DIABETOLOGY / CLINICAL RESEARCH
 
KEYWORDS
TOPICS
ABSTRACT
Introduction:
Diabetic foot ulcers (DFUs) are among the most severe and debilitating diabetic complications, often leading to extremely high morbidity and mortality. Recently, increasing evidence has highlighted the role of necroptosis, a distinct type of programmed cell death distinct from apoptosis, in the progression and severity of DFUs. Understanding necroptosis-associated genes in DFUs could open new therapeutic avenues aimed at modulating this form of cell death, potentially improving outcomes for patients suffering from this serious diabetic complication.

Material and methods:
This study aimed to identify and confirm potential necroptosis biomarkers associated with DFU through the application of machine learning and bioinformatics approaches. We obtained three microarray datasets associated with DFU patients from the Gene Expression Omnibus (GEO) database: GSE68183, GSE134431, and GSE80178.

Results:
In GSE134431, we identified necroptosis-associated genes (NRGs) with differential expression between DFU patients and healthy controls, totaling 37 NRGs. Additionally, we observed an activated immune response in both groups. Moreover, clustering analysis identified two distinct clusters within the DFU samples, highlighting immune heterogeneity. Subsequently, we constructed a random forest (RF) model using 5 genes (CENPB, TRIM56, ZNF768, PLIN4, and ATP1A1). Notably, this model demonstrated outstanding performance on the external validation datasets GSE134431, GSE68183 (AUC = 1.000). The study identified five genes linked to necroptosis in the context of DFU, revealing new potential biomarkers and targets for DFU therapy.

Conclusions:
Bioinformatics analysis indicated that CENPB, TRIM56, ZNF768, PLIN4, and ATP1A1 could serve as potential biomarkers for future DFU research.
REFERENCES (61)
1.
Zhang Y, Lazzarini PA, Mcphail SM, et al. Global disability burdens of diabetes-related lower-extremity complications in 1990 and 2016. Diabetes Care 2020; 43: 964-74.
 
2.
Davies AH. The seriousness of chronic venous disease: a review of real-world evidence. Adv Ther 2019; 36 (Suppl 1): 5-12.
 
3.
Mcdermott K, Fang M, Boulton AJM, et al. Etiology, epidemiology, and disparities in the burden of diabetic foot ulcers. Diabetes Care 2023; 46: 209-21.
 
4.
Armstrong DG, Tan TW, Boulton AJM, et al. Diabetic foot ulcers. JAMA 2023; 330: 62-75.
 
5.
Shofler D, Rai V, Mansager S, et al. Impact of resolvin mediators in the immunopathology of diabetes and wound healing. Expert Rev Clin Immunol 2021; 17: 681-90.
 
6.
Sun H, Pulakat L, Anderson DW. Challenges and new therapeutic approaches in the management of chronic wounds. Curr Drug Targets 2020; 21: 1264-75.
 
7.
Cano Sanchez M, Lancel S, Boulanger E, et al. Targeting oxidative stress and mitochondrial dysfunction in the treatment of impaired wound healing: a systematic review. Antioxidants 2018; 7: 98.
 
8.
Patel S, Srivastava S, Singh MR, et al. Mechanistic insight into diabetic wounds: pathogenesis, molecular targets and treatment strategies to pace wound healing. Biomed Pharmacother 2019; 112: 108615.
 
9.
Grennan D. Diabetic foot ulcers. JAMA 2019; 321: 114.
 
10.
Kang Y, Zheng C, Ye J, et al. Effects of advanced glycation end products on neutrophil migration and aggregation in diabetic wounds. Aging 2021; 13: 12143-59.
 
11.
Liao S, Apaijai N, Chattipakorn N, et al. The possible roles of necroptosis during cerebral ischemia and ischemia/reperfusion injury. Arch Biochem Biophys 2020; 695: 108629.
 
12.
Balusu S, Horre K, Thrupp N, et al. MEG3 activates necroptosis in human neuron xenografts modeling Alzheimer’s disease. Science 2023; 381: 1176-82.
 
13.
Vucur M, Ghallab A, Schneider AT, et al. Sublethal necroptosis signaling promotes inflammation and liver cancer. Immunity 2023; 56: 1578-95.
 
14.
Li F, Sun H, Yu Y, et al. RIPK1-dependent necroptosis promotes vasculogenic mimicry formation via eIF4E in triple-negative breast cancer. Cell Death Dis 2023; 14: 335.
 
15.
Li Z, Dai R, Chen M, et al. p55gamma degrades RIP3 via MG53 to suppress ischaemia-induced myocardial necroptosis and mediates cardioprotection of preconditioning. Cardiovasc Res 2023; 119: 2421-40.
 
16.
Wu X, Nagy LE, Gautheron J. Mediators of necroptosis: from cell death to metabolic regulation. EMBO Mol Med 2024; 16: 219-37.
 
17.
Zhong B, Wang Y, Liao Y, et al. MLKL and other necroptosis-related genes promote the tumor immune cell infiltration, guiding for the administration of immunotherapy in bladder urothelial carcinoma. Apoptosis 2023; 28: 892-911.
 
18.
Zhang T, Xu D, Liu J, et al. Prolonged hypoxia alleviates prolyl hydroxylation-mediated suppression of RIPK1 to promote necroptosis and inflammation. Nat Cell Biol 2023; 25: 950-62.
 
19.
Zou J, Zhang W, Chen X, et al. Data mining reveal the association between diabetic foot ulcer and peripheral artery disease. Front Public Health 2022; 10: 963426.
 
20.
Wang X, Meng L, Zhang J, et al. Identification of ferroptosis-related molecular clusters and genes for diabetic osteoporosis based on the machine learning. Front Endocrinol 2023; 14: 1189513.
 
21.
Yang L, Li LP, Yi HC. DeepWalk based method to predict lncRNA-miRNA associations via lncRNA-miRNA-disease-protein-drug graph. BMC Bioinformatics 2022; 22 (Suppl 12): 621.
 
22.
Sheng N, Wang Y, Huang L, et al. Multi-task prediction-based graph contrastive learning for inferring the relationship among lncRNAs, miRNAs and diseases. Brief Bioinform 2023; 24: bbad276.
 
23.
Li J, Wang H, Dong C, et al. The underlying mechanisms of FGF2 in carotid atherosclerotic plaque development revealed by bioinformatics analysis. Arch Med Sci 2024; 20: 1209-19.
 
24.
Sun F, Sun J, Zhao Q. A deep learning method for predicting metabolite-disease associations via graph neural network. Brief Bioinform 2022; 23: bbac266.
 
25.
Gao H, Sun J, Wang Y, et al. Predicting metabolite-disease associations based on auto-encoder and non-negative matrix factorization. Brief Bioinform 2023; 24: bbad259.
 
26.
Wu Z, Gao Y, Cao L, et al. Purine metabolism-related genes and immunization in thyroid eye disease were validated using bioinformatics and machine learning. Sci Rep 2023; 13: 18391.
 
27.
Chen Z, Zhang L, Sun J, et al. DCAMCP: A deep learning model based on capsule network and attention mechanism for molecular carcinogenicity prediction. J Cell Mol Med 2023; 27: 3117-26.
 
28.
Hu H, Feng Z, Lin H, et al. Gene function and cell surface protein association analysis based on single-cell multiomics data. Comput Biol Med 2023; 157: 106733.
 
29.
Ramirez HA, Pastar I, Jozic I, et al. Staphylococcus aureus triggers induction of miR-15B-5P to diminish DNA repair and deregulate inflammatory response in diabetic foot ulcers. J Invest Dermatol 2018; 138: 1187-96.
 
30.
Sawaya AP, Stone RC, Brooks SR, et al. Deregulated immune cell recruitment orchestrated by FOXM1 impairs human diabetic wound healing. Nat Commun 2020; 11: 4678.
 
31.
Zhabotynsky V, Inoue K, Magnuson T, et al. A statistical method for joint estimation of cis-eQTLs and parent-of-origin effects under family trio design. Biometrics 2019; 75: 864-74.
 
32.
Wu Z, Zhu M, Kang Y, et al. Do we need different machine learning algorithms for QSAR modeling? A comprehensive assessment of 16 machine learning algorithms on 14 QSAR data sets. Brief Bioinform 2021; 22: bbaa321.
 
33.
Krause L, Mchardy AC, Nattkemper TW, et al. GISMO: gene identification using a support vector machine for ORF classification. Nucleic Acids Res 2007; 35: 540-9.
 
34.
Rigatti SJ. Random forest. J Insur Med 2017; 47: 31-9.
 
35.
Pinheiro-Machado E, Gurgul-Convey E, Marzec MT. Immunometabolism in type 2 diabetes mellitus: tissue-specific interactions. Arch Med Sci 2023; 19: 895-911.
 
36.
Polk C, Sampson MM, Roshdy D, et al. Skin and soft tissue infections in patients with diabetes mellitus. Infect Dis Clin North Am 2021; 35: 183-97.
 
37.
Fitridge R, Pena G, Mills JL. The patient presenting with chronic limb-threatening ischaemia. Does diabetes influence presentation, limb outcomes and survival? Diabetes Metab Res Rev 2020; 36 Suppl 1: e3242.
 
38.
Gan Y, Huang X, Zou G, et al. Deep structural clustering for single-cell RNA-seq data jointly through autoencoder and graph neural network. Brief Bioinform 2022; 23: bbac018.
 
39.
Wang T, Sun J, Zhao Q. Investigating cardiotoxicity related with hERG channel blockers using molecular fingerprints and graph attention mechanism. Comput Biol Med 2023; 153: 106464.
 
40.
Shi H, Yuan X, Yang X, et al. A novel diabetic foot ulcer diagnostic model: identification and analysis of genes related to glutamine metabolism and immune infiltration. BMC Genomics 2024; 25: 125.
 
41.
Guo B, Chen JH, Zhang JH, et al. Pattern-recognition receptors in endometriosis: a narrative review. Front Immunol 2023; 14: 1161606.
 
42.
Ying L, Benjanuwattra J, Chattipakorn SC, et al. The role of RIPK3-regulated cell death pathways and necroptosis in the pathogenesis of cardiac ischaemia-reperfusion injury. Acta Physiol 2021; 231: e13541.
 
43.
Siegmund D, Zaitseva O, Wajant H. Fn14 and TNFR2 as regulators of cytotoxic TNFR1 signaling. Front Cell Dev Biol 2023; 11: 1267837.
 
44.
Zhou Y, Cai Z, Zhai Y, et al. Necroptosis inhibitors: mechanisms of action and therapeutic potential. Apoptosis 2024; 29: 22-44.
 
45.
Naito MG, Xu D, Amin P, et al. Sequential activation of necroptosis and apoptosis cooperates to mediate vascular and neural pathology in stroke. Proc Natl Acad Sci USA 2020; 117: 4959-70.
 
46.
Lee JY, Won D, Lee K. Machine learning-based identification and related features of depression in patients with diabetes mellitus based on the Korea National Health and Nutrition Examination Survey: a cross-sectional study. PLoS One 2023; 18: e288648.
 
47.
Gamba R, Fachinetti D. From evolution to function: two sides of the same CENP-B coin? Exp Cell Res 2020; 390: 111959.
 
48.
Ohzeki JI, Otake K, Masumoto H. Human artificial chromosome: chromatin assembly mechanisms and CENP-B. Exp Cell Res 2020; 389: 111900.
 
49.
Mohibi S, Srivastava S, Wang-France J, et al. Alteration/deficiency in activation 3 (ADA3) protein, a cell cycle regulator, associates with the centromere through CENP-B and regulates chromosome segregation. J Biol Chem 2015; 290: 28299-310.
 
50.
Wang B, Wang Z, Li Y, et al. TRIM56: a promising prognostic immune biomarker for glioma revealed by pan-cancer and single-cell analysis. Front Immunol 2024; 15: 1327898.
 
51.
Crawley SW, Weck ML, Grega-Larson NE, et al. ANKS4B is essential for intermicrovillar adhesion complex formation. Dev Cell 2016; 36: 190-200.
 
52.
Low B, Lim CS, Ding S, et al. Decreased GLUT2 and glucose uptake contribute to insulin secretion defects in MODY3/HNF1A hiPSC-derived mutant beta cells. Nat Commun 2021; 12 :3133.
 
53.
Schlingmann KP, Bandulik S, Mammen C, et al. Germline de novo mutations in ATP1A1 cause renal hypomagnesemia, refractory seizures, and intellectual disability. Am J Hum Genet 2018; 103: 808-16.
 
54.
Ygberg S, Akkuratov EE, Howard RJ, et al. A missense mutation converts the Na(+),K(+)-ATPase into an ion channel and causes therapy-resistant epilepsy. J Biol Chem 2021; 297: 101355.
 
55.
Lee JS, Lee BI, Park CB. Photo-induced inhibition of Alzheimer’s beta-amyloid aggregation in vitro by rose bengal. Biomaterials 2015; 38: 43-9.
 
56.
Sumiyoshi S, Shiozaki A, Kosuga T, et al. Functional analysis and clinical importance of ATP1A1 in colon cancer. Ann Surg Oncol 2023; 30: 6898-910.
 
57.
Louiselle AE, Niemiec SM, Zgheib C, et al. Macrophage polarization and diabetic wound healing. Transl Res 2021; 236: 109-16.
 
58.
Kaltsas A. Oxidative stress and male infertility: the protective role of antioxidants. Medicina 2023; 59: 1769.
 
59.
Lee YS, Kang SU, Lee MH, et al. GnRH impairs diabetic wound healing through enhanced NETosis. Cell Mol Immunol 2020; 17: 856-64.
 
60.
Liu Y, Zhang X, Yang L, et al. Proteomics and transcriptomics explore the effect of mixture of herbal extract on diabetic wound healing process. Phytomedicine 2023; 116: 154892.
 
61.
Wang Y, Pi Y, Hu L, et al. Proteomic analysis of foot ulcer tissue reveals novel potential therapeutic targets of wound healing in diabetic foot ulcers. Comput Biol Med 2023; 159: 106858.
 
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