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Abuzaid O, Idris AB, Yılmaz S, Idris EB, Idris LB, Hassan MA. Prediction of the most deleterious non-synonymous SNPs in the human IL1B gene: evidence from bioinformatics analyses. BMC Genom Data 2024; 25:56. [PMID: 38858637 PMCID: PMC11163699 DOI: 10.1186/s12863-024-01233-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 05/22/2024] [Indexed: 06/12/2024] Open
Abstract
BACKGROUND Polymorphisms in IL1B play a significant role in depression, multiple inflammatory-associated disorders, and susceptibility to infection. Functional non-synonymous SNPs (nsSNPs) result in changes in the encoded amino acids, potentially leading to structural and functional alterations in the mutant proteins. So far, most genetic studies have concentrated on SNPs located in the IL1B promoter region, without addressing nsSNPs and their association with multifactorial diseases. Therefore, this study aimed to explore the impact of deleterious nsSNPs retrieved from the dbSNP database on the structure and functions of the IL1B protein. RESULTS Six web servers (SIFT, PolyPhen-2, PROVEAN, SNPs&GO, PHD-SNP, PANTHER) were used to analyze the impact of 222 missense SNPs on the function and structure of IL1B protein. Five novel nsSNPs (E100K, T240I, S53Y, D128Y, and F228S) were found to be deleterious and had a mutational impact on the structure and function of the IL1B protein. The I-mutant v2.0 and MUPro servers predicted that these mutations decreased the stability of the IL1B protein. Additionally, these five mutations were found to be conserved, underscoring their significance in protein structure and function. Three of them (T240I, D128Y, and F228S) were predicted to be cancer-causing nsSNPs. To analyze the behavior of the mutant structures under physiological conditions, we conducted a 50 ns molecular dynamics simulation using the WebGro online tool. Our findings indicate that the mutant values differ from those of the IL1B wild type in terms of RMSD, RMSF, Rg, SASA, and the number of hydrogen bonds. CONCLUSIONS This study provides valuable insights into nsSNPs located in the coding regions of IL1B, which lead to direct deleterious effects on the functional and structural aspects of the IL1B protein. Thus, these nsSNPs could be considered significant candidates in the pathogenesis of disorders caused by IL1B dysfunction, contributing to effective drug discovery and the development of precision medications. Thorough research and wet lab experiments are required to verify our findings. Moreover, bioinformatic tools were found valuable in the prediction of deleterious nsSNPs.
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Affiliation(s)
- Ola Abuzaid
- Faculty of Medicine, Erciyes University, Kayseri, Turkey
| | - Abeer Babiker Idris
- Department of Medical Microbiology, Faculty of Medical Laboratory Sciences, University of Khartoum, Khartoum, Sudan.
| | - Semih Yılmaz
- Department of Agricultural Biotechnology, Faculty of Agriculture, Erciyes University, Kayseri, Turkey
- Erciyes Teknopark, Promoseed Biotechnology A.Ş, Kayseri, Turkey
| | - Einass Babikir Idris
- Department of Medical Microbiology, Rashid Medical Complex, Riyadh, Saudi Arabia
| | | | - Mohamed A Hassan
- Department of Bioinformatics, Africa City of Technology, Khartoum, Sudan
- Sanimed International Lab and Management L.L.C, Abu Dhabi, UAE
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Zervou MI, Tarlatzis BC, Grimbizis GF, Spandidos DA, Niewold TB, Goulielmos GN. Association of endometriosis with Sjögren's syndrome: Genetic insights (Review). Int J Mol Med 2024; 53:20. [PMID: 38186322 PMCID: PMC10781419 DOI: 10.3892/ijmm.2024.5344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Accepted: 12/20/2023] [Indexed: 01/09/2024] Open
Abstract
Patients with a history of endometriosis have an increased risk of developing various autoimmune diseases such as rheumatoid arthritis, ankylosing spondylitis, systemic lupus erythematosus, multiple sclerosis and celiac disease. There is a potential association between endometriosis and an increased susceptibility for Sjögren's syndrome (SS). SS is a common chronic, inflammatory, systemic, autoimmune, multifactorial disease of complex pathology, with genetic, epigenetic and environmental factors contributing to the development of this condition. It occurs in 0.5‑1% of the population, is characterized by the presence of ocular dryness, lymphocytic infiltrations and contributes to neurological, gastrointestinal, vascular and dermatological manifestations. Endometriosis is an inflammatory, estrogen‑dependent, multifactorial, heterogeneous gynecological disease, affecting ≤10% of reproductive‑age women. It is characterized by the occurrence of endometrial tissue outside the uterine cavity, mainly in the pelvic cavity, and is associated with pelvic pain, dysmenorrhea, deep dyspareunia and either subfertility or infertility. It is still unclear whether SS appears as a secondary response to endometriosis, or it is developed due to any potential shared mechanisms of these conditions. The aim of the present review was to explore further the biological basis only of the co‑occurrence of these disorders but not their association at clinical basis, focusing on the analysis of the partially shared genetic background between endometriosis and SS, and the clarification of the possible similarities in the underlying pathogenetic mechanisms and the relevant molecular pathways.
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Affiliation(s)
- Maria I. Zervou
- Section of Molecular Pathology and Human Genetics, Department of Internal Medicine, School of Medicine, University of Crete, 71403 Heraklion, Greece
| | - Basil C. Tarlatzis
- First Department of Obstetrics and Gynecology, School of Medicine, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Grigoris F. Grimbizis
- Unit for Human Reproduction, First Department of Obstetrics and Gynecology, 'Papageorgiou' General Hospital, Aristotle University Medical School, 56403 Thessaloniki, Greece
| | - Demetrios A. Spandidos
- Laboratory of Clinical Virology, School of Medicine, University of Crete, 71403 Heraklion, Greece
| | - Timothy B. Niewold
- Barbara Volcker Center for Women and Rheumatic Disease, New York, NY 10021, USA
- Hospital for Special Surgery, New York, NY 10021, USA
| | - George N. Goulielmos
- Section of Molecular Pathology and Human Genetics, Department of Internal Medicine, School of Medicine, University of Crete, 71403 Heraklion, Greece
- Department of Internal Medicine, University Hospital of Heraklion, 71500 Heraklion, Greece
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Oală IE, Mitranovici MI, Chiorean DM, Irimia T, Crișan AI, Melinte IM, Cotruș T, Tudorache V, Moraru L, Moraru R, Caravia L, Morariu M, Pușcașiu L. Endometriosis and the Role of Pro-Inflammatory and Anti-Inflammatory Cytokines in Pathophysiology: A Narrative Review of the Literature. Diagnostics (Basel) 2024; 14:312. [PMID: 38337827 PMCID: PMC10855755 DOI: 10.3390/diagnostics14030312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 01/29/2024] [Accepted: 01/29/2024] [Indexed: 02/12/2024] Open
Abstract
Endometriosis is a chronic inflammatory disease, which explains the pain that such patients report. Currently, we are faced with ineffective, non-invasive diagnostic methods and treatments that come with multiple side effects and high recurrence rates for both the disease and pain. These are the reasons why we are exploring the possibility of the involvement of pro-inflammatory and anti-inflammatory molecules in the process of the appearance of endometriosis. Cytokines play an important role in the progression of endometriosis, influencing cell proliferation and differentiation. Pro-inflammatory molecules are found in intrafollicular fluid. They have an impact on the number of mature and optimal-quality oocytes. Endometriosis affects fertility, and the involvement of endometriosis in embryo transfer during in vitro fertilization (IVF) is being investigated in several studies. Furthermore, the reciprocal influence between anti-inflammatory and pro-inflammatory cytokines and their role in the pathogenesis of endometriosis has been assessed. Today, we can affirm that pro-inflammatory and anti-inflammatory cytokines play roles in survival, growth, differentiation, invasion, angiogenesis, and immune escape, which provides a perspective for approaching future clinical implications and can be used as biomarkers or therapy.
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Affiliation(s)
- Ioan Emilian Oală
- Department of Obstetrics and Gynecology, Emergency County Hospital Hunedoara, 331057 Hunedoara, Romania;
| | - Melinda-Ildiko Mitranovici
- Department of Obstetrics and Gynecology, Emergency County Hospital Hunedoara, 331057 Hunedoara, Romania;
| | - Diana Maria Chiorean
- Department of Pathology, County Clinical Hospital of Targu Mures, 540072 Targu Mures, Romania;
| | - Traian Irimia
- Doctoral School of Medicine and Pharmacy, George Emil Palade University of Medicine, Pharmacy, Science, and Technology of Targu Mures, 540142 Targu Mures, Romania; (T.I.); (A.I.C.); (I.M.M.); (T.C.)
| | - Andrada Ioana Crișan
- Doctoral School of Medicine and Pharmacy, George Emil Palade University of Medicine, Pharmacy, Science, and Technology of Targu Mures, 540142 Targu Mures, Romania; (T.I.); (A.I.C.); (I.M.M.); (T.C.)
- Department of 1st Gynecology Clinic, Emergency County Hospital Targu Mures, 540136 Targu Mures, Romania
| | - Ioana Marta Melinte
- Doctoral School of Medicine and Pharmacy, George Emil Palade University of Medicine, Pharmacy, Science, and Technology of Targu Mures, 540142 Targu Mures, Romania; (T.I.); (A.I.C.); (I.M.M.); (T.C.)
| | - Teodora Cotruș
- Doctoral School of Medicine and Pharmacy, George Emil Palade University of Medicine, Pharmacy, Science, and Technology of Targu Mures, 540142 Targu Mures, Romania; (T.I.); (A.I.C.); (I.M.M.); (T.C.)
| | - Vlad Tudorache
- Department of 2nd Gynecology Clinic, County Clinical Hospital Targu Mures, 540072 Targu Mures, Romania;
| | - Liviu Moraru
- Department of Anatomy, George Emil Palade University of Medicine, Pharmacy, Sciences and Technology, 540142 Targu Mures, Romania; (L.M.); (R.M.)
| | - Raluca Moraru
- Department of Anatomy, George Emil Palade University of Medicine, Pharmacy, Sciences and Technology, 540142 Targu Mures, Romania; (L.M.); (R.M.)
| | - Laura Caravia
- Department of Morphological Sciences, Division of Cellular and Molecular Biology and Histology, Carol Davila University of Medicine and Pharmacy, 050474 Bucharest, Romania;
| | - Mihai Morariu
- Department of Obstretics and Gynecology, George Emil Palade University of Medicine and Pharmacies, Science and Technology of Targu Mures, 540142 Targu Mures, Romania; (M.M.); (L.P.)
| | - Lucian Pușcașiu
- Department of Obstretics and Gynecology, George Emil Palade University of Medicine and Pharmacies, Science and Technology of Targu Mures, 540142 Targu Mures, Romania; (M.M.); (L.P.)
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Zhang L, Yang X. Association between exposure to polycyclic aromatic hydrocarbons and endometriosis: data from the NHANES 2001-2006. Front Public Health 2024; 11:1267124. [PMID: 38259796 PMCID: PMC10801278 DOI: 10.3389/fpubh.2023.1267124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 09/25/2023] [Indexed: 01/24/2024] Open
Abstract
Aim To evaluate the association between urinary polycyclic aromatic hydrocarbon (PAH) metabolites and the risk of endometriosis. Methods This cross-sectional study obtained data on women aged 20-54 years from the National Health and Nutrition Examination Survey (NHANES) 2001-2006. The weighted multivariate logistic regression model was established to assess the association between the eight urinary PAH metabolites and the risk of endometriosis. In this multivariate analysis, the eight urinary PAH metabolites were adjusted with urinary creatinine, and were divided into three groups according to tertiles: Tertile 1, Tertile 2 and Tertile 3. To evaluate the overall association of mixed PAH metabolites with endometriosis, the Bayesian kernel machine regression (BKMR) model was applied. Results Totally 1,291 women were included, of which 90 (6.97%) had endometriosis and 1,201 (93.03%) did not have endometriosis. After adjusting for age, race, smoking, age at menarche, hysterectomy, ovary removed, female hormone use, and menopause, compared with the Tertile 1 group, the Tertile 2 and Tertile 3 groups of all PAH metabolites demonstrated no significant risk of endometriosis. A positive tendency was found between mixed PAH metabolites and endometriosis when all the metabolites were at their 60th percentile levels or above compared with their median levels. When all the other metabolites were fixed at their median levels, 1-hydroxynaphthalene was positively correlated with endometriosis. Potential interactions existed between 1-hydroxynaphthalene and 2-hydroxynaphthalene and between 2-hydroxyfluorene and 3-hydroxyfluorene. Conclusion No significant association was found between individual PAH metabolites and endometriosis. A positive association existed between mixed PAH metabolites and the risk of endometriosis.
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Affiliation(s)
| | - Xiaojun Yang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
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Cho SB. Molecular Mechanisms of Endometriosis Revealed Using Omics Data. Biomedicines 2023; 11:2210. [PMID: 37626707 PMCID: PMC10452455 DOI: 10.3390/biomedicines11082210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 07/22/2023] [Accepted: 08/05/2023] [Indexed: 08/27/2023] Open
Abstract
Endometriosis is a gynecological disorder prevalent in women of reproductive age. The primary symptoms include dysmenorrhea, irregular menstruation, and infertility. However, the pathogenesis of endometriosis remains unclear. With the advent of high-throughput technologies, various omics experiments have been conducted to identify genes related to the pathophysiology of endometriosis. This review highlights the molecular mechanisms underlying endometriosis using omics. When genes identified in omics experiments were compared with endometriosis disease genes identified in independent studies, the number of overlapping genes was moderate. However, the characteristics of these genes were found to be equivalent when functional gene set enrichment analysis was performed using gene ontology and biological pathway information. These findings indicate that omics technology provides invaluable information regarding the pathophysiology of endometriosis. Moreover, the functional characteristics revealed using enrichment analysis provide important clues for discovering endometriosis disease genes in future research.
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Affiliation(s)
- Seong Beom Cho
- Department of Biomedical Informatics, College of Medicine, Gachon University, 38-13, Dokgeom-ro 3 Street Namdon-gu, Incheon 21565, Republic of Korea
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Zhong S, Liang Y, Wu Z, Wei L. Association between polymorphisms of cytokine genes and endometriosis: A comprehensive systematic review and meta-analysis. J Reprod Immunol 2023; 158:103969. [PMID: 37295065 DOI: 10.1016/j.jri.2023.103969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 05/13/2023] [Accepted: 05/24/2023] [Indexed: 06/12/2023]
Abstract
INTRODUCTION There is abundant evidence to suggest that cytokines play a part in the mechanisms responsible for the formation of endometrium heterotopy. Cytokine synthesis is not only determined by the body's immunological reactivity but also by polymorphisms in the immune regulatory genes. The study of these polymorphisms in the immune regulatory genes offers up new possibilities in terms of prognosticating the risk of endometriosis and susceptibility to its treatment. The purpose of this comprehensive systematic review and meta-analysis was to investigate whether or not cytokine gene polymorphisms were linked to an increased chance of endometriosis. METHODS By searching MEDLINE, Scopus, and Web of Science databases, the relevant studies were identified. The odds ratio (OR) with 95% confidence interval (CI) was used to assess the association between TNF-α/IL-10/IL-6/TGF-β/IFN-γ/IL-1β gene polymorphisms and endometriosis risk. RESULTS A total of 5128 cases and 5334 controls in 32 eligible studies were included in the meta-analysis. Overall, results indicated the negative association between the cytokine gene polymorphisms and endometriosis in the dominant model of TNF-α (rs1799964): [OR] = 0.64, [CI]: 0.46-0.89) and a positive association in IFN-γ a13 allele: OR= 1.45, [CI]: 1.07-1.98; and IL-10 (rs1800872): [OR]= 1.60, [CI]: 1.21-2.12). CONCLUSION The present study suggests that IL-10 (rs1800872) and IFN-γ a13 allele may be a risk factors for endometriosis. Also, TNF-α (rs1799964) is associated with decreased susceptibility to endometriosis.
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Affiliation(s)
- Shulin Zhong
- Department of Obstetrics and Gynecology, Affiliated Dongguan Hospital, Southern Medical University (Dongguan People's Hospital), Dongguan 523018, China
| | - Yuzhen Liang
- Department of Obstetrics and Gynecology, Affiliated Dongguan Hospital, Southern Medical University (Dongguan People's Hospital), Dongguan 523018, China
| | - Zhixi Wu
- Department of Obstetrics and Gynecology, Affiliated Dongguan Hospital, Southern Medical University (Dongguan People's Hospital), Dongguan 523018, China
| | - Li Wei
- Department of Obstetrics and Gynecology, Affiliated Dongguan Hospital, Southern Medical University (Dongguan People's Hospital), Dongguan 523018, China.
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Evaluation of Tumor Necrosis Factor-Alpha Gene (−308 G/A, −238 G/A and −857 C/T) Polymorphisms and the Risk of Gastric Cancer in Eastern Indian Population. GASTROENTEROLOGY INSIGHTS 2022. [DOI: 10.3390/gastroent13040034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Introduction: Gastric cancer (GC) is one of the leading causes of cancer-related decimations worldwide. The gastric infection at both the stomach and duodenum with Helicobacter pylori causes inflammation by the tumor necrosis factor-alpha (TNF-α). The aim of the study was to associate and evaluate the three TNF-α gene polymorphisms at positions −308 G/A, −238 G/A, and −857 C/T with the risk of GC. Methods: A total of 156 individuals (consecutively diagnosed 95 GC patients and 61 controls) above the age of 18 years were enrolled in the study. Healthy individuals with normal upper gastrointestinal endoscopy (UGIE) irrespective of their family history of GC or peptic ulcer were included as controls. The cited three TNF-α gene polymorphisms were evaluated using polymerase chain reaction-restriction fragment length polymorphism (RFLP). Results: There was no significant difference in the distribution of gene polymorphisms as genetic factors, TNF-α−308 GA/AA (22.1% vs. 14.8%, p = 0.2), TNF-α−238 GA/AA (21% vs. 19.6%, p = 0.8), and TNF-α−857 CT/TT (8.4% vs. 11.5%, p = 0.5), between GC cases and healthy controls. A subgroup analysis of H. pylori-positive patients showed that there was no significant difference in the distribution of GA/AA polymorphisms in TNF-α−308 (15(45.5%) vs. 3(23%); p = 0.17) and −238 (12(36.3%) vs. 2(15.4%); p = 0.17), and the distribution of TT/CT −857 CT/TT (13(39.4%) vs. 2(15.4%); p = 0.13), among the GC cases and controls. Conclusion: The statistical comparisons of GA/AA vs. GG genotypes at −308 (with OR = 1.6, 95% CI: 0.6–3.8), −238 (OR = 1.09, 95% CI: 0.4–2.4) and TT/CT vs. CC genotypes at −857 (OR = 0.7, 95% CI: 0.2–2.1) did not suggest any association of TNF-α with GC in the population herein. Hence, the TNF-α (−308 G/A, −238 G/A and −857 C/T) may not be the associating factor for GC incidence determined by the PCR–RFLP method.
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