| Literature DB >> 35309115 |
Diana Feio da Veiga Borges Leal1, Mayara Natália Santana da Silva2, Lucas Favacho Pastana1, Marianne Rodrigues Fernandes1, Aidalucy do Socorro Costa de Athayde1, Débora Christina Ricardo Fernandes Porchera1, Cleonardo Augusto da Silva1, Antônio André Conde Modesto1, Paulo Pimentel De Assumpcão1, Sidney Emanuel Batista Dos Santos1,2, Ney Pereira Carneiro Dos Santos1.
Abstract
Tuberculosis (TB) is a chronic infection caused by Mycobacterium tuberculosis (Mtb) with high incidence and mortality. Studies reported that host genetic variants might be associated with the risk of tuberculosis. The aim of this study was to perform an association study between 26 single nucleotide polymorphisms (SNPs) and tuberculosis and evaluate whether these SNPs may confer risk factors to tuberculosis in the Amazon population. There were 52 males and 126 females, with total of 178 healthy controls. Genotyping was performed using TaqMan Open Array Genotyping. Ancestry-informative markers were used to estimate the ancestral proportions of the individuals in the case and control groups. The results indicated that the SNPs rs10035440 (DROSHA), rs7372209 (miR26-a1), rs1834306 (miR100), rs4919510 (miR608), and rs10739971 (pri-let-7a-1) were significantly associated with high risk and rs3746444 (miR499) and rs6505162 (miR423), with low risk of developing tuberculosis in the Amazon population. Our study concluded that seven miRNA polymorphisms were associated with tuberculosis. Our study contributes to a better understanding of TB pathogenesis and may promote the development of new diagnostic tools against M. tuberculosis infection.Entities:
Keywords: drosha; genetic variants; microRNA; risk factor; tuberculosis
Year: 2022 PMID: 35309115 PMCID: PMC8924412 DOI: 10.3389/fgene.2022.850058
Source DB: PubMed Journal: Front Genet ISSN: 1664-8021 Impact factor: 4.599
Clinical characteristics and genetic ancestry of subjects.
| Variable | Case ( | Control ( |
|
|---|---|---|---|
| Age (years) | 51.8 (49.2–54.4) | 70.82 (68.5–72.1) | <0.001 |
| Sex (male/female) | 88(46.3%)/102(53.7%) | 52(29.3%)/126(70.7%) | 0.001 |
| EUR ancestry | 0.25 (0.23–0.27) | 0.45 (0.42–0.48) | <0.001 |
| AMR ancestry | 0.42 (0.38–0.43) | 0.31 (0.28–0.32) | <0.001 |
| AFR ancestry | 0.33 (0.31–0.35) | 0.24 (0.22–0.26) | <0.001 |
Mann–Whitney test.
Fisher’s exact Test.
Multivariate regression logistic. Data are presented as median ±standard deviation.
All 26 SNPs in microRNA and DROSHA genes with Hardy-Weinberg equilibrium (HWE) tests with the Bonferroni correction.
| Gene |
|
|---|---|
| DROSHA (rs639174) | 0.001 |
| DROSHA (rs10035440) | 0.787* |
| miR453 (rs56103835) | 0.817* |
| miR 2053 (rs10505168) | 0.109* |
| miR300 (rs12894467) | 1* |
| miR-146A (rs2910164) | 0.861* |
| miR196A2 (rs11614913) | 1* |
| miR149 (rs2292832) | <0.001 |
| AGO01 (rs636832) | 0.850* |
| miR200B/200A/429 (rs9660710) | <0.001 |
| miR20b/miR-17-5P (rs3660) | 0.022 |
| miR608 (rs4919510) | 0.125* |
| miR499 (rs3746444) | 0.204* |
| miR605 (rs2043556) | 0.003 |
| miR570 (rs4143815) | 0.008 |
| miR200C (rs12904) | 0.340* |
| pre-miR938 (rs2505901) | <0.001 |
| pri-let-7a-1 (rs10739971) | 0.113* |
| miR219A1 (rs107822) | 0.211* |
| miR604 (rs2368392) | 0.002 |
| miR26-a1 (rs7372209) | 0.183* |
| miR100 (rs1834306) | 0.718* |
| miR219-1 (rs213210) | <0.001 |
| miR4513 (rs2168518) | 0.073* |
| miR423 (rs6505162) | 1* |
| DROSHA (rs3805500) | <0.001 |
Association analysis of 16 SNPS with risk of TB disease in accordance with the Hardy–Weinberg equilibrium.
| Genotype (SNP ID) | Case (%) | Control (%) |
| OR (95% CI) |
|---|---|---|---|---|
| DROSHA (rs10035440) |
|
| <0.001* | TT + CT vs. CC |
| CC | 35 (33%) | 06 (04%) | 15.58 (5.04-48.15)a | |
| CT | 72 (67%) | 44 (30%) | 0.996 | TT vs. CT + CCb |
| TT | 0 (0%) | 98 (66%) | ||
| miR453 (rs56103835) |
|
| 0.322 | TT + CT vs. CC |
| CC | 09 (12%) | 07 (05%) | 1.80 (0.56–5.77)a | |
| CT | 33 (44%) | 54 (38%) | 0.142 | TT vs. CT + CC |
| TT | 33 (44%) | 81 (57%) | 1.60 (0.85-3.00)b | |
| miR 2053 (rs10505168) |
|
| 0.975 | TT + CT vs. CC |
| CC | 10 (15%) | 19 (15%) | 1.05 (0.39-2.58)a | |
| CT | 29 (43%) | 47 (39%) | 0.931 | TT vs. CT + CC |
| TT | 28 (42%) | 56 (46%) | 1.03 (0.52–2.03)b | |
| miR300 (rs12894467) |
|
| 0.266 | TT + CT vs. CC |
| CC | 17 (11%) | 20 (14%) | 1.56 (0.71-3.44)a | |
| CT | 80 (55%) | 46 (33%) | 0.654 | TT vs. CT + CC |
| TT | 49 (34%) | 75 (53%) | 1.12 (0.66–1.90)b | |
| miR146A (rs2910164) |
|
| 0.696 | GG + CG vs. CC |
| CC | 13 (10%) | 18 (11%) | 0.845 (0.36-1.96)a | |
| CG | 59 (45%) | 74 (46%) | 0.590 | GG vs. CG + CC |
| GG | 59 (45%) | 68 (43%) | 1.15 (0.67–1.97)b | |
| miR196A2 (rs11614913) |
|
| 0.634 | TT + CT vs. CC |
| CC | 50 (52%) | 65 (45%) | 1.15 (0.64-2.07)a | |
| CT | 41 (43%) | 65 (45%) | 0.239 | TT vs. CT + CC |
| TT | 05 (05%) | 15 (10%) | 1.98 (0.63–6.18)b | |
| AGO01 (rs636832) |
|
| 0.643 | GG + AG vs. AA |
| AA | 15 (14%) | 14 (09%) | 1.22 (0.51-2.90)a | |
| AG | 45 (43%) | 67 (45%) | 0.450 | GG vs. AG + AA |
| GG | 45 (43%) | 69 (46%) | 0.80 (0.45–1.42)b | |
| miR608 (rs4919510) |
|
| <0.001* | GG + CG vs. CC |
| CC | 21 (18%) | 85 (53%) | 4.53 (2.30-8.92)a | |
| CG | 46 (40%) | 58 (36%) | <0.001* | GG vs. CG + CC |
| GG | 49 (42%) | 18 (11%) | 4.13 (2.25-7.60)b | |
| miR499 (rs3746444) |
|
| 0.995 | GG + AG vs. AAa |
| AA | 0 (0%) | 126 (75%) | ||
| AG | 31 (25%) | 36 (22%) | <0.001* | GG vs. AG + AA |
| GG | 96 (75%) | 05 (3%) | 0.009 (0.003–0.26)b | |
| miR200C (rs12904) |
|
| 0.474 | GG + AG vs. AA |
| AA | 35 (33%) | 38 (24%) | 1.25 (0.67–2.33)a | |
| AG | 42 (39%) | 72 (46%) | 0.717 | GG vs. AG + AA |
| GG | 29 (28%) | 46 (30%) | 1.12 (0.60-2.07)b | |
| pri-let-7a-1 (rs10739971) |
|
| <0.001* | GG + AG vs. AA |
| AA | 70 (76.92%) | 32 (38%) | 6.14 (2.88-13.08)a | |
| AG | 17 (18.68%) | 33 (40%) | <0.001* | GG vs. AG + AA |
| GG | 4 (4.4%) | 18 (22%) | 7.25 (2.13-24.69)b | |
| miR219-1(rs107822) |
|
| 0.528 | TT + CT vs. CC |
| CC | 50 (55%) | 85 (56%) | 1.20 (0.67–2.17)a | |
| CT | 33 (37%) | 53 (35%) | 0.994 | TT vs. CT + CC |
| TT | 7 (8%) | 14 (9%) | 0.99 (0.34-2.87)b | |
| miR26-a1 (rs7372209) |
|
| 0.752 | TT + CT vs. CC |
| CC | 49 (44%) | 70 (48%) | 0.91 (0.52-1.59)a | |
| CT | 58 (51%) | 56 (39%) | 0.017* | TT vs. CT + CC |
| TT | 6 (5%) | 19 (13%) | 3.75 (1.26–11.15)b | |
| miR100 (rs1834306) |
|
| 0.001* | GG + AG vs. AA |
| AA | 35 (46%) | 33 (27%) | 3.39 (1.67–6.85)a | |
| AG | 31 (41%) | 64 (52%) | 0.128 | GG vs. AG + AA |
| GG | 10 (13%) | 26 (21%) | 1.99 (0.81-4.86)b | |
| miR4513 (rs2168518) |
|
| 0.505 | GG + AG vs. AA |
| AA | 9 (7%) | 22 (13%) | 0.73 (0.29–1.82)a | |
| AG | 51 (41) | 61 (38%) | 0.931 | GG vs. AG + AA |
| GG | 65 (52%) | 80 (49%) | 1.02 (0.60-1.73)b | |
| miR423 (rs6505162) |
|
| 0.021* | CC + AC vs. AA |
| AA | 8 (10%) | 30 (24%) | 0.33 (0.13–0.84)a | |
| AC | 52 (68%) | 62 (50%) | 0.449 | CC vs. AC + AA |
| CC | 17 (22%) | 32 (26%) | 1.34 (0.62-2.90)b |
p-values for logistic analyses of alternative models (dominant a and recessive b models) are shown. Multivariate logistic regression with sex and ancestry is used as covariates.
Association analysis of seven significant SNPs with the risk of TB disease.
| Genotype (SNP ID) | Case (%) | Control (%) |
| OR (95% CI) |
|---|---|---|---|---|
| DROSHA (rs10035440) |
|
| <0.001* | TT + CT vs. CC |
| CC | 35 (33%) | 06 (04%) | 15.58 (5.04-48.15)a | |
| CT | 72 (67%) | 44 (30%) | 0.996 | TT vs. CT + CC b |
| TT | 0 (0%) | 98 (66%) | ||
| miR608 (rs4919510) |
|
| <0.001* | GG + CG vs. CC |
| CC | 21 (18%) | 85 (53%) | 4.53 (2.30-8.92)a | |
| CG | 46 (40%) | 58 (36%) | <0.001* | GG vs. CG + CC |
| GG | 49 (42%) | 18 (11%) | 4.13 (2.25-7.60)b | |
| miR499 (rs3746444) |
|
| 0.995 | GG + AG vs. AAa |
| AA | 0 (0%) | 126 (75%) | ||
| AG | 31 (25%) | 36 (22%) | <0.001* | GG vs. AG + AA |
| GG | 96 (75%) | 05 (3%) | 0.009 (0.003–0.26)b | |
| pri-let-7a-1 (rs10739971) |
|
| <0.001* | GG + AG vs. AA |
| AA | 70 (76.92%) | 32 (38%) | 6.14 (2.88-13.08)a | |
| AG | 17 (18.68%) | 33 (40%) | <0.001* | GG vs. AG + AA |
| GG | 4 (4.4%) | 18 (22%) | 7.25 (2.13-24.69)b | |
| miR26-a1 (rs7372209) |
|
| 0.752 | TT + CT vs. CC |
| CC | 49 (44%) | 70 (48%) | 0.91 (0.52-1.59)a | |
| CT | 58 (51%) | 56 (39%) | 0.017* | TT vs. CT + CC |
| TT | 6 (5%) | 19 (13%) | 3.75 (1.26–11.15)b | |
| miR100 (rs1834306) |
|
| 0.001* | GG + AG vs. AA |
| AA | 35 (46%) | 33 (27%) | 3.39 (1.67–6.85)a | |
| AG | 31 (41%) | 64 (52%) | 0.128 | GG vs. AG + AA |
| GG | 10 (13%) | 26 (21%) | 1.99 (0.81-4.86)b | |
| miR423 (rs6505162) |
|
| 0.021* | CC + AC vs. AA |
| AA | 8 (10%) | 30 (24%) | 0.33 (0.13–0.84)a | |
| AC | 52 (68%) | 62 (50%) | 0.449 | CC vs. AC + AA |
| CC | 17 (22%) | 32 (26%) | 1.34 (0.62-2.90)b |
p-values for logistic analyses of alternative models (dominant a and recessive b models) are shown. Multivariate logistic regression with sex and ancestry is used as covariates. Genotypic frequency distributions are in accordance with the Hardy–Weinberg equilibrium (HWE, p > 0.05).