Fig. 2

AD human grafts exhibit significant proteomic alterations, but do not show main AD hallmarks a and b Overview of representative PET/CT images of ¹⁸F-flutemetamol in control and AD iPSC-derived grafts six months after transplantation into mouse hippocampus. Sagittal and axial views showed no specific uptake related to AD in the brain. Color scale bar shows (from black to white) activity values in PET ¹⁸F-flutemetamol image. The diagram shows relative uptake values presented as %IA/g. Results are presented as mean ± S.E.M. N = 3–4 animals. c and d Characterization of Aβ deposition in hippocampi of 6-month-old 5xFAD transgenic mice and control and AD iPSC-derived grafts. Congo Red staining and immunostaining for H31L21 show presence of Aβ deposits only in 5xFAD mice. Scale bars: 200 µm. Results are presented as mean ± S.E.M. N = 4 animals. e Accumulation of Aβ measured by MSD in control and AD iPSC-derived human grafts. Results are presented as mean ± S.E.M. N = 4 animals. Statistical analysis by two-tailed t-test. f Diagram reflecting the β-sheet structure content in control and AD iPSC-derived human grafts as shown by the absorbance ratios 1,628 cm⁻¹, a band characteristic for β-sheet structure, to 1,656 cm.⁻¹, a band typically assigned to α-helical or random structures, main components of protein structures used here as a normalization parameter. Results are presented as individual values. n = 42—81 spectra per sample for N = 3–4 animals. P value: **** = P < 0.0001. Statistical analysis by two-tailed t-test. g Venn diagram representing the number of identified proteins exclusively derived from AD iPSC-derived human grafts and/or from host mouse brain tissue. N = 4 animals. h Principal component analysis using the normalized intensities of proteins quantified in control and AD iPSC-derived human grafts. i 1D annotation enrichment analysis of quantified proteins in control and AD iPSC-derived human grafts (Benjamini–Hochberg FDR: 0.02). Underrepresented pathways in ADHG (blue) are mainly enriched by mitochondrial function. Overrepresented biological pathways in ADHG (red) are mostly associated with the dysregulation of RNA metabolism. j Hierarchical clustering analysis of dysregulated proteins in AD iPSC-derived human grafts (Two-tailed t-test; p-value < 0.05; Benjamini–Hochberg FDR: 0.05) using Pearson correlation distance. The abundance of protein groups decreased and increased is represented in blue and red, respectively. k Biological pathways enriched in the protein clusters of the hierarchical clustering analysis of AD iPSC-derived human graft proteome (p-value < 0.01). p-values are denoted as the –log10 (p-value). The grey color symbolizes the absence of that specific biological pathway. l Cluster bar representation of significantly altered proteins linked to well-established markers of early molecular dysfunction in AD (Two-tailed t-test; p-value < 0.05; Benjamini–Hochberg FDR: 0.05)