Journal of Shandong University (Health Sciences) ›› 2024, Vol. 62 ›› Issue (11): 40-53.doi: 10.6040/j.issn.1671-7554.0.2024.0162

• Personalized Diagnosis and Treatment of Cardiovascular Diseases • Previous Articles    

Comprehensive analysis of single-cell transcriptomics and machine learning reveals potential biomarkers for abdominal aortic aneurysm

WANG Yutao1,2, SUN Yan3   

  1. 1. The First Clinical College, Shandong University of Traditional Chinese Medicine, Jinan 250355, Shandong, China;;
    2. Department of Peripheral Vascular Disease, Jinan Municipal Hospital of Traditional Chinese Medicine, Jinan 250012, Shandong, China;;
    3. Department of Vascular Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan 250021, Shandong, China
  • Published:2024-11-25

Abstract: Objective To screen for potential biomarkers of abdominal aortic aneurysm(AAA)using single-cell RNA(scRNA)data analysis, weighted gene co-expression network analysis(WGCNA), machine learning, and immune infiltration analysis. Methods The scRNA sequencing data containing AAA and normal aorta control(NAC)in the gene expression database were downloaded and processed by data quality control, dimensionality reduction, differential analysis, and cell type annotation. Chronological analysis was proposed to screen for the earliest differentiated cell types during AAA genesis, and to screen for differentially expressed genes(DEGs). High dimensional WGCNA(hdWGCNA)was performed to identify AAA-related gene modules, and enrichment analysis was conducted. Conventional transcriptome sequencing data containing AAA and NAC was downloaded for differential analysis and WGCNA. DEGs of scRNA samples, DEGs of conventional transcriptomes and WGCNA results were integrated to screen genes associated with AAA lesions. Gene ontology(GO)and Kyoto Encyclopedia of Genes and Genomes(KEGG)signaling pathway enrichment analysis were carried out. The potential biomarkers of AAA were screened using the least absolute shrinkage and selection operator(LASSO), support vector machine recursive feature elimination(SVM-RFE), and random forest(RF)machine learning methods. The immune infiltration analysis was performed. Results The results of scRNA data analysis showed that endothelial cell was the earliest cell type to differentiate during AAA development, and a total of 853 scRNA DEGs were obtained. hdWGCNA identified 2 gene modules associated with AAA, which were significantly enriched in the signaling pathways of T helper 17 cell differentiation, and T helper 1 and 2 cell differentiation. Conventional transcriptome analysis yielded a total of 162 DEGs. Integration yielded 17 AAA-associated genes, which significantly enriched in signaling pathways such as chemokines, T helper 17 cell differentiation, and T helper 1 and 2 cell differentiation. The machine learning algorithm identified a potential biomarker for AAA, ecotropic viral integration site 2B(EVI2B). The expression of EVI2B was higher in AAA samples than in NAC samples. The immune infiltration results showed that the proportions of naive B cells, plasma cells, activated dendritic cells and neutrophils were higher in AAA samples than in NAC samples. EVI2B was positively correlated with M2 macrophages, M1 macrophages, CD8 T cells, plasma cells, helper follicular T cells, M0 macrophages, and neutrophils; and it was negatively correlated with resting dendritic cells. Conclusion AAA pathogenesis involves a variety of immune cells and signaling pathways, and EVI2B expression is significantly increased in AAA samples, correlating with a variety of immune cells, which may be a new target for AAA treatment.

Key words: Abdominal aortic aneurysm, Weighted gene co-expression network analysis, Machine learning, Biomarkers, Immune infiltration

CLC Number: 

  • R654.4
[1] 张韬, 郭伟. 腹主动脉瘤诊断和治疗中国专家共识(2022版)[J]. 中国实用外科杂志, 2022, 42(4): 380-387.
[2] Yuan Z, Lu Y, Wei J, et al. Abdominal aortic aneurysm: roles of inflammatory cells[J]. Front Immunol, 2020, 11: 609161. doi:10.3389/fimmu.2020.609161.
[3] 王颖, 顾慧, 于鑫鑫, 等. 71例腹主动脉瘤的基线CT特征与病变进展的相关性[J]. 山东大学学报(医学版), 2022, 60(10): 62-67. WANG Ying, GU Hui, YU Xinxin, et al. Correlation between baseline CT features and progression of abdominal aortic aneurysm in 71 cases[J]. Journal of Shandong University(Health Sciences), 2022, 60(10): 62-67.
[4] Kindon AJ, McCombie AM, Frampton C, et al. Early relative growth rate of abdominal aortic aneurysms and future risk of rupture or repair[J]. Eur J Vasc Endovasc Surg, 2023, 66(6): 797-803.
[5] Lancaster EM, Gologorsky R, Hull MM, et al. The natural history of large abdominal aortic aneurysms in patients without timely repair[J]. J Vasc Surg, 2022, 75(1): 109-117.
[6] Leone N, Broda MA, Eiberg JP, et al. Systematic review and meta-analysis of the incidence of rupture, repair, and death of small and large abdominal aortic aneurysms under surveillance[J]. J Clin Med, 2023, 12(21): 6837.
[7] Roychowdhury T, Klarin D, Levin MG, et al. Genome-wide association meta-analysis identifies risk loci for abdominal aortic aneurysm and highlights PCSK9 as a therapeutic target[J]. Nat Genet, 2023, 55(11): 1831-1842.
[8] Zhang S, Gu H, Chang N, et al. Assessing abdominal aortic aneurysm progression by using perivascular adipose tissue attenuation on computed tomography angiography[J]. Korean J Radiol, 2023, 24(10): 974-982.
[9] Hofmann A, Khorzom Y, Klimova A, et al. Associations of tissue and soluble LOX-1 with human abdominal aortic aneurysm[J]. J Am Heart Assoc, 2023,12(14):e027537. doi: 10.1161/JAHA.122.027537.
[10] Davis FM, Tsoi LC, Melvin WJ, et al. Inhibition of macrophage histone demethylase JMJD3 protects against abdominal aortic aneurysms[J]. J Exp Med, 2021, 218(6): e20201839. doi:10.1084/jem.20201839.
[11] Pahl MC, Erdman R, Kuivaniemi H, et al. Transcriptional(ChIP-chip)analysis of ELF1, ETS2, RUNX1 and STAT5 in human abdominal aortic aneurysm[J]. Int J Mol Sci, 2015, 16(5): 11229-11258.
[12] Biros E, Moran CS, Rush CM, et al. Differential gene expression in the proximal neck of human abdominal aortic aneurysm[J]. Atherosclerosis, 2014, 233(1): 211-218.
[13] Biros E, Gäbel G, Moran CS, et al. Differential gene expression in human abdominal aortic aneurysm and aortic occlusive disease[J]. Oncotarget, 2015,6(15):12984-12996.
[14] Zhang KJ, Yue JN, Yin L, et al. Comprehensive bioinformatics analysis revealed potential key genes and pathways underlying abdominal aortic aneurysm[J]. Comput Struct Biotechnol J, 2023, 21: 5423-5433. doi:10.1016/j.csbj.2023.10.052.
[15] Davis FM, Tsoi LC, Melvin WJ, et al. Inhibition of macrophage histone demethylase JMJD3 protects against abdominal aortic aneurysms[J]. J Exp Med, 2021, 218(6): e20201839. doi:10.1084/jem.20201839.
[16] Manenti A, Farinetti A, Manco G, et al. Intraluminal Thrombus and abdominal aortic aneurysm complications[J]. Ann Vasc Surg, 2022, 83: e11-e12.
[17] Zheng DD, Liu J, Piao HL, et al. ROS-triggered endothelial cell death mechanisms: focus on pyroptosis, parthanatos, and ferroptosis[J]. Front Immunol, 2022, 13: 1039241. doi:10.3389/fimmu.2022.1039241.
[18] DeRoo E, Stranz A, Yang H, et al. Endothelial dysfunction in the pathogenesis of abdominal aortic aneurysm[J]. Biomolecules. 2022,12(4): 509. doi: 10.3390/biom12040509.
[19] Spartalis E, Spartalis M, Athanasiou A, et al. Endothelium in aortic aneurysm disease: new insights[J]. Curr Med Chem, 2020, 27(7): 1081-1088.
[20] Zhao W, Yao MY, Zhang YY, et al. Endothelial cyclin I reduces vulnerability to angiotensin II-induced vascular remodeling and abdominal aortic aneurysm risk[J]. Microvasc Res, 2022, 142: 104348. doi:10.1016/j.mvr.2022.104348.
[21] Sharma AK, Lu GY, Jester A, et al. Experimental abdominal aortic aneurysm formation is mediated by IL-17 and attenuated by mesenchymal stem cell treatment[J]. Circulation, 2012, 126(Suppl 1): S38-S45.
[22] López-Sanz L, Bernal S, Jiménez-Castilla L, et al. The presence of activating IgG Fc receptors in macrophages aggravates the development of experimental abdominal aortic aneurysm[J]. Clin Investig Arterioscler, 2023, 35(4): 185-194.
[23] Lu L, Jin Y, Tong YH, et al. Myeloid-derived suppressor cells promote the formation of abdominal aortic aneurysms through the IL-3-ICOSL-ICOS axis[J]. BBA Adv, 2023, 4: 100103. doi:10.1016/j.bbadva.2023.100103.
[24] Zhu HL, Qu XQ, Zhang CS, et al. Interleukin-10 promotes proliferation of vascular smooth muscle cells by inhibiting inflammation in rabbit abdominal aortic aneurysm[J]. Int J Clin Exp Pathol, 2019, 12(4): 1260-1271.
[25] Wang H, Wei GD, Cheng S, et al. Circulatory CD4-positive T-lymphocyte imbalance mediated by homocysteine-induced AIM2 and NLRP1 inflammasome upregulation and activation is associated with human abdominal aortic aneurysm[J]. J Vasc Res, 2020, 57(5): 276-290.
[26] Zjablovskaja P, Kardosova M, Danek P, et al. EVI2B is a C/EBPα target gene required for granulocytic differentiation and functionality of hematopoietic progenitors[J]. Cell Death Differ, 2017, 24(4): 705-716.
[27] Dai ZL, Liu ZQ, Yang R, et al. EVI2B is a prognostic biomarker and is correlated with monocyte and macrophage infiltration in osteosarcoma based on an integrative analysis[J]. Biomolecules, 2023, 13(2): 327.
[28] Yap C, Mieremet A, de Vries CJM, et al. Six shades of vascular smooth muscle cells illuminated by KLF4(Krüppel-like factor 4)[J]. Arterioscler Thromb Vasc Biol, 2021, 41(11): 2693-2707.
[29] Gu JQ, Yang WW, Lin S, et al. Identification of co-expressed genes and immune infiltration features related to the progression of atherosclerosis[J]. J Appl Genet, 2024, 65(2): 331-339.
[30] Wierer M, Prestel M, Schiller HB, et al. Compartment-resolved proteomic analysis of mouse aorta during atherosclerotic plaque formation reveals osteoclast-specific protein expression[J]. Mol Cell Proteomics, 2018, 17(2): 321-334.
[31] Petsophonsakul P, Furmanik M, Forsythe R, et al. Role of vascular smooth muscle cell phenotypic switching and calcification in aortic aneurysm formation[J]. Arterioscler Thromb Vasc Biol, 2019, 39(7): 1351-1368.
[1] WEI Ren, GUO Wei. Current status of endovascular therapy for abdominal aortic aneurysm [J]. Journal of Shandong University (Health Sciences), 2024, 62(9): 13-18.
[2] SHI Xiaoxi, XIN Shijie. Open aortic repair of abdominal aortic aneurysm [J]. Journal of Shandong University (Health Sciences), 2024, 62(9): 26-29.
[3] HUO Zhengkun, KONG Xiangqian, WU Xuejun. Progress in diagnosis and treatment of infective native aortic aneurysm [J]. Journal of Shandong University (Health Sciences), 2024, 62(9): 42-48.
[4] ZHOU Yongkang, SUN Jing, ZHANG Shuai, QIAN Xiangyang. Progress in spinal cord protection strategies for open repair of thoracoabdominal aortic aneurysms [J]. Journal of Shandong University (Health Sciences), 2024, 62(9): 49-54.
[5] FAN Libin, ZHANG Hongkun. Progress in prevention and treatment of type Ⅱ endoleak after endovascular abdominal aortic aneurysm repair [J]. Journal of Shandong University (Health Sciences), 2024, 62(9): 55-60.
[6] NIU Shuai, WU Xuejun. Research progress of ferroptosis in abdominal aortic aneurysm [J]. Journal of Shandong University (Health Sciences), 2024, 62(9): 74-79.
[7] SUN Jing, ZHANG Shuai, QI Hongxia, LI Yuan, ZHOU Yongkang, HU Kejian, QIAN Xiangyang. Spinal cord protection by normothermic auto-arterial bypass and distal-anastomosis-first strategy in thoracoabdominal aortic replacement surgery [J]. Journal of Shandong University (Health Sciences), 2024, 62(9): 80-85.
[8] WANG Zheyu, XU Yi, ZHAO Changbo, YANG Shuofei, NI Qihong, CHEN Jiaquan, WANG Weilun, LI Yinan, GUO Xiangjiang, YE Meng, ZHANG Lan, XUE Guanhua. Risk factors and management for iliac branch occlusion after endovascular abdominal aortic aneurysm repair [J]. Journal of Shandong University (Health Sciences), 2024, 62(9): 101-107.
[9] WANG Jing, LIU Xiaofei, ZENG Rong, XU Changjuan, ZHANG Jintao, DONG Liang. Identification of necroptosis-related biomarkers in asthma based on machine learning algorithms [J]. Journal of Shandong University (Health Sciences), 2024, 62(7): 21-32.
[10] GUO Zhenjiang, WANG Ning, ZHAO Guangyuan, DU Liqiang, CUI Zhaobo, LIU Fangzhen. Development of preoperative models for predicting positive esophageal margin in proximal gastric cancer based on machine learning [J]. Journal of Shandong University (Health Sciences), 2024, 62(7): 78-83.
[11] SHI Shuochuan, ZENG Rong, ZHANG Jintao, ZHANG Dong, PAN Yun, LIU Xiaofei, XU Changjuan, WANG Ying, DONG Liang. Bioinformatics-based exploration of potential differential immune genes and immune infiltration signatures in bronchial asthma [J]. Journal of Shandong University (Health Sciences), 2024, 62(5): 43-53.
[12] LIANG Yongyuan, CAI Peifei, ZHENG Guixi. Establishment and value assessment of colon cancer diagnostic models based on multiple variables and different machine learning algorithms [J]. Journal of Shandong University (Health Sciences), 2024, 62(2): 51-59.
[13] QU Jin, ZENG Zhaoxiang, HE Mengwei, HUO Weixue, ZHANG Heng, LU Ye, TIAN Wen, FENG Rui. Comparative outcomes of endovascular aortic repair for post-dissection and degenerative thoracoabdominal aortic aneurysms [J]. Journal of Shandong University (Health Sciences), 2024, 62(11): 14-21.
[14] ZHANG Jinghui, WANG Juan, ZHAO Yujie, DUAN Miao, LIU Yiran, LIN Minjuan, QIAO Xu, LI Zhen, ZUO Xiuli. Construction of a machine learning-based tongue diagnosis model for gastrointestinal diseases [J]. Journal of Shandong University (Health Sciences), 2024, 62(1): 38-47.
[15] MENG Jianli, WANG Qinggang. Expression and potential mechanism of VPS72 in lung adenocarcinoma/ squamous cell carcinoma by integrated bioinformatics analysis [J]. Journal of Shandong University (Health Sciences), 2023, 61(8): 40-49.
Viewed
Full text


Abstract

Cited

  Shared   
  Discussed   
No Suggested Reading articles found!