Table 4.
Association with antemortem cognitive measures as well as neuropathological indices for transcripts that were consistently differentially expressed in this study and in the same brain region from the MSSB study. Samples from different brain regions were pooled and the statistical model corrected for the brain region in addition to the top five surrogate variables and gender using a linear regression model, while the main effect of interest was coded as a quantitative variable.
| genes | beta | AveExpr | T | P.Value∗ |
|---|---|---|---|---|
| Association with last MMSE score | ||||
| CDK2AP1 | −0.02 | 7.20 | −5.06 | 1.89E-06 |
| GEM | −0.03 | 2.55 | −3.21 | 1.77E-03 |
| CD74 | −0.02 | 8.21 | −2.61 | 1.04E-02 |
| ATG16L2 | −0.01 | 4.54 | −2.36 | 2.01E-02 |
| HLA-DRA | −0.02 | 5.97 | −2.19 | 3.08E-02 |
| MEIS3 | 0.01 | 6.38 | 1.86 | 6.58E-02 |
| OLR1 | −0.02 | 2.45 | −2.03 | 4.54E-02 |
| ITGAX | −0.01 | 3.42 | −1.03 | 3.06E-01 |
| TREM2 | 0.00 | 3.85 | −0.57 | 5.69E-01 |
| C3AR1 | 0.00 | 2.46 | −0.07 | 9.41E-01 |
| Association with Braak scorea | ||||
| CDK2AP1 | 0.12 | 7.18 | 4.97 | 1.88E-06 |
| MEIS3 | −0.10 | 6.34 | −2.54 | 1.23E-02 |
| OLR1 | 0.10 | 2.45 | 2.39 | 1.80E-02 |
| GEM | 0.11 | 2.59 | 2.28 | 2.41E-02 |
| HLA-DRA | 0.07 | 5.97 | 1.80 | 7.46E-02 |
| ATG16L2 | 0.03 | 4.47 | 1.79 | 7.62E-02 |
| CD74 | 0.04 | 8.17 | 1.11 | 2.71E-01 |
| C3AR1 | 0.06 | 2.51 | 1.40 | 1.63E-01 |
| ITGAX | 0.05 | 3.41 | 1.17 | 2.43E-01 |
| TREM2 | 0.02 | 3.84 | 0.46 | 6.45E-01 |
| Association with tangle total | ||||
| CDK2AP1 | 0.05 | 7.18 | 4.93 | 2.26E-06 |
| GEM | 0.06 | 2.59 | 3.66 | 3.52E-04 |
| OLR1 | 0.04 | 2.47 | 2.84 | 5.25E-03 |
| ATG16L2 | 0.02 | 4.46 | 2.45 | 1.55E-02 |
| MEIS3 | −0.04 | 6.33 | −2.09 | 3.88E-02 |
| HLA-DRA | 0.02 | 5.98 | 1.50 | 1.36E-01 |
| C3AR1 | 0.02 | 2.52 | 1.36 | 1.75E-01 |
| CD74 | 0.01 | 8.18 | 0.62 | 5.36E-01 |
| TREM2 | 0.01 | 3.86 | 0.57 | 5.68E-01 |
| ITGAX | 0.01 | 3.43 | 0.42 | 6.74E-01 |
| Association with plaque total | ||||
| OLR1 | 0.04 | 2.47 | 3.93 | 1.32E-04 |
| GEM | 0.04 | 2.59 | 3.58 | 4.68E-04 |
| MEIS3 | −0.04 | 6.33 | −3.28 | 1.32E-03 |
| CDK2AP1 | 0.02 | 7.18 | 2.47 | 1.47E-02 |
| HLA-DRA | 0.02 | 5.98 | 2.13 | 3.50E-02 |
| TREM2 | 0.02 | 3.86 | 2.05 | 4.21E-02 |
| ATG16L2 | 0.01 | 4.46 | 1.68 | 9.52E-02 |
| CD74 | 0.02 | 8.18 | 1.37 | 1.73E-01 |
| C3AR1 | 0.02 | 2.52 | 1.74 | 8.34E-02 |
| ITGAX | 0.00 | 3.43 | −0.17 | 8.63E-01 |
| Association with plaque densityb | ||||
| OLR1 | 0.17 | 2.45 | 3.87 | 1.64E-04 |
| MEIS3 | −0.16 | 6.34 | −3.28 | 1.31E-03 |
| CDK2AP1 | 0.08 | 7.18 | 2.98 | 3.34E-03 |
| TREM2 | 0.14 | 3.84 | 2.90 | 4.38E-03 |
| GEM | 0.15 | 2.59 | 2.90 | 4.39E-03 |
| HLA-DRA | 0.11 | 5.97 | 2.35 | 2.04E-02 |
| CD74 | 0.09 | 8.17 | 1.92 | 5.73E-02 |
| C3AR1 | 0.09 | 2.51 | 1.99 | 4.85E-02 |
| ATG16L2 | 0.03 | 4.47 | 1.60 | 1.12E-01 |
| ITGAX | 0.07 | 3.41 | 1.46 | 1.45E-01 |
p-value less than 0.05/10 = 0.005 is deemed significant.
Braak score is the Braak neurofibrillary stage (0-VI) as defined originally by Braak and Braak (1991). Thick 40–80 μm sections stained with Gallyas, Campbell-Switzer and thioflavine S stains are used to obtain this. These scores were converted to numerals (0–6) for statistical purposes.
Plaque density is the CERAD neuritic and/or cored plaque density (Mirra et al., 1991) defined using the CERAD templates as none, sparse, moderate and frequent. The value listed represents the highest density score seen in any of the three evaluated cerebral neocortex regions (frontal, temporal and parietal). However, if frequent neuritic or cored plaques are a rare finding, the score may be adjusted downwards to reflect this. These scores were converted to numerals (1–4) for statistical purposes.