| Literature DB >> 25019165 |
Julia M Hofstra1, Marieke J H Coenen2, Mascha M V A P Schijvenaars2, Jo H M Berden1, Johan van der Vlag1, Lies H Hoefsloot2, Nine V A M Knoers2, Jack F M Wetzels1, Tom Nijenhuis1.
Abstract
BACKGROUND: Activating mutations in the Transient Receptor Potential channel C6 (TRPC6) cause autosomal dominant focal segmental glomerular sclerosis (FSGS). TRPC6 expression is upregulated in renal biopsies of patients with idiopathic membranous glomerulopathy (iMN) and animal models thereof. In iMN, disease progression is characterized by glomerulosclerosis. In addition, a context-dependent TRPC6 overexpression was recently suggested in complement-mediated podocyte injury in e.g. iMN. Hence, we hypothesized that genetic variants in TRPC6 might affect susceptibility to development or progression of iMN. METHODS &Entities:
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Year: 2014 PMID: 25019165 PMCID: PMC4096511 DOI: 10.1371/journal.pone.0102065
Source DB: PubMed Journal: PLoS One ISSN: 1932-6203 Impact factor: 3.240
Figure 1TRPC6 topology.
Structure of the TRPC6 monomer. TRPC6 belongs to the large family of TRP channels, which contain six transmembrane domains, one pore-forming region and large intracellular N- and C-tails. Four subunits are required to assemble a functional channel. In the pococyte, TRPC6 is part of the slit diaphragm multiprotein complex. TRP: transient receptor potential, ANK: Ankyrin repeat, cc: coiled–coiled domain, CIRB: CaM/IP3R-binding domain.
Primers used to sequence the 13 exons of TRPC6.
| Exon | F/R primer | Primer sequence 5′—3′ |
| 1 | F primer |
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| 1 | R primer |
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| 2_01 | F primer |
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| 2_01 | R primer |
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| 2_02 | F primer |
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| 2_02 | R primer |
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| 2_03 | F primer |
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| 2_03 | R primer |
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| 3 | F primer |
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| 3 | R primer |
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| 4 | F primer |
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| 4 | R primer |
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| 5 | F primer |
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| 5 | R primer |
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| 6 | F primer |
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| 6 | R primer |
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| 7 | F primer |
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| 7 | R primer |
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| 8 | F primer |
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| 8 | R primer |
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| 9 | F primer |
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| 9 | R primer |
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| 10 | F primer |
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| 10 | R primer |
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| 11 | F primer |
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| 11 | R primer |
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| 12 | F primer |
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| 12 | R primer |
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| 13 | F primer |
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| 13 | R primer |
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F, forward; R, reverse.
TRPC6 variants in patients with iMN (n = 101).
| Chr | position | name | ref | All | CEU AF | AF patients | p-value | AF PLA2R | p-value* | ref cDNA | cDNA | prot. level | effect | exon | observations |
| 11 | 101454244 | rs191383391 | G | G/T | 0.017** | 0.025 | 0.44 | 0.024 | 0.56 | C | c.-10C>A | 5′-ÚTR | 1 | ||
| 11 | 101454192 | rs3802829 | G | G/A | 0.093** | 0.089 | 0.85 | 0.113 | 0.48 | C | c.43C>T | p.Pro15Ser | missense | 1 | NH2-terminal region |
| 11 | 101453995 | rs17096918 | C | C/T | 0.083 | 0.069 | 0.52 | 0.081 | 0.93 | G | c.170+70G>A | intron | |||
| 11 | 101375549 | rs10501986 | T | T/C | 0.480 | 0.495 | 0.71 | 0.492 | 0.81 | A | c.171-20A>G | intron | |||
| 11 | 101374812 | rs144891994 | C | C/T | 0 ∧ | 0.005 | NA | 0.008 | NA | G | c.888G>A | p.Thr296Thr | synonymous | 2 | CCD |
| 11 | 101374626 | rs4542378 | G | G/A | 0.480 | 0.490 | 0.80 | 0.492 | 0.81 | C | c.945+129C>T | intron | |||
| 11 | 101359750 | rs36111323 | G | G/A | 0.135** | 0.165 | 0.24 | 0.156 | 0.52 | C | c.1211C>T | p.Ala404Val | missense | 4 | linker region between CCD & TMD1 |
| 11 | 101347093 | rs12366144 | A | A/G | 0.250** | 0.292 | 0.20 | 0.347 | 0.02 | T | c.1683T>C | p.Asn561Asn | synonymous | 6 | linker region between TMD3 & TMD4 |
| 11 | 101342958 | rs61743044 | G | G/A | 0.020 | 0.020 | 1.00 | 0.024 | 0.75 | C | c.2115C>T | p.Tyr705Tyr | synonymous | 8 | linker region between TMD5 & TMD6 |
| 11 | 101342931 | rs144891994 | C | C/A | 0.008 | 0.005 | 0.66 | 0 | 0.32 | G | c.2142G>T | p.Thr714Thr | synonymous | 8 | TMD 6 |
| 11 | 101325970 | rs7105083 | G | G/A | 0.263 | 0.238 | 0.47 | 0.266 | 0.93 | C | c.2485-138C>T | intron | |||
| 11 | 101325788 | rs72984209 | G | G/A | 0.077 | 0.054 | 0.28 | 0.081 | 0.87 | C | c.2529C>T | p.Phe843Phe | synonymous | 11 | |
| 11 | 101323770 | rs12805398 | C | C/T | 0.140** | 0.158 | 0.49 | 0.153 | 0.69 | G | c.2712G>A | p.Gln904Gln | synonymous | 13 |
Chr = chromosome; position = basepair position based on UCSC genome browser version Human Feb. 2009 (GRCh37/hg19) assembly; name = rs identifier; ref = genomic reference allele; all = alleles; CEU AF = allele frequencies variant allele in control population. Control population consists of Caucasian population from 1000 Genomes project (release 10 - March 2012), complemented with data form 292 geographically matched controls for variants marked with **; ∧ = not reported in 1000 Genomes project; AF patient = patient minor allele frequencies; p-value = comparison allele frequencies controls and patients; AF PLA2R = minor allele frequencies in PLA2R positive patients (n = 62); p-value* = comparison allele frequencies controls and PLA2R positive patients; genomic level = NC_000002.11; ref cDNA = reference allele cDNA (given that TRPC6 is on the negative strand); cDNA = NM_004621.5; prot. level = NP_004612.2; CCD = coiled-coiled domain; TMD = transmembrane domain.
Genotypes in iMN patients with clinical remission versus patients with renal failure.
| Genotype | Remission n = 26 (%) | Renal Failure n = 46 (%) | p-value | |||
| rs191383391 | CC | 25 | (96.2) | 43 | (93.5) | 0.64 |
| CA | 1 | (3.8) | 3 | (6.5) | ||
| rs3802829 | CC | 22 | (84.6) | 37 | (80.4) | 0.68 |
| CT | 4 | (15.4) | 9 | (19.6) | ||
| rs17096918 | GG | 23 | (88.5) | 37 | (80.4) | 0.40 |
| GA | 3 | (11.5) | 9 | (19.6) | ||
| rs10501986 | AA | 9 | (34.6) | 10 | (21.7) | 0.09 |
| AG | 15 | (57.7) | 25 | (54.3) | ||
| GG | 2 | (7.7) | 11 | (23.9) | ||
| rs144891994 | GG | 26 | (100) | 46 | (100) | 1.00 |
| rs4542378 | CC | 9 | (34.6) | 9 | (19.6) | 0.09 |
| CT | 15 | (57.7) | 27 | (58.7) | ||
| TT | 2 | (7.7) | 10 | (21.7) | ||
| rs36111323 | GG | 19 | (73.1) | 31 | (67.4) | 0.74 |
| GA | 7 | (26.9) | 14 | (30.4) | ||
| rs61743044 | CC | 26 | (100) | 43 | (93.5) | 1.00 |
| CT | 0 | (0) | 3 | (6.5) | ||
| rs12366144 | TT | 16 | (61.5) | 20 | (43.5) | 0.18 |
| TC | 9 | (34.6) | 23 | (50.0) | ||
| CC | 1 | (3.8) | 3 | (6.5) | ||
| rs145077205 | GG | 25 | (96.2) | 46 | (100) | 0.18 |
| GT | 1 | (3.8) | 0 | (0) | ||
| rs7105083 | CC | 15 | (57.7) | 26 | (56.5) | 0.91 |
| CT | 10 | (38.5) | 18 | (39.1) | ||
| TT | 1 | (3.8) | 2 | (4.3) | ||
| rs72984209 | CC | 23 | (88.5) | 41 | (89.1) | 0.93 |
| CT | 3 | (11.5) | 5 | (10.9) | ||
| rs12805398 | GG | 18 | (69.2) | 32 | (69.6) | 0.88 |
| GA | 8 | (30.8) | 14 | (30.4) | ||
*N = 45 for renal failure.
*P-value for minor allele frequencies-comparison (Mann-Whitney U).