Association of DNA damage response pathway genes with rheumatoid arthritis risks: a case-control study

Abstract

Rheumatoid arthritis (RA) is an autoimmune disease affecting the joints and other extra-articular organs. RA has the symptoms of inflammation, joint dysfunction, and reduction in life expectancy. The main causes of RA are family history, immunogenicity, smoking, and genetic factors. Among the genetic factors, DNA damage response pathway genes are primarily involved in repairing damage caused by smoking and other carcinogens. Studies have reported an increased DNA damage frequency in RA patients. The present study is designed to illuminate the association between the DNA damage response pathway genes (PARP1, TREX1, ATM, and TP53) and RA in the Pakistani population. Methods For this purpose, 500 RA patients and 500 age/gender-matched controls were collected and DNA/RNA was extracted. The genotype frequency of selected SNPs [PARP1 (Val76Ala), ATM (Pro1054Arg), TP53 (Ala138Val), and TREX (Tyr177Tyr)] was measured using the Tetra-ARMS PCR. Expression analysis of selected genes was measured using quantitative PCR. Statistical analysis showed a significantly increased frequency of mutant allele Val76Ala (p < 0.0001), Pro1054Arg (p < 0.0001), Ala138Val (p < 0.0001), and Tyr177Tyr (p < 0.0001) in RA patients compared to controls. Linkage disequilibrium showed a strong linkage disequilibrium between selected SNPs in RA patients compared to controls. Quantitative PCR showed a significant downregulation of PARP1 (p < 0.0001), ATM (p < 0.0001), TP53 (p < 0.0001), and TREX (p < 0.0001) in RA patients. ROC curve analysis showed a good diagnostic value for selected genes in RA patients. The present study showed that increased mutant genotype frequency and expression deregulation of DNA damage response pathway genes was linked with significant increased risk of RA. This study showed that DNA damage response pathway genes can act as efficient/specific diagnostic markers for said disease. Furthermore, these findings also lay a solid foundation for further research based on targeted metabolomics/genomics, which may lead to the development of more effective treatment strategies in the future.

Keywords: ATM; DNA damage response pathway genes; PARP1; Rheumatoid arthritis; TP53; TREX1.

Fig. 1

Expression analysis of PARP1 gene in RA patients. (A) Significant downregulation of PARP1 gene was observed in RA compared to controls. (B) Non significant association of PARP1 gene with different gender (males vs. females) and age group (< 45years vs. > 45years) of RA patients. (C) Significant deregulation of PARP1 gene in different clinicopathological parameters of RA patients such as Anti-CCP, ESR, and CRP. (D) Significant downregulation of PARP1 gene was observed in RA patients using the different treatment modalities such as methotrexate and biologics. Level of significance p < 0.05.

Fig. 2

Expression analysis of ATM gene in RA patients. (A) Significant downregulation of ATM gene was observed in RA patients compared to controls. (B) Non-significant association of ATM gene with different gender (males vs. females) and age group (< 45years vs. > 45years) of RA patients. (C) Significant deregulation of the ATM gene was observed in different clinicopathological parameters of RA patients such as Anti-CCP, ESR, and CRP. (D) Significant downregulation of ATM gene was observed in RA patients using the methotrexate compared to patients using biologics. Level of significance p < 0.05.

Fig. 3

Expression analysis of TP53 gene in RA patients. (A) Significant downregulation of TP53 gene was observed in RA compared to controls. (B) Non-significant downregulation TP53 gene in different gender (males vs. females) and age group (< 45years vs. > 45years) of RA patients. (C) Significant downregulated expression of the TP53 gene was observed in different clinicopathological parameters of RA patients such as Anti-CCP, ESR, and CRP. (D) Significant downregulated expression level of TP53 gene was observed in patients using the methotrexate compared to patients using biologics. Level of significance p < 0.05.

Fig. 4

Expression analysis of TREX1 gene in RA patients. (A) Significant downregulation of TREX1 gene was observed in RA compared to controls. (B) Non-significant difference in the expression level of the TREX1 gene was observed in different gender (males vs. females) and age group (< 45years vs. > 45years) of RA patients. (C) Significant downregulated expression level of the TREX1 gene was observed in different clinicopathological parameters of RA patients such as Anti-CCP, ESR, and CRP. (D) Significant downregulated expression level of the TREX1 gene was observed in patients using the methotrexate compared to patients using biologics. Level of significance p < 0.05.

Fig. 5

Measurement of diagnostic value of selected genes in RA patients using the ROC curve analysis. Area under the curve (AUC) was generated to measure the diagnostic value of (A) PARP1 (specificity 100% and sensitivity 100%), (B) ATM (specificity 100% and sensitivity 100%), (C) TP53 PARP1 (specificity 100% and sensitivity 100.

Fig. 6

Linkage disequilibrium (LD) was used to measure the nonrandom co-occurrence of alleles at different loci in RA patients and controls. LD frequency was measured for the selected SNPs of DNA damage response pathway genes. Strong LD was observed in (A) controls, (B) patients.