Predictive network analysis identifies JMJD6 and other potential key drivers in Alzheimer’s disease

• Published in: Communications biology Vol. 6; no. 1; pp. 503 - 19
• Main Authors: Merchant, Julie P., Zhu, Kuixi, Henrion, Marc Y. R., Zaidi, Syed S. A., Lau, Branden, Moein, Sara, Alamprese, Melissa L., Pearse, Richard V., Bennett, David A., Ertekin-Taner, Nilüfer, Young-Pearse, Tracy L., Chang, Rui
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 15-05-2023; Nature Publishing Group; Nature Portfolio
• Subjects: 13/89; 38; 38/89; 38/91; 631/553/2714; 692/617/375/132/1283; 96/100; Alzheimer Disease - metabolism; Alzheimer's disease; Amyloid beta-Peptides - genetics; Amyloid beta-Peptides - metabolism; Biology; Biomedical and Life Sciences; Cell culture; Gene expression; Humans; Induced Pluripotent Stem Cells - metabolism; Jumonji Domain-Containing Histone Demethylases - metabolism; Life Sciences; Molecular modelling; Neurodegenerative diseases; Neurons - metabolism; Pathology; Pluripotency; Tau protein; tau Proteins - genetics; tau Proteins - metabolism; Therapeutic targets; Transcriptomics
• ISSN: 2399-3642; 2399-3642
• DOI: 10.1038/s42003-023-04791-5

Despite decades of genetic studies on late-onset Alzheimer’s disease, the underlying molecular mechanisms remain unclear. To better comprehend its complex etiology, we use an integrative approach to build robust predictive (causal) network models using two large human multi-omics datasets. We delineate bulk-tissue gene expression into single cell-type gene expression and integrate clinical and pathologic traits, single nucleotide variation, and deconvoluted gene expression for the construction of cell type-specific predictive network models. Here, we focus on neuron-specific network models and prioritize 19 predicted key drivers modulating Alzheimer’s pathology, which we then validate by knockdown in human induced pluripotent stem cell-derived neurons. We find that neuronal knockdown of 10 of the 19 targets significantly modulates levels of amyloid-beta and/or phosphorylated tau peptides, most notably
JMJD6
. We also confirm our network structure by RNA sequencing in the neurons following knockdown of each of the 10 targets, which additionally predicts that they are upstream regulators of REST and VGF. Our work thus identifies robust neuronal key drivers of the Alzheimer’s-associated network state which may represent therapeutic targets with relevance to both amyloid and tau pathology in Alzheimer’s disease.
A network analysis on deconvoluted bulk transcriptomic data from human Alzheimer’s disease cohorts identifies several potential key disease drivers, including
JMJD6
.