Metabolites, the biochemical products of the cellular process, can be used to measure alterations in biochemical pathways related to the pathogenesis of Alzheimer's disease (AD). However, the relationships between systemic abnormalities in metabolism and the pathogenesis of AD are poorly understood. In this study, we aim to identify AD-specific metabolomic changes and their potential upstream genetic and transcriptional regulators through an integrative systems biology framework for analyzing genetic, transcriptomic, metabolomic, and proteomic data in AD. Metabolite co-expression network analysis of the blood metabolomic data in the Alzheimer's Disease Neuroimaging Initiative (ADNI) shows short-chain acylcarnitines/amino acids and medium/long-chain acylcarnitines are most associated with AD clinical outcomes, including episodic memory scores and disease severity. Integration of the gene expression data in both the blood from the ADNI and the brain from the Accelerating Medicines Partnership Alzheimer's Disease (AMP-AD) program reveals ABCA1 and CPT1A are involved in the regulation of acylcarnitines and amino acids in AD. Gene co-expression network analysis of the AMP-AD brain RNA-seq data suggests the CPT1A- and ABCA1-centered subnetworks are associated with neuronal system and immune response, respectively. Increased ABCA1 gene expression and adiponectin protein, a regulator of ABCA1, correspond to decreased short-chain acylcarnitines and amines in AD in the ADNI. In summary, our integrated analysis of large-scale multiomics data in AD systematically identifies novel metabolites and their potential regulators in AD and the findings pave a way for not only developing sensitive and specific diagnostic biomarkers for AD but also identifying novel molecular mechanisms of AD pathogenesis.
GrantsFNIH Alzheimer's Disease Neuroimaging Initiative (ADNI) (National Institutes of Health) DOD ADNI (Department of Defense) National Institute on Aging National Institute of Biomedical Imaging and Bioengineering AbbVie National Institutes of Health (NIH)/National Institute on Aging National Institute on Aging (NIA) NIA Alzheimer's Association Alzheimer's Drug Discovery Foundation Araclon Biotech Lumosity Lundbeck Merck Co., Inc. Meso Scale Diagnostics, LLC NeuroRx Research Neurotrack Technologies Novartis Pharmaceuticals Corporation Pfizer Inc. Piramal Imaging Servier Takeda Pharmaceutical Company Transition Therapeutics Canadian Institutes of Health Research Illinois Department of Public Health Johnson & Johnson Pharmaceutical Research & Development LLC Janssen Alzheimer Immunotherapy Research & Development, LLC BioClinica, Inc. Biogen Bristol-Myers Squibb Company CereSpir, Inc. Cogstate Eisai Inc. Elan Pharmaceuticals, Inc. Eli Lilly and Company F. Hoffmann-La Roche Ltd EuroImmun Genentech, Inc. Fujirebio GE Healthcare IXICO Ltd. Translational Genomics Research Institute