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Safdar et al. (2017), 1(1), 56-67 T he I nter na t io na l J o ur na l o f I n no v a tiv e R es ea rch i n B io s cie nc es S a fd a r et a l. (2 0 1 7 ) , 1 (1 ), 5 6 - 6 7 ht tp : // www. ij ir b .o r g Full length Article Association of SNPs with Rheumatoid Arthritis Susceptibility Shakeel Safdar*1, Mahmood Kayani1, Hina Iqbal1, and Sohail Safdar2 1 Department of Biosciences, COMSATS Institute of Information Technology, Islamabad, Pakistan 2 Ahlia University, Bahrain *For correspondence: [email protected] ABSTRACT Rheumatoid Arthritis is one of the types of Arthritis in which the joints swell up. It has been found that there are approximately 340 genes involved in causing the Rheumatoid Arthritis. Moreover, it has also been observed that SNPs of these genes are associated with the disease. In this study, four genes were analyzed for their possible association with Rheumatoid Arthritis using bioinformatics tools. The results showed how SNPs are associated with this disease. Some of the SNPs brought some structural changes in particular proteins while others SNPs produced no change in the structure. SNPs that made the proteins abnormal and brought some structural changes in the protein can be considered as SNPs associated with Rheumatoid Arthritis, as by change of normal amino acid, the orientations of proteins can be disturbed and protein are not involved in specific pathways thus being pathogenic. In some cases, the structural change leads to disruption of the protein structure while sometimes, the structure remains unchanged i.e. due to synonymous mutations. This is due to a reason that sometimes, due to SNPs the abnormal amino acid is coded, which can either disrupt or mutate the whole structure. This fact can be supported by an evidence that the hydrophobic and hydrophilic amino acids provide specific orientations to proteins and whenever some polar amino acid is replaced by non-polar amino acid or some non-polar amino acid is replaced by polar amino acid or some cyclic amino acid is replaced by non-cyclic amino acid, the abnormality occurs, which can lead to disruption of protein structure making it abnormal. In this study, the changes in protein structure by SNPs are observed and such SNPs are predicted to be involved in causing Rheumatoid Arthritis. Keywords: Rheumatoid Arthritis, SNPs, Mutation, Genes, Proteins, Nucleotides, MIA, CST3, CTLA4, HMGB1 INTRODUCTION infections and includes joint pain. The suffix - The name Rheumatoid Arthritis is derived from oid means "resembling", i.e. resembling the Greek word rheumatos, means "flowing" rheumatic fever. Arthr means "joint" and the which initially gave rise to the term "rheumatic suffix fever", an illness that can follow throat inflammation". Thus Rheumatoid Arthritis is a -itis, a "condition involving To cite this paper: S a f d a r , S , K a y a n i , M , I q b a l , H . , & S a f d a r , S . ( 2 0 1 7 ) . A s s o c i a t i o n o f S N P s w i t h R h e u m a t o i d A r t h r i t i s Sus ceptibilit y). The International J our nal Of Innov ative Res ear ch In Biosc iences , 1(1), 56 -67. Safdar et al. (2017), 1(1), 56-67 form of joint inflammation, which resembles The cause of Rheumatoid Arthritis is a very rheumatic fever. Rheumatoid Arthritis appears active area of worldwide research. Genes and to have been described in paintings more than their SNPs have been found to be involved in a century before the first detailed medical Rheumatoid Arthritis, and in addition, the description of the condition in 1800 (Azaola, scientists believe that the environmental 2013). factors Rheumatoid arthritis (RA) is believed to be an Rheumatoid Arthritis. Moreover, it is also ‘inflammatory autoimmune disorder’, in which believed that smoking tobacco also increases the joints get severely affected (Voll et al., the severity of Rheumatoid Arthritis (Baka et 2008). It is such a condition, in which the al., 2009). inflammation and joint pains destructure the Many studies have reported the involvement of joints, hence resulting in restriction of joint genes and SNPs in the pathogenesis of the mobility (William et al., 2004). RA is a disease, some of which are mentioned here systemic disease, often affecting ‘extra- (Mattyasouszky et al., 2006; Kochil et al., articular tissues’ all over the body, which 2004; Arlehaq et al., 2005; Vazgiourakis et al., includes blood vessels, skin, lungs, heart, and 2007; Shimada et al., 2007). The above- the 2010). mentioned studies signify the involvement of Rheumatoid Arthritis normally affects the SNPs of various genes in Rheumatoid Arthritis. joints but sometimes it affects the organs as We have conducted experiments on MIA, well. Normally small joints are affected but CST3, CTLA 4 and HMGB 1 gene. About larger joints can also be affected by the CST3, Rheumatoid 2010). association of CST3 gene with Rheumatoid Rheumatoid arthritis affects women three times Arthritis. Gang Li (2014) mentioned in his more than men and it can develop at any age. research work that certain polymorphism in the Women aged 40 to 50 years usually suffer from nucleotides in CTLA4 gene has signified its this disease. Moreover, Rheumatoid Arthritis association with the Rheumatoid Arthritis. occurs 4 times more in smokers than the non- Earlier, Gonzalez (1994) also mentioned in his smokers (Williams et al., 2004). The research research that how CTLA4 is possibly linked work in Bioinformatics made it evident that with certain change at genetic level is one of the highlighted CTLA4’s association with RA in major Arthritis. Chinese population. About HMGB1, Arnandis Nucleotide (2010) and Voll (2008) elaborated that they had Polymorphism (SNP) is the reported to be one found certain elevated range of HMGB1 genes of the major causes of Rheumatoid Arthritis in the synovial fluid samples of the patients (Saad et al, 2016). with Rheumatoid Arthritis (Arnandis, 2010). muscles causes (Cojocaru Arthritis of Significantly, et at., (Wilke, Rheumatoid Single are Gauthier Rheumatoid Earlier, 57 also Bosserhoff involved (2012) in causing signified Arthritis. (2002), Lie and the (2005) then Safdar et al. (2017), 1(1), 56-67 Yeremenko and his research team, highlighted Polymorphism, so we used ClustalW® for MIA gene’s association with the Rheumatoid better sequential analysis. The next step was to Arthritis (Bosserhoff, 2002; Yeremenko et al, observe the replaced amino acid position in 2013). normal protein sequence. As the SNP region MATERIALS AND METHODS sequences were only available in nucleotide In this study, SNPs of Four genes were sequence form, so they needed to be translated analyzed namely MIA, CST3, CTLA4, and in order to align with normal protein sequence. HMGB1. The main objective of the project was So for this purpose, TranSeq was applied which to observe the structural changes in the protein can translate nucleotide sequence into protein structures, which are mentioned by NCBI to be sequence. After translation, the translated SNP involved in causing RA. However, in order to region sequence and normal protein sequence attain that objective, there were some minor were aligned by using a protein alignment tool objectives i.e. searching for SNPs using SNP Tcoffee. The alignment sometimes gave the database, selection of SNPs present in Exon signified region of DNA sequence, identification of allingmnents were dispersed or scattered. The mutation of reason was that different protein translation synonymous from nonsynonymous SNPs and tools translates nucleotide sequences by using to find the particular region of SNP in gene different frames, so shattered alignments can be sequence. observed in such cases. After the application of causing SNPs, filteration result, but sometimes the Various databases and bioinformatics tools Tcoffee, the next step was towards the major were applied in order to attain the minor objective i.e Structural analysis through objectives leading to major objective. The gene structure modeling. The tools that were applied sequences, protein sequences and the SNP for structural analysis were Swiss Model server region sequences were retrieved by NCBI. The and Swiss PDB viewer. The Swiss model takes tools were applied further to locate the exact the input sequence of protein and models it. SNP region in the gene and protein sequences. The normal protein sequences were manually The initial step was to align the gene sequence mutated according to the mutation mentioned with the SNP region sequence to locate the by NCBI and then the structures were modeled. exact SNP position in the gene sequence. The In the case of MIA, when the 17th SNP applied tool was ClustalW®, which is a mutation was manually inserted in the normal multiple sequence alignment tool. Higgins protein sequence, the structure was not (1988) in his research work has elaborated that modeled which indicated towards disruption of how multiple sequence pairwise alignments protein structure due to the insertion of can better initiate a gene/protein similarity abnormal amino acid in protein sequence. The study. As we had to do the sequence alignments Swiss Model server models the protein for structure on homology basis i.e. it searches the analyzing the Single Nucleotide 58 Safdar et al. (2017), 1(1), 56-67 relevent or homolog protein in database and structure. When the normal and the abnormal designs the homology modeling. As the protein structures were overlapped by using structure was not designed in case of MIA 17th Swiss PDB viewer, the result obtained shows SNP, so we predict that there is no such protein that the orientation of the protein structure has present in protein database, which resembles been changed. Therefore, we predict that SNP with mutated protein having the abnormal is RA causing SNP as it produces structural amino acid, this means that such abnormal change in protein. protein does not exists normally in nature, so The encircled area in the result obtained by the we predicted the involved SNP as the RA overlapping of normal and abnormal MIA causing SNP. The remaining six proteins were (consist of few residues of SNP region) shows also analysed by using this Swiss Model server the difference in the orientation of both the but the models were produced. The final step proteins. The 2nd analyzed gene was CST3 was the application of Swiss PDB viewer. In which has total of 58 SNPs out of which 4 order to use this tools, the PDB files were SNPs were selected i.e. SNP number 10, 14, 19 needed which were obtained by Swiss Model and 20. In case of 10th SNP, the conversion was as well as by Protein Data Bank. The Swiss C to A and the amino acid change was Arg to PDB veiwer modeled the structures for every Ser at position 71. Arg is hydrophillic basic SNP including the 17th SNP of MIA gene. residue whereas Ser is hydrophillic polar RESULTS AND DISCUSSION residues which are of completely opposite The intermediate steps including ClustalW, natures. The result obtained by Swiss PDB TranSeq and TCoffee were used to obtain the viewer is mentioned in Fig 2. minor objectives i.e. to move towards the The fig 2 shows the change in orientations of structural analysis. The reults that were both the overlapped proteins. The secondly obtained by the structural analysis are selected SNP of CST3 was 14th number SNP in mentioned in this paper. The first analyzed which the polymorphism or conversion is G to gene was MIA whose total SNPs, mentioned in A and the amino acid change is Arg to His at NCBI, are 20 out of which one SNP was 71 amino acid position. The polymorphism is selected for analysis due to its occurance in at the same position as that of SNP number 10. Exon region. The SNP change was C to T that Arg and His both are hydrophillic basic results in replacing Thr to Ile at at 113th amino residues but the change in structure was acid position of the protein. Thr is a observed because His has cyclic structure hydrophillic polar residue, that is why it is where as Arg does not have cyclic structure. usually present on outer region of protein The structural analysis obtained by Swiss PDB structure but Ile is hydrophobic non-polar viewer is shown in Fig 3. residue which tends to move inward of protein 59 Safdar et al. (2017), 1(1), 56-67 Fig 1: Result caused by C to T polymorphism Fig 2: Result caused by C to A polymorphism 60 Safdar et al. (2017), 1(1), 56-67 Fig 3: Result caused by G to A polymorphism Fig 4: Result caused by C toG polymorphism 61 Safdar et al. (2017), 1(1), 56-67 Fig 5: Result caused by G to C polymorphism Fig 6: Result caused by T to C polymorphism 62 Safdar et al. (2017), 1(1), 56-67 Fig 7: Result caused by A to G polymorphism Fig 8: Result caused by C to T polymorphism 63 Safdar et al. (2017), 1(1), 56-67 Fig 9: Result caused by C to T polymorphism 64 Safdar et al. (2017), 1(1), 56-67 The SNP number 19 has a conversion of C to abnormal protein structures shows the change G and the amino acid change is Arg to Gly at in protein orientation, mentioned in Fig 7. amino acid position 96. Arg is hydrophillic The fourth gene analyzed was HMGB1 which basic residue and Gly is hydrophillic polar has a total of 60 SNPs out of which 2 SNPs residue. The result obtained by Swiss PDB were selected for analysis. As the purpose was viewer is shown in Fig 4. in which change in to analyze the effect of polymorphism on the protein orientation can be noticed. protein creation, so we took only 2 SNPs out of 60. The conversion of nucleotide base and the The fourth analyzed SNP of CST3 was 20th amino acid change was same in both the SNPs number SNP in which the conversion is G to C i.e. C to T nucleotide conversion and Pro to Leu and the amino acid change is Gly to Ala at 38th amino acid change. The first SNP was 33rd amino acid position. Gly is hydrophillic polar number SNP in which the mutation was at 143rd residue where as Ala is hydrophobic non-polar position and in case of second analyzed SNP residue. The overlaping of normal and abnormal protein structures i.e. SNP number 47, the mutation was at 98th showed the position. Pro and Leu both are hydrophobic orientation change in protein structure. non-polar residues but Pro has cyclic structure The third gene analyzed was CTLA4, which while Leu has linear, non-cyclic structure. The has total 79 SNPs out of which 2 SNPs were overlaping of normal and abnormal protein selected for analysis. The first analyzed SNP structures of both the cases i.e. Fig 8 shows the was number 28 in which the nucleotide 33rd SNP case and Fig 9 shows 47th SNP case. conversion was T to C and the amio acid CONCLUSION change was Met to Thr at amino acid position It is evident that various genes are involved in 91. Met is a hydrophobic non-polar amino acid Rheumatoid Arthritis and it has been observed while Thr is a hydrophillic polar amino acid. that various SNPs of different genes are Thr tends to arrange itself towards outer region of protein surface while Met associated with Rheumatoid Arthritis. Our being research was based on analyzing the structural hydrophobic residue, tends to move inward of changes caused by the SNPs in the respective the protein structure. When the normal and the proteins of above-mentioned genes. In order to abnormal protein structures were overlapped, analyze the relationship of SNPs with the change in protein orientation was observed Rheumatoid Arthritis, the SNPs of four genes which is mentioned in Fig 6. namely MIA, CST3, CTLA4, and HMGB1 The second analyzed SNP was 37th SNP in were analyzed and the effects of SNPs were which the nucleotide conversion was A to G pointed out that how SNP was changing the and the amino acid change was Thr to Ala at structure of a protein. The SNPs of the exon 17th amino acid position. Thr is hydrophillic regions were only selected for the analysis residue while Ala is hydrophobic non-polar (excluding the SNPs of intronic region). The residue. The overlaping of normal and 65 Safdar et al. (2017), 1(1), 56-67 Database used for the data collection was single genetically homologous population. NCBI. There were about 17 SNPs of the above- Lupus. 16, 867-874. mentioned genes which were found to be mutation causing. These SNPs replaced the Mattyasouszky, S., Skapeoko, A., Kalden, JR., normal amino acids with the mutated ones. Lipsky, PE. And Schulze, H. (2006). When the normal and mutated proteins were INFGR1 Single Nucleotide Polymorphism over lapped, the proteins were not able to in Rheumatoid Arthritis. Arthritis Resther, overlap properly at the point of mutation, which 8, 63. indicates that there was a structural difference Xu, B., Ärlehag, L., Rantapää-Dahlquist, S. B., caused by the SNP and this mutation can & Lefvert, A. K. (2005). β2 Adrenoceptor become the cause of Rheumatoid Arthritis. gene single nucleotide polymorphisms are REFERENCES associated with rheumatoid arthritis in Shimada, M., Onizuka, M., Machida, S., northern Sweden. Annals of the rheumatic Suzuki, R., Kojima, M., Miyamura, K., ... diseases, 64(5), 773-776. & Ando, K. (2007). Association of autoimmune disease‐related Voll, RE., Urbonaviciute, V., Herrmann, M. and Kalden, JR. (2008). HMGB1 in the gene polymorphisms with chronic graft‐versus‐ pathogenesis host autoimmune disease. British journal of of inflammatory diseases. Israel and Medical Association Journal, 10, 26-28. haematology, 139(3), 458-463. Kochi, Y., Yamada, R., Kobayashi, K., Gonzalez‐Escribano, M. F., Rodriguez, R., Takahashi, A., Suzuki, A., Sekine, A., ... & Valenzuela, A., Garcia, A., Garcia‐Lozano, Yamamoto, K. (2004). Analysis of single‐ J. R., & Nunez‐Roldan, A. (1999). CTLA4 nucleotide polymorphisms in Japanese polymorphisms in Spanish patients with rheumatoid rheumatoid arthritis patients shows additional susceptibility markers besides Arthritis Lie, C., Donging, Z., Yegging, S., Oaks, MK., & Lishan, C., Jianzhong, J., Jie, Q., Fang, D., Rheumatology, 50(1), 63-71. Ningli, L., Xinghai, H. and Daming, R. Vazgiourakis, V., Sidiropoulos, P., Bertsias, G., Koutsounaki, E., Fraqouli, (2005). Association of CTLA4 gene with E., RA in Chinese Han population. European Raptopoulou, A., Kritikos, H., Boumpas, DT. and Goulielmos, GN. Tissue antigens, 53(3), 296-300. the classic shared epitope susceptibility sequences. arthritis. Journal of Human Genetic, 13, 823-828. (2007). Higgins, D. G., & Sharp, P. M. (1988). Association of Nitric Oxide Synthetase (e CLUSTAL: a package for performing Nos) gene polymorphism with increase risk multiple of Lupus gloueruloreplperitis and RA in microcomputer. Gene, 73(1), 237-244. 66 sequence alignment on a Safdar et al. (2017), 1(1), 56-67 William, David, S. and Barton, F. (2004). Role of Epidemiology in improving Hinojosa-Azaola, A., & Alcocer-Varela, J. our (2014). Art and rheumatology: the artist understanding of Rheumatoid Arthritis. and Lippincot Williams and Wilkins, 4, 1-5. Rheumatology, ket459. Majithia, V., & Geraci, S. A. (2007). Rheumatoid arthritis: diagnosis the rheumatologist’s perspective. Baka, Z., Buzás, E., & Nagy, G. (2009). and Rheumatoid arthritis and smoking: putting management. The American journal of the pieces together. Arthritis research & medicine, 120(11), 936-939. therapy, 11(4), 238. Bosserhoff, A. K., & Buettner, R. (2002). Cojocaru, M., Cojocaru, I. M., Silosi, I., Expression, function and clinical relevance Vrabie, C. D., & Tanasescu, R. (2010). of Extra-articular MIA (melanoma inhibitory manifestations in activity). Histology and histopathology, 17, rheumatoid arthritis. Maedica A Journal of 289-300. Clinical Medicine, 5(4), 286–291. Yeremenko, N., Härle, P., Cantaert, T., van Wilke, W. (2010). Rheumatoid Arthritis. Tok, M., van Duivenvoorde, L. M., Cleveland Clinic. Bosserhoff, A., & Baeten, D. (2013). The cartilage protein melanoma inhibitory activity contributes to inflammatory arthritis. Rheumatology, 53. Gauthier, S., Kaur, G., Mi, W., Tizon, B., & Levy, E. (2011). Protective mechanisms by cystatin C in neurodegenerative diseases. Frontiers in bioscience (Scholar edition), 3, 541-554. Li, G., Shi, F., Liu, J., & Li, Y. (2014). The effect of CTLA-4 A49G polymorphism on rheumatoid arthritis risk: a meta- analysis. Diagnostic pathology, 9(1), 157. García-Arnandis, I., Guillén, M. I., Gomar, F., Pelletier, J. P., Martel-Pelletier, J., & Alcaraz, M. J. (2010). High mobility group box 1 potentiates the pro-inflammatory effects of interleukin-1β in osteoarthritic synoviocytes. Arthritis research & therapy, 12(4), 165. 67