PMC:3216508 / 10737-16332 JSONTXT

{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/3216508","sourcedb":"PMC","sourceid":"3216508","source_url":"https://www.ncbi.nlm.nih.gov/pmc/3216508","text":"Discussion\nIL-22 has been reported to play a role in host defense against bacterial pathogens11. It is involved in host defense at environmental interfaces, such as mucosal surfaces of the airways and gastrointestinal tract. IL-22 can activate STAT3, which is a transcription activator that mediates the expression of a variety of genes in response to various cytokines14. It regulates genes that are involved in antimicrobial defense and cellular differentiation15. IL-22 can restrict the growth of M. tuberculosis in macrophages by enhancing phagolysosomal fusion10. However, the associations between genetic variations in the IL-22 gene and its promoter region and TB susceptibility have never been reported. In this study, we carried out this association study between the IL-22 gene, and found several SNPs in the IL-22 promoter region that influence TB susceptibility.\nOur approach of SNP selection is different from the traditional way of tagging SNPs, where SNPs were usually selected based only on the linkage disequilibrium in a genomic region. The SNP selection process focuses more on efficiency, which maximizes the coverage but minimizes the cost (the number of SNPs for genotyping)16. After genotyping, one can search for the functional SNPs with close LD to the tagged SNP that shows significant associations, as we did previously in breast cancer scanning17. However, there are disadvantages of this approach. (1) The LD is usually inferred from a limited number of previously genotyped data, such as HapMap. It might be different in the current studied population. (2) It ignores the functional role of the SNP, and many tagged SNPs are in the gene desert regions, and have little biological meanings1819. Our SNP selection approach focuses on the functional role of the SNPs, particularly in the promoter region of the gene that might affect the transcription factor binding sites. We found this simple approach very effective in identifying functional SNPs for our IL22 promoter study. Among the thirteen regulatory SNPs we selected, five (38.5%) showed significant association with TB susceptibility. This number is very high compared with non-regulatory SNPs, of which we selected seven SNPs, with none of them showing significant association. However, the effectiveness of this approach on other genes is unknown and yet to be tested.\nThe SNPs we found are biologically meaningful. The SNP rs2227473 alters the putative binding sites of several transcription factors from multiple databases, including Cgd2_3490 and PF14_0633, from the UniPROBE database, and RCGCANGCGY, and TCCCRNNRTG from the Jaspar database. Both Cgd2_3490 and PF14_0633 are hypothetical transcription factors containing AP2 domain. Cgd2_3490 is from Cryptosporidium parvum2021 and PF14_0633 is from Plasmodium falciparum222324. We propose that the two proteins from pathogens can target the host genes and regulate IL-22's expression. The variations in the binding sites of the two proteins provide a differential way of regulation. The two motifs, RCGCANGCGY and TCCCRNNRTG, were discovered by scanning the promoters of all human genes for conserved motifs25. RCGCANGCGY matches the binding consensus of transcription factor NRF1 (nuclear respiratory factor 1), which binds to the cytochrome c promotor26, and is essential for cell survival in oxidative stress inducing agents27.\nConsistent with previous research that patients with tuberculosis have significantly lower Th22 response than healthy donors28, our functional assay indicated that PBMCs from individuals carrying rs2227473G allele in IL-22, which is associated with susceptibility to tuberculosis, produce significantly lower IL-22 in response to polyclonal and Mtb antigen stimulation. Although we are currently uncertain with the mechanism of predisposition to tuberculosis in individuals with the rs2227473G allele, it probably lies at the level of the macrophage as well as lung epithelial cell. The macrophage is not only the most important effector of immunity to kill infected Mycobacterium tuberculosis, but also the niche to host them. It has been well recognized that Mycobacterium tuberculosis resides in phagosomes within macrophages, and killing these mycobacteria tuberculosis requires fusion of the phagosome with a lysosome. Importantly, Dhiman et al demonstrated that human IL-22 inhibits growth of mycobacterium tuberculosis by enhancing phagolysosomal fusion10. While there is no evidence to show the effect of IL-22 on epithelial cells to kill Mycobacterium tuberculosis, IL-22 has been known to enhance lung epithelial cells to produce β-defensin1529, which is beneficial to clear infected Mycobacterium30. Besides, several studies have shown that IL-22 participates in the protective immunity against tuberculosis283132. Taken together, our findings indicate that rs2227473 polymorphism controls IL-22 response upon Mycobacterium tuberculosis infection, which in turn determines, at least in part, the outcome of infection.\nIn summary, our study demonstrates an association between polymorphisms in the promoter of IL-22 gene and TB susceptibility. The rs2227473 polymorphism and associated SNPs in the promoter region of the IL-22 gene are associated with decreased susceptibility to pulmonary TB in Chinese. The ‘TGTAG' haplotype, which presents in 45.6% of the Chinese population, is associated with increased susceptibility to TB. The rs2227473 polymorphism affects IL-22's protein expression. Our SNP selection strategy focusing on regulatory SNPs is effective in identifying susceptive loci for the IL22 gene.","divisions":[{"label":"title","span":{"begin":0,"end":10}},{"label":"p","span":{"begin":11,"end":874}},{"label":"p","span":{"begin":875,"end":2357}},{"label":"p","span":{"begin":2358,"end":3374}},{"label":"p","span":{"begin":3375,"end":5003}}],"tracks":[{"project":"2_test","denotations":[{"id":"22355539-18264110-135382454","span":{"begin":93,"end":95},"obj":"18264110"},{"id":"22355539-15308104-135382455","span":{"begin":369,"end":371},"obj":"15308104"},{"id":"22355539-16619290-135382456","span":{"begin":463,"end":465},"obj":"16619290"},{"id":"22355539-19864591-135382457","span":{"begin":565,"end":567},"obj":"19864591"},{"id":"22355539-17060359-135382458","span":{"begin":1196,"end":1198},"obj":"17060359"},{"id":"22355539-17529973-135382459","span":{"begin":1372,"end":1374},"obj":"17529973"},{"id":"22355539-19474294-135382460","span":{"begin":1718,"end":1720},"obj":"19474294"},{"id":"22355539-16381902-135382461","span":{"begin":2766,"end":2768},"obj":"16381902"},{"id":"22355539-18957442-135382462","span":{"begin":2814,"end":2816},"obj":"18957442"},{"id":"22355539-18541913-135382463","span":{"begin":2814,"end":2818},"obj":"18541913"},{"id":"22355539-15735639-135382464","span":{"begin":3151,"end":3153},"obj":"15735639"},{"id":"22355539-2166701-135382465","span":{"begin":3297,"end":3299},"obj":"2166701"},{"id":"22355539-10601325-135382466","span":{"begin":3371,"end":3373},"obj":"10601325"},{"id":"22355539-18209095-135382467","span":{"begin":3499,"end":3501},"obj":"18209095"},{"id":"22355539-19864591-135382468","span":{"begin":4435,"end":4437},"obj":"19864591"},{"id":"22355539-16619290-135382469","span":{"begin":4625,"end":4627},"obj":"16619290"},{"id":"22355539-15039135-135382470","span":{"begin":4625,"end":4629},"obj":"15039135"},{"id":"22355539-18363594-135382471","span":{"begin":4682,"end":4684},"obj":"18363594"},{"id":"22355539-18209095-135382472","span":{"begin":4793,"end":4795},"obj":"18209095"},{"id":"22355539-20195465-135382473","span":{"begin":4793,"end":4797},"obj":"20195465"},{"id":"22355539-18811584-135382474","span":{"begin":4793,"end":4799},"obj":"18811584"}],"attributes":[{"subj":"22355539-18264110-135382454","pred":"source","obj":"2_test"},{"subj":"22355539-15308104-135382455","pred":"source","obj":"2_test"},{"subj":"22355539-16619290-135382456","pred":"source","obj":"2_test"},{"subj":"22355539-19864591-135382457","pred":"source","obj":"2_test"},{"subj":"22355539-17060359-135382458","pred":"source","obj":"2_test"},{"subj":"22355539-17529973-135382459","pred":"source","obj":"2_test"},{"subj":"22355539-19474294-135382460","pred":"source","obj":"2_test"},{"subj":"22355539-16381902-135382461","pred":"source","obj":"2_test"},{"subj":"22355539-18957442-135382462","pred":"source","obj":"2_test"},{"subj":"22355539-18541913-135382463","pred":"source","obj":"2_test"},{"subj":"22355539-15735639-135382464","pred":"source","obj":"2_test"},{"subj":"22355539-2166701-135382465","pred":"source","obj":"2_test"},{"subj":"22355539-10601325-135382466","pred":"source","obj":"2_test"},{"subj":"22355539-18209095-135382467","pred":"source","obj":"2_test"},{"subj":"22355539-19864591-135382468","pred":"source","obj":"2_test"},{"subj":"22355539-16619290-135382469","pred":"source","obj":"2_test"},{"subj":"22355539-15039135-135382470","pred":"source","obj":"2_test"},{"subj":"22355539-18363594-135382471","pred":"source","obj":"2_test"},{"subj":"22355539-18209095-135382472","pred":"source","obj":"2_test"},{"subj":"22355539-20195465-135382473","pred":"source","obj":"2_test"},{"subj":"22355539-18811584-135382474","pred":"source","obj":"2_test"}]}],"config":{"attribute types":[{"pred":"source","value type":"selection","values":[{"id":"2_test","color":"#d5ec93","default":true}]}]}}