| Literature DB >> 19258388 |
Mai Tuyet Vuong1, Sigrid Lundberg, Iva Gunnarsson, Lars Wramner, Maria Seddighzadeh, Mirjana Hahn-Zoric, Anders Fernström, Lars A Hanson, Lieu Thi Do, Stefan H Jacobson, Leonid Padyukov.
Abstract
BACKGROUND: There is growing evidence of genetic risk for susceptibility to IgA nephropathy. Among several candidate genes related to immunological regulation in renal tissue, TGFB1 is known to be a contributor to proliferation and the development of fibrosis.Entities:
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Year: 2009 PMID: 19258388 PMCID: PMC2747497 DOI: 10.1093/ndt/gfp079
Source DB: PubMed Journal: Nephrol Dial Transplant ISSN: 0931-0509 Impact factor: 5.992
Glomerular filtration rate of the patients in the different stages of chronic kidney diseasea
| >90 ml/min | 90–60 ml/min | 30–59 ml/min | 15–29 ml/min | <15 ml/min | |
|---|---|---|---|---|---|
| Males, | 19 (18.1%) | 28 (26.7%) | 20 (19.0%) | 6 (5.7%) | 4 (3.8%) |
| Females, | 4 (3.8%) | 15 (14.3%) | 6 (5.7%) | 2 (1.9%) | 1 (1%) |
| Total, | 23 (21.9%) | 43 (41.0%) | 26 (24.7%) | 8 (7.6%) | 5 (4.8%) |
aCalculated for individuals with available clinical data.
Polymorphisms of the TGFB1 gene in IgA nephropathy patients
| Chromosome | Heterozygosity | |||||||
|---|---|---|---|---|---|---|---|---|
| SNP | Position | Alternative name | position | Alleles | from NCBI | MAFa | ABI assay | Methods |
| rs6957 | Downstream 3′ genomic region | 46522446 | C/T | 0.414 | 0.167 | C___7818385_10 | TaqMan | |
| rs2241715 | Intron 1 | 46548726 | G/T | 0.467 | 0.289 | Assay by design | TaqMan | |
| rs1800471 | Signal sequence of exone 1 | Codon 25 or G915C (arginine→proline) | 46550716 | C/G | 0.112 | 0.081 | NA | REMb |
| rs1982073 | Signal sequence of exone 1 | Codon 10 or T869C (leucine→proline) | 46550761 | C/T | 0.397 | 0.378 | C___22272997_10 | TaqMan |
| rs1800469 | Promoter | C-509T | 46552136 | A/G | 0.485 | 0.295 | C___8708473_10 | TaqMan |
aMinor allele frequency from current study.
bRestriction Endonuclease Mapping method.
Genotype frequencies of TGFB1 polymorphisms in (a) male and (b) female IgA nephropathy patients in a co-dominant model
| SNPs | Genotype frequency in co-dominant model | Chi-square | |||||
|---|---|---|---|---|---|---|---|
| (a) Male IgA nephropathy patients | |||||||
| TGFB1 rs6957 | Totalb | CC | CT | TT | |||
| Group | Control | 314 (100%) | 3 (1%) | 85 (27%) | 226 (72%) | 11.5 | 0.003 |
| Patient | 144 (100%) | 9 (6.3%) | 42 (29.1%) | 93 (64.6%) | |||
| TGFB1 rs2241715 | Total | GG | GT | TT | |||
| Group | Control | 315 (100%) | 171 (54.3%) | 120 (38.1%) | 24 (7.6%) | 7.4 | 0.02 |
| Patient | 145 (100%) | 59 (40.7%) | 73 (50.3%) | 13 (9%) | |||
| TGFB1 rs1800471 | Total | CC | CG | GG | |||
| Group | Control | 319 (100%) | 0 (0%) | 48 (15%) | 271 (85%) | 9.1 | 0.01 |
| Patient | 143 (100%) | 4 (2.8%) | 19 (13.3%) | 120 (83.9%) | |||
| TGFB1 rs1982073 | Total | CC | CT | TT | |||
| Group | Control | 314 (100%) | 132 (42%) | 147 (46.8%) | 35 (11.2%) | 9.9 | 0.007 |
| Patient | 144 (100%) | 40 (27.8%) | 78 (54.2%) | 26 (18%) | |||
| TGFB1 rs1800469 | Total | AA | AG | GG | |||
| Group | Control | 314 (100%) | 24 (7.6%) | 120 (38.2%) | 170 (54.2%) | 10.2 | 0.006 |
| Patient | 144 (100%) | 13 (9%) | 76 (52.8%) | 55 (38.2%) | |||
| (b) Female IgA nephropathy patients | |||||||
| TGFB1 rs6957 | Totalb | CC | CT | TT | |||
| Group | Control | 152 (100%) | 4 (2.6%) | 44 (28.9%) | 104 (68.5%) | 0.9 | 0.6 |
| Patient | 65 (100%) | 3 (4.6%) | 16 (24.6%) | 46 (70.8%) | |||
| TGFB1 rs2241715 | Total | GG | GT | TT | |||
| Group | Control | 153 (100%) | 75 (49%) | 64 (41.8%) | 14 (9.2%) | 1.4 | 0.5 |
| Patient | 66 (100%) | 35 (53%) | 28 (42.4%) | 3 (4.6%) | |||
| TGFB1 rs1800471 | Total | CC | CG | GG | |||
| Group | Control | 156 (100%) | 0 (0%) | 23 (14.7%) | 133 (85.3%) | 2.4 | 0.3 |
| Patient | 66 (100%) | 1 (1.5%) | 10 (15.2%) | 55 (83.3%) | |||
| TGFB1 rs1982073 | Total | CC | CT | TT | |||
| Group | Control | 153 (100%) | 56 (36.6%) | 78 (51%) | 19 (12.4%) | 0.3 | 0.8 |
| Patient | 66 (100%) | 26 (39.4%) | 31 (47%) | 9 (13.6%) | |||
| TGFB1 rs1800469 | Total | AA | AG | GG | |||
| Group | Control | 154 (100%) | 14 (9.1%) | 65 (42.2%) | 75 (48.7%) | 0.5 | 0.8 |
| Patient | 65 (100%) | 4 (6.2%) | 28 (43%) | 33 (50.8%) | |||
aUncorrected.
bTotal number for different variations may be different due to genotyping failure.
Allelic frequencies of TGFB1 polymorphisms in (a) male and (b) female IgA nephropathy patients and healthy controls
| Control, case | Control, case | 100 000 permutation, | |||
|---|---|---|---|---|---|
| SNPs | ratio counts | frequencies | Chi-square | ||
| (a) Male IgA nephropathy patients | |||||
| rs6957 | 537:91, 228:60 | 0.855, 0.792 | 5.77 | 0.016 | 0.08 |
| rs2241715 | 462:168, 191:99 | 0.733, 0.659 | 5.381 | 0.020 | 0.09 |
| rs1800471 | 581:47, 259:27 | 0.925, 0.906 | 1.011 | 0.314 | NS |
| rs1982073 | 411:217, 158:130 | 0.654, 0.549 | 9.401 | 0.002 | 0.02 |
| rs1800469 | 460:168, 186:102 | 0.732, 0.646 | 7.132 | 0.007 | 0.04 |
| (b) Female IgA nephropathy patients | |||||
| rs6957 | 52:252, 22:108 | 0.171, 0.169 | 0.002 | 0.9631 | NS |
| rs2241715 | 92:214, 34:98 | 0.301, 0.258 | 0.835 | 0.3608 | NS |
| rs1800471 | 285:23, 120:12 | 0.925, 0.909 | 0.333 | 0.5641 | NS |
| rs1982073 | 116:190, 49:83 | 0.379, 0.371 | 0.024 | 0.876 | NS |
| rs1800469 | 93:215, 36:94 | 0.302, 0.277 | 0.276 | 0.5996 | NS |
aUncorrected.
Haplotype frequencies of TGFB1 polymorphisms in (a) male and (b) female IgA nephropathy patients and healthy controls
| Haplotype | Control/case | 100 000 permutation | ||||
|---|---|---|---|---|---|---|
| Block | frequencies | Control/case ratio counts | frequencies | Chi-square | ||
| (a) Male IgA nephropathy patients | ||||||
| TGGCG | 0.528 | 355.5: 274.5, 130.5: 159.5 | 0.564, 0.450 | 10.42 | 0.0012 | 0.006 |
| TTGTA | 0.214 | 131.1: 498.9, 65.5: 224.5 | 0.208, 0.226 | 0.374 | 0.5411 | NS |
| CGGCG | 0.089 | 55.5: 574.5, 26.5: 263.5 | 0.088, 0.091 | 0.026 | 0.8709 | NS |
| TGCTG | 0.080 | 47.0: 583.0, 27.0: 263.0 | 0.075, 0.093 | 0.919 | 0.3378 | NS |
| CTGTA | 0.075 | 35.9: 594.1, 33.5: 256.5 | 0.057, 0.116 | 9.749 | 0.0018 | 0.008 |
| (b) Female IgA nephropathy patients | ||||||
| TGGCG | 0.526 | 161.8: 146.2, 69.6: 62.4 | 0.525, 0.527 | 0.001 | 0.9709 | NS |
| TTGTA | 0.220 | 69.4: 238.6, 27.2: 104.8 | 0.225, 0.206 | 0.194 | 0.6599 | NS |
| CGGCG | 0.092 | 27.2: 280.8, 13.4: 118.6 | 0.088, 0.101 | 0.194 | 0.6595 | NS |
| TGCTG | 0.070 | 19.8: 288.2, 10.9: 121.1 | 0.064, 0.082 | 0.455 | 0.4998 | NS |
| CTGTA | 0.064 | 21.6: 286.4, 6.8: 125.2 | 0.070, 0.051 | 0.545 | 0.4602 | NS |
aUncorrected.
Fig. 1Meta-analysis with rs1800469 in two different populations and our own data; the genetic marker displayed a protective effect for the common genotype with CC and passed test for heterogeneity between the studies.