Table V. Abundant Bruch membrane/choroid proteins by AMD category of progression.
Adjusted mean protein ratios (AMD/control), S.E., and p values for abundant Bruch membrane proteins based on category of AMD progression are shown. Abundant proteins exhibited mean ratios at least 1 S.D. above the category median and p values <0.05 (from supplemental Tables 37–39 and Fig. 4). Protein subcellular source is from the Swiss Protein Database: A, secreted; B, cytoplasmic; C, membrane; D, nuclear.
| Swiss-Prot accession number | Subcellular source | Protein | Donor frequency | Mean protein ratio | S.E. | p value |
|---|---|---|---|---|---|---|
| Early/mid-stage AMD (n = 10 donors) | ||||||
| Only abundant in early/mid-stage AMD | ||||||
| P10643 | A | Complement C7 | 3 | 2.01a | 0.13 | 0.032 |
| Q16518 | B | Retinal pigment epithelium-specific 65-kDa protein | 4 | 1.86a | 0.14 | 0.011 |
| P02489 | B | α-Crystallin A chain | 6 | 1.58a | 0.19 | 0.049 |
| P02763 | A | α1-Acid glycoprotein 1 | 4 | 1.46a | 0.03 | <0.001 |
| P01031 | A | Complement C5 | 5 | 1.45a | 0.09 | 0.006 |
| P01903 | C | HLA class II histocompatibility antigen, DRα chain | 4 | 1.44a | 0.09 | 0.029 |
| Q01995 | B | Transgelin | 6 | 1.42a | 0.10 | 0.012 |
| P30086 | B | Phosphatidylethanolamine-binding protein 1 | 3 | 1.41a | 0.08 | 0.024 |
| P29762 | B | Cellular retinoic acid-binding protein 1 | 3 | 1.35a | 0.03 | 0.009 |
| P02511 | B | α-Crystallin B chain | 10 | 1.27 | 0.06 | 0.003 |
| Q14103 | D | Heterogeneous nuclear ribonucleoprotein D0 | 5 | 1.24 | 0.05 | 0.006 |
| P39019 | D | 40 S ribosomal protein S19 | 4 | 1.21 | 0.06 | 0.021 |
| P12271 | B | Cellular retinaldehyde-binding protein 1 | 5 | 1.21 | 0.07 | 0.034 |
| P08195 | C | 4F2 cell surface antigen heavy chain | 4 | 1.20 | 0.04 | 0.008 |
| P01011 | A | α1-Antichymotrypsin | 10 | 1.20 | 0.08 | 0.047 |
| Also abundant in other AMD categories | ||||||
| P05109 | B | Protein S100-A8 | 5 | 1.60a | 0.08 | 0.001 |
| P35625 | A | Metalloproteinase inhibitor 3 | 10 | 1.38a | 0.10 | 0.006 |
| Q05707 | A | Collagen α1(XIV) chain | 3 | 1.37a | 0.04 | 0.005 |
| P02748 | A | Complement C9 | 10 | 1.21 | 0.08 | 0.032 |
| Advanced dry AMD (n = 6 donors) | ||||||
| Only abundant in advanced dry AMD | ||||||
| P17931 | A, B, C | Galectin-3 | 3 | 1.83a | 0.13 | 0.020 |
| Q9NQC3 | C | Reticulon-4 | 3 | 1.34a | 0.07 | 0.016 |
| P11166 | C | Solute carrier family 2, facilitated glucose transporter | 3 | 1.25 | 0.03 | 0.001 |
| P06899 | D | Histone H2B type 1-J | 3 | 1.23 | 0.07 | 0.040 |
| P62805 | D | Histone H4 | 6 | 1.22 | 0.08 | 0.036 |
| P04216 | C | Thy-1 membrane glycoprotein | 4 | 1.21 | 0.06 | 0.039 |
| Also abundant in other AMD categories | ||||||
| P06702 | B | Protein S100-A9 | 3 | 1.66a | 0.14 | 0.023 |
| P35625 | A | Metalloproteinase inhibitor 3 | 6 | 1.32a | 0.10 | 0.021 |
| Q05707 | A | Collagen α1(XIV) chain | 5 | 1.19 | 0.05 | 0.012 |
| Advanced neovascular AMD (n = 8 donors) | ||||||
| Only abundant in advanced neovascular AMD | ||||||
| P59666 | A | Neutrophil α-defensins 1–3 | 4 | 3.26a | 0.15 | 0.004 |
| P04004 | A | Vitronectin | 8 | 1.33 | 0.07 | 0.001 |
| P02452 | A | Collagen α1(I) chain | 5 | 1.33 | 0.08 | 0.027 |
| P02675 | A | Fibrinogen β chain | 3 | 1.28 | 0.08 | 0.028 |
| P01024 | A | Complement C3 | 7 | 1.22 | 0.06 | 0.011 |
| Q09666 | D | Neuroblast differentiation-associated protein AHNAK | 4 | 1.19 | 0.03 | 0.002 |
| Also abundant in other AMD categories | ||||||
| P06702 | B | Protein S100-A9 | 4 | 1.92a | 0.18 | 0.011 |
| P05109 | B | Protein S100-A8 | 4 | 1.73a | 0.15 | 0.016 |
| P02748 | A | Complement C9 | 8 | 1.51a | 0.13 | 0.010 |
| P35625 | A | Metalloproteinase inhibitor 3 | 8 | 1.36 | 0.07 | 0.001 |
a Ratios at least 2 S.D. above the category median.