Exploration of blood-derived coding and non-coding RNA diagnostic immunological panels for COVID-19 through a co-expressed-based machine learning procedure

Front Immunol. 2022 Nov 3;13:1001070. doi: 10.3389/fimmu.2022.1001070. eCollection 2022.

Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS- CoV-2) is the causative virus of the pandemic coronavirus disease 2019 (COVID-19). Evaluating the immunological factors and other implicated processes underlying the progression of COVID-19 is essential for the recognition and then the design of efficacious therapies. Therefore, we analyzed RNAseq data obtained from PBMCs of the COVID-19 patients to explore coding and non-coding RNA diagnostic immunological panels. For this purpose, we integrated multiple RNAseq data and analyzed them overall as well as by considering the state of disease including severe and non-severe conditions. Afterward, we utilized a co-expressed-based machine learning procedure comprising weighted-gene co-expression analysis and differential expression gene as filter phase and recursive feature elimination-support vector machine as wrapper phase. This procedure led to the identification of two modules containing 5 and 84 genes which are mostly involved in cell dysregulation and innate immune suppression, respectively. Moreover, the role of vitamin D in regulating some classifiers was highlighted. Further analysis disclosed the role of discriminant miRNAs including miR-197-3p, miR-150-5p, miR-340-5p, miR-122-5p, miR-1307-3p, miR-34a-5p, miR-98-5p and their target genes comprising GAN, VWC2, TNFRSF6B, and CHST3 in the metabolic pathways. These classifiers differentiate the final fate of infection toward severe or non-severe COVID-19. The identified classifier genes and miRNAs may help in the proper design of therapeutic procedures considering their involvement in the immune and metabolic pathways.

Keywords: COVID-19; SARS- CoV-2; WGCNA; innate immune pathways; machine learning; vitamin D.

MeSH terms

  • COVID-19* / diagnosis
  • COVID-19* / genetics
  • Humans
  • Machine Learning
  • MicroRNAs* / genetics
  • MicroRNAs* / metabolism
  • SARS-CoV-2 / genetics

Substances

  • MicroRNAs
  • MIRN340 microRNA, human
  • MIRN98 microRNA, human