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Huang M, Zheng J, Chen L, You S, Huang H. Advances in the study of the pathogenesis of obesity: Based on apolipoproteins. Clin Chim Acta 2023; 545:117359. [PMID: 37086940 DOI: 10.1016/j.cca.2023.117359] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 04/14/2023] [Accepted: 04/17/2023] [Indexed: 04/24/2023]
Abstract
Obesity is a state presented by excessive accumulation and abnormal distribution of body fat, with metabolic disorders being one of its distinguishing features. Obesity is associated with dyslipidemia, apolipoproteins are important structural components of plasma lipoproteins, which influence lipid metabolism in the body by participating in lipoprotein metabolism and are closely related to the progression of obesity. Apolipoproteins influence the progression of obesity from lipid metabolism, energy expenditure and inflammatory response. In this review, we discuss the alterations of apolipoproteins in obesity, understand the potential mechanisms by which apolipoproteins affect obesity, as well as provide new targets for the treatment of obesity.
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Affiliation(s)
- Mingjing Huang
- The Second Clinical Medical College of Fujian Medical University, Quanzhou, Fujian Province China; Department of Endocrinology, the Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian Province, China
| | - Jingyi Zheng
- The Second Clinical Medical College of Fujian Medical University, Quanzhou, Fujian Province China; Department of Endocrinology, the Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian Province, China
| | - Lijun Chen
- Department of Endocrinology, the Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian Province, China
| | - Sufang You
- The Second Clinical Medical College of Fujian Medical University, Quanzhou, Fujian Province China; Department of Endocrinology, the Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian Province, China
| | - Huibin Huang
- Department of Endocrinology, the Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian Province, China.
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Head ST, Leslie EJ, Cutler DJ, Epstein MP. POIROT: a powerful test for parent-of-origin effects in unrelated samples leveraging multiple phenotypes. Bioinformatics 2023; 39:btad199. [PMID: 37067493 PMCID: PMC10148680 DOI: 10.1093/bioinformatics/btad199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 04/03/2023] [Accepted: 04/06/2023] [Indexed: 04/18/2023] Open
Abstract
MOTIVATION There is widespread interest in identifying genetic variants that exhibit parent-of-origin effects (POEs) wherein the effect of an allele on phenotype expression depends on its parental origin. POEs can arise from different phenomena including genomic imprinting and have been documented for many complex traits. Traditional tests for POEs require family data to determine parental origins of transmitted alleles. As most genome-wide association studies (GWAS) sample unrelated individuals (where allelic parental origin is unknown), the study of POEs in such datasets requires sophisticated statistical methods that exploit genetic patterns we anticipate observing when POEs exist. We propose a method to improve discovery of POE variants in large-scale GWAS samples that leverages potential pleiotropy among multiple correlated traits often collected in such studies. Our method compares the phenotypic covariance matrix of heterozygotes to homozygotes based on a Robust Omnibus Test. We refer to our method as the Parent of Origin Inference using Robust Omnibus Test (POIROT) of multiple quantitative traits. RESULTS Through simulation studies, we compared POIROT to a competing univariate variance-based method which considers separate analysis of each phenotype. We observed POIROT to be well-calibrated with improved power to detect POEs compared to univariate methods. POIROT is robust to non-normality of phenotypes and can adjust for population stratification and other confounders. Finally, we applied POIROT to GWAS data from the UK Biobank using BMI and two cholesterol phenotypes. We identified 338 genome-wide significant loci for follow-up investigation. AVAILABILITY AND IMPLEMENTATION The code for this method is available at https://github.com/staylorhead/POIROT-POE.
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Affiliation(s)
- S Taylor Head
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, GA 30322, United States
| | - Elizabeth J Leslie
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, United States
| | - David J Cutler
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, United States
| | - Michael P Epstein
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, United States
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3
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Workalemahu T, Enquobahrie DA, Gelaye B, Tadesse MG, Sanchez SE, Tekola-Ayele F, Hajat A, Thornton TA, Ananth CV, Williams MA. Maternal-fetal genetic interactions, imprinting, and risk of placental abruption. J Matern Fetal Neonatal Med 2022; 35:3473-3482. [PMID: 32972274 PMCID: PMC8601203 DOI: 10.1080/14767058.2020.1822314] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Revised: 09/02/2020] [Accepted: 09/08/2020] [Indexed: 12/17/2022]
Abstract
RESULTS Abruption cases were more likely to experience preeclampsia, have shorter gestational age, and deliver infants with lower birthweight compared with controls. Models with MFGI effects provided improved fit than models with only maternal and fetal genotype main effects for SNP rs12530904 (p-value = 1.2e-04) in calcium/calmodulin-dependent protein kinase [CaM kinase] II beta (CAMK2B), and, SNP rs73136795 (p-value = 1.9e-04) in peroxisome proliferator-activated receptor-gamma (PPARG), both MB genes. We identified 320 SNPs in 45 maternally-imprinted genes (including potassium voltage-gated channel subfamily Q member 1 [KCNQ1], neurotrimin [NTM], and, ATPase phospholipid transporting 10 A [ATP10A]) associated with abruption. Top hits included rs2012323 (p-value = 1.6E-16) and rs12221520 (p-value1.3e-13) in KCNQ1, rs8036892 (p-value = 9.3E-17) and rs188497582 in ATP10A, rs12589854 (p-value = 2.9E-11) and rs80203467 (p-value = 4.6e-11) in maternally expressed 8, small nucleolar RNA host (MEG8), and rs138281088 in solute carrier family 22 member 2 (SLC22A2) (p-value = 6.8e-9). CONCLUSIONS We identified novel PA-related maternal-fetal MB gene interactions and imprinting effects that highlight the role of the fetus in PA risk development. Findings can inform mechanistic investigations to understand the pathogenesis of PA.
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Affiliation(s)
- Tsegaselassie Workalemahu
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, Washington
- Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, University of Utah, Salt Lake City, Utah
| | - Daniel A. Enquobahrie
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, Washington
- Center for Perinatal Studies, Swedish Medical Center, Seattle, Washington
| | - Bizu Gelaye
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Mahlet G. Tadesse
- Department of Mathematics and Statistics, Georgetown University, Washington, District of Columbia
| | - Sixto E. Sanchez
- Facultad de Medicina Humana, Universidad de San Martín de Porres, Lima, Peru
- Asociación Civil PROESA, Lima, Peru
| | - Fasil Tekola-Ayele
- Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, University of Utah, Salt Lake City, Utah
| | - Anjum Hajat
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, Washington
| | | | - Cande V. Ananth
- Division of Epidemiology and Biostatistics, Department of Obstetrics, Gynecology and Reproductive Sciences, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ
- Department of Biostatistics and Epidemiology, Rutgers School of Public Health, Piscataway, NJ
- Cardiovascular Institute of New Jersey (CVI-NJ), Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ
- Environmental and Occupational Health Sciences Institute (EOHSI), Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ
| | - Michelle A. Williams
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
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4
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Kong YF, Li MK, Yuan YX, Yang ZY, Yu WY, Zhao PZ, Zhou JY. Detection of Parent-of-Origin Effects for the Variants Associated With Behavioral Disinhibition in the MCTFR Data. Front Genet 2022; 13:831685. [PMID: 35559008 PMCID: PMC9086303 DOI: 10.3389/fgene.2022.831685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 03/28/2022] [Indexed: 11/13/2022] Open
Abstract
Behavioral disinhibition is one of the important characteristics of many mental diseases. It has been reported in literature that serious behavioral disinhibition will affect people's health and greatly reduce people's quality of life. Meanwhile, behavioral disinhibition can easily lead to illegal drug abuse and violent crimes, etc., which will bring great harm to the society. At present, large-scale genome-wide association analysis has identified many loci associated with behavioral disinhibition. However, these studies have not incorporated the parent-of-origin effects (POE) into analysis, which may ignore or underestimate the genetic effects of loci on behavioral disinhibition. Therefore, in this article, we analyzed the five phenotypes related to behavioral disinhibition in the Minnesota Center for Twin and Family Research data (nicotine, alcohol consumption, alcohol dependence, illicit drugs, and non-substance use related behavioral disinhibition), to further explore the POE of variants on behavioral disinhibition. We applied a linear mixed model to test for the POE at a genome-wide scale on five transformed phenotypes, and found nine SNPs with statistically significant POE at the significance level of 5 × 10-8. Among them, SNPs rs4141854, rs9394515, and rs4711553 have been reported to be associated with two neurological disorders (restless legs syndrome and Tourette's syndrome) which are related to behavioral disinhibition; SNPs rs12960235 and rs715351 have been found to be associated with head and neck squamous cell carcinoma, skin cancer and type I diabetes, while both SNPs have not been identified to be related to behavioral disinhibition in literature; SNPs rs704833, rs6837925, rs1863548, and rs11067062 are novel loci identified in this article, and their function annotations have not been reported in literature. Follow-up study in molecular genetics is needed to verify whether they are surely related to behavioral disinhibition.
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Affiliation(s)
- Yi-Fan Kong
- Department of Biostatistics, State Key Laboratory of Organ Failure Research, Ministry of Education, and Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China.,Guangdong-Hong Hong-Macao Joint Laboratory for Contaminants Exposure and Health, Guangzhou, China
| | - Meng-Kai Li
- Department of Biostatistics, State Key Laboratory of Organ Failure Research, Ministry of Education, and Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China.,Guangdong-Hong Hong-Macao Joint Laboratory for Contaminants Exposure and Health, Guangzhou, China
| | - Yu-Xin Yuan
- Department of Biostatistics, State Key Laboratory of Organ Failure Research, Ministry of Education, and Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Zi-Ying Yang
- Department of Biostatistics, State Key Laboratory of Organ Failure Research, Ministry of Education, and Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Wen-Yi Yu
- Department of Biostatistics, State Key Laboratory of Organ Failure Research, Ministry of Education, and Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Pei-Zhen Zhao
- Department of Biostatistics, State Key Laboratory of Organ Failure Research, Ministry of Education, and Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Ji-Yuan Zhou
- Department of Biostatistics, State Key Laboratory of Organ Failure Research, Ministry of Education, and Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China.,Guangdong-Hong Hong-Macao Joint Laboratory for Contaminants Exposure and Health, Guangzhou, China
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5
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St Pierre CL, Macias-Velasco JF, Wayhart JP, Yin L, Semenkovich CF, Lawson HA. Genetic, epigenetic, and environmental mechanisms govern allele-specific gene expression. Genome Res 2022; 32:1042-1057. [PMID: 35501130 PMCID: PMC9248887 DOI: 10.1101/gr.276193.121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 04/14/2022] [Indexed: 12/03/2022]
Abstract
Allele-specific expression (ASE) is a phenomenon in which one allele is preferentially expressed over the other. Genetic and epigenetic factors cause ASE by altering the final composition of a gene's product, leading to expression imbalances that can have functional consequences on phenotypes. Environmental signals also impact allele-specific expression, but how they contribute to this cross talk remains understudied. Here, we explored how genotype, parent-of-origin, tissue, sex, and dietary fat simultaneously influence ASE biases. Male and female mice from a F1 reciprocal cross of the LG/J and SM/J strains were fed a high or low fat diet. We harnessed strain-specific variants to distinguish between two ASE classes: parent-of-origin-dependent (unequal expression based on parental origin) and sequence-dependent (unequal expression based on nucleotide identity). We present a comprehensive map of ASE patterns in 2853 genes across three tissues and nine environmental contexts. We found that both ASE classes are highly dependent on tissue and environmental context. They vary across metabolically relevant tissues, between males and females, and in response to dietary fat. We also found 45 genes with inconsistent ASE biases that switched direction across tissues and/or environments. Finally, we integrated ASE and QTL data from published intercrosses of the LG/J and SM/J strains. Our ASE genes are often enriched in QTLs for metabolic and musculoskeletal traits, highlighting how this orthogonal approach can prioritize candidate genes. Together, our results provide novel insights into how genetic, epigenetic, and environmental mechanisms govern allele-specific expression, which is an essential step toward deciphering the genotype-to-phenotype map.
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Affiliation(s)
| | | | | | - Li Yin
- Washington University in Saint Louis
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6
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Basavaraju P, Balasubramani R, Kathiresan DS, Devaraj I, Babu K, Alagarsamy V, Puthamohan VM. Genetic Regulatory Networks of Apolipoproteins and Associated Medical Risks. Front Cardiovasc Med 2022; 8:788852. [PMID: 35071357 PMCID: PMC8770923 DOI: 10.3389/fcvm.2021.788852] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Accepted: 11/22/2021] [Indexed: 12/22/2022] Open
Abstract
Apolipoproteins (APO proteins) are the lipoprotein family proteins that play key roles in transporting lipoproteins all over the body. There are nearly more than twenty members reported in the APO protein family, among which the A, B, C, E, and L play major roles in contributing genetic risks to several disorders. Among these genetic risks, the single nucleotide polymorphisms (SNPs), involving the variation of single nucleotide base pairs, and their contributing polymorphisms play crucial roles in the apolipoprotein family and its concordant disease heterogeneity that have predominantly recurred through the years. In this review, we have contributed a handful of information on such genetic polymorphisms that include APOE, ApoA1/B ratio, and A1/C3/A4/A5 gene cluster-based population genetic studies carried throughout the world, to elaborately discuss the effects of various genetic polymorphisms in imparting various medical conditions, such as obesity, cardiovascular, stroke, Alzheimer's disease, diabetes, vascular complications, and other associated risks.
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Affiliation(s)
- Preethi Basavaraju
- Biomaterials and Nano-Medicine Laboratory, Department of Human Genetics and Molecular Biology, Bharathiar University, Coimbatore, India
| | - Rubadevi Balasubramani
- Biomaterials and Nano-Medicine Laboratory, Department of Human Genetics and Molecular Biology, Bharathiar University, Coimbatore, India
| | - Divya Sri Kathiresan
- Biomaterials and Nano-Medicine Laboratory, Department of Human Genetics and Molecular Biology, Bharathiar University, Coimbatore, India
| | - Ilakkiyapavai Devaraj
- Biomaterials and Nano-Medicine Laboratory, Department of Human Genetics and Molecular Biology, Bharathiar University, Coimbatore, India
| | - Kavipriya Babu
- Biomaterials and Nano-Medicine Laboratory, Department of Human Genetics and Molecular Biology, Bharathiar University, Coimbatore, India
| | - Vasanthakumar Alagarsamy
- Biomaterials and Nano-Medicine Laboratory, Department of Human Genetics and Molecular Biology, Bharathiar University, Coimbatore, India
| | - Vinayaga Moorthi Puthamohan
- Department of Human Genetics and Molecular Biology, Bharathiar University, Coimbatore, India
- *Correspondence: Vinayaga Moorthi Puthamohan
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7
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Lipid-Associated Variants near ANGPTL3 and LPL Show Parent-of-Origin Specific Effects on Blood Lipid Levels and Obesity. Genes (Basel) 2021; 13:genes13010091. [PMID: 35052431 PMCID: PMC8774740 DOI: 10.3390/genes13010091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 12/16/2021] [Accepted: 12/25/2021] [Indexed: 11/23/2022] Open
Abstract
Parent-of-origin effects (POE) and sex-specific parental effects have been reported for plasma lipid levels, and a strong relationship exists between dyslipidemia and obesity. We aim to explore whether genetic variants previously reported to have an association to lipid traits also show POE on blood lipid levels and obesity. Families from the Botnia cohort and the Hungarian Transdanubian Biobank (HTB) were genotyped for 12 SNPs, parental origin of alleles were inferred, and generalized estimating equations were modeled to assess parental-specific associations with lipid traits and obesity. POE were observed for the variants at the TMEM57, DOCK7/ANGPTL3, LPL, and APOA on lipid traits, the latter replicated in HTB. Sex-specific parental effects were also observed; variants at ANGPTL3/DOCK7 showed POE on lipid traits and obesity in daughters only, while those at LPL and TMEM57 showed POE on lipid traits in sons. Variants at LPL and DOCK7/ANGPTL3 showed POE on obesity-related traits in Botnia and HTB, and POE effects on obesity were seen to a higher degree in daughters. This highlights the need to include analysis of POEs in genetic studies of complex traits.
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Li X, Fu Z, Xu H, Zou J, Zhu H, Li Z, Su K, Huai D, Yi H, Guan J, Yin S. Influence of multiple apolipoprotein A-I and B genetic variations on insulin resistance and metabolic syndrome in obstructive sleep apnea. Nutr Metab (Lond) 2020; 17:83. [PMID: 33005209 PMCID: PMC7523361 DOI: 10.1186/s12986-020-00501-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Accepted: 09/09/2020] [Indexed: 01/01/2023] Open
Abstract
Background The relationships between apolipoprotein A-I (APOA-I), apolipoprotein B (APOB) with insulin resistance, metabolic syndrome (MetS) are unclear in OSA. We aimed to evaluate whether the multiple single nucleotide polymorphism (SNP) variants of APOA-I and APOB exert a collaborative effect on insulin resistance and MetS in OSA. Methods Initially, 12 APOA-I SNPs and 30 APOB SNPs in 5259 subjects were examined. After strict screening, four APOA-I SNPs and five APOB SNPs in 4007 participants were included. For each participant, the genetic risk score (GRS) was calculated based on the cumulative effect of multiple genetic variants of APOA-I and APOB. Logistic regression analyses were used to evaluate the relationships between APOA-I/APOB genetic polymorphisms, insulin resistance, and MetS in OSA. Results Serum APOB levels increased the risk of insulin resistance and MetS adjusting for age, gender and BMI [odds ratio (OR = 3.168, P < 0.001; OR = 6.098, P < 0.001, respectively]. APOA-I GRS decreased the risk of insulin resistance and MetS after adjustments (OR = 0.917, P = 0.001; OR = 0.870, P < 0.001, respectively). APOB GRS had no association with insulin resistance (OR = 1.364, P = 0.610), and had weak association with MetS after adjustments (OR = 1.072, P = 0.042). In addition, individuals in the top quintile of the APOA-I genetic score distribution had a lower risk of insulin resistance and MetS after adjustments (OR = 0.761, P = 0.007; OR = 0.637, P < 0.001, respectively). Conclusions In patients with OSA, cumulative effects of APOA-I genetic variations decreased the risk of insulin resistance and MetS, whereas multiple APOB genetic variations had no associations with insulin resistance and weak association with MetS.
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Affiliation(s)
- Xinyi Li
- Department of Otorhinolaryngology-Head and Neck Surgery, Center of Sleep Medicine, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, 600 Yishan Road, Shanghai, 200233 People's Republic of China.,Otolaryngological Institute of Shanghai Jiao Tong University, Yishan Road 600, Shanghai, 200233 People's Republic of China.,Shanghai Key Laboratory of Sleep Disordered Breathing, Shanghai, People's Republic of China
| | - Zhihui Fu
- Department of Otorhinolaryngology-Head and Neck Surgery, Center of Sleep Medicine, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, 600 Yishan Road, Shanghai, 200233 People's Republic of China.,Otolaryngological Institute of Shanghai Jiao Tong University, Yishan Road 600, Shanghai, 200233 People's Republic of China.,Shanghai Key Laboratory of Sleep Disordered Breathing, Shanghai, People's Republic of China
| | - Huajun Xu
- Department of Otorhinolaryngology-Head and Neck Surgery, Center of Sleep Medicine, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, 600 Yishan Road, Shanghai, 200233 People's Republic of China.,Otolaryngological Institute of Shanghai Jiao Tong University, Yishan Road 600, Shanghai, 200233 People's Republic of China.,Shanghai Key Laboratory of Sleep Disordered Breathing, Shanghai, People's Republic of China
| | - Jianyin Zou
- Department of Otorhinolaryngology-Head and Neck Surgery, Center of Sleep Medicine, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, 600 Yishan Road, Shanghai, 200233 People's Republic of China.,Otolaryngological Institute of Shanghai Jiao Tong University, Yishan Road 600, Shanghai, 200233 People's Republic of China.,Shanghai Key Laboratory of Sleep Disordered Breathing, Shanghai, People's Republic of China
| | - Huaming Zhu
- Department of Otorhinolaryngology-Head and Neck Surgery, Center of Sleep Medicine, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, 600 Yishan Road, Shanghai, 200233 People's Republic of China.,Otolaryngological Institute of Shanghai Jiao Tong University, Yishan Road 600, Shanghai, 200233 People's Republic of China.,Shanghai Key Laboratory of Sleep Disordered Breathing, Shanghai, People's Republic of China
| | - Zhiqiang Li
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Bio-X Institutes, Ministry of Education, Shanghai Jiao Tong University, Huashan Road 1954, Shanghai, 200030 People's Republic of China
| | - Kaiming Su
- Department of Otorhinolaryngology-Head and Neck Surgery, Center of Sleep Medicine, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, 600 Yishan Road, Shanghai, 200233 People's Republic of China.,Otolaryngological Institute of Shanghai Jiao Tong University, Yishan Road 600, Shanghai, 200233 People's Republic of China.,Shanghai Key Laboratory of Sleep Disordered Breathing, Shanghai, People's Republic of China
| | - De Huai
- Department of Otorhinolaryngology, Huai'an Second People's Hospital, Huai'an Hospital Affiliated to Xuzhou Medical University, 62 Huaihai South Road, Huai'an, 223002 Jiangsu People's Republic of China
| | - Hongliang Yi
- Department of Otorhinolaryngology-Head and Neck Surgery, Center of Sleep Medicine, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, 600 Yishan Road, Shanghai, 200233 People's Republic of China.,Otolaryngological Institute of Shanghai Jiao Tong University, Yishan Road 600, Shanghai, 200233 People's Republic of China.,Shanghai Key Laboratory of Sleep Disordered Breathing, Shanghai, People's Republic of China
| | - Jian Guan
- Department of Otorhinolaryngology-Head and Neck Surgery, Center of Sleep Medicine, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, 600 Yishan Road, Shanghai, 200233 People's Republic of China.,Otolaryngological Institute of Shanghai Jiao Tong University, Yishan Road 600, Shanghai, 200233 People's Republic of China.,Shanghai Key Laboratory of Sleep Disordered Breathing, Shanghai, People's Republic of China
| | - Shankai Yin
- Department of Otorhinolaryngology-Head and Neck Surgery, Center of Sleep Medicine, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, 600 Yishan Road, Shanghai, 200233 People's Republic of China.,Otolaryngological Institute of Shanghai Jiao Tong University, Yishan Road 600, Shanghai, 200233 People's Republic of China.,Shanghai Key Laboratory of Sleep Disordered Breathing, Shanghai, People's Republic of China
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9
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Senaldi L, Smith-Raska M. Evidence for germline non-genetic inheritance of human phenotypes and diseases. Clin Epigenetics 2020; 12:136. [PMID: 32917273 PMCID: PMC7488552 DOI: 10.1186/s13148-020-00929-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 08/26/2020] [Indexed: 12/20/2022] Open
Abstract
It is becoming increasingly apparent that certain phenotypes are inherited across generations independent of the information contained in the DNA sequence, by factors in germ cells that remain largely uncharacterized. As evidence for germline non-genetic inheritance of phenotypes and diseases continues to grow in model organisms, there are fewer reports of this phenomenon in humans, due to a variety of complications in evaluating this mechanism of inheritance in humans. This review summarizes the evidence for germline-based non-genetic inheritance in humans, as well as the significant challenges and important caveats that must be considered when evaluating this process in human populations. Most reports of this process evaluate the association of a lifetime exposure in ancestors with changes in DNA methylation or small RNA expression in germ cells, as well as the association between ancestral experiences and the inheritance of a phenotype in descendants, down to great-grandchildren in some cases. Collectively, these studies provide evidence that phenotypes can be inherited in a DNA-independent manner; the extent to which this process contributes to disease development, as well as the cellular and molecular regulation of this process, remain largely undefined.
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Affiliation(s)
- Liana Senaldi
- Division of Newborn Medicine, Department of Pediatrics, Weill Cornell Medicine, New York-Presbyterian Hospital, New York, NY, USA
| | - Matthew Smith-Raska
- Division of Newborn Medicine, Department of Pediatrics, Weill Cornell Medicine, New York-Presbyterian Hospital, New York, NY, USA. .,Drukier Institute for Children's Health, Weill Cornell Medicine, New York, NY, USA.
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10
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Blanco-Vaca F, Martin-Campos JM, Beteta-Vicente Á, Canyelles M, Martínez S, Roig R, Farré N, Julve J, Tondo M. Molecular analysis of APOB, SAR1B, ANGPTL3, and MTTP in patients with primary hypocholesterolemia in a clinical laboratory setting: Evidence supporting polygenicity in mutation-negative patients. Atherosclerosis 2019; 283:52-60. [PMID: 30782561 DOI: 10.1016/j.atherosclerosis.2019.01.036] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 01/17/2019] [Accepted: 01/24/2019] [Indexed: 12/24/2022]
Abstract
BACKGROUND AND AIMS Primary hypobetalipoproteinemia is generally considered a heterogenic group of monogenic, inherited lipoprotein disorders characterized by low concentrations of LDL cholesterol and apolipoprotein B in plasma. Lipoprotein disorders include abetalipoproteinemia, familial hypobetalipoproteinemia, chylomicron retention disease, and familial combined hypolipidemia. Our aim was to review and analyze the results of the molecular analysis of hypolipidemic patients studied in our laboratory over the last 15 years. METHODS The study included 44 patients with clinical and biochemical data. Genomic studies were performed and genetic variants were characterized by bioinformatics analysis. A weighted LDL cholesterol gene score was calculated to evaluate common variants associated with impaired lipid concentrations and their distribution among patients. RESULTS Twenty-three patients were genetically confirmed as affected by primary hypobetalipoproteinemia. In this group of patients, the most prevalent mutated genes were APOB (in 17 patients, with eight novel mutations identified), SAR1B (in 3 patients, with one novel mutation identified), ANGPTL3 (in 2 patients), and MTTP (in 1 patient). The other 21 patients could not be genetically diagnosed with hypobetalipoproteinemia despite presenting suggestive clinical and biochemical features. In these patients, two APOB genetic variants associated with lower LDL cholesterol were more frequent than in controls. Moreover, the LDL cholesterol gene score, calculated with 11 SNPs, was significantly lower in mutation-negative patients. CONCLUSIONS Around half of the patients could be genetically diagnosed. The results suggest that, in at least some of the patients without an identified mutation, primary hypobetalipoproteinemia may have a polygenic origin.
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Affiliation(s)
- Francisco Blanco-Vaca
- Hospital de la Santa Creu i Sant Pau, Servei de Bioquímica - IIB Sant Pau, Barcelona, Spain; CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Barcelona, Spain; Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Spain.
| | - Jesús M Martin-Campos
- CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Barcelona, Spain; Institut de Recerca de l'Hospital de la Santa Creu i Sant Pau- IIB Sant Pau, Barcelona, Spain
| | - Ángel Beteta-Vicente
- Hospital de la Santa Creu i Sant Pau, Servei de Bioquímica - IIB Sant Pau, Barcelona, Spain
| | - Marina Canyelles
- Hospital de la Santa Creu i Sant Pau, Servei de Bioquímica - IIB Sant Pau, Barcelona, Spain; Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Spain
| | - Susana Martínez
- Hospital de la Santa Creu i Sant Pau, Servei de Bioquímica - IIB Sant Pau, Barcelona, Spain
| | - Rosa Roig
- Hospital de la Santa Creu i Sant Pau, Servei de Bioquímica - IIB Sant Pau, Barcelona, Spain
| | - Núria Farré
- Institut de Recerca de l'Hospital de la Santa Creu i Sant Pau- IIB Sant Pau, Barcelona, Spain
| | - Josep Julve
- CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Barcelona, Spain; Institut de Recerca de l'Hospital de la Santa Creu i Sant Pau- IIB Sant Pau, Barcelona, Spain
| | - Mireia Tondo
- Hospital de la Santa Creu i Sant Pau, Servei de Bioquímica - IIB Sant Pau, Barcelona, Spain.
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11
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Pervjakova N, Kukushkina V, Haller T, Kasela S, Joensuu A, Kristiansson K, Annilo T, Perola M, Salomaa V, Jousilahti P, Metspalu A, Mägi R. Genome-wide analysis of nuclear magnetic resonance metabolites revealed parent-of-origin effect on triglycerides in medium very low-density lipoprotein in PTPRD gene. Biomark Med 2018. [DOI: 10.2217/bmm-2018-0020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: The aim of the study was to explore the parent-of-origin effects (POEs) on a range of human nuclear magnetic resonance metabolites. Materials & methods: We search for POEs in 14,815 unrelated individuals from Estonian and Finnish cohorts using POE method for the genotype data imputed with 1000 G reference panel and 82 nuclear magnetic resonance metabolites. Results: Meta-analysis revealed the evidence of POE for the variant rs1412727 in PTPRD gene for the metabolite: triglycerides in medium very low-density lipoprotein. No POEs were detected for genetic variants that were previously known to have main effect on circulating metabolites. Conclusion: We demonstrated possibility to detect POEs for human metabolites, but the POEs are weak, and therefore it is hard to detect those using currently available sample sizes.
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Affiliation(s)
- N Pervjakova
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
- Department of Biotechnology, Institute of Molecular & Cell Biology, University of Tartu, Tartu 51010, Estonia
- Department of Genomics of Common Disease, School of Public Health, Imperial College London, Hammersmith Hospital, UK
| | - V Kukushkina
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
- Department of Biotechnology, Institute of Molecular & Cell Biology, University of Tartu, Tartu 51010, Estonia
| | - T Haller
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
| | - S Kasela
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
| | - A Joensuu
- National Institute for Health & Welfare (THL), Department of Public Health Solutions, Helsinki, Finland
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Finland
| | - K Kristiansson
- National Institute for Health & Welfare (THL), Department of Public Health Solutions, Helsinki, Finland
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Finland
| | - T Annilo
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
- Department of Biotechnology, Institute of Molecular & Cell Biology, University of Tartu, Tartu 51010, Estonia
| | - M Perola
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
- National Institute for Health & Welfare (THL), Department of Public Health Solutions, Helsinki, Finland
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Finland
| | - V Salomaa
- National Institute for Health & Welfare (THL), Department of Public Health Solutions, Helsinki, Finland
| | - P Jousilahti
- National Institute for Health & Welfare (THL), Department of Public Health Solutions, Helsinki, Finland
| | - A Metspalu
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
- Department of Biotechnology, Institute of Molecular & Cell Biology, University of Tartu, Tartu 51010, Estonia
| | - R Mägi
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
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12
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Harris RA, Alcott CE, Sullivan EL, Takahashi D, McCurdy CE, Comstock S, Baquero K, Blundell P, Frias AE, Kahr M, Suter M, Wesolowski S, Friedman JE, Grove KL, Aagaard KM. Genomic Variants Associated with Resistance to High Fat Diet Induced Obesity in a Primate Model. Sci Rep 2016; 6:36123. [PMID: 27811965 PMCID: PMC5095882 DOI: 10.1038/srep36123] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 10/07/2016] [Indexed: 12/28/2022] Open
Abstract
Maternal obesity contributes to an increased risk of lifelong morbidity and mortality for both the mother and her offspring. In order to better understand the molecular mechanisms underlying these risks, we previously established and extensively characterized a primate model in Macaca fuscata (Japanese macaque). In prior studies we have demonstrated that a high fat, caloric dense maternal diet structures the offspring’s epigenome, metabolome, and intestinal microbiome. During the course of this work we have consistently observed that a 36% fat diet leads to obesity in the majority, but not all, of exposed dams. In the current study, we sought to identify the genomic loci rendering resistance to obesity despite chronic consumption of a high fat diet in macaque dams. Through extensive phenotyping together with exon capture array and targeted resequencing, we identified three novel single nucleotide polymorphisms (SNPs), two in apolipoprotein B (APOB) and one in phospholipase A2 (PLA2G4A) that significantly associated with persistent weight stability and insulin sensitivity in lean macaques. By application of explicit orthogonal modeling (NOIA), we estimated the polygenic and interactive nature of these loci against multiple metabolic traits and their measures (i.e., serum LDL levels) which collectively render an obesity resistant phenotype in our adult female dams.
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Affiliation(s)
- R Alan Harris
- Department of Obstetrics &Gynecology, Division of Maternal-Fetal Medicine at Baylor College of Medicine and Texas Children's Hospital, Houston, TX, USA.,Department of Molecular and Human Genetics at Baylor College of Medicine, Houston, TX, USA
| | - Callison E Alcott
- Developmental Biology Interdisciplinary Program at Baylor College of Medicine, Houston, TX, USA
| | - Elinor L Sullivan
- Oregon National Primate Research Center, Oregon Health &Science University (OHSU), Beaverton, OR, USA.,Department of Biology, University of Portland, USA
| | - Diana Takahashi
- Oregon National Primate Research Center, Oregon Health &Science University (OHSU), Beaverton, OR, USA
| | - Carrie E McCurdy
- Department of Human Physiology, University of Oregon, Eugene, OR, USA
| | - Sarah Comstock
- Department of Biology, Corban University, Salem, OR, USA
| | - Karalee Baquero
- Oregon National Primate Research Center, Oregon Health &Science University (OHSU), Beaverton, OR, USA
| | - Peter Blundell
- Oregon National Primate Research Center, Oregon Health &Science University (OHSU), Beaverton, OR, USA
| | - Antonio E Frias
- Oregon National Primate Research Center, Oregon Health &Science University (OHSU), Beaverton, OR, USA.,Department of Obstetrics &Gynecology, Division of Maternal-Fetal Medicine, OHSU, Portland, OR, USA
| | - Maike Kahr
- Department of Obstetrics &Gynecology, Division of Maternal-Fetal Medicine at Baylor College of Medicine and Texas Children's Hospital, Houston, TX, USA
| | - Melissa Suter
- Department of Obstetrics &Gynecology, Division of Maternal-Fetal Medicine at Baylor College of Medicine and Texas Children's Hospital, Houston, TX, USA
| | - Stephanie Wesolowski
- Departments of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Jacob E Friedman
- Departments of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Kevin L Grove
- Oregon National Primate Research Center, Oregon Health &Science University (OHSU), Beaverton, OR, USA
| | - Kjersti M Aagaard
- Department of Obstetrics &Gynecology, Division of Maternal-Fetal Medicine at Baylor College of Medicine and Texas Children's Hospital, Houston, TX, USA.,Department of Molecular and Human Genetics at Baylor College of Medicine, Houston, TX, USA.,Developmental Biology Interdisciplinary Program at Baylor College of Medicine, Houston, TX, USA.,Oregon National Primate Research Center, Oregon Health &Science University (OHSU), Beaverton, OR, USA.,Department of Molecular and Cell Biology at Baylor College of Medicine, Houston, TX, USA
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