Background
Methods
Sources of blood transcriptomic and phenotypic data
APOE genotype | Blood batch 1 | Blood batch 2 | Combined blood | Brain | Blood-brain overlap | |||||
---|---|---|---|---|---|---|---|---|---|---|
AD | CTRL | AD | CTRL | AD | CTRL | AD | CTRL | AD | CTRL | |
ɛ2/ɛ2** | 0 | 0 | 0 | 1 | 0 | 1 | 0 | 5 | 0 | 1 |
ɛ2/ɛ3 | 5 | 3 | 9 | 9 | 14 | 12 | 32 | 39 | 12 | 8 |
ɛ3/ɛ3 | 16 | 11 | 44 | 31 | 60 | 42 | 197 | 158 | 49 | 33 |
ɛ2/ɛ4** | 1 | 1 | 5 | 0 | 6 | 1 | 9 | 4 | 4 | 1 |
ɛ3/ɛ4* | 8 | 1 | 21 | 10 | 21 | 10 | 101 | 25 | 22 | 8 |
ɛ4/ɛ4** | 1 | 0 | 1 | 0 | 0 | 0 | 5 | 1 | 2 | 0 |
NA | 0 | 0 | 1 | 0 | 1 | 0 | 0 | 0 | 0 | 0 |
Total | 31 | 16 | 81 | 51 | 112 | 67 | 344 | 232 | 89 | 51 |
Sources of brain transcriptomic and phenotypic data
Quality control, mapping, and quantification of gene expression data and sample
Gene expression analysis in the blood and brain
Differential expression analysis
Single-cell gene expression analysis
Gene set enrichment analysis
Co-expressed gene network analysis in the blood and brain
Measurements and association with vascular injury-related proteins
Results
Differentially expressed genes in the blood and brain
Gene | Dataset | APOE ɛ2/ɛ3 | APOE ɛ3/ɛ3 | APOE ɛ3/ɛ4 | Total | ||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
N | Z-score | P-value | N | Z-score | P-value | N | Z-score | P-value | N | Z-score | P-value | ||
INPP5D | Blood | 26 | −0.62 | 0.53 | 102 | 1.67 | 0.10 | 31 | 2.12 | 0.03 | 179 | 2.16 | 0.03 |
Brain | 71 | 1.80 | 0.07 | 355 | 0.92 | 0.36 | 126 | 0.66 | 0.51 | 576 | 2.30 | 0.02 | |
Combined | 97 | 1.51 | 0.13 | 457 | 1.29 | 0.20 | 157 | 1.31 | 0.19 | 755 | 2.42 | 0.02 | |
HLA-DQA1 | Blood | 26 | −1.49 | 0.14 | 102 | −1.80 | 0.07 | 31 | 0.96 | 0.34 | 179 | −2.26 | 0.03 |
Brain | 71 | 0.30 | 0.76 | 355 | −3.13 | 1.7 × 10−3 | 126 | −1.01 | 0.31 | 576 | −2.23 | 0.03 | |
Combined | 97 | −0.16 | 0.87 | 457 | −2.84 | 4.6 × 10−3 | 157 | −0.66 | 0.51 | 755 | −2.42 | 0.02 | |
SPDYE3 | Blood | 26 | −0.08 | 0.94 | 102 | −0.76 | 0.45 | 31 | −0.96 | 0.34 | 179 | −1.47 | 0.14 |
Brain | 71 | −0.79 | 0.43 | 355 | −0.97 | 0.33 | 126 | −2.16 | 0.03 | 576 | −2.73 | 6.4 × 10−3 | |
Combined | 97 | −0.77 | 0.44 | 457 | −0.96 | 0.33 | 157 | −2.37 | 0.02 | 755 | −2.26 | 0.02 | |
TSPOAP1 | Blood | 26 | −1.38 | 0.17 | 102 | 0.30 | 0.77 | 31 | −0.16 | 0.87 | 179 | −0.55 | 0.58 |
Brain | 71 | −1.04 | 0.30 | 355 | −2.17 | 0.03 | 126 | −1.85 | 0.06 | 576 | −3.65 | 2.6 × 10−4 | |
Combined | 97 | −1.39 | 0.16 | 457 | −1.35 | 0.18 | 157 | −1.82 | 0.07 | 755 | −2.24 | 0.03 | |
SIGLEC11 | Blood | 26 | 1.43 | 0.15 | 102 | 0.47 | 0.64 | 31 | 0.24 | 0.81 | 179 | 0.33 | 0.74 |
Brain | 71 | 1.05 | 0.29 | 355 | 2.46 | 0.01 | 126 | 2.58 | 9.9 × 10−3 | 576 | 3.77 | 1.6 × 10−4 | |
Combined | 97 | 1.42 | 0.16 | 457 | 1.86 | 0.06 | 157 | 2.54 | 0.01 | 755 | 2.17 | 0.03 |
Gene | Dataset | APOE ɛ2/ɛ3 | APOE ɛ3/ɛ3 | APOE ɛ3/ɛ4 | Total | ||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
N | Z-score | P-value | N | Z-score | P-value | N | Z-score | P-value | N | Z-score | P-value | ||
FRAS1 | Blood | NA | NA | NA | 75 | −0.24 | 0.81 | 31 | −4.66 | 3.2 × 10−6 | 132 | −2.26 | 0.02 |
Brain | NA | NA | NA | 355 | −0.97 | 0.33 | 126 | 0.28 | 0.78 | 576 | −0.49 | 0.62 | |
Combined | NA | NA | NA | 430 | −0.75 | 0.45 | 157 | −1.23 | 0.22 | 708 | −1.27 | 0.20 | |
PIGHP1 | Blood | 26 | 1.67 | 0.09 | 102 | 0.43 | 0.67 | 31 | 1.30 | 0.19 | 179 | 1.14 | 0.25 |
Brain | 71 | 4.42 | 9.8 × 10−6 | 355 | 0.53 | 0.59 | 126 | 0.47 | 0.64 | 576 | 1.98 | 0.05 | |
Combined | 97 | 4.67 | 3.1 × 10−6 | 457 | 0.53 | 0.59 | 157 | 0.87 | 0.39 | 755 | 1.68 | 0.09 |
APOE genotype-dependent pathways in combined blood and brain expression profiles
Hallmark pathway | APOE genotype | NES | Adjusted P-value | Leading-edge genes |
---|---|---|---|---|
Allograft rejection | ɛ3/ɛ3 | −1.89 | 0.02 | C2, HLA-DQA1, FAS, HLA-A, UBE2N, HLA-DOB, LTB, F2R, HLA-DRA, TAP2, B2M, CD1D, CD74, MAP3K7 |
ɛ3/ɛ4 | 2.16 | 7.4 × 10−3 | IRF4, CCL22, IRF7, CD74, HLA-DRA, ELF4, IL16, IFNGR2, IL27RA, IL1B | |
Interferon gamma response | ɛ3/ɛ3 | −2.56 | 1.3 × 10−5 | HLA-DQA1, FAS, CFB, BPGM, C1S, HLA-A, LAP3, MVP, PSME2, PSMA2, UBE2L6, SERPING1, DHX58, IFITM2, CD38, B2M, CD74 |
ɛ3/ɛ4 | 1.80 | 0.04 | CD274, CD69, BTG1, ISG20, PML, IRF4, NFKBIA, IRF7, CD74, IL10RA, IRF9 | |
Peroxisome | ɛ3/ɛ3 | −1.81 | 0.03 | IDH2, EHHADH, MVP, ALDH1A1, SCP2, SOD1, ABCD2, MSH2 |
ɛ3/ɛ4 | 1.90 | 0.03 | RDH11, ELOVL5, SLC25A19, CTPS1, SLC23A2, SEMA3C | |
Tnfa signaling via nfkb | ɛ2/ɛ3 | −2.03 | 0.01 | DUSP4, NR4A1, NR4A3, MARCKS, NFAT5, PHLDA1, DUSP2, KYNU, G0S2, ETS2, PTGS2, GCH1, MSC, SOD2, EGR2 |
ɛ3/ɛ4 | 2.27 | 2.5 × 10−3 | TRIP10, CD69, BTG1, DENND5A, PFKFB3, FOS, NFKBIA, LDLR, IER2, JUN, IL1A, PANX1, PNRC1, DUSP1, IFNGR2, OLR1, MAFF, IL1B, TNIP2, CCL20, BIRC2, IER3, GADD45B, KYNU, LITAF, CCRL2, SPHK1, FOSL1 |
Gene | APOE genotype | Pathway(s) | I-CAM1 | SAA | V-CAM1 | |||
---|---|---|---|---|---|---|---|---|
β | P-value | β | P-value | β | P-value | |||
C1S | ɛ3/ɛ3 | IGR | 0.11 | 0.13 | 0.24 | 2.5 × 10−3 | 0.30 | 2.0 × 10−4 |
C2 | ɛ3/ɛ3 | AR | 0.05 | 0.53 | 0.17 | 0.04 | 0.30 | 2.2 × 10−4 |
CD1D | ɛ3/ɛ3 | AR | 0.28 | 3.4 × 10−3 | 0.21 | 0.05 | 0.46 | 1.7 × 10−5 |
CD38 | ɛ3/ɛ4 | IGR | 0.09 | 0.25 | 0.07 | 0.41 | 0.39 | 6.1 × 10−6 |
CFB | ɛ3/ɛ3 | IGR | 0.16 | 0.05 | 0.46 | 2.2 × 10−7 | 0.26 | 5.4 × 10−3 |
DHX58 | ɛ3/ɛ3 | IGR | 0.11 | 0.34 | 0.20 | 0.13 | 0.51 | 7.1 × 10−5 |
ELF4 | ɛ3/ɛ4 | AR | 0.32 | 8.7 × 10−4 | 0.46 | 1.9 × 10−5 | 0.26 | 0.02 |
FOSL1 | ɛ3/ɛ4 | TSN | 0.20 | 3.1 × 10−4 | 0.18 | 3.1 × 10−3 | 0.08 | 0.21 |
HLA-A | ɛ3/ɛ3 | AR; IGR | 0.27 | 0.03 | 0.38 | 3.9 × 10−3 | 0.53 | 7.0 × 10−5 |
IDH2 | ɛ3/ɛ3 | P | 0.09 | 0.43 | 0.24 | 0.05 | 0.61 | 3.6 × 10−7 |
IER3 | ɛ3/ɛ4 | TSN | 0.14 | 0.06 | 0.37 | 3.5 × 10−6 | 0.07 | 0.43 |
IFITM2 | ɛ3/ɛ3 | IGR | 0.19 | 0.01 | 0.48 | 2.9 × 10−9 | 0.18 | 0.03 |
IRF7 | ɛ3/ɛ4 | AR; IGR | 0.24 | 9.5 × 10−4 | 0.41 | 2.8 × 10−7 | 0.20 | 0.02 |
ISG20 | ɛ3/ɛ4 | IGR | 0.21 | 3.6 × 10−3 | 0.34 | 1.9 × 10−5 | 0.29 | 4.4 × 10−4 |
LITAF | ɛ3/ɛ4 | TSN | 0.27 | 4.1 × 10−3 | 0.39 | 2.1 × 10−4 | 0.43 | 3.9 × 10−5 |
MVP | ɛ3/ɛ3 | IGR; P | 0.21 | 0.01 | 0.42 | 7.0 × 10−6 | 0.45 | 2.4 × 10−6 |
PFKFB3 | ɛ3/ɛ4 | TSN | 0.30 | 5.6 × 10−4 | 0.30 | 2.6 × 10−3 | 0.35 | 4.0 × 10−4 |
PML | ɛ3/ɛ4 | IGR | 0.28 | 0.02 | 0.47 | 3.8 × 10− | 0.50 | 2.0 × 10−4 |
SERPING1 | ɛ3/ɛ3 | IGR | 0.17 | 0.13 | 0.35 | 4.4 × 10−3 | 0.50 | 4.7 × 10−5 |
TNIP2 | ɛ3/ɛ4 | TSN | 0.36 | 1.9 × 10−3 | 0.59 | 4.7 × 10−6 | 0.19 | 0.15 |
TRIP10 | ɛ3/ɛ4 | TSN | 0.32 | 2.1 × 10−4 | 0.35 | 3.4 × 10−4 | 0.06 | 0.58 |