Genome-wide association study identifies COL2A1 locus involved in the hand development failure of Kashin-Beck disease

An integrative analysis of DNA methylation and transcriptome showed the dysfunction of MAPK pathway was involved in the damage of human chondrocyte induced by T-2 toxin

Background

T-2 toxin is thought to induce the growth plate and articular cartilage damage of Kashin-Beck disease (KBD), an endemic osteochondropathy in China. This study aims to explore the potential underlying mechanism of such toxic effects by integrating DNA methylation and gene expression profiles.

Methods

In this study, C28/I2 chondrocytes were treated with T-2 toxin (5 ng/mL) for 24 h and 72 h. Global DNA methylation level of chondrocyte was tested by Enzyme-Linked Immuno Sorbent Assay. Genome-wide DNA methylation and expression profiles were detected using Illumina Infinium HumanMethylation850 BeadChip and RNA-seq technique, respectively. Differentially methylated genes (DMGs) and differentially expressed genes (DEGs) were identified mainly for two stages including 24 h group versus Control group and 72 h group versus 24 h group. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses were performed by Metascape. DMGs and DEGs were further validated by Sequenom MassARRAY system and quantitative real-time polymerase chain reaction.

Results

The global DNA methylation levels of chondrocytes exposed to T-2 toxin were significantly increased (P < 0.05). For 24 h group versus Control group (24 VS C), 189 DEGs and 590 DMGs were identified, and 4 of them were overlapping. For 72 h group versus 24 h group (72 VS 24), 1671 DEGs and 637 DMGs were identified, and 45 of them were overlapping. The enrichment analysis results of DMGs and DEGs both showed that MAPK was the one of the mainly involved signaling pathways in the regulation of chondrocytes after T-2 toxin exposure (DEGs: P_24VSc = 1.62 × 10^− 7; P_72VS24 = 1.20 × 10^− 7; DMGs: P_24VSc = 0.0056; P_72VS24 = 3.80 × 10^− 5).

Conclusions

The findings depicted a landscape of genomic methylation and transcriptome changes of chondrocytes after T-2 toxin exposure and suggested that dysfunction of MAPK pathway may play important roles in the chondrocytes damage induced by T-2 toxin, which could provide new clues for understanding the potential biological mechanism of KBD cartilage damage induced by T-2 toxin.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12860-021-00404-3.

Multiple variants in collagen genes are associated with the susceptibility to lumbar disc herniation in the Chinese population

PURPOSE

Lumbar disc herniation (LDH) is an important cause of back pain and sciatica, but its aetiology is not fully understood. Single-nucleotide polymorphisms (SNPs) in specific collagen genes are known to increase the risk of lumbar disc degeneration. We performed a case-control study among the Chinese Han population to investigate whether genetic variations in collagen genes were associated with the risk of LDH or not.

METHODS

We genotyped SNPs selected from 1000 Genome Projects using Agena MassARRAY technology. Three hundred and eighty-four LDH cases were compared with 384 controls of similar age, using the odds ratio and 95% confidence interval to calculate the susceptibility in several genetic models.

RESULTS

Our results revealed that subjects with the rs6122316-C variant of the COL9A3 gene had a higher likelihood of LDH than subjects with the allele T variant in both the codominant and recessive models. In addition, after gender stratification analysis, we found significant associations between rs16970089 and rs740024 and LDH risk in females. Age stratification analysis illustrated that rs16970089 and rs6122316 were also correlated with LDH risk in people over 50 years. The smoking stratification illustrated that rs2071358 and rs740024 had an increased association with LDH risk in smokers. And after drinking stratification, we also observed the significance between rs740024 and LDH risk.

CONCLUSIONS

Variants in genes for COL1A1, COL9A3 and COL2A1 significantly influence the risk of LDH. Large and well-designed studies are needed to confirm and explain these conclusions. These slides can be retrieved under Electronic Supplementary Material.

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.

Pathway-based network analyses and candidate genes associated with Kashin-Beck disease

To perform a comprehensive analysis focusing on the biological functions and interactions of Kashin-Beck disease (KBD)-related genes to provide information towards understanding the pathogenesis of KBD.A retrospective, integrated bioinformatics analysis was designed and conducted. First, by reviewing the literature deposited in PubMed, we identified 922 genes genetically associated with KBD. Then, biological function and network analyses were conducted with Cytoscape software. Moreover, KBD specific molecular network analysis was conducted by Cytocluster using the Molecular Complex Detection Algorithm (MCODE).The biological function enrichment analysis suggested that collagen catabolic process, protein activation cascade, cellular response to growth factor stimulus, skeletal system development, and extrinsic apoptosis played important roles in KBD development. The apoptosis pathway, NF-kappa B signaling pathway, and the glutathione metabolism pathway were significantly enriched in the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway network, suggesting that these pathways may play key roles in KBD occurrence and development. MCODE clusters showed that in top 3 clusters, 54 of KBD-related genes were included in the network and 110 candidate genes were discovered might be potentially related to KBD.The 110 candidate genes discovered in the current study may be related to the development of KBD. The expression changes of apoptosis and oxidative stress-related genes might serve as biomarkers for early diagnosis and treatment of KBD.