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Article ; Online: Response to Letter to the Editor from Christina Parisi.

Li, Dadong / Cantor, Michael N

2020 Volume 224, Issue 2, Page(s) 373

Language	English
Publishing date	2020-11-18
Publishing country	United States
Document type	Letter ; Comment
ZDB-ID	3019-3
ISSN	1537-6613 ; 0022-1899
ISSN (online)	1537-6613
ISSN	0022-1899
DOI	10.1093/infdis/jiaa721
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Article ; Online: Corrigendum to 'Concentrations, leachability, and health risks of mercury in green tea from major production areas in China' Ecotoxicol. Environ. Saf. 232 (2022) 113279.

Wang, Qingfeng / Wang, Dan / Li, Zhonggen / Wang, Yuyu / Yang, Yan / Liu, Mengxun / Li, Dadong / Sun, Guangyi / Zeng, Boping

Ecotoxicology and environmental safety

2024 Volume 274, Page(s) 116233

Language	English
Publishing date	2024-03-18
Publishing country	Netherlands
Document type	Published Erratum
ZDB-ID	436536-7
ISSN	1090-2414 ; 0147-6513
ISSN (online)	1090-2414
ISSN	0147-6513
DOI	10.1016/j.ecoenv.2024.116233
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Article ; Online: Identification of cuproptosis-associated subtypes and signature genes for diagnosis and risk prediction of Ulcerative colitis based on machine learning.

Tang, Dadong / Pu, Baoping / Liu, Shiru / Li, Hongyan

Frontiers in immunology

2023 Volume 14, Page(s) 1142215

Abstract: Background: Ulcerative colitis (UC) is a chronic and debilitating inflammatory bowel disease that impairs quality of life. Cuproptosis, a recently discovered form of cell death, has been linked to many inflammatory diseases, including UC. This study ... ...

Abstract	Background: Ulcerative colitis (UC) is a chronic and debilitating inflammatory bowel disease that impairs quality of life. Cuproptosis, a recently discovered form of cell death, has been linked to many inflammatory diseases, including UC. This study aimed to examine the biological and clinical significance of cuproptosis-related genes in UC. Methods: Three gene expression profiles of UC were obtained from the Gene Expression Omnibus (GEO) database to form the combined dataset. Differential analysis was performed based on the combined dataset to identify differentially expressed genes, which were intersected with cuproptosis-related genes to obtain differentially expressed cuproptosis-related genes (DECRGs). Machine learning was conducted based on DECRGs to identify signature genes. The prediction model of UC was established using signature genes, and the molecular subtypes related to cuproptosis of UC were identified. Functional enrichment analysis and immune infiltration analysis were used to evaluate the biological characteristics and immune infiltration landscape of signature genes and molecular subtypes. Results: Seven signature genes (ABCB1, AQP1, BACE1, CA3, COX5A, DAPK2, and LDHD) were identified through the machine learning algorithms, and the nomogram built from these genes had excellent predictive performance. The 298 UC samples were divided into two subtypes through consensus cluster analysis. The results of the functional enrichment analysis and immune infiltration analysis revealed significant differences in gene expression patterns, biological functions, and enrichment pathways between the cuproptosis-related molecular subtypes of UC. The immune infiltration analysis also showed that the immune cell infiltration in cluster A was significantly higher than that of cluster B, and six of the characteristic genes (excluding BACE1) had higher expression levels in subtype B than in subtype A. Conclusions: This study identified several promising signature genes and developed a nomogram with strong predictive capabilities. The identification of distinct subtypes of UC enhances our current understanding of UC's underlying pathogenesis and provides a foundation for personalized diagnosis and treatment in the future.
MeSH term(s)	Humans ; Amyloid Precursor Protein Secretases ; Aspartic Acid Endopeptidases ; Colitis, Ulcerative/diagnosis ; Colitis, Ulcerative/genetics ; Inflammatory Bowel Diseases ; Quality of Life ; Copper ; Apoptosis
Chemical Substances	Amyloid Precursor Protein Secretases (EC 3.4.-) ; Aspartic Acid Endopeptidases (EC 3.4.23.-) ; Copper (789U1901C5)
Language	English
Publishing date	2023-04-05
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2606827-8
ISSN	1664-3224 ; 1664-3224
ISSN (online)	1664-3224
ISSN	1664-3224
DOI	10.3389/fimmu.2023.1142215
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Article ; Online: Role of PFKFB3-driven glycolysis in sepsis

Min Xiao / Dadong Liu / Yao Xu / Wenjian Mao / Weiqin Li

Annals of Medicine, Vol 55, Iss 1, Pp 1278-

2023 Volume 1289

Abstract: AbstractSepsis is still the leading cause of death as a result of infection. Metabolic disorder plays a vital role in sepsis progression. Glycolysis intensification is the most characteristic feature of sepsis-related metabolic disorders. The enzyme 6- ... ...

Abstract	AbstractSepsis is still the leading cause of death as a result of infection. Metabolic disorder plays a vital role in sepsis progression. Glycolysis intensification is the most characteristic feature of sepsis-related metabolic disorders. The enzyme 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 (PFKFB3) is a critical engine that controls the rate of glycolysis. Recent studies have revealed that sepsis accelerates the rate of PFKFB3-driven glycolysis in different cells, including macrophages, neutrophils, endothelial cells and lung fibroblasts. Furthermore, increased PFKFB3 is closely related to the excessive inflammatory response and high mortality in sepsis. Interestingly, inhibition of PFKFB3 alone or in combination has also shown great potential in the treatment of sepsis. Therefore, an improved understanding of the canonical and noncanonical functions of PFKFB3 may provide a novel combinatorial therapeutic target for sepsis. This review summarizes the role of PFKFB3-driven glycolysis in the regulation of immunocyte activation and nonimmune cell damage in sepsis. In addition, we present recent achievements in the development of PFKFB3 drugs and discuss their potential therapeutic roles in sepsis.KEY MESSAGESepsis induces high expression of PFKFB3 in immunocytes and nonimmune cells, thereby enhancing cellular glycolytic flux.PFKFB3-driven glycolysis reprogramming is closely related to an excessive inflammatory response and high mortality in sepsis.Inhibition of PFKFB3 alone or in combination provides a novel combinatorial therapeutic target for sepsis.
Keywords	sepsis ; glycolysis ; PFKFB3 ; Medicine ; R
Subject code	610
Language	English
Publishing date	2023-12-01T00:00:00Z
Publisher	Taylor & Francis Group
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Identification of platelet-related subtypes and diagnostic markers in pediatric Crohn's disease based on WGCNA and machine learning.

Tang, Dadong / Huang, Yingtao / Che, Yuhui / Yang, Chengjun / Pu, Baoping / Liu, Shiru / Li, Hongyan

Frontiers in immunology

2024 Volume 15, Page(s) 1323418

Abstract: Background: The incidence of pediatric Crohn's disease (PCD) is increasing worldwide every year. The challenges in early diagnosis and treatment of PCD persist due to its inherent heterogeneity. This study's objective was to discover novel diagnostic ... ...

Abstract	Background: The incidence of pediatric Crohn's disease (PCD) is increasing worldwide every year. The challenges in early diagnosis and treatment of PCD persist due to its inherent heterogeneity. This study's objective was to discover novel diagnostic markers and molecular subtypes aimed at enhancing the prognosis for patients suffering from PCD. Methods: Candidate genes were obtained from the GSE117993 dataset and the GSE93624 dataset by weighted gene co-expression network analysis (WGCNA) and differential analysis, followed by intersection with platelet-related genes. Based on this, diagnostic markers were screened by five machine learning algorithms. We constructed predictive models and molecular subtypes based on key markers. The models were evaluated using the GSE101794 dataset as the validation set, combined with receiver operating characteristic curves, decision curve analysis, clinical impact curves, and calibration curves. In addition, we performed pathway enrichment analysis and immune infiltration analysis for different molecular subtypes to assess their differences. Results: Through WGCNA and differential analysis, we successfully identified 44 candidate genes. Following this, employing five machine learning algorithms, we ultimately narrowed it down to five pivotal markers: GNA15, PIK3R3, PLEK, SERPINE1, and STAT1. Using these five key markers as a foundation, we developed a nomogram exhibiting exceptional performance. Furthermore, we distinguished two platelet-related subtypes of PCD through consensus clustering analysis. Subsequent analyses involving pathway enrichment and immune infiltration unveiled notable disparities in gene expression patterns, enrichment pathways, and immune infiltration landscapes between these subtypes. Conclusion: In this study, we have successfully identified five promising diagnostic markers and developed a robust nomogram with high predictive efficacy. Furthermore, the recognition of distinct PCD subtypes enhances our comprehension of potential pathogenic mechanisms and paves the way for future prospects in early diagnosis and personalized treatment.
MeSH term(s)	Child ; Humans ; Genes, Regulator ; Crohn Disease/diagnosis ; Crohn Disease/genetics ; Algorithms ; Machine Learning ; Phosphatidylinositol 3-Kinases
Chemical Substances	PIK3R3 protein, human (EC 2.7.1.137) ; Phosphatidylinositol 3-Kinases (EC 2.7.1.-)
Language	English
Publishing date	2024-02-14
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2606827-8
ISSN	1664-3224 ; 1664-3224
ISSN (online)	1664-3224
ISSN	1664-3224
DOI	10.3389/fimmu.2024.1323418
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Article ; Online: MMPs-related risk model identification and SAA1 promotes clear cell renal cell carcinoma migration via ERK-AP1-MMPs axis.

Wei, Haotian / Li, Yajun / Zhang, Jian / Xu, Chenglong / Wei, Dadong / Quan, Changyi / Zhu, Shimiao

Scientific reports

2024 Volume 14, Issue 1, Page(s) 9411

Abstract: Matrix Metalloproteinases (MMPs) have been demonstrated to be essential in facilitating the migration and metastasis of clear cell renal cell carcinoma (ccRCC). However, the ability of the MMP family to predict clinical outcomes and guide optimal ... ...

Abstract	Matrix Metalloproteinases (MMPs) have been demonstrated to be essential in facilitating the migration and metastasis of clear cell renal cell carcinoma (ccRCC). However, the ability of the MMP family to predict clinical outcomes and guide optimal therapeutic strategies for ccRCC patients remains incompletely understood. In this investigation, we initially conducted a thorough examination of the MMP family in pan-cancer. Notably, MMPs exhibited distinctive significance in ccRCC. Following this, we undertook an extensive analysis to evaluate the clinical value of MMPs and potential mechanisms by which MMPs contribute to the progression of ccRCC. A novel stratification method and prognostic model were developed based on MMPs in order to enhance the accuracy of prognosis prediction for ccRCC patients and facilitate personalized treatment. By conducting multi-omics analysis and transcriptional regulation analysis, it was hypothesized that SAA1 plays a crucial role in promoting ccRCC migration through MMPs. Subsequently, in vitro experiments confirmed that SAA1 regulates ccRCC cell migration via the ERK-AP1-MMPs axis. In conclusion, our study has explored the potential value of the MMP family as prognostic markers for ccRCC and as guides for medication regimens. Additionally, we have identified SAA1 as a crucial factor in the migration of ccRCC.
MeSH term(s)	Carcinoma, Renal Cell/genetics ; Carcinoma, Renal Cell/pathology ; Carcinoma, Renal Cell/metabolism ; Humans ; Cell Movement/genetics ; Kidney Neoplasms/genetics ; Kidney Neoplasms/pathology ; Kidney Neoplasms/metabolism ; Matrix Metalloproteinases/metabolism ; Matrix Metalloproteinases/genetics ; Prognosis ; Cell Line, Tumor ; Serum Amyloid A Protein/metabolism ; Serum Amyloid A Protein/genetics ; Gene Expression Regulation, Neoplastic ; MAP Kinase Signaling System ; Female ; Extracellular Signal-Regulated MAP Kinases/metabolism ; Male ; Signal Transduction
Chemical Substances	SAA1 protein, human ; Matrix Metalloproteinases (EC 3.4.24.-) ; Serum Amyloid A Protein ; Extracellular Signal-Regulated MAP Kinases (EC 2.7.11.24)
Language	English
Publishing date	2024-04-24
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-024-59112-5
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Article ; Online: Role of PFKFB3-driven glycolysis in sepsis.

Xiao, Min / Liu, Dadong / Xu, Yao / Mao, Wenjian / Li, Weiqin

Annals of medicine

2023 Volume 55, Issue 1, Page(s) 1278–1289

Abstract: Sepsis is still the leading cause of death as a result of infection. Metabolic disorder plays a vital role in sepsis progression. Glycolysis intensification is the most characteristic feature of sepsis-related metabolic disorders. The enzyme 6- ... ...

Abstract	Sepsis is still the leading cause of death as a result of infection. Metabolic disorder plays a vital role in sepsis progression. Glycolysis intensification is the most characteristic feature of sepsis-related metabolic disorders. The enzyme 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 (PFKFB3) is a critical engine that controls the rate of glycolysis. Recent studies have revealed that sepsis accelerates the rate of PFKFB3-driven glycolysis in different cells, including macrophages, neutrophils, endothelial cells and lung fibroblasts. Furthermore, increased PFKFB3 is closely related to the excessive inflammatory response and high mortality in sepsis. Interestingly, inhibition of PFKFB3 alone or in combination has also shown great potential in the treatment of sepsis. Therefore, an improved understanding of the canonical and noncanonical functions of PFKFB3 may provide a novel combinatorial therapeutic target for sepsis. This review summarizes the role of PFKFB3-driven glycolysis in the regulation of immunocyte activation and nonimmune cell damage in sepsis. In addition, we present recent achievements in the development of PFKFB3 drugs and discuss their potential therapeutic roles in sepsis.KEY MESSAGESepsis induces high expression of PFKFB3 in immunocytes and nonimmune cells, thereby enhancing cellular glycolytic flux.PFKFB3-driven glycolysis reprogramming is closely related to an excessive inflammatory response and high mortality in sepsis.Inhibition of PFKFB3 alone or in combination provides a novel combinatorial therapeutic target for sepsis.
MeSH term(s)	Humans ; Phosphofructokinase-2/metabolism ; Endothelial Cells/metabolism ; Lung ; Sepsis/complications ; Glycolysis/physiology
Chemical Substances	Phosphofructokinase-2 (EC 2.7.1.105) ; PFKFB3 protein, human (EC 2.7.1.105)
Language	English
Publishing date	2023-05-17
Publishing country	England
Document type	Journal Article ; Review ; Research Support, Non-U.S. Gov't
ZDB-ID	1004226-x
ISSN	1365-2060 ; 1651-2219 ; 0785-3890 ; 1743-1387
ISSN (online)	1365-2060 ; 1651-2219
ISSN	0785-3890 ; 1743-1387
DOI	10.1080/07853890.2023.2191217
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Article ; Online: Structural, energetic and dynamic investigation of poly(ethylene oxide) in imidazolium-based ionic liquids with different cationic structures.

Dan, Yongjie / Luo, Huan / Gong, Pengjian / Yan, Dadong / Niu, Yanhua / Li, Guangxian

Physical chemistry chemical physics : PCCP

2023 Volume 25, Issue 43, Page(s) 29783–29796

Abstract: In this work, two imidazolium-based ionic liquids (ILs) with different cations including dications (DIL) and monocations (MIL) were blended with poly(ethylene oxide) (PEO). The influence of ILs' structure on the structural and dynamic properties of a PEO/ ...

Abstract	In this work, two imidazolium-based ionic liquids (ILs) with different cations including dications (DIL) and monocations (MIL) were blended with poly(ethylene oxide) (PEO). The influence of ILs' structure on the structural and dynamic properties of a PEO/IL system was investigated by molecular dynamics (MD) simulation and density functional theory (DFT) methods. The simulation results show that DIL exhibits weaker interaction with PEO than MIL due to a stronger IL aggregation effect. The intermolecular interaction also makes the PEO chain tend to organize around the imidazolium ring of ILs, which causes the conformational entropy loss. Compared with PEO/MIL, this phenomenon is more significant in PEO/DIL because of the double positive centers of the dication and a longer hydrogen bond lifetime. MD simulation also demonstrates that DIL could act as a "crosslinker" to promote the formation of a physical crosslinking network which has strong dependence on the concentration of IL. The competition between physical crosslinking and plasticizing effects induces non-monotonic variations of relaxation time in PEO/DIL, which is consistent with its unusual change of the glass transition temperature (
Language	English
Publishing date	2023-11-08
Publishing country	England
Document type	Journal Article
ZDB-ID	1476244-4
ISSN	1463-9084 ; 1463-9076
ISSN (online)	1463-9084
ISSN	1463-9076
DOI	10.1039/d3cp01946b
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Article ; Online: Effects of Waterlogging Stress on the Neighboring Relationships between Cleistocalyx operculatus (Roxb.) Merr. and Dalbergia odorifera T. Chen Saplings

Li, Dadong / Guo, Luyao / Tian, Mengjie / Miao, Lingfeng / Xiang, Lishan / Yang, Fan

Forests. 2023 Feb. 13, v. 14, no. 2

2023

Abstract: Neighboring relationships among plants have been extensively reported, but little is known about the effect of waterlogging. In this study, Cleistocalyx operculatus (Roxb.) Merr. and Dalbergia odorifera T. Chen saplings were used in investigating the ... ...

Abstract	Neighboring relationships among plants have been extensively reported, but little is known about the effect of waterlogging. In this study, Cleistocalyx operculatus (Roxb.) Merr. and Dalbergia odorifera T. Chen saplings were used in investigating the neighboring relationships between legumes and non-leguminous woody plants under different planting and watering regimes. Results showed that C. operculatus and D. odorifera are waterlogging-tolerant species, and C. operculatus with high proportion of adventitious roots would be at an advantage during waterlogging. The growth performance of D. odorifera was better than that of C. operculatus under well-watered single-planting conditions. However, under well-watered mixed-planting conditions, C. operculatus had an obvious inhibitory effect on the growth traits (increments in stem height and leaf number, total leaf area, and total plant fresh weight) and physiological responses (net photosynthesis rate, stomatal conductance, and transpiration) of D. odorifera, whereas the growth of C. operculatus slightly increased in the presence of D. odorifera. Under waterlogging mixed-planting conditions, the facilitative effect was more intensive; the total leaf area, underground fresh weight, and total plant fresh weight of C. operculatus significantly increased, but a negative effect was found in D. odorifer. These results showed that the neighboring relationship between these two species is predominantly favorable to C. operculatus. This research sheds new light on screening waterlogging-tolerant arbor species and species collocation during vegetation restoration and reconstruction activities in wetland systems.
Keywords	Dalbergia odorifera ; Syzygium nervosum ; ecological restoration ; growth performance ; leaf area ; leaves ; photosynthesis ; stomatal conductance ; wetlands
Language	English
Dates of publication	2023-0213
Publishing place	Multidisciplinary Digital Publishing Institute
Document type	Article ; Online
ZDB-ID	2527081-3
ISSN	1999-4907
ISSN	1999-4907
DOI	10.3390/f14020377
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Poly (vinyl alcohol)/sodium alginate/carboxymethyl chitosan multifunctional hydrogel loading HKUST-1 nanoenzymes for diabetic wound healing.

Chai, Guodong / Wang, Ning / Xu, Meiling / Ma, Lina / Liu, Xinglong / Ding, Qiteng / Zhang, Shuai / Li, Anning / Xia, Guofeng / Zhao, Yingchun / Liu, Wencong / Liang, Dadong / Ding, Chuanbo

International journal of biological macromolecules

2024 , Page(s) 131670

Abstract: Bacterial infection, hyperinflammation and hypoxia, which can lead to amputation in severe cases, are frequently observed in diabetic wounds, and this has been a critical issue facing the repair of chronic skin injuries. In this study, a copper-based MOF ...

Abstract	Bacterial infection, hyperinflammation and hypoxia, which can lead to amputation in severe cases, are frequently observed in diabetic wounds, and this has been a critical issue facing the repair of chronic skin injuries. In this study, a copper-based MOF (TAX@HKUST-1) highly loaded with taxifolin (TAX) with a drug loading of 41.94 ± 2.60 % was prepared. In addition, it has excellent catalase activity, and by constructing an oxygen-releasing hydrogel (PTH) system with calcium peroxide (CaO
Language	English
Publishing date	2024-04-19
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	282732-3
ISSN	1879-0003 ; 0141-8130
ISSN (online)	1879-0003
ISSN	0141-8130
DOI	10.1016/j.ijbiomac.2024.131670
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