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A complete linkage disequilibrium in a haplotype of three SNPs in Fat Mass and Obesity associated (FTO) gene was strongly associated with anthropometric indices after controlling for calorie intake and physical activity
BMC Medical Genetics volume 19, Article number: 146 (2018)
The underlying mechanism of the effect of FTO genotype on body mass index (BMI) and body composition is unknown. The objective of the study was to investigate the association of FTO gene polymorphisms with anthropometric indices in adolescent boys after adjustments for dietary intake and physical activity.
In this school-based study, we enrolled 123 male adolescents without extra weight and 110 male adolescents with body mass index (BMI) higher than + 1 Z-score. The DNA samples were genotyped for the FTO gene polymorphisms by DNA Sequencing. BMI and body composition were assessed using bioelectrical impedance analyzer scale. Association of the FTO polymorphisms with Weight, height, BMI, body fat percent and skeletal muscle percent were investigated. Data on potential confounders (calorie intake and physical activity) were collected through the use of pre-tested questionnaires.
Adolescents with higher BMI and body fat percent and lower skeletal muscle percent were more likely to have a newly found haplotype of rs9930506, rs9930501 & rs9932754 (GGT) in the first intron of the FTO with complete linkage disequilibrium (LD) compared with those with the lower BMI (6.15;2.28–16.63), body fat percent (9.54;0.92–47.44) and higher skeletal muscle percent (9.26;1.85–46.38). This association was not changed after controlling for age. Additional adjustments for calorie intake and physical activity did not alter the association.
A haplotype in the first intron of the FTO gene had a strong association with obesity indices in adolescent boys after adjustments for calorie intake and physical activity. It’s suggested that the FTO genotype exert its effects on adolescents’ anthropometric indices as haplotype and through mechanisms other than changes in calorie intake and expenditure.
This paper reports the first phase of a comprehensive interventional study (Interactions of Genetics, lifestyle and anthropometrics study or IGLA study) and is retrospectively registered in the Iranian Registry of Clinical Trials as IRCT2016020925699N2. Date registered: April 24, 2016. (http://www.irct.ir/searchresult.php?id=25699&number=2).
The relationship between FTO and obesity is reported by several studies [1,2,3,4,5,6,7,8,9,10,11]. Still there is no general agreement on the underlying mechanisms of effects of FTO on body weight. Recent studies showed that polymorphisms of FTO play key role on control of food intake. People with the AA or AT genotypes of rs9939609 polymorphism had significantly higher calorie intake than people with the TT genotype . Moreover, obesity risk allele of FTO was associated with the less level of lipolysis in adipocytes that it shows possible primary role of the FTO gene in adipose tissue . Many polymorphisms of the FTO gene are studied for the possible association with obesity. Some of these SNPs are rs178117449, rs9939609, rs3751812, rs1421085, rs9930506, and rs7202116  and the recent studies have shown that the genotype of the rs9930506 polymorphism has the strongest influence on body weight and body composition [14, 15].
Although the aforementioned studies provide compelling evidence that the FTO gene is involved in determining anthropometric indices [12,13,14,15], the underlying mechanisms of the polymorphisms effect and whether the rs9930506 polymorphism has correlation with other SNPs or not is not clear. Hence, this study used DNA sequencing method to assess the genotype of the rs9930506 polymorphism and two other adjacent polymorphisms (rs9930501 & rs9932754) in the first intron of the FTO gene. This study aimed to investigation of the association between these SNPs and anthropometric indices (i.e. weight, height, BMI, body fat percent and skeletal muscle percent) after adjustments for dietary intake and physical activity.
The following details are presented in accordance with the STROBE guidelines for cross-sectional studies.
This paper reports the first phase of a comprehensive interventional study (Interactions of Genetics, lifestyle and anthropometrics study or IGLA study) and is registered in the Iranian Registry of Clinical Trials as IRCT2016020925699N2. The first phase of this study was carried out on adolescent male students of two schools from one district of Tehran over one school year from January to June 2016. The inclusion criteria were age 12 to 16 years, students’ willingness to participate in the study, and reaching the puberty stage (140 students of each schools). Stage of puberty was assessed by a pediatric psychologist using Tanner criteria of genital and pubic hair stage. The students who were suffering from diseases effective on body weight (n = 20), treated with the drugs that effect on body weight (n = 14), fear of blood sampling (n = 5), implausible data on BMI (n = 4) or difficulty in finding the veins (n = 4) were excluded. Finally, a total of 233 adolescent boys were studied (Additional file 1).
A.ll students were assessed in terms of anthropometric parameters (i.e. weight, height, BMI, body fat percent (BF), and skeletal muscle percent (SM)). Heights were measured in the standing position and without shoes using a standard measuring tape attached to the wall. Students’ weights were measured and the values of BMI, BF and SM were determined using a validated bioelectrical impedance analysis scale (Omron company model BF-511)  after entering their age, gender and height. The extracted data was classified according to World Health Organization z scores (for height, weight and BMI) and the published criteria reported by the recent studies (for BF and BM) . Moreover, maturity situation of the students was examined by a psychologist.
AS the FTO gene is large encompassing > 410 kb of genomic region , a targeted approach was adopted to search for common SNPs within 300 bp upstream and 300 bp downstream of the original and most significantly associated SNP, rs9930506 reported by Sentinelli et al. . Five ml of blood samples were collected in EDTA tubes from each participants and were transported to the cellular and molecular laboratory at nutritional sciences and food technology school of Shahid Beheshti university of medical sciences to isolation of buffy coat, DNA extraction, and PCR.
DNA extraction kit of GeneAll Company was used to extract and purify the DNA sample. The NanoDrop device (Thermo Scientific, Wilmington, DE, USA) was used to quantify the DNA concentration. The Optical Density (OD) of samples were obtained in the absorption rate of 260 to 280 and confirmed if it was from 1.8 to 2. Moreover, to check the quality of extracted DNA, electrophoresis on agarose gel technique was used. After primer design (Additional file 2), genomic DNAs were amplified by PCR by use of Taq DNA Pol 2X Master Mix Red (cat. No A180301; Ampliqon, Denmark). The PCR product were sent to Geneall company for DNA sequencing. The quality and average length of sequence library for each sample was assessed using Chromas software (version 2.33, http://www.technelysium.com.au/chromas.html). The population were tested to determine whether the genotypes were in Hardy-Weinberg equilibrium by comparing the observed genotype frequencies in AAA cases and controls with their expected frequencies.
Assessment of other variables
Usual dietary intakes of participants were examined by a validated 168-item semi-quantitative FFQ . The FFQ consisted of 168 food items with standard portion sizes commonly consumed by Iranian people. A trained interviewer administered the FFQ through face-to-face interviews. All reported consumption frequencies were converted to grams per day by using household measures. Daily intakes of energy were measured for each person by using the modified US Department of Agriculture food consumption database, which was modified for Iranian foods.
The International Physical Activity Questionnaire (IPAQ) was used for measuring physical activity of participants through the face-to-face interview . All results of the IPAQ were expressed as metabolic equivalents per minute (MET-minutes per week).
Participants were categorized based on BMI in: no overweight, overweight (+ 1 z score), or obese (+ 2 z score). General characteristics and dietary intakes of study participants across categories of BMI were examined using one-way ANOVA for continuous variables and Chi square for categorical variables. The association of SNPs with quantitative anthropometric measures was assessed by using multinomial logistic regression in two models. Age (years) was adjusted in the first model. Additional controlling for calorie intake (kcal/day) physical activity (METs/week) was done in the second model. The statistical analyses were carried out by using SPSS version 23. P values were considered significant at < 0.05.
Students’ age and weigh mean were about 14 years (Table 1) and all of the students had passed the sexual maturity stage. Students with higher BMI had more calorie intake, lower physical activity, and shorter height, but these differences were not statistically significant. Moreover, overweight and obese students had significantly higher BF and lower SM compared to subjects without overweight.
The FTO genotype
The A and G allele frequencies for these polymorphisms were 0.6 and 0.4, respectively, and the genotypes were in Hardy–Weinberg equilibrium. A complete LD in a haplotype block composed of 3 SNPs (rs993275 (allele G), rs9930506 (allele G), rs9930501 (allele C)) encompassing 40 bp in all students was identified. The rs930506 GG genotype was more frequent in overweight and obese subjects than subjects without overweight. Distribution of risk genotype of FTO according to categories of BMI are presented in Table 2.
Association between the FTO haplotype and anthropometric indices
Multivariable-adjusted odds ratios and 95% confidence intervals for risk genotype of FTO across categories of BMI are shown in Table 3. Obese subjects were more likely to have risk genotype of FTO compared with those without overweight (5.87; 2.16–15.99). This association was not changed after controlling for age. Additional adjustments for calorie intake and physical activity did not alter the association (6.06; 2.19–16.58).
Multivariable-adjusted odds ratios and 95% confidence intervals for risk genotype of FTO across categories of BF are shown in Table 4. Higher BF was positively associated with odds of risk genotype of FTO (9.54; 0.92–47.44). This positive association did not alter even after controlling for age (9.12; 1.83–45.5). Even after controlling for confounders, including dietary intakes and physical activity, the association remained significant (9.26; 1.85–46.38).
Multivariable-adjusted odds ratios and 95% confidence intervals for risk genotype of FTO across categories of SM are shown in Table 5. Higher SM was negatively associated with odds of risk genotype of FTO (0.28; 0.12–0.62). This association was not changed after controlling for age (0.26; 0.11–0.59). Additional adjustments for calorie intake and physical activity did not significantly alter the association. (0.26;0.11–0.59).
The results of the study identified that male adolescents with overweight, higher BF and lower SM were more likely to have the risk genotype of FTO haplotype compared with those without overweight. This association remained statistically significant even after controlling for common confounders, including calorie intake and physical activity. This study is the first to examine the association between a newly found FTO haplotype and anthropometric indices in adolescents.
The relationship between rs9930506 polymorphism and BMI has been studied frequently and the GG genotype of rs9930506 polymorphism was positively correlated with BMI. For example, in a study by Scuteri et al. to evaluate the polymorphisms associated with obesity, the results showed that the rs9930506 polymorphism had the strongest correlation with BMI . Also, in the study conducted by Sentinelli et al. to determine the effects of rs9930506 polymorphism on BMI, the results showed that both polymorphisms were associated with higher BMI. In addition, rs9930506 was correlated with early onset of childhood obesity . Although some studies have reported contradictory results [23–25]. Li et al. studied on the association between three polymorphisms of the FTO gene (rs8050136, rs9939609, and rs9930506) with obesity, the results showed that none of the studied SNPs are associated with obesity and waist circumference . Moreover, Wang et al. studied the relationship between FTO polymorphisms (including rs9930506) and metabolic syndrome and the rs9930506 polymorphism did not show a significant relationship with the pathogenesis of metabolic syndrome including abdominal obesity . However, both of these negative studies were conducted on the Chinese people. The MAF of this polymorphism in Chinese communities is significantly less than that in European populations .
Two other SNPs (rs9930501 & rs9932754) have been less studied for their potential impact on anthropometric measurements [26, 27]. The association between rs9932754 and BMI and its same MAF with rs9930506 was previously reported . In the present study a complete LD was interestingly found between three neighboring SNPs of intron 1 region of the FTO gene. Although the linkage disequilibrium (LD) between rs9930506, rs9930501 and rs9932754 has been indirectly mentioned in genome-wide association studies [24, 28, 29]. The results of the present study suggested that the FTO gene polymorphisms play their roles as a haplotype (and not single SNPs). Given the close proximity of these polymorphisms, it can be also considered as a new hypothesis that these polymorphisms exert their effects on expression of the other genes through a sequence of intron 1 region. Recent studies suggested that rather than affecting FTO itself, FTO polymorphisms in this region influence expression of a distant gene, IRX3. It’s suggested that this non-coding region of FTO gene interacts with the IRX3 promoter and changes its expression level .
This study has some limitations as well. We used self-reported data on dietary intake and physical activity. It was frequently reported that obese persons underestimate their food intake and overestimate their physical activities. Moreover, we enrolled only male adolescents mainly due to gender segregation in schools. The association between FTO genotype and anthropometric measurements may be affected by gender.
The results of this study showed that a haplotype in the first intron of the FTO gene had a strong association with obesity indices in Iranian adolescent boys after adjustments for calorie intake and physical activity. It seems that the effects of FTO genotype on anthropometric indices is independent from energy intake and energy expenditure. Future studies in this field are warranted to identify the underlying mechanisms to gain a better understanding into the interactions between the FTO gene polymorphisms and anthropometric measurements.
Body fat percent
Body mass index
Fat mass and obesity-associated
A genome-wide association study
Skeletal muscle percent
Melka MG, Gillis J, Bernard M, Abrahamowicz M, Chakravarty MM, Leonard GT, Perron M, Richer L, Veillette S, Banaschewski T, Barker GJ. FTO, obesity and the adolescent brain. Hum Mol Genet. 2012;22(5):1050–8.
Wardle J, Carnell S, Haworth CM, Plomin R. Evidence for a strong genetic influence on childhood adiposity despite the force of the obesogenic environment. Am J Clin Nutr. 2008;87(2):398–404.
Hirschhorn JN, Daly MJ. Genome-wide association studies for common diseases and complex traits. Nat Rev Genet. 2005;6(2):95–108.
Wardle J, Carnell S, Haworth CM, et al. Obesity associated genetic variation in FTO is associated with diminished satiety. J Clin Endocrinol Metab. 2008;93(9):3640–3.
Luan J, Browne PO, Harding AH, et al. Evidence for gene-nutrient interaction at the PPARgamma locus. Diabetes. 2001;50(3):686–9.
Jalba MS, Rhoads GG, Demissie K. Association of codon 16 and codon 27 beta 2-adrenergic receptor gene polymorphisms with obesity: a meta-analysis. Obesity (Silver Spring). 2008;16(9):2096–106.
Corella D, Qi L, Sorli JV, et al. Obese subjects carrying the 11482G>a polymorphism at the perilipin locus are resistant to weight loss after dietary energy restriction. J Clin Endocrinol Metab. 2005;90(9):5121–6.
Fawcett KA, Barroso I. The genetics of obesity: FTO leads the way. Trends Genet. 2010;26(6):266–74.
Gerken T, Girard CA, Tung YC, Webby CJ, Saudek V, Hewitson KS, et al. The obesity-associated FTO gene encodes a 2-oxoglutarate-dependent nucleic acid demethylase. Science. 2007;318(5855):1469–72.
Freathy RM, Timpson NJ, Lawlor DA, Pouta A, Ben-Shlomo Y, Ruokonen A, et al. Common variation in the FTO gene alters diabetes-related metabolic traits to the extent expected, given its effect on BMI. Diabetes. 2008;57(5):1419–26.
Frayling TM, Timpson NJ, Weedon MN, Zeggini E, Freathy RM, Lindgren CM, et al. A common variant in the FTO gene is associated with body mass index and predisposes to childhood and adult obesity. Science. 2007;316(5826):889–94.
Speakman JR, Rance KA, Johnstone AM. Polymorphisms of the FTO gene are associated with variation in energy intake, but not energy expenditure. Obesity. 2008;16(8):1961–5.
Do R, Bailey SD, Desbiens K, Belisle A, Montpetit A, Bouchard C, et al. Genetic variants of FTO influence adiposity, insulin sensitivity, leptin levels, and resting metabolic rate in the Quebec family study. Diabetes. 2008;57(4):1147–50.
Saldaña-Alvarez Y, Salas-Martínez MG, García-Ortiz H, Luckie-Duque A, García-Cárdenas G, Vicenteño-Ayala H, Cordova EJ, Esparza-Aguilar M, Contreras-Cubas C, Carnevale A, Chávez-Saldaña M. Gender-dependent association of FTO polymorphisms with body mass index in Mexicans. PLoS One. 2016;11(1):e0145984.
Sentinelli F, Incani M, Coccia F, Capoccia D, Cambuli VM, Romeo S, Cossu E, Cavallo MG, Leonetti F, Baroni MG. Association of FTO polymorphisms with early age of obesity in obese Italian subjects. Exp Diabetes Res. 2012;20:2012.
Pietiläinen KH, Kaye S, Karmi A, Suojanen L, Rissanen A, Virtanen KA. Agreement of bioelectrical impedance with dual-energy X-ray absorptiometry and MRI to estimate changes in body fat, skeletal muscle and visceral fat during a 12-month weight loss intervention. Br J Nutr. 2013;109(10):1910–6.
Onis MD, Onyango AW, Borghi E, Siyam A, Nishida C, Siekmann J. Development of a WHO growth reference for school-aged children and adolescents. Bull World Health Organ. 2007;85(9):660–7.
Borradaile KE, Foster GD, May H, Karpyn A, Sherman S, Grundy K, Nachmani J, Vander Veur S, Boruch RF. Associations between the youth/adolescent questionnaire, the youth/adolescent activity questionnaire, and body mass index z score in low-income inner-city fourth through sixth grade children. Am J Clin Nutr. 2008;87(6):1650–5.
Qi L, Kang K, Zhang C, van Dam RM, Kraft P, Hunter D, Lee CH, Hu FB. Fat mass–and obesity-associated (FTO) gene variant is associated with obesity. Diabetes. 2008;57(11):3145–51.
Esfahani FH, Asghari G, Mirmiran P, Azizi F. Reproducibility and relative validity of food group intake in a food frequency questionnaire developed for the Tehran lipid and glucose study. J Epidemiol. 2010;20(2):150–8.
Moghaddam MB, Aghdam FB, Jafarabadi MA, Allahverdipour H, Nikookheslat SD, Safarpour S. The Iranian version of international physical activity questionnaire (IPAQ) in Iran: content and construct validity, factor structure, internal consistency and stability. World Appl Sci. 2012;18(8):1073–80.
Scuteri A, Sanna S, Chen WM, Uda M, Albai G, Strait J, et al. Genome-wide association scan shows genetic variants in the FTO gene are associated with obesity-related traits. PLoS Genet. 2007;3(7):e115.
Li H, Wu Y, Loos RJ, Hu FB, Liu Y, Wang J, et al. Variants in the fat mass- and obesity-associated (FTO) gene are not associated with obesity in a Chinese Hanpopulation. Diabetes. 2008;57(1):264–8.
Coto E, Tavira B, Gómez J, Tranche S, Corte CD. Effect of the FTO rs9930506 polymorphism on the main comorbidities of the Cardiorenal metabolic syndrome in an elderly Spanish cohort. Cardiorenal Med. 2014;4(2):82–7.
Wang T, Huang Y, Xiao XH, Wang DM, Diao CM, Zhang F, Xu LL, Zhang YB, Li WH, Zhang LL, Zhang Y. The association between common genetic variation in the FTO gene and metabolic syndrome in Han Chinese. Chin Med J (Engl). 2010;123(14):1852.
Doaei S, Kalantari N, Mohammadi NK, Tabesh GA, Gholamalizadeh M. Macronutrients and the FTO gene expression in hypothalamus; a systematic review of experimental studies. Indian Heart J. 2017;69(2):277–81.
Kalantari N, Doaei S, Keshavarz-Mohammadi N, Gholamalizadeh M, Pazan N. Review of studies on the fat mass and obesity-associated (FTO) gene interactions with environmental factors affecting on obesity and its impact on lifestyle interventions. ARYA atherosclerosis. 2016;12(6):281–90.
Doaei S, Gholamalizadeh M, Jarrahi AM, Badakhanian M, Najafi R. The IRX3 Gene; the Missing Link between the FTO Gene and Obesity. Asian Pac J Cancer Biol. 2016;1(2):31–33.
Lindgren CM, Heid IM, Randall JC, Lamina C, Steinthorsdottir V, Qi L, Speliotes EK, Thorleifsson G, Willer CJ, Herrera BM, Jackson AU. Genome-wide association scan meta-analysis identifies three loci influencing adiposity and fat distribution. PLoS Genet. 2009;5(6):e1000508.
Heard-Costa NL, Zillikens MC, Monda KL, Johansson Å, Harris TB, Fu M, Haritunians T, Feitosa MF, Aspelund T, Eiriksdottir G, Garcia M. NRXN3 is a novel locus for waist circumference: a genome-wide association study from the CHARGE consortium. PLoS Genet. 2009;5(6):e1000539.
This study was conducted at the Department of public health nutrition of the Shahid Beheshti university of medical sciences, Tehran, Iran (Code: 2842). We acknowledge all the schools staff for their excellent cooperation.
The study was funded by Shahid Beheshti University of Medical Sciences and Health Education and Promotion, Department of Ministry of Health, Tehran, Iran (code 2842). The funding body was not involved in study design, the collection, analysis or interpretation of data, nor in the writing of the manuscript and the decision to submit the manuscript for publication.
Availability of data and materials
Because of the large amount of individual-level data that was collected for this study, there is a small potential for re-identification of the subjects involved, and therefore we feel that it is not ethically appropriate to make the data publically available for anonymous and unrestricted downloading.
Ethics approval and consent to participate
The study was approved by the Ethics Committee of the National Nutrition and Food Technology Research Institute, Tehran, Iran (reference number: Ir.sbmu.nnftri.rec.1394.22). The schools which were involved in this study were asked permission to be part of this trial and consented for their students to participate. The details of the study were explained to students and their parents with explanatory letter and written informed consent was obtained from parents and students prior to joining the project.
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Written informed consent for publication of this clinical detail was obtained from the subjects and their parents.
The authors declare that they have no competing interests.
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Kalantari, N., Keshavarz Mohammadi, N., Izadi, P. et al. A complete linkage disequilibrium in a haplotype of three SNPs in Fat Mass and Obesity associated (FTO) gene was strongly associated with anthropometric indices after controlling for calorie intake and physical activity. BMC Med Genet 19, 146 (2018) doi:10.1186/s12881-018-0664-z
- Fat mass and obesity associated (FTO)