Confirmation that SNPs in the high mobility group-A2 gene (HMGA2) are associated with adult height in the Japanese population; wide-ranging population survey of height-related SNPs in HMGA2

Association of a single nucleotide polymorphism (rs27434) in the ERAP1 gene with plural tissue weight

Our study was designed to examine the correlation between single nucleotide polymorphism (SNP) in the endoplasmic reticulum aminopeptidase 1 (ERAP1) gene, specifically focusing on rs27434, and plural tissue weight. We conducted this investigation using autopsy samples from the Japanese population. Blood samples were collected from 178 Japanese subjects who had undergone autopsies in Shimane Prefecture. Genomic DNA was subsequently extracted from these samples. SNP (rs27434, G＞A substitution) was analyzed by polymerase chain reaction (PCR) followed by restriction fragment length polymorphism (RFLP) analysis. In the present study, rs27434 exhibited a statistically significant association with brain weight (g) in both female and male individuals. Among males, rs27434 displayed significant relationships with liver weight (g), and body surface area (m2). In females, rs27434 was significantly related to the length of the appendix. Across both genders, individuals with GA and AA genotypes tended to exhibit higher levels in these respective measurements compared to those with the GG genotype. These results suggest that genetic variant of ERAP1 gene may influence the weight of the organs. To the best of our knowledge, this is the first study investigating the interaction between the association of rs27434 in the ERAP1 gene and data routinely measured at autopsy, such as tissue weight. However, conducting further investigations with larger population samples could provide more comprehensive insights to clarify this issue.

A Novel Approach Integrating Hierarchical Clustering and Weighted Combination for Association Study of Multiple Phenotypes and a Genetic Variant

As a pivotal research tool, genome-wide association study has successfully identified numerous genetic variants underlying distinct diseases. However, these identified genetic variants only explain a small proportion of the phenotypic variation for certain diseases, suggesting that there are still more genetic signals to be detected. One of the reasons may be that one-phenotype one-variant association study is not so efficient in detecting variants of weak effects. Nowadays, it is increasingly worth noting that joint analysis of multiple phenotypes may boost the statistical power to detect pathogenic variants with weak genetic effects on complex diseases, providing more clues for their underlying biology mechanisms. So a Weighted Combination of multiple phenotypes following Hierarchical Clustering method (WCHC) is proposed for simultaneously analyzing multiple phenotypes in association studies. A series of simulations are conducted, and the results show that WCHC is either the most powerful method or comparable with the most powerful competitor in most of the simulation scenarios. Additionally, we evaluated the performance of WCHC in its application to the obesity-related phenotypes from Atherosclerosis Risk in Communities, and several associated variants are reported.

Association of HMGA2 Polymorphisms with Glioma Susceptibility in Chinese Children

Background

Glioma is a malignant central nervous system tumor in children, with poor outcomes and prognosis. HMGA2 is a proto-oncogene with increased expression in various malignancies.

Methods

We explored the association of HMGA2 polymorphisms with glioma susceptibility in Chinese children using a case-control study (191 cases, 248 controls). HMGA2 single nucleotide polymorphisms (rs6581658 A>G; rs8756 A>C; rs968697 T>C) were genotyped using PCR-based TaqMan.

Results

Increased glioma susceptibility was associated with rs6581658 A>G; AG (adjusted odds ratio (OR) = 1.71, 95% confidence interval (CI) = 1.13–2.58, P = 0.010) or GG (adjusted OR = 3.12, 95% CI = 1.26–7.74, P = 0.014) genotype carriers had significantly raised glioma risk compared with AA genotype carriers. The rs6581658 AG/GG (adjusted OR = 1.85, 95% CI = 1.25–2.73, P = 0.002) and AA/GG (adjusted OR = 2.58, 95% CI = 1.05–6.33, P = 0.038) genotypes were associated with an increased risk of glioma relative to the AA genotype. Subjects with 2–3 risk genotypes had a significantly elevated risk (adjusted OR = 1.93, 95% CI = 1.31–2.84, P = 0.001) relative to those with 0–1 risk genotype.

Conclusion

HMGA2 rs6581658 A>G is associated with glioma susceptibility in Chinese children.

Development of a predictive model of growth hormone deficiency and idiopathic short stature in children

The aim of the present study was to develop predictive models using clinical features and MRI texture features for distinguishing between growth hormone deficiency (GHD) and idiopathic short stature (ISS) in children with short stature. This retrospective study included 362 children with short stature from Children's Hospital of Hebei Province. GHD and ISS were identified via the GH stimulation test using arginine. Overall, there were 190 children with GHD and 172 with ISS. A total of 57 MRI texture features were extracted from the pituitary gland region of interest using C++ language and Matlab software. In addition, the laboratory examination data were collected. Receiver operating characteristic (ROC) regression curves were generated for the predictive performance of clinical features and MRI texture features. Logistic regression models based on clinical and texture features were established for discriminating children with GHD and ISS. Two clinical features [IGF-1 (insulin growth factor-1) and IGFBP-3 (IGF binding protein-3) levels] were used to build the clinical predictive model, whereas the three best MRI textures were used to establish the MRI texture predictive model. The ROC analysis of the two models revealed predictive performance for distinguishing GHD from ISS. The accuracy of predicting ISS from GHD was 64.5% in ROC analysis [area under the curve (AUC), 0.607; sensitivity, 57.6%; specificity, 72.1%] of the clinical model. The accuracy of predicting ISS from GHD was 80.4% in ROC analysis (AUC, 0.852; sensitivity, 93.6%; specificity, 65.8%) of the MRI texture predictive model. In conclusion, these findings indicated that a texture predictive model using MRI texture features was superior for distinguishing children with GHD from those with ISS compared with the model developed using clinical features.

The Mammalian High Mobility Group Protein AT-Hook 2 (HMGA2): Biochemical and Biophysical Properties, and Its Association with Adipogenesis

The mammalian high-mobility-group protein AT-hook 2 (HMGA2) is a small DNA-binding protein and consists of three “AT-hook” DNA-binding motifs and a negatively charged C-terminal motif. It is a multifunctional nuclear protein directly linked to obesity, human height, stem cell youth, human intelligence, and tumorigenesis. Biochemical and biophysical studies showed that HMGA2 is an intrinsically disordered protein (IDP) and could form homodimers in aqueous buffer solution. The “AT-hook” DNA-binding motifs specifically bind to the minor groove of AT-rich DNA sequences and induce DNA-bending. HMGA2 plays an important role in adipogenesis most likely through stimulating the proliferative expansion of preadipocytes and also through regulating the expression of transcriptional factor Peroxisome proliferator-activated receptor γ (PPARγ) at the clonal expansion step from preadipocytes to adipocytes. Current evidence suggests that a main function of HMGA2 is to maintain stemness and renewal capacity of stem cells by which HMGA2 binds to chromosome and lock chromosome into a specific state, to allow the human embryonic stem cells to maintain their stem cell potency. Due to the importance of HMGA2 in adipogenesis and tumorigenesis, HMGA2 is considered a potential therapeutic target for anticancer and anti-obesity drugs. Efforts are taken to identify inhibitors targeting HMGA2.

Analysis of the value and correlation of IGF-1 with GH and IGFBP-3 in the diagnosis of dwarfism

Correlation between the value of insulin-like growth factor-1 (IGF-1) in the diagnosis of dwarfism and the levels of growth hormone (GH) and insulin-like growth factor binding protein-3 (IGFBP-3) was investigated. From April 2014 to June 2017, 122 children with dwarfism who were treated in The Affiliated Wuxi No. 2 People's Hospital of Nanjing Medical University and The First Affiliated Hospital of Xinxiang Medical University were selected as the experimental group, and 51 normal children as the control group. The basic information was recorded in detail; serum GH and IGFBP-3 levels were measured using an arginine stimulation test and an insulin hypoglycemia stimulation test, respectively. According to the peak of GH in the experimental group, there were 65 cases of growth hormone deficiency (GHD) and 57 cases of idiopathic short stature (ISS). The expression levels of IGF-1 of the serum in the experimental and control group were detected by chemiluminescence immunoassay (CLIA). The correlation between IGF-1 and GH, IGF-1 and IGFBP-3 was analyzed. The expression level of serum IGF-1 in GHD group was significantly lower than that in the ISS group (P<0.05). The expression level of serum IGF-1 in GHD group was significantly lower than that in the control group (P<0.05). The expression level of serum IGF-1 in ISS group was significantly lower than that in the control group (P<0.05). The results of partial correlation studies showed that IGF-1 is positively correlated with GH and IGFBP-3. Detection of GH and IGFBP-3 are important for the early diagnosis and comprehensive evaluation of children with dwarfism, and also in the detection of IGF-1 can reflect the therapeutic effect of dwarfism on recombinant human growth hormone (rhGH) treatment, which is worthy of application in clinics.

Association of SNPs in genes encoding zinc transporters on blood zinc levels in humans

Zinc homeostasis in cells depends on zinc transporters, which are divided into 2 families: ZnT (SLC30A) and ZIP (SLC39A). In this study, we examined the effect of 20 single nucleotide polymorphisms (SNPs) in 10 genes encoding zinc transporters on blood zinc concentration in Japanese subjects (n = 102). Blood zinc levels were determined by microwave plasma-atomic emission spectrometry, and SNPs were analyzed by polymerase chain reaction followed by restriction fragment length polymorphism analysis. Among the 20 SNPs examined, 3 SNPs (SLC30A3 rs11126936, SLC39A8 rs233804, and SLC39A14 rs4872479) were significantly associated with blood zinc concentration. Individuals with genotype TT and TG in rs11126936 showed significantly higher blood zinc concentrations than those with GG. As for rs233804, individuals harboring the A allele had significantly higher blood zinc concentrations than those without this allele. Furthermore, the genotype TT and TG in rs4872479 had significantly higher blood zinc concentrations than those with GG. Among these three SNPs, combination of SLC30A3 rs11126936 and SLC39A8 rs233804 may strongly affect blood zinc levels. This study is the first comprehensive investigation of the effect of SNPs in genes encoding zinc transporters on blood zinc concentration. Adverse effects of zinc deficiency are reported and above 3 SNPs may be related to genetic susceptibility to zinc deficiency.

Simple screening method for copy number variations associated with physical features

Recent studies of copy number variations (CNVs) associated with physical features, such as body mass index, body height or bone length, have suggested that such CNVs could serve as markers in forensic cases involving unidentified individuals. However, the process of cataloging CNVs has been slow because of the cumbersome nature and low reliability of the procedures involved. Here we describe a simple quantitative real-time PCR (Q-PCR) method for screening of medicolegally useful CNVs, which does not require reference DNA with known copy number. The first step is to prepare a chimeric plasmid vector including one copy each of the single-copy gene-specific sequence as the internal standard, and the target CNV-specific sequence. To assess the validity of this new method, we analyzed CNVs in the LTBP1 and ETV6 gene regions, both of which are candidate CNVs associated with body height. The PCR efficiencies for the single-copy (reference) gene and the target CNV were similar, indicating that quantitation was reliable. Furthermore, simulated analysis of the LTBP1 CNV using mock samples prepared by mixing vectors in varying proportions showed that this analytical method allowed correct determination of the LTBP1 copy number. These results demonstrated that our simple method has considerable potential for screening of trait-related CNVs that would be useful for forensic casework.

Single nucleotide polymorphisms in microRNA genes are associated with cervical cancer susceptibility in a population from Xinjiang Uygur

The goal of this study was to explore the correlation between single nucleotide polymorphisms (SNPs) and susceptibility to cervical cancer (CC) in a population from Xinjiang Uygur. Participating were 247 patients with CC and 285 healthy women. Fourteen SNPs in nine miRNA genes were selected. Odds ratios (ORs) and 95% confidence intervals (95% CIs) were calculated using unconditional logistic regression analysis. Multivariate logistic regression analysis was used to assess the correlation of SNPs with CC. The minor allele "C" of rs300574 in SPRY1 was associated with an increased risk of CC based on analysis of the allele, codominant, recessive and log-additive models, but an opposite result was found with the over-dominant model. The minor allele "C" of rs1042725 in HMGA2 was associated with an increased risk of CC in the allele, dominant and log-additive models. In clinical stage III/IVCC patients, rs4728 in SPRY2 was associated with decreased risk. Finally, rs3744935 in BCL2 was associated with CC in the allele and codominant models. In sum, we have detected associations between four SNPs, rs300574 (SPRY1), rs3744935 (BCL2), rs1042725 (HMGA2), and rs4728 (SPRY2), and CC risk in women from Xinjiang Uygur.

Variations in the high-mobility group-A2 gene (HMGA2) are associated with idiopathic short stature

BACKGROUND

Several association studies confirmed high-mobility group-A2 gene (HMGA2) polymorphisms as the most relevant variants contributing to height variability. Animal models and deletions in humans suggest that alterations of HMGA2 might be relevant in causing short stature. Together, these observations led us to investigate the involvement of HMGA2 in idiopathic short stature (ISS) through an association study and a mutation screening.

METHODS

We conducted an association study (155 ISS patients and 318 normal stature controls) with three HMGA2 single-nucleotide polymorphisms (SNPs) (SNPs rs1042725, rs7968682, and rs7968902) using a TaqMan-based assay. The patients were then analyzed by direct sequencing and multiplex ligation-dependent probe amplification (MLPA) to detect point mutations and genomic micro-rearrangements.

RESULTS

Considering a recessive model, an OR value >1 was observed for genotypes rs7968682 TT (Odds ratio (OR) = 1.72, confidence interval (CI): 1.14-2.58) and rs1042725 TT (OR = 1.51, CI: 1.00-2.28) in accordance to the effect exhibited by the single alleles in the general population. None of the patients carried possibly causative HMGA2 mutations.

CONCLUSION

Besides the already known role in determining variability in human height, HMGA2 polymorphisms also contribute to susceptibility to ISS. Moreover, we here report the first mutation screening performed in ISS concluding that HMGA2 has not a significant impact on the monogenic form of ISS.

Replication study of the association of SNPs in the LHX3-QSOX2 and IGF1 loci with adult height in the Japanese population; wide-ranging comparison of each SNP genotype distribution

Adult height is a highly heritable trait involving multiple genes. Recent genome-wide association studies have identified that SNP rs12338076 in the LHX3-QSOX2 locus, and rs1457595 and rs17032362 in the IGF1 locus are associated with human height in the Japanese population (Okada et al. (2010)). We performed a replication study to examine the associations between these three SNPs and adult height in the Japanese population based on autopsy cases. However, it was not possible to confirm that all these SNPs influenced adult height in the study population. We first conducted a wide-ranging survey of these three SNPs in the above genes using nine different populations including Asians, Africans and Caucasians, and demonstrated that the genotypes of rs12338076 and rs17032362 were distributed in an ethnicity-dependent manner; even within Asian populations, the genotype distributions of the SNPs differed widely. Although there are differences in height distribution between different populations, possibly due to genetic factors and/or gene-environmental interactions, the contradictory results of the association study and ethnic differences in genotype distribution allow us to assume that these height-related SNPs in the genes may contribute to adult height to a slight extent, at least in the Japanese population. It is anticipated that the present information will be useful for developing a reliable tool for personal identification through elucidation of the genetic basis of human height.