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MicroRNA-3148 modulates allelic expression of toll-like receptor 7 variant associated with systemic lupus erythematosus.

Deng Y, Zhao J, Sakurai D, Kaufman KM, Edberg JC, Kimberly RP, Kamen DL, Gilkeson GS, Jacob CO, Scofield RH, Langefeld CD, Kelly JA, Ramsey-Goldman R, Petri MA, Reveille JD, Vilá LM, Alarcón GS, Vyse TJ, Pons-Estel BA, Argentine Collaborative GroupFreedman BI, Gaffney PM, Sivils KM, James JA, Gregersen PK, Anaya JM, Niewold TB, Merrill JT, Criswell LA, Stevens AM, Boackle SA, Cantor RM, Chen W, Grossman JM, Hahn BH, Harley JB, Alarcόn-Riquelme ME, BIOLUPUS and GENLES networksBrown EE, Tsao BP - PLoS Genet. (2013)

Bottom Line: Overexpression of miR-3148 in HEK-293 cells led to significant dose-dependent decrease in luciferase activity for construct driven by TLR7 3'UTR segment bearing the C allele (P = 0.0003).Compared with the G-allele construct, the C-allele construct showed greater than two-fold reduction of luciferase activity in the presence of miR-3148.These data establish rs3853839 of TLR7 as a shared risk variant of SLE in 22,613 subjects of Asian, EA, AA, and Amerindian/Hispanic ancestries (Pmeta  = 2.0×10(-19), OR = 1.25 [1.20-1.32]), which confers allelic effect on transcript turnover via differential binding to the epigenetic factor miR-3148.

View Article: PubMed Central - PubMed

Affiliation: Division of Rheumatology, University of California Los Angeles, Los Angeles, California, USA.

ABSTRACT
We previously reported that the G allele of rs3853839 at 3'untranslated region (UTR) of Toll-like receptor 7 (TLR7) was associated with elevated transcript expression and increased risk for systemic lupus erythematosus (SLE) in 9,274 Eastern Asians [P = 6.5×10(-10), odds ratio (OR) (95%CI) = 1.27 (1.17-1.36)]. Here, we conducted trans-ancestral fine-mapping in 13,339 subjects including European Americans, African Americans, and Amerindian/Hispanics and confirmed rs3853839 as the only variant within the TLR7-TLR8 region exhibiting consistent and independent association with SLE (Pmeta = 7.5×10(-11), OR = 1.24 [1.18-1.34]). The risk G allele was associated with significantly increased levels of TLR7 mRNA and protein in peripheral blood mononuclear cells (PBMCs) and elevated luciferase activity of reporter gene in transfected cells. TLR7 3'UTR sequence bearing the non-risk C allele of rs3853839 matches a predicted binding site of microRNA-3148 (miR-3148), suggesting that this microRNA may regulate TLR7 expression. Indeed, miR-3148 levels were inversely correlated with TLR7 transcript levels in PBMCs from SLE patients and controls (R(2) = 0.255, P = 0.001). Overexpression of miR-3148 in HEK-293 cells led to significant dose-dependent decrease in luciferase activity for construct driven by TLR7 3'UTR segment bearing the C allele (P = 0.0003). Compared with the G-allele construct, the C-allele construct showed greater than two-fold reduction of luciferase activity in the presence of miR-3148. Reduced modulation by miR-3148 conferred slower degradation of the risk G-allele containing TLR7 transcripts, resulting in elevated levels of gene products. These data establish rs3853839 of TLR7 as a shared risk variant of SLE in 22,613 subjects of Asian, EA, AA, and Amerindian/Hispanic ancestries (Pmeta  = 2.0×10(-19), OR = 1.25 [1.20-1.32]), which confers allelic effect on transcript turnover via differential binding to the epigenetic factor miR-3148.

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The SLE-risk G allele of rs3853839 displays reduced transcript modulation by miR-3148.(A) TargetScan's predicted miR-3148-binding site in TLR7 3′UTR. The C allele, rather than G allele of rs3853839 corresponds to the second base of this seed region. (B) Inverse correlation of miR-3148 and TLR7 transcript levels in PBMCs from 16 patients with SLE (solid circles) and 21 controls (open diamonds). (C) HEK-293 cells were cotransfected with empty reporter vector (EV), luciferase constructs driven by TLR7 3′UTR segment containing either C or G allele of rs3853839 and increasing concentrations (1, 6, 12, and 48 nM) of miR-3148 or nontarget control (NC) mimics. Luciferase activity was determined 24 hours after transfection. Normalized luciferase activity is the Renilla/Firefly ratio of miR-3148-treated reporter vector compared with the same NC-treated reporter vector. Data show the mean ± SEM and are representative of cumulative data from three independent experiments. P = 0.0003 over all miR-3148-treated C-allele vector groups, and not significant over all miR-3148-treated G-allele or empty vector groups (ANOVA test). P* = 0.02, P**<0.0001 (Student's t test) for the comparison of indicated groups.
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pgen-1003336-g003: The SLE-risk G allele of rs3853839 displays reduced transcript modulation by miR-3148.(A) TargetScan's predicted miR-3148-binding site in TLR7 3′UTR. The C allele, rather than G allele of rs3853839 corresponds to the second base of this seed region. (B) Inverse correlation of miR-3148 and TLR7 transcript levels in PBMCs from 16 patients with SLE (solid circles) and 21 controls (open diamonds). (C) HEK-293 cells were cotransfected with empty reporter vector (EV), luciferase constructs driven by TLR7 3′UTR segment containing either C or G allele of rs3853839 and increasing concentrations (1, 6, 12, and 48 nM) of miR-3148 or nontarget control (NC) mimics. Luciferase activity was determined 24 hours after transfection. Normalized luciferase activity is the Renilla/Firefly ratio of miR-3148-treated reporter vector compared with the same NC-treated reporter vector. Data show the mean ± SEM and are representative of cumulative data from three independent experiments. P = 0.0003 over all miR-3148-treated C-allele vector groups, and not significant over all miR-3148-treated G-allele or empty vector groups (ANOVA test). P* = 0.02, P**<0.0001 (Student's t test) for the comparison of indicated groups.

Mentions: MicroRNAs (miRNAs) that bind to target sequences located within the 3′UTR of mRNAs by base pairing have been shown to result in accelerated mRNA turnover or translation repression [6]. Single nucleotide change either within or around the sequence of miRNA target sites can potentially alter the base-pairing patterns and affect miRNA-mediated regulation [7], [8]. The updated TargetScan database (Release 6.2; http://www.targetscan.org) indicates that rs3853839 is located within a binding site of miR-3148, where the non-risk allele (C), but not the risk allele (G), is predicted to match miR-3148 at the second position (Figure 3A). We hypothesized that the C to G variation of rs3853839 could reduce the binding and regulation incurred by miR-3148, therefore, leading to dysregulated TLR7 expression. We first showed that transcript levels of miR-3148 and TLR7 were inversely correlated in PBMCs from 16 patients with SLE and 21 healthy controls (R2 = 0.255, P = 0.001; Figure 3B), suggesting the possible regulation of TLR7 expression by miR-3148. Next, to verify whether allelic variation of rs3853839 affects the interaction of miR-3148 with TLR7 3′UTR, psiCHECK-2 vectors containing TLR7 3′UTR segment with either the C or G allele of rs3853839 were cotransfected with various doses of miR-3148 or nontarget control mimic into HEK-293 cells. As shown in Figure 3C, we observed significant dose-dependent miR-3148-mediated decrease in luciferase activity for the C-allele construct (P = 0.0003 over all miR-3148-treated C-allele vector groups, ANOVA test), but not for the G-allele construct (P = 0.14). Cotransfection with miR-3148 at a concentration of 6, 12, and 48 nM, respectively, led to greater than two-fold reduction of luciferase activity in the C-allele than the G-allele construct [reduction in C-allele vs. G-allele construct: 13.2% vs. 4.8%, P = 0.023 (6 nM); 22.5% vs. 9.9%, P = 0.0012 (12 nM); 21.4% vs. 8.5%, P = 0.0031 (48 nM)]. These data supported the bioinformatic prediction that miR-3148 directly targets TLR7 3′UTR and the C to G variation of rs3853839 within the binding site alters the inhibitory effect of miR-3148 on modulating TLR7 expression.


MicroRNA-3148 modulates allelic expression of toll-like receptor 7 variant associated with systemic lupus erythematosus.

Deng Y, Zhao J, Sakurai D, Kaufman KM, Edberg JC, Kimberly RP, Kamen DL, Gilkeson GS, Jacob CO, Scofield RH, Langefeld CD, Kelly JA, Ramsey-Goldman R, Petri MA, Reveille JD, Vilá LM, Alarcón GS, Vyse TJ, Pons-Estel BA, Argentine Collaborative GroupFreedman BI, Gaffney PM, Sivils KM, James JA, Gregersen PK, Anaya JM, Niewold TB, Merrill JT, Criswell LA, Stevens AM, Boackle SA, Cantor RM, Chen W, Grossman JM, Hahn BH, Harley JB, Alarcόn-Riquelme ME, BIOLUPUS and GENLES networksBrown EE, Tsao BP - PLoS Genet. (2013)

The SLE-risk G allele of rs3853839 displays reduced transcript modulation by miR-3148.(A) TargetScan's predicted miR-3148-binding site in TLR7 3′UTR. The C allele, rather than G allele of rs3853839 corresponds to the second base of this seed region. (B) Inverse correlation of miR-3148 and TLR7 transcript levels in PBMCs from 16 patients with SLE (solid circles) and 21 controls (open diamonds). (C) HEK-293 cells were cotransfected with empty reporter vector (EV), luciferase constructs driven by TLR7 3′UTR segment containing either C or G allele of rs3853839 and increasing concentrations (1, 6, 12, and 48 nM) of miR-3148 or nontarget control (NC) mimics. Luciferase activity was determined 24 hours after transfection. Normalized luciferase activity is the Renilla/Firefly ratio of miR-3148-treated reporter vector compared with the same NC-treated reporter vector. Data show the mean ± SEM and are representative of cumulative data from three independent experiments. P = 0.0003 over all miR-3148-treated C-allele vector groups, and not significant over all miR-3148-treated G-allele or empty vector groups (ANOVA test). P* = 0.02, P**<0.0001 (Student's t test) for the comparison of indicated groups.
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC3585142&req=5

pgen-1003336-g003: The SLE-risk G allele of rs3853839 displays reduced transcript modulation by miR-3148.(A) TargetScan's predicted miR-3148-binding site in TLR7 3′UTR. The C allele, rather than G allele of rs3853839 corresponds to the second base of this seed region. (B) Inverse correlation of miR-3148 and TLR7 transcript levels in PBMCs from 16 patients with SLE (solid circles) and 21 controls (open diamonds). (C) HEK-293 cells were cotransfected with empty reporter vector (EV), luciferase constructs driven by TLR7 3′UTR segment containing either C or G allele of rs3853839 and increasing concentrations (1, 6, 12, and 48 nM) of miR-3148 or nontarget control (NC) mimics. Luciferase activity was determined 24 hours after transfection. Normalized luciferase activity is the Renilla/Firefly ratio of miR-3148-treated reporter vector compared with the same NC-treated reporter vector. Data show the mean ± SEM and are representative of cumulative data from three independent experiments. P = 0.0003 over all miR-3148-treated C-allele vector groups, and not significant over all miR-3148-treated G-allele or empty vector groups (ANOVA test). P* = 0.02, P**<0.0001 (Student's t test) for the comparison of indicated groups.
Mentions: MicroRNAs (miRNAs) that bind to target sequences located within the 3′UTR of mRNAs by base pairing have been shown to result in accelerated mRNA turnover or translation repression [6]. Single nucleotide change either within or around the sequence of miRNA target sites can potentially alter the base-pairing patterns and affect miRNA-mediated regulation [7], [8]. The updated TargetScan database (Release 6.2; http://www.targetscan.org) indicates that rs3853839 is located within a binding site of miR-3148, where the non-risk allele (C), but not the risk allele (G), is predicted to match miR-3148 at the second position (Figure 3A). We hypothesized that the C to G variation of rs3853839 could reduce the binding and regulation incurred by miR-3148, therefore, leading to dysregulated TLR7 expression. We first showed that transcript levels of miR-3148 and TLR7 were inversely correlated in PBMCs from 16 patients with SLE and 21 healthy controls (R2 = 0.255, P = 0.001; Figure 3B), suggesting the possible regulation of TLR7 expression by miR-3148. Next, to verify whether allelic variation of rs3853839 affects the interaction of miR-3148 with TLR7 3′UTR, psiCHECK-2 vectors containing TLR7 3′UTR segment with either the C or G allele of rs3853839 were cotransfected with various doses of miR-3148 or nontarget control mimic into HEK-293 cells. As shown in Figure 3C, we observed significant dose-dependent miR-3148-mediated decrease in luciferase activity for the C-allele construct (P = 0.0003 over all miR-3148-treated C-allele vector groups, ANOVA test), but not for the G-allele construct (P = 0.14). Cotransfection with miR-3148 at a concentration of 6, 12, and 48 nM, respectively, led to greater than two-fold reduction of luciferase activity in the C-allele than the G-allele construct [reduction in C-allele vs. G-allele construct: 13.2% vs. 4.8%, P = 0.023 (6 nM); 22.5% vs. 9.9%, P = 0.0012 (12 nM); 21.4% vs. 8.5%, P = 0.0031 (48 nM)]. These data supported the bioinformatic prediction that miR-3148 directly targets TLR7 3′UTR and the C to G variation of rs3853839 within the binding site alters the inhibitory effect of miR-3148 on modulating TLR7 expression.

Bottom Line: Overexpression of miR-3148 in HEK-293 cells led to significant dose-dependent decrease in luciferase activity for construct driven by TLR7 3'UTR segment bearing the C allele (P = 0.0003).Compared with the G-allele construct, the C-allele construct showed greater than two-fold reduction of luciferase activity in the presence of miR-3148.These data establish rs3853839 of TLR7 as a shared risk variant of SLE in 22,613 subjects of Asian, EA, AA, and Amerindian/Hispanic ancestries (Pmeta  = 2.0×10(-19), OR = 1.25 [1.20-1.32]), which confers allelic effect on transcript turnover via differential binding to the epigenetic factor miR-3148.

View Article: PubMed Central - PubMed

Affiliation: Division of Rheumatology, University of California Los Angeles, Los Angeles, California, USA.

ABSTRACT
We previously reported that the G allele of rs3853839 at 3'untranslated region (UTR) of Toll-like receptor 7 (TLR7) was associated with elevated transcript expression and increased risk for systemic lupus erythematosus (SLE) in 9,274 Eastern Asians [P = 6.5×10(-10), odds ratio (OR) (95%CI) = 1.27 (1.17-1.36)]. Here, we conducted trans-ancestral fine-mapping in 13,339 subjects including European Americans, African Americans, and Amerindian/Hispanics and confirmed rs3853839 as the only variant within the TLR7-TLR8 region exhibiting consistent and independent association with SLE (Pmeta = 7.5×10(-11), OR = 1.24 [1.18-1.34]). The risk G allele was associated with significantly increased levels of TLR7 mRNA and protein in peripheral blood mononuclear cells (PBMCs) and elevated luciferase activity of reporter gene in transfected cells. TLR7 3'UTR sequence bearing the non-risk C allele of rs3853839 matches a predicted binding site of microRNA-3148 (miR-3148), suggesting that this microRNA may regulate TLR7 expression. Indeed, miR-3148 levels were inversely correlated with TLR7 transcript levels in PBMCs from SLE patients and controls (R(2) = 0.255, P = 0.001). Overexpression of miR-3148 in HEK-293 cells led to significant dose-dependent decrease in luciferase activity for construct driven by TLR7 3'UTR segment bearing the C allele (P = 0.0003). Compared with the G-allele construct, the C-allele construct showed greater than two-fold reduction of luciferase activity in the presence of miR-3148. Reduced modulation by miR-3148 conferred slower degradation of the risk G-allele containing TLR7 transcripts, resulting in elevated levels of gene products. These data establish rs3853839 of TLR7 as a shared risk variant of SLE in 22,613 subjects of Asian, EA, AA, and Amerindian/Hispanic ancestries (Pmeta  = 2.0×10(-19), OR = 1.25 [1.20-1.32]), which confers allelic effect on transcript turnover via differential binding to the epigenetic factor miR-3148.

Show MeSH
Related in: MedlinePlus