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Abu-Alghayth MH, Khan FR, Belali TM, Abalkhail A, Alshaghdali K, Nassar SA, Almoammar NE, Almasoudi HH, Hessien KBG, Aldossari MS, Binshaya AS. The emerging role of noncoding RNAs in the PI3K/AKT/mTOR signalling pathway in breast cancer. Pathol Res Pract 2024; 255:155180. [PMID: 38330621 DOI: 10.1016/j.prp.2024.155180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/25/2024] [Accepted: 01/27/2024] [Indexed: 02/10/2024]
Abstract
Breast cancer persists as a major problem for the world's healthcare, thus it is essential to fully understand the complex molecular processes that cause its growth and development. ncRNAs had been discovered to serve critical roles in a variety of cellular functions, including the regulation of signalling pathways. Within different pathways, the AKT/PI3K/mTOR signalling cascade has received a lot of interest because of its role in cancer. A complex interaction between ncRNAs, notably miRNAs, lncRNAs, and circRNAs, and the AKT/PI3K/mTOR signalling pathway exerts both oncogenic and tumor-suppressive activities by targeting critical components of the pathway directly or indirectly. Through miRNA-mediated post-transcriptional regulation, lncRNA-guided chromatin remodelling, and circRNA sequestration, ncRNAs modulate the activity of PI3K, AKT, and mTOR, influencing cell proliferation, survival, and metastasis. Furthermore, ncRNAs can serve as promising biomarkers for breast cancer prognosis, diagnosis, and treatment response, as their dysregulation is commonly observed in breast cancer patients. Harnessing the potential of ncRNAs as therapeutic targets or tools for restoring pathway homeostasis holds promise for innovative treatment strategies in breast cancer. Understanding the intricate regulatory networks orchestrated by ncRNAs in this context may pave the way for novel diagnostic approaches, therapeutic interventions, and a deeper comprehension of breast cancer's molecular landscape, ultimately improving patient outcomes. This abstract underscores the emerging significance of ncRNAs in the AKT/PI3K/mTOR signaling pathway in breast cancer.
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Affiliation(s)
- Mohammed H Abu-Alghayth
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, University of Bisha, Bisha, P.O. Box 255, 67714, Saudi Arabia
| | - Farhan R Khan
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Al- Quwayiyah, Shaqra University, Riyadh, Saudi Arabia
| | - Tareg M Belali
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, University of Bisha, Bisha, P.O. Box 255, 67714, Saudi Arabia
| | - Adil Abalkhail
- Department of Public Health, College of Applied Medical Sciences, Qassim University, Qassim, Saudi Arabia
| | - Khalid Alshaghdali
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, University of Hail, P.O Box 2440, Saudi Arabia
| | - Somia A Nassar
- Department of Medical Laboratory Science, College of Applied Medical Sciences, Prince Sattam bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia; Department of Parasitology & Animal Diseases, National Research Centre, 33 Bohouth St., Dokki, Giza 12622, Egypt
| | - Nasser Eissa Almoammar
- Department of Medical Laboratory Science, College of Applied Medical Sciences, Prince Sattam bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia
| | - Hassan H Almasoudi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Najran University, Najran 61441, Saudi Arabia
| | - Khater Balatone G Hessien
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Al- Quwayiyah, Shaqra University, Riyadh, Saudi Arabia
| | | | - Abdulkarim S Binshaya
- Department of Medical Laboratory Science, College of Applied Medical Sciences, Prince Sattam bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia.
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Thapa R, Afzal O, Gupta G, Bhat AA, Almalki WH, Alzarea SI, Kazmi I, Altamimi ASA, Subramaniyan V, Thangavelu L, Singh SK, Dua K. Unveiling the connection: Long-chain non-coding RNAs and critical signaling pathways in breast cancer. Pathol Res Pract 2023; 249:154736. [PMID: 37579591 DOI: 10.1016/j.prp.2023.154736] [Citation(s) in RCA: 44] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 08/01/2023] [Accepted: 08/02/2023] [Indexed: 08/16/2023]
Abstract
Breast cancer is a complex and diverse condition that disrupts multiple signaling pathways essential for cell proliferation, survival, and differentiation. Recently, the significant involvement of long-chain non-coding RNAs (lncRNAs) in controlling key signaling pathways associated with breast cancer development has been discovered. This review aims to explore the interaction between lncRNAs and various pathways, including the AKT/PI3K/mTOR, Wnt/β-catenin, Notch, DNA damage response, TGF-β, Hedgehog, and NF-κB signaling pathways, to gain a comprehensive understanding of their roles in breast cancer. The AKT/PI3K/mTOR pathway regulates cell growth, survival, and metabolic function. Recent data suggests that specific lncRNAs can influence the functioning of this pathway, acting as either oncogenes or tumor suppressors. Dysregulation of this pathway is commonly observed in breast cancer cases. Moreover, breast cancer development has been associated with other pathways such as Wnt/β-catenin, Notch, TGF-β, Hedgehog, and NF-κB. Emerging studies have identified lncRNAs that modulate breast cancer's growth, progression, and metastasis by interacting with these pathways. To advance the development of innovative diagnostic tools and targeted treatment options, it is crucial to comprehend the intricate relationship between lncRNAs and vital signaling pathways in breast cancer. By fully harnessing the therapeutic potential of lncRNAs, there is a possibility of developing more effective and personalized therapy choices for breast cancer patients. Further investigation is necessary to comprehensively understand the role of lncRNAs within breast cancer signaling pathways and fully exploit their therapeutic potential.
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Affiliation(s)
- Riya Thapa
- School of Pharmacy, Suresh Gyan Vihar University, Jagatpura, Mahal Road, Jaipur, India
| | - Obaid Afzal
- Department of Pharmaceutical Chemistry, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al Kharj 11942, Saudi Arabia
| | - Gaurav Gupta
- School of Pharmacy, Suresh Gyan Vihar University, Jagatpura, Mahal Road, Jaipur, India; Uttaranchal Institute of Pharmaceutical Sciences, Uttaranchal University, Dehradun, India; School of Pharmacy, Graphic Era Hill University, Dehradun 248007, India
| | - Asif Ahmad Bhat
- School of Pharmacy, Suresh Gyan Vihar University, Jagatpura, Mahal Road, Jaipur, India
| | - Waleed Hassan Almalki
- Department of Pharmacology, College of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Sami I Alzarea
- Department of Pharmacology, College of Pharmacy, Jouf University, Sakaka, Al-Jouf, Saudi Arabia
| | - Imran Kazmi
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | | | - Vetriselvan Subramaniyan
- Department of Pharmacology, Jeffrey Cheah School of Medicine and Health Sciences, MONASH University, Malaysia
| | - Lakshmi Thangavelu
- Center for Global Health Research , Saveetha Medical College , Saveetha Institute of Medical and Technical Sciences, Saveetha University, India.
| | - Sachin Kumar Singh
- School of Pharmaceutical Sciences, Lovely Professional University, Phagwara 144411, India; Faculty of Health, Australian Research Centre in Complementary and Integrative Medicine, University of Technology, Sydney, Ultimo-NSW 2007, Australia
| | - Kamal Dua
- Faculty of Health, Australian Research Centre in Complementary and Integrative Medicine, University of Technology, Sydney, Ultimo-NSW 2007, Australia; Discipline of Pharmacy, Graduate School of Health, University of Technology, Sydney, Ultimo-NSW 2007, Australia
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Cataloging the potential SNPs (single nucleotide polymorphisms) associated with quantitative traits, viz. BMI (body mass index), IQ (intelligence quotient) and BP (blood pressure): an updated review. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2022. [DOI: 10.1186/s43042-022-00266-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Single nucleotide polymorphism (SNP) variants are abundant, persistent and widely distributed across the genome and are frequently linked to the development of genetic diseases. Identifying SNPs that underpin complex diseases can aid scientists in the discovery of disease-related genes by allowing for early detection, effective medication and eventually disease prevention.
Main body
Various SNP or polymorphism-based studies were used to categorize different SNPs potentially related to three quantitative traits: body mass index (BMI), intelligence quotient (IQ) and blood pressure, and then uncovered common SNPs for these three traits. We employed SNPedia, RefSNP Report, GWAS Catalog, Gene Cards (Data Bases), PubMed and Google Scholar search engines to find relevant material on SNPs associated with three quantitative traits. As a result, we detected three common SNPs for all three quantitative traits in global populations: SNP rs6265 of the BDNF gene on chromosome 11p14.1, SNP rs131070325 of the SL39A8 gene on chromosome 4p24 and SNP rs4680 of the COMT gene on chromosome 22q11.21.
Conclusion
In our review, we focused on the prevalent SNPs and gene expression activities that influence these three quantitative traits. These SNPs have been used to detect and map complex, common illnesses in communities for homogeneity testing and pharmacogenetic studies. High blood pressure, diabetes and heart disease, as well as BMI, schizophrenia and IQ, can all be predicted using common SNPs. Finally, the results of our work can be used to find common SNPs and genes that regulate these three quantitative features across the genome.
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Identifying potential functional lncRNAs in metabolic syndrome by constructing a lncRNA-miRNA-mRNA network. J Hum Genet 2020; 65:927-938. [PMID: 32690864 DOI: 10.1038/s10038-020-0753-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 03/18/2020] [Accepted: 03/25/2020] [Indexed: 11/09/2022]
Abstract
The metabolic syndrome (MS) is a cluster of interrelated risk factors including diabetes mellitus, abdominal obesity, high cholesterol, and hypertension, which can significantly increase mortality and disability. Accumulating evidence suggest that long non-coding RNAs (lncRNAs) are involved in the pathogenesis of human metabolic diseases. However, little is known about the regulatory role of lncRNAs in MS. In this work, we proposed a method for identifying potential MS-associated lncRNAs by constructing an lncRNA-miRNA-mRNA network (LMMN). Firstly, we constructed LMMN by integrating MS-associated genes, miRNA-mRNA interactions, miRNA-lncRNA interactions and mRNA/miRNA expression profiles in patients with MS. Then, we predicted potential MS-associated lncRNAs based on the topological properties of LMMN. As a result, we identified XIST as the most important lncRNA in LMMN. Furthermore, we focused on XIST/miR-214-3p and mir-181a-5p/PTEN axis and validated their expression in MS using real-time quantitative polymerase chain reaction (RT-qPCR). The RT-qPCR results showed that the expression of XIST and PTEN was significantly decreased (P < 0.05) while the expression of miR-214-3p was significantly increased (P < 0.05) in peripheral blood mononuclear cells (PBMCs) of patients with MS, compared with healthy controls. In addition, correlation analysis showed that XIST was negatively correlated with serum C peptide and PTEN was positively correlated with BMI of MS patients. Our findings provided new evidence for further exploring the regulatory role of XIST and other lncRNAs in MS.
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Yu GI, Song DK, Shin DH. Associations of IL1RAP and IL1RL1 gene polymorphisms with obesity and inflammation mediators. Inflamm Res 2020; 69:191-202. [PMID: 31897507 DOI: 10.1007/s00011-019-01307-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 11/30/2019] [Accepted: 12/17/2019] [Indexed: 12/15/2022] Open
Abstract
OBJECTIVES Obesity is attributable to high free fatty acids, ER stress, oxidative stress and inflammation. The expression of IL-33, IL-1RL1 and IL-1RAP gene was observed in human visceral white fats, pre-adipocytes and adipocytes. The aim of this study was to determine whether IL1RAP and IL1RL1 gene variants were associated with obesity and inflammation mediators. METHODS 3 SNPs of IL1RAP (rs9990107, rs3836449 and rs9290936) and 11 SNPs of IL1RL1 (rs3771180, rs13431828, rs3214363, rs1420101, rs12905, rs3771175, rs3821204, rs12712142, rs10204137, rs4988958, and rs10206753) were genotyped for 175 obesity (BMI ≥ 25) and 358 non-obesity (BMI < 25.0) subjects. The genotype of SNPs was determined by the Axiom Genome-Wide Human Assay. RESULTS The allele and genotype frequencies of 2 SNPs in the IL1RAP gene (rs9990107 and rs3836449) and 11 SNPs in the IL1RL1 gene (rs3771180, rs13431828, rs3214363, rs1420101, rs12905, rs3771175, rs3821204, rs12712142, rs10204137, rs4988958 and rs10206753) were significantly associated between the obesity and non-obesity groups. The two haplotypes (GCTTATGAATT and TT-CGACCGCC) in block1 were associated with obesity. In the non-obesity group, genotype frequencies of rs3771180, rs13431828, rs3214363, rs10204137, rs4988958 and rs10206753 SNPs of IL1RL1 showed significant differences in the dominant models in lymphatic cell percentage. The genotype frequencies of rs1420101, rs21905, rs3821024 and rs12712142 SNPs of IL1RL1 showed significant differences in the dominant models in eosinophil percentage. CONCLUSIONS Our results suggest that IL1RAP and IL1RL1 gene polymorphisms may be associated with obesity and inflammation mediators.
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Affiliation(s)
- Gyeong Im Yu
- Department of Preventive Medicine, School of Medicine, Keimyung University, 1095 Dalgubeoldaero, Dalseo-Gu, Daegu, 42601, South Korea
| | - Dae Kyu Song
- Department of Physiology, School of Medicine, Keimyung University, 1095 Dalgubeoldaero, Dalseo-Gu, Daegu, 42601, South Korea
| | - Dong Hoon Shin
- Department of Preventive Medicine, School of Medicine, Keimyung University, 1095 Dalgubeoldaero, Dalseo-Gu, Daegu, 42601, South Korea.
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Guevara-Cruz M, Medina-Vera I, Flores-López A, Aguilar-López M, Smith CE, Parnell LD, Lee YC, Lai CQ, Tovar AR, Ordovás JM, Torres N. Development of a Genetic Score to Predict an Increase in HDL Cholesterol Concentration After a Dietary Intervention in Adults with Metabolic Syndrome. J Nutr 2019; 149:1116-1121. [PMID: 31070756 DOI: 10.1093/jn/nxz060] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 09/28/2018] [Accepted: 03/11/2019] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Dietary intervention (DI) is a primary strategy to attenuate some of the metabolic abnormalities associated with metabolic syndrome (MetS), including low HDL cholesterol. There is no biomarker that can identify individuals who respond to DI by increasing HDL cholesterol. OBJECTIVE The aim of this study was to assess the predictive power of a genetic predisposition score (GPS) in Mexican adults with MetS to identify HDL cholesterol responders to DI. METHODS This study followed a prospective cohort design. Sixty-seven Mexican adults aged 20-60 y (21% men) with BMI ≥25 and ≤39.9 kg/m², who had at least 3 of 5 positive criteria for MetS, were included. Participants consumed a low saturated fat diet for 2.5 mo (<7% energy as saturated fat, <200 mg of cholesterol/d) and reduced their usual diet by ∼440 kcal/d, a reduction in total energy intake of about 25%. Anthropometry and serum biochemical markers, including HDL cholesterol, were measured before and after DI. A multilocus GPS was constructed using previously reported genetic variants associated with response to diet in subjects with MetS. GPS values, designed to predict the response of HDL cholesterol to the DI, were computed for each individual as the sum of the number of effect alleles across 14 SNPs. RESULTS Individuals were dichotomized as high and low GPS according to median GPS (-2.12) and we observed a difference in HDL cholesterol changes on DI of +3 mg/dL (6.3%) in subjects with low GPS, whereas those with high GPS had HDL cholesterol decreases of -3 mg/dL (-7.9%) (P = 0.04). CONCLUSIONS Individuals with low GPS showed greater increases in their HDL cholesterol than those with high GPS. Therefore, the GPS can be useful for predicting the HDL cholesterol response to diet.
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Affiliation(s)
- Martha Guevara-Cruz
- Department of Physiology of Nutrition, National Institute of Medical Science and Nutrition Salvador Zubiran, Mexico City, Mexico
| | - Isabel Medina-Vera
- Department of Physiology of Nutrition, National Institute of Medical Science and Nutrition Salvador Zubiran, Mexico City, Mexico
| | - Adriana Flores-López
- Department of Physiology of Nutrition, National Institute of Medical Science and Nutrition Salvador Zubiran, Mexico City, Mexico
| | - Miriam Aguilar-López
- Department of Physiology of Nutrition, National Institute of Medical Science and Nutrition Salvador Zubiran, Mexico City, Mexico
| | - Caren E Smith
- Nutrition and Genomics' Laboratory, Jean Mayer United States Department of Agriculture Human Nutrition Research Center on Aging at Tufts University, Boston, MA
| | - Laurence D Parnell
- Nutrition and Genomics' Laboratory, Jean Mayer United States Department of Agriculture Human Nutrition Research Center on Aging at Tufts University, Boston, MA
| | - Yu-Chi Lee
- Nutrition and Genomics' Laboratory, Jean Mayer United States Department of Agriculture Human Nutrition Research Center on Aging at Tufts University, Boston, MA
| | - Chao-Qiang Lai
- Nutrition and Genomics' Laboratory, Jean Mayer United States Department of Agriculture Human Nutrition Research Center on Aging at Tufts University, Boston, MA
| | - Armando R Tovar
- Department of Physiology of Nutrition, National Institute of Medical Science and Nutrition Salvador Zubiran, Mexico City, Mexico
| | - Jose M Ordovás
- Nutrition and Genomics' Laboratory, Jean Mayer United States Department of Agriculture Human Nutrition Research Center on Aging at Tufts University, Boston, MA
| | - Nimbe Torres
- Department of Physiology of Nutrition, National Institute of Medical Science and Nutrition Salvador Zubiran, Mexico City, Mexico
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Miranda-Lora AL, Molina-Díaz M, Cruz M, Sánchez-Urbina R, Martínez-Rodríguez NL, López-Martínez B, Klünder-Klünder M. Genetic polymorphisms associated with pediatric-onset type 2 diabetes: A family-based transmission disequilibrium test and case-control study. Pediatr Diabetes 2019; 20:239-245. [PMID: 30652413 DOI: 10.1111/pedi.12818] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 11/12/2018] [Accepted: 01/04/2019] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND AND OBJECTIVE Genetics play a very strong role in the development of pediatric-onset type 2 diabetes (T2D); however, little information exists about specific common single nucleotide polymorphisms (SNPs) associated with T2D in this age group. The aim of the study was to analyze the association and parental transmission of 64 obesity-related SNPs with pediatric-onset T2D in Mexican families. METHODS A total of 57 pedigrees containing 171 probands with pediatric-onset T2D and 119 unrelated controls older than 18 years were included. The participants were genotyped for 64 polymorphisms. Association of each variant with pediatric-onset T2D was analyzed through a parent-offspring transmission disequilibrium test (TDT) and in a case-control comparison by χ2 analysis. RESULTS Five SNPs exhibited associations with pediatric-onset T2D in the combined case-parent trio and case-control analysis: LINGO/rs10968576 (odds ratio [OR] 1.82, P = 0.003), POC5/rs2112347 (OR 1.96, P = 2.4E-5), RPS10-NUDT3/rs206936 (OR 1.40, P = 0.023), GLIS3/rs7034200 (OR 2.34, P = 1.2E-6), and VEGFA/rs6905288 (OR 1.58, P = 0.015). The first three were also associated with obesity status. The SNPs POC5/rs2112347 and RPS10-NUDT3/rs206936 were significantly associated through the maternal allele and GLIS3/rs7034200 through the paternal allele (P < 0.05). CONCLUSIONS These findings suggest that certain SNPs associated with obesity and other metabolic traits may also be involved in risk of pediatric-onset T2D in Mexican families. We also identified preferential transmission of parental alleles in some variants.
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Affiliation(s)
- América L Miranda-Lora
- Research Unit of Medicine Based on Evidence, Mexico Children's Hospital Federico Gómez, Mexico City, Mexico
| | - Mario Molina-Díaz
- Department of Endocrinology, Mexico Children's Hospital Federico Gómez, Mexico City, Mexico
| | - Miguel Cruz
- Medical Research Unit in Biochemistry, Hospital de Especialidades Centro Médico Nacional SXXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Rocío Sánchez-Urbina
- Research Laboratory in Developmental Biology and Experimental Teratogenesis, Mexico Children's Hospital Federico Gómez, Mexico City, Mexico
| | - Nancy L Martínez-Rodríguez
- Departament of Community Health Research, Mexico Children's Hospital Federico Gómez, Mexico City, Mexico
| | - Briceida López-Martínez
- Deputy Director of Auxiliary Diagnostic Services, Mexico Children's Hospital Federico Gómez, Mexico City, Mexico
| | - Miguel Klünder-Klünder
- Deputy Director of Research, Mexico Children's Hospital Federico Gómez, Mexico City, Mexico.,Research Committee, Latin American Society for Pediatric Gastroenterology, Hepatology and Nutrition (LASPGHAN), Mexico City, Mexico
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Gong H, Xiao S, Li W, Huang T, Huang X, Yan G, Huang Y, Qiu H, Jiang K, Wang X, Zhang H, Tang J, Li L, Li Y, Wang C, Qiao C, Ren J, Huang L, Yang B. Unravelling the genetic loci for growth and carcass traits in Chinese Bamaxiang pigs based on a 1.4 million SNP array. J Anim Breed Genet 2019; 136:3-14. [PMID: 30417949 DOI: 10.1111/jbg.12365] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 08/29/2018] [Accepted: 09/22/2018] [Indexed: 12/21/2022]
Abstract
Bamaxiang pig is from Guangxi province in China, characterized by its small body size and two-end black coat colour. It is an important indigenous breed for local pork market and excellent animal model for biomedical research. In this study, we performed genomewide association studies (GWAS) on 43 growth and carcass traits in 315 purebred Bamaxiang pigs based on a 1.4 million SNP array. We observed considerable phenotypic variability in the growth and carcass traits in the Bamaxiang pigs. The corresponding SNP based heritability varied greatly across the 43 traits and ranged from 9.0% to 88%. Through a conditional GWAS, we identified 53 significant associations for 35 traits at p value threshold of 10-6 . Among which, 26 associations on chromosome 3, 7, 14 and X passed a genomewide significance threshold of 5 × 10-8 . The most remarkable loci were at around 30.6 Mb on chromosome 7, which had growth stage-dependent effects on body lengths and cannon circumferences and showed large effects on multiple carcass traits. We discussed HMGA1 NUDT3, EIF2AK1, TMEM132C and AFF2 that near the lead SNP of significant loci as plausible candidate genes for corresponding traits. We also showed that including phenotypic covariate in GWAS can help to reveal additional significant loci for the target traits. The results provide insight into the genetic architecture of growth and carcass traits in Bamaxiang pigs.
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Affiliation(s)
- Huanfa Gong
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Shijun Xiao
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Wanbo Li
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Tao Huang
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Xiaochang Huang
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Guorong Yan
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Yizhong Huang
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Hengqing Qiu
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Kai Jiang
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Xiaopeng Wang
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Hui Zhang
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Jianhong Tang
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Lin Li
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Yiping Li
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Chenbin Wang
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Chuanmin Qiao
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Jun Ren
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Lusheng Huang
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Bin Yang
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
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Chakraborty A. The inositol pyrophosphate pathway in health and diseases. Biol Rev Camb Philos Soc 2018; 93:1203-1227. [PMID: 29282838 PMCID: PMC6383672 DOI: 10.1111/brv.12392] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 11/28/2017] [Accepted: 12/05/2017] [Indexed: 12/11/2022]
Abstract
Inositol pyrophosphates (IPPs) are present in organisms ranging from plants, slime moulds and fungi to mammals. Distinct classes of kinases generate different forms of energetic diphosphate-containing IPPs from inositol phosphates (IPs). Conversely, polyphosphate phosphohydrolase enzymes dephosphorylate IPPs to regenerate the respective IPs. IPPs and/or their metabolizing enzymes regulate various cell biological processes by modulating many proteins via diverse mechanisms. In the last decade, extensive research has been conducted in mammalian systems, particularly in knockout mouse models of relevant enzymes. Results obtained from these studies suggest impacts of the IPP pathway on organ development, especially of brain and testis. Conversely, deletion of specific enzymes in the pathway protects mice from various diseases such as diet-induced obesity (DIO), type-2 diabetes (T2D), fatty liver, bacterial infection, thromboembolism, cancer metastasis and aging. Furthermore, pharmacological inhibition of the same class of enzymes in mice validates the therapeutic importance of this pathway in cardio-metabolic diseases. This review critically analyses these findings and summarizes the significance of the IPP pathway in mammalian health and diseases. It also evaluates benefits and risks of targeting this pathway in disease therapies. Finally, future directions of mammalian IPP research are discussed.
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Affiliation(s)
- Anutosh Chakraborty
- Department of Pharmacology and Physiology, Saint Louis University School of Medicine, Saint Louis, MO 63104, U.S.A
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Le X, Antony R, Razavi P, Treacy DJ, Luo F, Ghandi M, Castel P, Scaltriti M, Baselga J, Garraway LA. Systematic Functional Characterization of Resistance to PI3K Inhibition in Breast Cancer. Cancer Discov 2016; 6:1134-1147. [PMID: 27604488 DOI: 10.1158/2159-8290.cd-16-0305] [Citation(s) in RCA: 96] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 08/16/2016] [Indexed: 12/21/2022]
Abstract
PIK3CA (which encodes the PI3K alpha isoform) is the most frequently mutated oncogene in breast cancer. Small-molecule PI3K inhibitors have shown promise in clinical trials; however, intrinsic and acquired resistance limits their utility. We used a systematic gain-of-function approach to identify genes whose upregulation confers resistance to the PI3K inhibitor BYL719 in breast cancer cells. Among the validated resistance genes, Proviral Insertion site in Murine leukemia virus (PIM) kinases conferred resistance by maintaining downstream PI3K effector activation in an AKT-independent manner. Concurrent pharmacologic inhibition of PIM and PI3K overcame this resistance mechanism. We also observed increased PIM expression and activity in a subset of breast cancer biopsies with clinical resistance to PI3K inhibitors. PIM1 overexpression was mutually exclusive with PIK3CA mutation in treatment-naïve breast cancers, suggesting downstream functional redundancy. Together, these results offer new insights into resistance to PI3K inhibitors and support clinical studies of combined PIM/PI3K inhibition in a subset of PIK3CA-mutant cancers. SIGNIFICANCE PIM kinase overexpression confers resistance to small-molecule PI3K inhibitors. Combined inhibition of PIM and PI3K may therefore be warranted in a subset of breast cancers. Cancer Discov; 6(10); 1134-47. ©2016 AACR.This article is highlighted in the In This Issue feature, p. 1069.
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Affiliation(s)
- Xiuning Le
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA.,The Broad Institute of MIT and Harvard, Cambridge, MA.,Division of Hematology Oncology, Department of Medicine, Beth Israel Deaconess Medical Center, Boston MA
| | - Rajee Antony
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA.,The Broad Institute of MIT and Harvard, Cambridge, MA
| | - Pedram Razavi
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, NewYork, NY.,Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Daniel J Treacy
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA.,The Broad Institute of MIT and Harvard, Cambridge, MA
| | - Flora Luo
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA.,The Broad Institute of MIT and Harvard, Cambridge, MA
| | - Mahmoud Ghandi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA.,The Broad Institute of MIT and Harvard, Cambridge, MA
| | - Pau Castel
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, NewYork, NY
| | - Maurizio Scaltriti
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, NewYork, NY.,Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jose Baselga
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, NewYork, NY.,Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Levi A Garraway
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA.,The Broad Institute of MIT and Harvard, Cambridge, MA.,Department of Medicine, Brigham and Women's Hospital, Boston MA
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11
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Dechamethakun S, Muramatsu M. Long noncoding RNA variations in cardiometabolic diseases. J Hum Genet 2016; 62:97-104. [PMID: 27305986 DOI: 10.1038/jhg.2016.70] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Revised: 04/27/2016] [Accepted: 05/06/2016] [Indexed: 12/18/2022]
Abstract
Cardiometabolic diseases are characterized as a combination of multiple risk factors for cardiovascular disease (CVD) and metabolic diseases including diabetes mellitus, dyslipidemia, hypertension and abdominal obesity. This cluster of abnormalities individually and interdependently leads to atherosclerosis and CVD morbidity and mortality. In the past decade, genome-wide association studies (GWASs) have identified a series of cardiometabolic disease-associated variants that can collectively explain a small proportion of the variability. Intriguingly, the susceptibility variants imputed from GWASs usually do not reside in the coding regions, suggesting a crucial role of the noncoding elements of the genome. In recent years, emerging evidence suggests that noncoding RNA (ncRNA) is functional for physiology and pathophysiology of human diseases. These include microRNAs and long noncoding RNAs (lncRNAs) that are now implicated in human diseases. The ncRNAs can interact with each other and with proteins, to interfere gene expressions, leading to the development of many human disorders. Although evidence suggests the functional role of lncRNAs in cardiometabolic traits, the molecular mechanisms of gene regulation underlying cardiometabolic diseases remain to be better defined. Here, we summarize the recent discoveries of lncRNA variations in the context of cardiometabolic diseases.
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Affiliation(s)
- Sariya Dechamethakun
- Department of Molecular Epidemiology, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - Masaaki Muramatsu
- Department of Molecular Epidemiology, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
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12
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Sung YJ, Pérusse L, Sarzynski MA, Fornage M, Sidney S, Sternfeld B, Rice T, Terry G, Jacobs DR, Katzmarzyk P, Curran JE, Carr JJ, Blangero J, Ghosh S, Després JP, Rankinen T, Rao D, Bouchard C. Genome-wide association studies suggest sex-specific loci associated with abdominal and visceral fat. Int J Obes (Lond) 2016; 40:662-74. [PMID: 26480920 PMCID: PMC4821694 DOI: 10.1038/ijo.2015.217] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Revised: 10/05/2015] [Accepted: 10/06/2015] [Indexed: 12/21/2022]
Abstract
BACKGROUND To identify loci associated with abdominal fat and replicate prior findings, we performed genome-wide association (GWA) studies of abdominal fat traits: subcutaneous adipose tissue (SAT); visceral adipose tissue (VAT); total adipose tissue (TAT) and visceral to subcutaneous adipose tissue ratio (VSR). SUBJECTS AND METHODS Sex-combined and sex-stratified analyses were performed on each trait with (TRAIT-BMI) or without (TRAIT) adjustment for body mass index (BMI), and cohort-specific results were combined via a fixed effects meta-analysis. A total of 2513 subjects of European descent were available for the discovery phase. For replication, 2171 European Americans and 772 African Americans were available. RESULTS A total of 52 single-nucleotide polymorphisms (SNPs) encompassing 7 loci showed suggestive evidence of association (P<1.0 × 10(-6)) with abdominal fat in the sex-combined analyses. The strongest evidence was found on chromosome 7p14.3 between a SNP near BBS9 gene and VAT (rs12374818; P=1.10 × 10(-7)), an association that was replicated (P=0.02). For the BMI-adjusted trait, the strongest evidence of association was found between a SNP near CYCSP30 and VAT-BMI (rs10506943; P=2.42 × 10(-7)). Our sex-specific analyses identified one genome-wide significant (P<5.0 × 10(-8)) locus for SAT in women with 11 SNPs encompassing the MLLT10, DNAJC1 and EBLN1 genes on chromosome 10p12.31 (P=3.97 × 10(-8) to 1.13 × 10(-8)). The THNSL2 gene previously associated with VAT in women was also replicated (P=0.006). The six gene/loci showing the strongest evidence of association with VAT or VAT-BMI were interrogated for their functional links with obesity and inflammation using the Biograph knowledge-mining software. Genes showing the closest functional links with obesity and inflammation were ADCY8 and KCNK9, respectively. CONCLUSIONS Our results provide evidence for new loci influencing abdominal visceral (BBS9, ADCY8, KCNK9) and subcutaneous (MLLT10/DNAJC1/EBLN1) fat, and confirmed a locus (THNSL2) previously reported to be associated with abdominal fat in women.
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Affiliation(s)
- Yun Ju Sung
- Division of Biostatistics, Washington University School of Medicine, St-Louis, MO
| | - Louis Pérusse
- Department of Kinesiology, School of Medicine and Institute of Nutrition and Functional Foods, Laval University, Québec, QC
| | - Mark A. Sarzynski
- Human Genomics Laboratory, Pennington Biomedical Research Center, Baton Rouge, LA
| | - Myriam Fornage
- Center for Human Genetics, University of Texas Health Science Center, Houston, TX
| | - Steve Sidney
- Division of Research, Kaiser Permanente Northern California, Oakland, CA
| | - Barbara Sternfeld
- Division of Research, Kaiser Permanente Northern California, Oakland, CA
| | - Treva Rice
- Division of Biostatistics, Washington University School of Medicine, St-Louis, MO
| | - Gregg Terry
- Department of Radiology, School of Medicine, Vanderbilt University, Nahsville, TN
| | - David R. Jacobs
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, MN
| | - Peter Katzmarzyk
- Human Genomics Laboratory, Pennington Biomedical Research Center, Baton Rouge, LA
| | - Joanne E Curran
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley, TX
| | - John Jeffrey Carr
- Department of Radiology, School of Medicine, Vanderbilt University, Nahsville, TN
| | - John Blangero
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley, TX
| | - Sujoy Ghosh
- Cardiovascular and Metabolic Disorders Program and Center for Computational Biology, Duke-NUS Graduate Medical School, Singapore
| | - Jean-Pierre Després
- Department of Kinesiology, School of Medicine and Institute of Nutrition and Functional Foods, Laval University, Québec, QC
- Centre de recherché de l’Institut universitaire de cardiologie et de pneumologie de Québec, Québec, QC
| | - Tuomo Rankinen
- Human Genomics Laboratory, Pennington Biomedical Research Center, Baton Rouge, LA
| | - D.C. Rao
- Division of Biostatistics, Washington University School of Medicine, St-Louis, MO
| | - Claude Bouchard
- Human Genomics Laboratory, Pennington Biomedical Research Center, Baton Rouge, LA
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13
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Williams MJ, Eriksson A, Shaik M, Voisin S, Yamskova O, Paulsson J, Thombare K, Fredriksson R, Schiöth HB. The Obesity-Linked Gene Nudt3 Drosophila Homolog Aps Is Associated With Insulin Signaling. Mol Endocrinol 2015; 29:1303-19. [PMID: 26168034 DOI: 10.1210/me.2015-1077] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Several genome-wide association studies have linked the Nudix hydrolase family member nucleoside diphosphate-linked moiety X motif 3 (NUDT3) to obesity. However, the manner of NUDT3 involvement in obesity is unknown, and NUDT3 expression, regulation, and signaling in the central nervous system has not been studied. We performed an extensive expression analysis in mice, as well as knocked down the Drosophila NUDT3 homolog Aps in the nervous system, to determine its effect on metabolism. Detailed in situ hybridization studies in the mouse brain revealed abundant Nudt3 mRNA and protein expression throughout the brain, including reward- and feeding-related regions of the hypothalamus and amygdala, whereas Nudt3 mRNA expression was significantly up-regulated in the hypothalamus and brainstem of food-deprived mice. Knocking down Aps in the Drosophila central nervous system, or a subset of median neurosecretory cells, known as the insulin-producing cells (IPCs), induces hyperinsulinemia-like phenotypes, including a decrease in circulating trehalose levels as well as significantly decreasing all carbohydrate levels under starvation conditions. Moreover, lowering Aps IPC expression leads to a decreased ability to recruit these lipids during starvation. Also, loss of neuronal Aps expression caused a starvation susceptibility phenotype while inducing hyperphagia. Finally, the loss of IPC Aps lowered the expression of Akh, Ilp6, and Ilp3, genes known to be inhibited by insulin signaling. These results point toward a role for this gene in the regulation of insulin signaling, which could explain the robust association with obesity in humans.
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Affiliation(s)
- Michael J Williams
- Department of Neuroscience, Division of Functional Pharmacology, Uppsala University, 75 124 Uppsala, Sweden
| | - Anders Eriksson
- Department of Neuroscience, Division of Functional Pharmacology, Uppsala University, 75 124 Uppsala, Sweden
| | - Muksheed Shaik
- Department of Neuroscience, Division of Functional Pharmacology, Uppsala University, 75 124 Uppsala, Sweden
| | - Sarah Voisin
- Department of Neuroscience, Division of Functional Pharmacology, Uppsala University, 75 124 Uppsala, Sweden
| | - Olga Yamskova
- Department of Neuroscience, Division of Functional Pharmacology, Uppsala University, 75 124 Uppsala, Sweden
| | - Johan Paulsson
- Department of Neuroscience, Division of Functional Pharmacology, Uppsala University, 75 124 Uppsala, Sweden
| | - Ketan Thombare
- Department of Neuroscience, Division of Functional Pharmacology, Uppsala University, 75 124 Uppsala, Sweden
| | - Robert Fredriksson
- Department of Neuroscience, Division of Functional Pharmacology, Uppsala University, 75 124 Uppsala, Sweden
| | - Helgi B Schiöth
- Department of Neuroscience, Division of Functional Pharmacology, Uppsala University, 75 124 Uppsala, Sweden
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14
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Guénard F, Lamontagne M, Bossé Y, Deshaies Y, Cianflone K, Kral JG, Marceau P, Vohl MC. Influences of gestational obesity on associations between genotypes and gene expression levels in offspring following maternal gastrointestinal bypass surgery for obesity. PLoS One 2015; 10:e0117011. [PMID: 25603303 PMCID: PMC4300091 DOI: 10.1371/journal.pone.0117011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Accepted: 12/17/2014] [Indexed: 12/17/2022] Open
Abstract
METHODS Whole-genome genotyping and gene expression analyses in blood of 22 BMS and 23 AMS offspring from 19 mothers were conducted using Illumina HumanOmni-5-Quad and HumanHT-12 v4 Expression BeadChips, respectively. Using PLINK we analyzed interactions between offspring gene variations and maternal surgical status on offspring gene expression levels. Altered biological functions and pathways were identified and visualized using DAVID and Ingenuity Pathway Analysis. RESULTS Significant interactions (p ≤ 1.22 x 10(-12)) were found for 525 among the 16,060 expressed transcripts: 1.9% of tested SNPs were involved. Gene function and pathway analysis demonstrated enrichment of transcription and of cellular metabolism functions and overrepresentation of cellular stress and signaling, immune response, inflammation, growth, proliferation and development pathways. CONCLUSION We suggest that impaired maternal gestational metabolic fitness interacts with offspring gene variations modulating gene expression levels, providing potential mechanisms explaining improved cardiometabolic risk profiles of AMS offspring related to ameliorated maternal lipid and carbohydrate metabolism.
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Affiliation(s)
- Frédéric Guénard
- Institute of Nutrition and Functional Foods (INAF) and Department of Food Science and Nutrition, Laval University, Quebec, Canada
- Endocrinology and Nephrology, CHU de Quebec Research Center, Quebec, Canada
| | | | - Yohan Bossé
- Quebec Heart and Lung Institute, Quebec, Canada
- Department of Molecular Medicine, Laval University, Quebec, Canada
| | - Yves Deshaies
- Quebec Heart and Lung Institute, Quebec, Canada
- Department of Medicine, Laval University, Quebec, Canada
| | - Katherine Cianflone
- Quebec Heart and Lung Institute, Quebec, Canada
- Department of Medicine, Laval University, Quebec, Canada
| | - John G. Kral
- Department of Surgery, SUNY Downstate Medical Center, Brooklyn, New York, United States of America
| | - Picard Marceau
- Quebec Heart and Lung Institute, Quebec, Canada
- Department of Surgery, Laval University, Quebec, Canada
| | - Marie-Claude Vohl
- Institute of Nutrition and Functional Foods (INAF) and Department of Food Science and Nutrition, Laval University, Quebec, Canada
- Endocrinology and Nephrology, CHU de Quebec Research Center, Quebec, Canada
- * E-mail:
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