Association study of candidate genes for susceptibility to Kashin-Beck disease in a Tibetan population

In Silico Analysis of Collagens Missense SNPs and Human Abnormalities

Collagens are the most abundant proteins in the extra cellular matrix/ECM of human tissues that are encoded by different genes. There are single nucleotide polymorphisms/SNPs which are considered as the most useful biomarkers for some disease diagnosis or prognosis. The aim of this study is screening and identifying the functional missense SNPs of human ECM-collagens and investigating their correlation with human abnormalities. All of the missense SNPs were retrieved from the NCBI SNP database and screened for a global frequency of more than 0.1. Seventy missense SNPs that met the screening criteria were characterized for functional and stability impact using six and three protein analysis tools, respectively. Next, HOPE and geneMANIA analysis tools were used to show the effect of SNPs on three-dimensional structure (3D) and physical interaction of proteins. Results showed that 13 missense SNPs (rs2070739, rs28381984, rs13424243, rs1800517, rs73868680, rs12488457, rs1353613, rs59021909, rs9830253, rs2228547, rs3753841, rs2855430, and rs970547), which are in nine different collagen genes, affect the structure and function of different collagen proteins. Among these polymorphisms, COL4A3-rs13424243 and COL6A6-rs59021909 were predicted as the most effective ones. On the other hand, designed mutated and native 3D of rs13424243 variant illustrated that it can disturb the protein motifs. Also, geneMANIA predicted that COL4A3 and COL6A6 are interacting with some proteins including: DDR1, COL6A1, COL11A2 and so on. Based on our findings, ECM-collagens functional SNPs are important and may be considered as a risk factor or molecular marker for human disorders in the future studies.

An eQTL variant of ALDH1A2 is associated with Kashin-Beck disease in Chinese population

INTRODUCTION

The aims of the study were to investigate the relationship between aldehyde dehydrogenase 1 family member A2 (ALDH1A2) and Kashin-Beck disease (KBD), explore the effects of the rs3204689 polymorphism and methylation status on the expression levels of ALDH1A2, and further clarify the pathogenesis of KBD.

MATERIALS AND METHODS

The genotype of ALDH1A2 rs3204689 was detected by PCR-RFLP in 103 KBD patients and 109 healthy controls in the whole blood. The mRNA level of ALDH1A2 was measured by qRT-PCR, and the protein expression was detected using IHC staining and Western blotting. The MSP-PCR was used to identify the ALDH1A2 methylation level.

RESULTS

There were significant differences in G/G, G/C, and C/C frequencies of ALDH1A2 rs3204689 between the KBD and control groups (χ² = 7.113, P = 0.029); the minor allele G of ALDH1A2 was associated with the risk of KBD (χ² = 5.984, P = 0.014). The mRNA and protein levels of ALDH1A2 were increased in the whole blood and cartilage of KBD patients compared with the controls (P = 0.049, P < 0.0001, P = 0.019). Meanwhile, a statistically significant difference was observed between G/G, G/C and C/C genotype on mRNA expression (P = 0.039). The methylation level of the ALDH1A2 gene promoter region showed no significant difference between the KBD and control groups (χ² = 0.317, P = 0.573).

CONCLUSION

Our case-control study indicates that the common variant rs3204689 near ALDH1A2 is associated with KBD in Chinese population. The risk allele G of rs3204689 is statistically linked to the high expression of ALDH1A2, which is up-regulated in the cartilage and whole blood of KBD patients. Our findings suggest a potential role of ALDH1A2 in the pathogenesis of KBD.

Comprehensive analysis of lncRNA and mRNA based on expression microarray profiling reveals different characteristics of osteoarthritis between Tibetan and Han patients

Background

Osteoarthritis (OA) is thought to be the most prevalent chronic joint disease, especially in Tibet of China. Here, we aimed to explore the integrative lncRNA and mRNA landscape between the OA patients of Tibet and Han.

Methods

The lncRNA and mRNA expression microarray profiling was performed by SurePrint G3 Human Gene Expression 8x60K v2 Microarray in articular cartilage samples from OA patients of Han nationality and Tibetans, followed by GO, KEGG, and trans-regulation and cis-regulation analysis of lncRNA and mRNA.

Results

We found a total of 117 lncRNAs and 297 mRNAs differently expressed in the cartilage tissues of Tibetans (n = 5) comparing with those of Chinese Han (n = 3), in which 49 lncRNAs and 158 mRNAs were upregulated, and 68 lncRNAs and 139 mRNAs were downregulated. GO and KEGG analysis showed that several unreported biological processes and signaling pathways were particularly identified. LncRNA-mRNA co-expression analysis revealed a remarkable lncRNA-mRNA relationship, in which OTOA may play a critical role in the different mechanisms of the OA progression between Tibetans and Chinese Han.

Conclusion

This study identified different lncRNA/mRNA expression profiling between OA patients of Tibetans and Han, which were involved in many characteristic biological processes and signaling pathways.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13018-021-02213-y.

Association between DIO2 polymorphism and the risk of Kashin-Beck disease in the Tibetan population

BACKGROUND

Kashin-Beck disease (KBD) is a local, multiple and deformable osteoarthropathy, mostly occurring in Tibet. Type 2 iodothyronine deiodinase (DIO2) is implicated in the activation of thyroid hormones to which the bones are very sensitive. Therefore, it is necessary to explore the association between KBD and DIO2 in the Tibetan population.

METHODS

We carried out a case-control study among 316 cases and 320 controls from a Tibetan population. Seven single nucleotide polymorphisms in DIO2 were selected and genotyped using the Agena MassARRAY platform (Agena Bioscience, San Diego, CA, USA). Odds ratios (ORs) and 95% confidence intervals (CIs) were calculated by logistic regression analysis. HaploReg (https://pubs.broadinstitute.org/mammals/haploreg/haploreg.php) and GTEx (http://www.gtexportal.org) databases were applied for functional assessment of the polymorphisms.

RESULTS

The "A/C" genotype of rs1352815 (OR = 3.18, 95% CI = 1.14-8.85, p = 0.027) and the "A/G" genotype of rs1388382 (OR = 3.80, 95% CI = 1.30-11.11, p = 0.015) were associated with the susceptibility of KBD under the co-dominant model. With gender stratification analysis, rs1388382 showed obvious evidence for correlation with an elevated risk of KBD in females under the co-dominant model (OR = 3.32, 95% CI = 1.06-10.41, p = 0.039).

CONCLUSIONS

The results obtained in the present study indicate that DIO2 polymorphisms rs1352815 and rs1388382 were correlated with KBD susceptibility among Tibetans, which also sheds new light on the role of DIO2 in the development of KBD.

Genetic variants in the ITPR2 gene are associated with Kashin-Beck Disease in Tibetan

Background

Kashin‐Beck Disease (KBD) is a chronic, endemic osteoarthropathy. Inositol 1,4,5‐triphosphate receptor type 2 (ITPR2) gene is involved in chondrocytes. We speculated that single‐nucleotide polymorphisms (SNPs) in ITPR2 gene may have an association with KBD in Tibetan.

Methods

To prove this hypothesis, a total of eight SNPs (rs1049376, rs11048526, rs11048556, rs11048585, rs16931011, rs10842759, rs2230372, and rs7134213) were selected, and genotyped in 316 KBD patients and 320 controls. The association between ITPR2 variants and KBD risk was assessed by logistic regression analysis.

Results

The study identified significant association (p = 0.019) between KBD and a novel locus, ITPR2 SNP rs11048526 (OR = 1.49, 95% CI = 1.07–2.08). The variant A/G genotype frequency in rs11048526 had a significantly increased risk of KBD in co‐dominant model (OR = 3.70, 95% CI = 1.26–10.89, p = 0.018), dominant model (OR = 3.56, 95% CI = 1.22–10.40, p = 0.020), log‐additive model (OR = 3.00, 95% CI = 1.12–8.00, p = 0.029) after adjusted for age and gender.

Conclusion

The results indicate a potential association between ITPR2 and KBD risk in Tibetan. Further work is required to confirm these results and explore the mechanisms of these effects.

Biological Analysis of Gene Expression and Clinical Variables Suggest FZD1 as a Novel Biomarker for Patients with Kashin-Beck Disease, an Endemic Osteoarthritis in China

Clinical variables contribute to the severity of Kashin-Beck disease (KBD). However, it is unclear if there is a correlation between gene expression and clinical variables. Peripheral blood samples were collected from 100 patients with KBD and 100 healthy controls from KBD-endemic areas to identify differentially expressed genes in KBD. Correlation analysis and multiple logistic regression analysis were performed using gene expression and clinical parameters. Immunohistochemistry (IHC) was used to detect the expression of related proteins in articular cartilage tissues. Thirty-nine differentially expressed genes were identified in patients with KBD. Nine differentially expressed genes were correlated with the metacarpal length/metacarpal breadth index. FZD1 was identified as having statistical significance in establishing the regression model of clinical parameters and gene expression. FZD1 expression levels were remarkably reduced in patients with KBD. Our results indicate that FZD1 could be involved in the pathological process of phalanges tuberositas and brachydactylia and may provide new insight into the pathogenesis of articular cartilage destruction observed in patients with KBD.