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. 2019 Jan 28;12(1):8.
doi: 10.1186/s13041-019-0430-y.

Quantitative profiling brain proteomes revealed mitochondrial dysfunction in Alzheimer's disease

Sunil S Adav  1   2 , Jung Eun Park  3 , Siu Kwan Sze  4
Affiliations

Quantitative profiling brain proteomes revealed mitochondrial dysfunction in Alzheimer's disease

Sunil S Adav et al. Mol Brain. .

Abstract

Mitochondrial dysfunction is a key feature in both aging and neurodegenerative diseases including Alzheimer's disease (AD), but the molecular signature that distinguishes pathological changes in the AD from healthy aging in the brain mitochondria remain poorly understood. In order to unveil AD specific mitochondrial dysfunctions, this study adopted a discovery-driven approach with isobaric tag for relative and absolute quantitation (iTRAQ) and label-free quantitative proteomics, and profiled the mitochondrial proteomes in human brain tissues of healthy and AD individuals. LC-MS/MS-based iTRAQ quantitative proteomics approach revealed differentially altered mitochondriomes that distinguished the AD's pathophysiology-induced from aging-associated changes. Our results showed that dysregulated mitochondrial complexes including electron transport chain (ETC) and ATP-synthase are the potential driver for pathology of the AD. The iTRAQ results were cross-validated with independent label-free quantitative proteomics experiments to confirm that the subunit of electron transport chain complex I, particularly NDUFA4 and NDUFA9 were altered in AD patients, suggesting destabilization of the junction between membrane and matrix arms of mitochondrial complex I impacted the mitochondrial functions in the AD. iTRAQ quantitative proteomics of brain mitochondriomes revealed disparity in healthy aging and age-dependent AD.

Keywords: Alzheimer’s disease; Complex I; Mitochondrial dysfunction; Mitochondriome; Neurodegenerative diseases; Proteomics; iTRAQ.

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Conflict of interest statement

Ethics approval and consent to participate

Frozen brain samples of the medial frontal gyrus from AD patients and age-matched controls were obtained from Netherlands Brain Bank, Meibergdreef 47, 1105 BA Amsterdam, The Netherlands. The scientific use of the human material was conducted in accordance with the Declaration of Helsinki, and informed consent was obtained from all patients or the guardians of the patients prior to donation of brain tissues upon their death. All procedures were approved and performed in accordance with the ethical guidelines of the Nanyang Technological University ethics board.

Consent for publication

Not Applicable.

Competing interests

The authors declare that they have no competing interests.

Publisher’s Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Figures

Fig. 1
Fig. 1
Brain mitochondrial proteins properties, regulation and localization. a Molecular weight distribution of iTRAQ quantified brain mitochondrial proteins, b pI distribution of iTRAQ quantified brain mitochondrial proteins, c Volcano plot of the log10(p-values) as a function of log2(protein fold change). The statistical significance (p-value in a − log10 scale) is plotted as a function of the protein fold change (in a log2 scale), d Cellular localization of mitochondrial proteins as determined by gene ontology
Fig. 2
Fig. 2
Hierarchical clustering of differentially regulated (+/− 0.3) mitochondrial proteins exhibiting their expressions in early onset AD (log2 (115/114)), late onset AD (log2 (117/116)) and healthy aging subjects (log2 (116/114)). Up-regulated protein expression values are displayed in red, the down-regulation values are in blue, and the intermediate values are in shades of red and blue
Fig. 3
Fig. 3
iTRAQ-quantified subunits of complex I. The electron transport chain proteins that were iTRAQ quantified in this study are shown in red color (upper panel). The lower panel show the iTRAQ ratios with standard deviation indicates the abundances and regulation of these mitochondrial subunits in early onset AD (log2 (115/114)), late onset AD (log2 (117/116)), healthy aging subjects (log2 (116/114)) and aging AD (log2 (117/115))
Fig. 4
Fig. 4
Regulation of NDUFA4, NDUFAB1 and NDUFA9 in early onset AD. a iTRAQ quantitative abundances of NDUFA4, NDUFAB1 and NDUFA9 in early onset AD, b Western blot analysis of NDUFA9 and NDUFAB1 using mouse monoclonal anti-NDUFA9 and rabbit monoclonal anti-NDUFAB1 that were purchased from Abcam, c and d Quantitative analysis of immunoblot images by software ImageJ. Differences between means were assessed with the one-way ANOVA test. P-value < 0.05 was considered to indicate statistically significant differences. e Label free quantitative abundances of subunits NDUFA4, f Label free quantitative abundances of subunits NDUFAB1, g Label free quantitative abundances of subunits NDUFA9. The dot indicates values in individual brain sample, their biological and technical replicates). Brain mitochondria was isolated, purified using anti-TOM22 magnetic beads and analyzed using Q-Exactive mass spectrometry
Fig. 5
Fig. 5
Regulation of NDUFA4, NDUFAB1 and NDUFA9 in late onset AD. a iTRAQ quantitative abundances of NDUFA4, NDUFAB1 and NDUFA9 in late onset AD, b Western blot analysis of NDUFA9 and NDUFAB1 using mouse monoclonal anti-NDUFA9 and rabbit monoclonal anti-NDUFAB1 in individual samples of control and late onset AD, c and d Quantitative analysis of immunoblot images by software ImageJ. e Label free quantitative abundances of subunits NDUFA4, f Label free quantitative abundances of subunits NDUFAB1, g Label free quantitative abundances of subunits NDUFA9. The dot indicates values in individual brain sample, their biological and technical replicates. Brain mitochondria was isolated, purified using anti-TOM22 magnetic beads and analyzed using Q-Exactive mass spectrometry
Fig. 6
Fig. 6
Quantitative abundances of subunits of complex II, III, IV and ATP synthase in brain proteome of early onset AD (log2 (115/114)), late onset AD (log2 (117/116)) and healthy aging subjects (log2 (116/114)). a iTRAQ quantitative ratios with standard deviation of quantified subunits of complex II, b iTRAQ quantitative ratios with standard deviation of quantified subunits of complex III, c iTRAQ quantitative ratios with standard deviation of quantified subunits of complex IV, d iTRAQ quantitative ratios of ATP synthase
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