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Stejskalova K, Janova E, Splichalova P, Futas J, Oppelt J, Vodicka R, Horin P. Twelve toll-like receptor (TLR) genes in the family Equidae - comparative genomics, selection and evolution. Vet Res Commun 2024; 48:725-741. [PMID: 37874499 PMCID: PMC10998774 DOI: 10.1007/s11259-023-10245-4] [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: 07/18/2023] [Accepted: 10/18/2023] [Indexed: 10/25/2023]
Abstract
Toll-like receptors (TLRs) represent an important part of the innate immune system. While human and murine TLRs have been intensively studied, little is known about TLRs in non-model species. The order Perissodactyla comprises a variety of free-living and domesticated species exposed to different pathogens in different habitats and is therefore suitable for analyzing the diversity and evolution of immunity-related genes. We analyzed TLR genes in the order Perissodactyla with a focus on the family Equidae. Twelve TLRs were identified by bioinformatic analyses of online genomic resources; their sequences were confirmed in equids by genomic DNA re-sequencing of a panel of nine species. The expression of TLR11 and TLR12 was confirmed in the domestic horse by cDNA sequencing. Phylogenetic reconstruction of the TLR gene family in Perissodactyla identified six sub-families. TLR4 clustered together with TLR5; the TLR1-6-10 subfamily showed a high degree of sequence identity. The average estimated evolutionary divergence of all twelve TLRs studied was 0.3% among the Equidae; the most divergent CDS were those of Equus caballus and Equus hemionus kulan (1.34%) in the TLR3, and Equus africanus somaliensis and Equus quagga antiquorum (2.1%) in the TLR1 protein. In each TLR gene, there were haplotypes shared between equid species, most extensively in TLR3 and TLR9 CDS, and TLR6 amino acid sequence. All twelve TLR genes were under strong negative overall selection. Signatures of diversifying selection in specific codon sites were detected in all TLRs except TLR8. Differences in the selection patterns between virus-sensing and non-viral TLRs were observed.
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Affiliation(s)
- K Stejskalova
- Department of Animal Genetics, Faculty of Veterinary Medicine, University of Veterinary Sciences Brno, Brno, 61242, Czech Republic
| | - E Janova
- Department of Animal Genetics, Faculty of Veterinary Medicine, University of Veterinary Sciences Brno, Brno, 61242, Czech Republic
- RG Animal Immunogenomics, CEITEC VETUNI, University of Veterinary Sciences Brno, Brno, Czech Republic
| | - P Splichalova
- Department of Animal Genetics, Faculty of Veterinary Medicine, University of Veterinary Sciences Brno, Brno, 61242, Czech Republic
| | - J Futas
- Department of Animal Genetics, Faculty of Veterinary Medicine, University of Veterinary Sciences Brno, Brno, 61242, Czech Republic
- RG Animal Immunogenomics, CEITEC VETUNI, University of Veterinary Sciences Brno, Brno, Czech Republic
| | - J Oppelt
- RG Animal Immunogenomics, CEITEC VETUNI, University of Veterinary Sciences Brno, Brno, Czech Republic
| | | | - P Horin
- Department of Animal Genetics, Faculty of Veterinary Medicine, University of Veterinary Sciences Brno, Brno, 61242, Czech Republic.
- RG Animal Immunogenomics, CEITEC VETUNI, University of Veterinary Sciences Brno, Brno, Czech Republic.
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Zacher C, Schönfelder K, Rohn H, Siffert W, Möhlendick B. The single nucleotide polymorphism rs4986790 (c.896A>G) in the gene TLR4 as a protective factor in corona virus disease 2019 (COVID-19). Front Immunol 2024; 15:1355193. [PMID: 38433829 PMCID: PMC10904585 DOI: 10.3389/fimmu.2024.1355193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 01/29/2024] [Indexed: 03/05/2024] Open
Abstract
Background and aims Several factors, such as hypertension and diabetes mellitus, are known to influence the course of coronavirus disease 2019 (COVID-19). However, there is currently little information on genetic markers that influence the severity of COVID-19. In this study, we specifically investigated the single nucleotide polymorphism (SNP) rs4986790 in the TLR4 gene to identify a universal marker for preclinical prediction of COVID-19 disease progression. Methods We analyzed the influence of demographics, pre-existing conditions, inflammatory parameters at the time of hospitalization, and TLR4 rs4986790 genotype on the outcome of COVID-19 in a comprehensive cohort (N = 1570). We performed multivariable analysis to investigate the impact of each factor. Results We confirmed that younger patient age and absence of pre-existing conditions were protective factors against disease progression. Furthermore, when comparing patients with mild SARS-CoV-2 infection with patients who required hospitalization or intensive care or even died due to COVID-19, the AG/GG genotype of TLR4 rs4986790 was found to be a protective factor against COVID-19 disease progression (OR: 0.51, 95% CI: 0.34 - 0.77, p = 0.001). In addition, we demonstrated that low levels of interleukin-6 (IL-6) and procalcitonin (PCT) had a favorable effect on COVID-19 disease severity. In the subsequent multivariable analysis, we confirmed the absence of cardiovascular disease, low levels of IL-6 and PCT, and TLR4 rs4986790 AG/GG genotypes as independent predictors of potential hospitalization and reduction of severe or fatal disease course. Conclusion In this study, we identified an additional genetic factor that may serve as an invariant predictor of COVID-19 outcome. The TLR4 rs4986790 AG/GG genotype reduced by half the risk of COVID-19 patients requiring hospitalization, intensive care or to have a fatal outcome. In addition, we were able to confirm the influence of previously known factors such as pre-existing conditions and inflammatory markers upon the onset of disease on the course of COVID-19. Based on these observations, we hereby provide another prognostic biomarker that could be used in routine diagnostics as a predictive factor for the severity of COVID-19 prior to SARS-CoV-2 infection.
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Affiliation(s)
- Christoph Zacher
- Institute of Pharmacogenetics, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Kristina Schönfelder
- Department of Nephrology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Hana Rohn
- Department of Infectious Diseases, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Winfried Siffert
- Institute of Pharmacogenetics, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Birte Möhlendick
- Institute of Pharmacogenetics, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
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Flores-Gonzalez J, Chavez-Galan L, Falfán-Valencia R, Roldán IB, Fricke-Galindo I, Veronica-Aguilar A, Martínez-Morales A, Hernández-Zenteno RDJ, Guzmán-Guzmán IP, Pérez-Rubio G. Variant rs4986790 of toll-like receptor 4 affects the signaling and induces cell dysfunction in patients with severe COVID-19. Int J Infect Dis 2024; 138:102-109. [PMID: 38029833 DOI: 10.1016/j.ijid.2023.11.032] [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: 09/18/2023] [Revised: 10/18/2023] [Accepted: 11/23/2023] [Indexed: 12/01/2023] Open
Abstract
OBJECTIVES We investigated the expression of toll-like receptor (TLR)-4 on the cell surface of innate and adaptive cells from patients with COVID-19 carrying the rs4986790 GG genotype in the TLR4 gene and the functional profile of these cells. METHODS We included 1169 hospitalized patients with COVID-19. The rs4986790 in TLR4 was identified by real-time polymerase chain reaction. Peripheral blood mononuclear cells were isolated and cultured to evaluate TLR-4 expression on immune cells. Supernatants recovered culture assays were stored, and we measured cytokines and cytotoxic molecules. RESULTS We showed that the rs4986790 (GG) was significantly associated (P = 0.0310) with severe COVID-19. Cells of patients with COVID-19 carrying the GG genotype have increased the frequency of monocytes and activated naïve and non-switched B cells positive to TLR-4 when cells are stimulated with lipopolysaccharide and with spike protein of SARS-CoV-2. Also, cells from patients with GG COVID-19 cannot produce pro-inflammatory cytokines after lipopolysaccharide stimulus, but they are high producers of cytotoxic molecules at baseline. CONCLUSIONS The rs4986790 GG genotype of the TLR4 is associated with the risk of COVID-19 and acute respiratory distress syndrome. Peripheral blood mononuclear cells of patients carrying the rs4986790 (TLR4) GG genotype had a limited delivery of pro-inflammatory cytokines compared to the AA and AG genotypes in which TLR-4 stimulation induces IL-10, IL-6, tumor necrosis factor-α, and Fas ligand production.
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Affiliation(s)
- Julio Flores-Gonzalez
- Laboratory of Integrative Immunology, Instituto Nacional de Enfermedades Respiratorias Ismael Cosio Villegas, Mexico City, Mexico
| | - Leslie Chavez-Galan
- Laboratory of Integrative Immunology, Instituto Nacional de Enfermedades Respiratorias Ismael Cosio Villegas, Mexico City, Mexico
| | - Ramcés Falfán-Valencia
- HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, Mexico
| | - Ivette Buendía Roldán
- Translational Research Laboratory on Aging and Pulmonary Fibrosis, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, Mexico
| | - Ingrid Fricke-Galindo
- HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, Mexico
| | - Abigail Veronica-Aguilar
- HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, Mexico
| | - Alfonso Martínez-Morales
- HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, Mexico
| | | | - Iris Paola Guzmán-Guzmán
- Faculty of Chemical-Biological Sciences, Universidad Autónoma de Guerrero, Chilpancingo, Guerrero, Mexico
| | - Gloria Pérez-Rubio
- HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, Mexico.
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Silva MJA, Silva CS, Marinho RL, Cabral JG, Gurrão EPDC, dos Santos PAS, Casseb SMM, Lima KVB, Lima LNGC. Analysis of Epidemiological Factors and SNP rs3804100 of TLR2 for COVID-19 in a Cohort of Professionals Who Worked in the First Pandemic Wave in Belém-PA, Brazil. Genes (Basel) 2023; 14:1907. [PMID: 37895256 PMCID: PMC10606513 DOI: 10.3390/genes14101907] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 09/19/2023] [Accepted: 09/25/2023] [Indexed: 10/29/2023] Open
Abstract
COVID-19 is an infectious disease caused by coronavirus 2 of the severe acute syndrome (SARS-CoV-2). Single nucleotide polymorphisms (SNPs) in genes, such as TLR2, responsible for an effective human immune response, can change the course of infection. The objective of this article was to verify associations between epidemiological factors and TLR2 SNP rs3804100 (Thymine [T] > Cytosine [C]) in professionals from Health Institutions (HI) who worked during the first pandemic wave and COVID-19. A case-control study was conducted with Belém-PA HI workers (Northern Brazil), divided into symptomatology groups (Asymptomatic-AS; n = 91; and Symptomatic-SI; n = 123); and severity groups classified by Chest Computerized Tomography data (symptomatic with pulmonary involvement-SCP; n = 35; symptomatic without pulmonary involvement-SSP; n = 8). Genotyping was performed by Sanger sequencing, and Statistical Analysis was conducted through the SPSS program. Bioinformatics servers predicted the biological functions of the TLR2 SNP. There were associations between the presence of comorbidities and poor prognosis of COVID-19 (especially between symptomatology and severity of COVID-19 and overweight and obesity) and between the sickness in family members and kinship (related to blood relatives). The homozygous recessive (C/C) genotype was not found, and the frequency of the mutant allele (C) was less than 10% in the cohort. No significant associations were found for this SNP in this cohort. The presence of SNP was indicated to be benign and causes a decrease in the stability of the TLR2 protein. These data can help the scientific community and medicine find new forms of COVID-19 containment.
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Affiliation(s)
- Marcos Jessé Abrahão Silva
- Master Program in Epidemiology and Health Surveillance (PPGEVS), Evandro Chagas Institute (IEC), Ananindeua 67030-000, PA, Brazil
| | - Caroliny Soares Silva
- Master and PhD Program in Parasitic Biology in the Amazon (PPGBPA), University of State of Pará (UEPA), Belém 66087-670, PA, Brazil; (C.S.S.); (P.A.S.d.S.)
| | - Rebecca Lobato Marinho
- Evandro Chagas Institute (IEC), Ananindeua 67030-000, PA, Brazil; (R.L.M.); (J.G.C.); (E.P.d.C.G.); (S.M.M.C.); (K.V.B.L.)
| | - Jeanne Gonçalves Cabral
- Evandro Chagas Institute (IEC), Ananindeua 67030-000, PA, Brazil; (R.L.M.); (J.G.C.); (E.P.d.C.G.); (S.M.M.C.); (K.V.B.L.)
| | - Ellen Polyana da Costa Gurrão
- Evandro Chagas Institute (IEC), Ananindeua 67030-000, PA, Brazil; (R.L.M.); (J.G.C.); (E.P.d.C.G.); (S.M.M.C.); (K.V.B.L.)
| | - Pabllo Antonny Silva dos Santos
- Master and PhD Program in Parasitic Biology in the Amazon (PPGBPA), University of State of Pará (UEPA), Belém 66087-670, PA, Brazil; (C.S.S.); (P.A.S.d.S.)
| | - Samir Mansour Moraes Casseb
- Evandro Chagas Institute (IEC), Ananindeua 67030-000, PA, Brazil; (R.L.M.); (J.G.C.); (E.P.d.C.G.); (S.M.M.C.); (K.V.B.L.)
| | - Karla Valéria Batista Lima
- Evandro Chagas Institute (IEC), Ananindeua 67030-000, PA, Brazil; (R.L.M.); (J.G.C.); (E.P.d.C.G.); (S.M.M.C.); (K.V.B.L.)
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Alkudmani ZS, Alshammary AF, Ali Khan I. Molecular Effect of Variants in Toll-like Receptor 4 Gene in Saudi Patients with Type 2 Diabetes Mellitus. Cells 2023; 12:2340. [PMID: 37830554 PMCID: PMC10571932 DOI: 10.3390/cells12192340] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 09/15/2023] [Accepted: 09/21/2023] [Indexed: 10/14/2023] Open
Abstract
Single-nucleotide polymorphisms (SNPs) in the Toll-like receptor 4 (TLR4) gene have been documented in type 2 diabetes mellitus (T2DM) and other diseases in the Saudi population. We investigated the relationship between rs11536889, rs4986790, and rs4986791 SNPs in the TLR4 gene and T2DM in the Saudi population; 105 patients with T2DM and 105 healthy controls were analyzed. The TLR4 gene was amplified through PCR, followed by restriction fragment length polymorphism analysis for rs4986791 and Sanger sequencing for rs11536889 and rs4986790 SNPs. The clinical and biochemical characteristics were associated with T2DM (p < 0.05). The rs11536889, rs4986790, and rs4986791 SNPs in control subjects followed the Hardy-Weinberg equilibrium (p > 0.05). Alleles were associated with rs11536889, rs4986791, heterozygous codominant, and dominant models (p < 0.05). However, the rs4986790 SNP was not associated with T2DM (p > 0.05). Logistic regression analysis showed that high-density lipoprotein cholesterol (HDLc) levels were associated with T2DM (p < 0.001). Analysis of variance showed that waist (p = 0.0005) and hip circumferences (p = 0.002) in rs4986790 and rs4986791 SNPs, in SBP (p = 0.001), DBP (p = 0.002), and HDLc levels (p = 0.003), were associated with T2DM subjects. T2DM was also associated with the haplotype (p < 0.001) but not with linkage disequilibrium. The gene-gene interaction was associated with the three SNPs studied in patients with T2DM according to the generalized multifactor dimensionality reduction model (p < 0.0001). Dendrogram and graphical depletion analysis revealed a moderate association in patients with T2DM. The results suggest that rs11536889 and rs4986790 SNPs are genotypically and allelically associated with T2DM in Saudi patients. Future functional studies are recommended to validate the genetic roles of these SNPs in the pathogenesis and progression of diseases.
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Affiliation(s)
| | | | - Imran Ali Khan
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud University, Riyadh 11433, Saudi Arabia; (Z.S.A.); (A.F.A.)
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Silva MJA, Marinho RL, dos Santos PAS, dos Santos CS, Ribeiro LR, Rodrigues YC, Lima KVB, Lima LNGC. The Association between CCL5/RANTES SNPs and Susceptibility to HIV-1 Infection: A Meta-Analysis. Viruses 2023; 15:1958. [PMID: 37766364 PMCID: PMC10535444 DOI: 10.3390/v15091958] [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: 08/12/2023] [Revised: 09/10/2023] [Accepted: 09/11/2023] [Indexed: 09/29/2023] Open
Abstract
Genetic polymorphisms in genes that encode natural ligands of CCR5 (the main human HIV coreceptor), such as CCL5/RANTES, can alter the levels of secretion of these peptides. This article sought to review the relationship between single nucleotide polymorphisms (SNPs) of CCL5/RANTES and HIV-1 disease susceptibility. A meta-analysis was conducted through 17 articles found from January 1999 to December 2022 in the PUBMED, Science Direct, Medline, and SciELO databases. A total of three SNPs were identified and investigated under their dominant genotypic model and through a fixed-effects model. In terms of the SNP rs2107538 (G > A), in Africa and Asia, it has a protective role (OR = 0.56; 95% CI = 0.41-0.76; p = 0.0002, and OR = 0.88; 95% CI = 0.76-1.02; p = 0.08, respectively). In terms of the SNP rs2280788 (C > G), in Europe and America, it shows a higher risk role (OR = 1.92; 95% CI = 1.06-3.47; p = 0.03, and OR = 0.94; 95% CI = 0.94-1.11; p = 0.04, respectively), but in the population of Asia, with its mutant allele, it has a protective role (OR = 0.76; 95% CI = 0.63-0.93; p = 0.007). In terms of the SNP rs2280789 (T > C), no significant associations were found. Both SNPs rs2107538 and rs2280788 have a positive transcriptional effect on the RANTES/CCL5 gene, while SNP rs2280789 causes a decrease in gene expression levels. This study suggests that there is an association between the increased expression of CCL5/RANTES and a lower risk of AIDS. Therefore, further studies are needed to arrive at a definitive conclusion, and these results may help establish scientific bases for effective HIV/AIDS control strategies.
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Affiliation(s)
- Marcos Jessé Abrahão Silva
- Master Program in Epidemiology and Health Surveillance (PPGEVS), Evandro Chagas Institute (IEC), Ananindeua 67030-000, PA, Brazil;
| | - Rebecca Lobato Marinho
- Bacteriology and Mycology Section of the Evandro Chagas Institute (IEC), Ananindeua 67030-000, PA, Brazil; (R.L.M.); (L.R.R.); (K.V.B.L.); (L.N.G.C.L.)
| | - Pabllo Antonny Silva dos Santos
- Master and PhD Program in Parasitic Biology in the Amazon (PPGBPA), Department of Natural Science (DCNA/UEPA), University of Pará State (UEPA), Belém 66087-662, PA, Brazil; (P.A.S.d.S.); (C.S.d.S.)
| | - Carolynne Silva dos Santos
- Master and PhD Program in Parasitic Biology in the Amazon (PPGBPA), Department of Natural Science (DCNA/UEPA), University of Pará State (UEPA), Belém 66087-662, PA, Brazil; (P.A.S.d.S.); (C.S.d.S.)
| | - Layana Rufino Ribeiro
- Bacteriology and Mycology Section of the Evandro Chagas Institute (IEC), Ananindeua 67030-000, PA, Brazil; (R.L.M.); (L.R.R.); (K.V.B.L.); (L.N.G.C.L.)
| | - Yan Corrêa Rodrigues
- Master Program in Epidemiology and Health Surveillance (PPGEVS), Evandro Chagas Institute (IEC), Ananindeua 67030-000, PA, Brazil;
- Bacteriology and Mycology Section of the Evandro Chagas Institute (IEC), Ananindeua 67030-000, PA, Brazil; (R.L.M.); (L.R.R.); (K.V.B.L.); (L.N.G.C.L.)
- Department of Natural Science (DCNA/UEPA), University of Pará State (UEPA), Belém 66050-540, PA, Brazil
| | - Karla Valéria Batista Lima
- Bacteriology and Mycology Section of the Evandro Chagas Institute (IEC), Ananindeua 67030-000, PA, Brazil; (R.L.M.); (L.R.R.); (K.V.B.L.); (L.N.G.C.L.)
| | - Luana Nepomuceno Gondim Costa Lima
- Bacteriology and Mycology Section of the Evandro Chagas Institute (IEC), Ananindeua 67030-000, PA, Brazil; (R.L.M.); (L.R.R.); (K.V.B.L.); (L.N.G.C.L.)
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