Investigation of LncRNA part1 SNP (RS8176070) polymorphism in Turkey knee osteoartritis patient population by DNA sequence analysis

Osteoarthritis (OA); is a chronic disease that causes cartilage degradation, synovial inflammation, subchondral bone remodeling, and osteophyte formation. It is a degenerative disease associated with the progressive degradation of the subchondral bone and joint cartilage, leading to pain and loss of joint function that significantly impairs the patient's quality of life. Knee OA affects the 3 compartments of the knee joint (medial, lateral and patellofemoral joint) and usually progresses slowly within 10-15 years and disrupts daily life activities. In recent studies, non-coding RNA (lncRNA) PART1 expression has been detected in cartilage tissue and chondrocytes. It is indicated that PART1 stimulates OA development by regulating the miR-373-3p / SOX4 axis. LncRNA PART1 has been shown to be localized in the q12 arm of human chromosome 5. Numerous single nucleotide polymorphisms (SNPs) thought to be associated with OA have been identified. The aim of our study is to analyze SNP (rs8176070) seen in lncRNA PART1 using DNA sequencing method to test the risk it creates for the Turkey knee OA population. By obtaining the permission of the ethics committee for our study, the study group consisting of 102 primary OA patients and the control group consisting of 81 healthy individuals were included in our study. Physical and radiological examinations were performed by obtaining the voluntary consent of all participants. Individuals with knee OA were determined according to the Kellgren-Lawrence scale (grade 1-4) and Western Ontario and McMaster Universities Index (WOMAC) surveys were conducted. 5 ml of peripheral venous blood was taken from each participant and genomic DNA isolations were made with commercial kits. Spectrophotometric absorbance of purified genomic DNA was measured and concentrations were calculated and used for standard polymerase chain reaction (PCR) as 1 microgram (µg). Primers for the PART1 DNA sequence have been designed and the PCR conditions have been optimized. As a result of the PCR reaction, the product of 508 base pairs (bp) was obtained. By the Restriction fragment length polymorphism (RFLP) method, BseYI performed the enzyme cut process according to the recognition sequence (5'-C▼CCAGC-3 ') in the region of the restriction enzyme SNP (rs8176070) polymorphism. For DNA sequence analysis is the gold standard for polymorphism studies, DNA sequence analyzes of all individuals in our study has been carried out. The median age of the subjects included in the study was 60.5 years (MP: 53.8-67.0) in the OA group, and 46.0 years (MP: 40.5-51.0) in the control group. It was observed that 75.5% (n = 77) of the OA group and 55.6% (n = 45) of the control group were women. When the two groups were compared, it was determined that the mean age and women gender of the OA group patients were significantly higher than the control group (p <0.05). Similarly, Body Mass Index (BMI) and WOMAC score were higher in the patient group compared to the control group (p≤0.001). The distribution of the patient group according to the Kellgren-Lawrence degree is given in the demographic data table (Table 4.1). The wild type genotype (CC) is encoded as "bb", heterozygous polymorphic genotype (CN) "Bb" and homozygous polymorphic genotype (NN) "BB". When the genotype distribution in the OA and control groups was examined, 13.8% (n = 14) of the OA group and 13.6% (n = 11) of the control group were homozygous polymorphic genotype (NN) "BB", 43.1% (n = 44) of the OA group and the control group, 45.7% (n = 37) of the heterozygous polymorphic genotype (CN) "Bb" and 43.1% (n = 44) of the OA group and 40.7% (n = 33) of the control group, wild type genotype (CC) "bb" was detected (Table 4.2). As a result, odds ratios were not found to be statistically significant for BB or Bb genotypes (p> 0.05). Allele distributions in the groups are similar (p = 0.875). In the literature, some of the existing population studies that analyzed the possible relationship between SNP (rs8176070) and OA described a positive relationship, while some found a negative result. In our study, it was shown that there was no significant relationship between the lncRNA PART1 SNP (rs8176070) and knee OA in cases with Turkish knee OA. Further population studies analyzing the relationship between SNP (rs8176070) and OA are needed.