| Literature DB >> 31040692 |
Yan Qu1, Na Shao2, Wenjing Yang1, Jianbo Wang1, Yufeng Cheng1.
Abstract
OBJECTIVE: The main aim of this study was to investigate the association of polymorphisms in long non-coding RNA metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) with the risk of esophageal squamous cell carcinoma (ESCC) in a Chinese population.Entities:
Keywords: MALAT1; esophageal squamous cell carcinoma; polymorphism; single nucleotide polymorphism; susceptibility
Year: 2019 PMID: 31040692 PMCID: PMC6452823 DOI: 10.2147/OTT.S191155
Source DB: PubMed Journal: Onco Targets Ther ISSN: 1178-6930 Impact factor: 4.147
Logistic regression analysis for associations between selected SNPs and risk of ESCC
| Genotype | Cases | Controls | Crude OR | Adjusted OR | ||
|---|---|---|---|---|---|---|
| rs3200401 | ||||||
| CC | 148 | 338 | Ref | Ref | ||
| CT | 79 | 133 | 0.017 | 1.60 (1.09–2.35) | 1.59 (1.07–2.35) | |
| TT | 18 | 19 | 0.026 | 2.39 (1.11–5.14) | 2.27 (1.04–4.96) | |
| Dominant | ||||||
| CC | 148 | 338 | Ref | Ref | ||
| CT+TT | 97 | 152 | 0.004 | 1.70 (1.18–2.45) | 1.68 (1.16–2.43) | |
| Recessive | ||||||
| CC+CT | 227 | 471 | Ref | Ref | ||
| TT | 18 | 19 | 0.059 | 2.06 (0.97–4.36) | 0.084 | 1.96 (0.91–4.20) |
| rs1122709 | ||||||
| CC | 123 | 269 | Ref | Ref | ||
| CG | 105 | 198 | 0.558 | 1.11 (0.78–1.57) | 0.574 | 1.11 (0.78–1.57) |
| GG | 17 | 23 | 0.071 | 2.07 (0.94–4.57) | 0.092 | 2.01 (0.89–4.52) |
| Dominant | ||||||
| CC | 123 | 269 | Ref | Ref | ||
| CG+GG | 122 | 221 | 0.344 | 1.18 (0.84–1.65) | 0.370 | 1.17 (0.83–1.65) |
| Recessive | ||||||
| CC+CG | 228 | 467 | Ref | Ref | ||
| GG | 17 | 23 | 0.086 | 0.51 (0.23–1.10) | 0.110 | 0.52 (0.24–1.16) |
| rs664589 | ||||||
| CC | 106 | 205 | Ref | Ref | ||
| CG | 117 | 236 | 0.351 | 1.37 (0.71–2.62) | 0.466 | 1.28 (0.66–2.50) |
| GG | 22 | 49 | 0.656 | 1.15 (0.62–2.16) | 0.832 | 1.07 (0.56–2.04) |
| Dominant | ||||||
| CC | 106 | 205 | Ref | Ref | ||
| CG+GG | 139 | 285 | 0.310 | 1.21 (0.84–1.74) | 0.325 | 1.21 (0.83–1.76) |
| Recessive | ||||||
| CC+CG | 223 | 441 | Ref | Ref | ||
| GG | 22 | 49 | 0.510 | 0.81 (0.44–1.50) | 0.664 | 0.87 (0.47–1.63) |
| rs619586 | ||||||
| AA | 85 | 177 | Ref | Ref | ||
| AG | 132 | 248 | 0.619 | 0.90 (0.58–1.38) | 0.691 | 0.92 (0.59–1.41) |
| GG | 28 | 65 | 0.799 | 0.93 (0.51–1.68) | 0.968 | 1.01 (0.55–1.87) |
| Dominant | ||||||
| AA | 85 | 177 | Ref | Ref | ||
| AG+GG | 160 | 313 | 0.626 | 0.90 (0.60–1.36) | 0.755 | 0.94 (0.62–1.42) |
| Recessive | ||||||
| AA+AG | 217 | 425 | Ref | Ref | ||
| GG | 28 | 65 | 0. 964 | 0.99 (0.58–1.69) | 0.814 | 1.07 (0.62–1.85) |
Notes:
P-value and crude ORa: conditional logistic regression.
P-value and adjusted ORb: conditional logistic regression with adjustment for smoking status and alcohol use.
Significant P-values (P<0.05). Significant P-values (FDR <0.25) are given in bold after being adjusted by FDR; FDR = *,a0.168, *,b0.208, *,c0.096.
Abbreviations: ESCC, esophageal squamous cell carcinoma; SNP, single nucleotide polymorphism; FDR, false discovery rate.
Stratified analysis for associations between variant genotype of rs3200401 and ESCC risk
| Variables | rs3200401 C > T (ESCC/control) | Adjusted OR (95% CI); | |||||||
|---|---|---|---|---|---|---|---|---|---|
| CC | CT | TT | CT+TT | CC | CT | TT | CT+TT | TT vs (CT+CC) | |
| Smoking | |||||||||
| Ever | 46/98 | 26/37 | 4/3 | 30/40 | 1.00 | 1.69 (0.88–3.26) | 2.79 (0.54–14.38) | 1.78 (0.95–3.35) | 2.36 (0.47–11.95) |
| Never | 102/240 | 53/96 | 14/16 | 67/112 | 1.00 | 0.49 (0.23–1.03) | 0.63 (0.29–1.40) | 1.41 (0.96–2.06) | 1.90 (0.90–3.99) |
| Drinking | |||||||||
| Ever | 59/100 | 30/38 | 6/6 | 36/44 | 1.00 | 0.52 (0.16–1.75) | 0.73 (0.21–2.58) | 0.68 (0.39–1.20) | 1.72 (0.52–5.67) |
| Never | 89/238 | 49/95 | 12/13 | 61/10 | 1.00 | 1.40 (0.92–2.14) | 2.34 (1.02–5.34) | 1.52 (1.02–2.26) | 2.10 (0.93–4.74) |
Notes: P-value and adjusted OR: binary logistic regression with adjustment for smoking status and alcohol use (besides accordingly stratified factors).
Significant values (P<0.05). Significant P-values (FDR <0.25) are given in bold after being adjusted by FDR; FDR = *,a0.208, *,b0.208.
Abbreviations: ESCC, esophageal squamous cell carcinoma; FDR, false discovery rate.
Stratified analysis for associations between variant genotype of rs619586 and ESCC risk
| Variables | rs619586 A > G (ESCC/control) | Adjusted OR (95% CI); | |||||||
|---|---|---|---|---|---|---|---|---|---|
| AA | AG | GG | AG+GG | AA | AG | GG | AG + GG | GG vs (AG+AA) | |
| Smoking | |||||||||
| Ever | 25/39 | 43/74 | 8/25 | 51/99 | 1.00 | 0.68 (0.34–1.34) | 0.41 (0.15–1.12) | 0.61 (0.32–1.18) | 0.53 (0.22–1.30) |
| Never | 60/138 | 89/174 | 20/40 | 109/214 | 1.00 | 1.18 (0.79–1.75) | 1.16 (0.62–2.14) | 1.18 (0.80–1.72) | 1.05 (0.59–1.86) |
| Drinking | |||||||||
| Ever | 31/42 | 56/78 | 8/24 | 64/102 | 1.00 | 0.84 (0.46–1.52) | 0.38 (0.15–0.99) | 0.73 (0.41–1.31) | 2.32 (0.98–5.52) |
| Never | 54/135 | 76/170 | 20/41 | 96/211 | 1.00 | 1.12 (0.74–1.71) | 1.30 (0.69–2.43) | 1.16 (0.78–1.72) | 1.21 (0.68–2.16) |
Notes: P-value and adjusted OR: binary logistic regression with adjustment for smoking status and alcohol use (besides accordingly stratified factors).
Significant values (P<0.05). No significant P-values (FDR <0.25) are found after being adjusted by FDR.
Abbreviations: ESCC, esophageal squamous cell carcinoma; FDR, false discovery rate.
Primary information of selected SNPs for lncRNA MALAT1
| SNP | Primer | Primer sequence | Base change | Location in the chromosome | MAF in our controls | HWE |
|---|---|---|---|---|---|---|
|
| ||||||
| rs3200401 | Forward | GGGTGCCTG | C > T | 65,504,361 | 0.174 | 0.201 |
| TGGGGTTTT | ||||||
| Reverse | CCACCACCAGA | |||||
| AATGAACAAAA | ||||||
| rs11227209 | Forward | TTTTAGCAAC | C > G | 65,497,960 | 0.249 | 0.075 |
| GCAGAAGCCC | ||||||
| Reverse | TGTTATGCCTGG | |||||
| TTAGGTATGAGC | ||||||
| rs664589 | Forward | CTGTTGGCAC | C > G | 65,501,878 | 0.341 | 0.178 |
| GAACACCTTC | ||||||
| Reverse | TGGTACACCCA | |||||
| GTGGCTCATA | ||||||
| rs619586 | Forward | TGGGAGCAA | A > G | 65,498,698 | 0.386 | 0.132 |
| GTCGCAGGA | ||||||
| Reverse | GAGAACAACT | |||||
| CGCATCACCG | ||||||
Abbreviations: HWE, Hardy–Weinberg equilibrium; MAF, minor allele frequency; SNP, single nucleotide polymorphism; lncRNA, long non-coding RNA.
Selected characteristics in ESCC cases and controls
| Variables | Cases (N=245, n [%]) | Controls (N=490, n [%]) | |||
|---|---|---|---|---|---|
| Age (years) | 61.50 (39–79) | 62.00 (39–79) | 0.999 | ||
| ≥60 | 140 | 56.91% | 280 | 57.14% | |
| <60 | 105 | 43.09% | 210 | 42.86% | |
| Gender | 0.999 | ||||
| Male | 185 | 75.61% | 370 | 75.51% | |
| Female | 60 | 24.39% | 120 | 24.49% | |
| Smoking | 0.439 | ||||
| Ever | 76 | 30.89% | 138 | 28.16% | |
| Never | 169 | 69.11% | 352 | 71.84% | |
| Drinking | 0.012 | ||||
| Ever | 95 | 38.62% | 144 | 29.39% | |
| Never | 150 | 61.38% | 346 | 70.61% | |
Notes:
Two-sided chi-squared test.
Significant values (P<0.05).
Abbreviation: ESCC, esophageal squamous cell carcinoma.
Stratified analysis for associations between variant genotype of rs1122709 and ESCC risk
| Variables | rs1122709 C > G (ESCC/control) | Adjusted OR (95% CI); | |||||||
|---|---|---|---|---|---|---|---|---|---|
| CC | CG | GG | CG+GG | CC | CG | GG | CG+GG | GG vs (CG+CC) | |
| Smoking | |||||||||
| Ever | 37/85 | 32/49 | 7/4 | 39/53 | 1.00 | 1.30 (0.69–2.42) | 3.33 (0.86–12.97) | 1.45 (0.80–2.64) | 2.99 (0.79–11.36) |
| Never | 86/184 | 73/149 | 10/19 | 83/168 | 1.00 | 1.04 (0.71–1.52) | 1.12 (0.50–2.50) | 0.95 (0.66–1.38) | 1.10 (0.50–2.41) |
| Drinking | |||||||||
| Ever | 49/182 | 40/55 | 6/7 | 46/62 | 1.00 | 1.14 (0.66–1.99) | 1.25 (0.39–4.06) | 1.15 (0.68–1.97) | 1.18 (0.37–3.74) |
| Never | 74/187 | 65/143 | 11/16 | 76/158 | 1.00 | 1.09 (0.73–1.63) | 1.62 (0.72–3.68) | 1.14 (0.78–1.69) | 0.64 (0.29–1.42) |
Notes: P-value and adjusted OR: binary logistic regression with adjustment for smoking status and alcohol use (besides accordingly stratified factors).
Significant values (P<0.05).
Abbreviation: ESCC, esophageal squamous cell carcinoma.
Stratified analysis for associations between variant genotype of rs664589 and ESCC risk
| Variables | rs664589 C > G (ESCC/control) | Adjusted OR (95% CI); | |||||||
|---|---|---|---|---|---|---|---|---|---|
| CC | CG | GG | CG+GG | CC | CG | GG | CG+GG | GG vs (CG+CC) | |
| Smoking | |||||||||
| Ever | 37/67 | 31/62 | 8/9 | 39/71 | 1.00 | 0.95 (0.51–1.78) | 1.43 (0.48–4.27) | 1.02 (0.56–1.85) | 1.46 (0.51–4.20) |
| Never | 69/138 | 86/174 | 14/40 | 100/214 | 1.00 | 1.42 (0.72–2.79) | 1.41 (0.73–2.74) | 0.94 (0.65–1.37) | 0.71 (0.37–1.34) |
| Drinking | |||||||||
| Ever | 39/57 | 47/70 | 9/17 | 56/87 | 1.00 | 1.16 (0.65–2.05) | 0.86 (0.34–2.19) | 1.10 (0.63–1.90) | 0.80 (0.33–1.91) |
| Never | 67/148 | 70/166 | 13/32 | 83/198 | 1.00 | 0.91 (0.61–1.37) | 0.85 (0.42–1.72) | 0.90 (0.61–1.33) | 0.87 (0.45–1.75) |
Notes: P-value and adjusted OR: binary logistic regression with adjustment for smoking status and alcohol use (besides accordingly stratified factors).
Significant values (P<0.05).
Abbreviation: ESCC, esophageal squamous cell carcinoma.