The features of all subjects were summarized in Table 1. 563 BC patients (52.05 ± 9.81 years) and 552 healthy controls (51.88 ± 9.85 years) participated in the present study. No significant differences of age distribution between cases and controls (p = 0.767) was found. Most patients had tumor size > 2 cm (56.0%), stage I/II (64.8%), lymph node invasion (48.8%), positive hormone receptor status such as ER + (67.1%), PR +(60.6%), or HER2 + (48.5%) and positive Ki67 (64.8%).
Table 1
Characteristics of patients with breast cancer and controls
Characteristics | Cases (n = 563) | Controls ( n = 552) | p |
Age | Mean ± SD (years) | 52.05 ± 9.81 | 51.88 ± 9.85 | 0.767 |
| > 51 | 297 (52.8%) | 295 (53.4%) | |
| ≤ 51 | 266 (47.2%) | 257 (46.6%) | |
Tumor size (cm) | ≤ 2 cm | 107 (19.0%) | | |
> 2 cm | 315 (56.0%) | | |
| Missing | 141 (25.0%) | | |
Stage | Ⅰ-Ⅱ | 365 (64.8%) | | |
| Ⅲ-Ⅳ | 162 (28.8%) | | |
| Missing | 36 (6.4%) | | |
Lymph node invasion | No | 260 (46.2%) | | |
| Yes | 275 (48.8%) | | |
| Missing | 28 (5.0%) | | |
ER status | Negative | 161 (28.6%) | | |
| Positive | 378 (67.1%) | | |
| Missing | 24 (4.3%) | | |
PR status | Negative | 212 (37.7%) | | |
| Positive | 341 (60.6%) | | |
| Missing | 10 (1.8%) | | |
HER2 status | Negative | 91 (16.2%) | | |
| Positive | 273 (48.5%) | | |
| Missing | 199 (35.3%) | | |
Ki67 | Negative | 132 (23.4%) | | |
| Positive | 365 (64.8%) | | |
| Missing | 66 (11.7%) | | |
ER, estrogen receptor; RP, progesterone receptor; HER2, human epidermal growth factor receptor 2. |
The MAF of the LRRC3B SNPs were more than 0.05 (Supplementary Table 2). No deviation from the HWE for the polymorphisms examined was observed in the genotype distributions of the controls (p > 0.05), suggesting these subjects could represent the general population. In addition, LRRC3B variants were related to enhancer histone, changed motifs and GRASP QTL hits in silico analysis.
We performed allele and genetic model analyses of ten LRRC3B SNPs in the BC cases and control subjects. The genotype frequencies distribution of SNPs was shown in Table 2 and Supplementary Table 3. The distributions of A and T alleles of LRRC3B rs1907168 polymorphism were 84.6% and 15.4% in controls and 87.7% and 12.3% in patients. An association between T allele and BC risk (OR = 0.77, 95% CI: 0.61–0.99, p = 0.037) was found. Similarly, rs1907168 had a decreased risk of BC (heterozygous: OR = 0.71, 95% CI: 0.54–0.94, p = 0.017; dominant: OR = 0.72, 95% CI: 0.55–0.95, p = 0.019; and log-additive: OR = 0.76, 95% CI: 0.59–0.97, p = 0.030). However, no significant association was found for other SNPs (Supplementary Table 3).
Table 2
Relationships between LRRC3B rs1907168 polymorphism and breast cancer risk
Model | Genotype | Case | Control | Adjusted by age and gender |
OR (95%CI) | p |
Allele | A | 987 | 929 | 1.00 | 0.037 |
T | 139 | 169 | 0.77 (0.61–0.99) |
Genotype | AA | 432 | 388 | 1.00 | |
AT | 123 | 153 | 0.71 (0.54–0.94) | 0.017 |
TT | 8 | 8 | 0.90 (0.33–2.42) | |
Dominant | AA | 432 | 388 | 1.00 | 0.019 |
AT-TT | 131 | 161 | 0.72 (0.55–0.95) |
Recessive | AA-AT | 555 | 541 | 1.00 | 0.963 |
TT | 8 | 8 | 0.98 (0.36–2.62) |
Log-additive | --- | --- | --- | 0.76 (0.59–0.97) | 0.030 |
SNP, single nucleotide polymorphism; OR, odds ratio; 95% CI, 95% confidence interval. |
p values were calculated by logistic regression analysis with adjustments for age and gender. |
p < 0.05 means the data is statistically significant. |
We further conducted subgroup analyses by age to examine the effects of the LRRC3B SNPs on BC risk (Table 3). LRRC3B rs1907168 reduced the risk of BC among young participants (age < 51 years) under the allele (OR = 0.69, 95% CI: 0.48–0.99, p = 0.043), heterozygote (OR = 0.53, 95% CI: 0.35–0.80, p = 0.002), dominant (OR = 0.58, 95% CI: 0.39–0.86, p = 0.008) and log-additive (OR = 0.68, 95% CI: 0.47–0.98, p = 0.038) models. In addition, rs78205284 polymorphism (TT vs. GG, OR = 2.83, 95% CI: 1.08–7.41, p = 0.034; and TT vs. GG-GT, OR = 2.72, 95% CI: 1.05–7.07, p = 0.040) contributed to the increased BC risk at age ≤ 51 years.
Table 3
Relationships between LRRC3B polymorphisms and breast cancer risk according to the stratification by age
SNP ID | Model | Genotype | > 51 | ≤ 51 |
Case | Control | OR (95%CI) | p | Case | Control | OR (95%CI) | p |
rs1907168 | Allele | A | 515 | 500 | 1.00 | 0.336 | 472 | 429 | 1.00 | 0.043 |
T | 70 | 90 | 0.85 (0.62–1.18) | 60 | 79 | 0.69 (0.48–0.99) |
Genotype | AA | 220 | 211 | 1.00 | | 212 | 177 | 1.00 | |
AT | 75 | 78 | 0.91 (0.63–1.32) | 0.609 | 48 | 75 | 0.53 (0.35–0.80) | 0.002 |
TT | 2 | 6 | 0.32 (0.06–1.59) | 0.163 | 6 | 2 | 2.54 (0.51–12.77) | 0.257 |
Dominant | AA | 220 | 211 | 1.00 | 0.437 | 212 | 177 | 1.00 | 0.008 |
AT-TT | 77 | 84 | 0.87 (0.60–1.25) | 54 | 77 | 0.58 (0.39–0.86) |
Recessive | AA-AT | 295 | 289 | 1.00 | 0.172 | 260 | 252 | 1.00 | 0.188 |
TT | 2 | 6 | 0.33 (0.07–1.63) | 6 | 2 | 2.95 (0.59–14.77) |
Log-additive | --- | --- | --- | 0.83 (0.59–1.17) | 0.287 | --- | --- | 0.68 (0.47–0.98) | 0.038 |
rs78205284 | Allele | G | 482 | 477 | 1.00 | 0.993 | 419 | 428 | 1.00 | 0.063 |
T | 110 | 109 | 1.00 (0.74–1.34) | 113 | 86 | 1.34 (0.98–1.83) |
Genotype | GG | 201 | 197 | 1.00 | | 169 | 177 | 1.00 | |
GT | 80 | 83 | 0.95 (0.66–1.37) | 0.790 | 81 | 74 | 1.14 (0.78–1.66) | 0.505 |
TT | 15 | 13 | 1.15 (0.53–2.48) | 0.725 | 16 | 6 | 2.83 (1.08–7.41) | 0.034 |
Dominant | GG | 201 | 197 | 1.00 | 0.900 | 169 | 177 | 1.00 | 0.207 |
GT-TT | 95 | 96 | 0.98 (0.69–1.38) | 97 | 80 | 1.26 (0.88–1.82) |
Recessive | GG-GT | 281 | 280 | 1.00 | 0.694 | 250 | 251 | 1.00 | 0.040 |
TT | 15 | 13 | 1.17 (0.54-2,50) | 16 | 6 | 2.72 (1.05–7.07) |
Log-additive | --- | --- | --- | 1.01 (0.76–1.33) | 0.966 | | | 1.33 (0.98–1.80) | 0.071 |
SNP, single nucleotide polymorphism; OR, odds ratio; 95% CI, 95% confidence interval. |
p values were calculated by logistic regression analysis with adjustments for age. |
p < 0.05 indicates statistical significance. |
We also investigated the potential associations of LRRC3B polymorphisms with clinicopathological characteristics of BC, including tumor size, lymph node metastasis, clinical stage, the statuses of ER, PR, Her-2, and Ki67 (Table 4). We found that rs6551122 (OR = 0.51, p = 0.028) and rs12635768 (homozygote, OR = 0.36, p = 0.023; recessive, OR = 0.39, p = 0.032; log-additive, OR = 0.69, p = 0.043) polymorphisms were related to a smaller BC tumor size (< 2 cm). In addition, rs112276562, rs6551122 and rs73150416 variants contributed to a lower incidence of PR-positive breast cancer (for rs112276562, heterozygote OR = 0.56, p = 0.002 and dominant OR = 0.63, p = 0.011; for rs6551122, heterozygote OR = 0.63, p = 0.016 and dominant OR = 0.64, p = 0.018; and for rs73150416, heterozygote OR = 0.57, p = 0.005, dominant OR = 0.61, p = 0.008, log-additive OR = 0.72, p = 0.035, and allele OR = 0.71, p = 0.029). Moreover, rs6788033 was associated with a lower the expression level of Ki-67in dominant (OR = 0.64, p = 0.030), log-additive (OR = 0.68, p = 0.024) and allele (OR = 0.69, p = 0.025) models. There was no significant association of LRRC3B polymorphisms with respect to the other variables like lymph node metastasis, clinical stage and ER/HER2 status.
Table 4
The association between LRRC3B polymorphisms and clinical features of breast cancer
SNPs ID | Variables | OR (95%), p |
Homozygote | Heterozygote | Dominant | Recessive | Log-additive | Allele |
rs112276562 | Tumour size | < 2 cm/≥ 2 cm | 0.90 (0.31–2.64), 0.847 | 1.39 (0.83–2.34), 0.212 | 1.31 (0.80–2.13), 0.281 | 0.82 (0.28–2.40), 0.721 | 1.17 (0.78–1.76), 0.441 | 1.16 (0.77–1.75), 0.486 |
LNM | (-)/ (+) | 0.61 (0.25–1.47), 0.272 | 0.81 (0.56–1.18), 0.271 | 0.78 (0.55–1.12), 0.183 | 0.65 (0.27–1.56), 0.337 | 0.80 (0.59–1.08), 0.145 | 0.80 (0.59–1.08), 0.145 |
Stage | Ⅰ-Ⅱ/Ⅲ-Ⅳ | 0.75 (0.29–1.96), 0.560 | 0.81 (0.54–1.23), 0.326 | 0.80 (0.54–1.20), 0.282 | 0.80 (0.31–2.07), 0.648 | 0.83 (0.60–1.17), 0.289 | 0.84 (0.60–1.18), 0.310 |
ER | (-)/ (+) | 1.78 (0.59–5.40), 0.308 | 0.71 (0.48–1.06), 0.090 | 0.78 (0.53–1.14), 0.200 | 2.00 (0.66-6.00), 0.218 | 0.90 (0.65–1.24), 0.524 | 0.90 (0.65–1.24), 0.517 |
PR | (-)/ (+) | 1.54 (0.59–4.03), 0.375 | 0.56 (0.39–0.81), 0.002 | 0.63 (0.44–0.90), 0.011 | 1.87 (0.72–4.84), 0.196 | 0.77 (0.57–1.04), 0.093 | 0.77 (0.57–1.04), 0.085 |
HER2 | (-)/ (+) | 0.88 (0.27–2.91), 0.835 | 1.30 (0.76–2.22), 0.339 | 1.24 (0.74–2.06), 0.410 | 0.81 (0.25–2.66), 0.732 | 1.14 (0.74–1.76), 0.561 | 1.11 (0.72–1.72), 0.626 |
Ki-67 | < 10%/≥ 10% | 1.17 (0.41–3.34), 0.768 | 1.06 (0.69–1.64), 0.790 | 1.07 (0.70–1.63), 0.743 | 1.15 (0.41–3.24), 0.794 | 1.07 (0.75–1.53), 0.713 | 1.06 (0.74–1.51), 0.761 |
rs6551122 | Tumour size | < 2 cm/≥ 2 cm | 0.59 (0.30–1.13), 0.109 | 1.32 (0.81–2.14), 0.268 | 1.08 (0.69–1.69), 0.734 | 0.51 (0.28–0.93), 0.028 | 0.87 (0.63–1.20), 0.393 | 0.88 (0.64–1.21), 0.420 |
LNM | (-)/ (+) | 0.76 (0.44–1.30), 0.312 | 0.92 (0.64–1.33), 0.670 | 0.88 (0.62–1.26), 0.492 | 0.79 (0.48–1.31), 0.359 | 0.88 (0.69–1.14), 0.337 | 0.89 (0.70–1.14), 0.367 |
Stage | Ⅰ-Ⅱ/Ⅲ-Ⅳ | 0.66 (0.36–1.23), 0.194 | 1.06 (0.71–1.57), 0.794 | 0.96 (0.65–1.40), 0.825 | 0.64 (0.36–1.15), 0.135 | 0.88 (0.67–1.16), 0.355 | 0.89 (0.68–1.16), 0.389 |
ER | (-)/ (+) | 1.05 (0.58–1.92), 0.866 | 0.84 (0.56–1.25), 0.380 | 0.88 (0.60–1.29), 0.504 | 1.17 (0.67–2.03), 0.582 | 0.97 (0.74–1.28), 0.842 | 0.98 (0.75–1.28), 0.866 |
PR | (-)/ (+) | 0.71 (0.41–1.23), 0.218 | 0.63 (0.43–0.92), 0.016 | 0.64 (0.45–0.93), 0.018 | 0.93 (0.57–1.53), 0.776 | 0.79 (0.61–1.02), 0.064 | 0.80 (0.62–1.03), 0.078 |
HER2 | (-)/ (+) | 0.96 (0.42–2.17), 0.918 | 0.83 (0.49–1.39), 0.475 | 0.85 (0.52–1.40), 0.524 | 1.07 (0.50–2.28), 0.860 | 0.93 (0.65–1.34), 0.699 | 0.93 (0.66–1.32), 0.690 |
Ki-67 | < 10%/≥ 10% | 1.32 (0.69–2.52), 0.408 | 1.38 (0.90–2.13), 0.140 | 1.37 (0.91–2.06), 0.133 | 1.10 (0.60–2.02), 0.757 | 1.21 (0.90–1.65), 0.212 | 1.21 (0.90–1.63), 0.203 |
rs73150416 | Tumour size | < 2 cm/≥ 2 cm | 0.71 (0.26–1.95), 0.505 | 1.22 (0.71–2.07), 0.473 | 1.11 (0.68–1.82), 0.676 | 0.67 (0.25–1.85), 0.444 | 1.01 (0.68–1.51), 0.953 | 0.99 (0.66–1.50), 0.972 |
LNM | (-)/ (+) | 0.54 (0.22–1.34), 0.183 | 0.79 (0.54–1.16), 0.226 | 0.75 (0.52–1.09), 0.130 | 0.58 (0.24–1.42), 0.232 | 0.77 (0.56–1.04), 0.091 | 0.76 (0.55–1.04), 0.087 |
Stage | Ⅰ-Ⅱ/Ⅲ-Ⅳ | 0.47 (0.16–1.43), 0.183 | 0.84 (0.55–1.28), 0.405 | 0.78 (0.52–1.18), 0.236 | 0.50 (0.16–1.49), 0.211 | 0.78 (0.55–1.10), 0.151 | 0.78 (0.54–1.11), 0.159 |
ER | (-)/ (+) | 1.29 (0.46–3.60), 0.634 | 0.75 (0.50–1.13), 0.169 | 0.80 (0.54–1.18), 0.261 | 1.40 (0.50–3.89), 0.519 | 0.89 (0.64–1.23), 0.474 | 0.88 (0.63–1.24), 0.464 |
PR | (-)/ (+) | 0.95 (0.39–2.34), 0.916 | 0.57 (0.39–0.84), 0.005 | 0.61 (0.42–0.88), 0.008 | 1.13 (0.46–2.74), 0.792 | 0.72 (0.53–0.98), 0.035 | 0.71 (0.52–0.97), 0.029 |
HER2 | (-)/ (+) | 1.26 (0.34–4.66), 0.730 | 1.11 (0.65–1.89), 0.704 | 1.13 (0.67–1.88), 0.652 | 1.22 (0.33–4.48), 0.764 | 1.11 (0.72–1.72), 0.628 | 1.09 (0.70–1.69), 0.700 |
Ki-67 | < 10%/≥ 10% | 1.01 (0.38–2.67), 0.987 | 1.03 (0.66–1.62), 0.895 | 1.03 (0.67–1.58), 0.900 | 1.00 (0.38–2.62), 0.999 | 1.02 (0.72–1.45), 0.918 | 1.01 (0.70–1.45), 0.966 |
rs12635768 | Tumour size | < 2 cm/≥ 2 cm | 0.36 (0.15–0.87), 0.023 | 0.81 (0.50–1.30), 0.378 | 0.72 (0.46–1.12), 0.144 | 0.39 (0.16–0.92), 0.032 | 0.69 (0.48–0.99), 0.043 | 0.71 (0.50–1.01), 0.058 |
LNM | (-)/ (+) | 1.27 (0.59–2.71), 0.541 | 1.11 (0.77–1.59), 0.577 | 1.13 (0.8–1.59), 0.495 | 1.22 (0.58–2.57), 0.605 | 1.12 (0.84–1.48), 0.448 | 1.12 (0.84–1.48), 0.434 |
Stage | Ⅰ-Ⅱ/Ⅲ-Ⅳ | 1.32 (0.58–2.98), 0.506 | 1.16 (0.79–1.72), 0.454 | 1.18 (0.81–1.72), 0.386 | 1.24 (0.56–2.76), 0.594 | 1.16 (0.85–1.57), 0.359 | 1.15 (0.85–1.56), 0.364 |
ER | (-)/ (+) | 0.88 (0.38–2.01), 0.759 | 0.92 (0.62–1.35), 0.660 | 0.91 (0.63–1.33), 0.627 | 0.91 (0.40–2.05), 0.818 | 0.93 (0.68–1.26), 0.625 | 0.93 (0.69–1.27), 0.658 |
PR | (-)/ (+) | 0.96 (0.44–2.09), 0.910 | 0.87 (0.60–1.25), 0.448 | 0.88 (0.62–1.25), 0.470 | 1.01 (0.47–2.18), 0.981 | 0.92 (0.69–1.22), 0.557 | 0.93 (0.70–1.24), 0.628 |
HER2 | (-)/ (+) | 1.11 (0.35–3.51), 0.857 | 0.71 (0.43–1.16), 0.173 | 0.75 (0.46–1.21), 0.233 | 1.27 (0.41–3.95), 0.675 | 0.85 (0.57–1.26), 0.407 | 0.86 (0.58–1.27), 0.447 |
Ki-67 | < 10%/≥ 10% | 1.80 (0.59–5.44), 0.300 | 1.06 (0.69–1.62), 0.786 | 1.12 (0.74–1.69), 0.589 | 1.76 (0.59–5.26), 0.314 | 1.16 (0.82–1.64), 0.411 | 1.18 (0.84–1.67), 0.345 |
rs6788033 | Tumour size | < 2 cm/≥ 2 cm | 1.12 (0.43–2.96), 0.813 | 1.29 (0.81–2.07), 0.282 | 1.27 (0.81–1.99), 0.297 | 1.02 (0.39–2.64), 0.973 | 1.18 (0.81–1.72), 0.384 | 1.19 (0.82–1.72), 0.360 |
LNM | (-)/ (+) | 0.56 (0.24–1.32), 0.183 | 1.02 (0.71–1.45), 0.924 | 0.95 (0.68–1.35), 0.791 | 0.56 (0.24–1.29), 0.172 | 0.90 (0.67–1.20), 0.474 | 0.90 (0.68–1.20), 0.473 |
Stage | Ⅰ-Ⅱ/Ⅲ-Ⅳ | 0.33 (0.10–1.14), 0.079 | 1.02 (0.69–1.50), 0.941 | 0.92 (0.63–1.35), 0.685 | 0.33 (0.10–1.12), 0.076 | 0.85 (0.61–1.17), 0.317 | 0.85 (0.62–1.16), 0.302 |
ER | (-)/ (+) | 1.39 (0.54–3.58), 0.500 | 1.02 (0.69–1.50), 0.933 | 1.05 (0.72–1.53), 0.795 | 1.38 (0.54–3.52), 0.503 | 1.08 (0.78–1.48), 0.645 | 1.07 (0.78–1.47), 0.660 |
PR | (-)/ (+) | 1.72 (0.70–4.26), 0.239 | 1.11 (0.77–1.60), 0.572 | 1.16 (0.82–1.65), 0.401 | 1.66 (0.68–4.05), 0.269 | 1.19 (0.88–1.60), 0.268 | 1.17 (0.88–1.57), 0.286 |
HER2 | (-)/ (+) | 0.52 (0.17–1.62), 0.259 | 0.78 (0.47–1.28), 0.325 | 0.75 (0.46–1.21), 0.234 | 0.57 (0.19–1.76), 0.330 | 0.75 (0.50–1.13), 0.175 | 0.78 (0.53–1.16), 0.215 |
Ki-67 | < 10%/≥ 10% | 0.50 (0.21–1.20), 0.119 | 0.66 (0.44–1.01), 0.054 | 0.64 (0.43–0.96), 0.030 | 0.59 (0.25–1.39), 0.225 | 0.68 (0.49–0.95), 0.024 | 0.69 (0.50–0.95), 0.025 |
SNP, single nucleotide polymorphism; OR, odds ratio; 95% CI, 95% confidence interval; ER, estrogen receptor; RP, progesterone receptor; HER2, human epidermal growth factor receptor 2; LNM, lymph node metastasis. |
p values were calculated by logistic regression analysis with adjustments for age. |
p < 0.05 indicates statistical significance. |
Figure 1 represented the reconstructed LD plot, and had three blocks in LRRC3B SNPs (Block 1, rs112276562 and rs6790894; Block 2, rs6551121, rs6551122, rs1907168 and rs73150416; and Block 3, rs12635768, rs6551130, rs78205284 and rs6788033). Moreover, ‘GATT’ haplotype in the Block 2 had a higher risk for BC (OR = 1.29, 95% CI: 1.00-1.65, p = 0.048, Supplementary Table 4).
According to GEPIA database, LRRC3B gene was down-regulated in BC (p < 0.01, Supplementary Fig. 1). Kaplan–Meier plotter showed high expression of LRRC3B was related to better BC overall survival (HR = 0.83, 95% CI: 0.71–0.97, p = 0.017, Supplementary Fig. 2). We speculated that LRRC3B is a tumor suppressor gene, but more convincing studies are needed to validate the conclusions because these clinical data are from the database.