1. 1
GENETIC POLYMORPHISMS FROM CHRONIC OBSTRUCTIVE PULMONARY DISEASE GENOME-WIDE ASSOCIATION STUDIES IN ALPHA-1 ANTITRYPSIN DEFICIENCY
H Khiroya, PR Newby, R Edgar, RA Stockley, AM Turner
School of Clinical and Experimental Medicine, University of Birmingham, UK
INTRODUCTION
Patients with severe alpha-1 antitrypsin deficiency (AATD) constitute 0.63% of usual chronic obstructive disease (COPD)1. Several genetic factors have been put forward as being responsible for the variability within the COPD phenotype that cannot be accounted for by environmental factors such as cigarette smoke.
Genome-wide association studies of usual COPD have identified the following genes as contributing to the risk of COPD2,3,4
Family with sequence familiarity 13, member A (FAM13A)
Hedgehog interacting protein (HHIP)
5-hydroxytryptamine receptor 4 (HTR4)
We chose to explore single nucleotide polymorphisms (SNPs) of the above genes that have not previously been examined in AATD in order to see if these associations could be replicated within the AATD population.
METHODS
662 PiZZ and PiZnull AATD subjects underwent a full clinical assessment, which has been widely published for the UK AATD cohort5. In short, the clinical assessment comprises recording the date of birth, gender, weight and height of the patient, lung function testing, computed tomography scan and annual follow up.
DNA extraction was performed using a modified Nucleon Bacc II kit (Tepnel Life Sciences, UK) and quantified using Picogreen® (Molecular Probes Inc, UK).
Genotyping was carried out using TaqMan® genotyping technologies (Applied Biosystems, UK) on an ABI7900 HT.
Subjects were genotyped for the following 5 SNPs:
rs (FAM13A)
rs (FAM13A)
rs (HTR4)
rs (HHIP)
rs (HHIP)
Genetic association with post-bronchodilator forced expiratory volume (FEV1) was assessed by linear regression. Logistic regressions were performed to assess for associations with emphysema, chronic bronchitis and bronchiectasis, as defined on computed tomorgraphy scan. Adjustments were made for sex, age and smoking pack year history.
RESULTS: CLINICAL PHENOTYPE
Table 1 illustrates the demographics of our cohort. Data is shown as median (IQR) with the exception of age, which is shown as mean (SD).
TABLE 1
Figure 1 demonstrates the frequency of phenotypes in our AATD cohort.
FIGURE 1
RESULTS: GENETIC ASSOCIATION
Genotyping was successful in more than 95% of cases.
All 5 SNPs were in Hardy-Weinburg equilibrium.
Table 2 illustrates the association of our SNPs with emphysema. p<0.05 was set as the significance level.
TABLE 2
None of the 5 SNPs explored were significantly associated with post-bronchodilator FEV1, chronic bronchitis or bronchiectasis.
CONCLUSIONS
Our results add further replication to the background work on this topic, making it more likely that FAM13A and HHIP confer increased susceptibility to the COPD phenotype in the AATD population.
The HHIP SNPs we looked at are in significant linkage disequilibrium with each other (r2 > 0.99)6 which makes it difficult to say if one SNP is more responsible for emphysema than the other, or whether the effect is combined.
Despite rs (FAM13A) not having an effect in our study, previous work on this SNP has shown it to be in strong linkage disequilibrium (r2 = 0.852) with rs (FAM13A)7. It is therefore difficult to determine the separate effects of the SNPs.
This preliminary data could be used in the future to target these SNPs in terms of understanding their functionality and how this may relate to therapies for emphysema in AATD.
REFERENCES
1.Rahaghi, F.F. et al. The prevalence of alpha-1 antitrypsin deficiency among patients found to have airflow obstruction. COPD, (4): p
2.Hancock, D. B. et al. Meta-analyses of genome-wide association studies identify multiple loci associated with pulmonary function. Nat Genet Jan; 42(1):45-52.
3.Wilk, J. B. et al. Framingham Heart Study genome-wide association: results for pulmonary function measures. BMC Med Genet. 2007; 8(Suppl 1): S8
4.Wilk, J. B. et al. Genome-Wide Association Studies Identify CHRNA5/3 and HTR4 in the Development of Airflow Obstruction. Am J Respir Crit Care Med. Oct 1, 2012; 186(7): 622–632.
5.Dowson, L. J. et al. The relationship of chronic sputum expectoration to physiologic, radiologic, and health status characteristics in alpha(1)-antitrypsin deficiency (PiZ). Chest Oct;122(4):
6.Zhou, X. et al. Identification of a chronic obstructive pulmonary disease genetic determinant that regulates HHIP. Hum Mol Genet. Mar 15, 2012; 21(6): 1325–1335.
7.Cho, M. H. et al. Variants in FAM13A are associated with chronic obstructive pulmonary disease. Nat Genet. Mar 2010; 42(3):
FUNDING SOURCES
Subjects: UK AATD registry has unrestricted educational grants from Grifols
Genotyping: West Midlands Chest Fund rs
(FAM13A) rs rs
(HTR4) rs
(HHIP) rs
Age
50.66
(11.22)
50.68
(11.30)
50.85
(11.34)
51.06
(11.19)
50.76
(11.28)
Gender
(% female)
40.44
59.23
73.72
77.09
51.96
Pack year smoking history
13.67
(24.46)
13.29
(24.50)
12.70
(23.60)
12.49
(23.54)
12.58
(23.45)
Post bronchodilator FEV1 (litres)
1.54
(1.44)
1.60
(1.45)
1.58
(1.43)
(1.33)
1.55
(1.34)
KCO (% predicted)
64.02
(29.85)
64.34
(30.29)
63.23
63.67
(29.32)
64.00
(29.72)
SNP
p value in association with emphysema
Odds ratio (95% confidence interval)
rs (FAM13A)
0.033
0.70 ( )
rs (HHIP)
0.042
1.45 ( )
rs (HHIP)
0.079
0.71 ( )
Chronic bronchitis
(n=213)
Bronchiectasis
(n=94)
Emphysema
(n=248)
102 9 30 38