Functional interaction between SNPs and microsatellite in the transcriptional regulation of insulin-like growth factor 1

A case-control study coupling with meta-analysis elaborates decisive association between IGF-1 rs35767 and osteoporosis in Asian postmenopausal females

BACKGROUND

Osteoporosis (OP) is prevalent in postmenopausal women. Several studies investigated the association between IGF-1 polymorphisms and OP among postmenopausal females with conflicting outcomes.

OBJECTIVE

To investigate whether the IGF-1 (rs35767, rs2288377, rs5742612) were associated with OP in postmenopausal females.

METHODS

In case-control study, 95 OP cases and 222 healthy controls were recruited between March 2015 and July 2019. OP was diagnosed based on WHO criteria for diagnosis of OP as T score of bone mineral density (BMD) ≤-2.5; normal, as T score of BMD ≥-1. IGF-1 SNPs were genotyped by iPLEX Gold SNP genotyping. To be solid, related studies from PubMed, Embase, Cochrane, Web of science, and previous meta-analysis up until November 2020, along with our case-control study, were incorporated into a meta-analysis with criteria of significance using odds ratios (ORs) with corresponding 95% confidence intervals (CI) to evaluate risk factor of SNPs on OP. TSA was used to estimate the sample sizes required to achieve a conclusion.

RESULTS

In dominant model of our case-control study, we found nonsignificant association of rs35767 [Adj-OR: 0.95 (95% CI: 0.56-1.60)], rs2288377 [Adj-OR: 1.15 (95% CI: 0.67-1.97)], and rs5742612 [Adj-OR: 1.07 (95% CI: 0.62-1.83)] with OP in postmenopausal females. However, integration of our case-control study and 3 published studies, rs35767 [OR: 1.24 (95% CI: 1.05-1.47)] showed a conclusively risk association with OP in postmenopausal females judged by TSA with 2267 Asians.

CONCLUSIONS

This study demonstrates a crucial sample to conclude that IGF-1 rs35767 is significantly associated with OP in postmenopausal women.

A Poly(dA:dT) Tract in the IGF1 Gene Is a Genetic Marker for Growth Traits in Pigs

Insulin-like growth factor 1 (IGF1) is an important regulator of body growth, development, and metabolism. The poly(dA:dT) tract affects the accessibility of transcription factor binding sites to regulate transcription. Therefore, this study assessed the effects of two poly(dA:dT) tracts on the transcriptional activity of porcine IGF1. The luciferase assay results demonstrated that the poly(dA:dT) tract 2 (−264/−255) was a positive regulatory element for IGF1 gene expression, and the activities between the different lengths of the poly(dA:dT) tract 2 were significant (p<0.01). The transcription factor C/EBPα inhibited the transcription of IGF1 by binding to tract 2, and the expression levels between the lengths of tract 2 after C/EBPα binding were also statistically different (p<0.01). Only the alleles 10T and 11T were found in the tract 2 in commercial pig breeds, while the 9T, 10T, and 11T alleles were found in Chinese native pig breeds. The allele frequencies were in Hardy−Weinberg equilibrium in all pig breeds. The genotypes of tract 2 were significantly associated with the growth traits (days to 115 kg and average daily gain) (p<0.05) in commercial pig breeds. Based on these findings, it can be concluded that the tract 2 mutation could be applied as a candidate genetic marker for growth trait selection in pig breeding programs.

Association Between Insulin-like Growth Factor-1 rs35767 Polymorphism and Type 2 Diabetes Mellitus Susceptibility: A Meta-Analysis

Background: Insulin-like growth factor-1 (IGF-1) has been demonstrated to increase fatty acid β oxidation during fasting, and play an important role in regulating lipid metabolism and type 2 diabetes mellitus (T2DM). The rs35767 (T > C) polymorphism, a functional SNP was found in IGF-1 promoter, which may directly affect IGF-1 expression. However, the inconsistent findings showed on the IGF-1 rs35767 polymorphism and T2DM risk.

Methods: We performed a comprehensive meta-analysis to estimate the association between the IGF-1 rs35767 and T2DM risk among four genetic models (the allele, additive, recessive and dominant models).

Results: A total 49,587 T2DM cases and 97,906 NDM controls were included in the allele model, a total 2256 T2DM cases and 2228 NDM controls were included in the other three genetic models (the additive; recessive and dominant models). In overall analysis, the IGF-1 rs35767 was shown to be significantly associated with increased T2DM risk for the allele model (T vs. C: OR = 1.251, 95% CI: 1.082–1.447, p = 0.002), additive model (homozygote comparisons: TT vs. CC: OR = 2.433, 95% CI: 1.095–5.405, p = 0.029; heterozygote comparisons: TC vs. CC: OR = 1.623, 95% CI: 1.055–2.495, p = 0.027) and dominant model (TT + CT vs. CC: OR = 1.934, 95% CI: 1.148–3.257, p = 0.013) with random effects model. After omitting Gouda’s study could reduce the heterogeneity, especially in the recessive model (TT vs. CC + CT: I² = 38.7%, p = 0.163), the fixed effects model for recessive effect of the T allele (TT vs. CC + CT) produce results that were of borderline statistical significance (OR = 1.206, 95% CI: 1.004–1.448, p = 0.045). And increasing the risk of T2DM in Uyghur population of subgroup for the allele model.

Conclusion: The initial analyses that included all studies showed statistically significant associations between the rs35767 SNP and type 2 diabetes, but after removing the Gouda et al. study produced results that were mostly not statistically significant. Therefore, there is not enough evidence from the results of the meta-analysis to indicate that the rs35767 SNP has a statistically significant association with type 2 diabetes.

TLR4 rs1927914 polymorphism contributes to serum TLR4 levels in patients with aortic aneurysm

Toll-like receptor 4 (TLR4) is a crucial regulator of inflammatory reactions and vascular remodeling. Elevated TLR4 expression has been proved to be correlated with an increased risk of aortic aneurysm (AA). This study aimed to explore the influence of TLR4 gene polymorphisms on TLR4 expression levels and its probable functional significance in AA disease. A total of 294 AA patients and 285 controls were enrolled in the study and serum TLR4 levels were detected by ELISA. All the participants were genotyped for two tag-SNPs in TLR4 (rs1927914 in the promoter region and rs11536889 in the 3'-untranslated region) using the KASP method. Relative luciferase activity was measured by the dual-luciferase reporter assay system. The rs1927914 TC, TC/CC genotypes and C allele showed associations with increased serum TLR4 levels in the total population and AA patients (all P<0.05). Further stratified analysis demonstrated that AA subjects with TC or TC/CC genotype of rs1927914 had significantly higher serum levels of TLR4 than those with TT genotype in male, age>60y, hypertension, diabetes, TAA type and size>5.0 cm subgroups (all P<0.05). In binary logistic analysis, rs1927914 TC genotype and dominant model presented significant associations with high TLR4 levels (OR = 1.579 and 1.431, P = 0.020 and 0.049, respectively) after adjusting age, hypertension and diabetes. However, rs11536889 polymorphism had no significant influence on serum TLR4 levels. Regarding rs1927914, luciferase activity of the C allele construct was significantly increased in comparison with the T allele construct (0.589 ± 0.004 vs. 0.340 ± 0.014, P<0.001). Our results provided evidence that rs1927914 polymorphism contributed to serum TLR4 levels, possibly by influencing promoter activity of TLR4, and could be a novel genetic factor in the formation of AA.

Genome-Wide Search for SNP Interactions in GWAS Data: Algorithm, Feasibility, Replication Using Schizophrenia Datasets

In this study, we looked for potential gene-gene interaction in susceptibility to schizophrenia by an exhaustive searching for SNP-SNP interactions in 3 GWAS datasets (phs000021:phg000013, phs000021:phg000014, phs000167) using our recently published algorithm. The search space for SNP-SNP interaction was confined to 8 biologically plausible ways of interaction under dominant-dominant or recessive-recessive modes. First, we performed our search of all pair-wise combination of 729,454 SNPs after filtering by SNP genotype quality. All possible pairwise interactions of any 2 SNPs (5 × 10¹¹) were exhausted to search for significant interaction which was defined by p-value of chi-square tests. Nine out the top 10 interactions, protein coding genes were partnered with non-coding RNA (ncRNA) which suggested a new alternative insight into interaction biology other than the frequently sought-after protein-protein interaction. Therefore, we extended to look for replication among the top 10,000 interaction SNP pairs and high proportion of concurrent genes forming the interaction pairs were found. The results indicated that an enrichment of signals over noise was present in the top 10,000 interactions. Then, replications of SNP-SNP interaction were confirmed for 14 SNPs-pairs in both replication datasets. Biological insight was highlighted by a potential binding between FHIT (protein coding gene) and LINC00969 (lncRNA) which showed a replicable interaction between their SNPs. Both of them were reported to have expression in brain. Our study represented an early attempt of exhaustive interaction analysis of GWAS data which also yield replicated interaction and new insight into understanding of genetic interaction in schizophrenia.

Interaction between CA repeat microsatellites and HIF1α regulated the transcriptional activity of porcine IGF1 promoter

Insulin-like growth factor 1 (IGF1) is pivotal in the regulation of animal growth. Highly polymorphic CA repeat microsatellites have been identified in the IGF1 promoter region of different breeds of pigs. Previous studies showed that CA repeat microsatellites are associated with circulating IGF1 level. However, the mechanisms by which CA repeat microsatellites regulate IGF1 expression remain unclear. This study aimed to detect the association of CA repeat microsatellites with the transcriptional regulation of porcine IGF1 and the possible mechanisms. Results revealed that the number of CA repeats in porcine IGF1 promoter was 14-18, and a promoter with 14 or 15 CA repeats had a higher transcriptional activity (P < 0.01). Transcription factor hypoxia-inducible factor 1 subunit alpha (HIF1α) was confirmed to bind to the binding site upstream of CA repeat microsatellites. The microsatellites with 14 or 15 CA repeats were more sensitive to changes in the HIF1α expression level (P < 0.01). These results suggested that CA repeat microsatellites and HIF1α affected the transcriptional activity of each other in the regulation of IGF1 expression, thereby implying an interaction between them. Overall, this study provided novel evidence for elucidating the effects of CA repeat microsatellites on the transcriptional regulation of porcine IGF1.

The mechanism of transactivation regulation due to polymorphic short tandem repeats (STRs) using IGF1 promoter as a model

Functional short tandem repeats (STR) are polymorphic in the population, and the number of repeats regulates the expression of nearby genes (known as expression STR, eSTR). STR in IGF1 promoter has been extensively studied for its association with IGF1 concentration in blood and various clinical traits and represents an important eSTR. We previously used an in-vitro luciferase reporter model to examine the interaction between STRs and SNPs in IGF1 promoter. Here, we further explored the mechanism how the number of repeats of the STR regulates gene transcription. An inverse correlation between the number of repeats and the extent of transactivation was found in a haplotype consisting of three promoter SNPs (C-STR-T-T). We showed that these adjacent SNPs located outside the STR were required for the STR to function as eSTR. The C allele of rs35767 provides a binding site for CCAAT/enhancer-binding-protein δ (C/EBPD), which is essential for the gradational transactivation property of eSTR and FOXA3 may also be involved. Therefore, we propose a mechanism in which the gradational transactivation by the eSTR is caused by the interaction of one or more transcriptional complexes located outside the STR, rather than by direct binding to a repeat motif of the STR.

The influence of genetic polymorphisms in TLR4 and TIRAP, and their expression levels in peripheral blood, on susceptibility to sepsis

The present study aimed to investigate whether genetic polymorphisms in the Toll-like receptor (TLR)-4 and Toll/interleukin-1 receptor (TIR)-associated protein (TIRAP) genes, and/or their expression levels, influence the susceptibility of a patient to sepsis. A total of 106 patients with sepsis were divided into two groups on the basis of their acute physiology and chronic health evaluation (APACHE) II scores: i) Sepsis group A (APACHE II <20) and ii) Sepsis group B (APACHE II >20). In addition, 100 healthy volunteers were enrolled into the control group. Polymerase chain reaction-restriction fragment length polymorphism assay was used to detect the following genetic polymorphisms: The Ser180Leu allele of the TIRAP gene and the Asp299Gly and Thr399I1e alleles of the TLR4 gene. Furthermore, the protein expression levels of TLR4 and TIRAP were analyzed using an enzyme-linked immunosorbent assay. Genetic polymorphisms were not detected for the TLR4 and TIRAP genes; however, the protein expression levels of TLR4 and TIRAP differed significantly between the control, sepsis A and sepsis B groups (P<0.01). An APACHE II score of 20 was used as a baseline in order to differentiate sepsis severity. Pearson analysis demonstrated that TLR4 and TIRAP protein expression levels were positively correlated with sepsis severity (r=0.931 and 0.972; P<0.05), and TLR4 protein expression levels were positively correlated with those of TIRAP (r=0.936; P<0.05). The results of the present study suggested that the protein expression levels of, but not genetic polymorphisms in, TLR4 and TIRAP were associated with the severity of sepsis.

An exceptionally long CA-repeat in the core promoter of SCGB2B2 links with the evolution of apes and Old World monkeys

We have recently reported a genome-scale catalog of human protein-coding genes that contain "exceptionally long" STRs (≥6-repeats) in their core promoter, which may be of selective advantage in this species. At the top of that list, SCGB2B2 (also known as SCGBL), contains one of the longest CA-repeat STRs identified in a human gene core promoter, at 25-repeats. In the study reported here, we analyzed the conservation status of this CA-STR across evolution. The functional implication of this STR to alter gene expression activity was also analyzed in the HEK-293 cell line. We report that the SCGB2B2 core promoter CA-repeat reaches exceptional lengths, ranging from 9- to 25-repeats, across Apes (Hominoids) and the Old World monkeys (CA>2-repeats were not detected in any other species). The longest CA-repeats and highest identity in the SCGB2B2 protein sequence were observed between human and bonobo. A trend for increased gene expression activity was observed from the shorter to the longer CA-repeats (p<0.009), and the CA-repeat increased gene expression activity, per se (p<0.02). We propose that the SCGB2B2 gene core promoter CA-repeat functions as an expression code for the evolution of Apes and the Old World monkeys.

Type 2 diabetes-related variants influence the risk of developing multiple myeloma: results from the IMMEnSE consortium

Type 2 diabetes (T2D) has been suggested to be a risk factor for multiple myeloma (MM), but the relationship between the two traits is still not well understood. The aims of this study were to evaluate whether 58 genome-wide-association-studies (GWAS)-identified common variants for T2D influence the risk of developing MM and to determine whether predictive models built with these variants might help to predict the disease risk. We conducted a case-control study including 1420 MM patients and 1858 controls ascertained through the International Multiple Myeloma (IMMEnSE) consortium. Subjects carrying the KCNQ1rs2237892T allele or the CDKN2A-2Brs2383208G/G, IGF1rs35767T/T and MADDrs7944584T/T genotypes had a significantly increased risk of MM (odds ratio (OR)=1.32-2.13) whereas those carrying the KCNJ11rs5215C, KCNJ11rs5219T and THADArs7578597C alleles or the FTOrs8050136A/A and LTArs1041981C/C genotypes showed a significantly decreased risk of developing the disease (OR=0.76-0.85). Interestingly, a prediction model including those T2D-related variants associated with the risk of MM showed a significantly improved discriminatory ability to predict the disease when compared to a model without genetic information (area under the curve (AUC)=0.645 vs AUC=0.629; P=4.05×10(-) (06)). A gender-stratified analysis also revealed a significant gender effect modification for ADAM30rs2641348 and NOTCH2rs10923931 variants (Pinteraction=0.001 and 0.0004, respectively). Men carrying the ADAM30rs2641348C and NOTCH2rs10923931T alleles had a significantly decreased risk of MM whereas an opposite but not significant effect was observed in women (ORM=0.71 and ORM=0.66 vs ORW=1.22 and ORW=1.15, respectively). These results suggest that TD2-related variants may influence the risk of developing MM and their genotyping might help to improve MM risk prediction models.

Are polymorphisms of the immunoregulatory factor CD40LG implicated in acute transfusion reactions?

The CD40 ligand (CD40L/CD154), a member of TNF superfamily, is notably expressed on activated CD4+ T-cells and stimulated platelets. CD40L is linked to a variety of pathologies and to acute transfusion reactions (ATR). Mutations in this gene (CD40LG) lead to X-linked hyper-IgM syndrome. Some CD40LG polymorphisms are associated with variable protein expression. The rationale behind this study is that CD40L protein has been observed to be involved in ATR. We wondered whether genetic polymorphisms are implicated. We investigated genetic diversity in the CD40LG using DHPLC and capillary electrophoresis for screening and genotyping (n = 485 French and Tunisian blood donors). We identified significant difference in the CD40LG linkage pattern between the two populations. Variant minor alleles were significantly over-represented in Tunisian donors (P<0.0001 to 0.0270). We found higher heterogeneity in the Tunisian, including three novel low frequency variants. As there was not a particular pattern of CD40LG in single apheresis donors whose platelet components induced an ATR, we discuss how this information may be useful for future disease association studies on CD40LG.

GRK5 intronic (CA)n polymorphisms associated with type 2 diabetes in Chinese Hainan Island

A genome-wide association study had showed G-protein-coupled receptor kinase 5 (GRK5) rs10886471 was related to the risk of type 2 diabetes mellitus (T2DM) through upregulated GRK5 mRNA expression. Rs10886471 is located in the intron region of GRK5. However, the mechanism by which intronic SNP affects gene expression remains unclear, whether the effect on gene expression depends on the intronic short tandem repeat (STR) (CA)n splicing regulator or not. Here we investigated the STR (CA)n polymorphism in rs10886471 and further discussed its role in the T2DM risk of Chinese Hainan Island individuals. A total of 1164 subjects were recruited and classified into a normal fasting glucose (NFG) group, an impaired fasting glucose (IFG) group, an impaired glucose tolerance (IGT) group, and a T2DM group. STR (CA)n polymorphisms were detected through polymerase chain reaction and sequencing. Five intronic (CA)n alleles, (CA)15 to (CA)19, were identified in GRK5 rs10886471. Only the (CA)16 allele was significantly associated with increased prediabetes and T2DM risk [odds ratio (OR)>1, P<0.05]. Conversely, multiple alleles without any (CA)16 protected against prediabetes and T2DM (0<OR<1, P<0.05). In summary, rs10886471 acts as both an SNP and an STR. The rs10886471 intronic SNP causes GRK5 overexpression the subsequent risk of T2DM may be due to the rs10886471 intronic STR (CA)n splicing enhancer. Further studies should focus on verifying these finding using a large sample size and analyzing the splicing mechanism of intronic (CA)n in rs10886471.