Related Experiment Video
Updated: Jan 11, 2026
Mapping Alzheimer's Disease Variants to Their Target Genes Using Computational Analysis of Chromatin Configuration
Published on: January 9, 2020
Genetic variation in the Nr1d1 transcription factor binding site shapes metabolism-related protein networks
Yu Chen1, Tamara K Stevenson1, Yiding Cao1
1Department of Neurology, The University of Michigan, Ann Arbor, Michigan, USA.
Introduction:
Our previous work established the AD-BXD mouse panel as an innovative model for studying the genetic complexity and heterogeneity underlying Alzheimer's disease (AD). In this study, we leveraged this model and proteomics approach to identify protein signatures linked to cognitive resilience in AD.
Methods:
We assessed cognitive performance in 6-month-old AD-BXD mice using contextual fear conditioning and calculated a quantitative resilience score. Frontal cortex proteomes were analyzed using data-independent acquisition mass spectrometry. Protein quantitative trait loci (pQTL) mapping and transcription factor motif analysis were performed.
Results:
Cognitive resilience was highly heritable. Of nine pQTL proteins associated with resilience, eight mapped to a shared locus on chromosome 1, forming a genetically regulated module. This module mediates the link between specific SNPs and cognitive outcomes in AD.
Discussion:
These findings reveal a protein network underlying resilience to early AD pathology, with Nr1d1 emerging as a key transcriptional regulator.
Highlights:
Quantitative proteomics analysis using the genetically diverse AD-BXD mouse panel identified nine proteins whose abundances are under genetic control and associated with differences in cognitive response to early-onset AD mutations. Genetic mapping revealed that the abundances of eight of these nine proteins are regulated by the same genomic region on chromosome 1, forming a module that mediates the relationship between specific SNPs and cognitive outcomes in response to AD mutations. Integrating proteomic and genomic data suggests that SNP rs46128598, located in the transcription factor binding site of nuclear receptor subfamily 1 group D member 1 (Nr1d1), is a novel effector of metabolic pathways involved in cognitive performance differences in AD mutant carriers. This study indicates that targeting the molecular drivers of genetic resilience to AD mutations, including Nr1d1-mediated proteins (Ak1a1, Gars1, Nudt3, Ogdh, Ptpn11, Iars2, Uba1, Ppt1, and Tmem223), could lead to new therapeutic approaches to delay the onset and/or progression of AD.
