Identification of gene and protein signatures associated with long-term effects of COVID-19 on the immune system after patient recovery by analyzing single-cell multi-omics data using a machine learning approach

2019年冠状病毒病(COVID-19) 鉴定(生物学) 免疫系统 期限(时间) 组学 计算生物学 2019-20冠状病毒爆发 严重急性呼吸综合征冠状病毒2型(SARS-CoV-2) 生物 人工智能 计算机科学 机器学习 生物信息学 医学 免疫学 病毒学 疾病 传染病(医学专业) 病理 植物 物理 量子力学 爆发
作者
Jingxin Ren,Qian Gao,Xianchao Zhou,Lei Chen,Wei Guo,Kai‐Yan Feng,Jerry Hu,Tao Huang,Yu-Dong Cai
出处
期刊:Vaccine [Elsevier BV]
卷期号:42 (23): 126253-126253
标识
DOI:10.1016/j.vaccine.2024.126253
摘要

Viral infections significantly impact the immune system, and impact will persist until recovery. However, the influence of severe acute respiratory syndrome coronavirus 2 infection on the homeostatic immune status and secondary immune response in recovered patients remains unclear. To investigate these persistent alterations, we employed five feature-ranking algorithms (LASSO, MCFS, RF, CATBoost, and XGBoost), incremental feature selection, synthetic minority oversampling technique and two classification algorithms (decision tree and k-nearest neighbors) to analyze multi-omics data (surface proteins and transcriptome) from coronavirus disease 2019 (COVID-19) recovered patients and healthy controls post-influenza vaccination. The single-cell multi-omics dataset was divided into five subsets corresponding to five immune cell subtypes: B cells, CD4+ T cells, CD8+ T cells, Monocytes, and Natural Killer cells. Each cell was represented by 28,402 scRNA-seq (RNA) features, 3 Hash Tag Oligo (HTO) features, 138 Cellular indexing of transcriptomes and epitopes by sequencing (CITE) features and 23,569 Single Cell Transform (SCT) features. Some multi-omics markers were identified and effective classifiers were constructed. Our findings indicate a distinct immune status in COVID-19 recovered patients, characterized by low expression of ribosomal protein (RPS26) and high expression of immune cell surface proteins (CD33, CD48). Notably, TMEM176B, a membrane protein, was highly expressed in monocytes of COVID-19 convalescent patients. These observations aid in discerning molecular differences among immune cell subtypes and contribute to understanding the prolonged effects of COVID-19 on the immune system, which is valuable for treating infectious diseases like COVID-19.
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