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Zhang Y, Shi W, Sun Y. A functional gene module identification algorithm in gene expression data based on genetic algorithm and gene ontology. BMC Genomics 2023; 24:76. [PMID: 36797662 PMCID: PMC9936134 DOI: 10.1186/s12864-023-09157-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 01/31/2023] [Indexed: 02/18/2023] Open
Abstract
Since genes do not function individually, the gene module is considered an important tool for interpreting gene expression profiles. In order to consider both functional similarity and expression similarity in module identification, GMIGAGO, a functional Gene Module Identification algorithm based on Genetic Algorithm and Gene Ontology, was proposed in this work. GMIGAGO is an overlapping gene module identification algorithm, which mainly includes two stages: In the first stage (initial identification of gene modules), Improved Partitioning Around Medoids Based on Genetic Algorithm (PAM-GA) is used for the initial clustering on gene expression profiling, and traditional gene co-expression modules can be obtained. Only similarity of expression levels is considered at this stage. In the second stage (optimization of functional similarity within gene modules), Genetic Algorithm for Functional Similarity Optimization (FSO-GA) is used to optimize gene modules based on gene ontology, and functional similarity within gene modules can be improved. Without loss of generality, we compared GMIGAGO with state-of-the-art gene module identification methods on six gene expression datasets, and GMIGAGO identified the gene modules with the highest functional similarity (much higher than state-of-the-art algorithms). GMIGAGO was applied in BRCA, THCA, HNSC, COVID-19, Stem, and Radiation datasets, and it identified some interesting modules which performed important biological functions. The hub genes in these modules could be used as potential targets for diseases or radiation protection. In summary, GMIGAGO has excellent performance in mining molecular mechanisms, and it can also identify potential biomarkers for individual precision therapy.
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Affiliation(s)
- Yan Zhang
- grid.440686.80000 0001 0543 8253College of Environmental Science and Engineering, Dalian Maritime University, 116026 Dalian, Liaoning China
| | - Weiyu Shi
- grid.440686.80000 0001 0543 8253College of Maritime Economics & Management, Dalian Maritime University, 116026 Dalian, Liaoning China
| | - Yeqing Sun
- College of Environmental Science and Engineering, Dalian Maritime University, 116026, Dalian, Liaoning, China.
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Padala C, Puranam K, Shyamala N, Kupsal K, Kummari R, Galimudi RK, Gundapaneni KK, Tupurani MA, Suryadevera A, Chinta SK, Manavathi B, Hanumanth SR. Genotypic and haplotype analysis of Interleukin-6 and -18 gene polymorphisms in association with clinicopathological factors in breast cancer. Cytokine 2022; 160:156024. [DOI: 10.1016/j.cyto.2022.156024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 06/08/2022] [Accepted: 08/26/2022] [Indexed: 11/03/2022]
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Zakariya BF, Almohaidi AMS, Şimşek SA, Kamal AM, Al-Dabbagh WH, Al-Waysi SA. Associations between single-nucleotide polymorphisms of the interleukin-18 gene and breast cancer in Iraqi women. Genomics Inform 2022; 20:e18. [PMID: 35794698 PMCID: PMC9299566 DOI: 10.5808/gi.22026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 06/13/2022] [Indexed: 11/20/2022] Open
Abstract
According to long-term projections, by 2030, the world’s population is predicted to reach 7.5 billion individuals, and there will be roughly 27 million new cancer cases diagnosed. The global burden of breast cancer (BC) is expected to rise. According to the Ministry of Health-Iraqi Cancer Registry, cancer is the second largest cause of death after cardiovascular disease. This study investigated the interleukin-18 (IL18) single-nucleotide polymorphisms (SNPs) –607C/A rs1946518 and –137G/C rs187238 using the sequence-specific amplification-polymerase chain reaction approach. Regarding the position –607C/A, there was a highly significant difference between the observed and expected frequencies in patients and controls (χ2 = 3.16 and χ2 = 16.5), respectively. The AA and CA genotypes were associated with significantly increased BC risk (odds ratio [OR], 3.68; p = 0.004 and OR, 2.83; p = 0.04, respectively). Women with the A allele had a 5.03-fold increased susceptibility to BC. The C allele may be a protective allele against BC (OR, 0.19). Although position –137G/C showed no significant differences in the CC genotype distribution (p = 0.18), the frequency of the CC genotype was significantly higher in patients than in controls. In contrast, patients had a significantly higher frequency of GC genotypes than controls (p = 0.04), which was associated with an increased risk of developing BC (OR, 2.63). The G allele frequency was significantly lower in patients than in controls (55.0% vs. 76.2%, respectively). This SNP may be considered a common genotype in the Iraqi population, with the wild-type G allele having a protective function (OR, 0.19) and the mutant C allele having an environmental effect (OR, 2.63).
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Affiliation(s)
- Bilal Fadıl Zakariya
- Department of Biology, Institute of Sciences, Çankiri Karatekin University, Çankırı Merkez 18100, Turkey
| | - Asmaa M Salih Almohaidi
- Department of Biology, College of Science for Women, University of Baghdad, Baghdad 10022, Iraq
| | - Seçil Akilli Şimşek
- Department of Biology, Institute of Sciences, Çankiri Karatekin University, Çankırı Merkez 18100, Turkey
| | - Areege Mustafa Kamal
- Department of Pathology/Oncology, Medical City Teaching Hospital, Baghdad 10011, Iraq
| | | | - Safaa A Al-Waysi
- Department of Microbiology, Medical City Teaching Hospital, Baghdad 10011, Iraq
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Genomic Diversity in Sporadic Breast Cancer in a Latin American Population. Genes (Basel) 2020; 11:genes11111272. [PMID: 33126731 PMCID: PMC7716199 DOI: 10.3390/genes11111272] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 10/20/2020] [Accepted: 10/26/2020] [Indexed: 12/17/2022] Open
Abstract
Among Latin American women, breast cancer incidences vary across populations. Uruguay and Argentina have the highest rates in South America, which are mainly attributed to strong, genetic European contributions. Most genetic variants associated with breast cancer were described in European populations. However, the vast majority of genetic contributors to breast cancer risk remain unknown. Here, we report the results of a candidate gene association study of sporadic breast cancer in 176 cases and 183 controls in the Uruguayan population. We analyzed 141 variants from 98 loci that have been associated with overall breast cancer risk in European populations. We found weak evidence for the association of risk variants rs294174 (ESR1), rs16886165 (MAP3K1), rs2214681 (CNTNAP2), rs4237855 (VDR), rs9594579 (RANKL), rs8183919 (PTGIS), rs2981582 (FGFR2), and rs1799950 (BRCA1) with sporadic breast cancer. These results provide useful insight into the genetic susceptibility to sporadic breast cancer in the Uruguayan population and support the use of genetic risk scores for individualized screening and prevention.
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The lncRNA SOX2OT rs9839776 C>T Polymorphism Indicates Recurrent Miscarriage Susceptibility in a Southern Chinese Population. Mediators Inflamm 2019; 2019:9684703. [PMID: 31827385 PMCID: PMC6885167 DOI: 10.1155/2019/9684703] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 09/25/2019] [Accepted: 10/22/2019] [Indexed: 12/26/2022] Open
Abstract
Genetic susceptibility may be involved in the onset of recurrent miscarriage. Previous studies have shown that some genetic polymorphisms that regulate cell migration are associated with susceptibility to recurrent miscarriage. The SOX2 overlapping transcript (SOX2OT) may regulate the migration and invasion of multiple tumor cells and is related to susceptibility to various diseases. However, whether lncRNA SOX2OT polymorphisms are related to recurrent miscarriage susceptibility is unclear. Therefore, we investigated the relationship between the lncRNA SOX2OT rs9839776 C>T polymorphism and recurrent miscarriage susceptibility. We recruited 570 subjects with recurrent miscarriage and 578 healthy control subjects from a population in southern China and used the TaqMan method for genotyping. We found a significant association between the rs9839776 CT genotype in the SOX2OT gene and an increased risk for recurrent miscarriage (CT vs CC: adjusted OR = 1.357, 95%CI = 1.065 - 1.728, P = 0.0134). However, we did not observe any significant associations between the recurrent miscarriage risk and the number of miscarriages in different age groups. In conclusion, our study indicated that the rs9839776 CT genotype may contribute to an increased risk of recurrent miscarriage in the southern Chinese population and that rs9839776 may act as a prognostic biomarker in recurrent miscarriage patients. However, an experiment-based study with a larger sample size should be performed to confirm these results.
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Zavala VA, Serrano-Gomez SJ, Dutil J, Fejerman L. Genetic Epidemiology of Breast Cancer in Latin America. Genes (Basel) 2019; 10:E153. [PMID: 30781715 PMCID: PMC6410045 DOI: 10.3390/genes10020153] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 02/13/2019] [Accepted: 02/14/2019] [Indexed: 12/20/2022] Open
Abstract
The last 10 years witnessed an acceleration of our understanding of what genetic factors underpin the risk of breast cancer. Rare high- and moderate-penetrance variants such as those in the BRCA genes account for a small proportion of the familial risk of breast cancer. Low-penetrance alleles are expected to underlie the remaining heritability. By now, there are about 180 genetic polymorphisms that are associated with risk, most of them of modest effect. In combination, they can be used to identify women at the lowest or highest ends of the risk spectrum, which might lead to more efficient cancer prevention strategies. Most of these variants were discovered in populations of European descent. As a result, we might be failing to discover additional polymorphisms that could explain risk in other groups. This review highlights breast cancer genetic epidemiology studies conducted in Latin America, and summarizes the information that they provide, with special attention to similarities and differences with studies in other populations. It includes studies of common variants, as well as moderate- and high-penetrance variants. In addition, it addresses the gaps that need to be bridged in order to better understand breast cancer genetic risk in Latin America.
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Affiliation(s)
- Valentina A Zavala
- Department of Medicine, Division of General Internal Medicine, University of California San Francisco, San Francisco, CA 94143-1793, USA.
| | - Silvia J Serrano-Gomez
- Grupo de investigación en biología del cáncer, Instituto Nacional de Cancerología, Bogotá 11001000, Colombia.
| | - Julie Dutil
- Cancer Biology Division, Ponce Research Institute, Ponce Health Sciences University, Ponce, PR 00732, USA.
| | - Laura Fejerman
- Department of Medicine, Division of General Internal Medicine, University of California San Francisco, San Francisco, CA 94143-1793, USA.
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Qiao X, Xu D, Sun D, Sun S, Huang Z, Cui W. Association analysis of interleukin-18 gene promoter region polymorphisms and susceptibility to sporadic breast cancer in Chinese Han women. J Clin Lab Anal 2018; 32:e22591. [PMID: 29926984 DOI: 10.1002/jcla.22591] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 05/29/2018] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Interleukin-18-137G/C, -607G/T polymorphisms play multiple roles in various cancers. However, studies focused on its involvement in breast cancer remain controversial, and no study has taken the interaction between interleukin-18 (IL-18) gene polymorphism and body mass index (BMI), menopause into consideration. The study investigated the association between IL-18-137, -607 polymorphisms and risk of breast cancer and a possible interaction between the 2 single nucleotide polymorphisms (SNPs) and BMI, menopause in Chinese Han woman. METHODS A total of 488 participants, including 178 patients with breast cancer, 150 patients with benign breast disease and 160 healthy controls were recruited for this study. Polymerase chain reaction (PCR)-direct sequencing technology was used to identify the genotypes. RESULTS 137 G/C genotype can decrease the risk of breast cancer (OR = 0.54, 95% CI: 0.31-0.93; P = .025). In benign group, subjects with G/C genotype of IL-18-137G/C polymorphism had a 1.89-fold increased risk of developing breast cancer (95% CI = 1.05-3.41; P = .032). Among postmenopausal subjects, people with G/T genotype of IL-18-607 polymorphism had a 7.97-fold increased risk of lymph node metastasis compared with those with T/T homozygotes (95% CI = 1.95-32.65; P = .0045). Among Overweight and obese patients with breast cancer (BMI ≥ 24), people with G/T genotype of IL-18-607 polymorphism had a 5.45-fold increased risk of lymph node metastasis compared with those with T/T homozygotes (95% CI = 1.74-17.06; P = .034). CONCLUSIONS IL-18-137 G/C genotype may be a protective factor for healthy group, but a risk factor for benign group. IL-18-607 G/T genotype have an interaction with menopausal and BMI. The synergetic effect can further increase the risk of lymph node metastasis for breast cancer patients.
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Affiliation(s)
- Xuefeng Qiao
- Department of Clinical Laboratory, Beijing Meitan General Hospital, Beijing, China
| | - Danfei Xu
- Clinical Laboratory, Peking Union Medical College, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Dandan Sun
- Clinical Laboratory, Peking Union Medical College, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Sijin Sun
- Eight-Year Program of Clinical Medicine, Peking Union Medical College, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Zhiping Huang
- Heart Center, Beijing Meitan General Hospital, Beijing, China
| | - Wei Cui
- Clinical Laboratory, Peking Union Medical College, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences, Beijing, China
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Sabet S, El-Sayed SK, Mohamed HT, El-Shinawi M, Mohamed MM. Inflammatory breast cancer: High incidence of GCC haplotypes (−1082A/G, −819T/C, and −592A/C) in the interleukin-10 gene promoter correlates with over-expression of interleukin-10 in patients’ carcinoma tissues. Tumour Biol 2017; 39:1010428317713393. [DOI: 10.1177/1010428317713393] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Interleukin-10 is involved in carcinogenesis by supporting tumor escape from the immune response. The aim of this study was to assess the single nucleotide polymorphisms, −1082A/G, −819T/C and −592A/C, in interleukin-10 gene promoter in inflammatory breast cancer compared to non–inflammatory breast cancer and association of these polymorphisms with interleukin-10 gene expression. We enrolled 105 breast cancer tissue (72 non–inflammatory breast cancer and 33 inflammatory breast cancer) patients and we determined the three studied single nucleotide polymorphisms in all samples by polymerase chain reaction restriction fragment length polymorphism and investigated their association with the disease and with various prognostic factors. In addition, we assessed the expression of interleukin-10 gene by real-time quantitative reverse transcription polymerase chain reaction and the correlation between studied single nucleotide polymorphisms and interleukin-10 messenger RNA expression. We found co-dominant effect as the best inheritance model (in the three studied single nucleotide polymorphisms in non–inflammatory breast cancer and inflammatory breast cancer samples), and we didn’t identify any association between single nucleotide polymorphisms genotypes and breast cancer prognostic factors. However, GCC haplotype was found highly associated with inflammatory breast cancer risk (p < 0.001, odds ratio = 43.05). Moreover, the expression of interleukin-10 messenger RNA was significantly higher (p < 0.001) by 5.28-fold and 8.95-fold than non–inflammatory breast cancer and healthy control, respectively, where GCC haplotype significantly increased interleukin-10 gene expression (r = 0.9, p < 0.001).
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Affiliation(s)
- Salwa Sabet
- Department of Zoology, Faculty of Science, Cairo University, Giza, Egypt
| | | | | | - Mohamed El-Shinawi
- Department of General Surgery, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Mona M Mohamed
- Department of Zoology, Faculty of Science, Cairo University, Giza, Egypt
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Dai ZJ, Liu XH, Wang M, Guo Y, Zhu W, Li X, Lin S, Tian T, Liu K, Zheng Y, Xu P, Jin T, Li X. IL-18 polymorphisms contribute to hepatitis B virus-related cirrhosis and hepatocellular carcinoma susceptibility in Chinese population: a case-control study. Oncotarget 2017; 8:81350-81360. [PMID: 29113394 PMCID: PMC5655289 DOI: 10.18632/oncotarget.18531] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 06/04/2017] [Indexed: 12/17/2022] Open
Abstract
IL-18 polymorphisms influence the transcriptional activity of the IL-18 gene and associated with various diseases. However, their relationships with hepatitis B virus-related liver diseases had not reached a consensus. So we conducted this case-control study with a view to clarifying the association. We included four groups: healthy controls, chronic hepatitis B virus (CHB) carriers, liver cirrhosis (LC) and hepatocellular carcinoma (HCC) groups with each group of 250 persons. Odd ratios (ORs) and 95% confidence intervals (95%CIs) with or without adjustment were calculated. Haplotype analysis was also performed. The results showed people carrying rs187238 CG genotype had a lower risk of LC (CG vs. CC: OR = 0.59, 95%CI = 0.38–0.91, P = 0.02), while GG genotype carriers had a higher risk of HCC (GG vs. CC+CG: OR = 4.73, 95%CI = 1.01–22.1, P = 0.03) than those with CC and CG genotypes in healthy group. Rs187238 GG genotype increased the risk from CHB to LC status (GG vs. CC: OR = 4.81, 95%CI = 1.03–22.6; GG vs. CC+CG: OR = 4.73, 95%CI = 1.01–22.1), meanwhile the trend also existed by controlling confounding factors (GG vs. CC: OR = 6.25, 95%CI = 1.09–35.8; GG vs. CC+CG: OR = 5.91, 95%CI = 1.04–33.7). Haplotype Crs187238Trs1946518 moderately decreased the risk of CHB carriers developing into HCC (OR = 0.69, 95%CI = 0.50–0.96, P = 0.03) after adjustment. In conclusion, IL-18 rs187238 GG genotype may increase the risk of HCC in healthy population and the risk of LC in CHB carriers.
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Affiliation(s)
- Zhi-Jun Dai
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Xing-Han Liu
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Meng Wang
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Yan Guo
- School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Wenge Zhu
- Department of Biochemistry and Molecular Medicine, The George Washington University Medical School, Washington, DC, USA
| | - Xiao Li
- Department of Hepatobiliary Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Shuai Lin
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Tian Tian
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Kang Liu
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Yi Zheng
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Peng Xu
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Tianbo Jin
- National Engineering Research Center for Miniaturized Detection Systems, School of Life Sciences, Northwest University, Xi'an, China
| | - Xiaopeng Li
- Department of Ultrasound, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
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Wang H, Hua M, Wang S, Yu J, Chen C, Zhao X, Zhang C, Zhong C, Wang R, He N, Hou M, Ma D. Genetic polymorphisms of IL-18 rs1946518 and IL-1β rs16944 are associated with prognosis and survival of acute myeloid leukemia. Inflamm Res 2016; 66:249-258. [PMID: 27928589 DOI: 10.1007/s00011-016-1012-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Revised: 11/16/2016] [Accepted: 11/22/2016] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Though the pathogenesis of AML is still unknown, accumulating evidence revealed that immune response plays a vital part in it. NLRP3 inflammasome as a component of immune system has been found related to several cancers. The single nucleotide polymorphisms (SNPs) of NLRP3 inflammasome genes may be related to pathogenesis and prognosis of AML. METHODS AND RESULTS We determined polymorphisms of NLRP3 (rs35829419), CARD8 (rs2043211), IL-1β (rs16944), IL-18 (rs1946518) and NF-κB -94 ins/del ATTG in de novo AML patients to find out whether they play roles in the susceptibility and severity of AML. In our study, 383 AML cases and 300 randomly selected healthy individuals were examined for the polymorphisms and expression of NLRP3 genes. IL-1β (rs16944) polymorphism in different risk AML subgroups was found statistically different, with more GA genotype in favorable-risk cytogenetics group. We also demonstrated that the bone marrow blasts of patients carrying IL-18 (rs1946518) GG or GT genotype were higher than patients of TT genotype. IL-18 plasma level of patients with IL-18 (rs1946518) GT or TT genotype was higher than GG genotype. Moreover, the GT genotype of IL-18 (rs1946518) led to statistically poorer AML-specific survival. CONCLUSION IL-1β (rs16944) and IL-18 (rs1946518) may be served as potential predictors for AML.
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Affiliation(s)
- Hong Wang
- Department of Hematology, Qilu Hospital, Shandong University, 107 West Wenhua Rd, Jinan, 250012, People's Republic of China.,Department of Hematology, Zibo Central Hospital, Zibo, Shandong, People's Republic of China
| | - Mingqiang Hua
- Department of Hematology, Qilu Hospital, Shandong University, 107 West Wenhua Rd, Jinan, 250012, People's Republic of China
| | - Shukang Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Shandong University, Jinan, People's Republic of China
| | - Jie Yu
- Department of Hematology, Qilu Hospital, Shandong University, 107 West Wenhua Rd, Jinan, 250012, People's Republic of China
| | - Chen Chen
- Department of Hematology, Qilu Hospital, Shandong University, 107 West Wenhua Rd, Jinan, 250012, People's Republic of China
| | - Xueyun Zhao
- Department of Hematology, Qilu Hospital, Shandong University, 107 West Wenhua Rd, Jinan, 250012, People's Republic of China
| | - Chen Zhang
- Department of Hematology, Qilu Hospital, Shandong University, 107 West Wenhua Rd, Jinan, 250012, People's Republic of China
| | - Chaoqin Zhong
- Department of Hematology, Qilu Hospital, Shandong University, 107 West Wenhua Rd, Jinan, 250012, People's Republic of China
| | - Ruiqing Wang
- Department of Hematology, Qilu Hospital, Shandong University, 107 West Wenhua Rd, Jinan, 250012, People's Republic of China
| | - Na He
- Department of Hematology, Qilu Hospital, Shandong University, 107 West Wenhua Rd, Jinan, 250012, People's Republic of China
| | - Ming Hou
- Department of Hematology, Qilu Hospital, Shandong University, 107 West Wenhua Rd, Jinan, 250012, People's Republic of China
| | - Daoxin Ma
- Department of Hematology, Qilu Hospital, Shandong University, 107 West Wenhua Rd, Jinan, 250012, People's Republic of China.
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Karra VK, Gumma PK, Chowdhury SJ, Ruttala R, Polipalli SK, Chakravarti A, Kar P. IL-18 polymorphisms in hepatitis B virus related liver disease. Cytokine 2015; 73:277-82. [PMID: 25802197 DOI: 10.1016/j.cyto.2015.02.015] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Revised: 02/13/2015] [Accepted: 02/14/2015] [Indexed: 12/17/2022]
Abstract
Interleukine-18 (IL-18) was originally called interferon (INF-γ) inducing factor and plays a critical dual role in Th1 polarization and viral clearance. We aimed to explore whether single-nucleotide promoter polymorphisms (SNPs) are associated with the outcome of hepatitis B virus (HBV) infection. 271 HBV infected patients were recruited in this study out of these 109 were spontaneously recovered and 162 were diagnosed to be having persistent HBV infection which includes 48 chronic hepatitis, 84 liver cirrhosis, 30 HCC cases and were compared with 280 healthy controls. IL-18 promoter genotyping was performed with sequence-specific primers. The results demonstrated the significant involvement of genotype AA at position -607 in healthy controls (38.6%) when compared to cases (26.0%) (OR=0.54 (0.385-0.797)) and also associated with spontaneous clearance (37.6%) compared to persistent HBV infections (17.9%) (OR=2.76 (1.582-4.832)). Whereas, genotype CC at position -607 in cases (18.0%) when compared to healthy controls (6.7%) (OR=3.03 (1.734-5.303)) also associated with persistent HBV infections (24.1%) compared to spontaneous clearance (9.2%) (OR=0.31 (0.151-0.67)). And genotype GC at position -137 in cases (49.5%) compared to healthy controls (38.5%) (OR=1.55 (1.11-2.18)). Whereas, genotype GG at position -137 in healthy controls (56.8%) compared to cases (45.4%) (OR=0.63 (0.451-0.885)). No significant difference at position -137 was observed between spontaneous clearance and persistent HBV infections. These polymorphisms of the IL-18 gene promoter region at position -607 and -137 could be associated with different outcomes of HBV infection. The people with allele A at position -607 may be protected against HBV infection; moreover AA genotype is associated with spontaneous clearance.
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Affiliation(s)
- Vijay Kumar Karra
- PCR Hepatitis Lab, Dept. of Medicine, Maulana Azad Medical College, University of Delhi, New Delhi 110002, India
| | - Phani Kumar Gumma
- PCR Hepatitis Lab, Dept. of Medicine, Maulana Azad Medical College, University of Delhi, New Delhi 110002, India
| | - Soumya Jyoti Chowdhury
- PCR Hepatitis Lab, Dept. of Medicine, Maulana Azad Medical College, University of Delhi, New Delhi 110002, India
| | - Rajesh Ruttala
- PCR Hepatitis Lab, Dept. of Medicine, Maulana Azad Medical College, University of Delhi, New Delhi 110002, India
| | - Sunil Kumar Polipalli
- PCR Hepatitis Lab, Dept. of Medicine, Maulana Azad Medical College, University of Delhi, New Delhi 110002, India
| | - Anita Chakravarti
- Department of Medical Microbiology, Maulana Azad Medical College, University of Delhi, New Delhi 110002, India
| | - Premashis Kar
- PCR Hepatitis Lab, Dept. of Medicine, Maulana Azad Medical College, University of Delhi, New Delhi 110002, India.
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