Evaluation of genetic susceptibility of common variants in CACNA1D with schizophrenia in Han Chinese

CACNA1D-Related Channelopathies: From Hypertension to Autism

Tightly controlled Ca²⁺ influx through voltage-gated Ca²⁺ channels (Cavs) is indispensable for proper physiological function. Thus, it is not surprising that Cav loss and/or gain of function have been implicated in human pathology. Deficiency of Cav1.3 L-type Ca²⁺ channels (LTCCs) causes deafness and bradycardia, whereas several genetic variants of CACNA1D, the gene encoding the pore-forming α1 subunit of Cav1.3, have been linked to various disease phenotypes, such as hypertension, congenital hypoglycemia, or autism. These variants include not only common polymorphisms associated with an increased disease risk, but also rare de novo missense variants conferring high risk. This review provides a concise summary of disease-associated CACNA1D variants, whereas the main focus lies on de novo germline variants found in individuals with a neurodevelopmental disorder of variable severity. Electrophysiological recordings revealed activity-enhancing gating changes induced by these de novo variants, and tools to predict their pathogenicity and to study the resulting pathophysiological consequences will be discussed. Despite the low number of affected patients, potential phenotype-genotype correlations and factors that could impact the severity of symptoms will be covered. Since increased channel activity is assumed as the disease-underlying mechanism, pharmacological inhibition could be a treatment option. In the absence of Cav1.3-selective blockers, dihydropyridine LTCC inhibitors clinically approved for the treatment of hypertension may be used for personalized off-label trials. Findings from in vitro studies and treatment attempts in some of the patients seem promising as outlined. Taken together, due to advances in diagnostic sequencing techniques the number of reported CACNA1D variants in human diseases is constantly rising. Evidence from in silico, in vitro, and in vivo disease models can help to predict the pathogenic potential of such variants and to guide diagnosis and treatment in the clinical practice when confronted with patients harboring CACNA1D variants.

Zebrafish Larvae Carrying a Splice Variant Mutation in cacna1d: A New Model for Schizophrenia-Like Behaviours?

Persons with certain single nucleotide polymorphisms (SNPs) in the CACNA1D gene (encoding voltage-gated calcium channel subunit alpha 1-D) have increased risk of developing neuropsychiatric disorders such as bipolar, schizophrenia and autism. The molecular consequences of SNPs on gene expression and protein function are not well understood. Thus, the use of animal models to determine genotype-phenotype correlations is critical to understanding disease pathogenesis. Here, we describe the behavioural changes in larval zebrafish carrying an essential splice site mutation (sa17298) in cacna1da. Heterozygous mutation resulted in 50% reduction of splice variants 201 and 202 (haploinsufficiency), while homozygosity increased transcript levels of variant 201 above wild type (WT; gain-of-function, GOF). Due to low homozygote viability, we focused primarily on performing the phenotypic analysis on heterozygotes. Indeed, cacna1dasa17298/WT larvae displayed hyperlocomotion-a behaviour characterised in zebrafish as a surrogate phenotype for epilepsy, anxiety or psychosis-like behaviour. Follow-up tests ruled out anxiety or seizures, however, as neither thigmotaxis defects nor epileptiform-like discharges in larval brains were observed. We therefore focused on testing for potential "psychosis-like" behaviour by assaying cacna1dasa17298/WT larval locomotor activity under constant light, during light-dark transition and in startle response to dark flashes. Furthermore, exposure of larvae to the antipsychotics, risperidone and haloperidol reversed cacna1da-induced hyperactivity to WT levels while valproate decreased but did not reverse hyperactivity. Together, these findings demonstrate that cacna1da haploinsufficiency induces behaviours in larval zebrafish analogous to those observed in rodent models of psychosis. Future studies on homozygous mutants will determine how cacna1d GOF alters behaviour in this context.

Relationship of common variants in MPP7, TIMP2 and CASP8 genes with the risk of chronic achilles tendinopathy

Previous etiologic studies have indicated that both environmental and genetic factors play important roles in the occurrence and development of chronic Achilles tendinopathy (AT). A recent study documented the results of the largest genome-wide association study for chronic AT to date, indicating that MPP7, TIMP2 and CASP8 may be involved in the occurrence and development of chronic AT. In this study, we aimed to investigate whether MPP7, TIMP2 and CASP8 were associated with susceptibility to chronic AP in a Han Chinese population. A total of 3,680 study subjects comprised 1,288 chronic AT cases, and 2,392 healthy controls were recruited. Forty-four tag SNPs (7 from CASP8, 20 from MPP7, and 17 from TIMP2) were genotyped in the study. Genetic association analyses were performed at both single marker and haplotype levels. Functional consequences of significant SNPs were examined in the RegulomeDB and GTEx databases. Two SNPs, SNP rs1937810 (OR [95%CI] = 1.20 [1.09-1.32], χ2 = 13.50, P = 0.0002) in MPP7 and rs4789932 (OR [95%CI] = 1.24 [1.12-1.37], χ2 = 17.98, P = 2.23 × 10-5) in TIMP2, were significantly associated with chronic AT. Significant eQTL signals for SNP rs4789932 on TIMP2 were identified in human heart and artery tissues. Our results provide further supportive evidence for the association of the TIMP2 and MPP7 genes with chronic AT, which supports important roles for TIMP2 and MPP7 in the etiology of chronic AT, adding to the current understanding of the susceptibility of chronic AT.

Genetic Polymorphisms on 4q21.1 Contributed to the Risk of Hashimoto's Thyroiditis

Background: Hashimoto's thyroiditis (HT) is a common autoimmune disease characterized by lymphoid infiltration of the thyroid gland, including both T- and B-cells. Early studies have shown that HT is a complex disorder affected by both environmental and genetic factors. Recently, the single nucleotide polymorphism (SNP) rs2276886 associated with the CXCL9 gene was identified as associated with autoimmune thyroid disease susceptibility in Japanese populations. The aim of the present study was to validate this result for HT in a Chinese Han population. Methods: Study subjects, including 688 HT cases and 1456 healthy controls, were recruited, and 10 SNPs located within the CXCL9 gene were genotyped. Genetic association analyses were performed by fitting logistic models. Bioinformatics tools, including RegulomeDB and GTEx were utilized to investigate the functional consequences of the SNPs found to be significantly associated with HT. Results: SNP rs2276886 was identified as significantly associated with the risk of HT (odds ratio [OR] = 1.25, p = 0.0006). No significant expression quantitative trait loci (eQTL) signals could be identified for CXCL9. Significant eQTL signals were found for other genes, including ART3, CXCL10, CXCL11, NAAA, PPEF2, and SCARB2. This SNP physically maps to the CXCL9 gene region; however, further bioinformatic analyses indicated that this SNP might be associated with the gene NAAA. Conclusions: The rs2276886 SNP was found to be significantly associated with HT susceptibility. However, our findings suggest that this SNP which maps to the chromosomal region 4q21.1 likely effects the NAAA gene (as opposed to the CXCL9 gene), but still contributes to the susceptibility to HT in Han Chinese populations.

Genetic Associations between Voltage-Gated Calcium Channels and Psychiatric Disorders

Psychiatric disorders are mental, behavioral or emotional disorders. These conditions are prevalent, one in four adults suffer from any type of psychiatric disorders world-wide. It has always been observed that psychiatric disorders have a genetic component, however, new methods to sequence full genomes of large cohorts have identified with high precision genetic risk loci for these conditions. Psychiatric disorders include, but are not limited to, bipolar disorder, schizophrenia, autism spectrum disorder, anxiety disorders, major depressive disorder, and attention-deficit and hyperactivity disorder. Several risk loci for psychiatric disorders fall within genes that encode for voltage-gated calcium channels (CaVs). Calcium entering through CaVs is crucial for multiple neuronal processes. In this review, we will summarize recent findings that link CaVs and their auxiliary subunits to psychiatric disorders. First, we will provide a general overview of CaVs structure, classification, function, expression and pharmacology. Next, we will summarize tools to study risk loci associated with psychiatric disorders. We will examine functional studies of risk variations in CaV genes when available. Finally, we will review pharmacological evidence of the use of CaV modulators to treat psychiatric disorders. Our review will be of interest for those studying pathophysiological aspects of CaVs.

Evaluation of genetic susceptibility between systemic lupus erythematosus and GRB2 gene

Multiple lines of evidence have shown that systemic lupus erythematosus (SLE) is attributable to both genetic and environmental factors. The product of GRB2 is a key factor in the activation of B cells and has been reported to be significantly associated with SLE in European populations. In the study, we aimed to investigate the relationship between GRB2 and SLE. A total of 1,710 Han Chinese women comprising 567 SLE patients and 1,143 controls were recruited to genotype 20 selected tagging SNPs. We tested the potential association between 13 clinical variables of SLE and the significant polymorphisms related to SLE. The eQTL data were extracted from the GTEx database to examine the functional consequences of the targeted SNPs. A significant association signal was identified between rs36023980 and SLE in both genotypic and allelic analyses (OR = 0.61, P = 0.0003). Complement inhibition was shown to be significantly associated with the genotypes of SNP rs36023980 in SLE patients (P_genotype = 0.003). Further stratification analyses showed that the genetic association signal of SNP rs36023980 on SLE could only be identified in cases with complement inhibition. SNP rs36023980 was also identified to be significantly associated with the expression of GRB2 in whole blood and sun-exposed skin. In conclusion, our findings confirm the results from the previous GWAS and are the first to report the association of GRB2 with SLE in Han Chinese population.

Evaluation of the Relationship Between Common Variants in the TLR-9 Gene and Hip Osteoarthritis Susceptibility

Objective: Hip osteoarthritis (HOA) is one of the most common types of osteoarthritis and affects nearly 10% of men and 18% of women who are >60 years of age worldwide. It has been demonstrated to be a genetic disease with a 50% heritability risk. Recently, the TLR-9 gene has been associated with knee OA in both Turkish and Chinese populations, but the relationship between the TLR-9 gene and HOA has not been evaluated. In this study, we aimed to evaluate the relationship between the common genetic variants in the TLR-9 gene and the predisposition of Han Chinese individuals to HOA. Methods: A total of 730 HOA patients and 1220 healthy controls were recruited in a hospital-based case-control study. Six common single nucleotide polymorphisms (SNPs) of the TLR-9 gene were selected for genotyping, and genetic association analyses were performed using both single-marker and haplotype-based methods. Results: The SNP rs187084 was found to be significantly associated with the risk of HOA after a Bonferroni correction (adjusted allelic p-values with age, gender, and body mass index [BMI] = 0.0008). The results indicated that the A allele of rs187084 is a risk allele for HOA and is likely to be a predisposing factor leading to an increased risk of HOA (adjusted odds ratio with age, gender, and BMI = 1.26, 95% confidence interval = 1.10-1.43). The results of the haplotype analyses confirmed a similar pattern to the SNP analyses. Conclusions: Our study provides strong evidence that variations in the TLR-9 gene are closely linked with genetic susceptibility to HOA in the Han Chinese population. This finding furthers the role of TLR-9 in the development and occurrence of OA in general.

Relationship Between Genetic Polymorphisms of the TNF Gene and Hallux Valgus Susceptibility

Background: Hallux valgus (HV) is a type of forefoot deformity affecting ∼23% of adults. Previous studies have shown that HV is highly heritable. Tumor necrosis factor (TNF) is an important proinflammatory cytokine involved in bone remodeling and plays essential roles in osteoarthritis and chronic inflammatory bone diseases, including HV. Methods: A total of 1,788 Chinese women comprising 637 HV subjects and 1,151 controls were recruited. Twelve single nucleotide polymorphisms (SNPs) located in TNF and its promoter regions were selected and genotyped. Genetic association analyses were performed to investigate potential susceptibility SNPs. Bioinformatic and expression quantitative trait loci (eQTL) analyses were conducted to examine the functional consequences of the SNPs identified as being significantly associated with HV. Results: SNP rs1800629, which is located at the 5' end of the promoter region of TNF, was identified as significantly associated with HV status in Chinese women (OR = 0.56, p = 2.12 × 10^-6). Bioinformatic analyses using RegulomeDB indicated that this SNP has important functional significance, but subsequent eQTL analyses did not identify a significant association between rs1800629 and TNF gene expression. In addition, 26 genes with cis-eQTL for rs1800629 were identified. Conclusions: This study identified a susceptibility SNP for HV located within the promoter region of the TNF gene. Bioinformatic and eQTL analyses linked this SNP to 26 genes but not to TNF. Functional studies are needed to more fully characterize the effects of this SNP.

Relationship of common variants in Interleukin 33 gene with susceptibility and prognosis of osteosarcoma in Han Chinese population

Osteosarcoma (OS) is one of the most common malignant bone tumors. Many previous studies have indicated that OS is a complex disease and that its development may be affected by multiple genetic factors, which may contribute to its carcinogenesis. The aim of the present study was to evaluate the relationship of IL-33 with susceptibility and prognosis of OS in Han Chinese individuals. A total of 1,605 study subjects including 507 OS patients and 1,098 controls were recruited. Eighteen SNPs mapped to IL-33 were selected for genotyping. Genetic associations between selected SNPs and OS disease status were evaluated. Survival analyses, including Kaplan-Meier analysis and Cox model fitting for significant SNPs, were performed. The functional consequences of significant SNPs were analyzed using a publicly available database. SNP rs1048274 was identified to be significantly associated with OS disease status (OR=0.75, P=1.53×10-4). Compared to the GA and GG groups, OS patients with the AA genotype of rs1048274 had better survival rate. The hazard ratio of SNP rs1048274 (AA group compared to GG+GA group) was 0.35 (95% confidence interval of 0.25-0.5) following adjustment for several clinical variables. In conclusion, our results suggested that IL-33 may play a key role in the etiology of OS, indicating IL-33 as a potential genetic risk factor of the development and prognosis of OS.

Genetic effects of BDKRB2 and KNG1 on deep venous thrombosis after orthopedic surgery and the potential mediator

Deep venous thrombosis (DVT) is a common complication of orthopedic surgery. Genetic risk factors and high heritability carried a substantial risk of DVT. In this study, we aimed to investigate the potential association in the Han Chinese population between the polymorphisms of BDKRB2 and KNG1 and DVT after orthopedic surgery (DVTAOS). A total of 3,010 study subjects comprising 892 DVT cases and 2,118 controls were included in the study, and 39 single nucleotide polymorphisms (SNPs) in total (30 for BDKRB2 and 9 for KNG1) were chosen for genotyping. Two SNPs, rs710446 (OR = 1.27, P = 0.00016) and rs2069588 (OR = 1.29, P = 0.00056), were identified as significantly associated with DVTAOS. After adjusting for BMI, the significance of rs2069588 decreased (P = 0.0013). Haplotype analyses showed that an LD block containing rs2069588 significantly correlated with the DVTAOS risk. Moreover, bioinformatics analysis indicated that hsa-miR-758-5p and BDKRB2 formed miRNA/SNP target duplexes if the rs2069588 allele was in the T form, suggesting that rs2069588 may alter BDKRB2 expression by affecting hsa-miR-758-5p/single-nucleotide polymorphism target duplexes. Our results demonstrate additional evidence supporting that there is an important role for the KNG1 and BDKRB2 genes in the increased susceptibility of DVTAOS.

Relationship of WNT4 Gene with the Risk of Epithelial Ovarian Cancer: A Han Chinese Population-Based Association Study

OBJECTIVE

In China, epithelial ovarian cancer (EOC) patients account for the majority of ovarian cancer patients. The pathogenesis of EOC, one of the most lethal gynecological malignancies, remains unclear. Recently, the role of WNT4 in gynecological disease and tumor development was reported, and a suspicious association of WNT4 with EOC was identified in Europeans. However, the contributions of the WNT4 gene to EOC and the underlying molecular mechanisms remains largely unknown. To determine whether the WNT4 gene is associated with EOC, this study investigated polymorphisms of the WNT4 gene in Han Chinese individuals.

MATERIALS AND METHODS

We designed a case/control study with 707 EOC patients and 1563 unrelated healthy controls of Han Chinese descent. A total of eight tag single-nucleotide polymorphisms (SNPs) were genotyped successfully, and both single SNP and haplotype analyses were performed to detect the potential association of variations in the WNT4 gene with EOC.

RESULTS

The SNP rs56318008 was found to be strongly associated with EOC risk. In the serous EOC subgroup, individuals harboring the T allele of rs56318008 exhibited a higher risk of EOC than individuals harboring the C allele. Moreover, the odds ratios and 95% confidence intervals revealed an increased risk of EOC in individuals with the T allele of the SNP, and haplotypic analyses confirmed the results, showing a similar pattern.

CONCLUSION

Our results show that the WNT4 gene is associated with EOC risk, indicating that this gene may be a potential genetic risk factor for developing EOC.

Relationship of common variants in VEGFA gene with osteonecrosis of the femoral head: A Han Chinese population based association study

The pathology of non-traumatic osteonecrosis of the femoral head (ONFH) is complex. Several studies have linked some polymorphisms of vascular endothelial growth factors A (VEGFA) with ONFH, but the results are not consistent and are even conflicting. In the study, 22 single nucleotide polymorphisms (SNPs) in VEGFA were genotyped in 1,762 subjects (489 cases and 1,273 controls). Genetic association analyses were performed in single markers and haplotype levels. Stratification analysis was conducted for ONFH patients. Gene by environment interactions were tested between VEGFA and the smoking status of the subjects. Gene expression and eQTL data of significant SNPs were extracted from GTEx to examine their potential biological function. The SNP, rs2010963, was identified to be significantly associated with ONFH (χ² = 11.66, P = 0.0006, OR = 1.29). Haplotypes including rs2010963 were also identified to be correlated with ONFH in the haplotype-based analyses. After stratifying by the causes of ONFH, a significant signal from rs2010963 could only be identified in alcohol-induced patients (P_allelic = 0.0009) but not in steroid-induced patients (P_allelic = 0.055). No significant results were obtained from the gene by environmental interaction analyses. Significant expression differences of VEGFA were identified in multiple human tissues for different genotypes of rs2010963. Our findings indicate that SNP rs2010963 is significantly associated with ONFH.

Evaluation of Common Variants in Matrix Metalloproteinase-9 Gene with Lumbar Disc Herniation in Han Chinese Population

OBJECTIVE

Lumbar disc herniation (LDH) is a common and frequent orthopedic disease with strong genetic determinants. The disruption of the intervertebral disc extracellular matrix has been found to play a key role in the development of LDH, suggesting that abnormal matrix metalloproteinases (MMPs) may promote the degradation of the disc matrix. MMP-9, an important member of the MMP family, is a good candidate for the LDH susceptibility gene. The present study aimed to investigate the association of common variants in the MMP-9 gene with the risk, severity, and clinical characteristic variables of LDH.

MATERIALS AND METHODS

Fourteen tag single nucleotide polymorphisms (SNPs) entirely covering the region of the MMP-9 gene were analyzed in a sample of 845 patients and 1751 healthy controls.

RESULTS

The SNP rs17576 was found to be significantly associated with susceptibility to LDH (OR = 0.77, p = 0.0002), which was also confirmed by haplotype-based analyses (rs79845319-rs17576-rs45437897, global p < 0.001). Our results indicated that the A allele of rs17576 reduced the risk of LDH by ∼23% on average. Furthermore, the G allele of rs17576 was found to correlate with more severe grades of disc degeneration.

CONCLUSION

Our results provide additional evidence supporting an important role of the MMP-9 gene in the pathogenesis of LDH.

Genetic susceptibility of postmenopausal osteoporosis on sulfide quinone reductase-like gene

Postmenopausal osteoporosis is a major health problem with important genetic factors in postmenopausal women. We explored the relationship between SQRDL and osteoporosis in a cohort of 1006 patients and 2027 controls from Han Chinese postmenopausal women. Our evidence supported the significant role of SQRDL in the etiology of postmenopausal osteoporosis.

INTRODUCTION

Postmenopausal osteoporosis (PMOP) is a metabolic bone disease leading to progressive bone loss and the deterioration of the bone microarchitecture. The sulfide-quinone reductase-like protein is an important enzyme regulating the cellular hydrogen sulfide levels, and it can regulate bone metabolism balance in postmenopausal women. In this study, we aimed to investigate whether SQRDL is associated with susceptibility to PMOP in the Han Chinese population.

METHODS

A total of 3033 postmenopausal women, comprised of 1006 cases and 2027 controls, were recruited in the study. Twenty-two SNPs were selected for genotyping to evaluate the association of SQRDL gene with BMD and PMOP. Association analyses in both single marker and haplotype levels were performed for PMOP. Bone mineral density (BMD) was also utilized as a quantitative phenotype in further analyses. Bioinformatics tools were applied to predict the functional consequences of targeted polymorphisms in SQRDL.

RESULTS

The SNP rs1044032 (P = 6.42 × 10^-5, OR = 0.80) was identified as significantly associated with PMOP. Three SNPs (rs1044032, rs2028589, and rs12913151) were found to be significantly associated with BMD. Although limited functional significance can be obtained for these polymorphisms, significant hits for association with PMOP were found. Moreover, further association analyses with BMD identified three SNPs with significantly independent effects.

CONCLUSIONS

Our evidence supported the significant role of SQRDL in the etiology of PMOP and suggest that it may be a genetic risk factor for BMD and osteoporosis in Han Chinese postmenopausal women.

Genetic polymorphisms of GZMB and vitiligo: A genetic association study based on Chinese Han population

Vitiligo is a skin disease that affects 1% of the population worldwide. Both environmental and genetic factors contribute to the risk of vitiligo. GZMB encodes the enzyme Granzyme B, which plays an important role in cytotoxic T cell-induced apoptosis, and it has been considered one of the candidate genes for vitiligo because of its connections with human immune system. Overall, 3,120 study subjects with Chinese Han ancestry were recruited, and 15 pre-selected SNPs of GZMB were genotyped. Genetic association analyses were performed to evaluate the genetic risk of these SNPs to vitiligo. Further bioinformatic analyses were conducted to examine the potential biological function of targeted SNPs. The SNP rs8192917, a non-synonymous coding SNP, was identified to be significantly associated with the disease status of vitiligo, with OR = 1.39 and P = 1.92 × 10-8. Differences in the association signal can be observed in the stratification analyses of multiple clinical variables. Our positive results provide additional supportive evidence that GZMB gene is an important locus for vitiligo in Han Chinese population.

A common polymorphism of COMT was associated with symptomatic lumbar disc herniation based on a large sample with Chinese Han ancestry

Lumbar disc herniation (LDH) is a common spine disease characterized by a tear in the disc ring and bulges out at the soft portion. COMT is a protein coding gene located at 22q11.21, and its gene product is a major mammalian enzyme involved in the degradation of catecholamines. A total of 2,678 study subjects with Chinese Han ancestry were recruited and 15 SNPs were selected for genotyping in our study subjects. A synonymous coding SNP, rs4633, was identified to be significantly associated with the disease status of LDH after adjusting for BMI (OR = 0.76, P = 4.83 × 10⁻⁵). This SNP was also identified to be significantly associated with COMT gene expression in three types of human tissues. Minor alleles of rs4633 (T) increased the expression of COMT in these 3 tissues. We have identified a significant SNP of COMT, rs4633, which is associated with symptomatic LDH in a large Chinese Han-based sample of the study subjects. This significant finding is further replicated by haplotypic analysis. Evidence from bioinformatics analyses have shown that rs4633 is also significantly associated with the gene expression of COMT. Our findings provide additional supportive evidence for an important role of COMT gene in the symptomatic LDH susceptibility.

MDM4 contributes to the increased risk of glioma susceptibility in Han Chinese population

Recently, MDM4 gene has been reported to be a susceptibility gene for glioma in Europeans, but the molecular mechanism of glioma pathogenesis remains unknown. The aim of this study was to investigate whether common variants of MDM4 contribute to the risk of glioma in Han Chinese individuals. A total of 24 single-nucleotide polymorphisms (SNPs) of the MDM4 gene were assessed in a dataset of 562 glioma patients (non-glioblastoma) and 1,192 cancer-free controls. The SNP rs4252707 was found to be strongly associated with the risk of non-GBM (P = 0.000101, adjusted odds ratio (OR) = 1.34, 95% confidence interval (CI) = 1.16–1.55). Further analyses indicated that there was a significant association between A allele of rs4252707 associated with the increased non-GBM risk. Haplotype analysis also confirmed a result similar to that of the single-SNP analysis. Using stratification analyses, we found the association of rs4252707 with an increased non-GBM risk in adults (≥18 years, P = 0.0016) and individuals without IR exposure history (P = 0.0013). Our results provide strong evidence that the MDM4 gene is tightly linked to genetic susceptibility for non-GBM risk in Han Chinese population, indicating a important role for MDM4 gene in the etiology of glioma.

Common variants in the GNL3 contribute to the increasing risk of knee osteoarthritis in Han Chinese population

Osteoarthritis (OA) is a complex degenerative joint disorder, which is caused by both environmental and genetic factors. Previous studies have indicated that the GNL3 gene is associated with knee osteoarthritis (KOA) susceptibility in Europeans; however, the exact molecular mechanism is still unclear. In the present study, we investigated the potential genetic association of GNL3 with KOA in a two-stage sample of 6,704 individuals from the Han Chinese population. Subjects containing 1,052 KOA patients and 2,117 controls were considered the discovery dataset, while subjects consisting of 1,173 KOA patients and 2,362 controls were utilized as the replication dataset. Single-SNP association, imputation, and haplotypic association analyses were performed. The SNP of rs11177 in GNL3 was identified to be significantly associated with KOA after accounting for age, gender and BMI in both stages. The imputed SNP of rs6617 in SPCS1 was found to be strongly associated with KOA risk, and the significant association signal was confirmed in the replication stage. Moreover, a haplotype-based analysis also indicated a positive genetic effect of GNL3 on KOA susceptibility. In summary, our results proved that GNL3 plays an important role in the etiology of KOA, suggesting that GNL3 is a potential genetic modifier for KOA development.

Association of BET1L and TNRC6B with uterine leiomyoma risk and its relevant clinical features in Han Chinese population

Previous studies have shown that uterine leiomyomas (UL) are benign tumours with contributions from environmental and genetic factors. We aimed to replicate two initial significant genetic factors, TNRC6B and BET1L, in a Han Chinese population. A total of 2,055 study subjects were recruited, and 55 SNPs mapped to TNRC6B and BET1L were selected and genotyped in samples from these subjects. Genetic associations were analysed at both the single marker and haplotype levels. Associations between targeted SNPs and relevant clinical features of UL were analysed in case only samples. Functional consequences of significant SNPs were analysed by bioinformatics tools. Two SNPs, rs2280543 from BET1L (χ² = 18.3, OR = 0.64, P = 1.87 × 10⁻⁵) and rs12484776 from TNRC6B (χ² = 19.7, OR = 1.40, P = 8.91 × 10⁻⁶), were identified as significantly associated with the disease status of UL. Rs2280543 was significantly associated with the number of fibroid nodes (P = 0.0007), while rs12484776 was significantly associated with node size (χ² = 54.88, P = 3.44 × 10⁻¹¹). Both SNPs were a significant eQTL for their genes. In this study, we have shown that both BET1L and TNRC6B contributed to the risk of UL in Chinese women. Significant SNPs from BET1L and TNRC6B were also identified as significantly associated with the number of fibroid nodes and the size of the node, respectively.

Genetic polymorphisms of NOS2 and predisposition to fracture non-union: A case control study based on Han Chinese population

A non-union, especially atrophic non-unions, is a permanent failure of healing following a fracture and can be difficult to treat. Approximately 5–10% of fractures will result in a non-union during the healing process. non-unions can be classified into two types: atrophic non-union which is often due to impaired bone healing with a potential biological mechanism, and hypertrophic non-union which is due to inadequate fixation after fracture. Genetic variations also play an important role in the fracture healing response. Previous studies based on animal models have indicated that NOS2 might be greatly involved in the bone fracture healing process. In this case-control study, 346 nonunion patients were compared to 883 patients with normal fracture healing to investigate the potential genetic association between NOS2 and the fracture healing process using study subjects of Chinese Han ancestry. Twenty-seven single nucleotide polymorphisms (SNPs) covering NOS2 were genotyped in our study subjects and analyzed. In addition to the single marker-based analysis, we performed a gene-by-environment analysis to examine the potential interactions between genetic polymorphisms and some environmental factors. SNP rs2297514 showed significant association with the fracture healing process after adjusting for age and gender (OR = 1.38, P = 0.0005). Our results indicated that the T allele of rs2297514 significantly increased the risk of a non-union during the fracture healing process by 38% compared to the C allele. Further stratification analyses conducted for this SNP using data from subgroups classified by different sites of fracture indicated that significance could only be observed in the tibial diaphysis subgroup (N = 428, OR = 1.77, P = 0.0007) but not other groups including femur diaphysis, humeral shaft, ulnar shaft, and femur neck. Gene-by-environment interaction analyses of the three environmental factors showed no significant results. In this study, rs2297514 was significantly associated with the non-union status of fracture healing using a large Chinese population-based study sample. Our findings replicated those of a previous preliminary study and offered strong evidence linking NOS2 and fracture healing.

Common Variants in ALPL Gene Contribute to the Risk of Kidney Stones in the Han Chinese Population

OBJECTIVE

Kidney stone formation is a complex disorder that likely results from both dietary and genetic factors. A recent study identified an association between the risk of kidney stones and polymorphisms in the ALPL gene, but the study needs replication. To confirm whether the ALPL gene is universally associated with kidney stones, the present study further investigated polymorphisms of the ALPL gene in a Han Chinese population.

METHODS

A total of 331 kidney stone patients and 553 unrelated healthy controls were included in the present case-control study. We conducted genetic analyses to detect the association of 19 tagging single nucleotide polymorphisms (SNPs) with kidney stones. In addition, we examined the relations between targeted SNP(s) and several clinical characteristics of kidney stones in the patients.

RESULTS

Genetic association analyses using logistic regression models identified one ALPL SNP, rs1256328, which was significantly associated with the kidney stone disease status (OR = 1.52, p = 0.0009). No significant results were obtained through association tests between genotypes of this SNP and the various clinical characteristics of kidney stone patients.

CONCLUSION

The ALPL SNP, rs1256328, was identified as being significantly associated with kidney stone disease status in a large Chinese Han cohort. Our study replicated a previous genome-wide association study that was conducted in an Icelandic population.

Transcriptional regulation of voltage-gated Ca2+ channels

The transcriptional regulation of voltage-gated Ca²⁺ (Ca_V ) channels is an emerging research area that promises to improve our understanding of how many relevant physiological events are shaped in the central nervous system, the skeletal muscle and other tissues. Interestingly, a picture of how transcription of Ca_V channel subunit genes is controlled is evolving with the identification of the promoter regions required for tissue-specific expression and the identification of transcription factors that control their expression. These promoters share several characteristics that include multiple transcriptional start sites, lack of a TATA box and the presence of elements conferring tissue-selective expression. Likewise, changes in Ca_V channel expression occur throughout development, following ischaemia, seizures or chronic drug administration. This review focuses on insights achieved regarding the control of Ca_V channel gene expression. To further understand the complexities of expression and to increase the possibilities of detecting Ca_V channel alterations causing human disease, a deeper knowledge on the structure of the 5' upstream regions of the genes encoding these remarkable proteins will be necessary.

Genetic association study identified a 20 kb regulatory element in WLS associated with osteoporosis and bone mineral density in Han Chinese

Previous studies have linked the WNT pathway and human skeleton formation; therefore, genes related to WNT might contribute to the onset and development of osteoporosis. In this study, we investigated the potential genetic association of WLS, which encodes an important mediator in the WNT pathway, with osteoporosis and its related quantitative traits in a sample of 6,620 individuals from Han Chinese population. A two-stage approach, with a discovery stage with 859 cases and 1,690 controls and a validation stage with 1,039 cases and 3,032 controls, was applied in the study. Forty SNPs were genotyped in the discovery stage. The intronic SNP rs2566752 was identified to be significantly associated with osteoporosis (OR_discovery = 0.78, P_discovery = 3.73 × 10⁻⁵; OR_validation = 0.80, P_validation = 1.96 × 10⁻⁵). Two SNPs surrounding rs2566752 (in addition to this SNP itself) were identified to be associated with bone mineral density. In addition, we have identified a 20 kb peak region of H3K27Ac histone mark enrichment between rs2772304 and rs2566752. Our study suggested that WLS is an important locus for osteoporosis and its related quantitative phenotypes in Han Chinese population. Additional sequencing-based studies are needed to investigate the genetic architecture of this regulatory region and its relationship with osteoporosis-related phenotypes.

Evaluation of the association of UBASH3A and SYNGR1 with rheumatoid arthritis and disease activity and severity in Han Chinese

Rheumatoid arthritis (RA) is a common complex autoimmune disorder. UBASH3A and SYNGR1 were identified recently as susceptibility genes for RA risk in Korean and European populations, but the genetic aetiology and pathogenesis of RA have not been fully elucidated. We designed a two-stage case-control study including 916 RA patients and 2,266 unrelated healthy controls to identify common genetic variants in UBASH3A and SYNGR1 that predispose Han Chinese individuals to RA. We also evaluated the role of associated variants in clinical manifestations of RA, which may provide clues to the mechanisms involved in the aetiology of RA. We successfully identified two SNPs, rs1893592 in UBASH3A and rs909685 in SYNGR1, as significantly associated with the disease status of RA using our two-stage strategy. The rs1893592 SNP in UBASH3A was related with DAS28, CRP level and bone erosion. In summary, our results indicate that genetic variants in UBASH3A and SYNGR1 may modify individual susceptibility to RA in the Han Chinese population and support the role of the UBASH3A gene in RA disease activity and severity.

Evaluating the Association of Common Variants of the SLC44A4 Gene with Ulcerative Colitis Susceptibility in the Han Chinese Population

OBJECTIVE

The SLC44A4 gene was recently reported to be associated with ulcerative colitis (UC) susceptibility in the Indian and Japanese populations. The aim of our study was to investigate the association of common variants within the SLC44A4 gene and the susceptibility to UC among the Han Chinese.

METHODS

We examined 16 tag single nucleotide polymorphisms (SNPs) within the SLC44A4 gene in a Han Chinese population that consisted of 311 UC patients and 675 healthy controls; both SNP and haplotypic association analyses were performed.

RESULTS

We found that rs2736428 was significantly associated with UC risk (allelic p = 0.0004), and the CT and TT genotypes of rs2736428 had a higher distribution compared with the CC genotypes (genotypic p = 0.001), suggesting that the T allele was a risk allele (odds ratio = 1.45, 95% confidence interval = 1.18-1.78). Moreover, one haplotype block that included rs2736428 was found to be strongly associated with UC risk as well (global p < 0.001).

CONCLUSION

Our results provide further supportive evidence for an important role of the SLC44A4 gene in the pathogenesis of UC.

From Gene to Behavior: L-Type Calcium Channel Mechanisms Underlying Neuropsychiatric Symptoms

The L-type calcium channels (LTCCs) Cav1.2 and Cav1.3, encoded by the CACNA1C and CACNA1D genes, respectively, are important regulators of calcium influx into cells and are critical for normal brain development and plasticity. In humans, CACNA1C has emerged as one of the most widely reproduced and prominent candidate risk genes for a range of neuropsychiatric disorders, including bipolar disorder (BD), schizophrenia (SCZ), major depressive disorder, autism spectrum disorder, and attention deficit hyperactivity disorder. Separately, CACNA1D has been found to be associated with BD and autism spectrum disorder, as well as cocaine dependence, a comorbid feature associated with psychiatric disorders. Despite growing evidence of a significant link between CACNA1C and CACNA1D and psychiatric disorders, our understanding of the biological mechanisms by which these LTCCs mediate neuropsychiatric-associated endophenotypes, many of which are shared across the different disorders, remains rudimentary. Clinical studies with LTCC blockers testing their efficacy to alleviate symptoms associated with BD, SCZ, and drug dependence have provided mixed results, underscoring the importance of further exploring the neurobiological consequences of dysregulated Cav1.2 and Cav1.3. Here, we provide a review of clinical studies that have evaluated LTCC blockers for BD, SCZ, and drug dependence-associated symptoms, as well as rodent studies that have identified Cav1.2- and Cav1.3-specific molecular and cellular cascades that underlie mood (anxiety, depression), social behavior, cognition, and addiction.

Polymorphisms of RAD51B are associated with rheumatoid arthritis and erosion in rheumatoid arthritis patients

Rheumatoid arthritis (RA) is a common, chronic autoimmune disease affecting 0.5–1.0% of adults worldwide, including approximately 4.5–5.0 million patients in China. The genetic etiology and pathogenesis of RA have not yet been fully elucidated. Recently, one new RA susceptibility gene (RAD51B) has been identified in Korean and European populations. In this study, we designed a two-stage case-control study to further assess the relationship of common variants in the RAD51B gene with increased risk of RA in a total of 965 RA patients and 2,511 unrelated healthy controls of Han Chinese ancestry. We successfully identified a common variant, rs911263, as being significantly associated with the disease status of RA (P = 4.8 × 10⁻⁵, OR = 0.64). In addition, this SNP was shown to be related to erosion, a clinical assessment of disease severity in RA (P = 2.89 × 10⁻⁵, OR = 0.52). These findings shed light on the role of RAD51B in the onset and severity of RA. More research in the future is needed to clarify the underlying functional link between rs911263 and the disease.

Association of a common variant of SYNPO2 gene with increased risk of serous epithelial ovarian cancer

In China, the majority of ovarian cancer patients (80%–90%) are women who are diagnosed with epithelial ovarian cancer. The SYNPO2 gene has recently been reported to be associated with epithelial ovarian cancer in Europeans. To investigate the association of common variants of SYNPO2 gene with epithelial ovarian cancer in Han Chinese individuals, we designed a case–control study with 719 epithelial ovarian cancer patients and 1568 unrelated healthy controls of Han Chinese descent. A total of 49 tagging single-nucleotide polymorphisms were genotyped; single-single-nucleotide polymorphism association, imputation, and haplotypic association analyses were performed. The single-nucleotide polymorphism rs17329882 was found to be strongly associated with serous epithelial ovarian cancer and with ages ≤49 years, consistent with the pre-menopausal status of analyzed epithelial ovarian cancer cases. Odds ratios and 95% confidence intervals provided evidence of the risk effects of the C allele of the single-nucleotide polymorphism on epithelial ovarian cancer. Imputation analyses also confirmed the results with a similar pattern. Additionally, haplotype analyses indicated that the haplotype block that contained rs17329882 was significantly associated with epithelial ovarian cancer risk, specifically with the serous epithelial ovarian cancer subtype. In conclusion, our results show that SYNPO2 gene plays an important role in the etiology of epithelial ovarian cancer, suggesting that this gene may be a potential genetic modifier for developing epithelial ovarian cancer.

Additional Evidence Supports Association of Common Variants in COL11A1 with Increased Risk of Hip Osteoarthritis Susceptibility

OBJECTIVE

In a recent study single nucleotide polymorphisms (SNPs) in the COL11A1 gene were found to be associated with hip osteoarthritis (OA) among European populations. In this study, our aim was to identify common genetic variants in COL11A1 predisposing to primary hip OA in Han Chinese individuals.

METHODS

We designed a case-control study that included 313 hip OA patients and 911 unrelated healthy controls. Fourteen tagging single-nucleotide polymorphisms (SNPs) were genotyped, and single SNP and haplotypic association analyses were performed.

RESULTS

Two SNPs (rs1241164 and rs4907986) were found to be significantly associated with hip OA risk (adjusted p = 0.000731 and 0.000477). An increased risk of OA was associated with possession of the C allele of rs1241164 (adjusted odds ratio [OR] = 1.73, 95% confidence interval [CI] = 1.27-2.36) and the T allele of rs4907986 (adjusted OR = 1.72, 95% CI = 1.24-2.35). Similar results were confirmed via genotypic association analyses. Moreover, two different haplotype blocks, including rs1241164 and rs4907986, respectively, were found to be strongly associated with hip OA risk as well.

CONCLUSION

Variants in the COL11A1 gene modify individual susceptibility to hip OA in the Han Chinese population.

Association of common variants in MTAP with susceptibility and overall survival of osteosarcoma: a two-stage population-based study in Han Chinese

Osteosarcoma (OS) is a common malignant tumor, which exists widely in the bone of children and adolescents, and genetic factors may influence its susceptibility. Recently, the gene MTAP has been reported to be associated with OS in a Caucasian population. To investigate the association of common variants in MTAP with OS risk in Han Chinese individuals, we designed a two-stage case-control study with 392 OS patients and 1,578 unrelated healthy controls of Han Chinese individuals. A total of 17 tagging single nucleotide polymorphisms (SNPs) were firstly genotyped in the discovery stage, and single-SNP association and haplotypic association analyses have been performed. The SNP rs7023329 was found to be strongly associated with the OS risk (adjusted P = 0.002908), and the results of odds ratios (ORs) and 95% confidence intervals (CI) revealed increased risks from A allele of the SNP on OS (OR=1.33, 95% CI=1.13-1.62). The results were confirmed with a similar pattern in the validation stage (adjusted P = 0.006737, OR=1.49, 95% CI=1.11-2.00). Moreover, haplotypic analyses indicated that one haplotype block containing rs7023329 was significantly associated with OS risk in both stages (both global P<0.0001). The statistically significant association between the rs7023329 genotype and poor survival in OS patients was also observed. To sum up, our results prove that MTAP plays an important role in the etiology of OS, suggesting this gene as a potential genetic modifier for OS development.

Evaluation of voltage-dependent calcium channel γ gene families identified several novel potential susceptible genes to schizophrenia

Voltage-gated L-type calcium channels (VLCC) are distributed widely throughout the brain. Among the genes involved in schizophrenia (SCZ), genes encoding VLCC subunits have attracted widespread attention. Among the four subunits comprising the VLCC (α − 1, α −2/δ, β, and γ), the γ subunit that comprises an eight-member protein family is the least well understood. In our study, to further investigate the risk susceptibility by the γ subunit gene family to SCZ, we conducted a large-scale association study in Han Chinese individuals. The SNP rs17645023 located in the intergenic region of CACNG4 and CACNG5 was identified to be significantly associated with SCZ (OR = 0.856, P = 5.43 × 10⁻⁵). Similar results were obtained in the meta-analysis with the current SCZ PGC data (OR = 0.8853). We also identified a two-SNP haplotype (rs10420331-rs11084307, P = 1.4 × 10⁻⁶) covering the intronic region of CACNG8 to be significantly associated with SCZ. Epistasis analyses were conducted, and significant statistical interaction (OR = 0.622, P = 2.93 × 10⁻⁶, P_perm < 0.001) was observed between rs192808 (CACNG6) and rs2048137 (CACNG5). Our results indicate that CACNG4, CACNG5, CACNG6 and CACNG8 may contribute to the risk of SCZ. The statistical epistasis identified between CACNG5 and CACNG6 suggests that there may be an underlying biological interaction between the two genes.

Two-stage comprehensive evaluation of genetic susceptibility of common variants in FBXO38, AP3B2 and WHAMM to severe chronic periodontitis

Chronic periodontitis is an oral disorder characterized with gingival inflammation and bone destruction. As the sixth-most prevalent condition affecting more than 743 million people around the world, it is classified as one of the seven destructive oral disorders. Early genetic epidemiological evidence indicated a major role for genetics in periodontal disease development. In this study, we conducted a two-stage comprehensive evaluation of the genetic susceptibility of FBXO38, AP3B2 and WHAMM with the diagnosis of severe chronic periodontitis. A total of 5,065 study subjects from the Han Chinese population consisting of 1,264 cases and 3,801 healthy controls were recruited, and 65 single nucleotide markers related to the three candidate genes were genotyped to investigate the susceptibility of patients with these polymorphisms to severe chronic periodontitis. To increase the coverage of genetic markers, we implemented imputation techniques to extend the number of tested makers to 416. Single marker and haplotype-based analyses were performed, and significant results were obtained for FBXO38 (rs10043775, P = 0.0009) and AP3B2 (rs11631963-rs11637433, CA, P = 9.98 × 10(-5); rs1864699-rs2099259-rs2278355, ATC, P = 3.84 × 10(-8)). Our findings provide direct evidence for the association of FBXO38 and AP3B2 with severe chronic periodontitis in the Han Chinese population.

Common variants of HTR1A and SLC6A4 confer the increasing risk of Schizophrenia susceptibility: A population-based association and epistasis analysis

Schizophrenia (SZ) is a complex psychiatric disorder strongly influenced by genetic variants, some of which are associated with mood disorders. The neurotransmitter 5-hydoxytryptamine (5-HT) and its related biochemical factors have been shown to play a significant role in maintaining mood balance. Recent studies evaluating the association between SZ and genetic polymorphisms in a serotonin transporter (encoded by SLC6A4) and serotonin receptor 1A (encoded by HTR1A) show conflicting results. In this study, we performed a case-control association analysis using 4,000 individuals with Chinese-Han ancestry. Of these participants, 1,000 were SZ cases and 3,000 were healthy controls. Thirty-six single nucleotide polymorphisms (SNPs) located in SLC6A4 and HTR1A were genotyped in our 4,000 study samples. Of those, 33 polymorphic SNPs with a minor allele frequency >0.05 were used for further analysis. We found that rs878567 in HTR1A (asymptotic P-value = 3.89×10(-4) , corrected P-value = 0.0106) was significantly associated with SZ. Further haplotype-based analyses revealed that a two-SNP haplotype, rs2054847-rs140701 (TG) in gene SLC6A4, was significantly associated with SZ (P-value = 1.63×10(-4) and corrected P-value = 0.002799). We did not identify any significant epistatic interactions between the two genes. Our findings provide supportive evidence that genetic polymorphisms in SLC6A4 and HTR1A may influence the risk of SZ in Han Chinese individuals. © 2015 Wiley Periodicals, Inc.

Common variants in SLC1A2 and schizophrenia: Association and cognitive function in patients with schizophrenia and healthy individuals

SLC1A2 is reported to be responsible for the majority of glutamate uptake, which has a crucial role in neural development and synaptic plasticity, and a disturbance in glutamatergic transmission has been suggested to be involved in the pathophysiology of schizophrenia (SCZ) and cognition. To evaluate the relationship of common variants within SLC1A2 with SCZ and cognition in Han Chinese, 28 tag SNPs were genotyped in the discovery stage, which included 1117 cases and 2289 controls; significantly associated markers were genotyped in the replication stage with 2128 cases and 3865 controls. The rs4354668 SNP was identified to be significantly associated with SCZ in both datasets, and a similar pattern was also observed in the two-stage study on conducting imputation and haplotype association analyses. In addition, significant associations between the rs4354668 SNP and cognition were observed when processing the perseverative error of the Wisconsin Card Sorting Test in patients and controls. Our results provide supportive evidence for an effect of SLC1A2 on the etiology of SCZ, suggesting that genetic variation (rs4354668 and its haplotypes) in SLC1A2 may be involved in impaired executive function, which adds to the current body of knowledge regarding the risk of SCZ and the impairment of cognitive performance.

Endochondral ossification pathway genes and postmenopausal osteoporosis: Association and specific allele related serum bone sialoprotein levels in Han Chinese

Osteoporosis is a systemic skeletal disorder characterized by reduced bone mineral density (BMD) and disrupted bone architecture, predisposing the patient to increased fracture risk. Evidence from early genetic epidemiological studies has indicated a major role for genetics in the development of osteoporosis and the variation in BMD. In this study, we focused on two key genes in the endochondral ossification pathway, IBSP and PTHLH. Over 9,000 postmenopausal Han Chinese women were recruited, and 54 SNPs were genotyped. Two significant SNPs within IBSP, rs1054627 and rs17013181, were associated with BMD and postmenopausal osteoporosis by the two-stage strategy, and rs17013181 was also significantly associated with serum IBSP levels. Moreover, one haplotype (rs12425376-rs10843047-rs42294) covering the 5' end of PTHLH was associated with postmenopausal osteoporosis. Our results provide evidence for the association of these two key endochondral ossification pathway genes with BMD and osteoporosis in postmenopausal Han Chinese women. Combined with previous findings, we provide evidence that a particular SNP in IBSP has an allele-specific effect on mRNA levels, which would, in turn, reflect serum IBSP levels.