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Updated: Jun 19, 2025
Mapping Alzheimer's Disease Variants to Their Target Genes Using Computational Analysis of Chromatin Configuration
Published on: January 9, 2020
Revealing Molecular Patterns of Alzheimer's Disease Risk Gene Expression Signatures in COVID-19 Brains
Yan Liu1, Weiyue Xu1, Pan Yang2
1Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Third Hospital of Shanxi Medical University, Tongji Shanxi Hospital, Taiyuan, China.
Background:
Various virus infections are known to predispose to Alzheimer's disease (AD), and a linkage between COVID-19 and AD has been established. COVID-19 infection modulates the gene expression of the genes implicated in progression of AD.
Objective:
Determination of molecular patterns and codon usage and context analysis for the genes that are modulated during COVID-19 infection and are implicated in AD was the target of the study.
Methods:
Our study employed a comprehensive array of research methods, including relative synonymous codon usage, Codon adaptation index analysis, Neutrality and parity analysis, Rare codon analyses, and codon context analysis. This meticulous approach was crucial in determining the molecular patterns present in genes up or downregulated during COVID-19 infection.
Results:
G/C ending codons were preferred in upregulated genes while not in downregulated genes, and in both gene sets, longer genes have high expressivity. Similarly, T over A nucleotide was preferred, and selection was the major evolutionary force in shaping codon usage in both gene sets. Apart from stops codons, codons CGU - Arg, AUA - Ile, UUA - Leu, UCG - Ser, GUA - Val, and CGA - Arg in upregulated genes, while CUA - Leu, UCG - Ser, and UUA - Leu in downregulated genes were present below the 0.5%. Glutamine-initiated codon pairs have high residual values in upregulated genes. Identical codon pairs GAG-GAG and GUG-GUG were preferred in both gene sets.
Conclusions:
The shared and unique molecular features in the up- and downregulated gene sets provide insights into the complex interplay between COVID-19 infection and AD. Further studies are required to elucidate the relationship of these molecular patterns with AD pathology.
