Decreased activity of RCAN1.4 is a potential risk factor for congenital heart disease in a Han Chinese population
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To investigate if the RCAN1.4 plays a role in heart development, we evaluated the expression of the RCAN1.1 and RCAN1.4 proteins in E10.5 mouse embryonic hearts and human hearts. The results revealed that both the RCAN1.1 and RCAN1.4 were expressed in mouse embryonic hearts and human hearts (Fig. 1B). In addition, the RCAN1.4 protein was easily detected in embryonic mouse hearts at E10.5 but not in embryonic mouse heads at E10.5, while RCAN1.1 protein levels were similar between embryonic mouse hearts and heads (Figs. 1B and S1A). These results demonstrate that not only RCAN1.4 is expressed in hearts, but also its expression is differentially regulated, at least during mouse heart development, suggesting that the expression level of RCAN1.4 might contribute to human CHD.
Association of SNP rs2243890 A>G in RCAN1.4 promoter region with CHDs in two independent case-control studies
A further stratified analysis of rs2243890 A>G was performed based on different subtypes of CHDs. The most significant differences in CHD vs. control were observed in an additive genetic model in septal defects, which had a 1.51-fold higher risk in sporadic CHD patients (OR = 1.51, 95% CI = 1.11–2.07, P = 0.01) and conotruncal defects, which had a 2.18-fold higher (OR = 2.18, 95% CI = 1.59–2.99, P = 1.33E−06) risk in sporadic CHD patients (Table S3). There were no significant associations observed between rs2243890 A>G and other CHD subtypes, including right ventricular outflow tract obstruction (RVOTO) (P = 0.12), left ventricular outflow tract obstruction (LVOTO) (P = 0.34) and patent ductus arteriosus (PDA) (P = 0.41) (Table S3).
Since the minor G allele of rs2243890 (at −1,712 bp) was located in the promoter region for RCAN1.4 transcript, we hypothesized that the G allele may contribute to the risk of CHD by influencing RCAN1.4 transcription. To test our hypothesis, we evaluated the RCAN1.4 mRNA level in human heart tissue samples from sporadic CHD patients by qRT-PCR. We found that RCAN1.4 mRNA level in human heart samples with heterozygous A/G alleles was almost threefold lower than that of samples with homozygous A/A alleles (Fig. 1C), while as a control, the difference in RCAN1.4 mRNA level between the heart samples carrying either heterozygous C/G alleles or homozygous G/G alleles of rs2300385 (at −1,885 bp) was not significant (Fig. 1C). These results suggest that the minor G allele of rs2243890 in RCAN1 may affect CHD by decreasing rather than enhancing the transcription of RCAN1.4. To further confirm the effect of rs2243890 A>G, we evaluated the RCAN1.4 promoter activity of the A and G alleles of rs2243890 using a dual-luciferase reporter assay in HEK293, H9C2 and C2C12 cells. The results showed that the transcriptional activity of the G allele was significantly lower than that of the A allele in all three cell lines (Fig. 1D), demonstrating that the G allele of rs2243890 attenuates RCAN1.4 transcription. Taken together, these results suggest that the minor G allele of rs2243890 in RCAN1 may contribute to CHD by inhibiting rather than enhancing RCAN1.4 transcription.
As the minor G allele of rs2243890 decreased RCAN1.4 promoter activity (Fig. 1D), we questioned whether these changes might be due to its different binding affinity for some transcription factors. Using a major probe and a minor probe containing the A allele and G allele, respectively (Table S5), we performed an EMSA to evaluate the binding affinity of these alleles for unknown transcription factors in 293T cells. The results showed that the G allele displayed a higher binding affinity for some nuclear protein(s) than the A allele did (Fig. 1E). As the minor G allele decreased RCAN1.4 promoter activity compared with the major A allele, we inferred that the specific binding protein(s) probably function as transcriptional repressors.
By Sanger sequencing we also confirmed the CHD-specific rare mutation RCAN1.4E25K identified from target-capture sequencing (Fig. 1F). The MAF for RCAN1.4E25K in the ExAC database was as rare as 3.35E−05 (4/119506). To assess whether this RCAN1.4E25K mutant plays a role in CHD development, we performed an NFAT promoter-mediated luciferase reporter assay. Results showed that mutant RCAN1.4E25K significantly impaired suppression of NFAT-mediated transcription (Figs. 1G and S1B), suggesting that RCAN1.4E25K may be a loss-of-function mutant.
The E25 of human RCAN1.4 protein is conserved from the zebrafish to human (Fig. S1C). About 70% of zebrafishes injected with antisense morpholino-modified oligonucleotides (MO) for zebrafish rcan1a-4 (a zebrafish homolog of human RCAN1.4) (Alghanem et al., 2017) displayed an enlarged pericardium (a CHD phenotype) and this rcan1a-4 MO-mediated CHD phenotype could be partially rescued by co-injected human RCAN1.4 mRNA in a dosage-dependent manner (Fig. 1H). However, human RCAN1.4E25K mRNA failed to rescue rcan1a-4 MO-mediated CHD phenotype, suggesting again that RCAN1.4E25K is a loss-of-function mutation in vivo.
In this study, the SNP rs2243890 in RCAN1.4 promoter region was found to be significantly associated with CHD and further validated to be significantly associated with septal and conotruncal defects of CHD by analysing blood samples from 870 sporadic CHD patients and 1,320 normal controls from a Han Chinese population. Our results, therefore, adds one more piece of evidence supporting the conclusion that genetic associations with CHD have a high phenotypic specificity (Soemedi et al., 2012; Cordell et al., 2013) and also suggest a population specificity for genetic association of SNP rs2243890 with CHD because reported GWAS studies did not find the association of SNP rs2243890 with CHD in Caucasian (Cordell et al., 2013).
Consistent with the results from two previous genetic association studies (Guo et al., 2015; Li et al., 2015), we confirmed that three other SNPs (rs765610, rs12481297 and rs36012405) in the RCAN1.1 promoter region were also not associated with CHD. Our Western blot analyses further showed that the RCAN1.4 protein was expressed in both mouse and human embryonic hearts and the RCAN1.4, but not RCAN1.1, protein level was differentially up-regulated in developing mouse embryonic hearts (Fig. 1B). These results support the notion that RCAN1.4, but not RCAN1.1, may contribute to CHD pathogenesis in the Han Chinese population.
RCAN1, also known as Down syndrome candidate region 1 (DSCR1), is located in syntenic regions of human chromosome 21. Approximately 40%–60% of DS patients are accompanied by CHD (Stoll et al., 1998; Vis et al., 2009; Elmagrpy et al., 2011). RCAN1 triplication was thought to be a potential cause for CHD in DS (Lange et al., 2004). However, Lyle et al. identified eight new DS cases of partial monosomy 21. One patient carried only a 1.48 Mb deletion containing eight genes, including RCAN1, and displayed a relatively severe DS phenotype, including cardiac anomaly (Lyle et al., 2009). Now, our study revealed that rs2243890 A>G in the RCAN1.4 promoter increases the risk of CHD by decreasing RCAN1.4 transcription. We not only demonstrated that the minor G allele of rs2243890 significantly decreased RCAN1.4 transcription but also showed that the rare mutation RCAN1.4E25K identified in a VSD patient almost completely abolished RCAN1.4 activity in both in vivo zebrafish model as well as in an in vitro luciferase reporter assay. Altogether, these studies suggest that the expression or activity of RCAN1, rather than the RCAN1 copy number, may contribute to DS-associated CHD. Our study may provide a new understanding of the role of the RCAN1 gene in human CHD.
This work was supported by the grants from National Key Research and Development Program of China (2016YFC1000500) to Hongyan Wang and Wufan Tao, the National Natural Science Foundation of China (Grant Nos. 31671330 and 31471380) to Wufan Tao and (81472050) to Xueyan Yang, the National Natural Science Foundation of China (Grant Nos. 81430005 and 31521003) and the Commission for Science and Technology of Shanghai Municipality (13JC1407600) to Hongyan Wang.
Liangping Cheng, Peiqiang Li, He Wang, Xueyan Yang, Huiming Zhou, Wufan Tao, Jie Tian and Hongyan Wang declare that they have no conflict of interest.
All procedures followed were in accordance with the ethical standards of the responsible committee on human experimentation (institutional and national) and with the Helsinki Declaration of 1975, as revised in 2000 (5). Informed consent was obtained from all patients for being included in the study. Additional informed consent was obtained from all patients for which identifying information is included in this article. All institutional and national guidelines for the care and use of laboratory animals were followed.
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