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Gao Y, Guo L, Liu X, Chen N, Yang X, Zhang Q. Advances in the synthesis and applications of macrocyclic polyamines. ROYAL SOCIETY OPEN SCIENCE 2024; 11:231979. [PMID: 39092147 PMCID: PMC11293801 DOI: 10.1098/rsos.231979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 03/03/2024] [Accepted: 04/10/2024] [Indexed: 08/04/2024]
Abstract
Macrocyclic polyamines constitute a significant class of macrocyclic compounds that play a pivotal role in the realm of supramolecular chemistry. They find extensive applications across diverse domains including industrial and agricultural production, clinical diagnostics, environmental protection and other multidisciplinary fields. Macrocyclic polyamines possess a distinctive cavity structure with varying sizes, depths, electron-richness degrees and flexibilities. This unique feature enables them to form specific supramolecular structures through complexation with diverse objects, thereby attracting considerable attention from chemists, biologists and materials scientists alike. However, there is currently a lack of comprehensive summaries on the synthesis methods for macrocyclic polyamines. In this review article, we provide an in-depth introduction to the synthesis of macrocyclic polyamines while analysing their respective advantages and disadvantages. Furthermore, we also present an overview of the recent 5-year advancements in using macrocyclic polyamines as non-viral gene vectors, fluorescent probes, diagnostic and therapeutic reagents as well as catalysts. Looking ahead to future research directions on the synthesis and application of macrocyclic polyamines across various fields will hopefully inspire new ideas for their synthesis and use.
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Affiliation(s)
- Yongguang Gao
- Department of Chemistry, Tangshan Normal University, Tangshan063000, People’s Republic of China
- Hebei Key Laboratory of Degradable Polymers, Tangshan Normal University, Tangshan063000, People’s Republic of China
- Tangshan Silicone Key Laboratory, Tangshan Normal University, Tangshan063000, People’s Republic of China
| | - Lina Guo
- Tangshan First Vocational Secondary Specialized School, Tangshan 063000, People’s Republic of China
| | - Xinhua Liu
- Department of Chemistry, Tangshan Normal University, Tangshan063000, People’s Republic of China
- Hebei Key Laboratory of Degradable Polymers, Tangshan Normal University, Tangshan063000, People’s Republic of China
- Tangshan Silicone Key Laboratory, Tangshan Normal University, Tangshan063000, People’s Republic of China
| | - Na Chen
- Department of Chemistry, Tangshan Normal University, Tangshan063000, People’s Republic of China
- Hebei Key Laboratory of Degradable Polymers, Tangshan Normal University, Tangshan063000, People’s Republic of China
- Tangshan Silicone Key Laboratory, Tangshan Normal University, Tangshan063000, People’s Republic of China
| | - Xiaochun Yang
- Department of Chemistry, Tangshan Normal University, Tangshan063000, People’s Republic of China
- Hebei Key Laboratory of Degradable Polymers, Tangshan Normal University, Tangshan063000, People’s Republic of China
- Tangshan Silicone Key Laboratory, Tangshan Normal University, Tangshan063000, People’s Republic of China
| | - Qing Zhang
- Department of Chemistry, Tangshan Normal University, Tangshan063000, People’s Republic of China
- Hebei Key Laboratory of Degradable Polymers, Tangshan Normal University, Tangshan063000, People’s Republic of China
- Tangshan Silicone Key Laboratory, Tangshan Normal University, Tangshan063000, People’s Republic of China
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Amniouel S, Yalamanchili K, Sankararaman S, Jafri MS. Evaluating Ovarian Cancer Chemotherapy Response Using Gene Expression Data and Machine Learning. BIOMEDINFORMATICS 2024; 4:1396-1424. [PMID: 39149564 PMCID: PMC11326537 DOI: 10.3390/biomedinformatics4020077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
Background Ovarian cancer (OC) is the most lethal gynecological cancer in the United States. Among the different types of OC, serous ovarian cancer (SOC) stands out as the most prevalent. Transcriptomics techniques generate extensive gene expression data, yet only a few of these genes are relevant to clinical diagnosis. Methods Methods for feature selection (FS) address the challenges of high dimensionality in extensive datasets. This study proposes a computational framework that applies FS techniques to identify genes highly associated with platinum-based chemotherapy response on SOC patients. Using SOC datasets from the Gene Expression Omnibus (GEO) database, LASSO and varSelRF FS methods were employed. Machine learning classification algorithms such as random forest (RF) and support vector machine (SVM) were also used to evaluate the performance of the models. Results The proposed framework has identified biomarkers panels with 9 and 10 genes that are highly correlated with platinum-paclitaxel and platinum-only response in SOC patients, respectively. The predictive models have been trained using the identified gene signatures and accuracy of above 90% was achieved. Conclusions In this study, we propose that applying multiple feature selection methods not only effectively reduces the number of identified biomarkers, enhancing their biological relevance, but also corroborates the efficacy of drug response prediction models in cancer treatment.
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Affiliation(s)
- Soukaina Amniouel
- School of System Biology, George Mason University, Fairfax, VA 22030, USA
| | - Keertana Yalamanchili
- School of System Biology, George Mason University, Fairfax, VA 22030, USA
- School of Engineering, Brown University, Providence, RI 02912, USA
| | - Sreenidhi Sankararaman
- School of System Biology, George Mason University, Fairfax, VA 22030, USA
- Department of Biomedical Engineering, The John Hopkins University, Baltimore, MD 21218, USA
| | - Mohsin Saleet Jafri
- School of System Biology, George Mason University, Fairfax, VA 22030, USA
- Center for Biomedical Engineering and Technology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
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Lin C, Tian Q, Guo S, Xie D, Cai Y, Wang Z, Chu H, Qiu S, Tang S, Zhang A. Metabolomics for Clinical Biomarker Discovery and Therapeutic Target Identification. Molecules 2024; 29:2198. [PMID: 38792060 PMCID: PMC11124072 DOI: 10.3390/molecules29102198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 04/10/2024] [Accepted: 04/25/2024] [Indexed: 05/26/2024] Open
Abstract
As links between genotype and phenotype, small-molecule metabolites are attractive biomarkers for disease diagnosis, prognosis, classification, drug screening and treatment, insight into understanding disease pathology and identifying potential targets. Metabolomics technology is crucial for discovering targets of small-molecule metabolites involved in disease phenotype. Mass spectrometry-based metabolomics has implemented in applications in various fields including target discovery, explanation of disease mechanisms and compound screening. It is used to analyze the physiological or pathological states of the organism by investigating the changes in endogenous small-molecule metabolites and associated metabolism from complex metabolic pathways in biological samples. The present review provides a critical update of high-throughput functional metabolomics techniques and diverse applications, and recommends the use of mass spectrometry-based metabolomics for discovering small-molecule metabolite signatures that provide valuable insights into metabolic targets. We also recommend using mass spectrometry-based metabolomics as a powerful tool for identifying and understanding metabolic patterns, metabolic targets and for efficacy evaluation of herbal medicine.
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Affiliation(s)
- Chunsheng Lin
- Graduate School and Second Affiliated Hospital, Heilongjiang University of Chinese Medicine, Harbin 150040, China; (C.L.); (S.G.); (Y.C.); (Z.W.)
| | - Qianqian Tian
- Faculty of Social Sciences, The University of Hong Kong, Hong Kong 999077, China;
| | - Sifan Guo
- Graduate School and Second Affiliated Hospital, Heilongjiang University of Chinese Medicine, Harbin 150040, China; (C.L.); (S.G.); (Y.C.); (Z.W.)
- International Advanced Functional Omics Platform, Scientific Experiment Center, International Joint Research Center on Traditional Chinese and Modern Medicine, Hainan Engineering Research Center for Biological Sample Resources of Major Diseases (First Affiliated Hospital of Hainan Medical University), Key Laboratory of Tropical Cardiovascular Diseases Research of Hainan Province, Hainan Medical University, Xueyuan Road 3, Haikou 571199, China; (D.X.); (S.Q.); (S.T.)
| | - Dandan Xie
- International Advanced Functional Omics Platform, Scientific Experiment Center, International Joint Research Center on Traditional Chinese and Modern Medicine, Hainan Engineering Research Center for Biological Sample Resources of Major Diseases (First Affiliated Hospital of Hainan Medical University), Key Laboratory of Tropical Cardiovascular Diseases Research of Hainan Province, Hainan Medical University, Xueyuan Road 3, Haikou 571199, China; (D.X.); (S.Q.); (S.T.)
| | - Ying Cai
- Graduate School and Second Affiliated Hospital, Heilongjiang University of Chinese Medicine, Harbin 150040, China; (C.L.); (S.G.); (Y.C.); (Z.W.)
- International Advanced Functional Omics Platform, Scientific Experiment Center, International Joint Research Center on Traditional Chinese and Modern Medicine, Hainan Engineering Research Center for Biological Sample Resources of Major Diseases (First Affiliated Hospital of Hainan Medical University), Key Laboratory of Tropical Cardiovascular Diseases Research of Hainan Province, Hainan Medical University, Xueyuan Road 3, Haikou 571199, China; (D.X.); (S.Q.); (S.T.)
| | - Zhibo Wang
- Graduate School and Second Affiliated Hospital, Heilongjiang University of Chinese Medicine, Harbin 150040, China; (C.L.); (S.G.); (Y.C.); (Z.W.)
- International Advanced Functional Omics Platform, Scientific Experiment Center, International Joint Research Center on Traditional Chinese and Modern Medicine, Hainan Engineering Research Center for Biological Sample Resources of Major Diseases (First Affiliated Hospital of Hainan Medical University), Key Laboratory of Tropical Cardiovascular Diseases Research of Hainan Province, Hainan Medical University, Xueyuan Road 3, Haikou 571199, China; (D.X.); (S.Q.); (S.T.)
| | - Hang Chu
- Department of Biomedical Sciences, Beijing City University, Beijing 100193, China;
| | - Shi Qiu
- International Advanced Functional Omics Platform, Scientific Experiment Center, International Joint Research Center on Traditional Chinese and Modern Medicine, Hainan Engineering Research Center for Biological Sample Resources of Major Diseases (First Affiliated Hospital of Hainan Medical University), Key Laboratory of Tropical Cardiovascular Diseases Research of Hainan Province, Hainan Medical University, Xueyuan Road 3, Haikou 571199, China; (D.X.); (S.Q.); (S.T.)
| | - Songqi Tang
- International Advanced Functional Omics Platform, Scientific Experiment Center, International Joint Research Center on Traditional Chinese and Modern Medicine, Hainan Engineering Research Center for Biological Sample Resources of Major Diseases (First Affiliated Hospital of Hainan Medical University), Key Laboratory of Tropical Cardiovascular Diseases Research of Hainan Province, Hainan Medical University, Xueyuan Road 3, Haikou 571199, China; (D.X.); (S.Q.); (S.T.)
| | - Aihua Zhang
- Graduate School and Second Affiliated Hospital, Heilongjiang University of Chinese Medicine, Harbin 150040, China; (C.L.); (S.G.); (Y.C.); (Z.W.)
- International Advanced Functional Omics Platform, Scientific Experiment Center, International Joint Research Center on Traditional Chinese and Modern Medicine, Hainan Engineering Research Center for Biological Sample Resources of Major Diseases (First Affiliated Hospital of Hainan Medical University), Key Laboratory of Tropical Cardiovascular Diseases Research of Hainan Province, Hainan Medical University, Xueyuan Road 3, Haikou 571199, China; (D.X.); (S.Q.); (S.T.)
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Amniouel S, Jafri MS. High-accuracy prediction of colorectal cancer chemotherapy efficacy using machine learning applied to gene expression data. Front Physiol 2024; 14:1272206. [PMID: 38304289 PMCID: PMC10830836 DOI: 10.3389/fphys.2023.1272206] [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: 08/03/2023] [Accepted: 12/26/2023] [Indexed: 02/03/2024] Open
Abstract
Introduction: FOLFOX and FOLFIRI chemotherapy are considered standard first-line treatment options for colorectal cancer (CRC). However, the criteria for selecting the appropriate treatments have not been thoroughly analyzed. Methods: A newly developed machine learning model was applied on several gene expression data from the public repository GEO database to identify molecular signatures predictive of efficacy of 5-FU based combination chemotherapy (FOLFOX and FOLFIRI) in patients with CRC. The model was trained using 5-fold cross validation and multiple feature selection methods including LASSO and VarSelRF methods. Random Forest and support vector machine classifiers were applied to evaluate the performance of the models. Results and Discussion: For the CRC GEO dataset samples from patients who received either FOLFOX or FOLFIRI, validation and test sets were >90% correctly classified (accuracy), with specificity and sensitivity ranging between 85%-95%. In the datasets used from the GEO database, 28.6% of patients who failed the treatment therapy they received are predicted to benefit from the alternative treatment. Analysis of the gene signature suggests the mechanistic difference between colorectal cancers that respond and those that do not respond to FOLFOX and FOLFIRI. Application of this machine learning approach could lead to improvements in treatment outcomes for patients with CRC and other cancers after additional appropriate clinical validation.
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Affiliation(s)
- Soukaina Amniouel
- School of Systems Biology, George Mason University, Fairfax, VA, United States
| | - Mohsin Saleet Jafri
- School of Systems Biology, George Mason University, Fairfax, VA, United States
- Center for Biomedical Engineering and Technology, University of Maryland School of Medicine, Baltimore, MD, United States
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Song L, Wang J, Zhang Y, Yan X, He J, Nie J, Zhang F, Han R, Yin H, Li J, Liu H, Huang L, Li Y. Association Between Human Metabolomics and Rheumatoid Arthritis: A Systematic Review and Meta-analysis. Arch Med Res 2024; 55:102907. [PMID: 38029644 DOI: 10.1016/j.arcmed.2023.102907] [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: 04/25/2023] [Revised: 09/23/2023] [Accepted: 10/24/2023] [Indexed: 12/01/2023]
Abstract
OBJECTIVE The underdiagnosis and inadequate treatment of rheumatoid arthritis (RA) can be attributed to the various clinical manifestations presented by patients. To address this concern, we conducted an extensive review and meta-analysis, focusing on RA-related metabolites. METHODS A comprehensive literature search was conducted in PubMed, the Cochrane Library, Web of Science, and Embase to identify relevant studies published up to October 5, 2022. The quality of the included articles was evaluated and, subsequently, a meta-analysis was conducted using Review Manager software to analyze the association between metabolites and RA. RESULTS Forty nine studies met the inclusion criteria for the systematic review, and six of these studies were meta-analyzed to evaluate the association between 28 reproducible metabolites and RA. The results indicated that, compared to controls, the levels of histidine (RoM = 0.83, 95% CI = 0.79-0.88, I2 = 0%), asparagine (RoM = 0.83, 95% CI = 0.75-0.91, I2 = 0%), methionine (RoM = 0.82, 95% CI = 0.69-0.98, I2 = 85%), and glycine (RoM = 0.81, 95% CI = 0.67-0.97, I2 = 68%) were significantly lower in RA patients, while hypoxanthine levels (RoM = 1.14, 95% CI = 1.09-1.19, I2 = 0%) were significantly higher. CONCLUSION This study identified histidine, methionine, asparagine, hypoxanthine, and glycine as significantly correlated with RA, thus offering the potential for the advancement of biomarker discovery and the elucidation of disease mechanisms in RA.
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Affiliation(s)
- Lili Song
- Tianjin University of Traditional Chinese Medicine, No.10, Poyang Lake Road, West zone, Tuanbo New-City, Jinghai-District, Tianjin, China
| | - Jiayi Wang
- Tianjin University of Traditional Chinese Medicine, No.10, Poyang Lake Road, West zone, Tuanbo New-City, Jinghai-District, Tianjin, China
| | - Yue Zhang
- Tianjin University of Traditional Chinese Medicine, No.10, Poyang Lake Road, West zone, Tuanbo New-City, Jinghai-District, Tianjin, China
| | - Xingxu Yan
- Tianjin University of Traditional Chinese Medicine, No.10, Poyang Lake Road, West zone, Tuanbo New-City, Jinghai-District, Tianjin, China
| | - Junjie He
- Tianjin University of Traditional Chinese Medicine, No.10, Poyang Lake Road, West zone, Tuanbo New-City, Jinghai-District, Tianjin, China
| | - Jiaxuan Nie
- Tianjin University of Traditional Chinese Medicine, No.10, Poyang Lake Road, West zone, Tuanbo New-City, Jinghai-District, Tianjin, China
| | - Fangfang Zhang
- Tianjin University of Traditional Chinese Medicine, No.10, Poyang Lake Road, West zone, Tuanbo New-City, Jinghai-District, Tianjin, China
| | - Rui Han
- Tianjin University of Traditional Chinese Medicine, No.10, Poyang Lake Road, West zone, Tuanbo New-City, Jinghai-District, Tianjin, China
| | - Hongqing Yin
- Tianjin University of Traditional Chinese Medicine, No.10, Poyang Lake Road, West zone, Tuanbo New-City, Jinghai-District, Tianjin, China
| | - Jingfang Li
- Tianjin University of Traditional Chinese Medicine, No.10, Poyang Lake Road, West zone, Tuanbo New-City, Jinghai-District, Tianjin, China
| | - Huimin Liu
- Tianjin University of Traditional Chinese Medicine, No.10, Poyang Lake Road, West zone, Tuanbo New-City, Jinghai-District, Tianjin, China
| | - Liping Huang
- Tianjin University of Traditional Chinese Medicine, No.10, Poyang Lake Road, West zone, Tuanbo New-City, Jinghai-District, Tianjin, China
| | - Yubo Li
- Tianjin University of Traditional Chinese Medicine, No.10, Poyang Lake Road, West zone, Tuanbo New-City, Jinghai-District, Tianjin, China.
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Chakraborty S, Anand S, Coe S, Reh B, Bhandari RK. The PCOS-NAFLD Multidisease Phenotype Occurred in Medaka Fish Four Generations after the Removal of Bisphenol A Exposure. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:12602-12619. [PMID: 37581432 PMCID: PMC10469501 DOI: 10.1021/acs.est.3c01922] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 07/17/2023] [Accepted: 07/18/2023] [Indexed: 08/16/2023]
Abstract
As a heterogeneous reproductive disorder, polycystic ovary syndrome (PCOS) can be caused by genetic, diet, and environmental factors. Bisphenol A (BPA) can induce PCOS and nonalcoholic fatty liver disease (NAFLD) due to direct exposure; however, whether these phenotypes persist in future unexposed generations is not currently understood. In a previous study, we observed that transgenerational NAFLD persisted in female medaka for five generations (F4) after exposure to an environmentally relevant concentration (10 μg/L) of BPA. Here, we demonstrate PCOS in the same F4 generation female medaka that developed NAFLD. The ovaries contained immature follicles, restricted follicular progression, and degenerated follicles, which are characteristics of PCOS. Untargeted metabolomic analysis revealed 17 biomarkers in the ovary of BPA lineage fish, whereas transcriptomic analysis revealed 292 genes abnormally expressed, which were similar to human patients with PCOS. Metabolomic-transcriptomic joint pathway analysis revealed activation of the cancerous pathway, arginine-proline metabolism, insulin signaling, AMPK, and HOTAIR regulatory pathways, as well as upstream regulators esr1 and tgf signaling in the ovary. The present results suggest that ancestral BPA exposure can lead to PCOS phenotypes in the subsequent unexposed generations and warrant further investigations into potential health risks in future generations caused by initial exposure to EDCs.
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Affiliation(s)
- Sourav Chakraborty
- Department of Biology, University of North Carolina at Greensboro, Greensboro 27412 North Carolina, United
States
| | - Santosh Anand
- Department of Biology, University of North Carolina at Greensboro, Greensboro 27412 North Carolina, United
States
| | - Seraiah Coe
- Department of Biology, University of North Carolina at Greensboro, Greensboro 27412 North Carolina, United
States
| | - Beh Reh
- Department of Biology, University of North Carolina at Greensboro, Greensboro 27412 North Carolina, United
States
| | - Ramji Kumar Bhandari
- Department of Biology, University of North Carolina at Greensboro, Greensboro 27412 North Carolina, United
States
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Cortada-Garcia J, Daly R, Arnold SA, Burgess K. Streamlined identification of strain engineering targets for bioprocess improvement using metabolic pathway enrichment analysis. Sci Rep 2023; 13:12990. [PMID: 37563133 PMCID: PMC10415327 DOI: 10.1038/s41598-023-39661-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 07/28/2023] [Indexed: 08/12/2023] Open
Abstract
Metabolomics is a powerful tool for the identification of genetic targets for bioprocess optimisation. However, in most cases, only the biosynthetic pathway directed to product formation is analysed, limiting the identification of these targets. Some studies have used untargeted metabolomics, allowing a more unbiased approach, but data interpretation using multivariate analysis is usually not straightforward and requires time and effort. Here we show, for the first time, the application of metabolic pathway enrichment analysis using untargeted and targeted metabolomics data to identify genetic targets for bioprocess improvement in a more streamlined way. The analysis of an Escherichia coli succinate production bioprocess with this methodology revealed three significantly modulated pathways during the product formation phase: the pentose phosphate pathway, pantothenate and CoA biosynthesis and ascorbate and aldarate metabolism. From these, the two former pathways are consistent with previous efforts to improve succinate production in Escherichia coli. Furthermore, to the best of our knowledge, ascorbate and aldarate metabolism is a newly identified target that has so far never been explored for improving succinate production in this microorganism. This methodology therefore represents a powerful tool for the streamlined identification of strain engineering targets that can accelerate bioprocess optimisation.
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Affiliation(s)
- Joan Cortada-Garcia
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, Edinburgh, EH8 9AB, UK
| | - Rónán Daly
- Institute of Infection, Immunity and Inflammation, Glasgow Polyomics, University of Glasgow, Glasgow, G61 1QH, UK
| | - S Alison Arnold
- Ingenza Ltd., Roslin Innovation Centre, Roslin, EH25 9RG, UK
| | - Karl Burgess
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, Edinburgh, EH8 9AB, UK.
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Chen J, Li S, Zhu J, Su W, Jian C, Zhang J, Wu J, Wang T, Zhang W, Zeng F, Chang S, Jia L, Su J, Zhao Y, Wang J, Zeng F. Multi-omics profiling reveals potential alterations in rheumatoid arthritis with different disease activity levels. Arthritis Res Ther 2023; 25:74. [PMID: 37138305 PMCID: PMC10155393 DOI: 10.1186/s13075-023-03049-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 04/07/2023] [Indexed: 05/05/2023] Open
Abstract
BACKGROUND Rheumatoid arthritis (RA) is a chronic, systemic autoimmune inflammatory disease, the pathogenesis of which is not clear. Clinical remission, or decreased disease activity, is the aim of treatment for RA. However, our understanding of disease activity is inadequate, and clinical remission rates for RA are generally poor. In this study, we used multi-omics profiling to study potential alterations in rheumatoid arthritis with different disease activity levels. METHODS Fecal and plasma samples from 131 rheumatoid arthritis (RA) patients and 50 healthy subjects were collected for 16S rRNA sequencing, internally transcribed spacer (ITS) sequencing, and liquid chromatography-tandem mass spectrometry (LC-MS/MS). The PBMCS were also collected for RNA sequencing and whole exome sequencing (WES). The disease groups, based on 28 joints and ESR (DAS28), were divided into DAS28L, DAS28M, and DAS28H groups. Three random forest models were constructed and verified with an external validation cohort of 93 subjects. RESULTS Our findings revealed significant alterations in plasma metabolites and gut microbiota in RA patients with different disease activities. Moreover, plasma metabolites, especially lipid metabolites, demonstrated a significant correlation with the DAS28 score and also associations with gut bacteria and fungi. KEGG pathway enrichment analysis of plasma metabolites and RNA sequencing data demonstrated alterations in the lipid metabolic pathway in RA progression. Whole exome sequencing (WES) results have shown that non-synonymous single nucleotide variants (nsSNV) of the HLA-DRB1 and HLA-DRB5 gene locus were associated with the disease activity of RA. Furthermore, we developed a disease classifier based on plasma metabolites and gut microbiota that effectively discriminated RA patients with different disease activity in both the discovery cohort and the external validation cohort. CONCLUSION Overall, our multi-omics analysis confirmed that RA patients with different disease activity were altered in plasma metabolites, gut microbiota composition, transcript levels, and DNA. Our study identified the relationship between gut microbiota and plasma metabolites and RA disease activity, which may provide a novel therapeutic direction for improving the clinical remission rate of RA.
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Affiliation(s)
- Jianghua Chen
- Institute of Basic Medicine and Forensic Medicine, North Sichuan Medical College, Nanchong, Sichuan, China
- Department of Clinical Research Center, Dazhou Central Hospital, Dazhou, Sichuan, China
| | - Shilin Li
- Department of Clinical Research Center, Dazhou Central Hospital, Dazhou, Sichuan, China
| | - Jing Zhu
- Department of Rheumatology and Immunology, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
- Department of Rheumatology and Immunology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Wei Su
- Department of Rheumatology and Immunology, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Congcong Jian
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Jie Zhang
- Department of Clinical Research Center, Dazhou Central Hospital, Dazhou, Sichuan, China
| | - Jianhong Wu
- Department of Rheumatology and Immunology, Dazhou Central Hospital, Dazhou, Sichuan, China
| | - Tingting Wang
- Department of Rheumatology and Immunology, Dazhou Central Hospital, Dazhou, Sichuan, China
| | - Weihua Zhang
- Department of Rheumatology and Immunology, Dazhou Central Hospital, Dazhou, Sichuan, China
| | - Fanwei Zeng
- Sichuan Province Orthopaedic Hospital, Chengdu, Sichuan, China
| | - Shengjia Chang
- Shantou University Medical College, Shantou University, Guangdong, China
| | - Lihua Jia
- Institute of Basic Medicine and Forensic Medicine, North Sichuan Medical College, Nanchong, Sichuan, China
| | - Jiang Su
- Department of Rheumatology and Immunology, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Yi Zhao
- Department of Rheumatology and Immunology, West China Hospital, Sichuan University, Chengdu, Sichuan, China.
- Clinical Institute of Inflammation and Immunology (CIII), Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan, China.
| | - Jing Wang
- The National Clinical Research Center for Mental Disorders, National Center for Mental Disorders, Beijing Anding Hospital, Capital Medical University, Beijing, China.
| | - Fanxin Zeng
- Institute of Basic Medicine and Forensic Medicine, North Sichuan Medical College, Nanchong, Sichuan, China.
- Department of Clinical Research Center, Dazhou Central Hospital, Dazhou, Sichuan, China.
- Department of Big Data and Biomedical AI, College of Future Technology, Peking University, Beijing, 100871, 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: 99] [Impact Index Per Article: 99.0] [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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10
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Huang R, Tang J, Wang S, Liu Y, Zhang M, Jin M, Qin H, Qian W, Lu Y, Yang Y, Lu B, Yao Y, Yan P, Huang J, Zhang W, Lu J, Gu M, Zhu Y, Guo X, Xian S, Liu X, Huang Z. Sequencing technology as a major impetus in the advancement of studies into rheumatism: A bibliometric study. Front Immunol 2023; 14:1067830. [PMID: 36875117 PMCID: PMC9982012 DOI: 10.3389/fimmu.2023.1067830] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 01/23/2023] [Indexed: 02/19/2023] Open
Abstract
Background Rheumatism covers a wide range of diseases with complex clinical manifestations and places a tremendous burden on humans. For many years, our understanding of rheumatism was seriously hindered by technology constraints. However, the increasing application and rapid advancement of sequencing technology in the past decades have enabled us to study rheumatism with greater accuracy and in more depth. Sequencing technology has made huge contributions to the field and is now an indispensable component and powerful tool in the study of rheumatism. Methods Articles on sequencing and rheumatism, published from 1 January 2000 to 25 April 2022, were retrieved from the Web of Science™ (Clarivate™, Philadelphia, PA, USA) database. Bibliometrix, the open-source tool, was used for the analysis of publication years, countries, authors, sources, citations, keywords, and co-words. Results The 1,374 articles retrieved came from 62 countries and 350 institutions, with a general increase in article numbers during the last 22 years. The leading countries in terms of publication numbers and active cooperation with other countries were the USA and China. The most prolific authors and most popular documents were identified to establish the historiography of the field. Popular and emerging research topics were assessed by keywords and co-occurrence analysis. Immunological and pathological process in rheumatism, classification, risks and susceptibility, and biomarkers for diagnosis were among the hottest themes for research. Conclusions Sequencing technology has been widely applied in the study of rheumatism and propells research in the area of discovering novel biomarkers, related gene patterns and physiopathology. We suggest that further efforts be made to advance the study of genetic patterns related to rheumatic susceptibility, pathogenesis, classification and disease activity, and novel biomarkers.
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Affiliation(s)
- Runzhi Huang
- Department of Orthopedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Department of Burn Surgery, The First Affiliated Hospital of Naval Medical University, Shanghai, People's Republic of China, Research Unit of Key Techniques for Treatment of Burns and Combined Burns and Trauma Injury, Chinese Academy of Medical Sciences, Shanghai, China
| | - Jieling Tang
- Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Siqiao Wang
- Tongji University School of Medicine, Shanghai, China
| | - Yifan Liu
- Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Mengyi Zhang
- Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Minghao Jin
- Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hengwei Qin
- Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Weijin Qian
- Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yuwei Lu
- Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yiting Yang
- Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Bingnan Lu
- Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yuntao Yao
- Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Penghui Yan
- Department of Orthopedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jie Huang
- Department of Burn Surgery, The First Affiliated Hospital of Naval Medical University, Shanghai, People's Republic of China, Research Unit of Key Techniques for Treatment of Burns and Combined Burns and Trauma Injury, Chinese Academy of Medical Sciences, Shanghai, China
| | - Wei Zhang
- Department of Burn Surgery, The First Affiliated Hospital of Naval Medical University, Shanghai, People's Republic of China, Research Unit of Key Techniques for Treatment of Burns and Combined Burns and Trauma Injury, Chinese Academy of Medical Sciences, Shanghai, China
| | - Jianyu Lu
- Department of Burn Surgery, The First Affiliated Hospital of Naval Medical University, Shanghai, People's Republic of China, Research Unit of Key Techniques for Treatment of Burns and Combined Burns and Trauma Injury, Chinese Academy of Medical Sciences, Shanghai, China
| | - Minyi Gu
- Department of Burn Surgery, The First Affiliated Hospital of Naval Medical University, Shanghai, People's Republic of China, Research Unit of Key Techniques for Treatment of Burns and Combined Burns and Trauma Injury, Chinese Academy of Medical Sciences, Shanghai, China
| | - Yushu Zhu
- Department of Burn Surgery, The First Affiliated Hospital of Naval Medical University, Shanghai, People's Republic of China, Research Unit of Key Techniques for Treatment of Burns and Combined Burns and Trauma Injury, Chinese Academy of Medical Sciences, Shanghai, China
| | - Xinya Guo
- Department of Burn Surgery, The First Affiliated Hospital of Naval Medical University, Shanghai, People's Republic of China, Research Unit of Key Techniques for Treatment of Burns and Combined Burns and Trauma Injury, Chinese Academy of Medical Sciences, Shanghai, China
| | - Shuyuan Xian
- Department of Orthopedics, Shibei Hospital, Shanghai, China
| | - Xin Liu
- Department of Rheumatology and Immunology, Second Affiliated Hospital of Naval Medical University, Shanghai, China
| | - Zongqiang Huang
- Department of Orthopedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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11
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Morabito A, De Simone G, Ferrario M, Falcetta F, Pastorelli R, Brunelli L. EASY-FIA: A Readably Usable Standalone Tool for High-Resolution Mass Spectrometry Metabolomics Data Pre-Processing. Metabolites 2022; 13:metabo13010013. [PMID: 36676938 PMCID: PMC9861133 DOI: 10.3390/metabo13010013] [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: 11/23/2022] [Revised: 12/15/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022] Open
Abstract
Flow injection analysis coupled with high-resolution mass spectrometry (FIA-HRMS) is a fair trade-off between resolution and speed. However, free software available for data pre-processing is few, web-based, and often requires advanced user specialization. These tools rarely embedded blank and noise evaluation strategies, and direct feature annotation. We developed EASY-FIA, a free standalone application that can be employed for FIA-HRMS metabolomic data pre-processing by users with no bioinformatics/programming skills. We validated the tool's performance and applicability in two clinical metabolomics case studies. The main functions of our application are blank subtraction, alignment of the metabolites, and direct feature annotation by means of the Human Metabolome Database (HMDB) using a minimum number of mass spectrometry parameters. In a scenario where FIA-HRMS is increasingly recognized as a reliable strategy for fast metabolomics analysis, EASY-FIA could become a standardized and feasible tool easily usable by all scientists dealing with MS-based metabolomics. EASY-FIA was implemented in MATLAB with the App Designer tool and it is freely available for download.
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Affiliation(s)
- Aurelia Morabito
- Laboratory of Mass Spectrometry, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 20156 Milan, Italy
- Department of Electronics, Information and Bioengineering, Politecnico di Milano, 20133 Milan, Italy
| | - Giulia De Simone
- Laboratory of Mass Spectrometry, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 20156 Milan, Italy
- Department of Biotechnologies and Biosciences, Università degli Studi Milano Bicocca, 20126 Milan, Italy
| | - Manuela Ferrario
- Department of Electronics, Information and Bioengineering, Politecnico di Milano, 20133 Milan, Italy
| | - Francesca Falcetta
- Unit of Biophysics, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 20156 Milan, Italy
| | - Roberta Pastorelli
- Laboratory of Mass Spectrometry, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 20156 Milan, Italy
| | - Laura Brunelli
- Laboratory of Mass Spectrometry, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 20156 Milan, Italy
- Correspondence: ; Tel.: +39-0239014742
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12
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Identification of Canine Pyometra-Associated Metabolites Using Untargeted Metabolomics. Int J Mol Sci 2022; 23:ijms232214161. [PMID: 36430638 PMCID: PMC9697130 DOI: 10.3390/ijms232214161] [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: 10/13/2022] [Revised: 11/09/2022] [Accepted: 11/14/2022] [Indexed: 11/18/2022] Open
Abstract
Canine pyometra frequently occurs in middle-aged to older intact bitches, which seriously affects the life of dogs and brings an economic loss to their owners. Hence, finding a key metabolite is very important for the diagnosis and development of a new safe and effective therapy for the disease. In this study, dogs with pyometra were identified by blood examinations, laboratory analyses and diagnostic imaging, and fifteen endometrium tissues of sick dogs with pyometra and fifteen controls were collected and their metabolites were identified utilizing a UHPLC-qTOF-MS-based untargeted metabolomics approach. The results indicated that the elevated inflammatory cells were observed in dogs with pyometra, suggesting that sick dogs suffered systemic inflammation. In the untargeted metabolic profile, 705 ion features in the positive polarity mode and 414 ion features in the negative polarity mode were obtained in endometrium tissues of sick dogs with pyometra, with a total of 275 differential metabolites (173 in positive and 102 in negative polarity modes). Moreover, the multivariate statistical analyses such as PCA and PLS-DA also showed that the metabolites were significantly different between the two groups. Then, these differential metabolites were subjected to pathway analysis using Metaboanalyst 4.0, and Galactose metabolism, cAMP signaling pathway and Glycerophospholipid metabolism were enriched, proving some insights into the metabolic changes during pyometra. Moreover, the receiver operating characteristic curves further confirmed kynurenic acid was expected to be a candidate biomarker of canine pyometra. In conclusion, this study provided a new idea for exploring early diagnosis methods and a safe and effective therapy for canine pyometra.
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13
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Zhu H, Xiong XG, Lu Y, Wu HC, Zhang ZH, Sun MJ. The mechanism of the anti-inflammatory effect of Oldenlandia diffusa on arthritis model rats: a quantitative proteomic and network pharmacologic study. ANNALS OF TRANSLATIONAL MEDICINE 2022; 10:1098. [PMID: 36388817 PMCID: PMC9652507 DOI: 10.21037/atm-22-3678] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 08/30/2022] [Indexed: 07/28/2023]
Abstract
BACKGROUND In China, Oldenlandia diffusa (OD) has been prescribed as a therapeutic herb for rheumatoid arthritis (RA). We previously conducted a preliminary study of the anti-inflammatory effect of OD, and the purpose of this study is to further investigate its mechanism. METHODS We performed a quantitative proteomic analysis of synovium, identified the differentially expressed proteins, and performed bioinformatics analyses. With the help of network pharmacology, we aimed to find the key synovial proteins which OD or its key compound might influence. To verify the result, liquid chromatography-mass spectrometry (LC-MS) was applied to quantify and qualify the absorbable potential compounds of OD. The anti-inflammatory effect was evaluated by morphological, histopathological, and cytokine analyses. Target proteins were observed by immunohistochemistry (IHC) and enzyme-linked immunosorbent assay (ELISA). RESULTS MMP3 and CAV1 were identified as 2 of the differentially expressed proteins in RA synovium, and might be influenced by quercetin, the active compound of OD. MMP3 might be altered through atherosclerosis signaling, while CAV1 might be altered through caveolar-mediated endocytosis signaling. According to our verification, quercetin was identified as the absorbed and effective compound of OD, and it could exert an anti-inflammatory effect on the collagen-induced arthritis (CIA) model, including serum cytokine expression, synovial hyperplasia and lymphocyte infiltration, articular cartilage lesion. Quercetin could also down-regulate the synovial expression of MMP3 and CAV1, and could exert better effects at a high dose. CONCLUSIONS Quercetin was the main active compound of OD in the treatment of RA. OD might alleviate inflammatory responses in CIA rats by suppressing the expression of MMP3 and CAV1 through quercetin, and at a high dose, quercetin could exert a better anti-inflammatory effect.
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Affiliation(s)
- Hao Zhu
- Department of Traditional Chinese Medicine, The First Affiliated Hospital of Soochow University, Soochow University, Suzhou, China
| | - Xin-Gui Xiong
- Institute of Combined Traditional Chinese and Western Medicine, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Changsha, China
| | - Ying Lu
- Department of General Practice, Dushu Lake Hospital, Soochow University, Suzhou, China
| | - Hui-Chun Wu
- Department of Infectious Disease, The First Affiliated Hospital of Soochow University, Soochow University, Suzhou, China
| | - Zhi-Hui Zhang
- Department of Traditional Chinese Medicine, The First Affiliated Hospital of Soochow University, Soochow University, Suzhou, China
| | - Mei-Juan Sun
- Department of Traditional Chinese Medicine, The First Affiliated Hospital of Soochow University, Soochow University, Suzhou, China
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14
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Xu L, Chang C, Jiang P, Wei K, Zhang R, Jin Y, Zhao J, Xu L, Shi Y, Guo S, He D. Metabolomics in rheumatoid arthritis: Advances and review. Front Immunol 2022; 13:961708. [PMID: 36032122 PMCID: PMC9404373 DOI: 10.3389/fimmu.2022.961708] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Accepted: 07/25/2022] [Indexed: 12/11/2022] Open
Abstract
Rheumatoid arthritis (RA) is an autoimmune disease accompanied by metabolic alterations. The metabolic profiles of patients with RA can be determined using targeted and non-targeted metabolomics technology. Metabolic changes in glucose, lipid, and amino acid levels are involved in glycolysis, the tricarboxylic acid cycle, the pentose phosphate pathway, the arachidonic acid metabolic pathway, and amino acid metabolism. These alterations in metabolic pathways and metabolites can fulfill bio-energetic requirements, promote cell proliferation, drive inflammatory mediator secretion, mediate leukocyte infiltration, induce joint destruction and muscle atrophy, and regulate cell proliferation, which may reflect the etiologies of RA. Differential metabolites can be used as biomarkers for the diagnosis, prognosis, and risk prediction, improving the specificity and accuracy of diagnostics and prognosis prediction. Additionally, metabolic changes associated with therapeutic responses can improve the understanding of drug mechanism. Metabolic homeostasis and regulation are new therapeutic strategies for RA. In this review, we provide a comprehensive overview of advances in metabolomics for RA.
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Affiliation(s)
- Lingxia Xu
- Guanghua Clinical Medical College, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Department of Rheumatology, Shanghai Guanghua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Institute of Arthritis Research in Integrative Medicine, Shanghai Academy of Traditional Chinese Medicine, Shanghai, China
| | - Cen Chang
- Guanghua Clinical Medical College, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Department of Rheumatology, Shanghai Guanghua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Institute of Arthritis Research in Integrative Medicine, Shanghai Academy of Traditional Chinese Medicine, Shanghai, China
| | - Ping Jiang
- Guanghua Clinical Medical College, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Department of Rheumatology, Shanghai Guanghua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Institute of Arthritis Research in Integrative Medicine, Shanghai Academy of Traditional Chinese Medicine, Shanghai, China
| | - Kai Wei
- Guanghua Clinical Medical College, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Department of Rheumatology, Shanghai Guanghua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Institute of Arthritis Research in Integrative Medicine, Shanghai Academy of Traditional Chinese Medicine, Shanghai, China
| | - Runrun Zhang
- Department of Rheumatology, The Second Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Yehua Jin
- Guanghua Clinical Medical College, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Department of Rheumatology, Shanghai Guanghua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Jianan Zhao
- Guanghua Clinical Medical College, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Department of Rheumatology, Shanghai Guanghua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Institute of Arthritis Research in Integrative Medicine, Shanghai Academy of Traditional Chinese Medicine, Shanghai, China
| | - Linshuai Xu
- Guanghua Clinical Medical College, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Department of Rheumatology, Shanghai Guanghua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yiming Shi
- Guanghua Clinical Medical College, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Department of Rheumatology, Shanghai Guanghua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Institute of Arthritis Research in Integrative Medicine, Shanghai Academy of Traditional Chinese Medicine, Shanghai, China
| | - Shicheng Guo
- Department of Medical Genetics, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States
- Computation and Informatics in Biology and Medicine, University of Wisconsin-Madison, Madison, WI, United States
- *Correspondence: Shicheng Guo, ; Dongyi He,
| | - Dongyi He
- Guanghua Clinical Medical College, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Department of Rheumatology, Shanghai Guanghua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Institute of Arthritis Research in Integrative Medicine, Shanghai Academy of Traditional Chinese Medicine, Shanghai, China
- *Correspondence: Shicheng Guo, ; Dongyi He,
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15
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Siqueira IR, de Souza Rodrigues A, Flores MS, Vieira Cunha EL, Goldberg M, Harmon B, Batabyal R, Freishtat RJ, Cechinel LR. Circulating Extracellular Vesicles and Particles Derived From Adipocytes: The Potential Role in Spreading MicroRNAs Associated With Cellular Senescence. FRONTIERS IN AGING 2022; 3:867100. [PMID: 36016863 PMCID: PMC9395989 DOI: 10.3389/fragi.2022.867100] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 06/13/2022] [Indexed: 11/13/2022]
Abstract
Aging is associated with adipose tissue dysfunction and is recognized as a risk factor for shortened life span. Considering that in vitro findings have shown the involvement of microRNA in extracellular vesicles and particles (EVPs) on senescence, we hypothesized that circulating EVPs derived from adipocytes can be involved in the aging process via their microRNA cargo. We aimed to determine the microRNA profiles of circulating EVPs derived from adipocytes (FABP4+) from aged and young adult animals and to perform in silico prediction of their downstream signaling effects. Plasma was obtained from Wistar rats (3 and 21 months old), and adipocyte-derived EVPs were isolated using the commercially available kit. Fatty acid-binding protein 4 (FABP4) was used for adipocyte-derived EVPs isolation; microRNA isolation and microarray expression analysis were performed. The analysis revealed 728 miRNAs, 32 were differentially between groups (p < 0.05; fold change ≥ |1.1|), of which 15 miRNAs were upregulated and 17 were downregulated in circulating EVPs from aged animals compared to young adults. A conservative filter was applied, and 18 microRNAs had experimentally validated and highly conserved predicted mRNA targets, with a total of 2,228 mRNAs. Canonical pathways, disease and functions, and upstream regulator analyses were performed using IPA-QIAGEN, allowing a global and interconnected evaluation. IPA categories impacted negatively were cell cycle, cellular development, cellular growth and proliferation, and tissue development, while those impacted positively were “digestive system cancer” and “endocrine gland tumor.” Interestingly, the upregulated miR-15-5p targets several cyclins, such as CCND1 and CCND2, and miR-24-3p seems to target CDK4 (cyclin-dependent kinase 4); then potentially inhibiting their expression, both miRNAs can induce a negative regulation of cell cycle progression. In contrast, silencing of negative cell cycle checkpoint regulators, such as p21 and p16, can be predicted, which can induce impairment in response to genotoxic stressors. In addition, predicted targets, such as SMAD family members, seem to be involved in the positive control of digestive and endocrine tumors. Taken together, this exploratory study indicates that miRNA signature in circulating adipocyte-derived EVPs may be involved with the double-edged sword of cellular senescence, including irreversible proliferation arrest and tissue-dependent cancer, and seems to be suitable for further validation and confirmatory studies.
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Affiliation(s)
- Ionara Rodrigues Siqueira
- Programa de Pós-Graduação em Ciências Biológicas: Farmacologia e Terapêutica, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
- Programa de Pós-Graduação em Ciências Biológicas: Fisiologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
- Departamento de Farmacologia, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
- *Correspondence: Ionara Rodrigues Siqueira,
| | - Andressa de Souza Rodrigues
- Programa de Pós-Graduação em Ciências Biológicas: Farmacologia e Terapêutica, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Marina Siqueira Flores
- Departamento de Farmacologia, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Eduarda Letícia Vieira Cunha
- Departamento de Farmacologia, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Madeleine Goldberg
- Center for Genetic Medicine Research, Children’s National Hospital, Washington, WC, United States
| | - Brennan Harmon
- Center for Genetic Medicine Research, Children’s National Hospital, Washington, WC, United States
| | - Rachael Batabyal
- Center for Genetic Medicine Research, Children’s National Hospital, Washington, WC, United States
| | - Robert J. Freishtat
- Center for Genetic Medicine Research, Children’s National Hospital, Washington, WC, United States
| | - Laura Reck Cechinel
- Programa de Pós-Graduação em Ciências Biológicas: Farmacologia e Terapêutica, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
- Programa de Pós-Graduação em Ciências Biológicas: Fisiologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
- Center for Genetic Medicine Research, Children’s National Hospital, Washington, WC, United States
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16
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Investigating the Mechanisms of Jieduquyuziyin Prescription Improves Lupus Nephritis and Fibrosis via FXR in MRL/lpr Mice. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:4301033. [PMID: 35855861 PMCID: PMC9288302 DOI: 10.1155/2022/4301033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 05/30/2022] [Accepted: 06/19/2022] [Indexed: 11/18/2022]
Abstract
Lupus nephritis (LN) is one of the most serious complications of systemic lupus erythematosus (SLE) and one of the leading causes of death. An alternative effective treatment to ameliorate and relieve LN and delay the process of renal tissue fibrosis is urgently needed in the clinical setting. Jieduquyuziyin prescription (JP) has been successfully used to treat SLE, but its potential mechanisms are not sufficiently understood. In this study, we treated MRL/lpr mice with JP for 8 weeks and treated human renal tubular epithelial cells (human kidney 2 (HK-2)) with drug-containing serum to observe the antagonistic effects of JP on inflammation and fibrosis, as well as to investigate the possible mechanisms. Results demonstrated that JP significantly reduced urinary protein and significantly improved pathological abnormalities. Metabolomics combined with ingenuity pathway analysis illustrated that the process of kidney injury in lupus mice may be closely related to farnesoid X receptor (FXR) pathway abnormalities. Microarray biomimetic analysis and LN patients indicated that FXR may play a protective role as an effective therapeutic target for LN and renal fibrosis. JP significantly increased the expression of FXR and inhibited the expression of its downstream targets, namely, nuclear transcription factor κB (NF-κB) and α-smooth muscle actin (α-SMA), in the kidney of MRL/lpr mice and HK-2 cells, as confirmed by in vitro and in vivo experiments. In conclusion, JP may mediate the activation of renal FXR expression and inhibit NF-κB and α-SMA expression to exert anti-inflammatory and antifibrotic effects for LN prevention and treatment.
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17
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Metabolic Profiling in Rheumatoid Arthritis, Psoriatic Arthritis, and Psoriasis: Elucidating Pathogenesis, Improving Diagnosis, and Monitoring Disease Activity. J Pers Med 2022; 12:jpm12060924. [PMID: 35743709 PMCID: PMC9225104 DOI: 10.3390/jpm12060924] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 05/23/2022] [Accepted: 05/30/2022] [Indexed: 11/16/2022] Open
Abstract
Immune-mediated inflammatory diseases (IMIDs), such as rheumatoid arthritis (RA), psoriatic arthritis (PsA), and psoriasis (Ps), represent autoinflammatory and autoimmune disorders, as well as conditions that have an overlap of both categories. Understanding the underlying pathogeneses, making diagnoses, and choosing individualized treatments remain challenging due to heterogeneous disease phenotypes and the lack of reliable biomarkers that drive the treatment choice. In this review, we provide an overview of the low-molecular-weight metabolites that might be employed as biomarkers for various applications, e.g., early diagnosis, disease activity monitoring, and treatment-response prediction, in RA, PsA, and Ps. The literature was evaluated, and putative biomarkers in different matrices were identified, categorized, and summarized. While some of these candidate biomarkers appeared to be disease-specific, others were shared across multiple IMIDs, indicating common underlying disease mechanisms. However, there is still a long way to go for their application in a routine clinical setting. We propose that studies integrating omics analyses of large patient cohorts from different IMIDs should be performed to further elucidate their pathomechanisms and treatment options. This could lead to the identification and validation of biomarkers that might be applied in the context of precision medicine to improve the clinical outcomes of these IMID patients.
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18
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Bartikoski BJ, de Oliveira MS, do Espírito Santo RC, dos Santos LP, dos Santos NG, Xavier RM. A Review of Metabolomic Profiling in Rheumatoid Arthritis: Bringing New Insights in Disease Pathogenesis, Treatment and Comorbidities. Metabolites 2022; 12:394. [PMID: 35629898 PMCID: PMC9146149 DOI: 10.3390/metabo12050394] [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: 03/08/2022] [Revised: 04/14/2022] [Accepted: 04/21/2022] [Indexed: 12/04/2022] Open
Abstract
Metabolomic analysis provides a wealth of information that can be predictive of distinctive phenotypes of pathogenic processes and has been applied to better understand disease development. Rheumatoid arthritis (RA) is an autoimmune disease with the establishment of chronic synovial inflammation that affects joints and peripheral tissues such as skeletal muscle and bone. There is a lack of useful disease biomarkers to track disease activity, drug response and follow-up in RA. In this review, we describe potential metabolic biomarkers that might be helpful in the study of RA pathogenesis, drug response and risk of comorbidities. TMAO (choline and trimethylamine oxide) and TCA (tricarboxylic acid) cycle products have been suggested to modulate metabolic profiles during the early stages of RA and are present systemically, which is a relevant characteristic for biomarkers. Moreover, the analysis of lipids such as cholesterol, FFAs and PUFAs may provide important information before disease onset to predict disease activity and treatment response. Regarding therapeutics, TNF inhibitors may increase the levels of tryptophan, valine, lysine, creatinine and alanine, whereas JAK/STAT inhibitors may modulate exclusively fatty acids. These observations indicate that different disease modifying antirheumatic drugs have specific metabolic profiles and can reveal differences between responders and non-responders. In terms of comorbidities, physical impairment represented by higher fatigue scores and muscle wasting has been associated with an increase in urea cycle, FFAs, tocopherols and BCAAs. In conclusion, synovial fluid, blood and urine samples from RA patients seem to provide critical information about the metabolic profile related to drug response, disease activity and comorbidities.
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Affiliation(s)
- Bárbara Jonson Bartikoski
- Laboratório de Doenças Autoimunes, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre 90035-903, RS, Brazil; (B.J.B.); (M.S.d.O.); (R.C.d.E.S.); (L.P.d.S.); (N.G.d.S.)
- Serviço de Reumatologia, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre 90035-903, RS, Brazil
- Postgraduate Program in Medical Science, Universidade Federal do Rio Grande do Sul, Ramiro Barcelos 2400, Porto Alegre 90035-003, RS, Brazil
| | - Marianne Schrader de Oliveira
- Laboratório de Doenças Autoimunes, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre 90035-903, RS, Brazil; (B.J.B.); (M.S.d.O.); (R.C.d.E.S.); (L.P.d.S.); (N.G.d.S.)
- Serviço de Reumatologia, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre 90035-903, RS, Brazil
- Postgraduate Program in Medical Science, Universidade Federal do Rio Grande do Sul, Ramiro Barcelos 2400, Porto Alegre 90035-003, RS, Brazil
| | - Rafaela Cavalheiro do Espírito Santo
- Laboratório de Doenças Autoimunes, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre 90035-903, RS, Brazil; (B.J.B.); (M.S.d.O.); (R.C.d.E.S.); (L.P.d.S.); (N.G.d.S.)
- Serviço de Reumatologia, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre 90035-903, RS, Brazil
- Postgraduate Program in Medical Science, Universidade Federal do Rio Grande do Sul, Ramiro Barcelos 2400, Porto Alegre 90035-003, RS, Brazil
| | - Leonardo Peterson dos Santos
- Laboratório de Doenças Autoimunes, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre 90035-903, RS, Brazil; (B.J.B.); (M.S.d.O.); (R.C.d.E.S.); (L.P.d.S.); (N.G.d.S.)
- Serviço de Reumatologia, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre 90035-903, RS, Brazil
- Postgraduate Program in Medical Science, Universidade Federal do Rio Grande do Sul, Ramiro Barcelos 2400, Porto Alegre 90035-003, RS, Brazil
| | - Natália Garcia dos Santos
- Laboratório de Doenças Autoimunes, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre 90035-903, RS, Brazil; (B.J.B.); (M.S.d.O.); (R.C.d.E.S.); (L.P.d.S.); (N.G.d.S.)
- Serviço de Reumatologia, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre 90035-903, RS, Brazil
- Postgraduate Program in Biological Sciences: Pharmacology and Therapeutics, Barcelos 2400, Porto Alegre 90035-003, RS, Brazil
| | - Ricardo Machado Xavier
- Laboratório de Doenças Autoimunes, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre 90035-903, RS, Brazil; (B.J.B.); (M.S.d.O.); (R.C.d.E.S.); (L.P.d.S.); (N.G.d.S.)
- Serviço de Reumatologia, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre 90035-903, RS, Brazil
- Postgraduate Program in Medical Science, Universidade Federal do Rio Grande do Sul, Ramiro Barcelos 2400, Porto Alegre 90035-003, RS, Brazil
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Plasma Metabolomic Profiling Reveals Four Possibly Disrupted Mechanisms in Systemic Sclerosis. Biomedicines 2022; 10:biomedicines10030607. [PMID: 35327409 PMCID: PMC8945346 DOI: 10.3390/biomedicines10030607] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 02/24/2022] [Accepted: 02/26/2022] [Indexed: 12/15/2022] Open
Abstract
Systemic sclerosis (SSc) is a rare systemic autoimmune disorder marked by high morbidity and increased risk of mortality. Our study aimed to analyze metabolomic profiles of plasma from SSc patients by using targeted and untargeted metabolomics approaches. Furthermore, we aimed to detect biochemical mechanisms relevant to the pathophysiology of SSc. Experiments were performed using high-performance liquid chromatography coupled to mass spectrometry technology. The investigation of plasma samples from SSc patients (n = 52) compared to a control group (n = 48) allowed us to identify four different dysfunctional metabolic mechanisms, which can be assigned to the kynurenine pathway, the urea cycle, lipid metabolism, and the gut microbiome. These significantly altered metabolic pathways are associated with inflammation, vascular damage, fibrosis, and gut dysbiosis and might be relevant for the pathophysiology of SSc. Further studies are needed to explore the role of these metabolomic networks as possible therapeutic targets of SSc.
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Metabolomics in Autoimmune Diseases: Focus on Rheumatoid Arthritis, Systemic Lupus Erythematous, and Multiple Sclerosis. Metabolites 2021; 11:metabo11120812. [PMID: 34940570 PMCID: PMC8708401 DOI: 10.3390/metabo11120812] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 11/24/2021] [Accepted: 11/24/2021] [Indexed: 12/18/2022] Open
Abstract
The metabolomics approach represents the last downstream phenotype and is widely used in clinical studies and drug discovery. In this paper, we outline recent advances in the metabolomics research of autoimmune diseases (ADs) such as rheumatoid arthritis (RA), multiple sclerosis (MuS), and systemic lupus erythematosus (SLE). The newly discovered biomarkers and the metabolic mechanism studies for these ADs are described here. In addition, studies elucidating the metabolic mechanisms underlying these ADs are presented. Metabolomics has the potential to contribute to pharmacotherapy personalization; thus, we summarize the biomarker studies performed to predict the personalization of medicine and drug response.
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