drug (5, 7.5, and 40 mg/L), which were administered to the perfusion circuit reservoir as a bolus after a full perfusion flow had been established. Along with OxPt levels, the biocompatible solid-phase microextraction (SPME) probes were employed to profile other low-molecular-weight compounds to provide spatial and temporal information about the toxicity of chemotherapy or lung injury. The resultant measurements revealed a rather heterogeneous distribution of OxPt (over the course of IVLP) in the two sampled sections of the lung. In most cases, the OxPt concentration in the lung tissue peaked during the second hour of IVLP, with this trend being more evident in the upper section. In turn, OxPt in supernatant samples represented ∼25% of the entire drug after the first hour of perfusion, which may be attributable to the binding of OxPt to albumin, its sequestration into erythrocytes, or its rapid nonenzymatic biotransformation. Additionally, the Bio-SPME probes also facilitated the extraction of various endogenous molecules for the purpose of screening biochemical pathways affected during IVLP (i.e., lipid and amino acid metabolism, steroidogenesis, or purine metabolism). Overall, the results of this study demonstrate that the minimally invasive SPME-based sampling approach presented in this work can serve as (pre)clinical and precise bedside medical tool.
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Affiliation(s)
- Mariola Olkowicz
- Department of Chemistry, University of Waterloo, Waterloo, ON, Canada
| | | | - Khaled Ramadan
- Latner Thoracic Surgery Research Laboratories, Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada
| | - Aizhou Wang
- Latner Thoracic Surgery Research Laboratories, Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada
| | - Marcelo Cypel
- Latner Thoracic Surgery Research Laboratories, Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada
- Division of Thoracic Surgery, Department of Surgery, University Health Network, University of Toronto, Toronto Lung Transplant Program, Toronto, ON, Canada
| | - Janusz Pawliszyn
- Department of Chemistry, University of Waterloo, Waterloo, ON, Canada
- *Correspondence: Janusz Pawliszyn,
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