| Literature DB >> 31744542 |
Haihua Wang1, Shufang Zhang2, Na Wang3, Jie Zhang2, Mingkai Chen3, Xiaohui He2, Yinghua Cui4, Shuchao Pang5, Bo Yan6.
Abstract
BACKGROUND: Coronary artery disease (CAD) including acute myocardial infarction (AMI) is a common complex disease caused by atherosclerosis. Vascular epithelial growth factor receptor-1 (VEGFR-1) stimulates angiogenesis and vascular permeability, and functions as a decoy to sequester VEGF and prevent initiation of intracellular signaling. VEGFR-1 knockout mice exhibit significantly higher mortality due to heart failure, cardiac hypertrophy, and cardiac dysfunction. An evident increase in macrophage infiltration and cardiac fibrosis are also observed after transverse aortic constriction. Therefore, VEGFR-1 gene variants may be involved in CAD. In this study, VEGFR-1 gene promoter was genetically and functionally analyzed in large cohorts of AMI patients and ethnic-matched controls.Entities:
Keywords: Acute myocardial infarction; DNA sequence variants; Genetics; Promoter; VEGFR-1
Mesh:
Substances:
Year: 2019 PMID: 31744542 PMCID: PMC6862733 DOI: 10.1186/s40246-019-0243-1
Source DB: PubMed Journal: Hum Genomics ISSN: 1473-9542 Impact factor: 4.639
Genetic variants in the VEGFR-1 gene promoter identified in AMI patients and controls
| DSVs and SNPs | Genotype | Locationa | Controls ( | AMI ( | |
|---|---|---|---|---|---|
| g.28495805C>T (rs111458691) | CT | − 677 bp | 0 | 1 | – |
| g.28495796G>T | GT | − 668 bp | 0 | 1 | – |
| g.28495678G>A | GA | − 550 bp | 1 | 0 | – |
| g.28495538C>T (rs17086747) | CC | − 410 bp | 388 | 357 | 0.574 |
| CT | 26 | 28 | |||
| TT | 0 | 1 | |||
| g.28495527G>A (rs117031451) | GG | − 399 bp | 380 | 360 | 0.748 |
| GA | 33 | 25 | |||
| AA | 1 | 1 | |||
| g.28495445G>T | GT | − 317 bp | 0 | 1 | – |
| g.28495412C>T (rs36204411) | CC | − 284 bp | 388 | 357 | 0.574 |
| CT | 26 | 28 | |||
| TT | 0 | 1 | |||
| g.28495356G>A | GA | − 228 bp | 1 | 0 | – |
| g.28495341A>G | AG | − 213 bp | 0 | 1 | – |
| g.28495138G>C | GC | − 10 bp | 0 | 1 | – |
| g.28495135 G>C (rs17086745) | GG | − 7 bp | 388 | 357 | 0.574 |
| GC | 26 | 28 | |||
| CC | 0 | 1 | |||
| g.28495029G>T | GT | + 99 bp | 1 | 1 | 1.000 |
| g.28495028C>A | CA | + 100 bp | 1 | 1 | 1.000 |
| g.28494902C>T (rs55927955) | CC | + 226 bp | 355 | 343 | 0.162 |
| CT | 58 | 43 | |||
| TT | 1 | 0 | |||
| g.28494900G>A | GA | + 228 bp | 0 | 1 | – |
| g.28494895G>T | GT | + 233 bp | 1 | 1 | 1.000 |
aDSVs are located upstream (−) and downstream (+) to the transcription start site at 28495128 of VEGFR-1 gene (NC_000013.11). AMI acute myocardial infarction, DSV DNA sequence variant, − not applicable
Fig. 1Locations of the identified DSVs and SNPs within the VEGFR-1 gene promoter and 5′-UTR. The genetic variants are named according to the genomic DNA sequence of the human VEGFR-1 gene (Genbank accession number NC_000013.11). The transcription start site is at the position of 28495128 in the first exon
Fig. 2Sequencing chromatograms of the DSVs and SNPs. a Sequencing chromatograms of the DSVs and SNPs only identified in AMI patients, g.28495805C>T (rs111458691), g.28495796 G>T, g.28495445 G>T, g.28495341 A>G, g.28495138 G>C, and g.28494900 G>A. b Sequencing chromatograms of the DSVs identified only in controls, g.28495678 G>A and g.28495356G>A. Top panels show wild-type and bottom panels heterozygous sequences, which are marked with arrows
Predicted binding sites for transcription factors and promoter activity affected by DSVs and SNPs
| DSVs/SNPs | Binding cites for transcription factors | Promoter activity | AMI/CTR | |
|---|---|---|---|---|
| Creating | Abolishing | |||
| g.28495805C>T (rs111458691) | ELF5, NFE2L1:MafG | EGR2 | ↑ | AMI |
| g.28495796G>T | – | ESRRA, NR2C2, PAX5, PPARG::RXRA, ZEB1 | No change | AMI |
| g.28495678G>A | NFATC1 | TFE3 | No change | CTR |
| g.28495445G>T | FOXO3, NFE2L1::MafG | NFKB1 | ↓ | AMI |
| g.28495356G>A | HINFP | E2F4, TFAP2C | No change | CTR |
| g.28495341A>G | EGR1, NRF1 | BRCA1, HIF1A::ARNT | No change | AMI |
| g.28495138G>C | – | NHLH1, HIF1A::ARNT | ↓ | AMI |
| g.28494900G>A | NF1C | – | ↑ | AMI |
Fig. 3Relative transcriptional activity of wild type and variant VEGFR-1 gene promoters. Wild-type and variant VEGFR-1 gene promoters were cloned into reporter gene vector pGL3 and transfected into cultured cells. The transfected cells were collected, and dual-luciferase activities were assayed. Empty vector pGL3-basic was used as a negative control. Transcriptional activity of the wild-type VEGFR-1 gene promoter was designed as 100%. Relative activities of variant VEGFR-1 gene promoters were calculated. a Relative activities of wild type and variant VEGFR-1 gene promoters in HEK-293 cells. b Relative activities of wild-type and variant VEGFR-1 gene promoters in H9c2 cells. Lanes 1, pGL3-basic; 2, pGL3-WT; 3, pGL3-28494900A; 4, pGL3-28495138C; 5, pGL3-28495341G; 6, pGL3-28,495,445 T; 7, pGL3-28,495,796 T; 8, pGL3-28,495,805 T; 9, pGL3-28495356A; and 10, pGL3-28495678A. WT wild type, AMI AMI patients, CTR healthy controls. *P < 0.05, compared to pGL3-WT; **P < 0.01, compared to PGL3-WT
Double-stranded biotinylated oligonucleotides containing DSVs in AMI for EMSA
| DSVs | Oligonucleotide sequences |
|---|---|
| g.28495805C>T (rs111458691) | 5′-AAAAAGACACGGACA(C/T)GCTCCCCTGGGACC-3′ |
| g.28495796G>T | 5′-CGGACACGCTCCCCT(G/T)GGACCTGAGCTGGT-3′ |
| g.28495445G>T | 5′-GGAGGGAGTCTGCAA(G/T)GATTTCCTGAGCGC-3′ |
| g.28495341A>G | 5′-GCCCGCGTCGCCAGC(A/G)CCTCCCCACGCGCG-3′ |
| g.28495138G>C | 5′-TCGCCCCCGCCCTCG(G/C)CTGCTCTTCATCGA-3′ |
| g.28494900G>A | 5′-CGGACTCTGGCGGCC(G/A)GGTCGTTGGCCGCG-3′ |
Fig. 4EMSA of biotin-labeled oligonucleotides. Wild-type and variant oligonucleotides (30 bp) were designed and labeled with biotin for genetic variants identified in AMI patients, including g.28495805C>T(rs111458691), g.28495138G>C, and g.28494900G>A. EMSA was conducted with biotinylated oligonucleotides and the nuclear extracts from HEK-293 and H9c2 cells. Free probe was marked with an arrow at the bottom. The affected binding for transcription factors was marked with an open arrow
PCR primers for the VEGFR-1 gene promoter and 5′-UTR region
| PCR primers | Sequences | Location | Position | Products |
|---|---|---|---|---|
| Sequencing | ||||
| VEGFR-1-F1 | 5′-ACATCCCTCTGACGGGTTCCA-3′ | 28496221 | − 1092 bp | 770 bp |
| VEGFR-1-R1 | 5′-GTAAGCCGGGTGGAGGGAGT-3′ | 28495471 | − 338 bp | |
| VEGFR-1-F2 | 5′-GCCTCAGTCCTCCGTGCCAAGA-3′ | 28495608 | − 479 bp | 788 bp |
| VEGFR-1-R2 | 5′-ATGGTCAGCTACTGGGACACCGG-3′ | 28494821 | + 308 bp | |
| Functioning | ||||
| VEGFR-1-F | 5′-(KpnI)-GCTCCGTGCAGCCAGGACGA-3′ | 28,496,151 | − 1022 bp | 1307 bp |
| VEGFR-1-R | 5′-(HindIII)-GTGAGCGCGACGCGGCCT-3′ | 28,494,845 | + 284 bp | |
PCR primers are designed based on the genomic DNA sequence of the VEGFR-1 gene (NC_000013.11). The transcription start is at the position of 28495128 (+ 1). PCR polymerase chain reaction