1
|
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.
Collapse
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
| |
Collapse
|
2
|
Nogawa S, Kanamori H, Tokuda K, Kawafune K, Chijiiwa M, Saito K, Takahashi S. A web-based genome-wide association study reveals the susceptibility loci of common adverse events following COVID-19 vaccination in the Japanese population. Sci Rep 2023; 13:20820. [PMID: 38012279 PMCID: PMC10682012 DOI: 10.1038/s41598-023-47632-5] [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: 06/15/2023] [Accepted: 11/16/2023] [Indexed: 11/29/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has spread rapidly worldwide. To prevent its spread, mRNA-based vaccines made by Pfizer/BioNTech (BNT162b1) and Moderna (mRNA-1273) have been widely used, including in Japan. Various adverse events have been reported following the COVID-19 mRNA vaccination, with differences observed among individuals. However, analyses of the genetic background associated with the susceptibility to side effects have been limited. In the present study, we performed genome-wide association studies (GWAS) for self-reported adverse events of the COVID-19 mRNA vaccination in 4545 Japanese individuals and identified 14 associated loci. Among these, 6p21 was associated with 37.5 °C or higher fever, 38 °C or higher fever, and muscle pain. HLA allele association analysis revealed that various HLA alleles were associated with the adverse effects; HLA-DQA1*03:01 and HLA-A*11:01 were more reliably associated with the adverse effects. Our results may enable the preparation and management of adverse effects by identifying the susceptibility to these adverse events. Furthermore, we obtained valuable data that may lead to a better understanding of the mechanisms of action of the COVID-19 mRNA vaccines.
Collapse
Affiliation(s)
- Shun Nogawa
- Genequest Inc., Siba 5-29-11, Minato-ku, Tokyo, 108-0014, Japan
| | - Hajime Kanamori
- Department of Infectious Diseases, Internal Medicine, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8574, Japan
- Division of Infection Control, Tohoku University Hospital, 1-1 Seiryo-machi, Aoba-ku, Sendai, 980-8574, Japan
| | - Koichi Tokuda
- Department of Infectious Diseases, Internal Medicine, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8574, Japan
- Division of Infection Control, Tohoku University Hospital, 1-1 Seiryo-machi, Aoba-ku, Sendai, 980-8574, Japan
| | - Kaoru Kawafune
- Genequest Inc., Siba 5-29-11, Minato-ku, Tokyo, 108-0014, Japan
| | - Miyuki Chijiiwa
- Genequest Inc., Siba 5-29-11, Minato-ku, Tokyo, 108-0014, Japan
| | - Kenji Saito
- Genequest Inc., Siba 5-29-11, Minato-ku, Tokyo, 108-0014, Japan
| | - Shoko Takahashi
- Genequest Inc., Siba 5-29-11, Minato-ku, Tokyo, 108-0014, Japan.
| |
Collapse
|
3
|
Hernandez-Mixteco M, Bernal-Morales B, Valenzuela OL, Rodríguez-Landa JF, Cerna-Cortes JF, García-Montalvo EA. TPH2-703 G/T polymorphism is associated with stress, depression, and psychosocial symptoms in mentally healthy Mexicans. Brain Res 2023; 1817:148479. [PMID: 37423455 DOI: 10.1016/j.brainres.2023.148479] [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: 05/19/2023] [Revised: 06/30/2023] [Accepted: 07/06/2023] [Indexed: 07/11/2023]
Abstract
Tryptophan hydroxylase (TPH) catalyzes the rate-limiting step of serotonin synthesis. TPH2 is the brain-specific isoform of this enzyme, and genetic variations in the TPH2 gene have been shown to impact its transcription and enzymatic activity and are associated with mood disorders. In this study we focused on the rs4570625 (-703G/T) single nucleotide polymorphism of TPH2 gene. By using conventional polymerase chain reaction (PCR), we examined the effect of this polymorphism on stress, anxiety, and depression symptoms as well as quality of life, evaluated based on the Holmes-Rahe Inventory, the Beck Anxiety Inventory, the Beck Depression Inventory, and the World Health Organization Quality of Life - Short Version, respectively. We found that individuals with the homozygous recessive T/T genotype had lower stress and depression scores. In addition, the quality of life in the psychological health domain was better in males with the T/T genotype. These results suggest that T/T genotype could decrease the susceptibility to developing stress and depression in the Mexican population without a diagnosis for an emotional disorder.
Collapse
Affiliation(s)
- Margarita Hernandez-Mixteco
- Programa de Doctorado en Neuroetología, Instituto de Neuroetología, Universidad Veracruzana, Xalapa, Veracruz, Mexico; Laboratorio de Neurofarmacología, Instituto de Neuroetología, Universidad Veracruzana, Xalapa, Veracruz, Mexico; Facultad de Ciencias Químicas, Universidad Veracruzana, Orizaba, Veracruz, Mexico
| | - Blandina Bernal-Morales
- Laboratorio de Neurofarmacología, Instituto de Neuroetología, Universidad Veracruzana, Xalapa, Veracruz, Mexico
| | | | | | - Jorge Francisco Cerna-Cortes
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, Mexico
| | | |
Collapse
|
4
|
Zhang J, Wang MG, He JQ. Association between a single nucleotide polymorphism of the ALOX5 gene and susceptibility to multisystem tuberculosis in a Chinese Han population. Microb Pathog 2023; 183:106289. [PMID: 37567324 DOI: 10.1016/j.micpath.2023.106289] [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: 05/26/2023] [Revised: 08/03/2023] [Accepted: 08/07/2023] [Indexed: 08/13/2023]
Abstract
BACKGROUND Host genetic single nucleotide polymorphisms can exert an influence susceptibility to tuberculosis infection. Previous investigations have demonstrated an association between the polymorphism in the ALOX5 gene and a range of diseases, encompassing not only noninfectious conditions like asthma, acute myocardial infarction, and cerebral infarction but also infections caused by various pathogens. However, the relationship between ALOX5 gene polymorphism and susceptibility to tuberculosis has received limited research attention. The ALOX5 gene encodes arachidonic acid 5-lipoxygenase(5-LO), which serves as the initiating catalyst in the generation of the inflammatory mediator leukotriene. Leukotrienes, products derived from the 5-LO pathway, are potent proinflammatory lipid mediators that assume a pivotal role in tuberculosis infections.Consequently, ALOX5 gene variants may be intricately associated with the pathogenesis of tuberculosis. In instances where the host exhibits immunocompromisation, infection with Mycobacterium tuberculosis can impact multiple systems. The involvement of multiple systems significantly augments the complexity of treatment and escalates patient mortality rates. Regrettably, the underlying mechanisms driving multisystem tuberculosis pathogenesis remain enigmatic, with clinicians paying scant attention to this aspect. Although the protein encoded by the ALOX5 gene represents a pivotal enzyme that catalyzes the metabolism of arachidonic acid into LXA4, and thereby plays a significant role in the inflammatory response during tuberculosis infection, studies investigating ALOX5 gene polymorphism and its association with susceptibility to multisystem tuberculosis in the Chinese Han population are exceptionally scarce. Therefore, the primary objective of this study is to comprehensively examine the correlation between ALOX5 gene polymorphisms and susceptibility to tuberculosis within the Chinese Han population, with particular emphasis on multisystemic tuberculosis. METHODS A case‒control study design was employed, encompassing 382 individuals with pulmonary tuberculosis and 367 individuals with multisystemic tuberculosis as the case groups, along with 577 healthy controls.Whole blood DNA was extracted from all patients and healthy controls. Subsequently, three tag polymorphisms (rs2029253, rs7896431, rs2115819) within the ALOX5 gene were selectively identified and genotyped. RESULTS After adjusting for age and sex, the presence of allele A at rs2029253 exhibited a pronounced association with an elevated risk of TB susceptibility when compared to the tuberculosis group and healthy control group. (ORa: 2.174, 95% CI: 1.827-2.587; Pa<0.001, respectively). Notably, the rs2029253 AG genotype and AA genotype displayed a significantly increased susceptibility to tuberculosis (ORa: 2.236, 95% CI: 1.769-2.825; Pa <0.001 and ORa: 4.577, 95% CI: 2.950-7.100; Pa <0.001, respectively) compared to the GG genotype. Moreover, in the analysis utilizing genetic models, rs2029253 also exhibited a markedly heightened susceptibility to tuberculosis in additive models, dominant models, and recessive models (Pa <0.001). Conversely, no significant association was observed between rs7896431, rs2115819, and tuberculosis. In the subgroup analysis, when comparing the pulmonary tuberculosis group with the healthy control group, we observed no significant disparities in the distribution frequencies of alleles, genotypes, and gene models (additive model, dominant model, and recessive model) for the three tag SNPs, with P-values were >0.05 after adjusting for age and sex. Additionally, we noted that the presence of allele A at rs2029253 was linked to an increased susceptibility to tuberculosis in the multisystemic tuberculosis group relative to the healthy control group (ORa: 2.292, 95% CI: 1.870-2.810; Pa<0.001). Similarly, the rs2029253 AG genotype, AA genotype, and gene models, including the additive model, dominant model, and recessive model, demonstrated a significantly elevated risk of tuberculosis susceptibility. CONCLUSIONS The polymorphism in the ALOX5 gene is associated with susceptibility to multisystemic tuberculosis in the Chinese Han population.
Collapse
Affiliation(s)
- Juan Zhang
- Department of Respiratory and Critical Care Medicine, West China Hospital of Sichuan University, No.37, Guo Xue Alley, Chengdu, 610041, Sichuan Province, People's Republic of China; Intensive Care Unit, Deyang People's Hospital, No 173, North Taishan Road, Deyang, 618000, Sichuan Province, People's Republic of China
| | - Ming-Gui Wang
- Department of Respiratory and Critical Care Medicine, West China Hospital of Sichuan University, No.37, Guo Xue Alley, Chengdu, 610041, Sichuan Province, People's Republic of China
| | - Jian-Qing He
- Department of Respiratory and Critical Care Medicine, West China Hospital of Sichuan University, No.37, Guo Xue Alley, Chengdu, 610041, Sichuan Province, People's Republic of China.
| |
Collapse
|
5
|
Gyawali PK, Le Guen Y, Liu X, Belloy ME, Tang H, Zou J, He Z. Improving genetic risk prediction across diverse population by disentangling ancestry representations. Commun Biol 2023; 6:964. [PMID: 37736834 PMCID: PMC10517023 DOI: 10.1038/s42003-023-05352-6] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Accepted: 09/12/2023] [Indexed: 09/23/2023] Open
Abstract
Risk prediction models using genetic data have seen increasing traction in genomics. However, most of the polygenic risk models were developed using data from participants with similar (mostly European) ancestry. This can lead to biases in the risk predictors resulting in poor generalization when applied to minority populations and admixed individuals such as African Americans. To address this issue, largely due to the prediction models being biased by the underlying population structure, we propose a deep-learning framework that leverages data from diverse population and disentangles ancestry from the phenotype-relevant information in its representation. The ancestry disentangled representation can be used to build risk predictors that perform better across minority populations. We applied the proposed method to the analysis of Alzheimer's disease genetics. Comparing with standard linear and nonlinear risk prediction methods, the proposed method substantially improves risk prediction in minority populations, including admixed individuals, without needing self-reported ancestry information.
Collapse
Affiliation(s)
- Prashnna K Gyawali
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA.
| | - Yann Le Guen
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
- Institut du Cerveau-Paris Brain Institute-ICM, Paris, France
| | - Xiaoxia Liu
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Michael E Belloy
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Hua Tang
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - James Zou
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA.
| | - Zihuai He
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA.
- Quantitative Sciences Unit, Department of Medicine (Biomedical Informatics Research), Stanford University, Stanford, CA, USA.
| |
Collapse
|
6
|
Sherva R, Zhang R, Sahelijo N, Jun G, Anglin T, Chanfreau C, Cho K, Fonda JR, Gaziano JM, Harrington KM, Ho YL, Kremen WS, Litkowski E, Lynch J, Neale Z, Roussos P, Marra D, Mez J, Miller MW, Salat DH, Tsuang D, Wolf E, Zeng Q, Panizzon MS, Merritt VC, Farrer LA, Hauger RL, Logue MW. African ancestry GWAS of dementia in a large military cohort identifies significant risk loci. Mol Psychiatry 2023; 28:1293-1302. [PMID: 36543923 PMCID: PMC10066923 DOI: 10.1038/s41380-022-01890-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 11/02/2022] [Accepted: 11/15/2022] [Indexed: 12/24/2022]
Abstract
While genome wide association studies (GWASs) of Alzheimer's Disease (AD) in European (EUR) ancestry cohorts have identified approximately 83 potentially independent AD risk loci, progress in non-European populations has lagged. In this study, data from the Million Veteran Program (MVP), a biobank which includes genetic data from more than 650,000 US Veteran participants, was used to examine dementia genetics in an African descent (AFR) cohort. A GWAS of Alzheimer's disease and related dementias (ADRD), an expanded AD phenotype including dementias such as vascular and non-specific dementia that included 4012 cases and 18,435 controls age 60+ in AFR MVP participants was performed. A proxy dementia GWAS based on survey-reported parental AD or dementia (n = 4385 maternal cases, 2256 paternal cases, and 45,970 controls) was also performed. These two GWASs were meta-analyzed, and then subsequently compared and meta-analyzed with the results from a previous AFR AD GWAS from the Alzheimer's Disease Genetics Consortium (ADGC). A meta-analysis of common variants across the MVP ADRD and proxy GWASs yielded GWAS significant associations in the region of APOE (p = 2.48 × 10-101), in ROBO1 (rs11919682, p = 1.63 × 10-8), and RNA RP11-340A13.2 (rs148433063, p = 8.56 × 10-9). The MVP/ADGC meta-analysis yielded additional significant SNPs near known AD risk genes TREM2 (rs73427293, p = 2.95 × 10-9), CD2AP (rs7738720, p = 1.14 × 10-9), and ABCA7 (rs73505251, p = 3.26 × 10-10), although the peak variants observed in these genes differed from those previously reported in EUR and AFR cohorts. Of the genes in or near suggestive or genome-wide significant associated variants, nine (CDA, SH2D5, DCBLD1, EML6, GOPC, ABCA7, ROS1, TMCO4, and TREM2) were differentially expressed in the brains of AD cases and controls. This represents the largest AFR GWAS of AD and dementia, finding non-APOE GWAS-significant common SNPs associated with dementia. Increasing representation of AFR participants is an important priority in genetic studies and may lead to increased insight into AD pathophysiology and reduce health disparities.
Collapse
Affiliation(s)
- Richard Sherva
- National Center for PTSD, Behavioral Sciences Division, VA Boston Healthcare System, Boston, MA, USA
- Boston University Chobanian & Avedisian School of Medicine, Biomedical Genetics, Boston, MA, USA
| | - Rui Zhang
- National Center for PTSD, Behavioral Sciences Division, VA Boston Healthcare System, Boston, MA, USA
| | - Nathan Sahelijo
- Boston University Chobanian & Avedisian School of Medicine, Biomedical Genetics, Boston, MA, USA
| | - Gyungah Jun
- Boston University Chobanian & Avedisian School of Medicine, Biomedical Genetics, Boston, MA, USA
| | - Tori Anglin
- VA Informatics and Computing Infrastructure (VINCI), Salt Lake City, UT, USA
| | - Catherine Chanfreau
- VA Informatics and Computing Infrastructure (VINCI), Salt Lake City, UT, USA
| | - Kelly Cho
- Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, MA, USA
- Division of Aging, Brigham & Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Jennifer R Fonda
- Department of Psychiatry, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, 02118, USA
- Translational Research Center for TBI and Stress Disorders (TRACTS) and Geriatric Research, Educational and Clinical Center (GRECC), VA Boston Healthcare System, Boston, MA, USA
- Department of Psychiatry, Harvard Medical School, Boston, MA, USA
| | - J Michael Gaziano
- Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, MA, USA
- Division of Aging, Brigham & Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Kelly M Harrington
- Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, MA, USA
- Department of Psychiatry, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, 02118, USA
| | - Yuk-Lam Ho
- Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, MA, USA
| | - William S Kremen
- Department of Psychiatry, School of Medicine, University of California, San Diego, La Jolla, CA, USA
- Center for Behavior Genetics of Aging, University of California, San Diego, La Jolla, CA, USA
| | - Elizabeth Litkowski
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- VA Eastern Colorado Healthcare System, Aurora, CO, USA
| | - Julie Lynch
- VA Informatics and Computing Infrastructure (VINCI), Salt Lake City, UT, USA
| | - Zoe Neale
- National Center for PTSD, Behavioral Sciences Division, VA Boston Healthcare System, Boston, MA, USA
- Department of Psychiatry, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, 02118, USA
| | - Panos Roussos
- Center for Disease Neurogenomics, Departments of Psychiatry and Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Dementia Research, Nathan Kline Institute for Psychiatric Research, Orangeburg, NY, USA
- Mental Illness Research Education and Clinical Center (MIRECC), James J. Peters VA Medical Center, Bronx, New York, NY, USA
| | - David Marra
- Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, MA, USA
- Department of Psychiatry, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, 02118, USA
| | - Jesse Mez
- Boston University Chobanian & Avedisian School of Medicine, Biomedical Genetics, Boston, MA, USA
- Department of Neurology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
- Boston University Alzheimer's Disease Research Center, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Mark W Miller
- National Center for PTSD, Behavioral Sciences Division, VA Boston Healthcare System, Boston, MA, USA
- Department of Psychiatry, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, 02118, USA
| | - David H Salat
- Neuroimaging Research for Veterans Center, VA Boston Healthcare System, Boston, MA, USA
| | - Debby Tsuang
- Geriatric Research, Education, and Clinical Center, VA Puget Sound Health Care System, Seattle, WA, USA
| | - Erika Wolf
- National Center for PTSD, Behavioral Sciences Division, VA Boston Healthcare System, Boston, MA, USA
- Department of Psychiatry, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, 02118, USA
| | - Qing Zeng
- VA Washington DC Healthcare System, Washington, DC, USA
| | - Matthew S Panizzon
- Department of Psychiatry, School of Medicine, University of California, San Diego, La Jolla, CA, USA
- Center for Behavior Genetics of Aging, University of California, San Diego, La Jolla, CA, USA
- Center of Excellence for Stress and Mental Health, VA San Diego Healthcare System, San Diego, CA, USA
| | - Victoria C Merritt
- Department of Psychiatry, School of Medicine, University of California, San Diego, La Jolla, CA, USA
- Center of Excellence for Stress and Mental Health, VA San Diego Healthcare System, San Diego, CA, USA
- VA San Diego Healthcare System, 3350 La Jolla Village Dr, San Diego, CA, USA
| | - Lindsay A Farrer
- Boston University Chobanian & Avedisian School of Medicine, Biomedical Genetics, Boston, MA, USA
- Department of Neurology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
- Boston University Alzheimer's Disease Research Center, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
- Department of Ophthalmology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
- Department of Epidemiology, Boston University School of Public Health, Boston, MA, USA
| | - Richard L Hauger
- Department of Psychiatry, School of Medicine, University of California, San Diego, La Jolla, CA, USA
- Center for Behavior Genetics of Aging, University of California, San Diego, La Jolla, CA, USA
- VA San Diego Healthcare System, 3350 La Jolla Village Dr, San Diego, CA, USA
| | - Mark W Logue
- National Center for PTSD, Behavioral Sciences Division, VA Boston Healthcare System, Boston, MA, USA.
- Boston University Chobanian & Avedisian School of Medicine, Biomedical Genetics, Boston, MA, USA.
- Department of Psychiatry, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, 02118, USA.
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA.
| |
Collapse
|
7
|
Sterrett-Hong EM, Aliev F, Dick DM, Hooper LM, Mustanski B. Genetic Risk, Neighborhood Characteristics, and Behavioral Difficulties Among African American Adolescents Living in Very Low-Income Neighborhoods. Res Child Adolesc Psychopathol 2023; 51:653-664. [PMID: 36645613 PMCID: PMC10121776 DOI: 10.1007/s10802-023-01021-8] [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] [Accepted: 12/30/2022] [Indexed: 01/17/2023]
Abstract
Behavioral difficulties among African American youth are disproportionately detrimental to their future well-being compared to when demonstrated by White American youth. The majority of gene-environment studies of behavior have been conducted with European ancestry samples, limiting our knowledge of these processes among African Americans. This study examined the influence of positive and negative neighborhood conditions, in the context of genetic risk, on behavioral difficulties among low-income African American adolescents. Data were from the Genes, Environment, and Neighborhood Initiative study of African American youth in high-poverty neighborhoods, n = 524, M age = 15.89, SD = 1.42. DNA samples were collected using the Oragene Discovery 500 series, and polygenic risk scores for behavioral difficulties computed. Neighborhood informal social control, social cohesion, physical disorder, and social disorder were assessed. Adolescent alcohol use, hyperactivity/inattention and conduct problems were examined as outcomes. After controlling for polygenic risk, lower levels of neighborhood social disorder and higher levels of social cohesion were associated with fewer youth-reported hyperactivity/inattention and conduct problems. Less social disorder also was associated with fewer parent-reported behavioral difficulties. Neighborhood characteristics did not moderate associations between genetic risk and the outcomes. Higher levels of positive and lower levels of negative neighborhood characteristics can be associated with lower levels of behavioral difficulties among African American youth living in poverty, even after taking into account genetic risk.
Collapse
Affiliation(s)
- Emma M Sterrett-Hong
- Kent School of Social Work & Family Science, University of Louisville, Oppenheimer Hall #102, 2217 S. 3rd St, 40292, Louisville, KY, USA.
| | - Fazil Aliev
- Rutgers University, New Brunswick, United States
| | | | - Lisa M Hooper
- University of Northern Iowa, Cedar Falls, United States
| | | |
Collapse
|
8
|
Abraham Daniel A, Silzer T, Sun J, Zhou Z, Hall C, Phillips N, Barber R. Hypermethylation at CREBBP Is Associated with Cognitive Impairment in a Mexican American Cohort. J Alzheimers Dis 2023; 92:1229-1239. [PMID: 36872777 PMCID: PMC10200223 DOI: 10.3233/jad-221031] [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] [Accepted: 02/01/2023] [Indexed: 03/06/2023]
Abstract
BACKGROUND The aging Mexican American (MA) population is the fastest growing ethnic minority group in the US. MAs have a unique metabolic-related risk for Alzheimer's disease (AD) and mild cognitive impairment (MCI), compared to non-Hispanic whites (NHW). This risk for cognitive impairment (CI) is multifactorial involving genetics, environmental, and lifestyle factors. Changes in environment and lifestyle can alter patterns and even possibly reverse derangement of DNA methylation (a form of epigenetic regulation). OBJECTIVE We sought to identify ethnicity-specific DNA methylation profiles that may be associated with CI in MAs and NHWs. METHODS DNA obtained from peripheral blood of 551 participants from the Texas Alzheimer's Research and Care Consortium was typed on the Illumina Infinium® MethylationEPIC chip array, which assesses over 850K CpG genomic sites. Within each ethnic group (N = 299 MAs, N = 252 NHWs), participants were stratified by cognitive status (control versus CI). Beta values, representing relative degree of methylation, were normalized using the Beta MIxture Quantile dilation method and assessed for differential methylation using the Chip Analysis Methylation Pipeline (ChAMP), limma and cate packages in R. RESULTS Two differentially methylated sites were significant: cg13135255 (MAs) and cg27002303 (NHWs) based on an FDR p < 0.05. Three suggestive sites obtained were cg01887506 (MAs) and cg10607142 and cg13529380 (NHWs). Most methylation sites were hypermethylated in CI compared to controls, except cg13529380 which was hypomethylated. CONCLUSION The strongest association with CI was at cg13135255 (FDR-adjusted p = 0.029 in MAs), within the CREBBP gene. Moving forward, identifying additional ethnicity-specific methylation sites may be useful to discern CI risk in MAs.
Collapse
Affiliation(s)
- Ann Abraham Daniel
- Department of Microbiology, Immunology and Genetics, School of Biomedical Sciences, University of North Texas Health Science Center, Fort Worth, TX, USA
| | - Talisa Silzer
- Department of Microbiology, Immunology and Genetics, School of Biomedical Sciences, University of North Texas Health Science Center, Fort Worth, TX, USA
| | - Jie Sun
- Department of Microbiology, Immunology and Genetics, School of Biomedical Sciences, University of North Texas Health Science Center, Fort Worth, TX, USA
| | - Zhengyang Zhou
- Department of Biostatistics and Epidemiology, School of Public Health, University of North Texas Health Science Center, Fort Worth, TX, USA
| | - Courtney Hall
- Department of Microbiology, Immunology and Genetics, School of Biomedical Sciences, University of North Texas Health Science Center, Fort Worth, TX, USA
| | - Nicole Phillips
- Department of Microbiology, Immunology and Genetics, School of Biomedical Sciences, University of North Texas Health Science Center, Fort Worth, TX, USA
| | - Robert Barber
- Department of Family and Manipulative Medicine, Texas College of Osteopathic Medicine, University of North Texas Health Science Center, Fort Worth, TX, USA
| |
Collapse
|
9
|
Chen YM, Xu P, Wang ZT, Zhu YM, Gong CM, Huang CH, Liu XL, Zhou JC. Polymorphisms of the Vitamin D Receptor Gene and Sex-Differential Associations with Lipid Profiles in Chinese Han Adults. Biomed Environ Sci 2022; 35:115-125. [PMID: 35197176 DOI: 10.3967/bes2022.016] [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] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 07/19/2021] [Indexed: 06/14/2023]
Abstract
OBJECTIVE To explore the association of single nucleotide polymorphisms (SNPs) of the vitamin D receptor gene ( VDR) with circulating lipids considering gender differences. METHODS Of the Han Chinese adults recruited from a health examination center for inclusion in the study, the circulating lipids, 25-hydroxyvitamin D (25OHD), and other parameters were measured. The VDR SNPs of Cdx2 (rs11568820), Fok1 (rs2228570), Apa1 (rs7975232), and Taq1 (rs731236) were genotyped with a qPCR test using blood DNA samples, and their associations with lipids were analyzed using logistic regression. RESULTS In the female participants ( n = 236 with dyslipidemia and 888 without dyslipidemia), multiple genotype models of Fok1 indicated a positive correlation of B (not A) alleles with LDLC level ( P < 0.05). In the male participants ( n = 299 with dyslipidemia and 564 without dyslipidemia), the recessive model of Cdx2 and the additive and recessive models of Fok1 differed ( P < 0.05) between the HDLC-classified subgroups, respectively, and Fok1 BB and Cdx2 TT presented interactions with 25OHD in the negative associations with HDLC ( P < 0.05). CONCLUSION In the Chinese Han adults included in the study, the Fok1 B-allele of VDR was associated with higher LDLC in females, and the Fok1 B-allele and the Cdx2 T-allele of VDR were associated with lower HDLC in males. The interaction of VD and Fok1 BB or Cdx2 TT in males synergistically decreased HDLC levels.
Collapse
Affiliation(s)
- Yan Mei Chen
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen 518100, Guangdong, China
| | - Ping Xu
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen 518100, Guangdong, China
| | - Zhou Tian Wang
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen 518100, Guangdong, China
| | - Yu Mei Zhu
- Shenzhen Center for Chronic Disease Control, Shenzhen 518020, Guangdong, China
| | - Chun Mei Gong
- Shenzhen Center for Chronic Disease Control, Shenzhen 518020, Guangdong, China
| | - Chang Hua Huang
- Shenzhen Qilinshan Sanatorium, Shenzhen 518055, Guangdong, China
| | - Xiao Li Liu
- Shenzhen Center for Chronic Disease Control, Shenzhen 518020, Guangdong, China
| | - Ji Chang Zhou
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen 518100, Guangdong, China;Shenzhen Center for Chronic Disease Control, Shenzhen 518020, Guangdong, China;Guangdong Province Engineering Laboratory for Nutrition Translation, Guangzhou 510080, Guangdong, China
| |
Collapse
|
10
|
Sun Q, Graff M, Rowland B, Wen J, Huang L, Miller-Fleming TW, Haessler J, Preuss MH, Chai JF, Lee MP, Avery CL, Cheng CY, Franceschini N, Sim X, Cox NJ, Kooperberg C, North KE, Li Y, Raffield LM. Analyses of biomarker traits in diverse UK biobank participants identify associations missed by European-centric analysis strategies. J Hum Genet 2022; 67:87-93. [PMID: 34376796 PMCID: PMC8792153 DOI: 10.1038/s10038-021-00968-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 07/09/2021] [Accepted: 07/27/2021] [Indexed: 12/13/2022]
Abstract
Despite the dramatic underrepresentation of non-European populations in human genetics studies, researchers continue to exclude participants of non-European ancestry, as well as variants rare in European populations, even when these data are available. This practice perpetuates existing research disparities and can lead to important and large effect size associations being missed. Here, we conducted genome-wide association studies (GWAS) of 31 serum and urine biomarker quantitative traits in African (n = 9354), East Asian (n = 2559), and South Asian (n = 9823) ancestry UK Biobank (UKBB) participants. We adjusted for all known GWAS catalog variants for each trait, as well as novel signals identified in a recent European ancestry-focused analysis of UKBB participants. We identify 7 novel signals in African ancestry and 2 novel signals in South Asian ancestry participants (p < 1.61E-10). Many of these signals are highly plausible, including a cis pQTL for the gene encoding gamma-glutamyl transferase and PIEZO1 and G6PD variants with impacts on HbA1c through likely erythrocytic mechanisms. This work illustrates the importance of using the genetic data we already have in diverse populations, with novel discoveries possible in even modest sample sizes.
Collapse
Affiliation(s)
- Quan Sun
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC, USA
| | - Misa Graff
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, USA
| | - Bryce Rowland
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC, USA
| | - Jia Wen
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Le Huang
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Tyne W Miller-Fleming
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jeffrey Haessler
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Michael H Preuss
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jin-Fang Chai
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
| | - Moa P Lee
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, USA
| | - Christy L Avery
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, USA
| | - Ching-Yu Cheng
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
- Ophthalmology & Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, Singapore, Singapore
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Nora Franceschini
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, USA
| | - Xueling Sim
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
| | - Nancy J Cox
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Kari E North
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, USA
- Carolina Center of Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Yun Li
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC, USA
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
- Department of Computer Science, University of North Carolina, Chapel Hill, NC, USA
| | - Laura M Raffield
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA.
| |
Collapse
|
11
|
Ouidir M, Zeng X, Chatterjee S, Zhang C, Tekola-Ayele F. Ancestry-Matched and Cross-Ancestry Genetic Risk Scores of Type 2 Diabetes in Pregnant Women and Fetal Growth: A Study in an Ancestrally Diverse Cohort. Diabetes 2022; 71:340-349. [PMID: 34789498 PMCID: PMC8914278 DOI: 10.2337/db21-0655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 11/11/2021] [Indexed: 02/03/2023]
Abstract
Maternal genetic variants associated with offspring birth weight and adult type 2 diabetes (T2D) risk loci show some overlap. Whether T2D genetic risk influences longitudinal fetal weight and the gestational timing when these relationships begin is unknown. We investigated the associations of T2D genetic risk scores (GRS) with longitudinal fetal weight and birth weight among 1,513 pregnant women from four ancestral groups. Women had up to five ultrasonography examinations. Ancestry-matched GRS were constructed separately using 380 European- (GRSeur), 104 African- (GRSafr), and 189 East Asian- (GRSeas) related T2D loci discovered in different population groups. Among European Americans, the highest quartile GRSeur was significantly associated with 53.8 g higher fetal weight (95% CI 19.2-88.5) over the pregnancy. The associations began at gestational week 24 and continued through week 40, with a 106.8 g (95% CI 6.5-207.1) increase in birth weight. The findings were similar in analysis further adjusted for maternal glucose challenge test results. No consistent association was found using ancestry-matched or cross-ancestry GRS in non-Europeans. In conclusion, T2D genetic susceptibility may influence fetal growth starting at midsecond trimester among Europeans. Absence of similar associations in non-Europeans urges the need for further genetic T2D studies in diverse ancestries.
Collapse
|
12
|
Sassano M, Mariani M, Quaranta G, Pastorino R, Boccia S. Polygenic risk prediction models for colorectal cancer: a systematic review. BMC Cancer 2022; 22:65. [PMID: 35030997 PMCID: PMC8760647 DOI: 10.1186/s12885-021-09143-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 12/02/2021] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Risk prediction models incorporating single nucleotide polymorphisms (SNPs) could lead to individualized prevention of colorectal cancer (CRC). However, the added value of incorporating SNPs into models with only traditional risk factors is still not clear. Hence, our primary aim was to summarize literature on risk prediction models including genetic variants for CRC, while our secondary aim was to evaluate the improvement of discriminatory accuracy when adding SNPs to a prediction model with only traditional risk factors. METHODS We conducted a systematic review on prediction models incorporating multiple SNPs for CRC risk prediction. We tested whether a significant trend in the increase of Area Under Curve (AUC) according to the number of SNPs could be observed, and estimated the correlation between AUC improvement and number of SNPs. We estimated pooled AUC improvement for SNP-enhanced models compared with non-SNP-enhanced models using random effects meta-analysis, and conducted meta-regression to investigate the association of specific factors with AUC improvement. RESULTS We included 33 studies, 78.79% using genetic risk scores to combine genetic data. We found no significant trend in AUC improvement according to the number of SNPs (p for trend = 0.774), and no correlation between the number of SNPs and AUC improvement (p = 0.695). Pooled AUC improvement was 0.040 (95% CI: 0.035, 0.045), and the number of cases in the study and the AUC of the starting model were inversely associated with AUC improvement obtained when adding SNPs to a prediction model. In addition, models constructed in Asian individuals achieved better AUC improvement with the incorporation of SNPs compared with those developed among individuals of European ancestry. CONCLUSIONS Though not conclusive, our results provide insights on factors influencing discriminatory accuracy of SNP-enhanced models. Genetic variants might be useful to inform stratified CRC screening in the future, but further research is needed.
Collapse
Affiliation(s)
- Michele Sassano
- Section of Hygiene, University Department of Life Sciences and Public Health, Università Cattolica del Sacro Cuore, 00168, Roma, Italy
| | - Marco Mariani
- Section of Hygiene, University Department of Life Sciences and Public Health, Università Cattolica del Sacro Cuore, 00168, Roma, Italy
| | - Gianluigi Quaranta
- Section of Hygiene, University Department of Life Sciences and Public Health, Università Cattolica del Sacro Cuore, 00168, Roma, Italy
- Department of Woman and Child Health and Public Health - Public Health Area, Fondazione Policlinico Universitario A. Gemelli IRCCS, Roma, Italy
| | - Roberta Pastorino
- Department of Woman and Child Health and Public Health - Public Health Area, Fondazione Policlinico Universitario A. Gemelli IRCCS, Roma, Italy.
| | - Stefania Boccia
- Section of Hygiene, University Department of Life Sciences and Public Health, Università Cattolica del Sacro Cuore, 00168, Roma, Italy
- Department of Woman and Child Health and Public Health - Public Health Area, Fondazione Policlinico Universitario A. Gemelli IRCCS, Roma, Italy
| |
Collapse
|
13
|
Lozano S, Padilla V, Avila ML, Gil M, Maestre G, Wang K, Xu C. APOE Gene Associated with Cholesterol-Related Traits in the Hispanic Population. Genes (Basel) 2021; 12:genes12111768. [PMID: 34828374 PMCID: PMC8619821 DOI: 10.3390/genes12111768] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 11/02/2021] [Accepted: 11/04/2021] [Indexed: 11/16/2022] Open
Abstract
Genetic variants in the apolipoprotein E (APOE) gene are associated with lipid metabolism and lipid-related traits in the non-Hispanic population. There have been limited studies regarding the association between the APOE gene and hypercholesterolemia in the Hispanic population; therefore, our aim for this study is to examine the APOE gene’s associations with cholesterol level and its related phenotypes. The APOE gene consists of three different alleles, ε2, ε3, and ε4, with ε4 being associated with dementia and cardiovascular diseases. A total of 1,382 subjects were collected from the Texas Alzheimer’s Research and Care Consortium (TARCC, N = 1320) and the Initial Study of Longevity and Dementia from the Rio Grande Valley (ISLD-RGV, N = 62). Questionnaires on demographics, medical history, and blood/saliva samples were collected and APOE genotypes were performed. We observed allele frequencies of the APOE ε3 (96.7%), ε4 (22.6%) and ε2 (6.8%) alleles, respectively. Multivariable logistic regression revealed a significant association between the APOE ε4 allele and hypercholesteremia (p = 1.8 × 10−4) in our studied Hispanic population. We prove for the first time, that the APOE ε4 allele increases the risk for hypercholesterol in Hispanics. Further research is needed to confirm and supports our current findings.
Collapse
Affiliation(s)
- Stephanie Lozano
- Department of Science, Graduate College of Biochemistry and Molecular Biology, University of Texas Rio Grande Valley, Edinburg, TX 78539, USA;
| | - Victoria Padilla
- Department of Health and Biomedical Science, College of Health Affairs, University of Texas Rio Grande Valley, Brownsville, TX 78520, USA; (V.P.); (M.L.A.)
| | - Manuel Lee Avila
- Department of Health and Biomedical Science, College of Health Affairs, University of Texas Rio Grande Valley, Brownsville, TX 78520, USA; (V.P.); (M.L.A.)
| | - Mario Gil
- Department of Psychological Science, University of Texas Rio Grande Valley, Brownsville, TX 78520, USA;
- Department of Neuroscience, School of Medicine, University of Texas Rio Grande Valley, Harlingen, TX 78539, USA
| | - Gladys Maestre
- Neuroscience and School of Medicine, University of Texas Rio Grande Valley, Edinburg, TX 78539, USA;
| | - Kesheng Wang
- Health Sciences Center, Department of Family and Community Health, School of Nursing, West Virginia University, Morgantown, WV 26506, USA
- Correspondence: (K.W.); (C.X.); Tel.: +1-304-581-1912 (K.W.); +1-956-882-4193 (C.X.)
| | - Chun Xu
- Department of Health and Biomedical Science, College of Health Affairs, University of Texas Rio Grande Valley, Brownsville, TX 78520, USA; (V.P.); (M.L.A.)
- Correspondence: (K.W.); (C.X.); Tel.: +1-304-581-1912 (K.W.); +1-956-882-4193 (C.X.)
| |
Collapse
|
14
|
Miyahira AK, Soule HR. The 27th Annual Prostate Cancer Foundation Scientific Retreat Report. Prostate 2021; 81:1107-1124. [PMID: 34469608 DOI: 10.1002/pros.24211] [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: 08/10/2021] [Accepted: 08/11/2021] [Indexed: 11/07/2022]
Abstract
BACKGROUND The 27th Annual Prostate Cancer Foundation (PCF) Scientific Retreat was held virtually from October 20 to 23, 2020. METHODS The Annual PCF Scientific Retreat is a global scientific research conference that highlights the most promising and cutting edge advances in prostate cancer basic, translational and clinical research, as well as research from other fields with a strong potential for advancing prostate cancer research. RESULTS Primary areas of research discussed at the 2020 PCF Retreat included: (i) the intersection between prostate cancer and COVID-19 research; (ii) lessons from the COVID-19 pandemic that may address prostate cancer disparities; (iv) the role of the microbiome in cancer; (v) current challenges in treatment of patients with metastatic prostate cancer; (viii) prostate cancer germline genetics and evolutionary genomics; (ix) advances in circulating DNA methylation biomarkers for diagnosis, prognosis, and treatment selection; (x) advances in the development of MYC-targeting therapeutics; (xi) advances in antibody-drug conjugates for the treatment of cancer; (xii) advances for immunotherapy in prostate cancer; and (xiii) updates from other recent prostate cancer clinical trials. CONCLUSIONS This article summarizes the research presented at the 2020 PCF Scientific Retreat. We hope that dissemination of this knowledge will help to accelerate and direct the next major advances in prostate cancer research and care.
Collapse
Affiliation(s)
- Andrea K Miyahira
- Department of Science, Prostate Cancer Foundation, Santa Monica, California, USA
| | - Howard R Soule
- Department of Science, Prostate Cancer Foundation, Santa Monica, California, USA
| |
Collapse
|
15
|
Elsayed I, Martinez-Carrasco A, Cornejo-Olivas M, Bandres-Ciga S. Mapping the Diverse and Inclusive Future of Parkinson's Disease Genetics and Its Widespread Impact. Genes (Basel) 2021; 12:1681. [PMID: 34828286 PMCID: PMC8624537 DOI: 10.3390/genes12111681] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 10/19/2021] [Accepted: 10/20/2021] [Indexed: 12/27/2022] Open
Abstract
Over the last decades, genetics has been the engine that has pushed us along on our voyage to understand the etiology of Parkinson's disease (PD). Although a large number of risk loci and causative mutations for PD have been identified, it is clear that much more needs to be done to solve the missing heritability mystery. Despite remarkable efforts, as a field, we have failed in terms of diversity and inclusivity. The vast majority of genetic studies in PD have focused on individuals of European ancestry, leading to a gap of knowledge on the existing genetic differences across populations and PD as a whole. As we move forward, shedding light on the genetic architecture contributing to PD in non-European populations is essential, and will provide novel insight into the generalized genetic map of the disease. In this review, we discuss how better representation of understudied ancestral groups in PD genetics research requires addressing and resolving all the challenges that hinder the inclusion of these populations. We further provide an overview of PD genetics in the clinics, covering the current challenges and limitations of genetic testing and counseling. Finally, we describe the impact of worldwide collaborative initiatives in the field, shaping the future of the new era of PD genetics as we advance in our understanding of the genetic architecture of PD.
Collapse
Affiliation(s)
- Inas Elsayed
- Faculty of Pharmacy, University of Gezira, Wad Medani P.O. Box 20, Sudan;
- International Parkinson Disease Genomics Consortium (IPDGC)-Africa, University of Gezira, Wad Medani P.O. Box 20, Sudan
| | | | - Mario Cornejo-Olivas
- Neurogenetics Research Center, Instituto Nacional de Ciencias Neurológicas, Lima 15003, Peru;
- Center for Global Health, Universidad Peruana Cayetano Heredia, Lima 15103, Peru
| | - Sara Bandres-Ciga
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, NIH, Bethesda, MD 20892, USA
| |
Collapse
|
16
|
Wang J, Conti DV, Bogumil D, Sheng X, Noureddin M, Wilkens LR, Le Marchand L, Rosen HR, Haiman CA, Setiawan VW. Association of Genetic Risk Score With NAFLD in An Ethnically Diverse Cohort. Hepatol Commun 2021; 5:1689-1703. [PMID: 34558842 PMCID: PMC8485887 DOI: 10.1002/hep4.1751] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 05/03/2021] [Indexed: 12/15/2022] Open
Abstract
Most genetic studies of nonalcoholic fatty liver disease (NAFLD) have been conducted in Whites. In this large and ethnically diverse cohort, we assessed the transportability of previously identified genetic variants for NAFLD, built a genetic risk score (GRS), and examined its association with NAFLD risk in multiple ethnic groups. Thirty previously identified genome-wide association studies (GWAS) variants (P < 5 × 10-8 ) and 17 other variants associated with NAFLD were examined in a nested case-control study of NAFLD (1,448 cases/8,444 controls) in this multi-ethnic cohort study. We then built a GRS using 11 independent single-nucleotide polymorphisms from these prior studies and examined its association with NAFLD by cirrhosis status across multiple ethnic groups. Of the 30 GWAS SNPs, 20 (67%) were replicated (P < 0.05) in the pooled multi-ethnic population. The highest percentage of replication was seen in Latinos (43%), followed by Japanese Americans (37%), Whites (17%), and Native Hawaiians and African Americans (≤10%). Several genetic variants, including those in PNPLA3 (patatin-like phospholipase domain containing 3), HSD17B13 (hydroxysteroid 17-beta dehydrogenase 13), TM6SF2 (transmembrane 6 superfamily member 2), GATAD2A (GATA zinc finger domain containing 2A), GCKR (glucokinase regulator), SUGP1 (SURP and G-patch domain containing 1), MBOAT7 (membrane bound O-acyltransferase domain containing 7), TRIB1 (tribbles pseudokinase 1), SAMM50 (sorting and assembly machinery component), and ERLIN1 (ER lipid raft associated 1)-CHUK (component of inhibitor of nuclear factor kappa B kinase complex)-CWF19L1 (CWF19 like cell cycle control factor 1) gene cluster, were replicated in at least two ethnic groups. An 11-SNP weighted GRS was associated with NAFLD risk in the multi-ethnic population (odds ratio [OR] per SD increase = 1.41; 95% confidence interval [CI] = 1.32-1.50), as well as in each ethnic group (OR ranged from 1.30 in African Americans to 1.52 in Latinos). The GRS-NAFLD association was stronger for NAFLD with cirrhosis (OR = 1.67; 95% CI = 1.46-1.92) compared to NAFLD without cirrhosis (OR = 1.37; 95% CI = 1.28-1.46) (P heterogeneity = 0.003). Conclusion: In this ethnically diverse cohort, we replicated several key genetic variants for NAFLD and showed the utility of GRS based on the risk alleles for NAFLD risk stratification in multiple ethnic groups.
Collapse
Affiliation(s)
- Jun Wang
- Department of Preventive MedicineKeck School of Medicine of University of Southern CaliforniaLos AngelesCAUSA
| | - David V. Conti
- Department of Preventive MedicineKeck School of Medicine of University of Southern CaliforniaLos AngelesCAUSA
- Center for Genetic EpidemiologyKeck School of MedicineUniversity of Southern CaliforniaLos AngelesCAUSA
- Norris Comprehensive Cancer CenterKeck School of Medicine of University of Southern CaliforniaLos AngelesCAUSA
| | - David Bogumil
- Department of Preventive MedicineKeck School of Medicine of University of Southern CaliforniaLos AngelesCAUSA
| | - Xin Sheng
- Department of Preventive MedicineKeck School of Medicine of University of Southern CaliforniaLos AngelesCAUSA
| | - Mazen Noureddin
- Division of Gastroenterology and HepatologyDepartment of MedicineCedars‐Sinai Medical CenterLos AngelesCAUSA
| | - Lynne R. Wilkens
- Epidemiology ProgramUniversity of Hawaii Cancer CenterHonoluluHIUSA
| | - Loic Le Marchand
- Epidemiology ProgramUniversity of Hawaii Cancer CenterHonoluluHIUSA
| | - Hugo R. Rosen
- Department of MedicineKeck School of Medicine of University of Southern CaliforniaLos AngelesCAUSA
| | - Christopher A. Haiman
- Department of Preventive MedicineKeck School of Medicine of University of Southern CaliforniaLos AngelesCAUSA
- Center for Genetic EpidemiologyKeck School of MedicineUniversity of Southern CaliforniaLos AngelesCAUSA
- Norris Comprehensive Cancer CenterKeck School of Medicine of University of Southern CaliforniaLos AngelesCAUSA
| | - Veronica Wendy Setiawan
- Department of Preventive MedicineKeck School of Medicine of University of Southern CaliforniaLos AngelesCAUSA
- Center for Genetic EpidemiologyKeck School of MedicineUniversity of Southern CaliforniaLos AngelesCAUSA
- Norris Comprehensive Cancer CenterKeck School of Medicine of University of Southern CaliforniaLos AngelesCAUSA
- Department of MedicineKeck School of Medicine of University of Southern CaliforniaLos AngelesCAUSA
| |
Collapse
|
17
|
Machipisa T, Chong M, Muhamed B, Chishala C, Shaboodien G, Pandie S, de Vries J, Laing N, Joachim A, Daniels R, Ntsekhe M, Hugo-Hamman CT, Gitura B, Ogendo S, Lwabi P, Okello E, Damasceno A, Novela C, Mocumbi AO, Madeira G, Musuku J, Mtaja A, ElSayed A, Elhassan HHM, Bode-Thomas F, Okeahialam BN, Zühlke LJ, Mulder N, Ramesar R, Lesosky M, Parks T, Cordell HJ, Keavney B, Engel ME, Paré G. Association of Novel Locus With Rheumatic Heart Disease in Black African Individuals: Findings From the RHDGen Study. JAMA Cardiol 2021; 6:1000-1011. [PMID: 34106200 PMCID: PMC8190704 DOI: 10.1001/jamacardio.2021.1627] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 03/25/2021] [Indexed: 01/02/2023]
Abstract
Importance Rheumatic heart disease (RHD), a sequela of rheumatic fever characterized by permanent heart valve damage, is the leading cause of cardiac surgery in Africa. However, its pathophysiologic characteristics and genetics are poorly understood. Understanding genetic susceptibility may aid in prevention, control, and interventions to eliminate RHD. Objective To identify common genetic loci associated with RHD susceptibility in Black African individuals. Design, Setting, and Participants This multicenter case-control genome-wide association study (GWAS), the Genetics of Rheumatic Heart Disease, examined more than 7 million genotyped and imputed single-nucleotide variations. The 4809 GWAS participants and 116 independent trio families were enrolled from 8 African countries between December 31, 2012, and March 31, 2018. All GWAS participants and trio probands were screened by use of echocardiography. Data analyses took place from May 15, 2017, until March 14, 2021. Main Outcomes and Measures Genetic associations with RHD. Results This study included 4809 African participants (2548 RHD cases and 2261 controls; 3301 women [69%]; mean [SD] age, 36.5 [16.3] years). The GWAS identified a single RHD risk locus, 11q24.1 (rs1219406 [odds ratio, 1.65; 95% CI, 1.48-1.82; P = 4.36 × 10-8]), which reached genome-wide significance in Black African individuals. Our meta-analysis of Black (n = 3179) and admixed (n = 1055) African individuals revealed several suggestive loci. The study also replicated a previously reported association in Pacific Islander individuals (rs11846409) at the immunoglobulin heavy chain locus, in the meta-analysis of Black and admixed African individuals (odds ratio, 1.16; 95% CI, 1.06-1.27; P = 1.19 × 10-3). The HLA (rs9272622) associations reported in Aboriginal Australian individuals could not be replicated. In support of the known polygenic architecture for RHD, overtransmission of a polygenic risk score from unaffected parents to affected probands was observed (polygenic transmission disequilibrium testing mean [SE], 0.27 [0.16] SDs; P = .04996), and the chip-based heritability was estimated to be high at 0.49 (SE = 0.12; P = 3.28 × 10-5) in Black African individuals. Conclusions and Relevance This study revealed a novel candidate susceptibility locus exclusive to Black African individuals and an important heritable component to RHD susceptibility in African individuals.
Collapse
Affiliation(s)
- Tafadzwa Machipisa
- Department of Medicine, University of Cape Town and Groote Schuur Hospital, Cape Town, South Africa
- Hatter Institute for Cardiovascular Diseases Research in Africa and Cape Heart Institute, Department of Medicine, University of Cape Town, Cape Town, South Africa
- Population Health Research Institute, David Braley Cardiac, Vascular and Stroke Research Institute, Hamilton, Ontario, Canada
- Thrombosis and Atherosclerosis Research Institute, David Braley Cardiac, Vascular and Stroke Research Institute, Hamilton, Ontario, Canada
- Department of Pathology and Molecular Medicine, McMaster University, Michael G. DeGroote School of Medicine, Hamilton, Ontario, Canada
| | - Michael Chong
- Population Health Research Institute, David Braley Cardiac, Vascular and Stroke Research Institute, Hamilton, Ontario, Canada
- Thrombosis and Atherosclerosis Research Institute, David Braley Cardiac, Vascular and Stroke Research Institute, Hamilton, Ontario, Canada
- Department of Pathology and Molecular Medicine, McMaster University, Michael G. DeGroote School of Medicine, Hamilton, Ontario, Canada
| | - Babu Muhamed
- Department of Medicine, University of Cape Town and Groote Schuur Hospital, Cape Town, South Africa
- Hatter Institute for Cardiovascular Diseases Research in Africa and Cape Heart Institute, Department of Medicine, University of Cape Town, Cape Town, South Africa
- Population Health Research Institute, David Braley Cardiac, Vascular and Stroke Research Institute, Hamilton, Ontario, Canada
- Thrombosis and Atherosclerosis Research Institute, David Braley Cardiac, Vascular and Stroke Research Institute, Hamilton, Ontario, Canada
- Department of Pathology and Molecular Medicine, McMaster University, Michael G. DeGroote School of Medicine, Hamilton, Ontario, Canada
| | - Chishala Chishala
- Department of Medicine, University of Cape Town and Groote Schuur Hospital, Cape Town, South Africa
- Hatter Institute for Cardiovascular Diseases Research in Africa and Cape Heart Institute, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Gasnat Shaboodien
- Department of Medicine, University of Cape Town and Groote Schuur Hospital, Cape Town, South Africa
- Hatter Institute for Cardiovascular Diseases Research in Africa and Cape Heart Institute, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Shahiemah Pandie
- Department of Medicine, University of Cape Town and Groote Schuur Hospital, Cape Town, South Africa
| | - Jantina de Vries
- Department of Medicine, University of Cape Town and Groote Schuur Hospital, Cape Town, South Africa
| | - Nakita Laing
- Department of Medicine, University of Cape Town and Groote Schuur Hospital, Cape Town, South Africa
| | - Alexia Joachim
- Department of Medicine, University of Cape Town and Groote Schuur Hospital, Cape Town, South Africa
| | - Rezeen Daniels
- Department of Medicine, University of Cape Town and Groote Schuur Hospital, Cape Town, South Africa
| | - Mpiko Ntsekhe
- Department of Medicine, University of Cape Town and Groote Schuur Hospital, Cape Town, South Africa
| | - Christopher T. Hugo-Hamman
- Rheumatic Heart Disease Clinic, Windhoek Central Hospital, Ministry of Health and Social Services, Windhoek, Republic of Namibia
| | - Bernard Gitura
- Cardiology Department of Medicine, Kenyatta National Hospital, University of Nairobi, Nairobi, Kenya
| | - Stephen Ogendo
- Cardiology Department of Medicine, Kenyatta National Hospital, University of Nairobi, Nairobi, Kenya
| | | | | | - Albertino Damasceno
- Faculty of Medicine, Eduardo Mondlane University/Nucleo de Investigaçao, Departamento de Medicina, Hospital Central de Maputo, Maputo, Mozambique
| | - Celia Novela
- Faculty of Medicine, Eduardo Mondlane University/Nucleo de Investigaçao, Departamento de Medicina, Hospital Central de Maputo, Maputo, Mozambique
| | - Ana O. Mocumbi
- Instituto Nacional de Saúde Ministério da Saúde, Maputo, Moçambique
| | - Goeffrey Madeira
- Emergency Department, World Health Organization Mozambique, Maputo, Mozambique
| | - John Musuku
- Department of Paediatrics and Child Health, University Teaching Hospital–Children’s Hospital, University of Zambia, Lusaka, Zambia
| | - Agnes Mtaja
- Department of Paediatrics and Child Health, University Teaching Hospital–Children’s Hospital, University of Zambia, Lusaka, Zambia
| | - Ahmed ElSayed
- Department of Cardiothoracic Surgery, Alshaab Teaching Hospital, Alazhari Health Research Center, Alzaiem Alazhari University, Khartoum, Sudan
| | - Huda H. M. Elhassan
- Department of Cardiothoracic Surgery, Alshaab Teaching Hospital, Alazhari Health Research Center, Alzaiem Alazhari University, Khartoum, Sudan
| | - Fidelia Bode-Thomas
- Department of Paediatrics, Jos University Teaching Hospital and University of Jos, Jos, Plateau State Nigeria
| | - Basil N. Okeahialam
- Department of Paediatrics, Jos University Teaching Hospital and University of Jos, Jos, Plateau State Nigeria
| | - Liesl J. Zühlke
- Department of Medicine, University of Cape Town and Groote Schuur Hospital, Cape Town, South Africa
- Division of Paediatric Cardiology, Department of Paediatrics and Child Health, Red Cross War Memorial Children’s Hospital and University of Cape Town, South Africa
| | - Nicola Mulder
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Raj Ramesar
- Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Maia Lesosky
- Department of Medicine, University of Cape Town and Groote Schuur Hospital, Cape Town, South Africa
| | - Tom Parks
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Heather J. Cordell
- Population Health Sciences Institute, Faculty of Medical Sciences, Newcastle University, International Centre for Life, Newcastle upon Tyne, United Kingdom
| | - Bernard Keavney
- Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine, and Health, The University of Manchester, Manchester, United Kingdom
- Manchester University National Health Service Foundation Trust, Manchester Academic Health Science CentreManchester, United Kingdom
| | - Mark E. Engel
- Department of Medicine, University of Cape Town and Groote Schuur Hospital, Cape Town, South Africa
| | - Guillaume Paré
- Population Health Research Institute, David Braley Cardiac, Vascular and Stroke Research Institute, Hamilton, Ontario, Canada
- Thrombosis and Atherosclerosis Research Institute, David Braley Cardiac, Vascular and Stroke Research Institute, Hamilton, Ontario, Canada
- Department of Pathology and Molecular Medicine, McMaster University, Michael G. DeGroote School of Medicine, Hamilton, Ontario, Canada
- Department of Clinical Epidemiology and Biostatistics, McMaster University, Hamilton Ontario, Canada
| |
Collapse
|
18
|
Sariya S, Felsky D, Reyes-Dumeyer D, Lali R, Lantigua RA, Vardarajan B, Jiménez-Velázquez IZ, Haines JL, Shellenberg GD, Pericak-Vance MA, Paré G, Mayeux R, Tosto G. Polygenic Risk Score for Alzheimer's Disease in Caribbean Hispanics. Ann Neurol 2021; 90:366-376. [PMID: 34038570 PMCID: PMC8435026 DOI: 10.1002/ana.26131] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 05/17/2021] [Accepted: 05/19/2021] [Indexed: 11/07/2022]
Abstract
OBJECTIVE Polygenic risk scores (PRSs) assess the individual genetic propensity to a condition by combining sparse information scattered across genetic loci, often displaying small effect sizes. Most PRSs are constructed in European-ancestry populations, limiting their use in other ethnicities. Here we constructed and validated a PRS for late-onset Alzheimer's Disease (LOAD) in Caribbean Hispanics (CH). METHODS We used a CH discovery (n = 4,312) and independent validation sample (n = 1,850) to construct an ancestry-specific PRS ("CH-PRS") and evaluated its performance alone and with other predictors using the area under curve (AUC) and logistic regression (strength of association with LOAD and statistical significance). We tested if CH-PRS predicted conversion to LOAD in a subsample with longitudinal data (n = 1,239). We also tested the CH-PRS in an independent replication CH cohort (n = 200) and brain autopsy cohort (n = 33). Finally, we tested the effect of ancestry on PRS by using European and African American discovery cohorts to construct alternative PRSs ("EUR-PRS", "AA-PRS"). RESULTS The full model (LOAD ~ CH-PRS + sex + age + APOE-ɛ4), achieved an AUC = 74% (ORCH-PRS = 1.51 95%CI = 1.36-1.68), raising to >75% in APOE-ɛ4 non-carriers. CH-PRS alone achieved an AUC = 72% in the autopsy cohort, raising to AUC = 83% in full model. Higher CH-PRS was significantly associated with clinical LOAD in the replication CH cohort (OR = 1.61, 95%CI = 1.19-2.17) and significantly predicted conversion to LOAD (HR = 1.93, CI = 1.70-2.20) in the longitudinal subsample. EUR-PRS and AA-PRS reached lower prediction accuracy (AUC = 58% and 53%, respectively). INTERPRETATION Enriching diversity in genetic studies is critical to provide an effective PRS in profiling LOAD risk across populations. ANN NEUROL 2021;90:366-376.
Collapse
Affiliation(s)
- Sanjeev Sariya
- Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, College of Physicians and Surgeons, Columbia University, New York, NY
- The Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, New York, NY
- Department of Neurology, College of Physicians and Surgeons, Columbia University and the New York Presbyterian Hospital, New York, NY
| | - Daniel Felsky
- Krembil Centre for Neuroinformatics, Centre for Addiction and Mental Health, Toronto, ON, Canada
| | - Dolly Reyes-Dumeyer
- Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, College of Physicians and Surgeons, Columbia University, New York, NY
- The Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, New York, NY
- Department of Neurology, College of Physicians and Surgeons, Columbia University and the New York Presbyterian Hospital, New York, NY
| | - Ricky Lali
- Population Health Research Institute, McMaster University, Hamilton, ON, Canada
| | - Rafael A. Lantigua
- Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, College of Physicians and Surgeons, Columbia University, New York, NY
- Department of Medicine, College of Physicians and Surgeons, Columbia University, and the New York Presbyterian Hospital, New York, NY
| | - Badri Vardarajan
- Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, College of Physicians and Surgeons, Columbia University, New York, NY
- The Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, New York, NY
- Department of Neurology, College of Physicians and Surgeons, Columbia University and the New York Presbyterian Hospital, New York, NY
| | | | - Jonathan L. Haines
- Department of Population & Quantitative Health SciencesCleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH
| | | | - Margaret A Pericak-Vance
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL
| | - Guillaume Paré
- Population Health Research Institute, McMaster University, Hamilton, ON, Canada
| | - Richard Mayeux
- Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, College of Physicians and Surgeons, Columbia University, New York, NY
- The Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, New York, NY
- Department of Neurology, College of Physicians and Surgeons, Columbia University and the New York Presbyterian Hospital, New York, NY
- Department of Medicine, College of Physicians and Surgeons, Columbia University, and the New York Presbyterian Hospital, New York, NY
- Department of Psychiatry, College of Physicians and Surgeons, Columbia University, New York, NY
| | - Giuseppe Tosto
- Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, College of Physicians and Surgeons, Columbia University, New York, NY
- The Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, New York, NY
- Department of Neurology, College of Physicians and Surgeons, Columbia University and the New York Presbyterian Hospital, New York, NY
| |
Collapse
|
19
|
Liu C, Zeinomar N, Chung WK, Kiryluk K, Gharavi AG, Hripcsak G, Crew KD, Shang N, Khan A, Fasel D, Manolio TA, Jarvik GP, Rowley R, Justice AE, Rahm AK, Fullerton SM, Smoller JW, Larson EB, Crane PK, Dikilitas O, Wiesner GL, Bick AG, Terry MB, Weng C. Generalizability of Polygenic Risk Scores for Breast Cancer Among Women With European, African, and Latinx Ancestry. JAMA Netw Open 2021; 4:e2119084. [PMID: 34347061 PMCID: PMC8339934 DOI: 10.1001/jamanetworkopen.2021.19084] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
IMPORTANCE Multiple polygenic risk scores (PRSs) for breast cancer have been developed from large research consortia; however, their generalizability to diverse clinical settings is unknown. OBJECTIVE To examine the performance of previously developed breast cancer PRSs in a clinical setting for women of European, African, and Latinx ancestry. DESIGN, SETTING, AND PARTICIPANTS This cohort study using the Electronic Medical Records and Genomics (eMERGE) network data set included 39 591 women from 9 contributing medical centers in the US that had electronic medical records (EMR) linked to genotype data. Breast cancer cases and controls were identified through a validated EMR phenotyping algorithm. MAIN OUTCOMES AND MEASURES Multivariable logistic regression was used to assess the association between breast cancer risk and 7 previously developed PRSs, adjusting for age, study site, breast cancer family history, and first 3 ancestry informative principal components. RESULTS This study included 39 591 women: 33 594 with European, 3801 with African, and 2196 with Latinx ancestry. The mean (SD) age at breast cancer diagnosis was 60.7 (13.0), 58.8 (12.5), and 60.1 (13.0) years for women with European, African, and Latinx ancestry, respectively. PRSs derived from women with European ancestry were associated with breast cancer risk in women with European ancestry (highest odds ratio [OR] per 1-SD increase, 1.46; 95% CI, 1.41-1.51), women with Latinx ancestry (highest OR, 1.31; 95% CI, 1.09-1.58), and women with African ancestry (OR, 1.19; 95% CI, 1.05-1.35). For women with European ancestry, this association with breast cancer risk was largest in the extremes of the PRS distribution, with ORs ranging from 2.19 (95% CI, 1.84-2.53) to 2.48 (95% CI, 1.89-3.25) for the 3 different PRSs examined for those in the highest 1% of the PRS compared with those in the middle quantile. Among women with Latinx and African ancestries at the extremes of the PRS distribution, there were no statistically significant associations. CONCLUSIONS AND RELEVANCE This cohort study found that PRS models derived from women with European ancestry for breast cancer risk generalized well for women with European, Latinx, and African ancestries across different clinical settings, although the effect sizes for women with African ancestry were smaller, likely because of differences in risk allele frequencies and linkage disequilibrium patterns. These results highlight the need to improve representation of diverse population groups, particularly women with African ancestry, in genomic research cohorts.
Collapse
Affiliation(s)
- Cong Liu
- Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, New York
| | - Nur Zeinomar
- Department of Epidemiology, Columbia University Irving Medical Center, New York, New York
- Division of Medical Oncology, Rutgers Cancer Institute of New Jersey, Robert Wood Johnson Medical School, New Brunswick, New Jersey
| | - Wendy K. Chung
- Department of Pediatrics, Columbia University Irving Medical Center, New York, New York
| | - Krzysztof Kiryluk
- Department of Medicine, Columbia University Irving Medical Center, New York, New York
| | - Ali G. Gharavi
- Department of Medicine, Columbia University Irving Medical Center, New York, New York
| | - George Hripcsak
- Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, New York
| | - Katherine D. Crew
- Department of Medicine, Columbia University Irving Medical Center, New York, New York
| | - Ning Shang
- Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, New York
| | - Atlas Khan
- Department of Medicine, Columbia University Irving Medical Center, New York, New York
| | - David Fasel
- Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, New York
| | - Teri A. Manolio
- National Human Genome Research Institute, Bethesda, Maryland
| | - Gail P. Jarvik
- Department of Medicine, University of Washington, Seattle
| | - Robb Rowley
- National Human Genome Research Institute, Bethesda, Maryland
| | - Ann E. Justice
- Department of Population Health Sciences, Geisinger, Danville, Pennsylvania
| | - Alanna K. Rahm
- Genomic Medicine Institute, Geisinger, Danville, Pennsylvania
| | | | - Jordan W. Smoller
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Eric B. Larson
- Kaiser Permanente Washington Health Research Institute, Seattle, Washington
| | - Paul K. Crane
- Department of Medicine, University of Washington, Seattle
| | - Ozan Dikilitas
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, Minnesota
| | - Georgia L. Wiesner
- Department of Medicine, Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Alexander G. Bick
- Department of Medicine, Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Mary Beth Terry
- Department of Epidemiology, Columbia University Irving Medical Center, New York, New York
| | - Chunhua Weng
- Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, New York
| |
Collapse
|
20
|
Abstract
AIM The aetiopathogenesis of the multigenic multifactorial endocrinopathy, polycystic ovary syndrome (PCOS) has been explored using linkage, candidate gene and genome-wide association studies. Contradictory reports of replication studies attributed to phenotypic, ethnic and geographic variations are available. In this study, we investigated the association of Han Chinese GWAS polymorphism (rs13429458) in thyroid adenoma-associated gene (THADA) with PCOS susceptibility and its related traits in Indian women. METHODS We genotyped rs13429458 of THADA by direct sequencing and investigated its association with PCOS and its related traits in controls (N = 150) and PCOS women (N = 348). All women were extensively phenotyped in terms of anthropometric, hormonal and metabolic parameters. Association of polymorphism with PCOS risk and its related traits was carried out by regression analysis. RESULTS Genotypic and allele frequencies for rs13429458 were not different between controls and PCOS. Women with PCOS carrying variant allele showed significantly reduced fasting glucose levels, and decreased free and bioavailable testosterone and free androgen index. CONCLUSION To our knowledge, this is the first study to demonstrate that although this polymorphism does not alter PCOS susceptibility, it favorably impacts glucose metabolism and hyperandrogenism in Indian women with PCOS only. This study highlights that genetic predisposition markers for PCOS may differ with ethnicity and phenotypic variations.
Collapse
Affiliation(s)
- Roshan Dadachanji
- Department of Molecular Endocrinology, National Institute for Research in Reproductive Health, Mumbai, India
| | - Divya Sawant
- Department of Molecular Endocrinology, National Institute for Research in Reproductive Health, Mumbai, India
| | - Anushree Patil
- Department of Clinical Research, National Institute for Research in Reproductive Health, Mumbai, India
| | - Srabani Mukherjee
- Department of Molecular Endocrinology, National Institute for Research in Reproductive Health, Mumbai, India
| |
Collapse
|
21
|
Choquet H, Yin J, Jacobson AS, Horton BH, Hoffmann TJ, Jorgenson E, Avins AL, Pressman AR. New and sex-specific migraine susceptibility loci identified from a multiethnic genome-wide meta-analysis. Commun Biol 2021; 4:864. [PMID: 34294844 PMCID: PMC8298472 DOI: 10.1038/s42003-021-02356-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 06/04/2021] [Indexed: 02/06/2023] Open
Abstract
Migraine is a common disabling primary headache disorder that is ranked as the most common neurological cause of disability worldwide. Women present with migraine much more frequently than men, but the reasons for this difference are unknown. Migraine heritability is estimated to up to 57%, yet much of the genetic risk remains unaccounted for, especially in non-European ancestry populations. To elucidate the etiology of this common disorder, we conduct a multiethnic genome-wide association meta-analysis of migraine, combining results from the GERA and UK Biobank cohorts, followed by a European-ancestry meta-analysis using public summary statistics. We report 79 loci associated with migraine, of which 45 were novel. Sex-stratified analyses identify three additional novel loci (CPS1, PBRM1, and SLC25A21) specific to women. This large multiethnic migraine study provides important information that may substantially improve our understanding of the etiology of migraine susceptibility.
Collapse
Affiliation(s)
- Hélène Choquet
- Division of Research, Kaiser Permanente Northern California (KPNC), Oakland, CA, USA.
| | - Jie Yin
- Division of Research, Kaiser Permanente Northern California (KPNC), Oakland, CA, USA
| | | | - Brandon H Horton
- Division of Research, Kaiser Permanente Northern California (KPNC), Oakland, CA, USA
| | - Thomas J Hoffmann
- Institute for Human Genetics, University of California, San Francisco (UCSF), San Francisco, CA, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Eric Jorgenson
- Division of Research, Kaiser Permanente Northern California (KPNC), Oakland, CA, USA
| | - Andrew L Avins
- Division of Research, Kaiser Permanente Northern California (KPNC), Oakland, CA, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Alice R Pressman
- Sutter Health, Walnut Creek, CA, USA.
- Department of Epidemiology and Biostatistics, University of California, San Francisco (UCSF), San Francisco, CA, USA.
| |
Collapse
|
22
|
Xia H, Huang X, Deng S, Xu H, Yang Y, Liu X, Yuan L, Deng H. DNAH11 compound heterozygous variants cause heterotaxy and congenital heart disease. PLoS One 2021; 16:e0252786. [PMID: 34133440 PMCID: PMC8208527 DOI: 10.1371/journal.pone.0252786] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 05/21/2021] [Indexed: 12/16/2022] Open
Abstract
Heterotaxy (HTX), a condition characterized by internal organs not being arranged as expected relative to each other and to the left-right axis, is often accompanied with congenital heart disease (CHD). The purpose was to detect the pathogenic variants in a Chinese family with HTX and CHD. A non-consanguineous Han Chinese family with HTX and CHD, and 200 unrelated healthy subjects were enlisted. Exome sequencing and Sanger sequencing were applied to identify the genetic basis of the HTX family. Compound heterozygous variants, c.3426-1G>A and c.4306C>T (p.(Arg1436Trp)), in the dynein axonemal heavy chain 11 gene (DNAH11) were identified in the proband via exome sequencing and further confirmed by Sanger sequencing. Neither c.3426-1G>A nor c.4306C>T variant in the DNAH11 gene was detected in 200 healthy controls. The DNAH11 c.3426-1G>A variant was predicted as altering the acceptor splice site and most likely affecting splicing. The DNAH11 c.4306C>T variant was predicted to be damaging, which may reduce the phenotype severity. The compound heterozygous variants, c.3426-1G>A and c.4306C>T, in the DNAH11 gene might be the pathogenic alterations resulting in HTX and CHD in this family. These findings broaden the variant spectrum of the DNAH11 gene and increase knowledge used in genetic counseling for the HTX family.
Collapse
Affiliation(s)
- Hong Xia
- Center for Experimental Medicine, the Third Xiangya Hospital, Central South University, Changsha, Hunan, China
- Department of Emergency, the Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Xiangjun Huang
- Department of General Surgery, The First Affiliated Hospital of Hunan University of Chinese Medicine, Changsha, Hunan, China
| | - Sheng Deng
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Hongbo Xu
- Center for Experimental Medicine, the Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yan Yang
- Department of Neurology, the Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Xin Liu
- Center for Experimental Medicine, the Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Lamei Yuan
- Center for Experimental Medicine, the Third Xiangya Hospital, Central South University, Changsha, Hunan, China
- * E-mail: (HD); (LY)
| | - Hao Deng
- Center for Experimental Medicine, the Third Xiangya Hospital, Central South University, Changsha, Hunan, China
- * E-mail: (HD); (LY)
| |
Collapse
|
23
|
Jee D, Park S. Hyperglycemia and Hypo-HDL-cholesterolemia Are Primary Risk Factors for Age-related Cataract, and a Korean-style Balanced Diet has a Negative Association, based on the Korean Genome and Epidemiology Study. J Korean Med Sci 2021; 36:e155. [PMID: 34128595 PMCID: PMC8203849 DOI: 10.3346/jkms.2021.36.e155] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 05/10/2021] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND The prevalence of cataracts is steadily increasing among the middle-aged and elderly worldwide. We hypothesized that adults aged > 50 years with age-related cataracts (ARCs) have an association with metabolic syndrome (MS) and its components, and MS has interactions with different dietary patterns and lifestyles that affect ARC risk. We examined the hypothesis using the Korean Genome and Epidemiology Study (KoGES; a large-scale hospital-based cohort study), which collected data between 2004-2013. METHODS Participants ≥ 50 years old were classified as cases (1,972 ARC patients) and controls (38,290 healthy controls) based on a diagnosis of cataract by a physician. MS and its components were defined using WHO definitions for Asians. Dietary consumption was evaluated using a validated semi-quantitative food frequency questionnaire (SQFFQ), which contained 106 foods, and dietary patterns were analyzed by principal component analysis. After adjusting for potential covariates, logistic regression was used to investigate associations between MS and its components and between dietary patterns and a positive cataract history. RESULTS ARC had a positive association with MS after 1.32-fold adjusting for age, sex, residence area, body mass index, and energy intake. Plasma glucose and HbA1c concentrations exhibited an increased ARC risk in the participants with MS by 1.50- and 1.92-fold and without MS by 1.35 and 1.88-fold, respectively. Serum high-density lipoprotein (HDL) concentrations were negatively associated with ARC risk only in the MS patients, but not without MS. However, blood pressure, abdominal obesity, and serum triglyceride concentrations did not associate with ARC risk regardless of MS. High intake of a Korean-balanced diet (KBD) containing fermented food exhibited a negative association with ARC risk (OR = 0.81) only in the MS group. The fat and coffee intake had a negative association with ARC only in the non-MS group. Current- and former-smokers were positively associated with ARC risk. CONCLUSION Persons who have hyperglycemia and low-HDL-cholesterolemia had increased susceptibility of ARC prevalence. A KBD with a proper amount of fat (≥ 15%) is recommended, and smoking should be prohibited.
Collapse
Affiliation(s)
- Donghyun Jee
- Division of Vitreous and Retina, Department of Ophthalmology, St. Vincent's Hospital, College of Medicine, The Catholic University of Korea, Suwon, Korea
| | - Sunmin Park
- Food and Nutrition, Obesity/Diabetes Research Center, Hoseo University, Asan, Korea.
| |
Collapse
|
24
|
Asselta R, Paraboschi EM, Gerussi A, Cordell HJ, Mells GF, Sandford RN, Jones DE, Nakamura M, Ueno K, Hitomi Y, Kawashima M, Nishida N, Tokunaga K, Nagasaki M, Tanaka A, Tang R, Li Z, Shi Y, Liu X, Xiong M, Hirschfield G, Siminovitch KA, Carbone M, Cardamone G, Duga S, Gershwin ME, Seldin MF, Invernizzi P. X Chromosome Contribution to the Genetic Architecture of Primary Biliary Cholangitis. Gastroenterology 2021; 160:2483-2495.e26. [PMID: 33675743 PMCID: PMC8169555 DOI: 10.1053/j.gastro.2021.02.061] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [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: 03/29/2020] [Revised: 02/15/2021] [Accepted: 02/25/2021] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS Genome-wide association studies in primary biliary cholangitis (PBC) have failed to find X chromosome (chrX) variants associated with the disease. Here, we specifically explore the chrX contribution to PBC, a sexually dimorphic complex autoimmune disease. METHODS We performed a chrX-wide association study, including genotype data from 5 genome-wide association studies (from Italy, United Kingdom, Canada, China, and Japan; 5244 case patients and 11,875 control individuals). RESULTS Single-marker association analyses found approximately 100 loci displaying P < 5 × 10-4, with the most significant being a signal within the OTUD5 gene (rs3027490; P = 4.80 × 10-6; odds ratio [OR], 1.39; 95% confidence interval [CI], 1.028-1.88; Japanese cohort). Although the transethnic meta-analysis evidenced only a suggestive signal (rs2239452, mapping within the PIM2 gene; OR, 1.17; 95% CI, 1.09-1.26; P = 9.93 × 10-8), the population-specific meta-analysis showed a genome-wide significant locus in East Asian individuals pointing to the same region (rs7059064, mapping within the GRIPAP1 gene; P = 6.2 × 10-9; OR, 1.33; 95% CI, 1.21-1.46). Indeed, rs7059064 tags a unique linkage disequilibrium block including 7 genes: TIMM17B, PQBP1, PIM2, SLC35A2, OTUD5, KCND1, and GRIPAP1, as well as a superenhancer (GH0XJ048933 within OTUD5) targeting all these genes. GH0XJ048933 is also predicted to target FOXP3, the main T-regulatory cell lineage specification factor. Consistently, OTUD5 and FOXP3 RNA levels were up-regulated in PBC case patients (1.75- and 1.64-fold, respectively). CONCLUSIONS This work represents the first comprehensive study, to our knowledge, of the chrX contribution to the genetics of an autoimmune liver disease and shows a novel PBC-related genome-wide significant locus.
Collapse
Affiliation(s)
- Rosanna Asselta
- Department of Biomedical Sciences, Humanitas University, Milan, Italy; IRCCS Humanitas Research Hospital, Milan, Italy
| | - Elvezia M Paraboschi
- Department of Biomedical Sciences, Humanitas University, Milan, Italy; IRCCS Humanitas Research Hospital, Milan, Italy
| | - Alessio Gerussi
- Division of Gastroenterology and Center for Autoimmune Liver Diseases, Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy; European Reference Network on Hepatological Diseases, San Gerardo Hospital, Monza, Italy
| | - Heather J Cordell
- Population Health Sciences Institute, Faculty of Medical Sciences, Newcastle University, United Kingdom
| | - George F Mells
- Academic Department of Medical Genetics, Cambridge University, Cambridge, United Kingdom
| | - Richard N Sandford
- Academic Department of Medical Genetics, Cambridge University, Cambridge, United Kingdom
| | - David E Jones
- Faculty of Medical Sciences, Newcastle University, Newcastle, United Kingdom
| | - Minoru Nakamura
- Clinical Research Center, National Hospital Organization, Nagasaki Medical Center, Nagasaki, Japan; Department of Hepatology, Nagasaki University Graduate School of Biomedical Sciences, Omura, Nagasaki, Japan
| | - Kazuko Ueno
- Genome Medical Science Project, National Center for Global Health and Medicine, Tokyo, Japan
| | - Yuki Hitomi
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Minae Kawashima
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Nao Nishida
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Katsushi Tokunaga
- Genome Medical Science Project, National Center for Global Health and Medicine, Tokyo, Japan; Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Masao Nagasaki
- Human Biosciences Unit for the Top Global Course Center for the Promotion of Interdisciplinary Education and Research, Kyoto University, Kyoto, Japan; Center for Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Atsushi Tanaka
- Department of Medicine, Teikyo University School of Medicine, Tokyo, Japan
| | - Ruqi Tang
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai, China
| | - Zhiqiang Li
- Affiliated Hospital of Qingdao University and Biomedical Sciences Institute of Qingdao University (Qingdao Branch of SJTU Bio-X Institutes), Qingdao University, Qingdao, China; Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, China
| | - Yongyong Shi
- Affiliated Hospital of Qingdao University and Biomedical Sciences Institute of Qingdao University (Qingdao Branch of SJTU Bio-X Institutes), Qingdao University, Qingdao, China; Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, China
| | - Xiangdong Liu
- Key Laboratory of Developmental Genes and Human Diseases, Institute of Life Sciences, Southeast University, Nanjing, Jiangsu, China
| | - Ma Xiong
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai, China
| | - Gideon Hirschfield
- Toronto General Hospital Research Institute, Toronto, Ontario, Canada; Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Katherine A Siminovitch
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada; Mount Sinai Hospital, Lunenfeld Tanenbaum Research Institute and Toronto General Research Institute, Toronto, Canada; Department of Immunology, University of Toronto, Toronto, Ontario, Canada; Institute of Medical Sciences, University of Toronto, Toronto, Ontario, Canada
| | - Marco Carbone
- Division of Gastroenterology and Center for Autoimmune Liver Diseases, Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy; European Reference Network on Hepatological Diseases, San Gerardo Hospital, Monza, Italy
| | - Giulia Cardamone
- Department of Biomedical Sciences, Humanitas University, Milan, Italy; IRCCS Humanitas Research Hospital, Milan, Italy
| | - Stefano Duga
- Department of Biomedical Sciences, Humanitas University, Milan, Italy; IRCCS Humanitas Research Hospital, Milan, Italy
| | | | | | - Pietro Invernizzi
- Division of Gastroenterology and Center for Autoimmune Liver Diseases, Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy; European Reference Network on Hepatological Diseases, San Gerardo Hospital, Monza, Italy.
| |
Collapse
|
25
|
Tan GX, Jiang L, Li GQ, Bai K. Evaluation of association between methylenetetrahydrofolate reductase and azoospermia: A meta-analysis. Medicine (Baltimore) 2021; 100:e24523. [PMID: 33847607 PMCID: PMC8051989 DOI: 10.1097/md.0000000000024523] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 11/19/2020] [Accepted: 01/08/2021] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Infertility affects childbearing age couples all over the world. One of the important reasons for infertility is genetic factors. Our study evaluated the association between methylenetetrahydrofolate reductase (MTHFR) and azoospermia. METHODS Multiple databases like MEDLINE, EMBASE, Cochrane library, and China journal full-text database were used to search for relevant studies, and full-text articles involved in the evaluation of MTHFR and azoospermia. The results were evaluated using STATA 12.0. Heterogeneity analysis, sensitivity analysis, and bias analysis were also performed on the data. RESULTS Thirteen related studies eventually met the inclusion criteria. Significant association between C677T polymorphism and azoospermia (relative risk [RR] = 0.94 [0.90, 0.99], I2 = 60.9%, P = .002), and between A1298C polymorphism and azoospermia (RR = 0.98 [0.94, 1.02], I2 = 56.3%, P = .011) was observed. Meanwhile, in subgroup analysis, Caucasians had higher risk than Mongolians in association between MTHFR and azoospermia. CONCLUSION There was association between MTHFR polymorphism and azoospermia. Caucasian populations had higher risk than Mongolian populations in association between MTHFR and azoospermia.
Collapse
|
26
|
Wu Z, Chen H, Pan L, Yu W, Lou C, Chen J, He D. Effect of TIMP2/TIMP3 genes on the risk of osteosarcoma in Zhejiang population. Medicine (Baltimore) 2021; 100:e24818. [PMID: 33725949 PMCID: PMC7982212 DOI: 10.1097/md.0000000000024818] [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] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 01/28/2021] [Indexed: 01/05/2023] Open
Abstract
Osteosarcoma is a malignant tumor that develops from a mesenchymal cell line and is caused by gene-environment interactions. This study aimed to explore whether TIMP2/TIMP3 polymorphisms influenced the osteosarcoma risk.The expression of the TIMP2 and TIMP3 genes in osteosarcoma histiocytes was analyzed by immunohistochemistry. In this case-control study, which includes samples from 499 patients and 500 healthy controls, 10 single-nucleotide polymorphisms (SNPs) in TIMP2 and TIMP3 were selected. Furthermore, we used the Agena MassARRAY platform for genotyping. The statistical analysis was performed using χ2 test/Fisher exact test, and logistic regression analysis.The immunohistochemistry results showed that the expression of TIMP2 is obvious higher in osteosarcoma histiocytes than in the normal histiocytes. The association study indicated that the allele of rs2277698 and rs4789936 were protective SNPs reducing the risk of osteosarcoma (odds ratios > 1, P < .05) by the χ2 test. In the genetic model, logistic regression analyses revealed that the rs2277698 and rs4789936 were associated with decreasing the risk of osteosarcoma under the codominant model, dominant model, and log-additive model. Stratification analysis revealed that 2 SNPs (rs2277698 and rs4789936) were significantly associated with a reduced risk of osteosarcoma in allele and genetic model after stratification by gender or age (P < .05). In addition, the haplotype "Trs2277698Crs2009169Crs7342880" of TIMP2 was associated with decreasing the osteosarcoma risk. The "Ars9609634Trs11547635" of TIMP3 was associated with reducing the osteosarcoma risk.This finding shed new light on the high expression of TIMP2 polymorphisms may contribute to decreasing the osteosarcoma risk in Zhejiang populations.
Collapse
Affiliation(s)
- Zhongwei Wu
- Spinal Surgery Department, The Central Hospital of Lishui City
| | - Huali Chen
- Orthopaedics Department, Lishui City People's Hospital, Lishui
| | - Liwei Pan
- Spinal Surgery Department, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Weiyang Yu
- Spinal Surgery Department, The Central Hospital of Lishui City
| | - Chao Lou
- Spinal Surgery Department, The Central Hospital of Lishui City
| | - Jian Chen
- Spinal Surgery Department, The Central Hospital of Lishui City
| | - Dengwei He
- Spinal Surgery Department, The Central Hospital of Lishui City
| |
Collapse
|
27
|
Wang Q, Zhao J, Chang H, Liu X, Zhu R. Association between lncRNA ANRIL genetic variants with the susceptibility to ischemic stroke: From a case-control study to meta-analysis. Medicine (Baltimore) 2021; 100:e25113. [PMID: 33725991 PMCID: PMC7982178 DOI: 10.1097/md.0000000000025113] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 01/18/2021] [Accepted: 02/17/2021] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Recent studies have reported that lncRNA (long noncoding RNAs) antisense non-coding RNA in the INK4 locus (ANRIL) plays important roles in the development of atherosclerosis through regulating cell apoptosis, proliferation, and adhesion. GWAS (genome-wide association studies) identified common genetic variants within ANRIL could confer risk of ischemic stroke (IS) in southern Sweden. METHODS We performed a case-control study, including 567 IS patients and 552 healthy controls from unrelated northern Chinese Han population, aiming to explore the association between lncRNA ANRIL rs2383207, rs4977574 polymorphisms and the risk of IS. Subsequently we implemented a meta-analysis to further assess the relationship of these variants and the disease. RESULTS In our case-control study, no significant associations were observed in all models between above 2 polymorphisms and IS. Next in our subgroup analysis, we detected significant association between GA genotype of rs4977574 and the increased risk of LAA-IS (large-artery atherosclerotic ischemic stroke), similar elevated risk also appeared in the GG + GA genotype under the dominant model (P = .048, OR = 1.385, 95% CIs 1.002-1.914; P = .040, OR = 1.378, 95% CIs 1.015-1.872, respectively). As for rs2383207, negative results were obtained under all models and subgroups. Our meta-analysis showed a significant association between rs4977574 polymorphism and IS risk in allele model (G vs A P = .002, OR = 1.137, 95% CIs 1.048-1.234); with respect to rs2383207 polymorphism, no significant association between that and the risk of IS was detected under the dominant model (GA + AA vs GG, P = .061, OR = 0.923, 95% CIs 0.849-1.004), or recessive model (AA vs GA + GG, P = .656, OR = 0.972, 95% CIs 0.858-1.101), or allele model (A vs G, P = .326, OR = 0.952, 95% CIs 0.863-1.050). Likewise, no significant association between rs2383207 and IS was found in different stoke subtypes (P > .05). CONCLUSIONS Our findings indicated G allele of lncRNA ANRIL rs4977574 could increase the risk of IS, and the variant may be associated with susceptibility to LAA-IS in Chinese Han population.
Collapse
|
28
|
Marozik P, Rudenka A, Kobets K, Rudenka E. Vitamin D Status, Bone Mineral Density, and VDR Gene Polymorphism in a Cohort of Belarusian Postmenopausal Women. Nutrients 2021; 13:nu13030837. [PMID: 33806559 PMCID: PMC7999336 DOI: 10.3390/nu13030837] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 02/16/2021] [Accepted: 02/17/2021] [Indexed: 01/18/2023] Open
Abstract
Vitamin D plays an important role in bone metabolism and is important for the prevention of multifactorial pathologies, including osteoporosis (OP). The biological action of vitamin is realized through its receptor, which is coded by the VDR gene. VDR gene polymorphism can influence individual predisposition to OP and response to vitamin D supplementation. The aim of this work was to reveal the effects of VDR gene ApaI rs7975232, BsmI rs1544410, TaqI rs731236, FokI rs2228570, and Cdx2 rs11568820 variants on bone mineral density (BMD), 25-hydroxyvitamin D level, and OP risk in Belarusian women. Methods. The case group included 355 women with postmenopausal OP, and the control group comprised 247 women who met the inclusion criteria. TaqMan genotyping assay was used to determine VDR gene variants. Results. Rs7975232 A/A, rs1544410 T/T, and rs731236 G/G single variants and their A-T-G haplotype showed a significant association with increased OP risk (for A-T-G, OR = 1.8, p = 0.0001) and decreased BMD (A-T-G, −0.09 g/cm2, p = 0.0001). The rs11568820 A-allele showed a protective effect on BMD (+0.22 g/cm2, p = 0.027). A significant dose effect with 25(OH)D was found for rs1544410, rs731236, and rs11568820 genotypes. Rs731236 A/A was associated with the 25(OH)D deficiency state. Conclusion. Our novel data on the relationship between VDR gene variants and BMD, 25(OH)D level, and OP risk highlights the importance of genetic markers for personalized medicine strategy.
Collapse
Affiliation(s)
- Pavel Marozik
- Laboratory of Human Genetics, Institute of Genetics and Cytology of the National Academy of Sciences of Belarus, 220072 Minsk, Belarus;
- Department of General Biology and Genetics, International Sakharov Environmental Institute of the Belarusian State University, 220070 Minsk, Belarus
- Correspondence: ; Tel.: +375-17-364-1614
| | - Alena Rudenka
- Department of Cardiology and Rheumatology, Belarusian Medical Academy of Post-Graduate Education, 220013 Minsk, Belarus;
| | - Katsiaryna Kobets
- Laboratory of Human Genetics, Institute of Genetics and Cytology of the National Academy of Sciences of Belarus, 220072 Minsk, Belarus;
| | - Ema Rudenka
- Department of Cardiology and Internal Diseases, Belarusian State Medical University, 220116 Minsk, Belarus;
| |
Collapse
|
29
|
Wang YF, Zhang Y, Lin Z, Zhang H, Wang TY, Cao Y, Morris DL, Sheng Y, Yin X, Zhong SL, Gu X, Lei Y, He J, Wu Q, Shen JJ, Yang J, Lam TH, Lin JH, Mai ZM, Guo M, Tang Y, Chen Y, Song Q, Ban B, Mok CC, Cui Y, Lu L, Shen N, Sham PC, Lau CS, Smith DK, Vyse TJ, Zhang X, Lau YL, Yang W. Identification of 38 novel loci for systemic lupus erythematosus and genetic heterogeneity between ancestral groups. Nat Commun 2021; 12:772. [PMID: 33536424 PMCID: PMC7858632 DOI: 10.1038/s41467-021-21049-y] [Citation(s) in RCA: 110] [Impact Index Per Article: 36.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Accepted: 01/11/2021] [Indexed: 02/07/2023] Open
Abstract
Systemic lupus erythematosus (SLE), a worldwide autoimmune disease with high heritability, shows differences in prevalence, severity and age of onset among different ancestral groups. Previous genetic studies have focused more on European populations, which appear to be the least affected. Consequently, the genetic variations that underlie the commonalities, differences and treatment options in SLE among ancestral groups have not been well elucidated. To address this, we undertake a genome-wide association study, increasing the sample size of Chinese populations to the level of existing European studies. Thirty-eight novel SLE-associated loci and incomplete sharing of genetic architecture are identified. In addition to the human leukocyte antigen (HLA) region, nine disease loci show clear ancestral differences and implicate antibody production as a potential mechanism for differences in disease manifestation. Polygenic risk scores perform significantly better when trained on ancestry-matched data sets. These analyses help to reveal the genetic basis for disparities in SLE among ancestral groups.
Collapse
Affiliation(s)
- Yong-Fei Wang
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
| | - Yan Zhang
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Zhiming Lin
- Department of Rheumatology, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Huoru Zhang
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
| | - Ting-You Wang
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
- The Hormel Institute, University of Minnesota, Austin, USA
| | - Yujie Cao
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
| | - David L Morris
- Division of Genetics and Molecular Medicine, King's College London, London, UK
| | - Yujun Sheng
- Department of Dermatology, No.1 Hospital, Anhui Medical University, Hefei, China
| | - Xianyong Yin
- Department of Dermatology, No.1 Hospital, Anhui Medical University, Hefei, China
| | - Shi-Long Zhong
- Guangdong Provincial Key Laboratory of Coronary Heart Disease Prevention, Guangdong Provincial People's Hospital, Guangzhou, China
| | - Xiaoqiong Gu
- Department of Clinical Biological Resource Bank, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou, China
| | - Yao Lei
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
| | - Jing He
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Qi Wu
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Jiangshan Jane Shen
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
| | - Jing Yang
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
| | - Tai-Hing Lam
- School of Public Health, The University of Hong Kong, Hong Kong, China
| | - Jia-Huang Lin
- School of Public Health, The University of Hong Kong, Hong Kong, China
| | - Zhi-Ming Mai
- School of Public Health, The University of Hong Kong, Hong Kong, China
- Radiation Epidemiology Branch, Division of Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, USA
| | - Mengbiao Guo
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
| | - Yuanjia Tang
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yanhui Chen
- Department of Pediatrics, Union Hospital Affiliated to Fujian Medical University, Fuzhou, China
| | - Qin Song
- Department of Rheumatology, Affiliated Hospital of Jining Medical University, Jining, China
| | - Bo Ban
- Department of Endocrinology, Affiliated Hospital of Jining Medical University, Jining, China
| | - Chi Chiu Mok
- Department of Medicine, Tuen Mun Hospital, Hong Kong, China
| | - Yong Cui
- Department of Dermatology, China-Japan Friendship Hospital, Chaoyang, China
| | - Liangjing Lu
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Nan Shen
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Pak C Sham
- Department of Psychiatry, The University of Hong Kong, Hong Kong, China
| | - Chak Sing Lau
- Department of Medicine, The University of Hong Kong, Hong Kong, China
| | - David K Smith
- School of Public Health, The University of Hong Kong, Hong Kong, China
| | - Timothy J Vyse
- Division of Genetics and Molecular Medicine, King's College London, London, UK
| | - Xuejun Zhang
- Department of Dermatology, No.1 Hospital, Anhui Medical University, Hefei, China
| | - Yu Lung Lau
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China.
| | - Wanling Yang
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China.
- Shenzhen Institute of Research and Innovation, The University of Hong Kong, Hong Kong, China.
| |
Collapse
|
30
|
Actkins KV, Singh K, Hucks D, Velez Edwards DR, Aldrich M, Cha J, Wellons M, Davis LK. Characterizing the Clinical and Genetic Spectrum of Polycystic Ovary Syndrome in Electronic Health Records. J Clin Endocrinol Metab 2021; 106:153-167. [PMID: 32961557 PMCID: PMC7765638 DOI: 10.1210/clinem/dgaa675] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [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: 04/17/2020] [Accepted: 09/19/2020] [Indexed: 02/08/2023]
Abstract
CONTEXT Polycystic ovary syndrome (PCOS) is one of the leading causes of infertility, yet current diagnostic criteria are ineffective at identifying patients whose symptoms reside outside strict diagnostic criteria. As a result, PCOS is underdiagnosed and its etiology is poorly understood. OBJECTIVE We aim to characterize the phenotypic spectrum of PCOS clinical features within and across racial and ethnic groups. METHODS We developed a strictly defined PCOS algorithm (PCOSkeyword-strict) using the International Classification of Diseases, ninth and tenth revisions and keywords mined from clinical notes in electronic health records (EHRs) data. We then systematically relaxed the inclusion criteria to evaluate the change in epidemiological and genetic associations resulting in 3 subsequent algorithms (PCOScoded-broad, PCOScoded-strict, and PCOSkeyword-broad). We evaluated the performance of each phenotyping approach and characterized prominent clinical features observed in racially and ethnically diverse PCOS patients. RESULTS The best performance came from the PCOScoded-strict algorithm, with a positive predictive value of 98%. Individuals classified as cases by this algorithm had significantly higher body mass index (BMI), insulin levels, free testosterone values, and genetic risk scores for PCOS, compared to controls. Median BMI was higher in African American females with PCOS compared to White and Hispanic females with PCOS. CONCLUSIONS PCOS symptoms are observed across a severity spectrum that parallels the continuous genetic liability to PCOS in the general population. Racial and ethnic group differences exist in PCOS symptomology and metabolic health across different phenotyping strategies.
Collapse
Affiliation(s)
- Ky’Era V Actkins
- Department of Microbiology, Immunology, and Physiology, Meharry Medical College, Nashville, Tennessee
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Kritika Singh
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Donald Hucks
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Digna R Velez Edwards
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee
- Vanderbilt Epidemiology Center, Institute of Medicine and Public Health, Vanderbilt University Medical Center, Nashville, Tennessee
- Division of Quantitative Sciences, Department of Obstetrics and Gynecology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Melinda Aldrich
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
- Department of Thoracic Surgery, Vanderbilt University Medical Center, Nashville, Tennessee
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Jeeyeon Cha
- Division of Diabetes, Endocrinology, and Metabolism, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Melissa Wellons
- Division of Diabetes, Endocrinology, and Metabolism, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Lea K Davis
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee
| |
Collapse
|
31
|
Yang Y, Zhang Y, Ren M, Wang Y, Cairang Z, Lin R, Sun H, Liu J. Association of cytochrome P450 2C19 polymorphisms with coronary heart disease risk: A protocol for systematic review and meta analysis. Medicine (Baltimore) 2020; 99:e23652. [PMID: 33327349 PMCID: PMC7738024 DOI: 10.1097/md.0000000000023652] [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] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Polymorphisms in the cytochrome P450 2C19 (CYP2C19) gene have been reported to be associated with coronary heart disease (CHD), but the results were not consistently analyzed among different patient groups. To derive a more precise estimation of these associations, we will conduct a meta-analysis to investigate the polymorphisms of CYP2C19 in all published studies. METHODS Electronic databases (Google Scholar, ISI Web of Science, Pubmed, Embase, China National Knowledge Infrastructure, Wanfang, and China Biological Medicine) will be used to search clinical case-control or cohort studies about CYP2C19 polymorphism and CHD published until November 2020. Two reviewers will independently select the study, extract the data, and evaluate the quality of the study. Odds ratios with 95% confidence interval will be used to evaluate the strength of the association between the CYP2C19 polymorphism and CHD susceptibility under 4 genetic models. Subgroup analysis will be conducted by different ethnicity and genotyping method. Sensitivity analysis will be performed via sequentially omitting each of the included studies 1 at a time. Begg funnel plots and Egger test will be used to examine the potential publication bias. All the statistical analyses will be performed using Review Manager 5.3 and Stata 12.0. RESULTS This study will provide a better understanding of the association between CYP2C19 polymorphisms and coronary heart disease risk. CONCLUSION The publication of this protocol will minimize the possibility of bias due to post hoc changes to the analysis protocol, thus helping to obtain reliable evidence. OSF REGISTRATION NUMBER DOI 10.17605/OSF.IO/R7U93.
Collapse
Affiliation(s)
- Yongxin Yang
- Department of Cardiology, The People's Hospital of Qinghai Province
| | - Yaping Zhang
- Department of Cardiology, The People's Hospital of Qinghai Province
| | - Ming Ren
- Department of Cardiology, Qinghai University Affiliated Hospital
| | - Yonglan Wang
- Department of Cardiology, The People's Hospital of Qinghai Province
| | - Zhuoma Cairang
- Department of Cardiology, The People's Hospital of Qinghai Province
| | - Rongxiang Lin
- Department of Cardiology, The People's Hospital of Qinghai Province
| | - Haixia Sun
- Echocardiography Room, The People's Hospital of Qinghai Province, Xining, China
| | - Jianju Liu
- Department of Cardiology, The People's Hospital of Qinghai Province
| |
Collapse
|
32
|
Zhao X, Chen Y, Wang L, Li X, Chen X, Zhang H. Associations of ATG7 rs1375206 polymorphism and elevated plasma ATG7 levels with late-onset sporadic Parkinson's disease in a cohort of Han Chinese from southern China. Int J Neurosci 2020; 130:1206-1214. [PMID: 32065549 DOI: 10.1080/00207454.2020.1731507] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [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: 02/14/2019] [Revised: 01/25/2020] [Accepted: 02/09/2020] [Indexed: 10/25/2022]
Abstract
Background: Autophagy-related gene 7 (ATG7) plays a key role in autophagy and is strongly implicated in Parkinson's disease (PD). This study investigated the associations of rs1375206 polymorphism in ATG7 gene promoter and plasma ATG7 levels with late-onset sporadic PD in a cohort of Han Chinese from southern China.Methods: Variant genotypes were identified using polymerase chain reaction-restriction fragment length polymorphism and gene sequencing in 124 patients with late-onset sporadic PD, as well as in 105 age- and sex-matched healthy controls. Plasma ATG7 levels were determined using an enzyme-linked immunosorbent assay.Results: No significant differences in genotype distributions were found between the two groups. Stratification analyses by sex and clinical motor subtypes revealed that the differences remained non-significant in each subgroup (all p > 0.05). Plasma ATG7 protein levels were significantly higher in the PD group than in the control group (p = 0.000). Haplotype analysis demonstrated that the A-T haplotype was significantly associated with late-onset sporadic PD (p = 0.045).Conclusion: Our study suggests that the rs1375206 polymorphism in ATG7 may not be associated with late-onset sporadic PD; however, high plasma ATG7 levels and the A-T haplotype may be associated with susceptibility to late-onset sporadic PD in the Han population from Zhejiang and Guangdong provinces.
Collapse
Affiliation(s)
- Xiyao Zhao
- Department of Neurology, The Second Affiliated Hospital (Jiande Branch), School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China
| | - Yusen Chen
- Department of Neurology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong Province, China
| | - Li Wang
- Department of Neurology, The Second Affiliated Hospital (Jiande Branch), School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China
| | - Xiangxin Li
- Department of Neurology, The Second Affiliated Hospital (Jiande Branch), School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China
| | - Xiaoyi Chen
- Department of Neurology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong Province, China
| | - Hao Zhang
- Department of Neurology, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
| |
Collapse
|
33
|
Yan L, Wang H, Liu P, Wang M, Chen J, Zhao X. Association between the A46G polymorphism (rs1042713) in the β2-adrenergic receptor gene and essential hypertension susceptibility in the Chinese population: A PRISMA-compliant meta-analysis. Medicine (Baltimore) 2020; 99:e23164. [PMID: 33181690 PMCID: PMC7668484 DOI: 10.1097/md.0000000000023164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Recently, many studies have been conducted to investigate the relationship between the A46G polymorphism in the β2-adrenergic receptor (ADRB2) gene and essential hypertension risk in the Chinese population. However, the results of previous studies were conflicting. OBJECTIVES The present study aimed to investigate the association between the ADRB2 A46G polymorphism and the risk of essential hypertension in the Chinese population. METHODS We performed a systematic search of possible relevant studies on PubMed, Embase, Ovid, Web of Science, China National Knowledge Infrastructure, Wanfang, and China Biology Medicine disc databases up to January 3, 2020. Two authors independently extracted information from included articles and assessed the quality of each study by the use of the Newcastle-Ottawa Scale. According to the extent of interstudy heterogeneity, either a random-effect model or a fixed-effect model was used to calculate the combined odds ratio (OR) and 95% confidence interval (CI). RESULTS Finally, 16 studies containing 3390 cases and 2528 controls were included in our meta-analysis. Significant associations were found between the ADRB2 A46G polymorphism and essential hypertension risk in the Chinese population under four genetic models: allele genetic model (OR: 1.14, 95% CI: 1.06-1.23, P = .001, Pheterogeneity = .09), homozygote genetic model (OR: 1.29, 95% CI: 1.11-1.51, P = .001, Pheterogeneity = .25), dominant genetic model (OR: 1.17, 95% CI: 1.05-1.32, P = .005, Pheterogeneity = .04), and recessive genetic model (OR: 1.21, 95% CI: 1.05-1.38, P = .007, Pheterogeneity = .72). CONCLUSION The ADRB2 A46G polymorphism may increase the risk of essential hypertension in the Chinese population.
Collapse
Affiliation(s)
- Liyuan Yan
- Department of Cardiology, the First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | | | | | | | | | | |
Collapse
|
34
|
Liu ZJ, Tian YT, Shi BY, Zhou Y, Jia XS. Association between mutation of interleukin 36 receptor antagonist and generalized pustular psoriasis: A PRISMA-compliant systematic review and meta-analysis. Medicine (Baltimore) 2020; 99:e23068. [PMID: 33157966 PMCID: PMC7647532 DOI: 10.1097/md.0000000000023068] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Generalized pustular psoriasis (GPP) is a systemic inflammatory disease with poor outcomes, and several studies have suggested that the mutation of the interleukin 36 receptor antagonist gene (IL36RN) is related to GPP, where the polymorphism c.115+6T>C is reported to be the most common mutation of IL36RN. This study was performed to clarify and comprehensively evaluate the relationship between IL36RN gene polymorphism and the susceptibility of GPP subtypes. METHODS To conduct a thorough literature review, studies were obtained using databases such as Pubmed, EMBASE, Cochrane, China National Knowledge Infrastructure, and the Wanfang database. Only studies published up to December 2019 were included. The quality of the research studies was estimated using the Newcastle-Ottawa scale. The total odds ratios (ORs) and corresponding 95% confidence intervals (95% CIs) were pooled and analysed using STATA 14. The publication bias was evaluated through the Egger test, performed using the aforementioned software. Five common gene models were built and analysed to assess the association between the polymorphism c.115+6T>C and subtypes of GPP. RESULTS A total of 10 studies were selected, including 683 cases of GPP patients. Meta-analyses showed that there was a significant statistical correlation of IL36RN mutation between GPP with or without psoriasis vulgaris (OR = 3.82, 95%CI 2.63-5.56) and between adult GPP and paediatric GPP (OR = 0.42, 95%CI 0.23-0.77). No obvious discrepancy between European patients (OR = 4.03, 95%CI 2.23-7.26) and Asian patients was found. The gene models showed clear associations between the polymorphism c.115+6T>C and GPP through the dominant model (CC+ TC vs TT, OR 2.74, 95%CI 2.06-3.64), recessive model (CC vs CT + TT, OR 4.33, 95%CI 2.84-6.60), homozygote model (CC vs TT, OR 4.37, 95%CI 2.88-6.62), heterozygote model (CT vs TT, OR 2.26, 95%CI 1.32-3.85) and allelic model (C vs T, OR 3.35, 95%CI 2.63-4.27). CONCLUSION The IL36RN mutation is strongly related to GPP without psoriasis vulgaris and the early onset of GPP. Furthermore, the single-nucleotide polymorphism c.115+6T>C of the IL36RN gene plays a significant role in GPP vulnerability, especially in homozygous mutation. GPP could be a different inflammatory disease, independent of psoriasis.
Collapse
Affiliation(s)
| | - Yu-Tong Tian
- Neurology Department, the First Affiliated Hospital of Shihezi University School of medicine, Shihezi city, Xinjiang, China
| | | | | | | |
Collapse
|
35
|
Hou B, Jia X, Deng Z, Liu X, Liu H, Yu H, Liu S. Exploration of CYP21A2 and CYP17A1 polymorphisms and preeclampsia risk among Chinese Han population: a large-scale case-control study based on 5021 subjects. Hum Genomics 2020; 14:33. [PMID: 32977860 PMCID: PMC7517682 DOI: 10.1186/s40246-020-00286-0] [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] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 06/17/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Several genome-wide association studies have identified single-nucleotide polymorphisms (SNPs), such as rs4409766, rs1004467, and rs3824755 in CYP17A1 and rs2021783 in CYP21A2, as new hypertension susceptibility genetic variants in the Chinese population. This study aimed to look into the relationship between preeclampsia (PE) and these SNPs in Chinese Han women. METHODS Overall, 5021 unrelated pregnant women were recruited, including 2002 patients with PE and 3019 normal healthy controls. The real-time PCR (TaqMan) method was applied to genotype these four polymorphisms. RESULTS A statistically obvious difference in the allelic frequencies was observed in CYP21A2 rs2021783 between cases and controls (χ2 = 7.201, Pc = 0.028 by allele), and the T allele was associated with the occurrence and development of PE (OR = 1.151, 95% CI 1.039-1.275). We also found a significant association between rs2021783 and the development of early-onset PE (Pc = 0.008 by genotype, Pc = 0.004 by allele). For rs1004467 and rs3824755, the distribution of allelic frequencies differed markedly between mild PE and control groups (χ2 = 6.843, Pc = 0.036; χ2 = 6.869, Pc = 0.036), and patients with the TT genotype of rs1004467 were less easy to develop mild PE than were those carrying the CT or CC genotype (χ2 = 7.002, Pc = 0.032, OR = 1.306, 95% CI 1.071-1.593). The GG genotype of rs3824755 appeared to a protective effect on the occurrence of mild PE (OR = 0.766, 95% CI 0.629-0.934). CONCLUSIONS CYP21A2 rs2021783 appears to be closely related to PE susceptibility, and CYP17A1 rs1004467 and rs3824755 seem to be closely associated with mild PE in Han women.
Collapse
Affiliation(s)
- Bo Hou
- Department of Cardiology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Xuewen Jia
- Department of Cardiology, The Affiliated Hospital of Qingdao University, Qingdao, China
- Emergency Department, Shengli Oilfield Central Hospital, Dongying, China
| | - Ziwen Deng
- Medical Genetic Department, The Affiliated Hospital of Qingdao University, Qingdao, China
- Prenatal Diagnosis Center, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Xin Liu
- Department of Blood Transfusion, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Huitang Liu
- Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Haichu Yu
- Department of Cardiology, The Affiliated Hospital of Qingdao University, Qingdao, China.
| | - Shiguo Liu
- Medical Genetic Department, The Affiliated Hospital of Qingdao University, Qingdao, China.
- Prenatal Diagnosis Center, The Affiliated Hospital of Qingdao University, Qingdao, China.
| |
Collapse
|
36
|
Affiliation(s)
- John R Giudicessi
- Clinician-Investigator Training Program, Department of Cardiovascular Medicine, Mayo Clinic, Rochester, Minnesota; Division of Heart Rhythm Services, Department of Cardiovascular Medicine, Mayo Clinic, Rochester, Minnesota
| | - Dan M Roden
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee; Department of Pharmacology, Vanderbilt University Medical Center, Nashville, Tennessee; Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Arthur A M Wilde
- Department of Clinical and Experimental Cardiology, Amsterdam Cardiovascular Sciences, Amsterdam UMC, University of Amsterdam, Heart Center, Amsterdam, The Netherlands; European Reference Network for Rare and Low Prevalence Complex Diseases of the Heart (ERN GUARD-Heart)
| | - Michael J Ackerman
- Division of Heart Rhythm Services, Department of Cardiovascular Medicine, Mayo Clinic, Rochester, Minnesota; Division of Pediatric Cardiology, Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, Minnesota; Department of Molecular Pharmacology & Experimental Therapeutics, Windland Smith Rice Sudden Death Genomics Laboratory, Mayo Clinic, Rochester, Minnesota.
| |
Collapse
|
37
|
Keene KL, Hyacinth HI, Bis JC, Kittner SJ, Mitchell BD, Cheng YC, Pare G, Chong M, O’Donnell M, Meschia JF, Chen WM, Sale MM, Rich SS, Nalls MA, Zonderman AB, Evans MK, Wilson JG, Correa A, Markus HS, Traylor M, Lewis CM, Carty CL, Reiner A, Haessler J, Langefeld CD, Gottesman R, Mosley TH, Woo D, Yaffe K, Liu Y, Longstreth WT, Psaty BM, Kooperberg C, Lange LA, Sacco R, Rundek T, Lee JM, Cruchaga C, Furie KL, Arnett DK, Benavente OR, Grewal RP, Peddareddygari LR, Dichgans M, Malik R, Worrall BB, Fornage M. Genome-Wide Association Study Meta-Analysis of Stroke in 22 000 Individuals of African Descent Identifies Novel Associations With Stroke. Stroke 2020; 51:2454-2463. [PMID: 32693751 PMCID: PMC7387190 DOI: 10.1161/strokeaha.120.029123] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [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: 10/15/2019] [Accepted: 06/18/2020] [Indexed: 01/07/2023]
Abstract
BACKGROUND AND PURPOSE Stroke is a complex disease with multiple genetic and environmental risk factors. Blacks endure a nearly 2-fold greater risk of stroke and are 2× to 3× more likely to die from stroke than European Americans. METHODS The COMPASS (Consortium of Minority Population Genome-Wide Association Studies of Stroke) has conducted a genome-wide association meta-analysis of stroke in >22 000 individuals of African ancestry (3734 cases, 18 317 controls) from 13 cohorts. RESULTS In meta-analyses, we identified one single nucleotide polymorphism (rs55931441) near the HNF1A gene that reached genome-wide significance (P=4.62×10-8) and an additional 29 variants with suggestive evidence of association (P<1×10-6), representing 24 unique loci. For validation, a look-up analysis for a 100 kb region flanking the COMPASS single nucleotide polymorphism was performed in SiGN (Stroke Genetics Network) Europeans, SiGN Hispanics, and METASTROKE (Europeans). Using a stringent Bonferroni correction P value of 2.08×10-3 (0.05/24 unique loci), we were able to validate associations at the HNF1A locus in both SiGN (P=8.18×10-4) and METASTROKE (P=1.72×10-3) European populations. Overall, 16 of 24 loci showed evidence for validation across multiple populations. Previous studies have reported associations between variants in the HNF1A gene and lipids, C-reactive protein, and risk of coronary artery disease and stroke. Suggestive associations with variants in the SFXN4 and TMEM108 genes represent potential novel ischemic stroke loci. CONCLUSIONS These findings represent the most thorough investigation of genetic determinants of stroke in individuals of African descent, to date.
Collapse
Affiliation(s)
- Keith L. Keene
- Department of Biology; Brody School of Medicine Center for Health Disparities, East Carolina University, Greenville, NC
| | - Hyacinth I. Hyacinth
- Aflac Cancer and Blood Disorder Center of Emory University and Children’s Healthcare of Atlanta University, Atlanta, GA
| | | | - Steven J. Kittner
- Baltimore Veterans Administration Medical Center and University of Maryland School of Medicine, Baltimore, MD
| | - Braxton D. Mitchell
- Baltimore Veterans Administration Medical Center and University of Maryland School of Medicine, Baltimore, MD
| | - Yu-Ching Cheng
- Baltimore Veterans Administration Medical Center and University of Maryland School of Medicine, Baltimore, MD
| | - Guillaume Pare
- McMaster University and Population Health Research Institute, Hamilton Ontario
| | - Michael Chong
- McMaster University and Population Health Research Institute, Hamilton Ontario
| | | | | | - Wei-Min Chen
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA
| | - Michele M. Sale
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA
| | - Stephen S. Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA
| | - Mike A. Nalls
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD
- Data Tecnica International, Glen Echo, MD
| | - Alan B. Zonderman
- Laboratory of Epidemiology and Population Science, National Institute on Aging, Baltimore, MD
| | - Michele K. Evans
- Laboratory of Epidemiology and Population Science, National Institute on Aging, Baltimore, MD
| | | | - Adolfo Correa
- University of Mississippi Medical Center, Jackson, MS
| | | | - Matthew Traylor
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, United Kingdom
| | - Cathryn M. Lewis
- Social, Genetic and Developmental Psychiatry Centre, King’s College London, London, United Kingdom
| | - Cara L. Carty
- Initiative for Research and Education to Advance Community Health, Washington State University, Seattle, WA
| | - Alexander Reiner
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Jeff Haessler
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Carl D. Langefeld
- Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, NC
| | | | | | - Daniel Woo
- Department of Neurology, University of Cincinnati, Cincinnati, OH
| | | | - YongMei Liu
- Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, NC
| | | | - Bruce M. Psaty
- Cardiovascular Health Research Unit, Departments of Medicine, Epidemiology and Health Services, University of Washington, Seattle, WA; Kaiser Permanente Washington Health Research Institute, Seattle, WA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA
| | | | - Ralph Sacco
- University of Miami, Miller School of Medicine, Miami, FL
| | - Tatjana Rundek
- University of Miami, Miller School of Medicine, Miami, FL
| | - Jin-Moo Lee
- Washington University School of Medicine, St. Louis, MO
| | | | - Karen L. Furie
- Brown University Warren Alpert Medical School, Providence, RI
| | - Donna K. Arnett
- University of Kentucky, College of Public Health, Lexington, KY
| | | | - Raji P. Grewal
- Neuroscience Institute, Saint Francis Medical Center, Trenton, NJ
| | | | - Martin Dichgans
- Institute for Stroke and Dementia Research (ISD), University Hospital, LMU Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Rainer Malik
- Institute for Stroke and Dementia Research (ISD), University Hospital, LMU Munich, Germany
| | | | - Myriam Fornage
- Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX
| |
Collapse
|
38
|
Hong SJ, Goodman M, Kaphingst KA. Relationships of Family History-related Factors and Causal Beliefs to Cancer Risk Perception and Mammography Screening Adherence Among Medically Underserved Women. J Health Commun 2020; 25:531-542. [PMID: 32673182 PMCID: PMC7749030 DOI: 10.1080/10810730.2020.1788677] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
This study examines how family history-related factors and causal beliefs affect underserved women's cancer risk perceptions and adherence to mammography. 1,010 patients at a primary care safety net clinic at a large urban hospital completed a survey in 2015. Of the 1,010 patients, 467 women 45 years of age or older were included in this analysis. The majority of participants were African American (68%). We built multivariable linear and logistic regression models to examine the dependent variables of cancer risk perception and mammography screening adherence. According to the results, those with a family history of cancer were significantly more likely to be adherent to mammography. Perceived importance of family health history also significantly predicted their mammography screening adherence. However, cancer risk perceptions did not predict underserved women's mammography adherence. Significant interaction effects on the associations 1) between family cancer history, cancer risk perceptions, and mammography screening adherence and 2) between race, behavioral causal beliefs, and risk perceptions were found. Findings suggest that implementing different strategies across racial groups and by cancer history may be necessary to promote regular mammography screening.
Collapse
Affiliation(s)
- Soo Jung Hong
- Department of Communications and New Media, National University of Singapore , Singapore
| | - Melody Goodman
- Department of Biostatistics, New York University School of Global Public Health , New York, New York, USA
| | - Kimberly A Kaphingst
- Huntsman Cancer Institute, University of Utah , Salt Lake City, Utah, USA
- Department of Communication, University of Utah , Salt Lake City, Utah, USA
| |
Collapse
|
39
|
Rivera-Paredez B, Hidalgo-Bravo A, de la Cruz-Montoya A, Martínez-Aguilar MM, Ramírez-Salazar EG, Flores M, Quezada-Sánchez AD, Ramírez-Palacios P, Cid M, Martínez-Hernández A, Orozco L, Denova-Gutiérrez E, Salmerón J, Velázquez-Cruz R. Association between vitamin D deficiency and common variants of Vitamin D binding protein gene among Mexican Mestizo and indigenous postmenopausal women. J Endocrinol Invest 2020; 43:935-946. [PMID: 31907821 DOI: 10.1007/s40618-019-01177-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [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: 09/06/2019] [Accepted: 12/30/2019] [Indexed: 12/13/2022]
Abstract
PURPOSE Vitamin D deficiency (VDD) and polymorphisms in the group-specific component (GC) gene are known to be associated in different populations. However, the effects of such genetic variants may vary across different populations. Thus, the objective of this study was to estimate the association between Vitamin D-Binding Protein (VDBP) haplotypes and VDD in mestizo postmenopausal women and Mexican Amerindian ethnic groups. METHODS This was a cross-sectional study of 726 postmenopausal Mexican women from the Health Workers Cohort Study (HWCS) and 166 postmenopausal women from the Metabolic Analysis in an Indigenous Sample (MAIS) cohort in Mexico. GC polymorphisms (rs7045 and rs4588) were analyzed by TaqMan probes. Serum 25-hydroxyvitamin D [25(OH)D] levels were measured by Chemiluminescent Microparticle Immuno Assay. RESULTS The prevalence of VDD serum 25(OH)D < 20 ng/mL was 43.7% in mestizo women and 44.6% in indigenous women. In HWCS, the single nucleotide polymorphisms (SNPs) rs7041 and rs4588 were associated with VDD. In addition, women from the HWCS, carrying the haplotypes GC2/2 and GC1f/2 had higher odds of VDD (OR = 2.83, 95% CI 1.14, 7.02; and OR = 2.30, 95% CI 1.40, 3.78, respectively) compared to women with haplotype 1f/1 s. These associations were not statistically significant in the MAIS cohort. CONCLUSIONS Our results show genetic association of the analyzed SNPs and related haplotypes, on the GC gene, with VDD in mestizo Mexican postmenopausal women. Moreover, a high prevalence of VDD with high genetic variability within the country was observed. Our results support the need for national policies for preventing VDD.
Collapse
Affiliation(s)
- B Rivera-Paredez
- Centro de Investigación en Políticas, Población Y Salud de La Facultad de Medicina de La Universidad Nacional Autónoma de México, Ciudad de México, México
| | - A Hidalgo-Bravo
- Departamento de Genética, Instituto Nacional de Rehabilitación, Ciudad de México, México
| | - A de la Cruz-Montoya
- Laboratorio de Genómica del Metabolismo Óseo, Instituto Nacional de Medicina Genómica (INMEGEN), Ciudad de México, México
| | - M M Martínez-Aguilar
- Laboratorio de Genómica del Metabolismo Óseo, Instituto Nacional de Medicina Genómica (INMEGEN), Ciudad de México, México
| | - E G Ramírez-Salazar
- CONACYT-Laboratorio de Genómica del Metabolismo Óseo, (INMEGEN), Ciudad de México, México
| | - M Flores
- Centro de Investigación en Nutrición y Salud, Instituto Nacional de Salud Pública, Cuernavaca, Morelos, México
| | - A D Quezada-Sánchez
- Centro de Información Para Decisiones en Salud Pública, Instituto Nacional de Salud Pública, Cuernavaca, Morelos, México
| | - P Ramírez-Palacios
- Unidad de Investigación Epidemiológica Y en Servicios de Salud, Instituto Mexicano del Seguro Social (IMSS), Delegación Morelos, Cuernavaca, México
| | - M Cid
- Laboratorio de Inmunogenómica Y Enfermedades Metabólicas Instituto Nacional de Medicina Genómica (INMEGEN), Ciudad de México, México
| | - A Martínez-Hernández
- Laboratorio de Inmunogenómica Y Enfermedades Metabólicas Instituto Nacional de Medicina Genómica (INMEGEN), Ciudad de México, México
| | - L Orozco
- Laboratorio de Inmunogenómica Y Enfermedades Metabólicas Instituto Nacional de Medicina Genómica (INMEGEN), Ciudad de México, México
| | - E Denova-Gutiérrez
- Centro de Investigación en Nutrición y Salud, Instituto Nacional de Salud Pública, Cuernavaca, Morelos, México
| | - J Salmerón
- Centro de Investigación en Políticas, Población Y Salud de La Facultad de Medicina de La Universidad Nacional Autónoma de México, Ciudad de México, México
| | - R Velázquez-Cruz
- Laboratorio de Genómica del Metabolismo Óseo, Instituto Nacional de Medicina Genómica (INMEGEN), Ciudad de México, México.
| |
Collapse
|
40
|
Li Z, Ye CY, Zhao TY, Yang L. Model of genetic and environmental factors associated with type 2 diabetes mellitus in a Chinese Han population. BMC Public Health 2020; 20:1024. [PMID: 32600448 PMCID: PMC7325035 DOI: 10.1186/s12889-020-09130-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 06/16/2020] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Type 2 diabetes mellitus (T2DM) is a metabolic disorder which accounts for high morbidity and mortality due to complications like renal failure, amputations, cardiovascular disease, and cerebrovascular events. METHODS We collected medical reports, lifestyle details, and blood samples of individuals and used the polymerase chain reaction-ligase detection reaction method to genotype the SNPs, and a visit was conducted in August 2016 to obtain the incidence of Type 2 diabetes in the 2113 eligible people. To explore which genes and environmental factors are associated with type 2 diabetes mellitus in a Chinese Han population, we used elastic net to build a model, which is to explain which variables are strongly associated with T2DM, rather than predict the occurrence of T2DM. RESULT The genotype of the additive of rs964184, together with the history of hypertension, regular intake of meat and waist circumference, increased the risk of T2DM (adjusted OR = 2.38, p = 0.042; adjusted OR = 3.31, p < 0.001; adjusted OR = 1.05, p < 0.001). The TT genotype of the additive and recessive models of rs12654264, the CC genotype of the additive and dominant models of rs2065412, the TT genotype of the additive and dominant models of rs4149336, together with the degree of education, regular exercise, reduced the risk of T2DM (adjusted OR = 0.46, p = 0.017; adjusted OR = 0.53, p = 0.021; adjusted OR = 0.59, p = 0.021; adjusted OR = 0.57, p = 0.01; adjusted OR = 0.59, p = 0.021; adjusted OR = 0.57, p = 0.01; adjusted OR = 0.50, p = 0.007; adjusted OR = 0.80, p = 0.032) . CONCLUSION Eventually we identified a set of SNPs and environmental factors: rs5805 in the SLC12A3, rs12654264 in the HMGCR, rs2065412 and rs414936 in the ABCA1, rs96418 in the ZPR1 gene, waistline, degree of education, exercise frequency, hypertension, and the intake of meat. Although there was no interaction between these variables, people with two risk factors had a higher risk of T2DM than those only having one factor. These results provide the theoretical basis for gene and other risk factors screening to prevent T2DM.
Collapse
Affiliation(s)
- Zheng Li
- Medical School, Hangzhou Normal University, 2318 Yuhangtang Rd, Hangzhou, 310000 Zhejiang China
| | - Cheng-yin Ye
- Medical School, Hangzhou Normal University, 2318 Yuhangtang Rd, Hangzhou, 310000 Zhejiang China
| | - Tian-Yu Zhao
- Medical School, Hangzhou Normal University, 2318 Yuhangtang Rd, Hangzhou, 310000 Zhejiang China
- Medical School, Shihezi University, Shihezi, 832000 China
| | - Lei Yang
- Medical School, Hangzhou Normal University, 2318 Yuhangtang Rd, Hangzhou, 310000 Zhejiang China
| |
Collapse
|
41
|
Sapkota BR, Sanghera DK. A rare missense variant in the milk fat globule-EGF factor 8 (MFGE8) increases T2DM susceptibility and cardiovascular disease risk with population-specific effects. Acta Diabetol 2020; 57:733-741. [PMID: 32025861 PMCID: PMC10502938 DOI: 10.1007/s00592-019-01463-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [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: 09/24/2019] [Accepted: 11/28/2019] [Indexed: 12/26/2022]
Abstract
AIMS The milk fat globule-epidermal growth factor 8 (MFGE8), also called lactadherin, is an integrin ligand and a known mediator of inflammation and atherosclerosis in T2DM in studies using animal models. However, its role in the pathophysiology of human T2DM, obesity, and cardiovascular disease has been poorly explored. Aim of this study was to investigate the role of a missense variant (rs371227978 C/T: Arg148His) in the MFGE8 gene identified through exome sequencing for its association with T2DM and cardiometabolic traits. METHODS Exome-wide sequencing was performed using DNA samples from 68 Sikh individuals from multi-generation pedigrees affected with diabetes on Illumina's GAIIx using "SureSelect Human All Exon" panels. We further replicated this variant by de novo genotyping in a total of 4242 individuals of the Asian Indian Diabetic Heart Study/Sikh Diabetes Study using custom TaqMan genotyping assay. We also measured circulating concentrations of Mfge8 using frozen serum aliquots by enzyme-linked immunosorbent assay. RESULTS Overall, only 1.78% of 4242 individuals were carriers of this variant with MAF being 0.009. Except for the significant correlation of this variant with T2DM and triglycerides, no other quantitative risk phenotype was significant. The minor per allele-associated increased risk for T2DM showed odds ratio of 1.95 (95% CI 1.18-3.23; p = 0.008) in unadjusted model and was 1.73 (95% CI 1.02-2.93; p = 0.043) after adjusting for the age, gender, and BMI. However, there was a strong correlation between serum Mfge8 concentrations with T2DM, (r2 = 0.38; p = 0.001), fasting glucose (r2= 0.36; p = 0.002), and triglycerides (r2 = 0.33; p = 0.005). Our data revealed a significant dose-related increase in MFGE8 genotypes for affecting serum Mfge8 (p = 2.1 × 10-3) and triglyceride concentrations (p = 3.2 × 10-3). For a per risk allele-associated increase of 4.74 ng/ml ± SD of 1.62 ng/ml of the Mfge8 concentration was found to increase T2DM risk to 1.7 fold (95% CI from 1 to 3 fold). CONCLUSIONS Here, we report for the first time a novel population-specific rare variant in the MFGE8 gene linked with the increased Mfge8 concentrations and the risk for developing T2DM and cardiovascular risk factors in a population of Punjabi Sikhs from India. In view of a strong evidence from animal studies supporting the role of Mfge8 in obesity, insulin resistance, and the development of atherosclerosis in T2DM, our findings are important and timely. If validated in a large independent dataset, early screening of Mfge8 in blood levels may especially benefit those patients with genetically elevated Mfge8 levels to preventing or reducing the risk of T2DM and cardiovascular disease.
Collapse
Affiliation(s)
- Bishwa R Sapkota
- Department of Pediatrics, College of Medicine, University of Oklahoma Health Sciences Center, 940 Stanton L. Young Blvd., Rm 317 BMSB, Oklahoma City, OK, 73104, USA
| | - Dharambir K Sanghera
- Department of Pediatrics, College of Medicine, University of Oklahoma Health Sciences Center, 940 Stanton L. Young Blvd., Rm 317 BMSB, Oklahoma City, OK, 73104, USA.
- Department of Pharmaceutical Sciences, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.
- Department of Physiology, College of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.
- Oklahoma Center for Neuroscience, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.
- Harold Hamm Diabetes Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.
| |
Collapse
|
42
|
Castro-Santos P, Verdugo RA, Alonso-Arias R, Gutiérrez MA, Suazo J, Aguillón JC, Olloquequi J, Pinochet C, Lucia A, Quiñones LA, Díaz-Peña R. Association analysis in a Latin American population revealed ethnic differences in rheumatoid arthritis-associated SNPs in Caucasian and Asian populations. Sci Rep 2020; 10:7879. [PMID: 32398702 PMCID: PMC7217883 DOI: 10.1038/s41598-020-64659-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 04/08/2020] [Indexed: 11/17/2022] Open
Abstract
Large genome-wide association studies (GWAS) have increased our knowledge of the genetic risk factors of rheumatoid arthritis (RA). However, little is known about genetic susceptibility in populations with a large admixture of Amerindian ancestry. The aim of the present study was to test the generalizability of previously reported RA loci in a Latin American (LA) population with admixed ancestry. We selected 128 single nucleotide polymorphisms (SNPs) in linkage equilibrium, with high association to RA in multiple populations of non-Amerindian origin. Genotyping of 118 SNPs was performed in 313 RA patients/487 healthy control subjects by mid-density arrays of polymerase chain reaction (PCR). Some of the identified associations were validated in an additional cohort (250 cases/290 controls). One marker, the SNP rs2451258, located upstream of T Cell Activation RhoGTPase Activating Protein (TAGAP) gene, showed significant association with RA (p = 5 × 10-3), whereas 18 markers exhibited suggestive associations (p < 0.05). Haplotype testing showed association of some groups of adjacent SNPs around the signal transducer and activator of transcription 4 (STAT4) gene (p = 9.82 × 10-3 to 2.04 × 10-3) with RA. Our major finding was little replication of previously reported genetic associations with RA. These results suggest that performing GWAS and admixture mapping in LA populations has the potential to reveal novel loci associated with RA. This in turn might help to gain insight into the 'pathogenomics' of this disease and to explore trans-population differences for RA in general.
Collapse
Affiliation(s)
- P Castro-Santos
- Facultad de Ciencias de la Salud, Universidad Autónoma de Chile, Talca, Chile
- Inmunología, Centro de Investigaciones Biomédicas (CINBIO), Universidad de Vigo, Vigo, Spain
| | - R A Verdugo
- Programa de Genética Humana, ICBM, Facultad de Medicina, Universidad de Chile, Santiago, Chile
- Departamento de Oncología Básico Clínica, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - R Alonso-Arias
- Facultad de Ciencias de la Salud, Universidad Autónoma de Chile, Talca, Chile
- Immunology Department, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - M A Gutiérrez
- Rheumatology, Almirante Nef Naval Hospital, Viña del Mar, Valparaíso, Chile
- Valparaíso University, Viña del Mar, Valparaíso, Chile
| | - J Suazo
- Instituto de Investigación en Ciencias Odontológicas, Facultad de Odontología, Universidad de Chile, Santiago, Chile
| | - J C Aguillón
- Immune Regulation and Tolerance Research Group, Programa de Inmunología, ICBM, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - J Olloquequi
- Facultad de Ciencias de la Salud, Universidad Autónoma de Chile, Talca, Chile
| | - C Pinochet
- Hospital Regional de Talca, Talca, Chile
| | - A Lucia
- Universidad Europea de Madrid (Faculty of Sports Sciences) and Research Institute Hospital 12 de Octubre ('i + 12'), Madrid, Spain
| | - L A Quiñones
- Laboratory of Chemical Carcinogenesis and Pharmacogenetics, Department de Basic-Clinical Oncology, Faculty of Medicine, University of Chile, Santiago, Chile.
- Latin American Network for Implementation and Validation of Clinical Pharmacogenomics Guidelines (RELIVAF-CYTED), Madrid, Spain.
| | - R Díaz-Peña
- Facultad de Ciencias de la Salud, Universidad Autónoma de Chile, Talca, Chile.
| |
Collapse
|
43
|
Xiao QY, Fang XC, Li XQ, Fei GJ. Ethnic differences in genetic polymorphism associated with irritable bowel syndrome. World J Gastroenterol 2020; 26:2049-2063. [PMID: 32536774 PMCID: PMC7267697 DOI: 10.3748/wjg.v26.i17.2049] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 03/25/2020] [Accepted: 04/04/2020] [Indexed: 02/06/2023] Open
Abstract
Genetic polymorphism is associated with irritable bowel syndrome (IBS) in terms of susceptibility and clinical manifestations. Previous studies have shown that genetic polymorphism might play a key role in the onset and progression of IBS by modulating components of its pathogenesis such as the gut-brain axis, gastrointestinal motility, inflammatory activity, and immune status. Although underlying pathophysiological mechanisms have not been fully clarified, the potential ethnic differences that are present in worldwide genetic studies of IBS deserve attention. This review surveyed numerous studies focusing on IBS-associated single nucleotide polymorphisms, and investigated the ethnic disparities revealed by them. The results demonstrate the need for more attention on ethnic factors in IBS-related genetic studies. Taking ethnic backgrounds into accounts and placing emphasis on disparities potentially ascribed to ethnicity could help lay a solid and generalized foundation for transcultural, multi-ethnic, or secondary analyses in IBS, for example, a meta-analysis. Broader genetic studies considering ethnic factors are greatly needed to obtain a better understanding of the pathophysiological mechanisms of IBS and to improve the prevention, intervention, and treatment of this disease.
Collapse
Affiliation(s)
- Qi-Yun Xiao
- Department of Gastroenterology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Xiu-Cai Fang
- Department of Gastroenterology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Xiao-Qing Li
- Department of Gastroenterology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Gui-Jun Fei
- Department of Gastroenterology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| |
Collapse
|
44
|
Xu C, Lin X, Qian W, Na R, Yu H, Jia H, Jiang H, Fang Z, Zheng SL, Ding Q, Wu Y, Zheng J, Xu J. Genetic risk scores based on risk-associated single nucleotide polymorphisms can reveal inherited risk of bladder cancer in Chinese population. Medicine (Baltimore) 2020; 99:e19980. [PMID: 32384449 PMCID: PMC7220229 DOI: 10.1097/md.0000000000019980] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Genome-wide association studies have identified single nucleotide polymorphisms (SNPs) associated with bladder cancer (BCa) risk in Caucasian and East Asian population. The objective of this study was to validate these SNPs in Chinese population and evaluate whether these SNPs could differentiate the individual inherited risk for BCa.A case-control study including 581 BCa cases and 1561 healthy controls was performed. Germline DNA samples from all individuals were genotyped for eight SNPs. Genetic risk score (GRS) was calculated for each individual based on the odds ratios and risk allele frequencies of five risk-associated SNPs.Among eight SNPs evaluated in this study, rs798766 at 4p16.3 [OR = 1.39 (1.15-1.67), P < .001], rs9642880 [OR = 1.17 (1.06-1.30), P < .001] and rs4813953 at 20p12.2 [OR = 1.09 (1.02-1.17), P = .016] were found associated with BCa risk in Chinese population. A genetic risk score was established based on five SNPs (including the above three SNPs and two other SNPs which have the consistent direction with previous reported genome-wide association study). The mean GRS was significantly higher in BCa cases than controls (1.22 vs. 1.01, P < .001). When subjects were categorized into low- (<0.8), average- (0.8-1.2), and high-risk (>1.2) groups, the likelihoods of BCa were 25.2%, 33.7% and 55.0%, respectively (P-trend < 2.2 × 10). In subgroup analyses, no significant difference was observed in mean GRS among BCa patients with different stages or grades.In conclusion, two SNPs derived from East Asian and one SNP from Caucasian were associated with BCa risk in Chinese population. These results provided additional information of genetic risks for BCa in Chinese population. Genetic risk score based on these SNPs can reveal inherited risk of BCa, and may have potential for modifying personalized cancer screening strategy.
Collapse
Affiliation(s)
- Chenyang Xu
- Department of Urology
- Fudan Institute of Urology, Huashan Hospital, Fudan University, Shanghai, PR China
| | - Xiaoling Lin
- Fudan Institute of Urology, Huashan Hospital, Fudan University, Shanghai, PR China
| | | | - Rong Na
- Department of Urology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, PR China
| | - Hongjie Yu
- Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, Illinois, USA
| | - Haifei Jia
- Department of Urology
- Fudan Institute of Urology, Huashan Hospital, Fudan University, Shanghai, PR China
| | - Haowen Jiang
- Department of Urology
- Fudan Institute of Urology, Huashan Hospital, Fudan University, Shanghai, PR China
| | - Zujun Fang
- Department of Urology
- Fudan Institute of Urology, Huashan Hospital, Fudan University, Shanghai, PR China
| | - S. Lilly Zheng
- Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, Illinois, USA
| | - Qiang Ding
- Department of Urology
- Fudan Institute of Urology, Huashan Hospital, Fudan University, Shanghai, PR China
| | - Yishuo Wu
- Department of Urology
- Fudan Institute of Urology, Huashan Hospital, Fudan University, Shanghai, PR China
- Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, Illinois, USA
| | - Jie Zheng
- Department of Urology
- Fudan Institute of Urology, Huashan Hospital, Fudan University, Shanghai, PR China
| | - Jianfeng Xu
- Fudan Institute of Urology, Huashan Hospital, Fudan University, Shanghai, PR China
- Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, Illinois, USA
| |
Collapse
|
45
|
Ohi K, Nishizawa D, Shimada T, Kataoka Y, Hasegawa J, Shioiri T, Kawasaki Y, Hashimoto R, Ikeda K. Polygenetic Risk Scores for Major Psychiatric Disorders Among Schizophrenia Patients, Their First-Degree Relatives, and Healthy Participants. Int J Neuropsychopharmacol 2020; 23:157-164. [PMID: 31900488 PMCID: PMC7171929 DOI: 10.1093/ijnp/pyz073] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 12/17/2019] [Accepted: 01/01/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The genetic etiology of schizophrenia (SCZ) overlaps with that of other major psychiatric disorders in samples of European ancestry. The present study investigated transethnic polygenetic features shared between Japanese SCZ or their unaffected first-degree relatives and European patients with major psychiatric disorders by conducting polygenic risk score (PRS) analyses. METHODS To calculate PRSs for 5 psychiatric disorders (SCZ, bipolar disorder [BIP], major depressive disorder, autism spectrum disorder, and attention-deficit/hyperactivity disorder) and PRSs differentiating SCZ from BIP, we utilized large-scale European genome-wide association study (GWAS) datasets as discovery samples. PRSs derived from these GWASs were calculated for 335 Japanese target participants [SCZ patients, FRs, and healthy controls (HCs)]. We took these PRSs based on GWASs of European psychiatric disorders and investigated their effect on risk in Japanese SCZ patients and unaffected first-degree relatives. RESULTS The PRSs obtained from European SCZ and BIP patients were higher in Japanese SCZ patients than in HCs. Furthermore, PRSs differentiating SCZ patients from European BIP patients were higher in Japanese SCZ patients than in HCs. Interestingly, PRSs related to European autism spectrum disorder were lower in Japanese first-degree relatives than in HCs or SCZ patients. The PRSs of autism spectrum disorder were positively correlated with a young onset age of SCZ. CONCLUSIONS These findings suggest that polygenic factors related to European SCZ and BIP and the polygenic components differentiating SCZ from BIP can transethnically contribute to SCZ risk in Japanese people. Furthermore, we suggest that reduced levels of an ASD-related genetic factor in unaffected first-degree relatives may help protect against SCZ development.
Collapse
Affiliation(s)
- Kazutaka Ohi
- Department of Neuropsychiatry, Kanazawa Medical University, Ishikawa, Japan
- Medical Research Institute, Kanazawa Medical University, Ishikawa, Japan
- Department of General Internal Medicine, Kanazawa Medical University, Ishikawa, Japan
- Department of Psychiatry and Psychotherapy, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Daisuke Nishizawa
- Addictive Substance Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Takamitsu Shimada
- Department of Neuropsychiatry, Kanazawa Medical University, Ishikawa, Japan
| | - Yuzuru Kataoka
- Department of Neuropsychiatry, Kanazawa Medical University, Ishikawa, Japan
| | - Junko Hasegawa
- Addictive Substance Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Toshiki Shioiri
- Department of Psychiatry and Psychotherapy, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Yasuhiro Kawasaki
- Department of Neuropsychiatry, Kanazawa Medical University, Ishikawa, Japan
| | - Ryota Hashimoto
- Department of Pathology of Mental Diseases, National Institute of Mental Health, National Center of Neurology and Psychiatry, Kodaira, Tokyo, Japan
- Molecular Research Center for Children’s Mental Development, United Graduate School of Child Development, Osaka University, Suita, Osaka, Japan
| | - Kazutaka Ikeda
- Addictive Substance Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| |
Collapse
|
46
|
Hou J, Lin L, Guo W, Luo D, Lan L. Association of methylenetetrahydrofolate reductase C677T polymorphism with the pre-eclampsia risk in Hakka pregnant women in Southern China. Gynecol Endocrinol 2020; 36:322-326. [PMID: 31452430 DOI: 10.1080/09513590.2019.1658188] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [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] [Indexed: 10/26/2022] Open
Abstract
The aim of this study is to clarify the possible association between methylenetetrahydrofolate reductase (MTHFR) C677T polymorphism and pre-eclampsia in Hakka pregnant women in southern China. Pre-eclampsia and normal pregnant women were consecutively collected and MTHFR C677T genotypes were determined by the DNA sequencing method. One hundred and thirteen pre-eclampsia patients were CC homozygote (113 of 191, 59.2%), 68 of 191 (35.6%) were CT heterozygote, and 10 of 191 (5.2%) were TT homozygote, with the frequency of the T allele equal to 0.77. This is in comparison with the normal control group where 106 of 202 (52.5%) were CC homozygote, 83 of 202 (41.1%) were CT heterozygote, and 13 of 202 (6.4%) were TT homozygote, with the frequency of the T allele equal to 0.27. No statistically significant differences were observed in genotype or allele frequencies between the pre-eclampsia and normal control for the C677T polymorphism of MTHFR gene (p > .05). The findings of this study suggest that polymorphisms of MTHFR C677T genes were not associated with pre-eclampsia in Hakka pregnant women from southern China, but additional studies are necessary to explore the mechanisms involving it.
Collapse
Affiliation(s)
- Jingyuan Hou
- Clinical Core Laboratory, Meizhou People's Hospital (Huangtang Hospital), Meizhou Hospital Affiliated to Sun Yat-Sen University, Meizhou, P. R. China
- Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou, P. R. China
| | - Lifang Lin
- Clinical Core Laboratory, Meizhou People's Hospital (Huangtang Hospital), Meizhou Hospital Affiliated to Sun Yat-Sen University, Meizhou, P. R. China
- Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou, P. R. China
- Prenatal Diagnosis Center, Meizhou People's Hospital (Huangtang Hospital), Meizhou Hospital Affiliated to Sun Yat-Sen University, Meizhou, P. R. China
| | - Wei Guo
- Clinical Core Laboratory, Meizhou People's Hospital (Huangtang Hospital), Meizhou Hospital Affiliated to Sun Yat-Sen University, Meizhou, P. R. China
- Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou, P. R. China
- Prenatal Diagnosis Center, Meizhou People's Hospital (Huangtang Hospital), Meizhou Hospital Affiliated to Sun Yat-Sen University, Meizhou, P. R. China
| | - Dandan Luo
- Prenatal Diagnosis Center, Meizhou People's Hospital (Huangtang Hospital), Meizhou Hospital Affiliated to Sun Yat-Sen University, Meizhou, P. R. China
| | - Liubing Lan
- Prenatal Diagnosis Center, Meizhou People's Hospital (Huangtang Hospital), Meizhou Hospital Affiliated to Sun Yat-Sen University, Meizhou, P. R. China
| |
Collapse
|
47
|
Nicolopoulos K, Mulugeta A, Zhou A, Hyppönen E. Association between habitual coffee consumption and multiple disease outcomes: A Mendelian randomisation phenome-wide association study in the UK Biobank. Clin Nutr 2020; 39:3467-3476. [PMID: 32284183 DOI: 10.1016/j.clnu.2020.03.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [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: 09/08/2019] [Revised: 03/03/2020] [Accepted: 03/07/2020] [Indexed: 01/24/2023]
Abstract
BACKGROUND Coffee is the most commonly consumed beverage in the world after water, however the debate as to whether coffee consumption is beneficial or detrimental to health continues. Current evidence of the link between coffee and health outcomes is predominately observational, thus subject to methodological issues such a confounding and reverse causation. METHODS This Mendelian randomisation phenome-wide association study (MR-PheWAS) used information from up to 333,214 participants of White-British ancestry in the UK Biobank to examine the causal association between genetically instrumented habitual coffee consumption and the full range of disease outcomes. We constructed a genetic risk score for habitual coffee consumption and screened for associations with disease outcomes across 1117 case-control series. All signals under false discovery rate controlled threshold (5.8 × 10-4) were followed by Mendelian randomisation (MR) analyses, with replication in independent data sources where possible. RESULTS The initial phenome-wide association analysis identified signals for 13 outcomes representing five distinct diseases. The strongest signal was seen for gout (P = 2.3 × 10-12), but there was notable pleiotropy (Pdistortion <0.001) and MR analyses did not support an association with habitual coffee consumption (inverse variance weighted MR OR 0.41, 95% CI 0.08 to 2.25, P = 0.31). Support for a possible causal relationship between habitual coffee consumption was only obtained for four distinct disease outcomes, including an increased odds of osteoarthrosis (OR 1.23, 95% CI 1.11 to 1.35), other arthropathies (OR 1.22, 95% CI 1.12 to 1.33) and overweight (OR 1.28, 95% CI 1.05 to 1.56), and a lower odds of postmenopausal bleeding (OR 0.72, 95% CI 0.63 to 0.82). Evidence for an association between habitual coffee consumption and these four diseases was also supported by phenotypic associations with self-reported coffee consumption. CONCLUSIONS This large-scale MR-PheWAS provided little evidence for notable harm or benefit with respect to higher habitual coffee consumption. The only evidence for harm was seen with respect to osteoarthrosis, other arthropathies and obesity.
Collapse
Affiliation(s)
- Konstance Nicolopoulos
- Australian Centre for Precision Health, University of South Australia Cancer Research Institute, Adelaide, Australia
| | - Anwar Mulugeta
- Australian Centre for Precision Health, University of South Australia Cancer Research Institute, Adelaide, Australia; Department of Pharmacology, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Ang Zhou
- Australian Centre for Precision Health, University of South Australia Cancer Research Institute, Adelaide, Australia
| | - Elina Hyppönen
- Australian Centre for Precision Health, University of South Australia Cancer Research Institute, Adelaide, Australia; Population, Policy and Practice, UCL Great Ormond Street Institute of Child Health, London, UK; South Australian Health and Medical Research Institute, Adelaide, Australia.
| |
Collapse
|
48
|
Shi C, Zhao H. Association between Tumor Necrosis Factor-308 G/A Polymorphism and Chronic Obstructive Pulmonary Disease Risk in Chinese Population: Evidence from a Meta-Analysis. Clin Lab 2020; 65. [PMID: 31625355 DOI: 10.7754/clin.lab.2019.190313] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
BACKGROUND Association studies of tumor necrosis factor (TNF)-308 G/A (rs1800629) polymorphism and chronic obstructive pulmonary disease (COPD) have shown inconsistent and contradictory results among different populations. In the present study, a meta-analysis was performed to evaluate the association between TNF-308 G/A polymorphism and COPD susceptibility in Chinese population. MATERIALS AND METHODS Systemic assessment was performed for the published studies from PubMed, Embase, Web of Science, the Cochrane Library, Wanfang Data, and CNKI prior to July 2018. Odds ratios (ORs) with their 95% confidence intervals (CIs) were pooled using STATA software. RESULTS A total of eighteen studies comprising 1,817 COPD cases and 2,056 controls were included in this meta-analysis. Overall, significant results were obtained between TNF-308 G/A polymorphism and COPD risk in Chinese population (A vs. G, OR = 2.45, 95% CI: 1.93 - 3.11; AA vs. GG, OR = 4.53, 95% CI: 2.67 - 7.68; AA vs. GA + GG, OR = 3.74, 95% CI: 2.21 - 6.33; AA + GA vs. GG, OR = 2.53, 95% CI: 1.97 - 3.26) under allele and homozygote models as well as recessive and dominant models. In the subgroup analyses, TNF-308 G/A polymorphism was significantly associated with increased COPD risk both in North China and South China, as well as in population-based studies. CONCLUSIONS This meta-analysis indicates that TNF-308A/G polymorphism may contribute to individual suscepti-bility to COPD in Chinese population.
Collapse
|
49
|
Zhao J, Li D, Tang H, Tang L. Association of vascular endothelial growth factor polymorphisms with polycystic ovarian syndrome risk: a meta-analysis. Reprod Biol Endocrinol 2020; 18:18. [PMID: 32164758 PMCID: PMC7069028 DOI: 10.1186/s12958-020-00577-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 02/24/2020] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Polycystic ovarian syndrome (PCOS) is a multi-gene hereditary disorder caused by the interaction of certain gene variation with environmental factors. Previous studies have shown that vascular endothelial growth factor (VEGF) gene polymorphisms are associated with the risk of polycystic ovarian syndrome. However, the results of these studies remain controversial. We performed the present meta-analysis aiming to further investigate the potential relationship between VEGF polymorphisms and susceptibility to PCOS. METHODS The following databases were systematically searched: PubMed, EMBASE, Web of Science (WOS), China National Knowledge Infrastructure (CNKI), and Wanfang Databases. The correlation between VEGF polymorphisms and PCOS risk was assessed by calculating pooled odds ratios (ORs) and their 95% confidence intervals (95% CIs). Subgroup analyses stratified by ethnicity and source of control were also conducted. Besides, trial sequential analysis (TSA) was done to verify the reliability of the pooled results. RESULTS 10 relevant case-control studies were incorporated in this meta-analysis, involving 1347 PCOS cases and 1378 controls. The VEGF rs2010963 polymorphism was associated with decreased PCOS risk in the whole population and the Asian populations. The VEGF rs3025039 polymorphism was associated with decreased PCOS susceptibility and the Asian populations, but increased risk of PCOS was observed among the Caucasian populations. In addition, the results of trial sequential analysis (TSA) showed the negative correlation between rs2010963 and PCOS risk, obtained by our meta-analysis, was stable and reliable. CONCLUSION Overall, different VEGF gene polymorphisms may exert different effects on PCOS susceptibility. The VEGF rs2010963 polymorphism decreases PCOS susceptibility in both the whole population and the Asian populations, and VEGF rs3025039 polymorphism causes lower PCOS susceptibility in the whole population and the Asian populations but higher in the Caucasian populations.
Collapse
Affiliation(s)
- Jiahui Zhao
- Department of Reproductive Medicine, Lianyungang Maternal and Child Health Hospital, NO.669 Qindongmen Road, Lianyungang, 222001, Jiangsu Province, China
| | - Da Li
- Department of Vascular Surgery, the First People's Hospital of Lianyungang, NO.182 North Tongguan Road, Lianyungang, Jiangsu Province, 222002, China
| | - Huaiyun Tang
- Department of Reproductive Medicine, Lianyungang Maternal and Child Health Hospital, NO.669 Qindongmen Road, Lianyungang, 222001, Jiangsu Province, China
| | - Lisha Tang
- Department of Reproductive Medicine, Lianyungang Maternal and Child Health Hospital, NO.669 Qindongmen Road, Lianyungang, 222001, Jiangsu Province, China.
| |
Collapse
|
50
|
Wang K, Fan J, Lin W, Zou C, He M, Cai Y, Pei H, Li M. Functional polymorphism of PIN1 rs2233679 is associated with the progression of CIN to early cervical cancer in Hunan Chinese. Taiwan J Obstet Gynecol 2020; 59:220-226. [PMID: 32127141 DOI: 10.1016/j.tjog.2020.01.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 11/17/2022] Open
Abstract
OBJECTIVE Peptidyl-prolyl cis/trans isomerase NIMA-interacting 1 (PIN1) involves alteration of the structure, function, intracellular localization and/or stability of the phosphorylated protein on serine or threonine residues which relates to inflammation and tumorigenesis. Association between PIN1 promoter polymorphisms and cancer risk were reported in several cancers. We intend to study the relationship between the polymorphism of PIN1 promoter and cervical cancer initiation and development. MATERIALS AND METHODS We genotyped two common single nucleotide polymorphisms (SNPs) (rs2233678 and rs2233679) in the promoter of the PIN1 gene in healthy controls, patients with CIN or cervical cancer. We used polymerase chain reaction and DNA sequencing methods to analyze these two SNPs in 179 patients and 223 healthy controls. Luciferase activity assay was used to detect PIN1 expression driven by the rs2233679. RESULTS The results revealed that the carriers of rs2233679 genotypes CT/TT had a significantly increased risk of cervical cancer in patients with CIN compared with genotype CC (odds ration [OR] = 2.924, 95% confidence interval [CI] = 1.093-7.819, P = 0.033). Luciferase activity assay results revealed that PIN1 expression driven by the rs2233679 genotype TT was higher than the genotype CC (P < 0.05). On the other hand, no significant correlation between the healthy controls and patients was found for PIN1 rs2233678 which showed that rs2233678 genotypes CG/GG is 95% in healthy controls and 100% in patients. CONCLUSION PIN1 rs2233679 genotype CT/TT may be a risk factor of early cervical cancer compared with genotype CC in Hunan populations. Our findings suggest that PIN1 rs2233679 genotype CT/TT might involve in the progression of the precancerous stage developing to early cancer by enhancing PIN1 expression.
Collapse
Affiliation(s)
- Kangtao Wang
- Department of Gastrointestinal Surgery, Xiangya Hospital, Central South University, Changsha, Hunan 410008 PR China.
| | - Jielin Fan
- Department of Gynecologic Tumor, Affiliated Cancer Hospital of Central South University, Changsha, Hunan 410013 PR China.
| | - Wenchao Lin
- Xiangya School of Medicine, Central South University, Changsha, Hunan 410008 PR China.
| | - Chun Zou
- Department of Immunology, College of Basic Medical Science, Central South University, Changsha, Hunan 410008 PR China.
| | - Mei He
- Department of Immunology, College of Basic Medical Science, Central South University, Changsha, Hunan 410008 PR China.
| | - Yubo Cai
- Department of Immunology, College of Basic Medical Science, Central South University, Changsha, Hunan 410008 PR China.
| | - Haiping Pei
- Department of Gastrointestinal Surgery, Xiangya Hospital, Central South University, Changsha, Hunan 410008 PR China.
| | - Ming Li
- Department of Immunology, College of Basic Medical Science, Central South University, Changsha, Hunan 410008 PR China.
| |
Collapse
|