Protein swarm-based cause-effect analysis: effects of microRNAs on cooperation networks linking COVID-19 infections, atherosclerosis, and Alzheimer's disease

Well-being depends on the integrated operation of biological processes at all levels of system organization, from individual cells to tissues and organ systems, collectively sustaining homeostasis and optimal bodily functions. The regulation of cooperation among these processes is mediated by information flow within networks possessing diverse structural, functional, and temporal properties. Disruption in these networks is observed in conditions such as infections, inflammatory diseases, and cancer. To advance understanding of immune system roles and to elucidate mechanisms underlying health vulnerability during disease, we utilized proteomics data related to 4,800 diseases along with protein swarm-based cause-effect analyses to identify principles governing plasticity and self-organizing capabilities of immune systems. Our findings demonstrate that the precision of immune system functions is regulated by dynamic alterations in the topologies of cooperation networks that are partially modulated by microRNAs. Additionally, our analysis indicates that investigating the underlying causes of diseases through the study of cooperative network functions and their interactions with microRNAs-rather than concentrating exclusively on individual protein targets or microRNAs-provides significant insights for devising effective treatment strategies for infections, cardiovascular conditions, Alzheimer's disease, cancer, aging, and related health concerns.