Common proteomic profiles of induced pluripotent stem cell-derived three-dimensional neurons and brain tissue from Alzheimer patients

Abstract

We established a unique platform for proteomic analysis of cultured three-dimensional (3D) neurons and brain tissue from Alzheimer's disease (AD) patients. We collected peripheral blood mononuclear cells (PBMC), converted PBMC to induced pluripotent stem cell (iPSC) lines, and differentiated the iPSC into human 3D neuro-spheroids. The postmortem brain tissue from the superior frontal cortex, inferior frontal cortex and cerebellum area of the AD patients was compared to the same regions from the control subjects. Proteomic analysis of 3D neuro-spheroids derived from AD subjects revealed the alteration of a number of proteins involved in axon growth, mitochondrial function, and antioxidant defense. Similar analysis of post-mortem AD brain tissue revealed significant alteration in proteins involved in oxidative stress, neuro-inflammation, along with proteins related to axonal injury. These results clearly indicate that the dysfunction of 3D neurons from AD patients in our in vitro environment is comparable to the post-mortem AD brain tissue in vivo. In conclusion, our study revealed a number of candidate proteins that have important implications in AD pathogenesis and supports the notion that the iPSC-derived 3D neuronal system functions as a model to examine novel aspects of AD pathology.

Significance: In this study, we present a unique platform for proteomic analysis of induced pluripotent stem cell-derived three dimensional (3D) neurons and compare the results to those from three regions of post-mortem brain tissue from Alzheimer's disease patients and normal control subjects. Our results show that the dysfunction of 3D neurons from AD patients in our in vitro environment is comparable to the post-mortem AD brain tissue in vivo. Our results revealed several candidate proteins that have important implications in AD pathogenesis.

Keywords: 3D; Alzheimer; Bioinformatic; Neuro-spheroid; Proteomics; iPSC.

Fig. 1.

The cellular and molecular process networks of the dysregulated proteins in three brain regions of AD patients. (SF: Superior frontal cortex; IF: Inferior frontal cortex; CRLM: Cerebellum.)

Fig. 2.

Protein network analysis of up- (A) and down-regulated (B) proteins in three brain regions (SF, IF and CRLM) from AD patients relative to control subjects using the web-based tool STRING 10.0. The enriched biological process and dysregulated proteins were analyzed by DAVID. (SF: Superior frontal cortex; IF: Inferior frontal cortex; CRLM: Cerebellum.)

Fig. 3.

Comparison of GO Process Networks of up-regulated proteins from 3D neuro-spheroid and AD vulnerable brain regions (SF and IF) from AD patients using Metacore. Sorting is carried out for the statistically significant networks only. (SF: Superior frontal cortex, IF: Inferior frontal cortex.)

Fig. 4.

Comparison of GO Localization of up-regulated proteins from AD-derived 3D neuro-spheroid and brain regions (IF and SF) from AD patients using Metacore. (SF: Superior frontal cortex; IF: Inferior frontal.)

Fig. 5.

Levels of S100B and Vimentin in the brain tissue and 3D neuro-spheroids from AD and control subjects. ELISA was performed to quantify levels of S100B (A) and Vimentin in brain tissue (B) and 3D neuro-spheroids (C). The difference between two groups of brain samples (A and B) is statistically significant, p < 0.05. The standard error of means (short lines) and means (long middle line) are illustrated for each group. (SF: Superior frontal cortex; IF: Inferior frontal cortex.)