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Dong X, Bai Y, Liao Z, Gritsch D, Liu X, Wang T, Borges-Monroy R, Ehrlich A, Serrano GE, Feany MB, Beach TG, Scherzer CR. Circular RNAs in the human brain are tailored to neuron identity and neuropsychiatric disease. Nat Commun 2023; 14:5327. [PMID: 37723137 PMCID: PMC10507039 DOI: 10.1038/s41467-023-40348-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 07/20/2023] [Indexed: 09/20/2023] Open
Abstract
Little is known about circular RNAs (circRNAs) in specific brain cells and human neuropsychiatric disease. Here, we systematically identify over 11,039 circRNAs expressed in vulnerable dopamine and pyramidal neurons laser-captured from 190 human brains and non-neuronal cells using ultra-deep, total RNA sequencing. 1526 and 3308 circRNAs are custom-tailored to the cell identity of dopamine and pyramidal neurons and enriched in synapse pathways. 29% of Parkinson's and 12% of Alzheimer's disease-associated genes produced validated circRNAs. circDNAJC6, which is transcribed from a juvenile-onset Parkinson's gene, is already dysregulated during prodromal, onset stages of common Parkinson's disease neuropathology. Globally, addiction-associated genes preferentially produce circRNAs in dopamine neurons, autism-associated genes in pyramidal neurons, and cancers in non-neuronal cells. This study shows that circular RNAs in the human brain are tailored to neuron identity and implicate circRNA-regulated synaptic specialization in neuropsychiatric diseases.
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Affiliation(s)
- Xianjun Dong
- APDA Center for Advanced Parkinson Disease Research, Harvard Medical School, Brigham & Women's Hospital, Boston, MA, USA
- Precision Neurology Program, Harvard Medical School and Brigham & Women's Hospital, Boston, MA, USA
- Genomics and Bioinformatics Hub, Harvard Medical School and Brigham & Women's Hospital, Boston, MA, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA
| | - Yunfei Bai
- APDA Center for Advanced Parkinson Disease Research, Harvard Medical School, Brigham & Women's Hospital, Boston, MA, USA
- Precision Neurology Program, Harvard Medical School and Brigham & Women's Hospital, Boston, MA, USA
- State Key Lab of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Zhixiang Liao
- APDA Center for Advanced Parkinson Disease Research, Harvard Medical School, Brigham & Women's Hospital, Boston, MA, USA
- Precision Neurology Program, Harvard Medical School and Brigham & Women's Hospital, Boston, MA, USA
| | - David Gritsch
- APDA Center for Advanced Parkinson Disease Research, Harvard Medical School, Brigham & Women's Hospital, Boston, MA, USA
- Precision Neurology Program, Harvard Medical School and Brigham & Women's Hospital, Boston, MA, USA
| | - Xiaoli Liu
- APDA Center for Advanced Parkinson Disease Research, Harvard Medical School, Brigham & Women's Hospital, Boston, MA, USA
- Precision Neurology Program, Harvard Medical School and Brigham & Women's Hospital, Boston, MA, USA
- Department of Neurology, Zhejiang Hospital, Zhejiang, China
| | - Tao Wang
- APDA Center for Advanced Parkinson Disease Research, Harvard Medical School, Brigham & Women's Hospital, Boston, MA, USA
- Precision Neurology Program, Harvard Medical School and Brigham & Women's Hospital, Boston, MA, USA
- School of Computer Science, Northwestern Polytechnical University, Xi'an, Shaanxi, China
| | - Rebeca Borges-Monroy
- APDA Center for Advanced Parkinson Disease Research, Harvard Medical School, Brigham & Women's Hospital, Boston, MA, USA
- Precision Neurology Program, Harvard Medical School and Brigham & Women's Hospital, Boston, MA, USA
| | - Alyssa Ehrlich
- APDA Center for Advanced Parkinson Disease Research, Harvard Medical School, Brigham & Women's Hospital, Boston, MA, USA
- Precision Neurology Program, Harvard Medical School and Brigham & Women's Hospital, Boston, MA, USA
- Department of Psychiatry, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Mel B Feany
- Departement of Pathology, Brigham & Women's Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Clemens R Scherzer
- APDA Center for Advanced Parkinson Disease Research, Harvard Medical School, Brigham & Women's Hospital, Boston, MA, USA.
- Precision Neurology Program, Harvard Medical School and Brigham & Women's Hospital, Boston, MA, USA.
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA.
- Program in Neuroscience, Harvard Medical School, Boston, MA, USA.
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Dong X, Bai Y, Liao Z, Gritsch D, Liu X, Wang T, Borges-Monroy R, Ehrlich A, Serano GE, Feany MB, Beach TG, Scherzer CR. Circular RNAs in the human brain are tailored to neuron identity and neuropsychiatric disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.01.535194. [PMID: 37066229 PMCID: PMC10103951 DOI: 10.1101/2023.04.01.535194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Little is known about circular RNAs (circRNAs) in specific brain cells and human neuropsychiatric disease. Here, we systematically identified over 11,039 circRNAs expressed in vulnerable dopamine and pyramidal neurons laser-captured from 190 human brains and non-neuronal cells using ultra-deep, total RNA sequencing. 1,526 and 3,308 circRNAs were custom-tailored to the cell identity of dopamine and pyramidal neurons and enriched in synapse pathways. 88% of Parkinson's and 80% of Alzheimer's disease-associated genes produced circRNAs. circDNAJC6, produced from a juvenile-onset Parkinson's gene, was already dysregulated during prodromal, onset stages of common Parkinson's disease neuropathology. Globally, addiction-associated genes preferentially produced circRNAs in dopamine neurons, autism-associated genes in pyramidal neurons, and cancers in non-neuronal cells. This study shows that circular RNAs in the human brain are tailored to neuron identity and implicate circRNA- regulated synaptic specialization in neuropsychiatric diseases.
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Affiliation(s)
- Xianjun Dong
- APDA Center for Advanced Parkinson Disease Research, Harvard Medical School, Brigham & Women’s Hospital, Boston, MA, USA
- Precision Neurology Program, Harvard Medical School and Brigham & Women’s Hospital, Boston, MA, USA
- Genomics and Bioinformatics Hub, Harvard Medical School and Brigham & Women’s Hospital, Boston, MA, USA
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815
| | - Yunfei Bai
- APDA Center for Advanced Parkinson Disease Research, Harvard Medical School, Brigham & Women’s Hospital, Boston, MA, USA
- Precision Neurology Program, Harvard Medical School and Brigham & Women’s Hospital, Boston, MA, USA
- State Key Lab of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Zhixiang Liao
- APDA Center for Advanced Parkinson Disease Research, Harvard Medical School, Brigham & Women’s Hospital, Boston, MA, USA
- Precision Neurology Program, Harvard Medical School and Brigham & Women’s Hospital, Boston, MA, USA
| | - David Gritsch
- APDA Center for Advanced Parkinson Disease Research, Harvard Medical School, Brigham & Women’s Hospital, Boston, MA, USA
- Precision Neurology Program, Harvard Medical School and Brigham & Women’s Hospital, Boston, MA, USA
| | - Xiaoli Liu
- APDA Center for Advanced Parkinson Disease Research, Harvard Medical School, Brigham & Women’s Hospital, Boston, MA, USA
- Precision Neurology Program, Harvard Medical School and Brigham & Women’s Hospital, Boston, MA, USA
- Department of Neurology, Zhejiang Hospital, Zhejiang, China
| | - Tao Wang
- APDA Center for Advanced Parkinson Disease Research, Harvard Medical School, Brigham & Women’s Hospital, Boston, MA, USA
- Precision Neurology Program, Harvard Medical School and Brigham & Women’s Hospital, Boston, MA, USA
- School of Computer Science, Northwestern Polytechnical University, Xi’an, Shaanxi, China
| | - Rebeca Borges-Monroy
- APDA Center for Advanced Parkinson Disease Research, Harvard Medical School, Brigham & Women’s Hospital, Boston, MA, USA
- Precision Neurology Program, Harvard Medical School and Brigham & Women’s Hospital, Boston, MA, USA
| | - Alyssa Ehrlich
- APDA Center for Advanced Parkinson Disease Research, Harvard Medical School, Brigham & Women’s Hospital, Boston, MA, USA
- Precision Neurology Program, Harvard Medical School and Brigham & Women’s Hospital, Boston, MA, USA
- Department of Psychiatry, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Mel B. Feany
- Departement of Pathology, Brigham & Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Clemens R. Scherzer
- APDA Center for Advanced Parkinson Disease Research, Harvard Medical School, Brigham & Women’s Hospital, Boston, MA, USA
- Precision Neurology Program, Harvard Medical School and Brigham & Women’s Hospital, Boston, MA, USA
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815
- Program in Neuroscience, Harvard Medical School, Boston, MA, USA
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Hubacek JA, Dlouha L, Adamkova V, Dlouha D, Pacal L, Kankova K, Galuska D, Lanska V, Veleba J, Pelikanova T. Genetic risk score is associated with T2DM and diabetes complications risks. Gene X 2022; 849:146921. [PMID: 36174902 DOI: 10.1016/j.gene.2022.146921] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 09/09/2022] [Accepted: 09/21/2022] [Indexed: 10/14/2022] Open
Abstract
BACKGROUND Type 2 diabetes mellitus (T2DM) is a prototypical complex disease with polygenic architecture playing an important role in determining susceptibility to develop the disease (and its complications) in subjects exposed to modifiable lifestyle factors. A current challenge is to quantify the degree of the individual's genetic risk using genetic risk scores (GRS) capturing the results of genome-wide association studies while incorporating possible ethnicity- or population-specific differences. METHODS This study included three groups of T2DM (T2DM-I, N=1,032; T2DM-II, N=353; and T2DM-III, N=399) patients and 2,481 diabetes-free subjects. The status of the microvascular and macrovascular diabetes complications were known for the T2DM-I patients. Overall, 21 single nucleotide polymorphisms (SNPs) were analyzed, and selected subsets were used to determine the GRS (both weighted - wGRS and unweighted - uGRS) for T2DM risk predictions (6 SNPs) and for predicting the risks of complications (7 SNPs). RESULTS The strongest T2DM markers (P<0.0001) were within the genes for TCF7L2 (transcription factor 7-like 2), FTO (fat mass and obesity associated protein) and ARAP1 (ankyrin repeat and PH domain 1). The T2DM-I subjects with uGRS values greater (Odds Ratio, 95% Confidence Interval) than six had at least twice (2.00, 1.72-2.32) the risk of T2DM development (P<0.0001), and these results were confirmed in the independent groups (T2DM-II 1.82, 1.45-2.27; T2DM-III 2.63, 2.11-3.27). The wGRS (>0.6) further improved (P<0.000001) the risk estimations for all three T2DM groups. The uGRS was also a significant predictor of neuropathy (P<0.0001), nephropathy (P<0.005) and leg ischemia (P<0.0005). CONCLUSIONS If carefully selected and specified, GRS, both weighted and unweighted, could be significant predictors of T2DM development, as well as the diabetes complications development.
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Affiliation(s)
- Jaroslav A Hubacek
- Experimental Medicine Centre, Institute for Clinical and Experimental Medicine, Prague, Czech Republic; 3rd Department of Internal Medicine, 1(st) Faculty of Medicine, Charles University, Prague, Czech Republic.
| | - Lucie Dlouha
- Experimental Medicine Centre, Institute for Clinical and Experimental Medicine, Prague, Czech Republic; Department of Anthropology and Human Genetics, Faculty of Science, Charles University, Prague, Czech Republic
| | - Vera Adamkova
- Department of Preventive Cardiology, Institute for Clinical and Experimental Medicine, Prague, Czech Republic; Czech Technical University of Prague, Faculty of Biomedical Engineering, Prague, Czech Republic
| | - Dana Dlouha
- Experimental Medicine Centre, Institute for Clinical and Experimental Medicine, Prague, Czech Republic
| | - Lukas Pacal
- Department of Pathophysiology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Katerina Kankova
- Department of Pathophysiology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - David Galuska
- Department of Pathophysiology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Vera Lanska
- Statistical Unit, Institute for Clinical and Experimental Medicine, Prague, Czech Republic
| | - Jiri Veleba
- Diabetes Centre, Institute for Clinical and Experimental Medicine, Prague, Czech Republic
| | - Terezie Pelikanova
- Diabetes Centre, Institute for Clinical and Experimental Medicine, Prague, Czech Republic
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Wang X, Jia J, Huang T. Coffee Types and Type 2 Diabetes Mellitus: Large-Scale Cross-Phenotype Association Study and Mendelian Randomization Analysis. Front Endocrinol (Lausanne) 2022; 13:818831. [PMID: 35222278 PMCID: PMC8873575 DOI: 10.3389/fendo.2022.818831] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Accepted: 01/10/2022] [Indexed: 11/24/2022] Open
Abstract
PURPOSE To explore whether coffee intake is associated with the risk of type 2 diabetes mellitus (T2DM) from a genetic perspective, and whether this association remains the same among different types of coffee consumers. METHODS We utilized the summary-level results of 12 genome-wide association studies. First, we used linkage disequilibrium score regression and cross-phenotype association analysis to estimate the genetic correlation and identify shared genes between coffee intake and T2DM in addition to some other T2DM-related phenotypes. Second, we used Mendelian randomization (MR) analysis to test whether there is a significant genetically predicted causal association between coffee intake and the risk of T2DM or other T2DM-related phenotypes. For all the analyses above, we also conducted a separate analysis for different types of coffee consumers, in addition to total coffee intake. RESULTS Genetically, choice for ground coffee was significantly negatively associated with the risk of T2DM and some other related risks. While coffee intake and choice for decaffeinated/instant coffee had significant positive correlation with these risks. Between these genetically related phenotypes, there were 1571 genomic shared regions, of which 134 loci were novel. Enrichment analysis showed that these shared genes were significantly enriched in antigen processing related biological processes. MR analysis indicated that higher genetically proxied choice for ground coffee can reduce the risk of T2DM (T2DM: b: -0.2, p-value: 4.70×10-10; T2DM adjusted for body mass index (BMI): b: -0.11, p-value: 4.60×10-5), and BMI (b: -0.08, p-value: 6.50×10-5). CONCLUSIONS Compared with other types of coffee, ground coffee has a significant negative genetic and genetically predicated causal relationship with the risk of T2DM. And this association is likely to be mediated by immunity. The effect of different coffee types on T2DM is not equal, researchers on coffee should pay more attention to distinguishing between coffee types.
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Affiliation(s)
- Xinpei Wang
- Department of Biostatistics, School of Public Health, Peking University, Beijing, China
| | - Jinzhu Jia
- Department of Biostatistics, School of Public Health, Peking University, Beijing, China
- Center for Statistical Science, Peking University, Beijing, China
- *Correspondence: Jinzhu Jia, ; Tao Huang,
| | - Tao Huang
- Department of Epidemiology & Biostatistics, School of Public Health, Peking University, Beijing, China
- Department of Global Health, School of Public Health, Peking University, Beijing, China
- Key Laboratory of Molecular Cardiovascular Sciences (Peking University), Ministry of Education, Beijing, China
- *Correspondence: Jinzhu Jia, ; Tao Huang,
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Vrablik M, Dlouha D, Todorovova V, Stefler D, Hubacek JA. Genetics of Cardiovascular Disease: How Far Are We from Personalized CVD Risk Prediction and Management? Int J Mol Sci 2021; 22:ijms22084182. [PMID: 33920733 PMCID: PMC8074003 DOI: 10.3390/ijms22084182] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 04/09/2021] [Accepted: 04/12/2021] [Indexed: 12/13/2022] Open
Abstract
Despite the rapid progress in diagnosis and treatment of cardiovascular disease (CVD), this disease remains a major cause of mortality and morbidity. Recent progress over the last two decades in the field of molecular genetics, especially with new tools such as genome-wide association studies, has helped to identify new genes and their variants, which can be used for calculations of risk, prediction of treatment efficacy, or detection of subjects prone to drug side effects. Although the use of genetic risk scores further improves CVD prediction, the significance is not unambiguous, and some subjects at risk remain undetected. Further research directions should focus on the “second level” of genetic information, namely, regulatory molecules (miRNAs) and epigenetic changes, predominantly DNA methylation and gene-environment interactions.
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Affiliation(s)
- Michal Vrablik
- 3rd Department of Internal Medicine, General University Hospital and 1st Faculty of Medicine, Charles University, 11636 Prague, Czech Republic; (V.T.); (J.A.H.)
- Correspondence: ; Tel.: +420-224-962-122
| | - Dana Dlouha
- Experimental Medicine Centre, Institute for Clinical and Experimental Medicine, 14021 Prague, Czech Republic;
| | - Veronika Todorovova
- 3rd Department of Internal Medicine, General University Hospital and 1st Faculty of Medicine, Charles University, 11636 Prague, Czech Republic; (V.T.); (J.A.H.)
| | - Denes Stefler
- Department of Epidemiology and Public Health, Institute of Epidemiology and Health Care, University College London, London WC1E 7HB, UK;
| | - Jaroslav A. Hubacek
- 3rd Department of Internal Medicine, General University Hospital and 1st Faculty of Medicine, Charles University, 11636 Prague, Czech Republic; (V.T.); (J.A.H.)
- Experimental Medicine Centre, Institute for Clinical and Experimental Medicine, 14021 Prague, Czech Republic;
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Doaei S, Bourbour F, Rastgoo S, Akbari ME, Gholamalizadeh M, Hajipour A, Moslem A, Ghorat F, Badeli M, Bagheri SE, Alizadeh A, Mokhtari Z, Pishdad S, JavadiKooshesh S, Azizi Tabesh G, Montazeri F, Joola P, Rezaei S, Dorosti M, Mosavi Jarrahi SA. Interactions of anthropometric indices, rs9939609 FTO gene polymorphism and breast cancer: A case-control study. J Cell Mol Med 2021; 25:3252-3257. [PMID: 33634577 PMCID: PMC8034447 DOI: 10.1111/jcmm.16394] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Revised: 02/07/2021] [Accepted: 02/09/2021] [Indexed: 12/19/2022] Open
Abstract
Contradictory results were reported on the effect of fat mass‐ and obesity‐associated (FTO) gene and anthropometric measurements on breast cancer (BC). This study aimed to assess the interactions between rs9939609 polymorphism of FTO gene, anthropometric indices and BC risk in Iranian women. This case‐control study was performed on 540 women including 180 women with BC and 360 healthy women in Tehran, Iran. Physical activity and dietary intakes were assessed by validated questionnaires. Data on sociodemographic and pathologic factors of the participants as well as their blood samples were collected. The rs9939609 FTO gene polymorphism was genotyped using the tetra‐primer amplification refractory mutation system‐polymerase chain reaction (T‐ARMS‐PCR). No significant association was found between BC and risk allele of FTO rs9939609 polymorphism after adjustments for the confounders. However, there was a significant association between rs9939609 polymorphism risk allele and BC risk in females with overweight, even after adjusting for age, family history of BC, abortion, BMI and the number of pregnancies (P < .05). The association was disappeared after further adjustments for lifestyle factors including smoking, alcohol consumption, calorie and macronutrients intake, and physical activity. The FTO gene polymorphism was associated with the risk of BC in overweight individuals. This association was influenced by environmental factors including diet, alcohol consumption and smoking. Future studies are required to confirm the association between the FTO gene and BC in overweight females and to identify the underlying mechanisms.
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Affiliation(s)
- Saeid Doaei
- Cancer Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Fatemeh Bourbour
- Department of Clinical Nutrition and Dietetics, Shahid Beheshti University of Medical Science, Tehran, Iran
| | - Samira Rastgoo
- Department of Clinical Nutrition and Dietetics, Shahid Beheshti University of Medical Science, Tehran, Iran
| | | | - Maryam Gholamalizadeh
- Student Research Committee, Cancer Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Azadeh Hajipour
- Department of Health Sciences in Nutrition, School of Health, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Alireza Moslem
- Iranian Research Center on Healthy Aging, Sabzevar University of Medical Sciences, Sabzevar, Iran
| | - Fereshteh Ghorat
- Non-Communicable Diseases Research Center, Sabzevar University of Medical Sciences, Sabzevar, Iran
| | - Mostafa Badeli
- Department of Nutrition, Urmia University of Medical Science, Urmia, Iran
| | | | - Atieh Alizadeh
- Department of Clinical Nutrition and Dietetics, Shahid Beheshti University of Medical Science, Tehran, Iran
| | - Zohreh Mokhtari
- Department of Clinical Biochemistry, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Samaneh Pishdad
- Nutrition and Food Security Research Center, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Sepehr JavadiKooshesh
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ghasem Azizi Tabesh
- Genomic Research center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Fateme Montazeri
- Cancer Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Parvin Joola
- Department of non-communicable diseases, deputy of health services, Dezful University of Medical Sciences, Dezful, Iran
| | - Shahla Rezaei
- Student Research Committee, Department of Clinical Nutrition, School of Nutrition and Food Sciences, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Masoomeh Dorosti
- Department of Nutrition, Urmia University of Medical Science, Urmia, Iran
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