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Cheng H, Ouyang Y, Li C. Impact of IRGM gene promoter polymorphisms on susceptibility to chronic HBV infection. Int J Immunogenet 2024; 51:149-156. [PMID: 38514898 DOI: 10.1111/iji.12661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 02/03/2024] [Accepted: 02/16/2024] [Indexed: 03/23/2024]
Abstract
The autophagy gene immunity-related GTPase M (IRGM) can affect the immune response against intracellular pathogens. The study was performed to determine any possible association between three IRGM single-nucleotide polymorphisms (SNPs) (rs4958842, rs4958843 and rs4958846) and chronic hepatitis B virus (HBV) infection. A total of 171 chronic HBV-infected individuals and 171 healthy controls were collected. Peripheral blood cells and Sanger sequencing were used to extract genomic DNA and determine the SNP genotypes, respectively. The C allele of rs4958843 is a risk factor for chronic HBV infection in various genetic models, including allelic, codominant and dominant models, with the following respective statistical data: allelic (T vs. C: OR = 1.371, 95% CI = 1.009-1.863, p = .043), codominant (TT vs. CC: OR = 2.137, 95% CI = 1.104-4.138, p = .024) and dominant (TT + TC vs. CC: OR = 1.976, 95% CI = 1.106-3.533, p = .021) models. The genotype and allele distributions of rs4958842 and rs4958846 showed no significant differences between chronic HBV infection patients and healthy controls. IRGM rs4958843 CC genotype carriers had significantly elevated values of alanine transaminase, aspartate transaminase alpha-fetoprotein and total bilirubin (OR = 3.467, 95%CI = 1.167-10.298), which was positively associated with the disease progression of HBV infection. Mutant allele C of IRGM rs4958843 polymorphism is associated with the risk of chronic HBV infection in the Han people in central China and contributes to the disease progression.
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Affiliation(s)
- Hai Cheng
- School of Medicine & Health Sciences, Jingzhou University, Jingzhou, China
| | - Yaoling Ouyang
- Department of Laboratory Medicine, Jingzhou Hospital Affiliated to Yangtze University, Jingzhou, China
| | - Chengbin Li
- Department of Laboratory Medicine, Jingzhou Hospital Affiliated to Yangtze University, Jingzhou, China
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2
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Saadat M. Evaluation of Hardy-Weinberg equilibrium in genetic association studies. Int J Immunogenet 2024; 51:183-186. [PMID: 38509453 DOI: 10.1111/iji.12668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Revised: 02/28/2024] [Accepted: 03/08/2024] [Indexed: 03/22/2024]
Abstract
STrengthening the REporting of Genetic Association (STREGA) studies strongly recommend that researchers assess the Hardy-Weinberg equilibrium (HWE) in their control groups. The exact frequency of studies in which their control subjects show a significant deviation from the HWE is not well established. Therefore, the present study was conducted. The electronic database PubMed was searched using the terms: 'meta-analysis' and 'polymorphism'. Data of original articles were extracted from meta-analysis. The STREGA statement was published in 2009. Therefore, studies were divided into two groups, before and after the statement. After data collection, quartiles for sample size and minor allele frequency (MAF) were determined separately. A total of 772 independent studies were extracted from these meta-analyses and included in the current study. Multivariate analysis revealed the following associations: (1) Reports published after the STREGA statement (compared to before the statement) were associated with an increased prevalence of deviation from HWE. (2) Reports with sample size Q2-Q4 versus Q1 were associated with an increased prevalence of deviation from HWE. (3) Studies with MAF Q4 versus Q1 were negatively associated with the prevalence of reports of deviation from HWE. We conclude that the STREGA statement failed to change the attitudes and practices of researchers and editors towards the importance of HWE.
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Affiliation(s)
- Mostafa Saadat
- Department of Biology, School of Science, Shiraz University, Shiraz, Iran
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Walton IS, McCann E, Weber A, Morton JEV, Noons P, Wilson LC, Ching RC, Cilliers D, Johnson D, Phipps JM, Shears DJ, Thomas GPL, Wall SA, Twigg SRF, Wilkie AOM. Reassessing the association: Evaluation of a polyalanine deletion variant of RUNX2 in non-syndromic sagittal and metopic craniosynostosis. J Anat 2024. [PMID: 38760592 DOI: 10.1111/joa.14052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 04/09/2024] [Accepted: 04/12/2024] [Indexed: 05/19/2024] Open
Abstract
The RUNT-related transcription factor RUNX2 plays a critical role in osteoblast differentiation, and alterations to gene dosage cause distinct craniofacial anomalies. Uniquely amongst the RUNT-related family, vertebrate RUNX2 encodes a polyglutamine/polyalanine repeat (Gln23-Glu-Ala17 in humans), with the length of the polyalanine component completely conserved in great apes. Surprisingly, a frequent 6-amino acid deletion polymorphism, p.(Ala84_Ala89)del, occurs in humans (termed 11A allele), and a previous association study (Cuellar et al. Bone 137:115395;2020) reported that the 11A variant was significantly more frequent in non-syndromic sagittal craniosynostosis (nsSag; allele frequency [AF] = 0.156; 95% confidence interval [CI] 0.126-0.189) compared to non-syndromic metopic craniosynostosis (nsMet; AF = 0.068; 95% CI 0.045-0.098). However, the gnomAD v.2.1.1 control population used by Cuellar et al. did not display Hardy-Weinberg equilibrium, hampering interpretation. To re-examine this association, we genotyped the RUNX2 11A polymorphism in 225 individuals with sporadic nsSag as parent-child trios and 164 singletons with sporadic nsMet, restricting our analysis to individuals of European ancestry. We compared observed allele frequencies to the non-transmitted alleles in the parent-child trios, and to the genome sequencing data from gnomAD v.4, which display Hardy-Weinberg equilibrium. Observed AFs (and 95% CI) were 0.076 (0.053-0.104) in nsSag and 0.082 (0.055-0.118) in nsMet, compared with 0.062 (0.042-0.089) in non-transmitted parental alleles and 0.065 (0.063-0.067) in gnomAD v.4.0.0 non-Finnish European control genomes. In summary, we observed a non-significant excess, compared to gnomAD data, of 11A alleles in both nsSag (relative risk 1.18, 95% CI 0.83-1.67) and nsMet (relative risk 1.29, 95% CI 0.87-1.92), but we did not replicate the much higher excess of RUNX2 11A alleles in nsSag previously reported (p = 0.0001).
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Affiliation(s)
- Isaac S Walton
- MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Emma McCann
- Department of Clinical Genetics, Liverpool Women's NHS Foundation Trust, Liverpool, England, UK
| | - Astrid Weber
- Department of Clinical Genetics, Liverpool Women's NHS Foundation Trust, Liverpool, England, UK
| | - Jenny E V Morton
- West Midlands Regional Clinical Genetics Service and Birmingham Health Partners, Birmingham Women's and Children's Hospitals NHS Foundation Trust, Birmingham, UK
- Birmingham Craniofacial Unit, Birmingham Women's and Children's Hospitals NHS Foundation Trust, Birmingham, UK
| | - Peter Noons
- Birmingham Craniofacial Unit, Birmingham Women's and Children's Hospitals NHS Foundation Trust, Birmingham, UK
| | - Louise C Wilson
- Clinical Genetics Service, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Rosanna C Ching
- Oxford Craniofacial Unit, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Deirdre Cilliers
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - David Johnson
- Oxford Craniofacial Unit, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Julie M Phipps
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Deborah J Shears
- Oxford Craniofacial Unit, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Gregory P L Thomas
- Oxford Craniofacial Unit, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Steven A Wall
- Oxford Craniofacial Unit, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Stephen R F Twigg
- MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Andrew O M Wilkie
- MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
- Oxford Craniofacial Unit, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
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Wahbeh MH, Boyd RJ, Yovo C, Rike B, McCallion AS, Avramopoulos D. A functional schizophrenia-associated genetic variant near the TSNARE1 and ADGRB1 genes. HGG Adv 2024; 5:100303. [PMID: 38702885 DOI: 10.1016/j.xhgg.2024.100303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 05/01/2024] [Accepted: 04/23/2024] [Indexed: 05/06/2024] Open
Abstract
Recent collaborative genome-wide association studies (GWAS) have identified >200 independent loci contributing to risk for schizophrenia (SCZ). The genes closest to these loci have diverse functions, supporting the potential involvement of multiple relevant biological processes, yet there is no direct evidence that individual variants are functional or directly linked to specific genes. Nevertheless, overlap with certain epigenetic marks suggest that most GWAS-implicated variants are regulatory. Based on the strength of association with SCZ and the presence of regulatory epigenetic marks, we chose one such variant near TSNARE1 and ADGRB1, rs4129585, to test for functional potential and assay differences that may drive the pathogenicity of the risk allele. We observed that the variant-containing sequence drives reporter expression in relevant neuronal populations in zebrafish. Next, we introduced each allele into human induced pluripotent cells and differentiated four isogenic clones homozygous for the risk allele and five clones homozygous for the non-risk allele into neural progenitor cells. Employing RNA sequencing, we found that the two alleles yield significant transcriptional differences in the expression of 109 genes at a false discovery rate (FDR) of <0.05 and 259 genes at a FDR of <0.1. We demonstrate that these genes are highly interconnected in pathways enriched for synaptic proteins, axon guidance, and regulation of synapse assembly. Exploration of genes near rs4129585 suggests that this variant does not regulate TSNARE1 transcripts, as previously thought, but may regulate the neighboring ADGRB1, a regulator of synaptogenesis. Our results suggest that rs4129585 is a functional common variant that functions in specific pathways likely involved in SCZ risk.
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Affiliation(s)
- Marah H Wahbeh
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Rachel J Boyd
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Christian Yovo
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Bailey Rike
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Andrew S McCallion
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Dimitrios Avramopoulos
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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Breeyear JH, Mautz BS, Keaton JM, Hellwege JN, Torstenson ES, Liang J, Bray MJ, Giri A, Warren HR, Munroe PB, Velez Edwards DR, Zhu X, Li C, Edwards TL. A new test for trait mean and variance detects unreported loci for blood-pressure variation. Am J Hum Genet 2024; 111:954-965. [PMID: 38614075 PMCID: PMC11080606 DOI: 10.1016/j.ajhg.2024.03.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 03/20/2024] [Accepted: 03/22/2024] [Indexed: 04/15/2024] Open
Abstract
Variability in quantitative traits has clinical, ecological, and evolutionary significance. Most genetic variants identified for complex quantitative traits have only a detectable effect on the mean of trait. We have developed the mean-variance test (MVtest) to simultaneously model the mean and log-variance of a quantitative trait as functions of genotypes and covariates by using estimating equations. The advantages of MVtest include the facts that it can detect effect modification, that multiple testing can follow conventional thresholds, that it is robust to non-normal outcomes, and that association statistics can be meta-analyzed. In simulations, we show control of type I error of MVtest over several alternatives. We identified 51 and 37 previously unreported associations for effects on blood-pressure variance and mean, respectively, in the UK Biobank. Transcriptome-wide association studies revealed 633 significant unique gene associations with blood-pressure mean variance. MVtest is broadly applicable to studies of complex quantitative traits and provides an important opportunity to detect novel loci.
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Affiliation(s)
- Joseph H Breeyear
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA; Biostatistics and Computational Biology Branch, Division of Intramural Research, National Institute of Environmental Health Sciences, Durham, NC, USA
| | - Brian S Mautz
- Population Analytics and Insights, Data Sciences, Janssen Research and Development, Spring House, PA, USA
| | - Jacob M Keaton
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jacklyn N Hellwege
- Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN, USA; Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Eric S Torstenson
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jingjing Liang
- Department of Pharmacy Practice and Science, University of Arizona, Tucson, AZ, USA
| | - Michael J Bray
- Department of Maternal and Fetal Medicine, Orlando Health, Orlando, FL, USA; Genetic Counseling Program, Bay Path University, Longmeadow, MA, USA
| | - Ayush Giri
- Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN, USA; Division of Quantitative Sciences, Department of Obstetrics and Gynecology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Helen R Warren
- Center of Clinical Pharmacology and Precision Medicine, Queen Mary University, London, England
| | - Patricia B Munroe
- Center of Clinical Pharmacology and Precision Medicine, Queen Mary University, London, England
| | - Digna R Velez Edwards
- Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN, USA; Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA; Division of Quantitative Sciences, Department of Obstetrics and Gynecology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Xiaofeng Zhu
- Department of Epidemiology and Biostatistics, Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, USA
| | - Chun Li
- Department of Population and Public Health Sciences, University of Southern California, Los Angeles, CA, USA
| | - Todd L Edwards
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.
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Ramírez-Rosete JA, Hurtado-Vazquez A, Miranda-Duarte A, Peralta-Cruz S, Cuevas-Olivo R, Martínez-Junco JA, Sevilla-Montoya R, Rivera-Paredez B, Velázquez-Cruz R, Valdes-Flores M, Rangel-Escareno C, Alanis-Funes GJ, Abad-Azpetia L, Grimaldo-Galeana SG, Santamaría-Olmedo MG, Hidalgo-Bravo A. Environmental and Genetic Risk Factors in Developmental Dysplasia of the Hip for Early Detection of the Affected Population. Diagnostics (Basel) 2024; 14:898. [PMID: 38732313 PMCID: PMC11083091 DOI: 10.3390/diagnostics14090898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 04/13/2024] [Accepted: 04/19/2024] [Indexed: 05/13/2024] Open
Abstract
Diagnosis of developmental dysplasia of the hip (DDH) mostly relies on physical examination and ultrasound, and both methods are operator-dependent. Late detection can lead to complications in young adults. Current evidence supports the involvement of environmental and genetic factors, such as single nucleotide variants (SNVs). Incorporating genetic factors into diagnostic methods would be useful for implementing early detection and management of affected individuals. Our aim was to analyze environmental factors and SNVs in DDH patients. We included 287 DDH cases and 284 controls. Logistic regression demonstrated an association for sex (OR 9.85, 95% CI 5.55-17.46, p = 0.0001), family history (OR 2.4, 95% CI 1.2-4.5, p = 0.006), fetal presentation (OR 3.19, 95% CI 1.55-6.54, p = 0.002), and oligohydramnios (OR 2.74, 95%CI 1.12-6.70, p = 0.026). A model predicting the risk of DDH including these variables showed sensitivity, specificity, PPV, and NPV of 0.91, 0.53, 0.74, and 0.80 respectively. The SNV rs1800470 in TGFB1 showed an association when adjusted for covariables, OR 0.49 (95% CI 0.27-0.90), p = 0.02. When rs1800470 was included in the equation, sensitivity, specificity, PPV and NPV were 0.90, 0.61, 0.84, and 0.73, respectively. Incorporating no-operator dependent variables and SNVs in detection methods could be useful for establishing uniform clinical guidelines and optimizing health resources.
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Affiliation(s)
- Judit A. Ramírez-Rosete
- Department of Genomics Medicine, National Institute of Rehabilitation (INRLGII), Calzada Mexico-Xochimilco 289, Arenal de Guadalupe, Mexico City 14389, Mexico; (J.A.R.-R.); (A.H.-V.); (A.M.-D.); (M.V.-F.); (L.A.-A.); (S.G.G.-G.); (M.G.S.-O.)
| | - Alonso Hurtado-Vazquez
- Department of Genomics Medicine, National Institute of Rehabilitation (INRLGII), Calzada Mexico-Xochimilco 289, Arenal de Guadalupe, Mexico City 14389, Mexico; (J.A.R.-R.); (A.H.-V.); (A.M.-D.); (M.V.-F.); (L.A.-A.); (S.G.G.-G.); (M.G.S.-O.)
| | - Antonio Miranda-Duarte
- Department of Genomics Medicine, National Institute of Rehabilitation (INRLGII), Calzada Mexico-Xochimilco 289, Arenal de Guadalupe, Mexico City 14389, Mexico; (J.A.R.-R.); (A.H.-V.); (A.M.-D.); (M.V.-F.); (L.A.-A.); (S.G.G.-G.); (M.G.S.-O.)
| | - Sergio Peralta-Cruz
- Department of Pediatric Orthopedics, National Institute of Rehabilitation (INRLGII), Calzada Mexico-Xochimilco 289, Arenal de Guadalupe, Mexico City 14389, Mexico; (S.P.-C.); (R.C.-O.); (J.A.M.-J.)
| | - Ramiro Cuevas-Olivo
- Department of Pediatric Orthopedics, National Institute of Rehabilitation (INRLGII), Calzada Mexico-Xochimilco 289, Arenal de Guadalupe, Mexico City 14389, Mexico; (S.P.-C.); (R.C.-O.); (J.A.M.-J.)
| | - José Antonio Martínez-Junco
- Department of Pediatric Orthopedics, National Institute of Rehabilitation (INRLGII), Calzada Mexico-Xochimilco 289, Arenal de Guadalupe, Mexico City 14389, Mexico; (S.P.-C.); (R.C.-O.); (J.A.M.-J.)
| | - Rosalba Sevilla-Montoya
- Department of Genetics and Human Genomics, National Institute of Perinatology, Montes Urales 800, Lomas-Virreyes, Lomas de Chapultepec IV Secc, Miguel Hidalgo, Mexico City 11000, Mexico;
| | - Berenice Rivera-Paredez
- Research Center in Policies, Population and Health, School of Medicine, National Autonomous University of Mexico, Zona Cultural s/n, CIPPS 2° Piso Ciudad Universitaria, Coyoacán, Mexico City 04510, Mexico;
| | - Rafael Velázquez-Cruz
- Genomics of Bone Metabolism Laboratory, National Institute of Genomic Medicine (INMEGEN), Arenal Tepepan, Tlalpan, Mexico City 14610, Mexico;
| | - Margarita Valdes-Flores
- Department of Genomics Medicine, National Institute of Rehabilitation (INRLGII), Calzada Mexico-Xochimilco 289, Arenal de Guadalupe, Mexico City 14389, Mexico; (J.A.R.-R.); (A.H.-V.); (A.M.-D.); (M.V.-F.); (L.A.-A.); (S.G.G.-G.); (M.G.S.-O.)
| | - Claudia Rangel-Escareno
- Computational Genomics Department, Instituto Nacional de Medicina Genómica (INMEGEN), Arenal Tepepan, Tlalpan, Mexico City 14610, Mexico;
| | - Gerardo J. Alanis-Funes
- School of Engineering and Sciences, Tecnologico de Monterrey, Campus Querétaro, Querétaro 76130, Mexico;
| | - Laura Abad-Azpetia
- Department of Genomics Medicine, National Institute of Rehabilitation (INRLGII), Calzada Mexico-Xochimilco 289, Arenal de Guadalupe, Mexico City 14389, Mexico; (J.A.R.-R.); (A.H.-V.); (A.M.-D.); (M.V.-F.); (L.A.-A.); (S.G.G.-G.); (M.G.S.-O.)
| | - Sacnicte G. Grimaldo-Galeana
- Department of Genomics Medicine, National Institute of Rehabilitation (INRLGII), Calzada Mexico-Xochimilco 289, Arenal de Guadalupe, Mexico City 14389, Mexico; (J.A.R.-R.); (A.H.-V.); (A.M.-D.); (M.V.-F.); (L.A.-A.); (S.G.G.-G.); (M.G.S.-O.)
| | - Monica G. Santamaría-Olmedo
- Department of Genomics Medicine, National Institute of Rehabilitation (INRLGII), Calzada Mexico-Xochimilco 289, Arenal de Guadalupe, Mexico City 14389, Mexico; (J.A.R.-R.); (A.H.-V.); (A.M.-D.); (M.V.-F.); (L.A.-A.); (S.G.G.-G.); (M.G.S.-O.)
| | - Alberto Hidalgo-Bravo
- Department of Genomics Medicine, National Institute of Rehabilitation (INRLGII), Calzada Mexico-Xochimilco 289, Arenal de Guadalupe, Mexico City 14389, Mexico; (J.A.R.-R.); (A.H.-V.); (A.M.-D.); (M.V.-F.); (L.A.-A.); (S.G.G.-G.); (M.G.S.-O.)
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Qiu Y, Hou Y, Wei X, Wang M, Yin Z, Xie M, Duan A, Ma C, Si K, Wang Z. Causal association between gut microbiomes and different types of aneurysms: a Mendelian randomization study. Front Microbiol 2024; 15:1267888. [PMID: 38659992 PMCID: PMC11039950 DOI: 10.3389/fmicb.2024.1267888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 03/28/2024] [Indexed: 04/26/2024] Open
Abstract
Background Previous studies suggests that gut microbiomes are associated with the formation and progression of aneurysms. However, the causal association between them remains unclear. Methods A two-sample Mendelian randomization was conducted to investigate whether gut microbiomes have a causal effect on the risk of intracerebral aneurysm (IA), thoracic aortic aneurysm (TAA) and abdominal aortic aneurysm (AAA), and aortic aneurysm (AA). Single nucleotide polymorphisms (SNPs) smaller than the locus-wide significance level (1 × 10-5) were selected as instrumental variables. We used inverse-variance weighted (IVW) test as the primary method for the evaluation of causal association. MR-Egger, weighted median, weighted mode, and MR Pleiotropy Residual Sum and Outlier (MR-PRESSO) methods were conducted for sensitive analysis. The p-value was adjusted by the false discovery rate (FDR) which adjust the results of multiple comparisons, a p < 0.05 and q < 0.1 was considered a significant causal association. Additionally, a p < 0.05 and q > 0.1 was considered a suggestive causal effect. Additionally, reverse MR was also performed to exclude the possibility of reverse causality. Results The phylum Firmicutes (OR = 0.62; 95% CI, 0.48-0.81), class Lentisphaeria (OR = 0.75; 95% CI, 0.62-0.89), and order Victivallales (OR = 0.75; 95% CI, 0.62-0.89) have a causal protective effect on the risk of AAA. Additionally, class Verrucomicrobia, class Deltaproteobacteria, order Verrucomicrobiale, family Verrucomicrobiacea, genus Eubacterium rectale group, genus Akkermansia, and genus Clostridium innocuum group were negatively associated with the risk of different types of aneurysms, whereas class Negativicutes, order Selenomonadales, and genus Roseburia had positive causal association with different types of aneurysms (p < 0.05; q > 0.1). Further sensitivity analysis validated the robustness of our MR results, and no reverse causality was found with these gut microbiomes (p > 0.05). Conclusion Our MR analysis confirmed the causal association of specific gut microbiomes with AAA, and these microbiomes were considered as protective factors. Our result may provide novel insights and theoretical basis for the prevention of aneurysms through regulation of gut microbiomes.
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Affiliation(s)
- Youjia Qiu
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Yucheng Hou
- Department of Cardiovascular Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Xingzhou Wei
- Suzhou Medical College of Soochow University, Suzhou, China
| | - Menghan Wang
- Suzhou Medical College of Soochow University, Suzhou, China
| | - Ziqian Yin
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Minjia Xie
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Aojie Duan
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Chao Ma
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Ke Si
- Department of Cardiovascular Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Zhong Wang
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, China
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8
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Zeng W, Wu Y, Liang X, Cun D, Ma L, Zhang J, Huang F, Jiang Z. Causal associations between human gut microbiota and osteomyelitis: a Mendelian randomization study. Front Cell Infect Microbiol 2024; 14:1338989. [PMID: 38655282 PMCID: PMC11035795 DOI: 10.3389/fcimb.2024.1338989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 03/26/2024] [Indexed: 04/26/2024] Open
Abstract
Background Recent studies have emphasized the role of gut microbiota in the onset and progression of osteomyelitis. However, the exact types of gut microbiota and their mechanisms of action remain unclear. Additionally, there is a lack of theoretical support for treatments that improve osteomyelitis by altering the gut microbiota. Methods In our study, we utilized the largest genome-wide association study (GWAS) meta-analysis to date from the MiBioGen consortium, involving 13,400 participants. The GWAS data for osteomyelitis were sourced from the UK Biobank, which included 4,836 osteomyelitis cases and 486,484 controls. We employed a two-sample Mendelian randomization framework for a detailed investigation into the causal relationship between gut microbiota and osteomyelitis. Our methods included inverse variance weighting, MR-Egger, weighted median, and weighted mode approaches. Additionally, we applied Cochran's Q statistic to assess the heterogeneity of the instrumental variable. Results At the class level, Bacilli and Bacteroidia were positively correlated with the risk of osteomyelitis. At the order level, only Bacteroidales showed a positive association with osteomyelitis. At the genus level, an increased abundance of Butyricimonas, Coprococcus3, and Tyzzerella3 was positively associated with the risk of osteomyelitis, whereas Lachnospira was negatively associated. Sensitivity analyses showed no evidence of heterogeneity or pleiotropy. Conclusion This study reveals that classes Bacilli and Bacteroidia, order Bacteroidales, and genera Butyricimonas, Coprococcus3, and Tyzzerella3 are implicated in increasing the risk of osteomyelitis, while the genus Lachnospira is associated with a reduced risk. Future investigations are warranted to elucidate the precise mechanisms through which these specific bacterial groups influence the pathophysiology of osteomyelitis.
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Affiliation(s)
- Wenxing Zeng
- First Clinical Medical College of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Yuheng Wu
- First Clinical Medical College of Guangzhou University of Chinese Medicine, Guangzhou, China
- Seventh Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, China
| | - Xiaoye Liang
- First Clinical Medical College of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Dejun Cun
- First Clinical Medical College of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Luyao Ma
- First Clinical Medical College of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Jingtao Zhang
- First Clinical Medical College of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Feng Huang
- First Clinical Medical College of Guangzhou University of Chinese Medicine, Guangzhou, China
- Department of Traumatology and Orthopedics, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Ziwei Jiang
- First Clinical Medical College of Guangzhou University of Chinese Medicine, Guangzhou, China
- Department of Traumatology and Orthopedics, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
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Salazar-García S, Ibáñez-Salazar A, Lares-Villaseñor E, Gaytan Pacheco N, Uresti-Rivera E, Portales-Pérez DP, De la Cruz-Mosso U, Vargas-Morales JM. Analysis of SIRT1 genetic variants in young Mexican individuals: relationships with overweight and obesity. Front Genet 2024; 15:1278201. [PMID: 38645486 PMCID: PMC11027998 DOI: 10.3389/fgene.2024.1278201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 03/18/2024] [Indexed: 04/23/2024] Open
Abstract
The high prevalence of obesity in Mexico starting from the early stages of life is concerning and represents a major public health problem. Genetic association studies have reported that single nucleotide variants (SNVs) in SIRT1, an NAD+-dependent deacetylase that plays an important role in the regulation of metabolic cellular functions, are associated with multiple metabolic disorders and the risk of obesity. In the present study, we analyzed the effect that the SNVs rs1467568 and rs7895833 of the SIRT1 gene may have on cardiometabolic risk factors in a young adult population from Mexico. A cross-sectional study was carried out with young adults between the ages of 18 and 25 who had a body mass index (BMI) greater than 18.5 kg/m2. This study included 1122 young adults who were classified into the normal weight (n = 731), overweight group (n = 277), and obesity group (n = 114) according to BMI of whom 405 and 404 volunteers were genotyped for rs1467568 and rs7895833 respectively using TaqMan probes through allelic discrimination assays. We found that the male sex carrying the G allele of rs7895833 had slightly lower BMI levels (p = 0.009). Furthermore, subjects carrying rs1467568 (G allele) showed a 34% lower probability of presenting with hyperbetalipoproteinemia where female carrying rs1467568 had lower levels of total cholesterol (p = 0.030), triglycerides (p = 0.026) and LDL cholesterol (p = 0.013). In conclusion, these findings suggest that the presence of both SNVs could have a non-risk effect against dyslipidemia in the Mexican population.
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Affiliation(s)
- S. Salazar-García
- Laboratorio de Análisis Clínicos, Facultad de Ciencias Químicas, Universidad Autónoma de San Luis Potosí, San Luis Potosí, México
| | - A. Ibáñez-Salazar
- Unidad Académica de Ciencias Químicas, Universidad Autónoma de Zacatecas ¨Francisco García Salinas, Zacatecas, México
| | - E. Lares-Villaseñor
- Laboratorio de Análisis Clínicos, Facultad de Ciencias Químicas, Universidad Autónoma de San Luis Potosí, San Luis Potosí, México
| | - Noemi Gaytan Pacheco
- Unidad Académica de Ciencias Químicas, Universidad Autónoma de Zacatecas ¨Francisco García Salinas, Zacatecas, México
| | - E. Uresti-Rivera
- Laboratorio de Biología, Facultad de Ciencias Químicas, Universidad Autónoma de San Luis Potosí, San Luis Potosí, México
| | - D. P. Portales-Pérez
- Centro de Investigación en Ciencias de la Salud y Biomedicina, Universidad Autónoma de San Luis Potosí, San Luis Potosí, México
| | - U. De la Cruz-Mosso
- Red de Inmunonutrición y Genómica Nutricional en las Enfermedades Autoinmunes, Instituto de Neurociencias Traslacionales, Departamento de Neurociencias, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, México
| | - J. M. Vargas-Morales
- Laboratorio de Análisis Clínicos, Facultad de Ciencias Químicas, Universidad Autónoma de San Luis Potosí, San Luis Potosí, México
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10
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Gautam B, Pandi A, Girija ASS, Arumugam P, Priyadharsini VJ. Genetic Association of Toll-Like Receptor 4 (TLR4) Gene Polymorphism (rs4986790) With Oral Squamous Cell Carcinoma (OSCC): A Pilot Case-Control Study. Cureus 2024; 16:e56021. [PMID: 38606218 PMCID: PMC11007480 DOI: 10.7759/cureus.56021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 03/12/2024] [Indexed: 04/13/2024] Open
Abstract
Introduction Oral squamous cell carcinoma (OSCC) is a highly prevalent and most common form of oral malignancy in the Indian population. Toll-like receptors belong to an important family of receptors that are involved in the process of pathogen recognition and mounting immune response. The expression of this receptor is dysregulated on the tumor cells as reported across several cancer types. The genetic variants in this gene could have a profound impact on the expression of the Toll-like receptor 4 (TLR4) gene. Objective This study aimed to understand the association of TLR4 gene polymorphism (rs4986790) with OSCC. The objective of this study was to compare the allele and genotype frequencies between the two groups, viz., OSCC and normal healthy subjects, recruited in the study. Materials and methods The blood samples were collected from normal healthy subjects (N = 25) and OSCC patients (N = 25). Genomic DNA was isolated from all samples, and genotyping was performed for the TLR4 gene polymorphism (rs4986790) employing the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) approach. The frequency distribution of genotypes and alleles across the study groups was determined by the Chi-square test. Results The allele frequency for TLR4 gene polymorphism (rs4986790) in the case group was found to be 60% (A allele) and 40% (G allele), respectively. The study population in both groups were found to agree with the Hardy-Weinberg equilibrium (HWE). The genotype frequency did not differ significantly among the two study groups which was evident from the p-value = 0.8285. Conclusion The present study did not report any significant association of the TLR4 polymorphic marker rs4986790 with OSCC. Further investigations into the association of other polymorphic markers in the TLR4 gene, among the larger population of OSCC patients, could provide evidence of their association with OSCC.
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Affiliation(s)
- Britina Gautam
- Department of Dentistry, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, IND
| | - Anitha Pandi
- Centre for Cellular and Molecular Research, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, IND
| | - A S Smiline Girija
- Department of Microbiology, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, IND
| | - Paramasivam Arumugam
- Centre for Cellular and Molecular Research, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, IND
| | - Vijayashree J Priyadharsini
- Centre for Cellular and Molecular Research, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, IND
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11
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Bajpai D, Rajasekar A. Genetic Association of ICAM-1 (rs5498) Gene Polymorphism With Susceptibility to Stage II Grade B Periodontitis: A Case-Control Study in South Indian Population. Cureus 2024; 16:e56629. [PMID: 38650775 PMCID: PMC11034711 DOI: 10.7759/cureus.56629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 03/21/2024] [Indexed: 04/25/2024] Open
Abstract
INTRODUCTION In the contemporary perspective, periodontitis is considered a complex issue triggered and perpetuated by bacteria but strongly influenced by the way the body reacts to bacterial plaque. Recent research has indicated that variations in genes might have an impact on the development of periodontitis. This study was conducted to explore a probable link between the genetic variations in intercellular adhesion molecule-1 (ICAM-1) represented by rs5498 and the occurrence of periodontitis. Methods: A total of 100 participants, 50 with periodontitis and 50 with periodontally healthy or mild gingivitis, were recruited for this study. Whole blood drawn from the participants was used to obtain genomic DNA. The ICAM-1 gene polymorphism (rs5498) was determined using polymerase chain reaction (PCR) amplification and digestion. The ICAM-1 gene's flanking primers were used to amp up the DNA. For statistical analysis, the genotype that was analyzed using the pattern of restriction fragment length polymorphism was recorded. The Chi-square test compared genotype and allele frequency distributions between both groups. The odds ratio with 95% confidence intervals with each individual allele or genotype was used to compute the risk. Statistical significance was established in all tests when the p-value was less than 0.05. RESULTS There was no discernible difference between the genotype frequencies of patients and controls χ2df (P = 0.6065). The findings demonstrated that no significant difference was present between the two groups for homozygous or heterozygous mutant genotypes (AA vs. AG+GG; P = 0.6854). There was no discernible difference in the detected frequencies of the A allele (58% vs. 61%), G allele (42% vs. 39%), TT (16% vs. 24%), AG (40% vs. 36%), and TT genotypes in the studied groups. CONCLUSION According to the results of the current investigation, the ICAM-1 (rs5498) gene polymorphism is not associated with periodontitis in the population investigated.
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Affiliation(s)
- Devika Bajpai
- Periodontics, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, IND
| | - Arvina Rajasekar
- Periodontics, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, IND
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12
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Yu C, Xu J, Xu S, Tang L, Han Q, Zeng X, Huang Y, Yu T, Sun Z. Exploring genetic associations of Crohn's disease and ulcerative colitis with extraintestinal cancers in European and East Asian populations. Front Immunol 2024; 15:1339207. [PMID: 38404590 PMCID: PMC10885353 DOI: 10.3389/fimmu.2024.1339207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 01/19/2024] [Indexed: 02/27/2024] Open
Abstract
Background Previous studies have reported associations of Crohn's disease (CD) and ulcerative colitis (UC) with the risks of extraintestinal cancers, but the causality remains unclear. Methods Using genetic variations robustly associated with CD and UC extracted from genome-wide association studies (GWAS) as instrumental variables. Nine types of extraintestinal cancers of European and Asian populations were selected as outcomes. We used the inverse variance weighted method as the primary approach for two-sample Mendelian randomization analysis. Sensitivity analyses were carried out to evaluate the reliability of our findings. Results In the European population, we found that CD showed a potential causal relationship with pancreatic cancer (OR: 1.1042; 95% CI: 1.0087-1.2088; P=0.0318). Meanwhile, both CD (outliers excluded: OR: 1.0208; 95% CI: 1.0079-1.0339; P=0.0015) and UC (outliers excluded: OR: 1.0220; 95% CI: 1.0051-1.0393; P=0.0108) were associated with a slight increase in breast cancer risk. Additionally, UC exhibited a potential causal effect on cervical cancer (outliers excluded: OR: 1.1091; 95% CI: 1.0286-1.1960; P=0.0071). In the East Asian population, CD had significant causal effects on pancreatic cancer (OR: 1.1876; 95% CI: 1.0741-1.3132; P=0.0008) and breast cancer (outliers excluded: OR: 0.9452; 95% CI: 0.9096-0.9822; P=0.0040). For UC, it exhibited significant causal associations with gastric cancer (OR: 1.1240; 95% CI: 1.0624-1.1891; P=4.7359×10-5), bile duct cancer (OR: 1.3107; 95% CI: 1.0983-1.5641; P=0.0027), hepatocellular carcinoma (OR: 1.2365; 95% CI: 1.1235-1.3608; P=1.4007×10-5) and cervical cancer (OR: 1.3941; 95% CI: 1.1708-1.6599; P=0.0002), as well as a potential causal effect on lung cancer (outliers excluded: OR: 1.1313; 95% CI: 1.0280-1.2449; P=0.0116). Conclusions Our study provided evidence that genetically predicted CD may be a risk factor for pancreatic and breast cancers in the European population, and for pancreatic cancer in the East Asian population. Regarding UC, it may be a risk factor for cervical and breast cancers in Europeans, and for gastric, bile duct, hepatocellular, lung, and cervical cancers in East Asians. Therefore, patients with CD and UC need to emphasize screening and prevention of site-specific extraintestinal cancers.
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Affiliation(s)
- Chengdong Yu
- Jiangxi Medical College, Nanchang University, Nanchang, China
| | - Jiawei Xu
- Jiangxi Medical College, Nanchang University, Nanchang, China
| | - Siyi Xu
- Jiangxi Medical College, Nanchang University, Nanchang, China
| | - Lei Tang
- Jiangxi Medical College, Nanchang University, Nanchang, China
| | - Qinyuan Han
- Jiangxi Medical College, Nanchang University, Nanchang, China
| | - Xiaoqiang Zeng
- Jiangxi Medical College, Nanchang University, Nanchang, China
| | - Yanxiao Huang
- Jiangxi Medical College, Nanchang University, Nanchang, China
| | - Tenghua Yu
- Department of breast surgery, Jiangxi Cancer Hospital, Nanchang, China
| | - Zhengkui Sun
- Department of breast surgery, Jiangxi Cancer Hospital, Nanchang, China
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13
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Yan P, Zhang L, Yang C, Zhang W, Wang Y, Zhang M, Cui H, Tang M, Chen L, Wu X, Zhao X, Zou Y, Xiao J, Liu Y, Xiao C, Yang Y, Zhang L, Yao Y, Li J, Liu Z, Yang C, Jiang X, Zhang B. Observational and genetic analyses clarify the relationship between type 2 diabetes mellitus and gallstone disease. Front Endocrinol (Lausanne) 2024; 14:1337071. [PMID: 38356679 PMCID: PMC10864641 DOI: 10.3389/fendo.2023.1337071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Accepted: 12/26/2023] [Indexed: 02/16/2024] Open
Abstract
Background The relationship between type 2 diabetes mellitus (T2DM) and gallstone disease (GSD) have been incompletely understood. We aimed to investigate their phenotypic and genetic associations and evaluate the biological mechanisms underlying these associations. Methods We first evaluated the phenotypic association between T2DM and GSD using data from the UK Biobank (n>450,000) using a prospective observational design. We then conducted genetic analyses using summary statistics from a meta-analysis of genome-wide association studies of T2DM, with and without adjusting for body mass index (BMI) (Ncase=74,124, Ncontrol=824,006; T2DMadjBMI: Ncase=50,409, Ncontrol=523,897) and GSD (Ncase=43,639, Ncontrol=506,798). Results A unidirectional phenotypic association was observed, where individuals with T2DM exhibited a higher GSD risk (hazard ratio (HR)=1.39, P<0.001), but not in the reverse direction (GSD→T2DM: HR=1.00, P=0.912). The positive T2DM-GSD genetic correlation (rg=0.35, P=7.71×10-23) remained even after adjusting for BMI (T2DMadjBMI: rg=0.22, P=4.48×10-10). Mendelian randomization analyses provided evidence of a unidirectional causal relationship (T2DM→GSD: odds ratio (OR)=1.08, P=4.6×10-8; GSD→T2DM: OR=1.02, P=0.48), even after adjusting for important metabolic confounders (OR=1.02, P=0.02). This association was further corroborated through a comprehensive functional analysis reflected by 23 pleiotropic single nucleotide polymorphisms, as well as multiple neural and motor-enriched tissues. Conclusion Through comprehensive observational and genetic analyses, our study clarified the causal relationship between T2DM and GSD, but not in the reverse direction. These findings might provide new insights into prevention and treatment strategies for T2DM and GSD.
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Affiliation(s)
- Peijing Yan
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Li Zhang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Chao Yang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
- School of Public Health, Southwest Medical University, Luzhou, Sichuan, China
| | - Wenqiang Zhang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yutong Wang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Min Zhang
- Clinical Research Center, Women and Children’s Hospital of Chongqing Medical University, Chongqing, China
| | - Huijie Cui
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Mingshuang Tang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Lin Chen
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Xueyao Wu
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Xunying Zhao
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yanqiu Zou
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Jinyu Xiao
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yunjie Liu
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Chenghan Xiao
- Department of Maternal, Child and Adolescent Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Yanfang Yang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Ling Zhang
- Department of Iatrical Polymer Material and Artificial Apparatus, School of Polymer Science and Engineering, Sichuan University, Chengdu, China
| | - Yuqin Yao
- Department of Occupational and Environmental Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Jiayuan Li
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Zhenmi Liu
- Department of Maternal, Child and Adolescent Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Chunxia Yang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Xia Jiang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
- Department of Nutrition and Food Hygiene, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
- Department of Clinical Neuroscience, Karolinska Institute, Stockholm, Sweden
| | - Ben Zhang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
- Department of Occupational and Environmental Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
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Shi H, Yuan X, Wu F, Li X, Fan W, Yang X, Liu G. Genetic support of the causal association between gut microbiota and peripheral artery disease: a bidirectional Mendelian randomization study. Aging (Albany NY) 2024; 16:762-778. [PMID: 38198148 PMCID: PMC10817407 DOI: 10.18632/aging.205417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 12/04/2023] [Indexed: 01/11/2024]
Abstract
BACKGROUND The causal relationship between gut microbiota and peripheral artery disease (PAD) is still not clear. In this research, we employed the Mendelian randomization (MR) technique to explore the potential causal connection between 211 gut microbiota species and PAD. We also investigated whether the causal effects operate in both directions. METHODS We used Genome-wide Association Studies (GWAS) summary statistics data from the MiBioGen and FinnGen consortia to conduct a two-sample MR analysis to explore the causal link between gut microbiota and PAD. Sensitivity analysis is conducted to assess the robustness of the MR results. In addition to that, reverse MR analysis was performed to examine the inverse causal relationship. RESULTS The inverse variance weighted (IVW) method provided evidence supporting a causal relationship between 9 specific gut microbiota taxa and PAD. The study findings indicated that family Family XI (OR=1.11, CI 1.00-1.24, P=0.048), genus Lachnoclostridium (OR=1.24, 1.02-1.50, P=0.033), and genus Lachnospiraceae UCG001 (OR=1.17, 1.01-1.35, P=0.031) are risk factors associated with PAD. class Actinobacteria (OR=0.84, 0.72-0.99, P=0.034), family Acidaminococcaceae (OR=0.80, 0.66-0.98, P=0.029), genus Coprococcus2 (OR=0.79, 0.64-0.98, P=0.029), genus Ruminococcaceae UCG004 (OR=0.84, 0.72-0.99, P=0.032), genus Ruminococcaceae UCG010 (OR=0.74, 0.58-0.96, P=0.022), and order NB1n (OR=0.88, 0.79-0.98, P=0.02) may be associated with the risk factors of PAD. Moreover, our analysis did not uncover any evidence of a reverse causal relationship between PAD and the nine specific gut microbiota taxa investigated. CONCLUSIONS Our MR research has confirmed the potential causal relationship between gut microbiota and PAD while also identifying specific gut bacterial communities associated with PAD.
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Affiliation(s)
- Hongshuo Shi
- Department of Peripheral Vascular Surgery, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Xin Yuan
- Department of Peripheral Vascular Surgery, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Fangfang Wu
- Department of Peripheral Vascular Surgery, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Xiaoyu Li
- Department of Peripheral Vascular Surgery, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Weijing Fan
- Department of Peripheral Vascular Surgery, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Xiao Yang
- Department of Peripheral Vascular Surgery, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Guobin Liu
- Department of Peripheral Vascular Surgery, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Guangming Traditional Chinese Medicine Hospital Pudong New Area, Shanghai, China
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Hirkane PS, Verma UP, Verma AK, Singh P. Exploring the Relation Between Interstitial Lung Diseases and Chronic Periodontitis: A Systematic Review. Cureus 2024; 16:e53157. [PMID: 38420070 PMCID: PMC10901193 DOI: 10.7759/cureus.53157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/29/2024] [Indexed: 03/02/2024] Open
Abstract
The objective of this systematic review is to determine the association between interstitial lung diseases and chronic periodontitis from various aspects such as microbial, biomarker, genetic, and environmental levels. A systematic review was carried out from 2000 to 2021 following Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) recommendations including studies searched in PubMed-Medline, Google Scholar, and Cochrane databases. A total of more than 100 articles were obtained in the initial screening process. Out of these 42 studies fulfilled the inclusion criteria and were included in the study. According to the extracted data, there is mounting evidence suggesting the association between these two diseases. Our systematic review raises the prospect of a connection between chronic periodontitis and interstitial lung diseases, within the limitations of the studies we included.
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Affiliation(s)
| | - Umesh P Verma
- Periodontology, King George's Medical University, Lucknow, IND
| | - Ajay K Verma
- Respiratory Medicine, King George's Medical University, Lucknow, IND
| | - Pooja Singh
- Periodontology, King George's Medical University, Lucknow, IND
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16
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Chase BA, Semenov I, Rubin S, Meyers S, Mark A, Makhlouf T, Chirayil TT, Maraganore D, Wei J, Zheng SL, Xu J, Epshteyn A, Pham A, Frigerio R, Markopoulou K. Characteristics associated with response to subcutaneously administered anti-CGRP monoclonal antibody medications in a real-world community cohort of persons living with migraine: A retrospective clinical and genetic study. Headache 2024; 64:68-92. [PMID: 38071464 DOI: 10.1111/head.14655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 10/12/2023] [Accepted: 10/20/2023] [Indexed: 01/23/2024]
Abstract
OBJECTIVE To evaluate response to anti-calcitonin gene-related peptide (CGRP) migraine preventives in a real-world community cohort of persons living with migraine and to identify clinical and genetic characteristics associated with efficacious response. BACKGROUND Erenumab-aooeb, fremanezumab-vrfm, and galcanezumab-gnlm target CGRP or its receptor; however, many patients are non-responsive. METHODS In this retrospective clinical and genetic study, we identified 1077 adult patients who satisfied the International Classification of Headache Disorders, 3rd edition, criteria for migraine without aura, migraine with aura, or chronic migraine and who were prescribed an anti-CGRP migraine preventive between May 2018 and May 2021. Screening of 558 patients identified 289 with data at baseline and first follow-up visits; data were available for 161 patients at a second follow-up visit. The primary outcome was migraine days per month (MDM). In 198 genotyped patients, we evaluated associations between responders (i.e., patients with ≥50% reduction in MDM at follow-up) and genes involved in CGRP signaling or pharmacological response, and genetic and polygenic risk scores. RESULTS The median time to first follow-up was 4.4 (0.9-22) months after preventive start. At the second follow-up, 5.7 (0.9-13) months later, 145 patients had continued on the same preventive. Preventives had strong, persistent effects in reducing MDM in responders (follow-up 1: η2 = 0.26, follow-up 2: η2 = 0.22). At the first but not second follow-up: galcanezumab had a larger effect than erenumab, while no difference was seen at either follow-up between galcanezumab and fremanezumab or fremanezumab and erenumab. The decrease in MDM at follow-up was generally proportional to baseline MDM, larger in females, and increased with months on medication. At the first follow-up only, patients with prior hospitalization for migraine or who had not responded to more preventive regimens had a smaller decrease in MDM. Reasons for stopping or switching a preventive varied between medications and were often related to cost and insurance coverage. At both follow-ups, patient tolerance (1: 92.2% [262/284]; 2: 95.2% [141/145]) and continued use (1: 77.5% [224/289]; 2: 80.6% [116/145]) were high and similar across preventives. Response consistency (always non-responders: 31.7% [46/145]; always responders: 56.5% [82/145], and one-time only responders: 11.7% [17/145]) was also similar across preventives. Non-responder status had nominally significant associations with rs12615320-G in RAMP1 (odds ratio [95% confidence interval]: 4.7 [1.5, 14.7]), and rs4680-A in COMT (0.6[0.4, 0.9]). Non-responders had a lower mean genetic risk score than responders (1.0 vs. 1.1; t(df) = -1.75(174.84), p = 0.041), and the fraction of responders increased with genetic and polygenic risk score percentile. CONCLUSIONS In this real-world setting, anti-CGRP preventives reduced MDM persistently and had similar and large effect sizes on MDM reduction; however, clinical and genetic factors influenced response.
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Affiliation(s)
- Bruce A Chase
- Health Information Technology, NorthShore University HealthSystem, Skokie, Illinois, USA
- Pritzker School of Medicine, Chicago, Illinois, USA
| | - Irene Semenov
- Pritzker School of Medicine, Chicago, Illinois, USA
- Department of Neurology, NorthShore University HealthSystem, Evanston, Illinois, USA
| | - Susan Rubin
- Department of Neurology, NorthShore University HealthSystem, Evanston, Illinois, USA
- University of Chicago Pritzker School of Medicine, Chicago, Illinois, USA
| | - Steven Meyers
- Department of Neurology, NorthShore University HealthSystem, Evanston, Illinois, USA
- University of Chicago Pritzker School of Medicine, Chicago, Illinois, USA
| | - Angela Mark
- Department of Neurology, NorthShore University HealthSystem, Evanston, Illinois, USA
- University of Chicago Pritzker School of Medicine, Chicago, Illinois, USA
| | - Thomas Makhlouf
- Pritzker School of Medicine, Chicago, Illinois, USA
- Department of Neurology, NorthShore University HealthSystem, Evanston, Illinois, USA
| | - Tanya T Chirayil
- Department of Neurology, NorthShore University HealthSystem, Evanston, Illinois, USA
| | | | - Jun Wei
- Center for Individualized Medicine, NorthShore University HealthSystem, Evanston, Illinois, USA
| | - Siqun L Zheng
- Center for Individualized Medicine, NorthShore University HealthSystem, Evanston, Illinois, USA
| | - Jianfeng Xu
- Center for Individualized Medicine, NorthShore University HealthSystem, Evanston, Illinois, USA
| | - Alexander Epshteyn
- Health Information Technology, NorthShore University HealthSystem, Skokie, Illinois, USA
| | - Anna Pham
- Department of Neurology, NorthShore University HealthSystem, Evanston, Illinois, USA
| | - Roberta Frigerio
- Pritzker School of Medicine, Chicago, Illinois, USA
- Department of Neurology, NorthShore University HealthSystem, Evanston, Illinois, USA
| | - Katerina Markopoulou
- Department of Neurology, NorthShore University HealthSystem, Evanston, Illinois, USA
- University of Chicago Pritzker School of Medicine, Chicago, Illinois, USA
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17
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Yu J, Varella Pereira GM, Allen-Brady K, Cuffolo R, Siddharth A, Koch M, Chua JWF, Sorrentino F, Dytko O, Ng KY, Violette P, Khullar V, Wang ZT, Cartwright R. Genetic polymorphisms associated with urinary tract infection in children and adults: a systematic review and meta-analysis. Am J Obstet Gynecol 2023:S0002-9378(23)02169-5. [PMID: 38128862 DOI: 10.1016/j.ajog.2023.12.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 12/13/2023] [Accepted: 12/13/2023] [Indexed: 12/23/2023]
Abstract
INTRODUCTION The lifetime risk of urinary tract infection is known from first-degree relative studies to be highly heritable. Associations have also been observed across the life course from pediatric urinary tract infection to recurrent urinary tract infection in adulthood, suggesting lifelong susceptibility factors. Candidate gene studies and genome-wide association studies have tested for genetic associations of urinary tract infection; however, no contemporary systematic synthesis of studies is available. OBJECTIVE We conducted a systematic review to identify all genetic polymorphisms tested for an association with urinary tract infection in children and adults; and to assess their strength, consistency, and risk of bias among reported associations. DATA SOURCES AND STUDY ELIGIBILITY CRITERIA PubMed, HuGE Navigator and Embase were searched from January 1, 2005 to November 16, 2023, using a combination of genetic and phenotype key words. STUDY APPRAISAL AND SYNTHESIS METHODS Fixed and random effects meta-analyses were conducted using codominant models of inheritance in metan. The interim Venice criteria were used to assess their credibility of pooled associations. RESULTS After removing 451 duplicates, 1821 studies reports were screened, with 106 selected for full-text review, 22 were included in the meta-analysis (7 adult studies and 15 pediatric studies). Our meta-analyses demonstrated significant pooled associations for pediatric urinary tract infection with variation in CXCR1, IL8, TGF, TLR4 and VDR; all of which have plausible roles in the pathogenesis of urinary tract infection. Our meta-analyses also demonstrated a significant pooled association for adult urinary tract infection with variation in CXCR1. All significant pooled associations were graded according to their epidemiological credibility, sample sizes, heterogeneity between studies, and risk of bias. CONCLUSION This systematic review provides a current synthesis of the known genetic architecture of urinary tract infection in childhood and adulthood; and should provide important information for researchers analysing future genetic association studies. Although, overall, the credibility of pooled associations was weak, the consistency of findings for rs2234671 single nucleotide polymorphisms of CXCR1 in both populations suggest a key role in the urinary tract infection pathogenesis.
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Affiliation(s)
- Jiakun Yu
- University Hospitals Sussex NHS Foundation Trust, Brighton, United Kingdom.
| | - Glaucia Miranda Varella Pereira
- Department of Epidemiology and Biostatistics, Imperial College London, Norfolk Place, London, United Kingdom; Department of Urogynaecology, LNWH NHS Trust, London, United Kingdom; Department of Obstetrics and Gynaecology, School of Medical Sciences, University of Campinas, Brazil
| | - Kristina Allen-Brady
- Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, UT
| | - Romana Cuffolo
- Department of Obstetrics and Gynaecology, John Radcliffe Hospital, Oxford University Hospitals NHS Trust, Oxford, United Kingdom
| | - Aditi Siddharth
- John Radcliffe Hospital, Headley Way, Headington, Oxford, United Kingdom
| | - Marianne Koch
- Department of Obstetrics and Gynecology, Medical University of Vienna, Vienna, Austria
| | - John W F Chua
- Frimley Health NHS Foundation Trust, Frimley, United Kingdom
| | - Felice Sorrentino
- Department of Medical and Surgical Sciences, Institute of Obstetrics and Gynecology, University of Foggia, Foggia, Italy
| | - Oskar Dytko
- Imperial College School of Medicine, Imperial College London, London, United Kingdom
| | - Kaa-Yung Ng
- Imperial College School of Medicine, Imperial College London, London, United Kingdom
| | - Philippe Violette
- Department of Health Research Methods, Evidence and Impact (HEI) and Surgery, McMaster University, Hamilton, Ontario, Canada
| | - Vik Khullar
- Department of Urogynaecology, Imperial College London, United Kingdom
| | - Zhan Tao Wang
- Department of Surgery, Division of Urology, University of Western Ontario, London, Ontario, Canada
| | - Rufus Cartwright
- Department of Epidemiology and Biostatistics, Imperial College London, Norfolk Place, London, United Kingdom; Department of Urogynaecology, LNWH NHS Trust, London, United Kingdom; Department of Urogynaecology, Chelsea and Westminster NHS Foundation Trust, London, United Kingdom
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18
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Wahbeh MH, Boyd RJ, Yovo C, Rike B, McCallion AS, Avramopoulos D. A Functional Schizophrenia-associated genetic variant near the TSNARE1 and ADGRB1 genes. bioRxiv 2023:2023.12.18.570831. [PMID: 38187620 PMCID: PMC10769312 DOI: 10.1101/2023.12.18.570831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Recent collaborative genome wide association studies (GWAS) have identified >200 independent loci contributing to risk for schizophrenia (SCZ). The genes closest to these loci have diverse functions, supporting the potential involvement of multiple relevant biological processes; yet there is no direct evidence that individual variants are functional or directly linked to specific genes. Nevertheless, overlap with certain epigenetic marks suggest that most GWAS-implicated variants are regulatory. Based on the strength of association with SCZ and the presence of regulatory epigenetic marks, we chose one such variant near TSNARE1 and ADGRB1, rs4129585, to test for functional potential and assay differences that may drive the pathogenicity of the risk allele. We observed that the variant-containing sequence drives reporter expression in relevant neuronal populations in zebrafish. Next, we introduced each allele into human induced pluripotent cells and differentiated 4 isogenic clones homozygous for the risk allele and 5 clones homozygous for the non-risk allele into neural precursor cells. Employing RNA-seq, we found that the two alleles yield significant transcriptional differences in the expression of 109 genes at FDR <0.05 and 259 genes at FDR <0.1. We demonstrate that these genes are highly interconnected in pathways enriched for synaptic proteins, axon guidance, and regulation of synapse assembly. Exploration of genes near rs4129585 suggests that this variant does not regulate TSNARE1 transcripts, as previously thought, but may regulate the neighboring ADGRB1, a regulator of synaptogenesis. Our results suggest that rs4129585 is a functional common variant that functions in specific pathways likely involved in SCZ risk.
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Affiliation(s)
- Marah H Wahbeh
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Rachel J Boyd
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Christian Yovo
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Bailey Rike
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Andrew S McCallion
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Dimitrios Avramopoulos
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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19
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Chang X, Qu HQ, Liu Y, Glessner JT, Hakonarson H. Mitochondrial DNA Haplogroup K Is Protective Against Autism Spectrum Disorder Risk in Populations of European Ancestry. J Am Acad Child Adolesc Psychiatry 2023:S0890-8567(23)02242-6. [PMID: 38072244 DOI: 10.1016/j.jaac.2023.09.550] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 09/23/2023] [Accepted: 12/01/2023] [Indexed: 12/23/2023]
Abstract
OBJECTIVE Accumulative evidence indicates a critical role of mitochondrial function in autism spectrum disorders (ASD), implying that ASD risk may be linked to mitochondrial dysfunction due to DNA (mtDNA) variations. Although a few studies have explored the association between mtDNA variations and ASD, the role of mtDNA in ASD is still unclear. Here, we aimed to investigate whether mitochondrial DNA haplogroups are associated with the risk of ASD. METHOD Two European cohorts and an Ashkenazi Jewish (AJ) cohort were analyzed, including 2,062 ASD patients in comparison with 4,632 healthy controls. DNA samples were genotyped using Illumina HumanHap550/610 and Illumina 1M arrays, inclusive of mitochondrial markers. Mitochondrial DNA (mtDNA) haplogroups were identified from genotyping data using HaploGrep2. A mitochondrial genome imputation pipeline was established to detect mtDNA variants. We conducted a case-control study to investigate potential associations of mtDNA haplogroups and variants with the susceptibility to ASD. RESULTS We observed that the ancient adaptive mtDNA haplogroup K was significantly associated with decreased risk of ASD by the investigation of 2 European cohorts including a total of 2,006 cases and 4,435 controls (odds ratio = 0.64, P=1.79 × 10-5), and we replicated this association in an Ashkenazi Jewish (AJ) cohort including 56 cases and 197 controls (odds ratio = 0.35, P = 9.46 × 10-3). Moreover, we demonstrate that the mtDNA variants rs28358571, rs28358584, and rs28358280 are significantly associated with ASD risk. Further expression quantitative trait loci (eQTLs) analysis indicated that the rs28358584 and rs28358280 genotypes are associated with expression levels of nearby genes in brain tissues, suggesting those mtDNA variants may confer risk for ASD via regulation of expression levels of genes encoded by the mitochondrial genome. CONCLUSION This study helps to shed light on the contribution of mitochondria in ASD and provides new insights into the genetic mechanism underlying ASD, suggesting the potential involvement of mtDNA-encoded proteins in the development of ASD.
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Affiliation(s)
- Xiao Chang
- Children's Hospital of Philadelphia, Pennsylvania, United States; Shandong First Medical University & Shandong Academy of Medical Sciences, Shandong, China.
| | - Hui-Qi Qu
- Children's Hospital of Philadelphia, Pennsylvania, United States
| | - Yichuan Liu
- Children's Hospital of Philadelphia, Pennsylvania, United States
| | | | - Hakon Hakonarson
- Children's Hospital of Philadelphia, Pennsylvania, United States; The Perelman School of Medicine, University of Pennsylvania, Pennsylvania, United States and Faculty of Medicine, University of Iceland, Reykjavik, Iceland
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20
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Kandeeban S, Ishwarya S, Nareshkumar RN, Gunalan V, Porkodi P, Shyam Sundar J, Asokan R, Sharada R, Sripriya K, George R, Sripriya S. A Study on the Candidate Gene Association and Interaction with Measures of UV Exposure in Pseudoexfoliation Patients from India. Curr Eye Res 2023; 48:1144-1152. [PMID: 37556844 DOI: 10.1080/02713683.2023.2246689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Revised: 07/18/2023] [Accepted: 08/05/2023] [Indexed: 08/11/2023]
Abstract
PURPOSE Environmental and genetic factors are associated with development of Pseudoexfoliation syndrome (XFS). Here we intended to elucidate the association of candidate genes in relevance to UV exposure in these patients. METHODS This is a case-control study of 309 subjects (N = 219 controls and 90 XFS cases) from India. PCR based direct sequencing was performed for candidate genes (LOXL1, POMP and TMEM136) followed by genotype and haplotype analysis. The promoter methylation status was assessed by Methylation specific PCR based direct sequencing of genomic DNA for all samples. The methylation status was compared with that of primary fibroblasts cultures established from patient's Tenon's tissue samples in subset of these patients. RESULTS SNPs rs3825942, rs41435250, rs8818 (LOXL1) and rs3737528 (POMP) showed significant association with XFS. LOXL1 gene haplotype GAGC (rs1048661- rs3825942- rs41435250-rs8818) was associated with lower risk for XFS with a p value 4.1961 × 10-6 (OR =0; 95%CI, 0.000-0.003). POMP gene haplotypes for intronic SNPs (rs1340815- rs3737528- rs913797) TCC and TTC were associated with increased risk for the disease (OR > 1.0). Significant correlation for SNPs rs3825942 of LOXL1 (ρ= -0.132) and rs3737528 of POMP (ρ = 0.12) was observed with measure of lifetime UV exposure (CUVAF value). Reduced LOXL1 gene expression was observed in cultured tenon fibroblasts from the patients that correlated with differential methylation of the Sp-1 binding sites at -253, -243bp upstream to the transcription start site of LOXL1 promoter region. CONCLUSION Our results suggest a possible interaction for LOXL1 gene haplotype (GAGC) with the measure of ocular UV exposure in pseudoexfoliation syndrome.
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Affiliation(s)
- Suganya Kandeeban
- SNONGC Department of Genetics and Molecular Biology, Vision Research Foundation, Chennai, India
- School of Chemical and Biotechnology, SASTRA University, Tanjavur, India
| | - Sureshkumar Ishwarya
- Glaucoma Services, Medical Research Foundation, Sankara Nethralaya, Chennai, India
| | - R N Nareshkumar
- Department of Biochemistry and Cell Biology, Vision Research Foundation, R S Mehta Jain, Chennai, India
| | - Vaishaali Gunalan
- Glaucoma Services, Medical Research Foundation, Sankara Nethralaya, Chennai, India
| | - P Porkodi
- SNONGC Department of Genetics and Molecular Biology, Vision Research Foundation, Chennai, India
| | - J Shyam Sundar
- Department of Biochemistry and Cell Biology, Vision Research Foundation, R S Mehta Jain, Chennai, India
| | - Rashima Asokan
- Glaucoma Services, Medical Research Foundation, Sankara Nethralaya, Chennai, India
| | - R Sharada
- Glaucoma Services, Medical Research Foundation, Sankara Nethralaya, Chennai, India
| | - Krishnamoorthy Sripriya
- Smt. Jadhavbai Nathamal Singhvee Glaucoma Services, Medical Research Foundation, Chennai, India
| | - Ronnie George
- Smt. Jadhavbai Nathamal Singhvee Glaucoma Services, Medical Research Foundation, Chennai, India
| | - Sarangapani Sripriya
- SNONGC Department of Genetics and Molecular Biology, Vision Research Foundation, Chennai, India
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21
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Mitok KA, Schueler KL, King SM, Orr J, Ryan KA, Keller MP, Krauss RM, Mitchell BD, Shuldiner AR, Attie AD. Missense variants in SORT1 are associated with LDL-C in an Amish population. J Lipid Res 2023; 64:100468. [PMID: 37913995 PMCID: PMC10711479 DOI: 10.1016/j.jlr.2023.100468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 10/23/2023] [Accepted: 10/26/2023] [Indexed: 11/03/2023] Open
Abstract
Common noncoding variants at the human 1p13.3 locus associated with SORT1 expression are among those most strongly associated with low-density lipoprotein cholesterol (LDL-C) in human genome-wide association studies. However, validation studies in mice and cell lines have produced variable results regarding the directionality of the effect of SORT1 on LDL-C. This, together with the fact that the 1p13.3 variants are associated with expression of several genes, has raised the question of whether SORT1 is the causal gene at this locus. Using whole exome sequencing in members of an Amish population, we identified coding variants in SORT1 that are associated with increased (rs141749679, K302E) and decreased (rs149456022, Q225H) LDL-C. Further, analysis of plasma lipoprotein particle subclasses by ion mobility in a subset of rs141749679 (K302E) carriers revealed higher levels of large LDL particles compared to noncarriers. In contrast to the effect of these variants in the Amish, the sortilin K302E mutation introduced into a C57BL/6J mouse via CRISPR/Cas9 resulted in decreased non-high-density lipoprotein cholesterol, and the sortilin Q225H mutation did not alter cholesterol levels in mice. This is indicative of different effects of these mutations on cholesterol metabolism in the two species. To our knowledge, this is the first evidence that naturally occurring coding variants in SORT1 are associated with LDL-C, thus supporting SORT1 as the gene responsible for the association of the 1p13.3 locus with LDL-C.
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Affiliation(s)
- Kelly A Mitok
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Kathryn L Schueler
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Sarah M King
- Department of Pediatrics, University of California-San Francisco, San Francisco, CA, USA
| | - Joseph Orr
- Department of Pediatrics, University of California-San Francisco, San Francisco, CA, USA
| | - Kathleen A Ryan
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Mark P Keller
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Ronald M Krauss
- Department of Pediatrics, University of California-San Francisco, San Francisco, CA, USA
| | - Braxton D Mitchell
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Alan R Shuldiner
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA; Regeneron Genetics Center, Tarrytown, NY, USA
| | - Alan D Attie
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA.
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22
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Higuchi T, Oka S, Furukawa H, Shimada K, Tsunoda S, Ito S, Okamoto A, Fujimori M, Nakamura T, Katayama M, Saisho K, Shinohara S, Matsui T, Migita K, Nagaoka S, Tohma S. Association of a Single Nucleotide Variant in TERT with Airway Disease in Japanese Rheumatoid Arthritis Patients. Genes (Basel) 2023; 14:2084. [PMID: 38003027 PMCID: PMC10671651 DOI: 10.3390/genes14112084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 11/11/2023] [Accepted: 11/15/2023] [Indexed: 11/26/2023] Open
Abstract
Interstitial lung disease and airway disease (AD) are often complicated with rheumatoid arthritis (RA) and have a poor prognosis. Several studies reported genetic associations with interstitial lung disease in RA. However, few genetic studies have examined the susceptibility to AD in RA patients. Here, we investigated whether single nucleotide variants susceptible to idiopathic pulmonary fibrosis might be associated with interstitial lung disease or AD in Japanese RA patients. Genotyping of rs2736100 [C/A] in TERT and rs1278769 [G/A] in ATP11A was conducted in 98 RA patients with usual interstitial pneumonia, 120 with nonspecific interstitial pneumonia (NSIP), 227 with AD, and 422 without chronic lung disease using TaqMan assays. An association with AD in RA was found for rs2736100 (p = 0.0043, Pc = 0.0129, odds ratio [OR] 1.40, 95% confidence interval [CI] 1.11-1.77). ATP11A rs1278769 was significantly associated with NSIP in older RA patients (>65 years, p = 0.0010, OR 2.15, 95% CI 1.35-3.40). This study first reported an association of rs2736100 with AD in RA patients and ATP11A rs1278769 with NSIP in older RA patients.
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Affiliation(s)
- Takashi Higuchi
- Department of Clinical Research, NHO Tokyo National Hospital, 3-1-1 Takeoka, Kiyose 204-8585, Japan; (T.H.); (S.O.); (S.T.)
| | - Shomi Oka
- Department of Clinical Research, NHO Tokyo National Hospital, 3-1-1 Takeoka, Kiyose 204-8585, Japan; (T.H.); (S.O.); (S.T.)
- Clinical Research Center for Allergy and Rheumatology, NHO Sagamihara National Hospital, 18-1 Sakuradai, Minami-ku, Sagamihara 252-0392, Japan;
| | - Hiroshi Furukawa
- Department of Clinical Research, NHO Tokyo National Hospital, 3-1-1 Takeoka, Kiyose 204-8585, Japan; (T.H.); (S.O.); (S.T.)
- Clinical Research Center for Allergy and Rheumatology, NHO Sagamihara National Hospital, 18-1 Sakuradai, Minami-ku, Sagamihara 252-0392, Japan;
| | - Kota Shimada
- Department of Rheumatology, NHO Sagamihara National Hospital, 18-1 Sakuradai, Minami-ku, Sagamihara 252-0392, Japan;
- Department of Rheumatic Diseases, Tokyo Metropolitan Tama Medical Center, 2-8-29 Musashi-dai, Fuchu 183-8524, Japan
| | - Shinichiro Tsunoda
- Division of Rheumatology, Department of Internal Medicine, Hyogo College of Medicine, 1-1 Mukogawa-cho, Nishinomiya 663-8501, Japan;
- Department of Nephrology, Sumitomo Hospital, 5-3-20 Nakanoshima, Kita-ku, Osaka 530-0005, Japan
| | - Satoshi Ito
- Department of Rheumatology, Niigata Rheumatic Center, 1-2-8 Hon-cho, Shibata 957-0054, Japan;
| | - Akira Okamoto
- Department of Rheumatology, NHO Himeji Medical Center, 68 Hon-machi, Himeji 670-8520, Japan; (A.O.)
| | - Misuzu Fujimori
- Department of Rheumatology, NHO Himeji Medical Center, 68 Hon-machi, Himeji 670-8520, Japan; (A.O.)
| | - Tadashi Nakamura
- Department of Rheumatology, Sakurajyuji Hospital, 1-1-1 Miyukikibe, Minami-ku, Kumamoto 861-4173, Japan;
| | - Masao Katayama
- Department of Internal Medicine, NHO Nagoya Medical Center, 4-1-1 Sannomaru, Naka-ku, Nagoya 460-0001, Japan;
| | - Koichiro Saisho
- Department of Orthopedics/Rheumatology, NHO Miyakonojo Medical Center, 5033-1 Iwayoshi-cho, Miyakonojo 885-0014, Japan;
- Tanimura Hospital, 10-2 Kitakoji, Nobeoka 882-0041, Japan
| | - Satoshi Shinohara
- Tochigi Rheumatology Clinic, 1-1-9 Ekimaedori, Utsunomiya 321-0964, Japan;
| | - Toshihiro Matsui
- Clinical Research Center for Allergy and Rheumatology, NHO Sagamihara National Hospital, 18-1 Sakuradai, Minami-ku, Sagamihara 252-0392, Japan;
- Department of Rheumatology, NHO Sagamihara National Hospital, 18-1 Sakuradai, Minami-ku, Sagamihara 252-0392, Japan;
| | - Kiyoshi Migita
- Clinical Research Center, NHO Nagasaki Medical Center, 2-1001-1 Kubara, Omura 856-8562, Japan;
- Department of Gastroenterology and Rheumatology, Fukushima Medical University School of Medicine, 1 Hikarigaoka, Fukushima 960-1295, Japan
| | - Shouhei Nagaoka
- Department of Rheumatology, Yokohama Minami Kyosai Hospital, 1-21-1 Rokuura-higashi, Kanazawa-ku, Yokohama 236-0037, Japan;
| | - Shigeto Tohma
- Department of Clinical Research, NHO Tokyo National Hospital, 3-1-1 Takeoka, Kiyose 204-8585, Japan; (T.H.); (S.O.); (S.T.)
- Clinical Research Center for Allergy and Rheumatology, NHO Sagamihara National Hospital, 18-1 Sakuradai, Minami-ku, Sagamihara 252-0392, Japan;
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23
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Liu Z, Turkmen AS, Lin S. Population stratification correction using Bayesian shrinkage priors for genetic association studies. Ann Hum Genet 2023; 87:302-315. [PMID: 37771252 DOI: 10.1111/ahg.12527] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 08/20/2023] [Accepted: 08/24/2023] [Indexed: 09/30/2023]
Abstract
INTRODUCTION Population stratification (PS) is a major source of confounding in population-based genetic association studies of quantitative traits. Principal component regression (PCR) and linear mixed model (LMM) are two commonly used approaches to account for PS in association studies. Previous studies have shown that LMM can be interpreted as including all principal components (PCs) as random-effect covariates. However, including all PCs in LMM may dilute the influence of relevant PCs in some scenarios, while including only a few preselected PCs in PCR may fail to fully capture the genetic diversity. MATERIALS AND METHODS To address these shortcomings, we introduce Bayestrat-a method to detect associated variants with PS correction under the Bayesian LASSO framework. To adjust for PS, Bayestrat accommodates a large number of PCs and utilizes appropriate shrinkage priors to shrink the effects of nonassociated PCs. RESULTS Simulation results show that Bayestrat consistently controls type I error rates and achieves higher power compared to its non-shrinkage counterparts, especially when the number of PCs included in the model is large. As a demonstration of the utility of Bayestrat, we apply it to the Multi-Ethnic Study of Atherosclerosis (MESA). Variants and genes associated with serum triglyceride or HDL cholesterol are identified in our analyses. DISCUSSION The automatic and self-selection features of Bayestrat make it particularly suited in situations with complex underlying PS scenarios, where it is unknown a priori which PCs are potential confounders, yet the number that needs to be considered could be large in order to fully account for PS.
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Affiliation(s)
- Zilu Liu
- Department of Statistics, The Ohio State University, Columbus, Ohio, USA
| | - Asuman S Turkmen
- Department of Statistics, The Ohio State University, Columbus, Ohio, USA
| | - Shili Lin
- Department of Statistics, The Ohio State University, Columbus, Ohio, USA
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Agarwal T, Lyngdoh T, Khadgawat R, Prabhakaran D, Chandak GR, Walia GK. Genetic architecture of adiposity measures among Asians: Findings from GWAS. Ann Hum Genet 2023; 87:255-273. [PMID: 37671428 DOI: 10.1111/ahg.12526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 08/17/2023] [Accepted: 08/18/2023] [Indexed: 09/07/2023]
Abstract
Adiposity has gradually become a global public threat over the years with drastic increase in the attributable deaths and disability adjusted life years (DALYs). Given an increased metabolic risk among Asians as compared to Europeans for any given body mass index (BMI) and considering the differences in genetic architecture between them, the present review aims to summarize the findings from genome-wide scans for various adiposity indices and related anthropometric measures from Asian populations. The search for related studies, published till February 2022, were made on PubMed and GWAS Catalog using search strategy built with relevant keywords joined by Boolean operators. It was recorded that out of a total of 47 identified studies, maximum studies are from Korean population (n = 14), followed by Chinese (n = 7), and Japanese (n = 6). Nearly 200 loci have been identified for BMI, 660 for height, 16 for weight, 28 for circumferences (waist and hip), 32 for ratios (waist hip ratio [WHR] and thoracic hip ratio [THR]), 5 for body fat, 16 for obesity, and 28 for adiposity-related blood markers among Asians. It was observed that though, most of the loci were unique for each trait, there were 3 loci in common to BMI and WHR. Apart from validation of variants identified in European setting, there were many novel loci discovered in Asian populations. Notably, 125 novel loci form Asian studies have been reported for BMI, 47 for height, 5 for waist circumference, and 2 for adiponectin level to the existing knowledge of the genetic framework of adiposity and related measures. It is necessary to examine more advanced adiposity measures, specifically of relevance to abdominal adiposity, a major risk factor for cardiometabolic disorders among Asians. Moreover, in spite of being one continent, there is diversity among different ethnicities across Asia in terms of lifestyle, climate, geography, genetic structure and consequently the phenotypic manifestations. Hence, it is also important to consider ethnic specific studies for identifying and validating reliable genetic variants of adiposity measures among Asians.
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Affiliation(s)
- Tripti Agarwal
- Indian Institute of Public Health-Delhi, Public Health Foundation of India, Delhi, India
| | | | | | | | - Giriraj Ratan Chandak
- Genomic Research in Complex diseases (GRC Group), CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
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25
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Melchiorsen JU, Sørensen KV, Bork-Jensen J, Kizilkaya HS, Gasbjerg LS, Hauser AS, Rungby J, Sørensen HT, Vaag A, Nielsen JS, Pedersen O, Linneberg A, Hartmann B, Gjesing AP, Holst JJ, Hansen T, Rosenkilde MM, Grarup N. Rare Heterozygous Loss-of-Function Variants in the Human GLP-1 Receptor Are Not Associated With Cardiometabolic Phenotypes. J Clin Endocrinol Metab 2023; 108:2821-2833. [PMID: 37235780 PMCID: PMC10584003 DOI: 10.1210/clinem/dgad290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 05/04/2023] [Accepted: 05/22/2023] [Indexed: 05/28/2023]
Abstract
CONTEXT Lost glucagon-like peptide 1 receptor (GLP-1R) function affects human physiology. OBJECTIVE This work aimed to identify coding nonsynonymous GLP1R variants in Danish individuals to link their in vitro phenotypes and clinical phenotypic associations. METHODS We sequenced GLP1R in 8642 Danish individuals with type 2 diabetes or normal glucose tolerance and examined the ability of nonsynonymous variants to bind GLP-1 and to signal in transfected cells via cyclic adenosine monophosphate (cAMP) formation and β-arrestin recruitment. We performed a cross-sectional study between the burden of loss-of-signaling (LoS) variants and cardiometabolic phenotypes in 2930 patients with type 2 diabetes and 5712 participants in a population-based cohort. Furthermore, we studied the association between cardiometabolic phenotypes and the burden of the LoS variants and 60 partly overlapping predicted loss-of-function (pLoF) GLP1R variants found in 330 566 unrelated White exome-sequenced participants in the UK Biobank cohort. RESULTS We identified 36 nonsynonymous variants in GLP1R, of which 10 had a statistically significant loss in GLP-1-induced cAMP signaling compared to wild-type. However, no association was observed between the LoS variants and type 2 diabetes, although LoS variant carriers had a minor increased fasting plasma glucose level. Moreover, pLoF variants from the UK Biobank also did not reveal substantial cardiometabolic associations, despite a small effect on glycated hemoglobin A1c. CONCLUSION Since no homozygous LoS nor pLoF variants were identified and heterozygous carriers had similar cardiometabolic phenotype as noncarriers, we conclude that GLP-1R may be of particular importance in human physiology, due to a potential evolutionary intolerance of harmful homozygous GLP1R variants.
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Affiliation(s)
- Josefine U Melchiorsen
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark
| | - Kimmie V Sørensen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark
| | - Jette Bork-Jensen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark
| | - Hüsün S Kizilkaya
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark
| | - Lærke S Gasbjerg
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark
| | - Alexander S Hauser
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2100, Denmark
| | - Jørgen Rungby
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark
| | - Henrik T Sørensen
- Department of Clinical Epidemiology, Aarhus University, Aarhus 8800, Denmark
- Department of Epidemiology, Boston University, Boston, MA 02118, USA
| | - Allan Vaag
- Steno Diabetes Center Copenhagen, Herlev Hospital, Herlev 2730, Denmark
| | - Jens S Nielsen
- Steno Diabetes Center Odense, Odense University Hospital, Odense 5000, Denmark
| | - Oluf Pedersen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark
- Center for Clinical Metabolic Research, Gentofte Hospital, Hellerup 2900, Denmark
| | - Allan Linneberg
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark
- Center for Clinical Research and Prevention, Copenhagen University Hospital—Bispebjerg and Frederiksberg, Frederiksberg 2000, Denmark
| | - Bolette Hartmann
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark
| | - Anette P Gjesing
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark
| | - Jens J Holst
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark
| | - Torben Hansen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark
| | - Mette M Rosenkilde
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark
| | - Niels Grarup
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark
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Sun W, Yang F, Yang Y, Su X, Xing Y. The causality between obstructive sleep apnea and ventricular structure and function: a bidirectional Mendelian randomization study. Front Genet 2023; 14:1266869. [PMID: 37881804 PMCID: PMC10597648 DOI: 10.3389/fgene.2023.1266869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 09/27/2023] [Indexed: 10/27/2023] Open
Abstract
Background: Multiple observational studies have discovered a substantial link between obstructive sleep apnea (OSA) and ventricular dysfunction. However, conventional observational studies are vulnerable to causal reversal and confounding, making it challenging to infer the causes of effects and their direction. Methods: With the help of a bidirectional, two-sample Mendelian randomization (MR) study, we assessed the potential causality between OSA and left and right ventricular (LV, RV) structure and function. We conducted our analysis utilizing summary data from genome-wide association studies of OSA (16,761 cases and 201,194 controls) in the FinnGen Study, as well as LV (36,041 participants) and RV (29,506 participants) in the UK Biobank cardiovascular magnetic resonance research. The inverse variance weighted (IVW) was selected as the main strategy, with the MR-Egger and weighted median methods serving as supplements. Other methods were employed as sensitivity analysis tools to look at heterogeneity and pleiotropy, including MR-Egger intercept, Cochran Q statistic, MR-PRESSO, and leave-one-out analysis. Results: In the primary IVW analysis, genetically predicted OSA was strongly causative on LV end-diastolic volume (β = 0.114, 95% CI = 0.034-0.194, p = 0.006) and LV stroke volume (β = 0.111, 95% CI = 0.031-0.191, p = 0.007), and genetically predicted LV ejection fraction was linked to an increased risk of OSA (OR = 1.161, 95% CI = 1.029-1.309, p = 0.015). However, there was no connection found between OSA and any RV parameters. Conclusion: Our genetic analysis raises a potential causative link between OSA and ventricular structure and function, which may improve the knowledge of OSA as a risk factor for cardiovascular disease by demonstrating a direct impact on cardiac structure and function.
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Affiliation(s)
| | | | | | | | - Yanwei Xing
- Guang’anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
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27
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Warren RA, Carew AS, Andreou P, Levy AP, Sapp J, Lache O, Ginsberg HN, Rimm EB, Herman C, Kirkland S, Cahill LE. Relationship Between Time-Varying Achieved High-Density Lipoprotein Cholesterol and Risk of Coronary Events Depends on Haptoglobin Phenotype Within the ACCORD Lipid Study. J Am Heart Assoc 2023; 12:e030288. [PMID: 37776200 PMCID: PMC10727244 DOI: 10.1161/jaha.123.030288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 08/08/2023] [Indexed: 10/02/2023]
Abstract
Background The Hp (haptoglobin)2-2 phenotype (~40% of people) is associated with dysfunctional high-density lipoprotein (HDL) that is heavily oxidized in hyperglycemia, which may explain why raising HDL-cholesterol (HDL-C) does not reliably prevent coronary artery disease (CAD) in diabetes. Methods and Results In this observational study using longitudinal data from the ACCORD (Action to Control Cardiovascular Risk in Diabetes) lipid trial, time-varying (achieved) HDL-C updated at 4, 8, and 12 months, and annually thereafter over a mean of 4.7 years, was analyzed in relation to risk of CAD and secondary outcomes using Cox proportional hazards regression with time-varying covariables among participants with (n=1781) and without (n=3191) the Hp2-2 phenotype. HDL-C did not differ between the phenotypes throughout the study. Having low HDL-C (<40 mg/dL for male participants and <50 mg/dL for female participants) was associated with a greater risk of CAD compared with non-low HDL-C among participants with the non-Hp2-2 phenotype (hazard ratio [HR], 1.48 [95% CI, 1.18-1.87]) but not among the Hp2-2 phenotype (HR, 0.97 [95% CI, 0.70-1.35]; P interaction=0.03). Similarly, an inverse relationship was observed between HDL-C quintiles and CAD risk among participants without the Hp2-2 phenotype, whereas no significant inverse relationship was observed among participants with the Hp2-2 phenotype (P interaction=0.38). Among the Hp2-2 phenotype group, having low HDL-C was associated with higher risk of CVD mortality (HR, 2.09 [95% CI, 1.05-4.13]), and compared with the lowest HDL-C quintile, higher quintiles were associated with lower risk of CVD mortality and congestive heart failure. Conclusions Hp phenotype modified the association between HDL-C and risk of CAD in the ACCORD lipid study, suggesting that HDL dysfunction in the Hp2-2 phenotype may hinder CAD-protective properties of HDL-C.
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Affiliation(s)
- Rachel A. Warren
- Department of MedicineDalhousie UniversityHalifaxNSCanada
- QEII Health Sciences CentreNova Scotia Health AuthorityHalifaxNSCanada
| | - Allie S. Carew
- Department of MedicineDalhousie UniversityHalifaxNSCanada
- QEII Health Sciences CentreNova Scotia Health AuthorityHalifaxNSCanada
- Department of Community Health and EpidemiologyDalhousie UniversityHalifaxNSCanada
| | - Pantelis Andreou
- Department of Community Health and EpidemiologyDalhousie UniversityHalifaxNSCanada
| | - Andrew P. Levy
- Rappaport Faculty of MedicineTechnion Israel Institute of TechnologyHaifaIsrael
| | - John Sapp
- Department of MedicineDalhousie UniversityHalifaxNSCanada
- QEII Health Sciences CentreNova Scotia Health AuthorityHalifaxNSCanada
| | - Orit Lache
- Rappaport Faculty of MedicineTechnion Israel Institute of TechnologyHaifaIsrael
| | | | - Eric B. Rimm
- Department of NutritionHarvard T. H. Chan School of Public HealthBostonMA
- Department of EpidemiologyHarvard T. H. Chan School of Public HealthBostonMA
| | - Christine Herman
- QEII Health Sciences CentreNova Scotia Health AuthorityHalifaxNSCanada
- Department of SurgeryDalhousie UniversityHalifaxNSCanada
| | - Susan Kirkland
- Department of MedicineDalhousie UniversityHalifaxNSCanada
- Department of Community Health and EpidemiologyDalhousie UniversityHalifaxNSCanada
| | - Leah E. Cahill
- Department of MedicineDalhousie UniversityHalifaxNSCanada
- QEII Health Sciences CentreNova Scotia Health AuthorityHalifaxNSCanada
- Department of Community Health and EpidemiologyDalhousie UniversityHalifaxNSCanada
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28
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Liang X, Sun H. Weighted Selection Probability to Prioritize Susceptible Rare Variants in Multi-Phenotype Association Studies with Application to a Soybean Genetic Data Set. J Comput Biol 2023; 30:1075-1088. [PMID: 37871292 DOI: 10.1089/cmb.2022.0487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2023] Open
Abstract
Rare variant association studies with multiple traits or diseases have drawn a lot of attention since association signals of rare variants can be boosted if more than one phenotype outcome is associated with the same rare variants. Most of the existing statistical methods to identify rare variants associated with multiple phenotypes are based on a group test, where a pre-specified genetic region is tested one at a time. However, these methods are not designed to locate susceptible rare variants within the genetic region. In this article, we propose new statistical methods to prioritize rare variants within a genetic region when a group test for the genetic region identifies a statistical association with multiple phenotypes. It computes the weighted selection probability (WSP) of individual rare variants and ranks them from largest to smallest according to their WSP. In simulation studies, we demonstrated that the proposed method outperforms other statistical methods in terms of true positive selection, when multiple phenotypes are correlated with each other. We also applied it to our soybean single nucleotide polymorphism (SNP) data with 13 highly correlated amino acids, where we identified some potentially susceptible rare variants in chromosome 19.
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Affiliation(s)
- Xianglong Liang
- Department of Statistic, Pusan National University, Busan, Korea
| | - Hokeun Sun
- Department of Statistic, Pusan National University, Busan, Korea
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29
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Li X, Li H, Christenson SA, Castro M, Denlinger LC, Erzurum SC, Fahy JV, Gaston BM, Israel E, Jarjour NN, Levy BD, Mauger DT, Moore WC, Zein J, Kaminski N, Wenzel SE, Woodruff PG, Bleecker ER, Meyers DA. Genetic analyses of chr11p15.5 region identify MUC5AC- MUC5B associated with asthma-related phenotypes. J Asthma 2023; 60:1824-1835. [PMID: 36946148 PMCID: PMC10524756 DOI: 10.1080/02770903.2023.2193631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 03/16/2023] [Indexed: 03/23/2023]
Abstract
OBJECTIVE Genome-wide association studies (GWASs) have identified single nucleotide polymorphisms (SNPs) in chr11p15.5 region associated with asthma and idiopathic interstitial pneumonias (IIPs). We sought to identify functional genes for asthma by combining SNPs and mRNA expression in bronchial epithelial cells (BEC) in the Severe Asthma Research Program (SARP). METHODS Correlation analyses of mRNA expression of six candidate genes (AP2A2, MUC6, MUC2, MUC5AC, MUC5B, and TOLLIP) and asthma phenotypes were performed in the longitudinal cohort (n = 156) with RNAseq in BEC, and replicated in the cross-sectional cohort (n = 155). eQTL (n = 114) and genetic association analysis of asthma severity (426 severe vs. 531 non-severe asthma) were performed, and compared with previously published GWASs of IIPs and asthma. RESULTS Higher expression of AP2A2 and MUC5AC and lower expression of MUC5B in BEC were correlated with asthma, asthma exacerbations, and T2 biomarkers (P < 0.01). SNPs associated with asthma and IIPs in previous GWASs were eQTL SNPs for MUC5AC, MUC5B, or TOLLIP, however, they were not in strong linkage disequilibrium. The risk alleles for asthma or protective alleles for IIPs were associated with higher expression of MUC5AC and lower expression of MUC5B. rs11603634, rs12788104, and rs28415845 associated with moderate-to-severe asthma or adult onset asthma in previous GWASs were not associated with asthma severity (P > 0.8). CONCLUSIONS SNPs associated with asthma in chr11p15.5 region are not associated with asthma severity neither with IIPs. Higher expression of MUC5AC and lower expression of MUC5B are risk for asthma but protective for IIPs.
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Affiliation(s)
- Xingnan Li
- Division of Genetics, Genomics and Precision Medicine, Department of Medicine, University of Arizona, Tucson, Arizona, USA
| | - Huashi Li
- Division of Genetics, Genomics and Precision Medicine, Department of Medicine, University of Arizona, Tucson, Arizona, USA
| | - Stephanie A. Christenson
- Division of Pulmonary, Critical Care, Sleep and Allergy, Department of Medicine, University of California at San Francisco, San Francisco, California, USA
| | - Mario Castro
- Division of Pulmonary, Critical Care and Sleep Medicine, University of Kansas School of Medicine, Kansas City, Kansas, USA
| | - Loren C. Denlinger
- Department of Medicine, University of Wisconsin School of Medicine & Public Health, Madison, Wisconsin, USA
| | - Serpil C. Erzurum
- Lerner Research Institute and the Respiratory Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - John V. Fahy
- Division of Pulmonary, Critical Care, Sleep and Allergy, Department of Medicine, University of California at San Francisco, San Francisco, California, USA
| | - Benjamin M. Gaston
- Wells Center for Pediatric Research and Riley Hospital for Children, Indiana University, Indianapolis, Indiana, USA
| | - Elliot Israel
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Nizar N. Jarjour
- Department of Medicine, University of Wisconsin School of Medicine & Public Health, Madison, Wisconsin, USA
| | - Bruce D. Levy
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - David T Mauger
- Department of Public Health Sciences, College of Medicine, Penn State University, Hershey, Pennsylvania, USA
| | - Wendy C. Moore
- Department of Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Joe Zein
- Lerner Research Institute and the Respiratory Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Naftali Kaminski
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, Connecticut, USA
| | - Sally E. Wenzel
- Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Prescott G. Woodruff
- Division of Pulmonary, Critical Care, Sleep and Allergy, Department of Medicine, University of California at San Francisco, San Francisco, California, USA
| | - Eugene R. Bleecker
- Division of Genetics, Genomics and Precision Medicine, Department of Medicine, University of Arizona, Tucson, Arizona, USA
| | - Deborah A. Meyers
- Division of Genetics, Genomics and Precision Medicine, Department of Medicine, University of Arizona, Tucson, Arizona, USA
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Coto-Segura P, Vázquez-Coto D, Velázquez-Cuervo L, García-Lago C, Coto E, Queiro R. The IFIH1/ MDA5 rs1990760 Gene Variant (946Thr) Differentiates Early- vs. Late-Onset Skin Disease and Increases the Risk of Arthritis in a Spanish Cohort of Psoriasis. Int J Mol Sci 2023; 24:14803. [PMID: 37834254 PMCID: PMC10572774 DOI: 10.3390/ijms241914803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Revised: 08/29/2023] [Accepted: 09/29/2023] [Indexed: 10/15/2023] Open
Abstract
The melanoma differentiation-associated protein 5 (MDA5; encoded by the IFIH1 gene) mediates the activation of the interferon pathway in response to a viral infection. This protein is also upregulated in autoimmune diseases and psoriasis skin lesions. IFIH1 gene variants that increase MDA5 activity have been associated with an increased risk for immune-mediated diseases, including psoriasis. Our aim is to determine the association between three IFIH1 variants (rs35337543 G/C, intron8 + 1; rs35744605 C/A, Glu627Stop; and rs1990760 C/T, Ala946Thr) and the main clinical findings in a cohort of Spanish patients with psoriasis (N = 572; 77% early-onset). Early-onset psoriasis patients (EOPs) had a significantly higher frequency of severe disease and the Cw6*0602 allele. Carriers of rs1990760 T (946Thr) were more common in the EOPs (p < 0.001), and the effect was more pronounced among Cw6*0602-negatives. This variant was also associated with an increased risk of psoriatic arthritis (PsA) independent from other factors (OR = 1.62, 95%CI = 1.11-2.37). The rs3533754 and rs35744605 polymorphisms did not show significant differences between the two onset age or PsA groups. Compared to the controls, the 946Thr variant was more common in the EOPs (nonsignificant difference) and significantly less common in patients aged >40 years (p = 0.005). In conclusion, the common IFIH1 rs1990760 T allele was significantly more frequent in early-onset compared to late-onset patients. This variant was also an independent risk factor for PsA in our cohort. Our study reinforces the widely reported role of the IFIH1 gene variants on psoriatic disease.
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Affiliation(s)
- Pablo Coto-Segura
- Dermatología, Hospital Universitario Vital Alvarez-Buylla, 33011 Mieres, Spain;
| | - Daniel Vázquez-Coto
- Genética Molecular, Hospital Universitario Central Asturias, 33011 Oviedo, Spain; (D.V.-C.); (L.V.-C.); (C.G.-L.); (E.C.)
| | - Lucinda Velázquez-Cuervo
- Genética Molecular, Hospital Universitario Central Asturias, 33011 Oviedo, Spain; (D.V.-C.); (L.V.-C.); (C.G.-L.); (E.C.)
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain
| | - Claudia García-Lago
- Genética Molecular, Hospital Universitario Central Asturias, 33011 Oviedo, Spain; (D.V.-C.); (L.V.-C.); (C.G.-L.); (E.C.)
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain
| | - Eliecer Coto
- Genética Molecular, Hospital Universitario Central Asturias, 33011 Oviedo, Spain; (D.V.-C.); (L.V.-C.); (C.G.-L.); (E.C.)
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain
- Departamento Medicina, Universidad de Oviedo, 33011 Oviedo, Spain
| | - Rubén Queiro
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain
- Departamento Medicina, Universidad de Oviedo, 33011 Oviedo, Spain
- Reumatología, Hospital Universitario Central Asturias, 33011 Oviedo, Spain
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Garcia-Etxebarria K, Etxart A, Barrero M, Nafria B, Segues Merino NM, Romero-Garmendia I, Goel A, Franke A, D’Amato M, Bujanda L. Genetic Variants as Predictors of the Success of Colorectal Cancer Treatments. Cancers (Basel) 2023; 15:4688. [PMID: 37835382 PMCID: PMC10571592 DOI: 10.3390/cancers15194688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 09/20/2023] [Accepted: 09/21/2023] [Indexed: 10/15/2023] Open
Abstract
BACKGROUND Some genetic polymorphisms (SNPs) have been proposed as predictors for different colorectal cancer (CRC) outcomes. This work aims to assess their performance in our cohort and find new SNPs associated with them. METHODS A total of 833 CRC cases were analyzed for seven outcomes, including the use of chemotherapy, and stratified by tumor location and stage. The performance of 63 SNPs was assessed using a generalized linear model and area under the receiver operating characteristic curve, and local SNPs were detected using logistic regressions. RESULTS In total 26 of the SNPs showed an AUC > 0.6 and a significant association (p < 0.05) with one or more outcomes. However, clinical variables outperformed some of them, and the combination of genetic and clinical data showed better performance. In addition, 49 suggestive (p < 5 × 10-6) SNPs associated with one or more CRC outcomes were detected, and those SNPs were located at or near genes involved in biological mechanisms associated with CRC. CONCLUSIONS Some SNPs with clinical data can be used in our population as predictors of some CRC outcomes, and the local SNPs detected in our study could be feasible markers that need further validation as predictors.
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Affiliation(s)
- Koldo Garcia-Etxebarria
- Biodonostia, Gastrointestinal Genetics Group, 20014 San Sebastián, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 08036 Barcelona, Spain;
| | - Ane Etxart
- Biodonostia, Gastrointestinal Disease Group, Universidad del País Vasco (UPV/EHU), 20014 San Sebastián, Spain; (A.E.); (M.B.); (B.N.); (N.M.S.M.)
| | - Maialen Barrero
- Biodonostia, Gastrointestinal Disease Group, Universidad del País Vasco (UPV/EHU), 20014 San Sebastián, Spain; (A.E.); (M.B.); (B.N.); (N.M.S.M.)
| | - Beatriz Nafria
- Biodonostia, Gastrointestinal Disease Group, Universidad del País Vasco (UPV/EHU), 20014 San Sebastián, Spain; (A.E.); (M.B.); (B.N.); (N.M.S.M.)
| | - Nerea Miren Segues Merino
- Biodonostia, Gastrointestinal Disease Group, Universidad del País Vasco (UPV/EHU), 20014 San Sebastián, Spain; (A.E.); (M.B.); (B.N.); (N.M.S.M.)
| | - Irati Romero-Garmendia
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (Universidad del País Vasco/Euskal Herriko Unibertsitatea), 48940 Leioa, Spain
| | - Ajay Goel
- Department of Molecular Diagnostics and Experimental Therapeutics, Beckman Research Institute, City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA;
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, 24105 Kiel, Germany;
| | - Mauro D’Amato
- Gastrointestinal Genetics Lab, CIC bioGUNE, Basque Research and Technology Alliance, 48160 Derio, Spain;
- IKERBASQUE, Basque Foundation for Sciences, 48009 Bilbao, Spain
- Department of Medicine and Surgery, LUM University, 70010 Casamassima, Italy
| | - Luis Bujanda
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 08036 Barcelona, Spain;
- Biodonostia, Gastrointestinal Disease Group, Universidad del País Vasco (UPV/EHU), 20014 San Sebastián, Spain; (A.E.); (M.B.); (B.N.); (N.M.S.M.)
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Jiang G, Reiter JL, Dong C, Wang Y, Fang F, Jiang Z, Liu Y. Genetic Regulation of Human isomiR Biogenesis. Cancers (Basel) 2023; 15:4411. [PMID: 37686687 PMCID: PMC10486453 DOI: 10.3390/cancers15174411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 08/31/2023] [Accepted: 08/31/2023] [Indexed: 09/10/2023] Open
Abstract
MicroRNAs play a critical role in regulating gene expression post-transcriptionally. Variations in mature microRNA sequences, known as isomiRs, arise from imprecise cleavage and nucleotide substitution or addition. These isomiRs can target different mRNAs or compete with their canonical counterparts, thereby expanding the scope of miRNA post-transcriptional regulation. Our study investigated the relationship between cis-acting single-nucleotide polymorphisms (SNPs) in precursor miRNA regions and isomiR composition, represented by the ratio of a specific 5'-isomiR subtype to all isomiRs identified for a particular mature miRNA. Significant associations between 95 SNP-isomiR pairs were identified. Of note, rs6505162 was significantly associated with both the 5'-extension of hsa-miR-423-3p and the 5'-trimming of hsa-miR-423-5p. Comparison of breast cancer and normal samples revealed that the expression of both isomiRs was significantly higher in tumors than in normal tissues. This study sheds light on the genetic regulation of isomiR maturation and advances our understanding of post-transcriptional regulation by microRNAs.
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Affiliation(s)
- Guanglong Jiang
- Department of BioHealth Informatics, Luddy School of Informatics, Computing, and Engineering, Indiana University, Indianapolis, IN 46202, USA
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Jill L. Reiter
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Chuanpeng Dong
- Department of Genetics, Yale University, New Haven, CT 06510, USA
| | - Yue Wang
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Fang Fang
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Zhaoyang Jiang
- Department of Computer Science, Purdue University, West Lafayette, IN 47907, USA
| | - Yunlong Liu
- Department of BioHealth Informatics, Luddy School of Informatics, Computing, and Engineering, Indiana University, Indianapolis, IN 46202, USA
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
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Shi Y, Kim HJ, Kim SY, Kim GE, Jin HJ. Lack of association between the VEGFA gene polymorphisms and preterm birth in Korean women. Genomics Inform 2023; 21:e29. [PMID: 37813625 PMCID: PMC10584649 DOI: 10.5808/gi.22064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 06/05/2023] [Accepted: 06/24/2023] [Indexed: 10/11/2023] Open
Abstract
Preterm birth (PTB), a pregnancy-related disease, is defined as a birth before 37 weeks of gestation. It is a major cause of maternal mortality and morbidity worldwide, and its incidence rate is steadily increasing. Various genetic factors can contribute to the etiology of PTB. Vascular endothelial growth factor A (VEGFA) gene is an important angiogenic gene and its polymorphisms have been reported to be associated with PTB development. Therefore, we conducted a case-control study to evaluate the association between VEGFA rs699947, rs2010963, and rs3025039 polymorphisms and PTB in Korean women. A total of 271 subjects (116 patients with PTB and 155 women at ≥38 weeks of gestation) were analyzed in this study. The genotyping of VEGFA gene polymorphisms was performed using polymerase chain reaction- restriction fragment length polymorphism. No significant association between the patients with PTB and the control groups was confirmed. In the combination analysis, we found a significant association between PTB and VEGFA rs699947 CC-rs2010963 GG-rs3025039 CC combination (odds ratio, 3.77; 95% confidence interval, 1.091 to 13.032; p = 0.031). The VEGFA rs699947, rs2010963, and rs3025039 polymorphisms might have no genetic association with the pathogenesis of PTB in Korean women. However, the combination analysis indicates the possibility that VEGFA acts in PTB pathophysiology. Therefore, larger sample sets and replication studies are required to further elucidate our findings.
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Affiliation(s)
- Yue Shi
- Department of Biological Sciences, College of Science & Technology, Dankook University, Cheonan 31116, Korea
| | - Hyung Jun Kim
- Department of Biological Sciences, College of Science & Technology, Dankook University, Cheonan 31116, Korea
| | - Seong Yong Kim
- Department of Biological Sciences, College of Science & Technology, Dankook University, Cheonan 31116, Korea
| | - Ga Eun Kim
- Department of Biological Sciences, College of Science & Technology, Dankook University, Cheonan 31116, Korea
| | - Han Jun Jin
- Department of Biological Sciences, College of Science & Technology, Dankook University, Cheonan 31116, Korea
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Zhang Q, Bhatia M, Park T, Ott J. A multi-threaded approach to genotype pattern mining for detecting digenic disease genes. Front Genet 2023; 14:1222517. [PMID: 37693313 PMCID: PMC10483394 DOI: 10.3389/fgene.2023.1222517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Accepted: 07/31/2023] [Indexed: 09/12/2023] Open
Abstract
To locate disease-causing DNA variants on the human gene map, the customary approach has been to carry out a genome-wide association study for one variant after another by testing for genotype frequency differences between individuals affected and unaffected with disease. So-called digenic traits are due to the combined effects of two variants, often on different chromosomes, while individual variants may have little or no effect on disease. Machine learning approaches have been developed to find variant pairs underlying digenic traits. However, many of these methods have large memory requirements so that only small datasets can be analyzed. The increasing availability of desktop computers with large numbers of processors and suitable programming to distribute the workload evenly over all processors in a machine make a new and relatively straightforward approach possible, that is, to evaluate all existing variant and genotype pairs for disease association. We present a prototype of such a method with two components, Vpairs and Gpairs, and demonstrate its advantages over existing implementations of such well-known algorithms as Apriori and FP-growth. We apply these methods to published case-control datasets on age-related macular degeneration and Parkinson disease and construct an ROC curve for a large set of genotype patterns.
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Affiliation(s)
- Qingrun Zhang
- Department of Mathematics and Statistics, University of Calgary, Calgary, AB, Canada
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB, Canada
| | - Muskan Bhatia
- Amity Institute of Biotechnology, Amity University Madhya Pradesh, Gwalior, India
| | - Taesung Park
- Department of Statistics, Seoul National University, Seoul, Republic of Korea
| | - Jurg Ott
- Laboratory of Statistical Genetics, Rockefeller University, New York, NY, United States
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Huang LC, Lee MY, Chien CF, Chang YP, Li KY, Yang YH. Age and sex differences in the association between APOE genotype and Alzheimer's disease in a Taiwan Chinese population. Front Aging Neurosci 2023; 15:1246592. [PMID: 37680541 PMCID: PMC10481952 DOI: 10.3389/fnagi.2023.1246592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Accepted: 08/07/2023] [Indexed: 09/09/2023] Open
Abstract
Introduction The Apolipoprotein E (APOE) epsilon (ε) 4 allele is a well-established risk factor for late-onset Alzheimer's disease (AD). Reports on white ancestry populations have showed that age, sex, and ethnicity have different effects on the association between APOE genotype and AD. However, studies on Asian populations such as Taiwan Chinese populations are limited. This study aimed to evaluate the association between APOE genotype and AD in a Taiwan Chinese population, and to explore if the association varies by age and sex. Methods We conducted a case-control study in 725 patients with AD and 1,067 age- and sex- matched controls without dementia from a Taiwan Chinese population. Logistic regression models were used to test the association between AD and APOE genotypes. Secondary analyses considered age (<75 or ≥75 years old), and sex stratified models. Results The risk of AD was significantly increased for people with at least one copy of APOE ε4 (OR = 2.52, 95% CI = 2.01-3.17, p < 0.001) and in a dose-dependent manner. Our results did not show an statistically significance different in AD risk when women and men carrying APOEε4 were compared. Despite not reaching statistical significance, the risk of APOE ε4 for AD was higher among younger participants (OR = 3.21, 95% CI = 2.26-4.56, p < 0.001) compared to older ones (OR = 2.13, 95% CI = 1.53-2.97, p < 0.001). When considering both sex and age, the risk of AD was higher among older men carrying APOE ε4 (OR = 2.64, 95% CI = 1.51-4.60 in men; OR = 1.90, 95% CI = 1.26-2.86 in women), while women carrying APOE ε4 appeared to have an increased risk at a younger age (OR = 3.29, 95% CI = 2.20-4.93 in women; OR = 2.91, 95% CI = 1.40-6.05 in men). Discussion The APOE ε4 allele represents a major risk factor for AD in the Taiwanese population. The effect of APOE ε4 allele on AD risk appeared to be stronger among men aged 75 years or more and among younger women.
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Affiliation(s)
- Ling-Chun Huang
- Department of Neurology, Kaohsiung Municipal Ta-Tung Hospital, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
- Department of Neurology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
- Neuroscience Research Center, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Mei-Yueh Lee
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
- Faculty of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Ching-Fang Chien
- Department of Neurology, Kaohsiung Municipal Ta-Tung Hospital, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
- Department of Neurology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
- Neuroscience Research Center, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Yang-Pei Chang
- Department of Neurology, Kaohsiung Municipal Ta-Tung Hospital, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
- Department of Neurology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
- Neuroscience Research Center, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Kuan-Ying Li
- Department of Neurology, Kaohsiung Municipal Ta-Tung Hospital, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
- Department of Neurology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
- Neuroscience Research Center, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Yuan-Han Yang
- Department of Neurology, Kaohsiung Municipal Ta-Tung Hospital, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
- Department of Neurology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
- Neuroscience Research Center, Kaohsiung Medical University, Kaohsiung, Taiwan
- School of Post-Baccalaureate Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
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Peng Q, Dai Z, Yin J, Lv D, Luo X, Xiong S, Yang Z, Chen G, Wei Y, Wang Y, Zhang D, Wang L, Yu D, Zhao Y, Lin D, Liao Z, Zhong Y, Lin Z, Lin J. Schizophrenia plausible protective effect of microRNA-137 is potentially related to estrogen and prolactin in female patients. Front Psychiatry 2023; 14:1187111. [PMID: 37680447 PMCID: PMC10482089 DOI: 10.3389/fpsyt.2023.1187111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 08/03/2023] [Indexed: 09/09/2023] Open
Abstract
Background Schizophrenia (SCZ) is a serious chronic mental disorder. Our previous case-control genetic association study has shown that microRNA-137 (miR-137) may only protect females against SCZ. Since estrogen, an important female sex hormone, exerts neuroprotective effects, the relationship between estrogen and miR-137 in the pathophysiology of SCZ was further studied in this study. Methods Genotyping of single-nucleotide polymorphism rs1625579 of miR-137 gene in 1,004 SCZ patients and 896 healthy controls was conducted using the iMLDR assay. The effect of estradiol (E2) on the miR-137 expression was evaluated on the human mammary adenocarcinoma cell line (MCF-7) and the mouse hippocampal neuron cell line (HT22). The relationships between serum E2, prolactin (PRL), and peripheral blood miR-137 were investigated in 41 SCZ patients and 43 healthy controls. The miR-137 and other reference miRNAs were detected by real-time fluorescent quantitative reverse transcription-PCR. Results Based on the well-known SNP rs1625579, the distributions of protective genotypes and alleles of the miR-137 gene were not different between patients and healthy controls but were marginally significantly lower in female patients. E2 upregulated the expression of miR-137 to 2.83 and 1.81 times in MCF-7 and HT22 cells, respectively. Both serum E2 and blood miR-137 were significantly decreased or downregulated in SCZ patients, but they lacked expected positive correlations with each other in both patients and controls. When stratified by sex, blood miR-137 was negatively correlated with serum E2 in female patients. On the other hand, serum PRL was significantly increased in SCZ patients, and the female patients had the highest serum PRL level and a negative correlation between serum PRL and blood miR-137. Conclusion The plausible SCZ-protective effect of miR-137 may be female specific, of which the underlying mechanism may be that E2 upregulates the expression of miR-137. This protective mechanism may also be abrogated by elevated PRL in female patients. These preliminary findings suggest a new genetic/environmental interaction mechanism for E2/miR-137 to protect normal females against SCZ and a novel E2/PRL/miR-137-related pathophysiology of female SCZ, implying some new antipsychotic ways for female patients in future.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Zhixiong Lin
- Department of Psychiatry, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Juda Lin
- Department of Psychiatry, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
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Lou C, Meng Z, Shi YY, Zheng R, Qian SZ, Pan J. Genetic association of lipids and lipid-lowering drugs with sepsis: a Mendelian randomization and mediation analysis. Front Cardiovasc Med 2023; 10:1217922. [PMID: 37621565 PMCID: PMC10446761 DOI: 10.3389/fcvm.2023.1217922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 07/24/2023] [Indexed: 08/26/2023] Open
Abstract
Background The impact of lipid-lowering medications on sepsis is still not well defined. A Mendelian randomization (MR) study was carried out to probe the causal connections between genetically determined lipids, lipid-reducing drugs, and the risk of sepsis. Materials and methods Data on total serum cholesterol (TC), high-density lipoprotein cholesterol (HDL-C), low-density lipoprotein cholesterol (LDL-C), apolipoprotein A-I (ApoA-I), apolipoprotein B (ApoB), and triglycerides (TG) were retrieved from the MR-Base platform and the Global Lipids Genetics Consortium in 2021 (GLGC2021). Our study categorized sepsis into two groups: total sepsis and 28-day mortality of sepsis patients (sepsis28). The inverse-variance weighted (IVW) method was the primary method used in MR analysis. Cochran's Q test and the MR-Egger intercept method were used to assess the heterogeneity and pleiotropy. Results In the MR analysis, we found that ApoA-I played a suggestively positive role in protecting against both total sepsis (OR, 0.863 per SD increase in ApoA-I; 95% CI, 0.780-0.955; P = 0.004) and sepsis28 (OR, 0.759; 95% CI, 0.598-0.963; P = 0.023). HDL-C levels were also found to suggestively reduce the incidence of total sepsis (OR, 0.891 per SD increase in HDL-C; 95% CI, 0.802-0.990; P = 0.031). Reverse-MR showed that sepsis28 led to a decrease in HDL-C level and an increase in TG level. In drug-target MR, we found that HMGCR inhibitors positively protected against total sepsis (1 OR , 0.719 per SD reduction in LDL-C; 95% CI, 0.540-0.958; P = 0.024). LDL-C and HDL-C proxied CETP inhibitors were found to have a protective effect on total sepsis, with only LDL-C proxied CETP inhibitors showing a suggestively protective effect on sepsis28. In Mediated-MR, BMI exhibited a negative indirect effect in HMGCR inhibitors curing sepsis. The indirect impact of ApoA-I explained over 50% of the curative effects of CETP inhibitors in sepsis. Conclusions Our MR study suggested that ApoA-I and HDL-C protected against sepsis, while HMGCR and CETP inhibitors showed therapeutic potential beyond lipid-lowering effects. ApoA-I explained the effects of CETP inhibitors. Our study illuminates how lipids affect sepsis patients and the effectiveness of new drugs, opening new avenues for sepsis treatment.
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Affiliation(s)
- Chen Lou
- School of The First Clinical Medical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Zhizhen Meng
- Department of Emergency, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, China
| | - Yi-Yi Shi
- Department of Anesthesiology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Rui Zheng
- Department of Critical Care Medicine, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Song-Zan Qian
- Department of Intensive Care Unit, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Jingye Pan
- Department of Intensive Care Unit, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
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Mikhalitskaya EV, Vyalova NM, Ermakov EA, Levchuk LA, Simutkin GG, Bokhan NA, Ivanova SA. Association of Single Nucleotide Polymorphisms of Cytokine Genes with Depression, Schizophrenia and Bipolar Disorder. Genes (Basel) 2023; 14:1460. [PMID: 37510364 PMCID: PMC10379485 DOI: 10.3390/genes14071460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 07/07/2023] [Accepted: 07/14/2023] [Indexed: 07/30/2023] Open
Abstract
Immune gene variants are known to be associated with the risk of psychiatric disorders, their clinical manifestations, and their response to therapy. This narrative review summarizes the current literature over the past decade on the association of polymorphic variants of cytokine genes with risk, severity, and response to treatment for severe mental disorders such as bipolar disorder, depression, and schizophrenia. A search of literature in databases was carried out using keywords related to depressive disorder, bipolar disorder, schizophrenia, inflammation, and cytokines. Gene lists were extracted from publications to identify common genes and pathways for these mental disorders. Associations between polymorphic variants of the IL1B, IL6, and TNFA genes were the most replicated and relevant in depression. Polymorphic variants of the IL1B, IL6, IL6R, IL10, IL17A, and TNFA genes have been associated with schizophrenia. Bipolar disorder has mainly been associated with polymorphic variants of the IL1B gene. Interestingly, the IL6R gene polymorphism (rs2228145) was associated with all three diseases. Some cytokine genes have also been associated with clinical presentation and response to pharmacotherapy. There is also evidence that some specific polymorphic variants may affect the expression of cytokine genes. Thus, the data from this review indicate a link between neuroinflammation and severe mental disorders.
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Affiliation(s)
- Ekaterina V Mikhalitskaya
- Mental Health Research Institute, Tomsk National Research Medical Center of the Russian Academy of Sciences, 634014 Tomsk, Russia
| | - Natalya M Vyalova
- Mental Health Research Institute, Tomsk National Research Medical Center of the Russian Academy of Sciences, 634014 Tomsk, Russia
| | - Evgeny A Ermakov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Lyudmila A Levchuk
- Mental Health Research Institute, Tomsk National Research Medical Center of the Russian Academy of Sciences, 634014 Tomsk, Russia
| | - German G Simutkin
- Mental Health Research Institute, Tomsk National Research Medical Center of the Russian Academy of Sciences, 634014 Tomsk, Russia
| | - Nikolay A Bokhan
- Mental Health Research Institute, Tomsk National Research Medical Center of the Russian Academy of Sciences, 634014 Tomsk, Russia
| | - Svetlana A Ivanova
- Mental Health Research Institute, Tomsk National Research Medical Center of the Russian Academy of Sciences, 634014 Tomsk, Russia
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Li YJ, Nuytemans K, La JO, Jiang R, Slifer SH, Sun S, Naj A, Gao XR, Martin ER. Identification of novel genes for age-at-onset of Alzheimer's disease by combining quantitative and survival trait analyses. Alzheimers Dement 2023; 19:3148-3157. [PMID: 36738287 DOI: 10.1002/alz.12927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 12/06/2022] [Accepted: 12/19/2022] [Indexed: 02/05/2023]
Abstract
INTRODUCTION Our understanding of the genetic predisposition for age-at-onset (AAO) of Alzheimer's disease (AD) is limited. Here, we sought to identify genes modifying AAO and examined whether any have sex-specific effects. METHODS Genome-wide association analysis were performed on imputed genetic data of 9219 AD cases and 10,345 controls from 20 cohorts of the Alzheimer's Disease Genetics Consortium. AAO was modeled from cases directly and as a survival outcome. RESULTS We identified 11 genome-wide significant loci (P < 5 × 10-8 ), including six known AD-risk genes and five novel loci, UMAD1, LUZP2, ARFGEF2, DSCAM, and 4q25, affecting AAO of AD. Additionally, 39 suggestive loci showed strong association. Twelve loci showed sex-specific effects on AAO including CD300LG and MLX/TUBG2 for females and MIR4445 for males. DISCUSSION Genes that influence AAO of AD are excellent therapeutic targets for delaying onset of AD. Several loci identified include genes with promising functional implications for AD.
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Affiliation(s)
- Yi-Ju Li
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, North Carolina, USA
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, North Carolina, USA
| | - Karen Nuytemans
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, USA
- John T. MacDonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, Florida, USA
| | - Jong Ok La
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, North Carolina, USA
| | - Rong Jiang
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, North Carolina, USA
- Department of Psychiatry and Behavior Science, Duke University School of Medicine, Durham, North Carolina, USA
| | - Susan H Slifer
- John T. MacDonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, Florida, USA
| | - Shuming Sun
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, North Carolina, USA
| | - Adam Naj
- Department of Biostatistics, Epidemiology, and Informatics, Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Xiaoyi Raymond Gao
- Department of Ophthalmology and Visual Sciences, Division of Human Genetics, The Ohio State University, Columbus, Ohio, USA
- Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio, USA
| | - Eden R Martin
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, USA
- John T. MacDonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, Florida, USA
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Yuan X, Hou M, Wang Y, Zhang S, Li L, Mi Y, Du H, Yu S, Nan Y. Mitofusin-2 gene polymorphisms and metabolic dysfunction associated fatty liver disease: a case-control study in a Chinese population. J Int Med Res 2023; 51:3000605231187953. [PMID: 37522325 PMCID: PMC10392247 DOI: 10.1177/03000605231187953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/01/2023] Open
Abstract
OBJECTIVES Mitofusion-2 (Mfn2) may have a role in mitochondrial oxidative stress and insulin resistance that can promote the development of metabolic dysfunction associated fatty liver disease (MAFLD). This retrospective and case control study aimed to explore the relationships between common Mfn2 single nucleotide polymorphisms (SNPs) and MAFLD in a northern Han Chinese population. METHODS Six Mfn2 SNPs (rs2336384, rs873458, rs873457, rs4846085, rs2878677, and rs2236057) were genotyped using the ligase detection reaction in 466 MAFLD patients and 423 healthy controls. Genotype and allele frequencies were calculated, along with haplotype analysis and pairwise linkage disequilibrium. RESULTS The genotype distribution of rs2336384, rs2878677, and rs2236057 among the MAFLD patients showed a significantly different pattern from that of healthy controls. The data showed that an increased risk of MAFLD was significantly correlated with patients carrying the GG genotype of rs2336384, CC genotype of rs873457, TT genotype of rs4846085, TT genotype of rs2878677, and the AA genotype of rs2236057. Moreover, The GGCTTA haplotype was found to be adversely linked with MAFLD by haplotype analysis. CONCLUSION The current findings suggest a strong link between certain Mfn2 gene polymorphisms and MAFLD.
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Affiliation(s)
- Xiwei Yuan
- Department of Traditional and Western Medical Hepatology & Hebei Key Laboratory of Mechanism of Liver Fibrosis in Chronic Liver Disease, Third Hospital of Hebei Medical University, Shijiazhuang, China
| | - Mengmeng Hou
- Department of Traditional and Western Medical Hepatology & Hebei Key Laboratory of Mechanism of Liver Fibrosis in Chronic Liver Disease, Third Hospital of Hebei Medical University, Shijiazhuang, China
| | - Yiqi Wang
- Department of Traditional and Western Medical Hepatology & Hebei Key Laboratory of Mechanism of Liver Fibrosis in Chronic Liver Disease, Third Hospital of Hebei Medical University, Shijiazhuang, China
| | - Siyu Zhang
- Department of Traditional and Western Medical Hepatology & Hebei Key Laboratory of Mechanism of Liver Fibrosis in Chronic Liver Disease, Third Hospital of Hebei Medical University, Shijiazhuang, China
| | - Lu Li
- Department of Traditional and Western Medical Hepatology & Hebei Key Laboratory of Mechanism of Liver Fibrosis in Chronic Liver Disease, Third Hospital of Hebei Medical University, Shijiazhuang, China
| | - Yingjun Mi
- School of Public Health, Hebei Medical University, Shijiazhuang, China
| | - Huijuan Du
- Department of Traditional and Western Medical Hepatology & Hebei Key Laboratory of Mechanism of Liver Fibrosis in Chronic Liver Disease, Third Hospital of Hebei Medical University, Shijiazhuang, China
| | - Songhao Yu
- Department of Traditional and Western Medical Hepatology & Hebei Key Laboratory of Mechanism of Liver Fibrosis in Chronic Liver Disease, Third Hospital of Hebei Medical University, Shijiazhuang, China
| | - Yuemin Nan
- Department of Traditional and Western Medical Hepatology & Hebei Key Laboratory of Mechanism of Liver Fibrosis in Chronic Liver Disease, Third Hospital of Hebei Medical University, Shijiazhuang, China
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Yang W, Cao J, McVey DG, Ye S. Allele-Specific Epigenetic Regulation of FURIN Expression at a Coronary Artery Disease Susceptibility Locus. Cells 2023; 12:1681. [PMID: 37443715 PMCID: PMC10341058 DOI: 10.3390/cells12131681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 06/12/2023] [Accepted: 06/19/2023] [Indexed: 07/15/2023] Open
Abstract
Genome-wide association studies have revealed an association between the genetic variant rs17514846 in the FURIN gene and coronary artery disease. We investigated the mechanism through which rs17514846 modulates FURIN expression. An analysis of isogenic monocytic cell lines showed that the cells of the rs17514846 A/A genotype expressed higher levels of FURIN than cells of the C/C genotype. Pyrosequencing showed that the cytosine (in a CpG motif) at the rs17514846 position on the C allele was methylated. Treatment with the DNA methylation inhibitor 5-aza-2'-deoxycytidine increased FURIN expression. An electrophoretic mobility super-shift assay with a probe corresponding to the DNA sequence at and around the rs17514846 position of the C allele detected DNA-protein complex bands that were altered by an anti-MeCP2 antibody. A chromatin immunoprecipitation assay with the anti-MeCP2 antibody showed an enrichment of the DNA sequence containing the rs17514846 site. siRNA-mediated knockdown of MeCP2 caused an increase in FURIN expression. Furthermore, MeCP2 knockdown increased monocyte migration and proliferation, and this effect was diminished by a FURIN inhibitor. The results of our study suggest that DNA methylation inhibits FURIN expression and that the coronary artery disease-predisposing variant rs17514846 modulates FURIN expression and monocyte migration via an allele-specific effect on DNA methylation.
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Affiliation(s)
- Wei Yang
- Department of Basic Medicine, Shantou University Medical College, Shantou 515041, China
| | - Junjun Cao
- Department of Basic Medicine, Shantou University Medical College, Shantou 515041, China
| | - David G. McVey
- Department of Cardiovascular Sciences, National Institute for Health Research, Leicester Biomedical Research Centre, University of Leicester, Leicester LE3 9QP, UK
| | - Shu Ye
- Department of Basic Medicine, Shantou University Medical College, Shantou 515041, China
- Department of Cardiovascular Sciences, National Institute for Health Research, Leicester Biomedical Research Centre, University of Leicester, Leicester LE3 9QP, UK
- Cardiovascular-Metabolic Disease Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore
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Li W, Ren A, Qin Q, Zhao L, Peng Q, Ma R, Luo S. Causal associations between human gut microbiota and cholelithiasis: a mendelian randomization study. Front Cell Infect Microbiol 2023; 13:1169119. [PMID: 37305422 PMCID: PMC10248444 DOI: 10.3389/fcimb.2023.1169119] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Accepted: 05/15/2023] [Indexed: 06/13/2023] Open
Abstract
Background There was some evidence that gut microbiota was closely related to cholelithiasis, but the causal relationship between them remained unclear. In this study, we try to use Two-sample Mendelian randomization (MR) to clarify the potential causal relationship between gut microbiota and cholelithiasis. Methods Summary Genome-Wide Association Studies (GWAS) statistical data for gut microbiota was obtained from MiBioGen, and the data of cholelithiasis was obtained from UK Biobank (UKB). Two-sample MR analyses were performed to assess causalities between gut microbiota and cholelithiasis mainly using the inverse-variance weighted (IVW) method. Sensitivity analyses were used to determine the robustness of the MR results. Reverse MR analyses were performed to examine the reverse causal association. Results Our research results, based primarily on the IVW method, support the existence of a causal relationship between nine gut microbial taxa and cholelithiasis. We observed a positive association between Genus Butyrivibrio (p=0.032), Genus Lachnospiraceae_UCG_001 (p=0.015), Genus Ruminococcaceae_NK4A214_group (p=0.003), Genus Ruminococcaceae_UCG_011 (p=0.010) and cholelithiasis, while Order Rhodospirillales (p=0.031), Genus Actinomyces (p=0.010), Genus Phascolarctobacterium (p=0.036), Genus Rikenellaceae_RC9_gutgroup (p=0.023), Genus Ruminococcaceae_UCG_013 (p=0.022) may be associated with a reduced risk of cholelithiasis. We did not find a reverse causal relationship between cholelithiasis and 9 specific gut microbial taxa. Conclusions This is the first mendelian randomization study to explore the causalities between specific gut microbiota taxa and cholelithiasis, which may provide new ideas and a theoretical basis for the prevention and treatment of cholelithiasis in the future.
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Blumhagen RZ, Schwartz DA, Langefeld CD, Fingerlin TE. Identification of influential rare variants in aggregate testing using random forest importance measures. Ann Hum Genet 2023. [PMID: 37221924 DOI: 10.1111/ahg.12509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 04/14/2023] [Accepted: 04/17/2023] [Indexed: 05/25/2023]
Abstract
Aggregate tests of rare variants are often employed to identify associated regions compared to sequentially testing each individual variant. When an aggregate test is significant, it is of interest to identify which rare variants are "driving" the association. We recently developed the rare variant influential filtering tool (RIFT) to identify influential rare variants and showed RIFT had higher true positive rates compared to other published methods. Here we use importance measures from the standard random forest (RF) and variable importance weighted RF (vi-RF) to identify influential variants. For very rare variants (minor allele frequency [MAF] < 0.001), the vi-RF:Accuracy method had the highest median true positive rate (TPR = 0.24; interquartile range [IQR]: 0.13, 0.42) followed by the RF:Accuracy method (TPR = 0.16; IQR: 0.07, 0.33) and both were superior to RIFT (TPR = 0.05; IQR: 0.02, 0.15). Among uncommon variants (0.001 < MAF < 0.03), the RF methods had higher true positive rates than RIFT while observing comparable false positive rates. Finally, we applied the RF methods to a targeted resequencing study in idiopathic pulmonary fibrosis (IPF), in which the vi-RF approach identified eight and seven variants in TERT and FAM13A, respectively. In summary, the vi-RF provides an improved, objective approach to identifying influential variants following a significant aggregate test. We have expanded our previously developed R package RIFT to include the random forest methods.
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Affiliation(s)
- Rachel Z Blumhagen
- Center for Genes, Environment and Health, National Jewish Health, Denver, Colorado, USA
- Department of Biostatistics and Informatics, Colorado School of Public Health, Aurora, Colorado, USA
| | - David A Schwartz
- School of Medicine, University of Colorado, Aurora, Colorado, USA
| | - Carl D Langefeld
- Department of Biostatistics and Data Science, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
- Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Winston-Salem, North Carolina, USA
- Center for Precision Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Tasha E Fingerlin
- Center for Genes, Environment and Health, National Jewish Health, Denver, Colorado, USA
- Department of Biostatistics and Informatics, Colorado School of Public Health, Aurora, Colorado, USA
- School of Medicine, University of Colorado, Aurora, Colorado, USA
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Meza-Alvarado JC, Page RA, Mallard B, Bromhead C, Palmer BR. VEGF-A related SNPs: a cardiovascular context. Front Cardiovasc Med 2023; 10:1190513. [PMID: 37288254 PMCID: PMC10242119 DOI: 10.3389/fcvm.2023.1190513] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 04/27/2023] [Indexed: 06/09/2023] Open
Abstract
Cardiovascular diseases (CVDs) are the leading cause of death worldwide. Currently, cardiovascular disease risk algorithms play a role in primary prevention. However, this is complicated by a lack of powerfully predictive biomarkers that could be observed in individuals before the onset of overt symptoms. A key potential biomarker for heart disease is the vascular endothelial growth factor (VEGF-A), a molecule that plays a pivotal role in blood vessel formation. This molecule has a complex biological role in the cardiovascular system due to the processes it influences, and its production is impacted by various CVD risk factors. Research in different populations has shown single nucleotide polymorphisms (SNPs) may affect circulating VEGF-A plasma levels, with some variants associated with the development of CVDs, as well as CVD risk factors. This minireview aims to give an overview of the VEGF family, and of the SNPs reported to influence VEGF-A levels, cardiovascular disease, and other risk factors used in CVD risk assessments.
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Affiliation(s)
| | | | | | | | - B. R. Palmer
- School of Health Sciences, Massey University, Wellington, New Zealand
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Xu SZ, Wang ZX, Fang X, Chen C, Yang XK, Shuai ZW, Tao SS. No genetic causal association between systemic lupus erythematosus and COVID-19. Front Immunol 2023; 14:1183570. [PMID: 37275906 PMCID: PMC10232808 DOI: 10.3389/fimmu.2023.1183570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 05/02/2023] [Indexed: 06/07/2023] Open
Abstract
Objective Emerging evidence suggests an increased prevalence of coronavirus disease 2019 (COVID-19) in patients with systemic lupus erythematosus (SLE), the prototype of autoimmune disease, compared to the general population. However, the conclusions were inconsistent, and the causal relationship between COVID-19 and SLE remains unknown. Methods In this study, we aimed to evaluate the bidirectional causal relationship between COVID-19 and SLE using bidirectional Mendelian randomization (MR) analysis, including MR-Egger, weighted median, weighted mode, and the inverse variance weighting (IVW) method. Results The results of IVW showed a negative effect of SLE on severe COVID-19 (OR = 0.962, p = 0.040) and COVID-19 infection (OR = 0.988, p = 0.025), which disappeared after Bonferroni correction. No causal effect of SLE on hospitalized COVID-19 was observed (OR = 0.983, p = 0.148). In the reverse analysis, no causal effects of severe COVID-19 infection (OR = 1.045, p = 0.664), hospitalized COVID-19 (OR = 0.872, p = 0.109), and COVID-19 infection (OR = 0.943, p = 0.811) on SLE were found. Conclusion The findings of our bidirectional causal inference analysis did not support a genetically predicted causal relationship between SLE and COVID-19; thus, their association observed in previous observational studies may have been caused by confounding factors.
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Affiliation(s)
- Shu-Zhen Xu
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China
- Institute of Kidney Disease, Inflammation and Immunity Mediated Diseases, The Second Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Zhi-Xin Wang
- Department of Rheumatology and Immunology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Xi Fang
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China
- Institute of Kidney Disease, Inflammation and Immunity Mediated Diseases, The Second Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Cong Chen
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China
- Institute of Kidney Disease, Inflammation and Immunity Mediated Diseases, The Second Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Xiao-Ke Yang
- Department of Rheumatology and Immunology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Zong-Wen Shuai
- Department of Rheumatology and Immunology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Sha-Sha Tao
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China
- Institute of Kidney Disease, Inflammation and Immunity Mediated Diseases, The Second Hospital of Anhui Medical University, Hefei, Anhui, China
- Experimental Teaching Center for Preventive Medicine, School of Public Health, Anhui Medical University, Hefei, Anhui, China
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Rada I, Calderón JF, Martínez G, Muñoz Venturelli P. Genetics of spontaneous cervical and coronary artery dissections. Front Glob Womens Health 2023; 4:1007795. [PMID: 37214559 PMCID: PMC10196206 DOI: 10.3389/fgwh.2023.1007795] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 04/14/2023] [Indexed: 05/24/2023] Open
Abstract
Objectives Spontaneous cervical artery dissections (SCeAD) and coronary artery dissections (SCoAD) are major causes of neurovascular and cardiovascular morbidity in young adults. Although multiple aspects of their etiology are still unknown, most consensuses are focused on the presence of constitutional genetic aspects and environmental triggers. Since recent evidence of genetic contribution points to a possible overlap between these conditions, we aimed to describe current information on SCeAD and SCoAD genetics and their potential shared pathological aspects. Materials and methods A narrative review is presented. Publications in English and Spanish were queried using database search. The articles were evaluated by one team member in terms of inclusion criteria. After collecting, the articles were categorized based on scientific content. Results Given that patients with SCeAD and SCoAD rarely present connective tissue disorders, other genetic loci are probably responsible for the increased susceptibility in some individuals. The common variant rs9349379 at PHACTR1 gene is associated with predisposition to pathologies of the arterial wall, likely mediated by variations in Endothelin-1 (ET-1) levels. The risk of arterial dissection may be increased for those who carry the rs9349379(A) allele, associated with lower expression levels of ET-1; however, the local effect of this vasomotor imbalance remains unclear. Sex differences seen in SCeAD and SCoAD support a role for sex hormones that could modulate risk, tilting the delicate balance and forcing vasodilator actions to prevail over vasoconstriction due to a reduction in ET-1 expression. Conclusions New evidence points to a common gene variation that could explain dissection in both the cervical and coronary vasculatures. To further confirm the risk conferred by the rs9349379 variant, genome wide association studies are warranted, hopefully in larger and ethnically diverse populations.
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Affiliation(s)
- Isabel Rada
- Instituto de Ciencias e Innovación en Medicina, Facultad de Medicina Clínica Alemana Universidad del Desarrollo, Santiago, Chile
| | - Juan Francisco Calderón
- Instituto de Ciencias e Innovación en Medicina, Facultad de Medicina Clínica Alemana Universidad del Desarrollo, Santiago, Chile
| | - Gonzalo Martínez
- División de Enfermedades Cardiovasculares, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Paula Muñoz Venturelli
- Instituto de Ciencias e Innovación en Medicina, Facultad de Medicina Clínica Alemana Universidad del Desarrollo, Santiago, Chile
- The George Institute for Global Health, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
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Choi GH, Cho SH, An HJ, Park HS, Lee JY, Ko EJ, Oh SH, Kim OJ, Kim NK. Association between PAI-1 Polymorphisms and Ischemic Stroke in a South Korean Case-Control Cohort. Int J Mol Sci 2023; 24:8041. [PMID: 37175749 PMCID: PMC10178745 DOI: 10.3390/ijms24098041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 04/24/2023] [Accepted: 04/26/2023] [Indexed: 05/15/2023] Open
Abstract
Stroke is the second leading cause of death in the world. Approximately 80% of strokes are ischemic in origin. Many risk factors have been linked to stroke, including an increased level of plasminogen activator inhibitor-1 (PAI-1). PAI-1 levels increase and remain elevated in blood during the acute phase of ischemic stroke, which can impair fibrinolytic activity, leading to coronary artery disease and arterial thrombotic disorders. Here, we present a case-control study of 574 stroke patients and 425 controls seen for routine health examination or treatment for nonspecific dizziness, nonorganic headache, or anxiety for positive family history of stroke at the Bundang Medical Center in South Korea. Polymorphisms in PAI-1 were identified by polymerase chain reaction/restriction fragment length polymorphism analysis using genomic DNA. Specifically, three variations (-675 4G>5G, 10692T>C, and 12068G>A) were linked to a higher overall prevalence of stroke as well as a higher prevalence of certain stroke subtypes. Haplotype analyses also revealed combinations of these variations (-844G>A, -675 4G>5G, 43G>A, 9785A>G, 10692T>C, 11053T>G, and 12068G>A) that were significantly associated with a higher prevalence of ischemic stroke. To the best of our knowledge, this is the first strong evidence that polymorphic sites in PAI-1 promoter and 3'-UTR regions are associated with higher ischemic stroke risk. Furthermore, the PAI-1 genotypes and haplotypes identified here have potential as clinical biomarkers of ischemic stroke and could improve the prognosis and future management of stroke patients.
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Affiliation(s)
- Gun Ho Choi
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam 13488, Republic of Korea
| | - Sung Hwan Cho
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam 13488, Republic of Korea
- College of Medicine, Konyang University, 158 Gwanjeodong-ro, Seo-gu, Daejeon 35365, Republic of Korea
| | - Hui Jeong An
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam 13488, Republic of Korea
- College of Life Science, Gangneung-Wonju National University, 7 Jukheon-gil, Gangneung 25457, Republic of Korea
| | - Han Sung Park
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam 13488, Republic of Korea
| | - Jeong Yong Lee
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam 13488, Republic of Korea
| | - Eun Ju Ko
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam 13488, Republic of Korea
| | - Seung Hun Oh
- Department of Neurology, CHA Bundang Medical Center, School of Medicine, CHA University, Seongnam 13496, Republic of Korea
| | - Ok Joon Kim
- Department of Neurology, CHA Bundang Medical Center, School of Medicine, CHA University, Seongnam 13496, Republic of Korea
| | - Nam Keun Kim
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam 13488, Republic of Korea
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Guo JZ, Xiao Q, Wu L, Chen F, Yin JL, Qin X, Gong TT, Wu QJ. Ovarian Cancer and Parkinson's Disease: A Bidirectional Mendelian Randomization Study. J Clin Med 2023; 12:jcm12082961. [PMID: 37109305 PMCID: PMC10146810 DOI: 10.3390/jcm12082961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 02/25/2023] [Accepted: 03/10/2023] [Indexed: 04/29/2023] Open
Abstract
(1) Background: Ovarian cancer (OC) and Parkinson's disease (PD) represent a huge public health burden. The relationship of these two diseases is suggested in the literature while not fully understood. To better understand this relationship, we conducted a bidirectional Mendelian ran-domization analysis using genetic markers as a proxy. (2) Methods: Utilizing single nucleotide polymorphisms associated with PD risk, we assessed the association between genetically predicted PD and OC risk, overall and by histotypes, using summary statistics from previously conducted genome-wide association studies of OC within the Ovarian Cancer Association Consortium. Similarly, we assessed the association between genetically predicted OC and PD risk. The inverse variance weighted method was used as the main method to estimate odds ratios (OR) and 95% confidence intervals (CI) for the associations of interest. (3) Results: There was no significant association between genetically predicted PD and OC risk: OR = 0.95 (95% CI: 0.88-1.03), or between genetically predicted OC and PD risk: OR = 0.80 (95% CI: 0.61-1.06). On the other hand, when examined by histotypes, a suggestive inverse association was observed between genetically predicted high grade serous OC and PD risk: OR = 0.91 (95% CI: 0.84-0.99). (4) Conclusions: Overall, our study did not observe a strong genetic association between PD and OC, but the observed potential association between high grade serous OC and reduced PD risk warrants further investigation.
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Affiliation(s)
- Jian-Zeng Guo
- Department of Clinical Epidemiology, Shengjing Hospital of China Medical University, Shenyang 110004, China
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang 110004, China
| | - Qian Xiao
- Department of Clinical Epidemiology, Shengjing Hospital of China Medical University, Shenyang 110004, China
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang 110004, China
| | - Lang Wu
- Cancer Epidemiology Division, Population Sciences in the Pacific Program, University of Hawaii Cancer Center, University of Hawaii at Manoa, Honolulu, HI 96813, USA
| | - Fa Chen
- Fujian Provincial Key Laboratory of Environment Factors and Cancer, Department of Epidemiology and Health Statistics, School of Public Health, Fujian Medical University, Fuzhou 350122, China
| | - Jia-Li Yin
- Department of Clinical Epidemiology, Shengjing Hospital of China Medical University, Shenyang 110004, China
- Clinical Research Center, Shengjing Hospital of China Medical University, Shenyang 110004, China
- Key Laboratory of Precision Medical Research on Major Chronic Disease, Shengjing Hospital of China Medical University, Shenyang 110004, China
| | - Xue Qin
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang 110004, China
| | - Ting-Ting Gong
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang 110004, China
| | - Qi-Jun Wu
- Department of Clinical Epidemiology, Shengjing Hospital of China Medical University, Shenyang 110004, China
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang 110004, China
- Clinical Research Center, Shengjing Hospital of China Medical University, Shenyang 110004, China
- Key Laboratory of Precision Medical Research on Major Chronic Disease, Shengjing Hospital of China Medical University, Shenyang 110004, China
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Deng WQ, Belisario K, Gray JC, Levitt EE, Mohammadi-Shemirani P, Singh D, Pare G, MacKillop J. Leveraging related health phenotypes for polygenic prediction of impulsive choice, impulsive action, and impulsive personality traits in 1534 European ancestry community adults. Genes Brain Behav 2023:e12848. [PMID: 37060189 DOI: 10.1111/gbb.12848] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 03/17/2023] [Accepted: 03/31/2023] [Indexed: 04/16/2023]
Abstract
Impulsivity refers to a number of conceptually related phenotypes reflecting self-regulatory capacity that are considered promising endophenotypes for mental and physical health. Measures of impulsivity can be broadly grouped into three domains, namely, impulsive choice, impulsive action, and impulsive personality traits. In a community-based sample of ancestral Europeans (n = 1534), we conducted genome-wide association studies (GWASs) of impulsive choice (delay discounting), impulsive action (behavioral inhibition), and impulsive personality traits (UPPS-P), and evaluated 11 polygenic risk scores (PRSs) of phenotypes previously linked to self-regulation. Although there were no individual genome-wide significant hits, the neuroticism PRS was positively associated with negative urgency (adjusted R2 = 1.61%, p = 3.6 × 10-7 ) and the educational attainment PRS was inversely associated with delay discounting (adjusted R2 = 1.68%, p = 2.2 × 10-7 ). There was also evidence implicating PRSs of attention-deficit/hyperactivity disorder, externalizing, risk-taking, smoking cessation, smoking initiation, and body mass index with one or more impulsivity phenotypes (adjusted R2 s: 0.35%-1.07%; FDR adjusted ps = 0.05-0.0006). These significant associations between PRSs and impulsivity phenotypes are consistent with established genetic correlations. The combined PRS explained 0.91%-2.46% of the phenotypic variance for individual impulsivity measures, corresponding to 8.7%-32.5% of their reported single-nucleotide polymorphism (SNP)-based heritability, suggesting a non-negligible portion of the SNP-based heritability can be recovered by PRSs. These results support the predictive validity and utility of PRSs, even derived from related phenotypes, to inform the genetics of impulsivity phenotypes.
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Affiliation(s)
- Wei Q Deng
- Peter Boris Centre for Addictions Research, St. Joseph's Healthcare Hamilton, Hamilton, Ontario, Canada
- Department of Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton, Canada
| | - Kyla Belisario
- Peter Boris Centre for Addictions Research, St. Joseph's Healthcare Hamilton, Hamilton, Ontario, Canada
- Department of Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton, Canada
| | - Joshua C Gray
- Department of Medical and Clinical Psychology, Uniformed Services University, Bethesda, Maryland, USA
| | - Emily E Levitt
- Peter Boris Centre for Addictions Research, St. Joseph's Healthcare Hamilton, Hamilton, Ontario, Canada
- Department of Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton, Canada
| | | | - Desmond Singh
- Peter Boris Centre for Addictions Research, St. Joseph's Healthcare Hamilton, Hamilton, Ontario, Canada
- Department of Biology, University of Waterloo, Wterloo, Canada
| | - Guillaume Pare
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Canada
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, Canada
| | - James MacKillop
- Peter Boris Centre for Addictions Research, St. Joseph's Healthcare Hamilton, Hamilton, Ontario, Canada
- Department of Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton, Canada
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Deng F, Laasik M, Salminen L, Lapatto L, Huhtinen K, Li Y, Hautaniemi S, Hynninen J, Niemi M, Lehtonen R. Toxicity and therapy outcome associations in LIG3, SLCO1B3, ABCB1, OPRM1, and GSTP1 in high-grade serous ovarian cancer. Basic Clin Pharmacol Toxicol 2023; 132:521-531. [PMID: 36988399 DOI: 10.1111/bcpt.13866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 03/23/2023] [Accepted: 03/24/2023] [Indexed: 03/30/2023]
Abstract
Adverse effects are the major limiting factor in combinatorial chemotherapies. To identify genetic associations in ovarian cancer chemotherapy-induced toxicities and therapy outcomes, we examined a cohort of 101 patients receiving carboplatin-paclitaxel treatment with advanced high-grade serous ovarian cancers. Based on literature and database searches, we selected 19 candidate polymorphisms, designed a multiplex single nucleotide polymorphism-genotyping assay, and applied Cox regression analysis, case-control association statistics, and the log-rank Mantel-Cox test. In the Cox regression analysis, the SLCO1B3 rs1052536 AA-genotype was associated with a reduced risk of any severe toxicity (hazard ratio = 0.35, p=0.023). In chi-square allelic test, the LIG3 rs1052536 T-allele was associated with an increased risk of neuropathy (odds ratio (OR) = 2.79, p=0.031) and GSTP1 rs1695 G-allele with a poorer response in the first-line chemotherapy (OR=2.65, p=0.026). In Kaplan-Meier survival analysis, ABCB1 rs2032582 TT-genotype was associated with shorter overall survival (uncorrected p=0.025), and OPRM1 rs544093 GG and GT genotypes with shorter platinum-free interval (uncorrected p=0.027) and progression-free survival (uncorrected p=0.012). Results suggest that SLCO1B3 and LIG3 variants are associated with the risk of adverse effects in patients receiving carboplatin-paclitaxel treatment, the GSTP1 variant may affect the treatment response, and ABCB1 and OPRM1 variants may influence the prognosis.
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Affiliation(s)
- Feng Deng
- Department of Clinical Pharmacology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Individualized Drug Therapy Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Maren Laasik
- Department of Obstetrics and Gynecology, Turku University Hospital and University of Turku, Turku, Finland
| | - Liina Salminen
- Department of Obstetrics and Gynecology, Turku University Hospital and University of Turku, Turku, Finland
| | - Lauri Lapatto
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Kaisa Huhtinen
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Institute of Biomedicine and FICAN West Cancer Centre, Turku University Hospital and University of Turku, Turku, Finland
| | - Yilin Li
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Sampsa Hautaniemi
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Johanna Hynninen
- Department of Obstetrics and Gynecology, Turku University Hospital and University of Turku, Turku, Finland
| | - Mikko Niemi
- Department of Clinical Pharmacology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Individualized Drug Therapy Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Clinical Pharmacology, HUS Diagnostic Center, Helsinki University Hospital, Helsinki, Finland
| | - Rainer Lehtonen
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Research Program in Tumor Genomics, Research Programs Unit, Biomedicum Helsinki, University of Helsinki, Finland
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