| Literature DB >> 25883525 |
Xiaoli Qu1, Chengye Che1, Ang Gao2, Jing Lin1, Nan Wang1, Xing Du1, Ying Liu1, Yanli Guo1, Wenjun Chen1, Guiqiu Zhao1.
Abstract
PURPOSE: Dendritic cell-associated C-type lectin-1 (Dectin-1) and dendritic cell-specific intercellular adhesion molecule-3-grabbing non-integrin (DC-SIGN) play a crucial role in the early procedure of fungal pathogen defenses. The present study evaluated the associations between Dectin-1 and DC-SIGN gene single nucleotide polymorphisms (SNPs) and susceptibility to fungal keratitis (FK) in the northern Han Chinese population.Entities:
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Year: 2015 PMID: 25883525 PMCID: PMC4392830
Source DB: PubMed Journal: Mol Vis ISSN: 1090-0535 Impact factor: 2.367
Primer sequences for each SNP and PCR conditions.
| Gene | Gene location | SNPs | Primer pairs | Product length | Anneling temperature (°C) | Extendding time(s) | |
|---|---|---|---|---|---|---|---|
| Dectin-1 | Intron | rs17206002 rs3901533 rs11053613 rs3901532 | F | TGACTACAATAATCAGGACACTACC | 777 bp | 64 | 47 |
| R | TAGCCATTGTCTTCTCCTCCA | ||||||
| DC-SIGN | Promoter | rs4804803 rs2287886 | F | ATTATGATTCTGCCCCAACTC | 424 bp | 63 | 27 |
| R | CAGCTTTTATTTCCCACCCT | ||||||
| DC-SIGN | Promoter | rs735239 rs735240 | F | TAGATGGTGGGGCTGAGACT | 407 bp | 62 | 25 |
| R | GCATACAGAAACCCCGTTGT | ||||||
Genotype and allele distribution of FK patients compared with controls.
| SNP | Genotype/Allele | Cases (n=109) N(%) | Controls (n=220) N(%) | | OR (95%CI) ** |
|---|---|---|---|---|---|
| rs17206002 | AA | 87 (79.8) | 184 (83.6) | 0.392 | 0.774(0.430–1.394) |
| TA | 22 (20.2) | 36 (16.4) | |||
| T | 22 (10.1) | 36(8.2) | 0.416 | 0.794 (0.455–1.386) | |
| A | 196 (89.9) | 404 (91.8) | |||
| rs11053613 | AA | 82 (75.2) | 169 (76.8) | 0.750 | 0.917(0.536–1.566) |
| GA | 27 (24.8) | 51 (23.2) | |||
| G | 27 (12.4) | 51 (11.6) | 0.767 | 0.927 (0.564–1.525) | |
| A | 191(87.6) | 389 (88.4) | |||
| rs3901532 | AA | 2 (1.8) | 6 (2.7) | 0.882 | |
| GA | 41 (37.6) | 81 (36.8) | |||
| GG | 66 (60.6) | 133 (60.5) | |||
| A | 45 (20.6) | 93 (21.1) | 0.883 | 0.977 (0.711–1.341) | |
| G | 173 (79.4) | 347 (78.9) | |||
| rs3901533 | GG | 2 (1.8) | 5 (2.3) | 0.949 | |
| GT | 42 (38.5) | 82 (37.3) | |||
| TT | 65 (59.6) | 133 (60.5) | |||
| G | 46 (21.1) | 92 (20.9) | 0.955 | 1.009 (0.737–1.382) | |
| T | 172 (78.9) | 348 (79.1) | |||
| rs4804803 | CC | 1 (0.9) | 5 (2.3) | 0.407 | |
| CT | 17 (15.6) | 44 (20.0) | |||
| TT | 91 (83.5) | 171 (77.7) | |||
| C | 19 (8.7) | 54 (12.3) | 0.171 | 0.710 (0.432–1.167) | |
| T | 199 (91.3) | 386 (87.7) | |||
| rs2287886 | CC | 14 (12.8) | 23 (10.5) | 0.407 | |
| TC | 46 (42.2) | 81 (36.8) | |||
| TT | 49 (45.0) | 116 (52.7) | |||
| C | 74 (33.9) | 127 (28.9) | 0.183 | 1.176 (0.929–1.489) | |
| T | 144 (66.1) | 313 (71.1) | |||
| rs735239 | AA | 73 (67.5) | 176 (80.0) | 0.019 | |
| GA | 30 (27.5) | 40 (18.2) | |||
| GG | 6 (5.5) | 4(1.8) | |||
| G | 42 (19.3) | 48 (10.9) | 0.003 | 1.766 (1.207–2.585) | |
| A | 176 (80.7) | 392 (89.1) | |||
| rs735240 | AA | 12 (11.0) | 9 (4.1) | 0.033 | |
| AG | 36 (33.0) | 66 (30.0) | |||
| GG | 61 (56.0) | 145 (65.9) | |||
| A | 60 (27.5) | 84 (19.1) | 0.014 | 1.609 (1.100–2.355) | |
| G | 158 (72.5) | 356 (80.9) |
*: χ2 test; **: OR=odds ratio, CI=confidence interval.
Allele and genotype distribution by severity of FK.
| SNP | Genotype /Allele | Cases (n=109) N (%) | Controls (n=220) N(%) | χ2 | | ||
|---|---|---|---|---|---|---|---|
| Mild | Moderate | Severe | |||||
| rs17206002 | AA | 8(61.5) | 25 (86.2) | 54 (80.6) | 184 (83.6) | 4.567 | 0.206 |
| TA | 5 (38.5) | 4 (13.8) | 13 (19.4) | 36 (16.4) | |||
| rs11053613 | AA | 11 (84.6) | 22 (75.9) | 49 (73.1) | 169 (76.8) | 0.904 | 0.824 |
| GA | 2 (15.4) | 7 (24.1) | 18 (26.9) | 51 (23.2) | |||
| rs3901532 | AA | 0 (0.0) | 0 (0.0) | 2 (3.0) | 6 (2.7) | 7.532 | 0.274 |
| GA | 9 (69.2) | 9 (31.0) | 23 (34.3) | 81 (36.8) | |||
| GG | 4 (30.8) | 20 (69.0) | 42 (62.7) | 133 (60.5) | |||
| rs3901533 | GG | 0 (0.00) | 0 (0.00) | 2(3.0) | 5 (2.3) | 7.246 | 0. 299 |
| GT | 9 (69.2) | 9 (31.0) | 24 (35.9) | 82 (37.3) | |||
| TT | 4 (30.8) | 20(69.0) | 41(61.1) | 133(60.5) | |||
| rs4804803 | CC | 0 (0.0) | 1 (3.4) | 0 (0.0) | 5 (2.3) | 4.408 | 0. 622 |
| CT | 1 (7.7) | 6 (20.7) | 10 (14.9) | 44 (20.0) | |||
| TT | 12 (92.3) | 22 (75.9) | 57 (85.1) | 171 (77.7) | |||
| rs2287886 | CC | 1 (7.7) | 5 (17.2) | 8 (11.9) | 23 (10.5) | 4.740 | 0. 578 |
| TC | 4 (30.8) | 14 (48.3) | 28 (41.8) | 81 (36.8) | |||
| TT | 8 (61.5) | 10 (34.5) | 31 (46.3) | 116 (52.7) | |||
Comparison the corneal trauma history cases with normal controls.
| SNP | Genotype/Allele | Cases (n=109) N (%) | Contorls (n=220) N (%) | χ2 | ||
|---|---|---|---|---|---|---|
| Corneal Trauma History (n=68) | No Corneal Trauma History (n=41) | |||||
| rs17206002 | AA | 55(80.9) | 32(78.0) | 184 (83.6) | 0.874 | 0.646 |
| TA | 13(19.1) | 9(22.0) | 36 (16.4) | |||
| rs11053613 | AA | 51(75.0) | 31(75.6) | 169 (76.8) | 0.107 | 0.948 |
| GA | 17(25.0) | 10(24.4) | 51 (23.2) | |||
| rs3901532 | AA | 1(1.5) | 1(2.4) | 6(2.7) | 0.429 | 0.980 |
| GA | 25(36.8) | 16(39.0) | 81(36.8) | |||
| GG | 42(61.8) | 24(59.5) | 133(60.5) | |||
| rs3901533 | GG | 1(1.5) | 1(2.4) | 5(2.3) | 0.235 | 0. 994 |
| GT | 26(38.2) | 16(39.0) | 82(37.3) | |||
| TT | 41(60.3) | 24(58.5) | 133(60.5) | |||
| rs4804803 | CC | 0(0.0) | 1(2.4) | 5(2.3) | 3.074 | 0. 546 |
| CT | 12(17.6) | 5(12.2) | 44(20.0) | |||
| TT | 56(82.4) | 35(85.4) | 171(77.7) | |||
| rs2287886 | CC | 7(10.3) | 7(17.1) | 23 (10.5) | 4.137 | 0.388 |
| TC | 32(47.1) | 14(34.1) | 81(36.8) | |||
| TT | 29(42.6) | 20(48.8) | 116(52.7) | |||
| rs735239 | AA | 48(70.6) | 25(61.0) | 176(80.0) | 9.446 | 0.051 |
| GA | 17(25.0) | 13(31.7) | 40(18.2) | |||
| GG | 3(4.4) | 3(7.3) | 4(1.8) | |||
| rs735240 | AA | 7(10.3) | 5(12.2) | 9(4.1) | 7.346 | 0.119 |
| AG | 24(35.3) | 12(29.3) | 66(30.0) | |||
| GG | 37(54.4) | 24(58.5) | 145(65.9) | |||
Haplotype analysis for DC-SIGN gene polymorphisms.
| No | Haplotype | Frequency | OR (95% CI) | | |||
|---|---|---|---|---|---|---|---|
| Total | Cases | Controls | |||||
| rs4804803 | rs2287886 | ||||||
| H1 | T | T | 0.691 | 0.656 | 0.709 | 0.728 (0.553–1.107) | 0.165 |
| H2 | T | C | 0.198 | 0.257 | 0.168 | 1.710 (1.154–2.534) | 0.007 |
| H3 | C | C | 0.107 | 0.083 | 0.120 | 0.657 (0.375–1.152) | 0.140 |
| rs735239 | rs735240 | ||||||
| H1 | A | G | 0.781 | 0. 725 | 0. 809 | 0.621 (0.425–0.909) | 0.014 |
| H2 | G | A | 0.137 | 0.193 | 0.109 | 1.949 (1.242–3.059) | 0.003 |
| H3 | A | A | 0.082 | 0.083 | 0.082 | 1.010 (0.560–1.823) | 0.974 |
Haplotype analysis for Dectin-1 gene polymorphisms.
| No | Haplotype | Frequency | OR (95% CI) | | |||||
|---|---|---|---|---|---|---|---|---|---|
| rs17206002 | rs3901533 | rs11053613 | rs3901532 | Total | Cases | Controls | |||
| H1 | A | T | A | G | 0.670 | 0.665 | 0.673 | 0.966(0.685–1.364) | 0.845 |
| H2 | A | G | A | A | 0.123 | 0.110 | 0.130 | 0.831(0.501–1.380) | 0. 475 |
| H3 | A | T | G | G | 0.112 | 0.115 | 0.111 | 1.034(0.620–1.724) | 0.899 |
| H4 | T | G | A | A | 0.081 | 0.096 | 0.075 | 1.1315(0.741–2.332) | 0.348 |
Figure 1Linkage disequilibrium structure of the SNPs and haplotype blocks analyzed by Haploview 4.2 software. The D’ value of each SNP pair is expressed as a percentage and shown within the respective square (D’= 1 not shown). Higher D’ values are indicated in brighter red. A: LD plot of four SNPs of the DC-SIGN gene in 109 study subjects. The four SNPs constitute two haplotype blocks, with substantial LD among the SNPs of both blocks (block 1: D’ =0.95; block 2: D’=1.00). B: LD plot of four SNPs of the Dectin-1 gene in 109 study subjects. The four SNPs constitute a haplotype block spanning 0.2 kb of the Dectin-1 gene, and the magnitude of LD between each SNP was extremely high, with pair-wise D’ ≥0.92.