- Email: [email protected]
LAMP3 and sporadic PD in the Chinese Han population
Neuroscience Letters 566 (2014) 206–209
Contents lists available at ScienceDirect
Neuroscience Letters journal homepage: www.elsevier.com/locate/neulet
Association analysis of STK39, MCCC1/LAMP3 and sporadic PD in the Chinese Han population Ya-qin Wang a , Bei-sha Tang a,b,c,d , Ri-li Yu a , Kai Li a , Zhen-hua Liu a , Qian Xu a,c,d , Qi-ying Sun a,c , Xin-xiang Yan a,c , Ji-feng Guo a,b,c,d,∗ a
Department of Neurology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, People’s Republic of China State Key Laboratory of Medical Genetics, Changsha 410008, Hunan, People’s Republic of China c Human Key Laboratory of Neurodegenerative Disorders, Central South University, Changsha 410008, Hunan, People’s Republic of China d Neurodegenerative Disorders Research Center, Central South University, Changsha 410008, Hunan, People’s Republic of China b
h i g h l i g h t s • The first polymorphism analysis of SNPs in the STK39 and MCCC1/LAMP3 in a Chinese Han population. • SNP rs11711441 has strong association with Chinese PD. • No association with Chinese PD was observed in the SNPs of rs2102808, rs3754775 and rs12493050.
a r t i c l e
i n f o
Article history: Received 17 December 2013 Received in revised form 2 March 2014 Accepted 4 March 2014 Keywords: Parkinson’s disease SNP GWAS
a b s t r a c t With the completion of the Human Genome Project, GWAS have been widely used in exploring the genetic studies of complex diseases. A meta-analysis of datasets from five Parkinson’s disease GWAS from the USA and Europe found 11 loci that surpassed the threshold for genome-wide significance (p < 5 × 10−8 ), and five were newly identified loci (ACMSD, STK39, MCCC1/LAMP3, SYT11 and CCDC62/HIP1R). Another GWAS of the Ashkenazi Jewish population also identified loci in STK39 and LAMP3. Because the association between the STK39 and MCCC1/LAMP3 genes and PD was confirmed in different populations, we conducted a case-control cohort to clarify the association between the four single nucleotide polymorphism (SNP) loci (rs2102808 and rs3754775 in the STK39; rs11711441 and rs12493050 in the MCCC1/LAMP3) and PD in the Chinese Han population. Polymerase chain reaction and direct DNA sequencing analyses were used to detect the four variations in a case-control cohort comprised of 993 ethnic Chinese subjects. We found that in the detection of the rs11711441, there was a significant difference between ungrouped populations, early-onset PD, late-onset PD, male PD, female PD and the corresponding control group in allele and genotype frequency (p < 0.001, OR < 1). In the detection of the rs2102808, rs3754775 and rs12493050, ungrouped populations, early-onset PD, late-onset PD, male PD or female PD with the corresponding control group showed no significant difference in allele and genotype frequency (p > 0.0125). Our findings suggested that the allele G of rs11711441 of the MCCC1/LAMP3 gene can decrease the risk of PD in Chinese population. No statistically significant difference in genotype frequency between cases and controls was observed for the other three SNPs. © 2014 Elsevier Ireland Ltd. All rights reserved.
1. Introduction Parkinson’s disease (PD) is the second most frequent neurodegenerative disorder, and its clinical features include resting tremor, rigidity, bradykinesia and impaired postural reflexes and a vari-
∗ Corresponding author at: Central South University, Department of Neurology, Xiangya Hospital, Changsha 410008, Hunan, People’s Republic of China. Tel.: +86 731 84327398; fax: +86 731 84327332. E-mail addresses: [email protected], [email protected] (J.-f. Guo). http://dx.doi.org/10.1016/j.neulet.2014.03.007 0304-3940/© 2014 Elsevier Ireland Ltd. All rights reserved.
ety of psychiatric symptoms. Its pathological features are the loss of dopaminergic neurons in the substantia nigra of the midbrain and the presence of Lewy bodies [12]. However, researchers have not yet determined the exact pathogeny of the disease. Until now, at least 13 genes and an additional five loci involved in familial and sporadic forms have been described (named PARK1-PARK18). With the completion of the Human Genome Project, GWAS have been widely used in exploring the genetics of complex diseases, such as cancer, diabetes and Parkinson’s disease [1,2,5,10,16]. So far, GWAS of Parkinson’s disease in various populations has found dozens of single nucleotide polymorphisms associated
Y.-q. Wang et al. / Neuroscience Letters 566 (2014) 206–209
207
Table 1 PCR primers of the four loci. SNP
F-primer
R-primer
rs2102808 rs3754775 rs11711441 rs12493050
5 -AGTTCAGAAGGGCTCAG-3 5 -TTTTCTCCATTCCTGTCCGTA-3 5 -GATTAGCCTAGATTAGCTAGATAC-3 5 -TCCTTACCACCTGATTGA-3
5 -CCATACATCTGGGAAAT-3 5 -GCAGCAACTTATCCTTCATCTTAG-3 5 -GAACCTTTACGTCTAGCTCAGGG-3 5 -AGAGTGCTCATCTCCCTA-3
Table 2 Genotype and allele frequencies of the four SNPs in cases and controls in the Chinese Han population. SNP
N
rs2102808 PD Controls rs3754775 PD Controls rs11711441 PD Controls rs12493050 PD Controls
Genotype GG 207(41.3%) 227(46.1%) GG 309(61.7%) 289(58.7%) GG 409(81.6%) 409(81.6%) AA 276(55.1%) 275(55.9%)
GT 294(58.7%) 265(53.9%) GA 167(33.3%) 184(37.4%) GA 87(17.4%) 87(17.4%) AG 185(36.9%) 185(37.6%)
TT 0 0 AA 25(5.0%) 19(3.9%) AA 5(1.0%) 5(1.0%) GG 40(8.0%) 32(6.5%)
with PD, although most of them have not been acknowledged [6,14,15]. A meta-analysis of datasets from five Parkinson’s disease GWAS from the USA and Europe found 11 loci that surpassed the threshold for genome-wide significance (p < 5 × 10−8 ). Five were newly identified loci, including the STK39 (rs2102808) and LAMP3 (rs11711441) genes [10]. Another GWAS of the Ashkenazi Jewish population also identified loci, including the STK39 (rs3754775) and LAMP3 (rs12493050) genes [8]. Because the association between the STK39 and MCCC1/LAMP3 genes and PD was confirmed in different populations, we suspected that these two genes were likely candidate genes for PD. Considering that there is no such research available in our population, we conducted a case-control cohort study to clarify the association between the four single nucleotide polymorphism (SNP) loci (rs2102808 and rs3754775 in STK39; rs11711441 and rs12493050 in MCCC1/LAMP3) and PD in the Chinese Han population.
P(OR)
Allele
CI 0.125(1.220) 0.947–1.573
G 708(70.7%) 719(73.1%) G 785(78.3%) 762(77.4%) G 905(90.3%) 787(80.0%) A 737(73.6%) 735(74.7%)
0.620(0.947) 0.763–1.175 <0.001(0.396) 0.300–0.522 0.570(1.059) 0.868–1.292
P(OR) T 294(29.3%) 265(26.9%) A 217(21.7%) 222(22.6%) A 97(9.7%) 197(20.0%) G 265(26.4%) 249(25.3%)
CI 0.255(1.121) 0.921–1.364 0.665(0.954) 0.771–1.180 <0.001(0.430) 0.331–0.559 0.564(1.061) 0.867–1.298
2. Materials and methods 2.1. Patients and controls Our study was comprised of 501 patients with PD and 492 age- and gender-matched controls. The mean age at onset was 54.77 ± 12.05 years (35–91 years old). All patients were consecutively recruited in only one center: Xiangya Hospital, Central South University. PD was diagnosed using established clinical criteria [7]. This study protocol was approved by the Ethics Committee of Central South University, and written informed consent was obtained from all subjects. 2.2. Genotyping Genotyping was performed in all cases and controls using polymerase chain reaction and direct DNA sequencing analysis. PCR amplification was carried out in a total volume of 10 l. PCR primer pairs are described in Table 1.
Table 3 Genotype and allele frequencies of the four SNPs in EOPD/LOPD and controls in the Chinese Han population. SNP rs2102808 EOPD Controls LOPD Controls rs3754775 EOPD Controls LOPD Controls rs11711441 EOPD Controls LOPD Controls rs12493050 EOPD Controls LOPD Controls
N 166 151 335 340 166 151 335 340 166 151 335 340 166 151 335 340
Genotype GG 72(0.434) 64(0.424) 135(0.403) 162(0.476) GG 100(0.603) 90(0.596) 209(0.624) 198(0.582) GG 131(0.789) 86(0.570) 278(0.830) 217(0.638) AA 82(0.494) 85(0.563) 194(0.579) 190(0.559)
GT 94(0.566) 87(0.576) 200(0.597) 178(0.524) GA 61(0.367) 55(0.364) 106(0.316) 128(0.376) GA 33(0.199) 63(0.417) 54(0.161) 120(0.353) AG 65(0.392) 55(0.364) 120(0.358) 130(0.382)
TT 0 0 0 0 AA 5(0.03) 6(0.04) 20(0.06) 14(0.042) AA 2(0.012) 2(0.013) 3(0.009) 5(0.015) GG 19(0.114) 11(0.073) 21(0.063) 20(0.059)
P(OR)
Allele
CI 0.395(0.816)
G 238(0.717) 218(0.722) 470(0.701) 502(0.738) G 261(0.786) 235(0.785) 524(0.782) 524(0.771) G 295(0.889) 235(0.778) 610(0.859) 554(0.815) A 229(0.690) 225(0.745) 508(0.758) 510(0.750)
0.080(1.319)
0.882(0.969) 0.643–1.460 0.500(0.914) 0.705–1.186 <0.001(0.377) 0.232–0.612 <0.001(0.403) 0.285–0.569 0.163(1.282) 0.904–1.819 0.664(0.946) 0.736–1.215
P(OR) T 94(0.283) 87(0.278) 200(0.299) 178(0.262) A 71(0.214) 67(0.215) 146(0.218) 156(0.229) A 37(0.111) 67(0.222) 60(0.141) 130(0.185) G 103(0.310) 77(0.255) 162(0.242) 172(0.250)
CI 0.567(0.901) 0.187(1.177)
0.720(0.931) 0.631–1.375 0.585(0.930) 0.716–1.207 <0.001(0.403) 0.257–0.632 <0.001(0.438) 0.314–0.611 0.131(1.319) 0.921–1.888 0.643(0.941) 0.732–1.209
208
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Table 4 Genotype and allele frequencies of the four SNPs in male PD/female PD and controls in the Chinese Han population. SNP rs2102808 Male PD Controls Female PD Controls rs3754775 Male PD Controls Female PD Controls rs11711441 Male PD Controls Female PD Controls rs12493050 Male PD Controls Female PD Controls
N 274 300 227 292 274 300 227 292 274 300 227 292 274 300 227 292
Genotype GG 117(0.427) 144(0.480) 90(0.396) 83(0.432) GG 164(0.599) 176(0.587) 145(0.639) 113(0.589) GG 225(0.821) 176(0.587) 184(0.811) 126(0.656) AA 140(0.511) 172(0.573) 136(0.599) 103(0.536)
GT 157(0.573) 156(0.520) 137(0.604) 109(0.568) GA 97(0.354) 114(0.380) 70(0.308) 70(0.365) GA 45(0.164) 120(0.400) 42(0.184) 63(0.328) AG 110(0.401) 112(0.373) 75(0.330) 73(0.380)
TT 0 0 0 0 AA 13(0.047) 10(0.033) 12(0.053) 9(0.046) AA 4(0.015) 4(0.013) 1(0.004) 3(0.016) GG 24(0.088) 16(0.054) 16(0.071) 16(0.084)
Each PCR product was purified and directly sequenced on an ABI 3100 automated sequencer (Applied Biosystems, Foster City, CA). Alignment and analysis was carried out with DNAStar (DNAStar, Inc, Madison, WI). All subjects were successfully genotyped. Moreover, 15% of samples were randomly selected for replication assays, the results of which were completely concordant with our original results. 2.3. Statistical analysis The allele and genotype frequencies of the PD and control groups were analysed using a Chi-square test with SPSS 17.0 software (SPSS Inc., Chicago, IL, USA). A p-value of <0.05 using a two-tailed test was considered to be statistically significant. 3. Results Genotype and allele frequencies for all subjects are shown in Tables 2–4. These four SNPs were in agreement with Hardy–Weinberg equilibrium in both the patient and control groups, and the two SNPs in one gene were not in linkage disequilibrium. Significant differences in the genotype and allele frequencies of the SNP rs11711441 were observed between cases and controls (p < 0.001, p < 0.001). Statistically significant differences in the genotype frequency between the early-onset and late-onset groups with controls were observed (p < 0.001, p < 0.001). Statistically significant differences in the genotype frequency between male cases and female cases with controls were observed (p < 0.001, p < 0.001). No statistically significant differences in the other three SNPs of genotype frequency between PD, EOPD, LOPD, male PD or female PD with the controls were observed. 4. Discussion The first meta-analysis of datasets from five Parkinson’s disease GWAS from the USA and Europe identified loci including the STK39 (rs2102808) and LAMP3 (rs11711441) genes. Later, another GWAS of the Ashkenazi Jewish population also identified loci, including the STK39 (rs3754775) and LAMP3 (rs12493050) genes. These results suggest a consistent association between the two genes and PD in different racial types. To detect the association in Chinese Han population, we conducted a replication analysis to verify the four SNPs. Our results demonstrated that statistically significant differences in genotype frequency and allele frequency for rs11711441
P(OR)
Allele
CI 0.206(1.237) 0.890–1.720 0.443(1.165) 0.788–1.722
G 391(71.4%) 444(74.0%) 317(69.8%) 275(71.6%) G 425(77.6%) 466(77.5%) 360(79.3%) 296(77.1%) G 495(90.3%) 472(78.7%) 410(90.5%) 315(82.0%) A 390(0.712) 456(0.760) 347(0.764) 279(0.727)
0.934(1.012) 0.760–1.348 0.397(0.868) 0.626–1.204 <0.001(0.358) 0.248–0.516 <0.001(0.456) 0.297–0.700 0.071(1.276) 0.979–1.663 0.228(0.830) 0.613–1.124
P(OR) T 157(28.6%) 156(26.0%) 137(30.2%) 109(28.4%) A 123(22.4%) 134(22.5%) 94(20.7% 88(22.9%) A 53(9.7%) 128(21.3%) 44(9.5%) 69(18.0%) G 158(0.288) 144(0.240) 107(0.236) 105(0.273)
CI 0.317(1.142) 0.880–1.481 0.558(1.094) 0.811–1.475 0.936(1.011) 0.766–1.336 0.444(0.879) 0.633–1.222 <0.001(0.394) 0.279–0.556 0.001(0.487) 0.325–0.732 0.071(1.275) 0.980–1.660 0.213(0.820) 0.600–1.121
between cases and controls was observed, which were stratified by age of onset and gender; however, differences were not observed for the other three SNPs. STK39 is abundant in the brain and pancreas, and the gene has been associated with autism, hypertension and inflammation. There have also been reports of the association with neurodegenerative disease [3,4,11]. Compared to STK39, the function of LAMP3 is less understood. It might partly cause the modulation of neuronal and neurosecretory functions in PC12 cell lines [9], and similar to STK39, it was not found to contribute to neurodegenerative disease. For the MCCC1, its product is part of MCC, which is a biotindependent carboxylase that catalyses the fourth step in the leucine catabolic pathway and is inherited as an autosomal recessive trait [13]. In summary, there is no biological evidence concerning the association of the two genes and Parkinson’s disease. Our study confirms the association of the loci rs11711441 near STK39 and sporadic PD in the Chinese Han population. We found that the variant decreases the risk of PD approximately 0.396-fold. However, there are several limitations that we cannot ignore. First, this is a clinic-based rather than a community-based study. Second, the number of EOPD patients is small in comparison with LOPD in our study. Some ascertainment bias of the PD patients might also be produced. Third, the sample size was moderate, which limited the statistical power of our study. We arrived at the conclusion in a statistical manner, without any biological evidence. In future works, well-designed studies in populations with different ethnic or geographic origins and further functional assays should be conducted to further evaluate the potential association between SNP and PD.
Conflicts of interest The authors have no actual or potential conflicts of interest to report.
Acknowledgments This work was supported by a grant from the Major State Basic Research Development Program of China (973 Program) (2011CB510001) and a grant from the National Natural Science Foundation of China (30900469, 81171198, 81200870, 81000542, 81130021, 81371405, 81361120404). We would like to thank the family for their participation in this study.
Y.-q. Wang et al. / Neuroscience Letters 566 (2014) 206–209
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Contents lists available at ScienceDirect
Neuroscience Letters journal homepage: www.elsevier.com/locate/neulet
Association analysis of STK39, MCCC1/LAMP3 and sporadic PD in the Chinese Han population Ya-qin Wang a , Bei-sha Tang a,b,c,d , Ri-li Yu a , Kai Li a , Zhen-hua Liu a , Qian Xu a,c,d , Qi-ying Sun a,c , Xin-xiang Yan a,c , Ji-feng Guo a,b,c,d,∗ a
Department of Neurology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, People’s Republic of China State Key Laboratory of Medical Genetics, Changsha 410008, Hunan, People’s Republic of China c Human Key Laboratory of Neurodegenerative Disorders, Central South University, Changsha 410008, Hunan, People’s Republic of China d Neurodegenerative Disorders Research Center, Central South University, Changsha 410008, Hunan, People’s Republic of China b
h i g h l i g h t s • The first polymorphism analysis of SNPs in the STK39 and MCCC1/LAMP3 in a Chinese Han population. • SNP rs11711441 has strong association with Chinese PD. • No association with Chinese PD was observed in the SNPs of rs2102808, rs3754775 and rs12493050.
a r t i c l e
i n f o
Article history: Received 17 December 2013 Received in revised form 2 March 2014 Accepted 4 March 2014 Keywords: Parkinson’s disease SNP GWAS
a b s t r a c t With the completion of the Human Genome Project, GWAS have been widely used in exploring the genetic studies of complex diseases. A meta-analysis of datasets from five Parkinson’s disease GWAS from the USA and Europe found 11 loci that surpassed the threshold for genome-wide significance (p < 5 × 10−8 ), and five were newly identified loci (ACMSD, STK39, MCCC1/LAMP3, SYT11 and CCDC62/HIP1R). Another GWAS of the Ashkenazi Jewish population also identified loci in STK39 and LAMP3. Because the association between the STK39 and MCCC1/LAMP3 genes and PD was confirmed in different populations, we conducted a case-control cohort to clarify the association between the four single nucleotide polymorphism (SNP) loci (rs2102808 and rs3754775 in the STK39; rs11711441 and rs12493050 in the MCCC1/LAMP3) and PD in the Chinese Han population. Polymerase chain reaction and direct DNA sequencing analyses were used to detect the four variations in a case-control cohort comprised of 993 ethnic Chinese subjects. We found that in the detection of the rs11711441, there was a significant difference between ungrouped populations, early-onset PD, late-onset PD, male PD, female PD and the corresponding control group in allele and genotype frequency (p < 0.001, OR < 1). In the detection of the rs2102808, rs3754775 and rs12493050, ungrouped populations, early-onset PD, late-onset PD, male PD or female PD with the corresponding control group showed no significant difference in allele and genotype frequency (p > 0.0125). Our findings suggested that the allele G of rs11711441 of the MCCC1/LAMP3 gene can decrease the risk of PD in Chinese population. No statistically significant difference in genotype frequency between cases and controls was observed for the other three SNPs. © 2014 Elsevier Ireland Ltd. All rights reserved.
1. Introduction Parkinson’s disease (PD) is the second most frequent neurodegenerative disorder, and its clinical features include resting tremor, rigidity, bradykinesia and impaired postural reflexes and a vari-
∗ Corresponding author at: Central South University, Department of Neurology, Xiangya Hospital, Changsha 410008, Hunan, People’s Republic of China. Tel.: +86 731 84327398; fax: +86 731 84327332. E-mail addresses: [email protected], [email protected] (J.-f. Guo). http://dx.doi.org/10.1016/j.neulet.2014.03.007 0304-3940/© 2014 Elsevier Ireland Ltd. All rights reserved.
ety of psychiatric symptoms. Its pathological features are the loss of dopaminergic neurons in the substantia nigra of the midbrain and the presence of Lewy bodies [12]. However, researchers have not yet determined the exact pathogeny of the disease. Until now, at least 13 genes and an additional five loci involved in familial and sporadic forms have been described (named PARK1-PARK18). With the completion of the Human Genome Project, GWAS have been widely used in exploring the genetics of complex diseases, such as cancer, diabetes and Parkinson’s disease [1,2,5,10,16]. So far, GWAS of Parkinson’s disease in various populations has found dozens of single nucleotide polymorphisms associated
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Table 1 PCR primers of the four loci. SNP
F-primer
R-primer
rs2102808 rs3754775 rs11711441 rs12493050
5 -AGTTCAGAAGGGCTCAG-3 5 -TTTTCTCCATTCCTGTCCGTA-3 5 -GATTAGCCTAGATTAGCTAGATAC-3 5 -TCCTTACCACCTGATTGA-3
5 -CCATACATCTGGGAAAT-3 5 -GCAGCAACTTATCCTTCATCTTAG-3 5 -GAACCTTTACGTCTAGCTCAGGG-3 5 -AGAGTGCTCATCTCCCTA-3
Table 2 Genotype and allele frequencies of the four SNPs in cases and controls in the Chinese Han population. SNP
N
rs2102808 PD Controls rs3754775 PD Controls rs11711441 PD Controls rs12493050 PD Controls
Genotype GG 207(41.3%) 227(46.1%) GG 309(61.7%) 289(58.7%) GG 409(81.6%) 409(81.6%) AA 276(55.1%) 275(55.9%)
GT 294(58.7%) 265(53.9%) GA 167(33.3%) 184(37.4%) GA 87(17.4%) 87(17.4%) AG 185(36.9%) 185(37.6%)
TT 0 0 AA 25(5.0%) 19(3.9%) AA 5(1.0%) 5(1.0%) GG 40(8.0%) 32(6.5%)
with PD, although most of them have not been acknowledged [6,14,15]. A meta-analysis of datasets from five Parkinson’s disease GWAS from the USA and Europe found 11 loci that surpassed the threshold for genome-wide significance (p < 5 × 10−8 ). Five were newly identified loci, including the STK39 (rs2102808) and LAMP3 (rs11711441) genes [10]. Another GWAS of the Ashkenazi Jewish population also identified loci, including the STK39 (rs3754775) and LAMP3 (rs12493050) genes [8]. Because the association between the STK39 and MCCC1/LAMP3 genes and PD was confirmed in different populations, we suspected that these two genes were likely candidate genes for PD. Considering that there is no such research available in our population, we conducted a case-control cohort study to clarify the association between the four single nucleotide polymorphism (SNP) loci (rs2102808 and rs3754775 in STK39; rs11711441 and rs12493050 in MCCC1/LAMP3) and PD in the Chinese Han population.
P(OR)
Allele
CI 0.125(1.220) 0.947–1.573
G 708(70.7%) 719(73.1%) G 785(78.3%) 762(77.4%) G 905(90.3%) 787(80.0%) A 737(73.6%) 735(74.7%)
0.620(0.947) 0.763–1.175 <0.001(0.396) 0.300–0.522 0.570(1.059) 0.868–1.292
P(OR) T 294(29.3%) 265(26.9%) A 217(21.7%) 222(22.6%) A 97(9.7%) 197(20.0%) G 265(26.4%) 249(25.3%)
CI 0.255(1.121) 0.921–1.364 0.665(0.954) 0.771–1.180 <0.001(0.430) 0.331–0.559 0.564(1.061) 0.867–1.298
2. Materials and methods 2.1. Patients and controls Our study was comprised of 501 patients with PD and 492 age- and gender-matched controls. The mean age at onset was 54.77 ± 12.05 years (35–91 years old). All patients were consecutively recruited in only one center: Xiangya Hospital, Central South University. PD was diagnosed using established clinical criteria [7]. This study protocol was approved by the Ethics Committee of Central South University, and written informed consent was obtained from all subjects. 2.2. Genotyping Genotyping was performed in all cases and controls using polymerase chain reaction and direct DNA sequencing analysis. PCR amplification was carried out in a total volume of 10 l. PCR primer pairs are described in Table 1.
Table 3 Genotype and allele frequencies of the four SNPs in EOPD/LOPD and controls in the Chinese Han population. SNP rs2102808 EOPD Controls LOPD Controls rs3754775 EOPD Controls LOPD Controls rs11711441 EOPD Controls LOPD Controls rs12493050 EOPD Controls LOPD Controls
N 166 151 335 340 166 151 335 340 166 151 335 340 166 151 335 340
Genotype GG 72(0.434) 64(0.424) 135(0.403) 162(0.476) GG 100(0.603) 90(0.596) 209(0.624) 198(0.582) GG 131(0.789) 86(0.570) 278(0.830) 217(0.638) AA 82(0.494) 85(0.563) 194(0.579) 190(0.559)
GT 94(0.566) 87(0.576) 200(0.597) 178(0.524) GA 61(0.367) 55(0.364) 106(0.316) 128(0.376) GA 33(0.199) 63(0.417) 54(0.161) 120(0.353) AG 65(0.392) 55(0.364) 120(0.358) 130(0.382)
TT 0 0 0 0 AA 5(0.03) 6(0.04) 20(0.06) 14(0.042) AA 2(0.012) 2(0.013) 3(0.009) 5(0.015) GG 19(0.114) 11(0.073) 21(0.063) 20(0.059)
P(OR)
Allele
CI 0.395(0.816)
G 238(0.717) 218(0.722) 470(0.701) 502(0.738) G 261(0.786) 235(0.785) 524(0.782) 524(0.771) G 295(0.889) 235(0.778) 610(0.859) 554(0.815) A 229(0.690) 225(0.745) 508(0.758) 510(0.750)
0.080(1.319)
0.882(0.969) 0.643–1.460 0.500(0.914) 0.705–1.186 <0.001(0.377) 0.232–0.612 <0.001(0.403) 0.285–0.569 0.163(1.282) 0.904–1.819 0.664(0.946) 0.736–1.215
P(OR) T 94(0.283) 87(0.278) 200(0.299) 178(0.262) A 71(0.214) 67(0.215) 146(0.218) 156(0.229) A 37(0.111) 67(0.222) 60(0.141) 130(0.185) G 103(0.310) 77(0.255) 162(0.242) 172(0.250)
CI 0.567(0.901) 0.187(1.177)
0.720(0.931) 0.631–1.375 0.585(0.930) 0.716–1.207 <0.001(0.403) 0.257–0.632 <0.001(0.438) 0.314–0.611 0.131(1.319) 0.921–1.888 0.643(0.941) 0.732–1.209
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Table 4 Genotype and allele frequencies of the four SNPs in male PD/female PD and controls in the Chinese Han population. SNP rs2102808 Male PD Controls Female PD Controls rs3754775 Male PD Controls Female PD Controls rs11711441 Male PD Controls Female PD Controls rs12493050 Male PD Controls Female PD Controls
N 274 300 227 292 274 300 227 292 274 300 227 292 274 300 227 292
Genotype GG 117(0.427) 144(0.480) 90(0.396) 83(0.432) GG 164(0.599) 176(0.587) 145(0.639) 113(0.589) GG 225(0.821) 176(0.587) 184(0.811) 126(0.656) AA 140(0.511) 172(0.573) 136(0.599) 103(0.536)
GT 157(0.573) 156(0.520) 137(0.604) 109(0.568) GA 97(0.354) 114(0.380) 70(0.308) 70(0.365) GA 45(0.164) 120(0.400) 42(0.184) 63(0.328) AG 110(0.401) 112(0.373) 75(0.330) 73(0.380)
TT 0 0 0 0 AA 13(0.047) 10(0.033) 12(0.053) 9(0.046) AA 4(0.015) 4(0.013) 1(0.004) 3(0.016) GG 24(0.088) 16(0.054) 16(0.071) 16(0.084)
Each PCR product was purified and directly sequenced on an ABI 3100 automated sequencer (Applied Biosystems, Foster City, CA). Alignment and analysis was carried out with DNAStar (DNAStar, Inc, Madison, WI). All subjects were successfully genotyped. Moreover, 15% of samples were randomly selected for replication assays, the results of which were completely concordant with our original results. 2.3. Statistical analysis The allele and genotype frequencies of the PD and control groups were analysed using a Chi-square test with SPSS 17.0 software (SPSS Inc., Chicago, IL, USA). A p-value of <0.05 using a two-tailed test was considered to be statistically significant. 3. Results Genotype and allele frequencies for all subjects are shown in Tables 2–4. These four SNPs were in agreement with Hardy–Weinberg equilibrium in both the patient and control groups, and the two SNPs in one gene were not in linkage disequilibrium. Significant differences in the genotype and allele frequencies of the SNP rs11711441 were observed between cases and controls (p < 0.001, p < 0.001). Statistically significant differences in the genotype frequency between the early-onset and late-onset groups with controls were observed (p < 0.001, p < 0.001). Statistically significant differences in the genotype frequency between male cases and female cases with controls were observed (p < 0.001, p < 0.001). No statistically significant differences in the other three SNPs of genotype frequency between PD, EOPD, LOPD, male PD or female PD with the controls were observed. 4. Discussion The first meta-analysis of datasets from five Parkinson’s disease GWAS from the USA and Europe identified loci including the STK39 (rs2102808) and LAMP3 (rs11711441) genes. Later, another GWAS of the Ashkenazi Jewish population also identified loci, including the STK39 (rs3754775) and LAMP3 (rs12493050) genes. These results suggest a consistent association between the two genes and PD in different racial types. To detect the association in Chinese Han population, we conducted a replication analysis to verify the four SNPs. Our results demonstrated that statistically significant differences in genotype frequency and allele frequency for rs11711441
P(OR)
Allele
CI 0.206(1.237) 0.890–1.720 0.443(1.165) 0.788–1.722
G 391(71.4%) 444(74.0%) 317(69.8%) 275(71.6%) G 425(77.6%) 466(77.5%) 360(79.3%) 296(77.1%) G 495(90.3%) 472(78.7%) 410(90.5%) 315(82.0%) A 390(0.712) 456(0.760) 347(0.764) 279(0.727)
0.934(1.012) 0.760–1.348 0.397(0.868) 0.626–1.204 <0.001(0.358) 0.248–0.516 <0.001(0.456) 0.297–0.700 0.071(1.276) 0.979–1.663 0.228(0.830) 0.613–1.124
P(OR) T 157(28.6%) 156(26.0%) 137(30.2%) 109(28.4%) A 123(22.4%) 134(22.5%) 94(20.7% 88(22.9%) A 53(9.7%) 128(21.3%) 44(9.5%) 69(18.0%) G 158(0.288) 144(0.240) 107(0.236) 105(0.273)
CI 0.317(1.142) 0.880–1.481 0.558(1.094) 0.811–1.475 0.936(1.011) 0.766–1.336 0.444(0.879) 0.633–1.222 <0.001(0.394) 0.279–0.556 0.001(0.487) 0.325–0.732 0.071(1.275) 0.980–1.660 0.213(0.820) 0.600–1.121
between cases and controls was observed, which were stratified by age of onset and gender; however, differences were not observed for the other three SNPs. STK39 is abundant in the brain and pancreas, and the gene has been associated with autism, hypertension and inflammation. There have also been reports of the association with neurodegenerative disease [3,4,11]. Compared to STK39, the function of LAMP3 is less understood. It might partly cause the modulation of neuronal and neurosecretory functions in PC12 cell lines [9], and similar to STK39, it was not found to contribute to neurodegenerative disease. For the MCCC1, its product is part of MCC, which is a biotindependent carboxylase that catalyses the fourth step in the leucine catabolic pathway and is inherited as an autosomal recessive trait [13]. In summary, there is no biological evidence concerning the association of the two genes and Parkinson’s disease. Our study confirms the association of the loci rs11711441 near STK39 and sporadic PD in the Chinese Han population. We found that the variant decreases the risk of PD approximately 0.396-fold. However, there are several limitations that we cannot ignore. First, this is a clinic-based rather than a community-based study. Second, the number of EOPD patients is small in comparison with LOPD in our study. Some ascertainment bias of the PD patients might also be produced. Third, the sample size was moderate, which limited the statistical power of our study. We arrived at the conclusion in a statistical manner, without any biological evidence. In future works, well-designed studies in populations with different ethnic or geographic origins and further functional assays should be conducted to further evaluate the potential association between SNP and PD.
Conflicts of interest The authors have no actual or potential conflicts of interest to report.
Acknowledgments This work was supported by a grant from the Major State Basic Research Development Program of China (973 Program) (2011CB510001) and a grant from the National Natural Science Foundation of China (30900469, 81171198, 81200870, 81000542, 81130021, 81371405, 81361120404). We would like to thank the family for their participation in this study.
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