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Liu X, Wu Z, Hu T, Lin X, Liang H, Li W, Jin X, Xiao L, Fang X, Zou Y. Comparative genomic analysis reveals niche adaption of Lactobacillus acidophilus. J Appl Microbiol 2023; 134:lxad287. [PMID: 38040628 DOI: 10.1093/jambio/lxad287] [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: 07/23/2023] [Revised: 11/01/2023] [Accepted: 11/30/2023] [Indexed: 12/03/2023]
Abstract
AIMS Lactobacillus acidophilus has been extensively applied in plentiful probiotic products. Although several studies have been performed to investigate the beneficial characteristics and genome function of L. acidophilus, comparative genomic analysis remains scarce. In this study, we collected 74 L. acidophilus genomes from our gut bacterial genome collection and the public database and conducted a comprehensive comparative genomic analysis. METHODS AND RESULTS This study revealed the potential correlation of the genomic diversity and niche adaptation of L. acidophilus from different perspectives. The pan-genome of L. acidophilus was found to be open, with metabolism, information storage, and processing genes mainly distributed in the core genome. Phage- and peptidase-associated genes were found in the genome of the specificity of animal-derived strains, which were related to the adaptation of the animal gut. SNP analysis showed the differences of the utilization of vitamin B12 in cellular of L. acidophilus strains from animal gut and others. CONCLUSIONS This work provides new insights for the genomic diversity analysis of L. acidophilus and uncovers the ecological adaptation of the specific strains.
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Affiliation(s)
- Xudong Liu
- BGI Research, Shenzhen 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhinan Wu
- BGI Research, Shenzhen 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | | | - Xiaoqian Lin
- BGI Research, Shenzhen 518083, China
- School of Bioscience and Biotechnology, South China University of Technology, Guangzhou 510006, China
| | | | - Wenxi Li
- BGI Research, Shenzhen 518083, China
- School of Bioscience and Biotechnology, South China University of Technology, Guangzhou 510006, China
| | - Xin Jin
- BGI Research, Shenzhen 518083, China
| | - Liang Xiao
- BGI Research, Shenzhen 518083, China
- Lars Bolund Institute of Regenerative Medicine Qingdao-Europe Advanced Institute for LifeSciences, Qingdao 266555, China
- Shenzhen Engineering Laboratory of Detection and Intervention of human intestinal microbiome, Shenzhen 518083, China
- BGI College and Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450052, PR China
| | | | - Yuanqiang Zou
- BGI Research, Shenzhen 518083, China
- Lars Bolund Institute of Regenerative Medicine Qingdao-Europe Advanced Institute for LifeSciences, Qingdao 266555, China
- Shenzhen Engineering Laboratory of Detection and Intervention of human intestinal microbiome, Shenzhen 518083, China
- BGI College and Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450052, PR China
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Firouzabadi N, Asadi‐Pooya AA, Alimoradi N, Simani L, Asadollahi M. Polymorphism of glucocorticoid receptor gene (rs41423247) in functional seizures (psychogenic nonepileptic seizures/attacks). Epilepsia Open 2023; 8:1425-1431. [PMID: 37593891 PMCID: PMC10690659 DOI: 10.1002/epi4.12816] [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: 04/12/2023] [Accepted: 08/14/2023] [Indexed: 08/19/2023] Open
Abstract
OBJECTIVE We investigated the association between the glucocorticoid receptor (GR) gene, also known as the nuclear receptor subfamily 3, group C, member 1 (NR3C1), rs41423247 polymorphism, and functional seizures (psychogenic nonepileptic seizures/attacks) in a case-control study. We hypothesized that the tested polymorphism has significant associations with functional seizures (psychogenic nonepileptic seizures/attacks) independent from comorbid depression. METHODS Seventy patients with functional seizures (psychogenic nonepileptic seizures/attacks), 70 with major depressive disorder (MDD), and 70 healthy controls (HCs) were studied. Their DNAs were analyzed for NR3C1 rs41423247 polymorphism. RESULTS Genotype and allele frequencies of rs41423247 were different between the three groups. G allele carriers were more frequent in patients with functional seizures (psychogenic nonepileptic seizures/attacks) and those with MDD compared to HCs (p = 0.0001). However no significant difference was observed with respect to allele distributions between functional seizures (psychogenic nonepileptic seizures/attacks) and MDD groups (p = 0.391). CC genotype was less often associated with functional seizures (psychogenic nonepileptic seizures/attacks) versus HC: Codominant model; p = 0.001, OR = 0.11, 95% CI = 0.05-0.24, and -2loglilkelihood = 231.7. In comparison between functional seizures (psychogenic nonepileptic seizures/attacks) group and other (MDD + HC) groups, we observed a significant association between CG genotype and functional seizures (psychogenic nonepileptic seizures/attacks) (Codominant model; p = 0.001, OR = 5.63, 95% CI = 2.60-12.40 and -2loglikelihood = 245.99). SIGNIFICANCE Patients with functional seizures (psychogenic nonepileptic seizures/attacks) and those with MDD were significantly more often G allele carriers in rs41423247 compared with HCs. We observed a significant association between CG genotype and functional seizures (psychogenic nonepileptic seizures/attacks). However, we could not exclude the possibility of confounding effects of depression. Future genetic studies of patients with functional seizures (psychogenic nonepileptic seizures/attacks) should include a comparison group with depression in addition to a comparison group of HCs.
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Affiliation(s)
- Negar Firouzabadi
- Department of Pharmacology and Toxicology, School of PharmacyShiraz University of Medical SciencesShirazIran
| | - Ali A. Asadi‐Pooya
- Epilepsy Research CenterShiraz University of Medical SciencesShirazIran
- Jefferson Comprehensive Epilepsy Center, Department of NeurologyThomas Jefferson UniversityPhiladelphiaPennsylvaniaUSA
| | - Nahid Alimoradi
- Department of Pharmacology and Toxicology, School of PharmacyShiraz University of Medical SciencesShirazIran
| | - Leila Simani
- Brain Mapping Research CenterShahid Beheshti University of Medical SciencesTehranIran
- Department of Pharmaceutical Sciences, College of PharmacyUniversity of KentuckyLexingtonKentuckyUSA
| | - Marjan Asadollahi
- Department of Epilepsy, Loghman Hakim HospitalShahid Beheshti University of Medical SciencesTehranIran
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Chen L, Zhao M, Zhou M, Luo J, Li S, Liu X, Cheng Z, Zhuo Y, Zeng W, Zhang Z, Zhou L. LncRNA RP1-276N6.2 Expression and RP1-276N6.2 Gene Polymorphisms Contribute to the Risk of Coronary Artery Disease in Chinese Han Population. DNA Cell Biol 2023; 42:746-752. [PMID: 37843894 DOI: 10.1089/dna.2023.0202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) have been implicated in coronary artery disease (CAD) processes. However, the relationship between the gene polymorphisms of lncRNA RP1-276N6.2 as a novel molecule and susceptibility to CAD remains unclear. In our case-control study, 949 CAD patients and 892 healthy controls were genotyped using the TaqMan genotyping assay. The quantitative real-time polymerase chain reaction and enzyme-linked immunosorbent assay were performed to examine the expression levels of RP1-276N6.2 and SLC22A3(OCT3). We observed that CAD patients had significantly lower RP1-276N6.2 levels than those healthy participants (p < 0.05). Compared to the wild-type genotype, the rs611950 T allele and the rs10499313 AG genotype and G allele significantly increased the premature CAD risk (p = 0.02, p = 0.002, and p = 0.01, respectively), while the rs505000 G allele reduced this risk (p = 0.01); moreover, the rs505000 CG genotype significantly enhanced the delayed CAD risk (p = 0.03), and the rs505000 G allele reduced the expression levels of RP1-276N6.2 and SLC22A3 (p < 0.05 and p < 0.05, respectively). In addition, RP1-276N6.2 positively regulated the mRNA and secreted protein levels of SLC22A3 (p < 0.05). In conclusion, the RP1-276N6.2 gene polymorphisms were closely associated with CAD risk. LncRNA RP1-276N6.2 may be a potential genetic target for CAD early diagnosis and treatment.
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Affiliation(s)
- Lijuan Chen
- Department of Epidemiology, School of Public Health, Chongqing Medical University, Chongqing, China
| | - Mingming Zhao
- Department of Epidemiology, School of Public Health, Chongqing Medical University, Chongqing, China
| | - Mingsha Zhou
- Department of Epidemiology, School of Public Health, Chongqing Medical University, Chongqing, China
| | - Jia Luo
- Department of Epidemiology, School of Public Health, Chongqing Medical University, Chongqing, China
| | - Shan Li
- Department of Epidemiology, School of Public Health, Chongqing Medical University, Chongqing, China
| | - Xing Liu
- Department of Epidemiology, School of Public Health, Chongqing Medical University, Chongqing, China
| | - Zheng Cheng
- Department of Epidemiology, School of Public Health, Chongqing Medical University, Chongqing, China
| | - Yang Zhuo
- Department of Epidemiology, School of Public Health, Chongqing Medical University, Chongqing, China
| | - Weiqi Zeng
- Department of Epidemiology, School of Public Health, Chongqing Medical University, Chongqing, China
| | - Zhiyu Zhang
- Department of Epidemiology, School of Public Health, Chongqing Medical University, Chongqing, China
| | - Li Zhou
- Department of Epidemiology, School of Public Health, Chongqing Medical University, Chongqing, China
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Mitarai Y, Tanino R, Nakashima K, Hotta T, Isobe T, Tsubata Y. Effects of single nucleotide polymorphisms of the folylpolyglutamate synthase gene on pemetrexed administration-induced nephropathy. Br J Clin Pharmacol 2023; 89:3551-3560. [PMID: 37452621 DOI: 10.1111/bcp.15851] [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: 01/06/2023] [Revised: 06/30/2023] [Accepted: 07/03/2023] [Indexed: 07/18/2023] Open
Abstract
AIMS Long-term administration of pemetrexed (PEM) in patients with lung cancer can cause renal damage, leading to treatment discontinuation. Previous reports have suggested that specific single nucleotide polymorphisms (SNPs) in the folylpolyglutamate synthase (FPGS) gene affect therapeutic efficacy; however, whether the FPGS SNPs affect renal function is unclear. Identifying SNPs related to renal damage during PEM administration may help predict the decrease in renal function caused by PEM. METHODS We retrospectively examined age, sex, body weight, total administered PEM, combined platinum, estimated glomerular filtration rate (eGFR) and serum creatinine (SCr) levels before and after PEM administration in patients with non-small cell lung cancer and searched for the alleles of FPGS SNPs (rs1544105 and rs10106) using DNA extracted from whole blood samples of patients. RESULTS Renal function decreased after PEM administration in 26 cases overall. The SCr and eGFR indices showed decreased renal function irrespective of concomitant cisplatin use. Based on promoter activity and miRNA binding predictions, rs1544105-C and rs10106-T were hypothesized to increase FPGS expression. Single SNP analyses showed no significant differences in renal function between groups with and without each SNP. Multiple regression analysis revealed that the most significant factors for decreased renal function were sex on SCr and the number of SNPs on eGFR. In subgroup analyses, the patients with rs10106-T showed a decline in renal function in the older group. CONCLUSIONS The number of FPGS SNPs may contribute to PEM-induced renal impairment. Detecting FPGS SNPs may help predict PEM-induced renal damage.
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Affiliation(s)
- Yuki Mitarai
- Department of Internal Medicine, Division of Medical Oncology & Respiratory Medicine, Shimane University Faculty of Medicine, Izumo, Japan
| | - Ryosuke Tanino
- Department of Internal Medicine, Division of Medical Oncology & Respiratory Medicine, Shimane University Faculty of Medicine, Izumo, Japan
| | - Kazuhisa Nakashima
- Department of Internal Medicine, Division of Medical Oncology & Respiratory Medicine, Shimane University Faculty of Medicine, Izumo, Japan
| | - Takamasa Hotta
- Department of Respiratory Medicine, Shimane Prefectural Central Hospital, Izumo, Japan
| | - Takeshi Isobe
- Department of Internal Medicine, Division of Medical Oncology & Respiratory Medicine, Shimane University Faculty of Medicine, Izumo, Japan
| | - Yukari Tsubata
- Department of Internal Medicine, Division of Medical Oncology & Respiratory Medicine, Shimane University Faculty of Medicine, Izumo, Japan
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Seral-Cortes M, Sabroso-Lasa S, Gonzalez-Gross M, Quesada-Gonzalez C, Stehle P, Gottrand F, Marcos A, Esperanza-Diaz L, Manios Y, Androutsos O, Widhalm K, Molnar D, Huybrechts I, Muntaner M, Meirhaeghe A, Salazar-Tortosa D, Ruiz JR, Esteban LM, Labayen I, Moreno LA. The body mass index increases the genetic risk scores' ability to predict risk of hepatic damage in European adolescents: The HELENA study. Eur J Clin Invest 2023; 53:e14081. [PMID: 37608495 DOI: 10.1111/eci.14081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 07/27/2023] [Accepted: 08/03/2023] [Indexed: 08/24/2023]
Abstract
BACKGROUND Hepatic disorders are often complex and multifactorial, modulated by genetic and environmental determinants. During the last years, the hepatic disease has been progressively established from early stages in life. The use of genetic risk scores (GRS) to predict the genetic susceptibility to a particular phenotype among youth has gained interest in recent years. Moreover, the alanine aminotransferase (ALT) blood biomarker is often considered as hepatic screening tool, in combination with imaging techniques. The aim of the present study was to develop an ALT-specific GRS to help in the evaluation of hepatic damage risk in European adolescents. METHODS A total of 972 adolescents (51.3% females), aged 12.5-17.5 years, from the Healthy Lifestyle in Europe by Nutrition in Adolescence study were included in the analyses. The sample incorporated adolescents in all body mass index (BMI) categories and was divided considering healthy/unhealthy ALT levels, using sex-specific cut-off points. From 1212 a priori ALT-related single nucleotide polymorphisms (SNPs) extracted from candidate gene selection, a first screening of 234 SNPs univariately associated was established, selecting seven significant SNPs (p < .05) in the multivariate model. An unweighted GRS (uGRS) was developed by summing the number of reference alleles, and a weighted GRS (wGRS), by multiplying each allele to its estimated coefficient. RESULTS The uGRS and wGRS were significantly associated with ALT (p < .001). The area under curve was obtained integrating BMI as clinical factor, improving the predictive ability for uGRS (.7039) and wGRS (.7035), using 10-fold internal cross-validation. CONCLUSIONS Considering BMI status, both GRSs could contribute as complementary tools to help in the early diagnosis of hepatic damage risk in European adolescents.
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Affiliation(s)
- Miguel Seral-Cortes
- Growth, Exercise, Nutrition and Development (GENUD) Research Group, Faculty of Health Sciences, Instituto Agroalimentario de Aragón (IA2), Instituto de Investigación Sanitaria Aragón (IIS Aragón), Universidad de Zaragoza, Zaragoza, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Instituto de Salud Carlos III, Madrid, Spain
| | - Sergio Sabroso-Lasa
- Genetic and Molecular Epidemiology Group (GMEG), Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Marcela Gonzalez-Gross
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Instituto de Salud Carlos III, Madrid, Spain
- ImFine Research Group, Department of Health and Human Performance, Facultad de Ciencias de la Actividad Física y del Deporte-INEF, Universidad Politécnica de Madrid, Madrid, Spain
- Institute of Nutritional and Food Sciences, Nutritional Physiology, University of Bonn, Bonn, Germany
| | - Carlos Quesada-Gonzalez
- ImFine Research Group, Department of Health and Human Performance, Facultad de Ciencias de la Actividad Física y del Deporte-INEF, Universidad Politécnica de Madrid, Madrid, Spain
- Department of Applied Mathematics to Information and Communication Technologies, Universidad Politécnica de Madrid, Madrid, Spain
| | - Peter Stehle
- Institute of Nutritional and Food Sciences, Nutritional Physiology, University of Bonn, Bonn, Germany
| | - Frederic Gottrand
- CHU Lille, Inserm U1286 INFINITE, University of Lille, Lille, France
| | - Ascension Marcos
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Instituto de Salud Carlos III, Madrid, Spain
- Immunonutrition Group, Department of Metabolism and Nutrition, Institute of Food Science, Technology and Nutrition (ICTAN), Spanish National Research Council (CSIC), Madrid, Spain
| | - Ligia Esperanza-Diaz
- Immunonutrition Group, Department of Metabolism and Nutrition, Institute of Food Science, Technology and Nutrition (ICTAN), Spanish National Research Council (CSIC), Madrid, Spain
| | - Yannis Manios
- Department of Nutrition and Dietetics, School of Health Science & Education, Harokopio University, Athens, Greece
- Institute of Agri-food and Life Sciences, Hellenic Mediterranean University Research Centre, Heraklion, Greece
| | - Odysseas Androutsos
- Lab of Clinical Nutrition and Dietetics, Department of Nutrition and Dietetics, School of Physical Education, Sport Science and Dietetics, University of Thessaly, Trikala, Greece
| | - Kurt Widhalm
- Division of Clinical Nutrition and Prevention, Department of Paediatrics, Medical University of Vienna, Vienna, Austria
- Austrian Academic Institute for Clinical Nutrition, Vienna, Austria
| | - Denes Molnar
- Department of Pediatrics, Medical School, University of Pécs, Pécs, Hungary
| | - Inge Huybrechts
- International Agency for Research on Cancer, World Health Organization, Lyon, France
- French Network for Nutrition and Cancer Research (NACRe network), Jouy-en-Josas, France
| | - Manon Muntaner
- UMR1167, RID-AGE, Risk Factors and Molecular Determinants of Aging-Related Diseases, Centre Hosp, Institut Pasteur de Lille, Université de Lille, Lille, France
| | - Aline Meirhaeghe
- UMR1167, RID-AGE, Risk Factors and Molecular Determinants of Aging-Related Diseases, Centre Hosp, Institut Pasteur de Lille, Université de Lille, Lille, France
| | - Diego Salazar-Tortosa
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona, USA
| | - Jonatan R Ruiz
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Instituto de Salud Carlos III, Madrid, Spain
- Department of Physical Education and Sports, Faculty of Sports Science, Sport and Health University Research Institute (iMUDS), Granada, Spain
- Instituto de Investigación Biosanitaria, ibs.Granada, Granada, Spain
| | | | - Idoia Labayen
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Instituto de Salud Carlos III, Madrid, Spain
- Department of Health Sciences, Public University of Navarra, Pamplona, Spain
| | - Luis A Moreno
- Growth, Exercise, Nutrition and Development (GENUD) Research Group, Faculty of Health Sciences, Instituto Agroalimentario de Aragón (IA2), Instituto de Investigación Sanitaria Aragón (IIS Aragón), Universidad de Zaragoza, Zaragoza, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Instituto de Salud Carlos III, Madrid, Spain
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Silva MA, Resende CMM, Louro MB, Ribeiro SAV, do Carmo Castro Franceschini S, Velasquez-Melendez G, Alvarez-Leite JI, Durso DF, de Novaes JF. Higher atherogenic risk in schoolchildren is associated with MTMR9 rs2293855 gene polymorphism and genetic score. NUTR BULL 2023; 48:559-571. [PMID: 37905391 DOI: 10.1111/nbu.12644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 10/02/2023] [Accepted: 10/03/2023] [Indexed: 11/02/2023]
Abstract
Childhood dyslipidaemia is associated with the occurrence of cardiovascular diseases in adulthood, so evaluating whether an individual has a genetic predisposition to this pathology is of great importance for early action of prevention and treatment. This study aimed to evaluate the association between the FTO (rs9939609), MC4R (rs17782313) and MTMR9 (rs2293855) polymorphisms, the obesity-related genetic risk score and atherogenic risk in Brazilian children. This is a cross-sectional study conducted in 544 children aged 4-9 years in the city of Viçosa, Minas Gerais state, Brazil. The single nucleotide polymorphisms rs9939609, rs17782313 and rs2293855, were identified by the system TaqMan SNP genotyping and the obesity-related genetic risk score was determined. The lipid profile (serum total cholesterol [TC], high density lipoprotein [HDL] cholesterol, low density lipoprotein [LDL] cholesterol, triglycerides) was analysed and the atherogenic indices (Castelli I and II indices), atherogenic coefficient (AC), lipoprotein combined index (LCI) and plasma atherogenic index (PAI) were calculated. A semi-structured questionnaire was applied, obtaining data on the sociodemographic, economic and lifestyle characteristics of the children. Weight and height measurements were performed in all children, and body composition was evaluated by Dual-Energy X-ray Absorptiometry (DXA). 55.5% of the sample had dyslipidaemia, while 28.5% of the sample had at least one polymorphism and 2.2% had three polymorphisms. Children with the AG/AA genotypes in the rs2293855 polymorphism had lower HDL cholesterol levels and higher TC/HDL cholesterol, LDL/HDL cholesterol ratios and AC. Those with one or more polymorphisms (rs9939609, rs17782313 and rs2293855) in the genetic risk score had lower HDL cholesterol levels and higher TC/HDL cholesterol ratios, AC, LCI and PAI. In conclusion, the risk allele of the rs2293855 polymorphism and a higher obesity-related genetic risk score were positively associated with higher atherogenic risk in Brazilian children.
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Affiliation(s)
- Mariane Alves Silva
- Faculty of Nutrition, Universidade Federal de Mato Grosso (UFMT), Cuiabá, Brazil
| | - Cristina Maria Mendes Resende
- Departament of Nutrition, Universidade Federal de Lavras, Trevo Rotatória Professor Edmir Sá Santos CEP: 37203-202, Lavras, Brazil
| | - Maíra Barros Louro
- Department of Maternal Child and Public Health, School of Nursing, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | | | | | - Gustavo Velasquez-Melendez
- Department of Maternal Child and Public Health, School of Nursing, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | | | - Danielle Fernandes Durso
- Department of Neurology, Wellstone Program, University of Massachusetts Medical School, Worcester, Massachusetts, USA
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Akhtar MS. The Variant Allele Frequency of CTLA-4 rs11571317 (-658 C/T) Polymorphism With Colorectal Cancer Susceptibility in the Saudi Population and Other Ethnic Groups. Cureus 2023; 15:e50091. [PMID: 38186404 PMCID: PMC10770638 DOI: 10.7759/cureus.50091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/05/2023] [Indexed: 01/09/2024] Open
Abstract
The single nucleotide polymorphisms (SNPs) in the promoter region of the cytotoxic T-lymphocyte antigen-4 (CTLA-4) gene are directly associated with the progression and onset of various human cancers. These SNPs are important prognostic biomarkers for the prediction and early onset of cancer risk. The variant frequency of the CTLA-4 rs11571317 (-658 C/T) polymorphism may be affecting the various ethnic groups differently. In the present study, the allelic frequency distribution of -658 C/T polymorphism was assessed in the population of Saudi Arabia and compared with other world populations. The data from different cancers were extracted from case-control studies in the various ethnic groups by using PubMed (MEDLINE) and similar web databases. The frequency of CTLA-4 rs11571317 (-658 C/T) variant allele (T) was observed to be 25.5% and different frequencies were found significant for India (p = 0.001), USA (p = 0.03), and China (p = 0.04), when the prevalence of Saudi Arabian population was compared to that of other population groups. The current finding reveals that there is a distinct pattern of CTLA-4 rs11571317 (-658 C/T) polymorphism variant allele in the populations of Saudi Arabia, may be because of the differences in ethnicity. The observed findings can help in the assessment of the risk for the population harboring the risk allele of rs11571317 (-658 C/T) SNP and toward their subsequent susceptibility to cancer.
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Affiliation(s)
- Mohammad Salman Akhtar
- Department of Basic Medical Sciences, Faculty of Applied Medical Sciences, Al Baha University, Al Baha, SAU
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Baghaei NN, Zhai G, Lamani E. Genetic and other factors contributing to external apical root resorption in orthodontic patients. Orthod Craniofac Res 2023; 26 Suppl 1:64-72. [PMID: 37526277 PMCID: PMC10830890 DOI: 10.1111/ocr.12701] [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: 11/24/2022] [Revised: 06/16/2023] [Accepted: 07/14/2023] [Indexed: 08/02/2023]
Abstract
OBJECTIVE External apical root resorption (EARR) is a multifactorial disorder with adverse clinical outcomes in orthodontic practices often resulting in significant root shortening. This study examined the effect that specific single nucleotide polymorphisms (SNPs) have on the risk of developing EARR in orthodontic patients in X. We also evaluated how other selected patient- and treatment-related factors may contribute to root resorption in these patients. SETTING/SAMPLE Patients included in this case-control study were treated at the University of Alabama at Birmingham School of Dentistry, Department of Orthodontics. METHODS Panoramic radiographs were used to measure root resorption of the maxillary incisors. EARR was recorded when at least 20% of the root length had been lost with orthodontic treatment. Factors evaluated for association with EARR included ethnicity, sex, age, dental and skeletal classifications, ANB, U1-SN, overjet, treatment type and time, and SNPs in IL-1A (rs1800587), IL-1B (rs1143634), IL-1RN (rs419598), P2RX7 (rs1718119 and rs2230912), IRAK1 (rs1059703) and CASP1 (rs530537, rs580253 and rs554344). Chi-square test, Student's t test, Wilcoxon test, Benjamin-Hochberg false discovery rate (FDR) adjustment and logistic regression were used to analyse the data. The significance level was defined as P < .05. RESULTS We found that extraction treatment protocol and dental classification displayed significant association with root resorption. Furthermore, the GG genotype of IL-1A rs1800587 variant (in individuals with an increased overjet) predisposed Caucasians to EARR. While CASP1 (rs530537) variant may contribute to the risk of root resorption, it was not statistically significant after FDR adjustment (P = .09). CONCLUSIONS Both patient- and treatment-related factors contributed to EARR.
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Affiliation(s)
- Nellie N. Baghaei
- Department of Orthodontics, School of Dentistry, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Guihua Zhai
- Center for Clinical and Translational Science, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Ejvis Lamani
- Department of Orthodontics, School of Dentistry, University of Alabama at Birmingham, Birmingham, Alabama, USA
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Zhang Y, Song Y, Zhang W, Xiao T, Peng H. Effect of NLR family pyrin domain containing 9 gene polymorphism on litter size in large white pigs. Anim Biotechnol 2023; 34:4547-4552. [PMID: 36651576 DOI: 10.1080/10495398.2023.2166840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
NLR family pyrin domain containing 9 (NLRP9) is a mammalian reproduction-related gene. In this study, we researched the associations between polymorphisms located in the coding sequence (CDS) of the NLRP9 gene, and both the total number of piglets born per litter (TNB) and the number of piglets born alive per litter (NBA) in Canada Large White pigs (CLW). We detected a single nucleotide polymorphism (SNP) within exon 3 (g.10910C > T). The allele frequencies at the NLRP9 locus were 0.474 for the C allele and 0.526 for the T allele. Three genotypes, CC, CT, and TT, occurred with frequencies of 0.216, 0.515, and 0.269, respectively. Sows with the CC genotype had the largest TNB and NBA, sows with TT had the smallest, and those with CT were in-between. This difference was statistically significant (p < 0.05). Furthermore, CC females grew faster than CT or TT females, and there was a significant relationship between NLRP9 polymorphism and the average daily gain (p < 0.05). Here, we provide the first evidence for a novel SNP in NLRP9 associated with litter size in CLW sows, which could be used as a genetic marker to improve litter size in pig breeding and production.
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Affiliation(s)
- Yanyan Zhang
- College of Animal Science and Technology, Hainan University, Haikou, Hainan, China
- College of Animal Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Yongqi Song
- Ruzhou Vocational and Technical College, Ruzhou, Henan, China
| | - Wenchang Zhang
- College of Animal Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Tianfang Xiao
- College of Animal Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Hui Peng
- College of Animal Science and Technology, Hainan University, Haikou, Hainan, China
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Lee JH, Ahn EH, Kwon MJ, Ryu CS, Ha YH, Ko EJ, Lee JY, Hwang JY, Kim JH, Kim YR, Kim NK. Genetic Correlation of miRNA Polymorphisms and STAT3 Signaling Pathway with Recurrent Implantation Failure in the Korean Population. Int J Mol Sci 2023; 24:16794. [PMID: 38069116 PMCID: PMC10706094 DOI: 10.3390/ijms242316794] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 11/24/2023] [Accepted: 11/24/2023] [Indexed: 12/18/2023] Open
Abstract
The growing prevalence of in vitro fertilization-embryo transfer procedures has resulted in an increased incidence of recurrent implantation failure (RIF), necessitating focused research in this area. STAT3, a key factor in maternal endometrial remodeling and stromal proliferation, is crucial for successful embryo implantation. While the relationship between STAT3 and RIF has been studied, the impact of single nucleotide polymorphisms (SNPs) in miRNAs, well-characterized gene expression modulators, on STAT3 in RIF cases remains uncharacterized. Here, we investigated 161 RIF patients and 268 healthy control subjects in the Korean population, analyzing the statistical association between miRNA genetic variants and RIF risk. We aimed to determine whether SNPs in specific miRNAs, namely miR-218-2 rs11134527 G>A, miR-34a rs2666433 G>A, miR-34a rs6577555 C>A, and miR-130a rs731384 G>A, were significantly associated with RIF risk. We identified a significant association between miR-34a rs6577555 C>A and RIF prevalence (implantation failure [IF] ≥ 2: adjusted odds ratio [AOR] = 2.264, 95% CI = 1.007-5.092, p = 0.048). These findings suggest that miR-34a rs6577555 C>A may contribute to an increased susceptibility to RIF. However, further investigations are necessary to elucidate the precise mechanisms underlying the role of miR-34a rs6577555 C>A in RIF. This study sheds light on the genetic and molecular factors underlying RIF, offering new avenues for research and potential advancements in the diagnosis and treatment of this complex condition.
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Affiliation(s)
- Jung Hun Lee
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam 13488, Republic of Korea; (J.H.L.); (M.J.K.); (C.S.R.); (Y.H.H.); (E.J.K.); (J.Y.L.)
| | - Eun Hee Ahn
- Department of Obstetrics and Gynecology, CHA Bundang Medical Center, CHA University, Seongnam 13496, Republic of Korea; (E.H.A.); (J.H.K.)
| | - Min Jung Kwon
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam 13488, Republic of Korea; (J.H.L.); (M.J.K.); (C.S.R.); (Y.H.H.); (E.J.K.); (J.Y.L.)
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, IA 50011, USA
| | - Chang Su Ryu
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam 13488, Republic of Korea; (J.H.L.); (M.J.K.); (C.S.R.); (Y.H.H.); (E.J.K.); (J.Y.L.)
| | - Yong Hyun Ha
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam 13488, Republic of Korea; (J.H.L.); (M.J.K.); (C.S.R.); (Y.H.H.); (E.J.K.); (J.Y.L.)
| | - Eun Ju Ko
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam 13488, Republic of Korea; (J.H.L.); (M.J.K.); (C.S.R.); (Y.H.H.); (E.J.K.); (J.Y.L.)
| | - Jeong Yong Lee
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam 13488, Republic of Korea; (J.H.L.); (M.J.K.); (C.S.R.); (Y.H.H.); (E.J.K.); (J.Y.L.)
| | - Ji Young Hwang
- Department of Obstetrics and Gynecology, Fertility Center of CHA Gangnam Medical Center, CHA University, Seoul 06135, Republic of Korea;
| | - Ji Hyang Kim
- Department of Obstetrics and Gynecology, CHA Bundang Medical Center, CHA University, Seongnam 13496, Republic of Korea; (E.H.A.); (J.H.K.)
| | - Young Ran Kim
- Department of Obstetrics and Gynecology, CHA Bundang Medical Center, CHA University, Seongnam 13496, Republic of Korea; (E.H.A.); (J.H.K.)
| | - Nam Keun Kim
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam 13488, Republic of Korea; (J.H.L.); (M.J.K.); (C.S.R.); (Y.H.H.); (E.J.K.); (J.Y.L.)
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Turczynowicz A, Jakubów P, Niedźwiecka K, Kondracka J, Pużyńska W, Tałałaj M, Guszczyn T, Grabala P, Kowalczuk O, Kocańda S. Mu-Opioid Receptor 1 and C-Reactive Protein Single Nucleotide Polymorphisms as Biomarkers of Pain Intensity and Opioid Consumption. Brain Sci 2023; 13:1629. [PMID: 38137077 PMCID: PMC10741726 DOI: 10.3390/brainsci13121629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 11/13/2023] [Accepted: 11/20/2023] [Indexed: 12/24/2023] Open
Abstract
Children constitute a special group in pain therapy. Single nucleotide polymorphisms that are associated with differences in postoperative, inflammatory pain perception and opioid requirement are the A118G SNP in the mu-opioid receptor 1 (OPRM1) gene and the rs1205 CRP. This study aimed to determine connection between OPRM1 and rs1205 CRP SNPs in pediatric patients postoperatively and pain intensity, the opioid dose needed to control pain after scoliosis correction, and other clinical aspects. Genotypes of rs1205 CRP and OPRM1 polymorphisms in a sample of 31 patients were specified, and statistical analysis was performed in terms of age, genotype frequency, pain assessment, sufentanil flow, post-anesthesia care unit stay, and the use of coanalgesics. The frequency of A/A and A/G genotypes in the OPRM1 gene was in line with 1000Genomes data for the European population. Patients from the AG group of OPRM1 SNP more frequently required coanalgesics for adequate pain control; however, it was of weak statistical significance. Other parameters measured in the study were not statistically significant in relation to OPRM1 and CRP polymorphisms. The effect of SNPs on postoperative pain management and opioid therapy in children was not confirmed by this study. An expansion of the study sample and other opioid-related SNPs is required.
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Affiliation(s)
- Aleksander Turczynowicz
- Department of Anesthesiology and Intensive Care for Children and Adolescents with Postoperative and Pain Treatment Unit, Medical University of Bialystok, 15-274 Bialystok, Poland; (P.J.); (J.K.); (M.T.)
| | - Piotr Jakubów
- Department of Anesthesiology and Intensive Care for Children and Adolescents with Postoperative and Pain Treatment Unit, Medical University of Bialystok, 15-274 Bialystok, Poland; (P.J.); (J.K.); (M.T.)
| | - Karolina Niedźwiecka
- Department of Cardiosurgery, Medical University of Bialystok, 15-276 Bialystok, Poland; (K.N.)
| | - Julia Kondracka
- Department of Anesthesiology and Intensive Care for Children and Adolescents with Postoperative and Pain Treatment Unit, Medical University of Bialystok, 15-274 Bialystok, Poland; (P.J.); (J.K.); (M.T.)
| | - Weronika Pużyńska
- Department of Palliative Medicine, Medical University of Bialystok, 15-276 Bialystok, Poland;
| | - Mariola Tałałaj
- Department of Anesthesiology and Intensive Care for Children and Adolescents with Postoperative and Pain Treatment Unit, Medical University of Bialystok, 15-274 Bialystok, Poland; (P.J.); (J.K.); (M.T.)
| | - Tomasz Guszczyn
- Department of Pediatric Orthopedics and Traumatology, Medical University of Bialystok, 15-274 Bialystok, Poland; (T.G.); (P.G.)
| | - Paweł Grabala
- Department of Pediatric Orthopedics and Traumatology, Medical University of Bialystok, 15-274 Bialystok, Poland; (T.G.); (P.G.)
| | - Oksana Kowalczuk
- Department of Clinical Molecular Biology, Medical University of Bialystok, 15-269 Bialystok, Poland
| | - Szymon Kocańda
- Department of Cardiosurgery, Medical University of Bialystok, 15-276 Bialystok, Poland; (K.N.)
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Islam MR, Sharma MK, KhunKhun R, Shandro C, Sekirov I, Tyrrell GJ, Soualhine H. Whole genome sequencing-based identification of human tuberculosis caused by animal-lineage Mycobacterium orygis. J Clin Microbiol 2023; 61:e0026023. [PMID: 37877705 PMCID: PMC10662373 DOI: 10.1128/jcm.00260-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 09/11/2023] [Indexed: 10/26/2023] Open
Abstract
A recently described member of the Mycobacterium tuberculosis complex (MTBC) is Mycobacterium orygis, which can cause disease primarily in animals but also in humans. Although M. orygis has been reported from different geographic regions around the world, due to a lack of proper identification techniques, the contribution of this emerging pathogen to the global burden of zoonotic tuberculosis is not fully understood. In the present work, we report single nucleotide polymorphism (SNP) analysis using whole genome sequencing (WGS) that can accurately identify M. orygis and differentiate it from other members of the MTBC species. WGS-based SNP analysis was performed for 61 isolates from different provinces in Canada that were identified as M. orygis. A total of 56 M. orygis sequences from the public databases were also included in the analysis. Several unique SNPs in the gyrB, PPE55, Rv2042c, leuS, mmpL6, and mmpS6 genes were used to determine their effectiveness as genetic markers for the identification of M. orygis. To the best of our knowledge, five of these SNPs, viz., gyrB 277 (A→G), gyrB 1478 (T→C), leuS 1064 (A→T), mmpL6 486 (T→C), and mmpS6 334 (C→G), are reported for the first time in this study. Our results also revealed several SNPs specific to other species within MTBC. The phylogenetic analysis shows that the studied genomes were genetically diverse and clustered with M. orygis sequences of human and animal origin reported from different geographic locations. Therefore, the present study provides a new insight into the high-confidence identification of M. orygis from MTBC species based on WGS data, which can be useful for reference and diagnostic laboratories.
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Affiliation(s)
- Md Rashedul Islam
- National Reference Centre for Mycobacteriology, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Meenu K. Sharma
- National Reference Centre for Mycobacteriology, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Rupinder KhunKhun
- BC Center for Disease Control Public Health Laboratory, Vancouver, British Columbia, Canada
| | - Cary Shandro
- Provincial Laboratory for Public Health, Alberta Precision Labs, Edmonton, Alberta, Canada
| | - Inna Sekirov
- BC Center for Disease Control Public Health Laboratory, Vancouver, British Columbia, Canada
| | - Gregory J. Tyrrell
- Provincial Laboratory for Public Health, Alberta Precision Labs, Edmonton, Alberta, Canada
| | - Hafid Soualhine
- National Reference Centre for Mycobacteriology, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Winnipeg, Manitoba, Canada
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113
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Fuentevilla-Álvarez G, Huesca-Gómez C, Paz-Torres YE, González-Moyotl N, Soto ME, García-Valdivia JA, Sámano R, Martínez-Rosas M, Meza-Toledo SE, Gamboa R. Evaluation of the participation of ABCA1 transporter in epicardial and mediastinal adipose tissue from patients with coronary artery disease. Arch Endocrinol Metab 2023; 68:e230188. [PMID: 37988669 PMCID: PMC10916836 DOI: 10.20945/2359-4292-2023-0188] [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] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 06/01/2023] [Indexed: 11/23/2023]
Abstract
Objective Recent studies have shown a relationship between adipose tissue and coronary artery disease (CAD). The ABCA1 transporter regulates cellular cholesterol content and reverses cholesterol transport. The aim of this study was to determine the relationship between single nucleotide polymorphisms (SNPs) R230C, C-17G, and C-69T and their expression in epicardial and mediastinal adipose tissue in Mexican patients with CAD. Subjects and methods The study included 71 patients with CAD and a control group consisting of 64 patients who underwent heart valve replacement. SNPs were determined using TaqMan probes. mRNA was extracted using TriPure Isolation from epicardial and mediastinal adipose tissue. Quantification and expression analyses were done using RT-qPCR. Results R230C showed a higher frequency of the GG genotype in the CAD group (70.4%) than the control group (57.8%) [OR 0.34, 95% CI (0.14-0.82) p = 0.014]. Similarly, C-17G (rs2740483) showed a statistically significant difference in the CC genotype in the CAD group (63.3%) in comparison to the controls (28.1%) [OR 4.42, 95% CI (2.13-9.16), p = 0.001]. mRNA expression in SNP R230C showed statistically significant overexpression in the AA genotype compared to the GG genotype in CAD patients [11.01 (4.31-15.24) vs. 3.86 (2.47-12.50), p = 0.015]. Conclusion The results suggest that the GG genotype of R230C and CC genotype of C-17G are strongly associated with the development of CAD in Mexican patients. In addition, under-expression of mRNA in the GG genotype in R230C is associated with patients undergoing revascularization.
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Affiliation(s)
- Giovanny Fuentevilla-Álvarez
- Departamento de Fisiología, Instituto Nacional de Cardiología "Ignacio Chávez", Ciudad de México, México
- Departamento de Bioquímica, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional (IPN), Ciudad de México, México
| | - Claudia Huesca-Gómez
- Departamento de Fisiología, Instituto Nacional de Cardiología "Ignacio Chávez", Ciudad de México, México
| | - Yazmín Estela Paz-Torres
- Departamento de Fisiología, Instituto Nacional de Cardiología "Ignacio Chávez", Ciudad de México, México
| | - Nadia González-Moyotl
- Departamento de Fisiología, Instituto Nacional de Cardiología "Ignacio Chávez", Ciudad de México, México
| | - María Elena Soto
- Departamento de Inmunología, Instituto Nacional de Cardiología "Ignacio Chávez", Ciudad de México, México
- Cardiovascular Line in American British Cowdray (ABC) Medical Center, I.A.P. A.B.C.,Mexico City, Mexico
| | | | - Reyna Sámano
- Coordinación de Nutrición y Bioprogramación, Instituto Nacional de Perinatología,Ciudad de México, México
| | - Martín Martínez-Rosas
- Departamento de Fisiología, Instituto Nacional de Cardiología "Ignacio Chávez", Ciudad de México, México
| | - Sergio Enrique Meza-Toledo
- Departamento de Bioquímica, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional (IPN), Ciudad de México, México
| | - Ricardo Gamboa
- Departamento de Fisiología, Instituto Nacional de Cardiología "Ignacio Chávez", Ciudad de México, México,
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Mera-Charria A, Nieto-Lopez F, Francès MP, Arbex PM, Vila-Vecilla L, Russo V, Silva CCV, De Souza GT. Genetic variant panel allows predicting both obesity risk, and efficacy of procedures and diet in weight loss. Front Nutr 2023; 10:1274662. [PMID: 38035352 PMCID: PMC10687570 DOI: 10.3389/fnut.2023.1274662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 10/24/2023] [Indexed: 12/02/2023] Open
Abstract
Purpose Obesity is a multifactorial condition with a relevant genetic correlation. Recent advances in genomic research have identified several single nucleotide polymorphisms (SNPs) in genes such as FTO, MCM6, HLA, and MC4R, associated with obesity. This study aimed to evaluate the association of 102 SNPs with BMI and weight loss treatment response in a multi-ethnic population. Methods The study analyzed 9,372 patients for the correlation between SNPs and BMI (dataset A). The correlation between SNP and weight loss was accessed in 474 patients undergoing different treatments (dataset B). Patients in dataset B were further divided into 3 categories based on the type of intervention: dietary therapy, intragastric balloon procedures, or surgeries. SNP association analysis and multiple models of inheritance were performed. Results In dataset A, ten SNPs, including rs9939609 (FTO), rs4988235 (MCM6), and rs2395182 (HLA), were significantly associated with increased BMI. Additionally, other four SNPs, rs7903146 (TCF7L2), (rs6511720), rs5400 (SLC2A2), and rs7498665 (SH2B1), showed sex-specific correlation. For dataset B, SNPs rs2016520 (PPAR-Delta) and rs2419621 (ACSL5) demonstrated significant correlation with weight loss for all treatment types. In patients who adhered to dietary therapy, SNPs rs6544713 (ABCG8) and rs762551 (CYP1A2) were strongly correlated with weight loss. Patients undergoing surgical or endoscopic procedures exhibited differential correlations with several SNPs, including rs1801725 (CASR) and rs12970134 (MC4R), and weight loss. Conclusion This study provides valuable insights into the genetic factors influencing BMI and weight loss response to different treatments. The findings highlight the potential for personalized weight management approaches based on individual genetic profiles.
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Affiliation(s)
| | - Francisco Nieto-Lopez
- Dorsia Clinics, Madrid, Spain
- Catedra UCAM Dorsia, Catholic University San Antonio of Murcia, Guadalupe, Spain
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Morales-Pison S, Tapia JC, Morales-González S, Maldonado E, Acuña M, Calaf GM, Jara L. Association of Germline Variation in Driver Genes with Breast Cancer Risk in Chilean Population. Int J Mol Sci 2023; 24:16076. [PMID: 38003265 PMCID: PMC10671568 DOI: 10.3390/ijms242216076] [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: 09/27/2023] [Revised: 11/02/2023] [Accepted: 11/04/2023] [Indexed: 11/26/2023] Open
Abstract
Cancer is a genomic disease, with driver mutations contributing to tumorigenesis. These potentially heritable variants influence risk and underlie familial breast cancer (BC). This study evaluated associations between BC risk and 13 SNPs in driver genes MAP3K1, SF3B1, SMAD4, ARID2, ATR, KMT2C, MAP3K13, NCOR1, and TBX3, in BRCA1/2-negative Chilean families. SNPs were genotyped using TaqMan Assay in 492 cases and 1285 controls. There were no associations between rs75704921:C>T (ARID2); rs2229032:A>C (ATR); rs3735156:C>G (KMT2C); rs2276738:G>C, rs2293906:C>T, rs4075943T:>A, rs13091808:C>T (MAP3K13); rs178831:G>A (NCOR1); or rs3759173:C>A (TBX3) and risk. The MAP3K1 rs832583 A allele (C/A+A/A) showed a protective effect in families with moderate BC history (OR = 0.7 [95% CI 0.5-0.9] p = 0.01). SF3B1 rs16865677-T (G/T+T/T) increased risk in sporadic early-onset BC (OR = 1.4 [95% CI 1.0-2.0] p = 0.01). SMAD4 rs3819122-C (A/C+C/C) increased risk in cases with moderate family history (OR = 2.0 [95% CI 1.3-2.9] p ≤ 0.0001) and sporadic cases diagnosed ≤50 years (OR = 1.6 [95% CI 1.1-2.2] p = 0.006). SMAD4 rs12456284:A>G increased BC risk in G-allele carriers (A/G + G/G) in cases with ≥2 BC/OC cases and early-onset cases (OR = 1.2 [95% CI 1.0-1.6] p = 0.04 and OR = 1.4 [95% CI 1.0-1.9] p = 0.03, respectively). Our study suggests that specific germline variants in driver genes MAP3K1, SF3B1, and SMAD4 contribute to BC risk in Chilean population.
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Affiliation(s)
- Sebastián Morales-Pison
- Centro de Oncología de Precisión (COP), Facultad de Medicina y Ciencias de la Salud, Universidad Mayor, Las Condes, Santiago 7560908, Chile;
| | - Julio C. Tapia
- Laboratorio de Transformación Celular, Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas (ICBM), Facultad de Medicina, Universidad de Chile, Independencia, Santiago 783090, Chile;
| | - Sarai Morales-González
- Laboratorio de Genética Humana, Programa de Genética Humana, Instituto de Ciencias Biomédicas (ICBM), Facultad de Medicina, Universidad de Chile, Independencia, Santiago 783090, Chile; (S.M.-G.); (M.A.)
| | - Edio Maldonado
- Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas (ICBM), Facultad de Medicina, Universidad de Chile, Independencia, Santiago 783090, Chile;
| | - Mónica Acuña
- Laboratorio de Genética Humana, Programa de Genética Humana, Instituto de Ciencias Biomédicas (ICBM), Facultad de Medicina, Universidad de Chile, Independencia, Santiago 783090, Chile; (S.M.-G.); (M.A.)
| | - Gloria M. Calaf
- Instituto de Alta Investigación, Universidad de Tarapacá, Arica 1010069, Chile;
| | - Lilian Jara
- Laboratorio de Genética Humana, Programa de Genética Humana, Instituto de Ciencias Biomédicas (ICBM), Facultad de Medicina, Universidad de Chile, Independencia, Santiago 783090, Chile; (S.M.-G.); (M.A.)
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Buraczynska M, Wrzos S, Zaluska W. MMP9 Gene Polymorphism (rs3918242) Increases the Risk of Cardiovascular Disease in Type 2 Diabetes Patients. J Clin Med 2023; 12:6990. [PMID: 38002605 PMCID: PMC10672737 DOI: 10.3390/jcm12226990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 10/20/2023] [Accepted: 11/04/2023] [Indexed: 11/26/2023] Open
Abstract
Matrix metalloproteinase 9 (MMP-9) C(-1562)T gene polymorphism has been considered a risk factor for cardiovascular disease (CVD). Our study aimed to evaluate the association between this polymorphism and CVD in diabetes patients. The genotyping was performed in 740 patients with T2DM and 400 healthy subjects. A significant difference in the polymorphism distribution was revealed between patients and controls. The T allele and TT homozygote were associated with increased risk of diabetes (OR 1.88, p < 0.0001 and OR 3.77, p = 0.0002, respectively). The comparison between CVD+ and CVD- subgroups showed a much higher frequency of the T allele in patients with CVD (OR 2.87, 95% CI 2.14-3.85, p < 0.0001). Patients with the TT genotype had a higher prevalence of CVD (OR 3.19, 95% CI 1.55-6.56, p = 0.0015). The carrier genotypes (CT/TT) were correlated with HDL levels in both CVD+ and CVD- subgroups (p < 0.001 for both). In the logistic regression analysis, only C(-1562)T SNP was a significant predictor of CVD in diabetic patients (p < 0.001). In conclusion, our study suggests an association between MMP-9 C(-1562)T polymorphism and an increased risk of CVD in T2DM. If replicated in other studies, it could be considered a genetic marker for predicting risk of T2DM and its cardiovascular comorbidity.
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Affiliation(s)
- Monika Buraczynska
- Department of Nephrology, Medical University of Lublin, 20-093 Lublin, Poland; (S.W.); (W.Z.)
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Xue D, Narisu N, Taylor DL, Zhang M, Grenko C, Taylor HJ, Yan T, Tang X, Sinha N, Zhu J, Vandana JJ, Nok Chong AC, Lee A, Mansell EC, Swift AJ, Erdos MR, Zhong A, Bonnycastle LL, Zhou T, Chen S, Collins FS. Functional interrogation of twenty type 2 diabetes-associated genes using isogenic human embryonic stem cell-derived β-like cells. Cell Metab 2023; 35:1897-1914.e11. [PMID: 37858332 PMCID: PMC10841752 DOI: 10.1016/j.cmet.2023.09.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 07/26/2023] [Accepted: 09/28/2023] [Indexed: 10/21/2023]
Abstract
Genetic studies have identified numerous loci associated with type 2 diabetes (T2D), but the functional roles of many loci remain unexplored. Here, we engineered isogenic knockout human embryonic stem cell lines for 20 genes associated with T2D risk. We examined the impacts of each knockout on β cell differentiation, functions, and survival. We generated gene expression and chromatin accessibility profiles on β cells derived from each knockout line. Analyses of T2D-association signals overlapping HNF4A-dependent ATAC peaks identified a likely causal variant at the FAIM2 T2D-association signal. Additionally, the integrative association analyses identified four genes (CP, RNASE1, PCSK1N, and GSTA2) associated with insulin production, and two genes (TAGLN3 and DHRS2) associated with β cell sensitivity to lipotoxicity. Finally, we leveraged deep ATAC-seq read coverage to assess allele-specific imbalance at variants heterozygous in the parental line and identified a single likely functional variant at each of 23 T2D-association signals.
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Affiliation(s)
- Dongxiang Xue
- Department of Surgery, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA; Center for Genomic Health, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
| | - Narisu Narisu
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - D Leland Taylor
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Meili Zhang
- Department of Surgery, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
| | - Caleb Grenko
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Henry J Taylor
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA; Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, CB1 8RN Cambridge, UK
| | - Tingfen Yan
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Xuming Tang
- Department of Surgery, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA; Center for Genomic Health, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
| | - Neelam Sinha
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jiajun Zhu
- Department of Surgery, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA; Center for Genomic Health, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
| | - J Jeya Vandana
- Department of Surgery, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA; Center for Genomic Health, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA; Tri-Institutional PhD Program in Chemical Biology, Weill Cornell Medicine, The Rockefeller University, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Angie Chi Nok Chong
- Department of Surgery, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA; Center for Genomic Health, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
| | - Angela Lee
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Erin C Mansell
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Amy J Swift
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Michael R Erdos
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Aaron Zhong
- Stem Cell Research Facility, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | - Lori L Bonnycastle
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ting Zhou
- Stem Cell Research Facility, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | - Shuibing Chen
- Department of Surgery, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA; Center for Genomic Health, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA.
| | - Francis S Collins
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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Abu-Farha M, Madhu D, Hebbar P, Mohammad A, Channanath A, Kavalakatt S, Alam-Eldin N, Alterki F, Taher I, Alsmadi O, Shehab M, Arefanian H, Ahmad R, Thanaraj TA, Al-Mulla F, Abubaker J. The Proinflammatory Role of ANGPTL8 R59W Variant in Modulating Inflammation through NF-κB Signaling Pathway under TNFα Stimulation. Cells 2023; 12:2563. [PMID: 37947641 PMCID: PMC10648545 DOI: 10.3390/cells12212563] [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: 07/14/2023] [Revised: 08/17/2023] [Accepted: 10/30/2023] [Indexed: 11/12/2023] Open
Abstract
BACKGROUND Angiopoietin-like protein 8 (ANGPTL8) is known to regulate lipid metabolism and inflammation. It interacts with ANGPTL3 and ANGPTL4 to regulate lipoprotein lipase (LPL) activity and with IKK to modulate NF-κB activity. Further, a single nucleotide polymorphism (SNP) leading to the ANGPTL8 R59W variant associates with reduced low-density lipoprotein/high-density lipoprotein (LDL/HDL) and increased fasting blood glucose (FBG) in Hispanic and Arab individuals, respectively. In this study, we investigate the impact of the R59W variant on the inflammatory activity of ANGPTL8. METHODS The ANGPTL8 R59W variant was genotyped in a discovery cohort of 867 Arab individuals from Kuwait. Plasma levels of ANGPTL8 and inflammatory markers were measured and tested for associations with the genotype; the associations were tested for replication in an independent cohort of 278 Arab individuals. Impact of the ANGPTL8 R59W variant on NF-κB activity was examined using approaches including overexpression, luciferase assay, and structural modeling of binding dynamics. RESULTS The ANGPTL8 R59W variant was associated with increased circulatory levels of tumor necrosis factor alpha (TNFα) and interleukin 7 (IL7). Our in vitro studies using HepG2 cells revealed an increased phosphorylation of key inflammatory proteins of the NF-κB pathway in individuals with the R59W variant as compared to those with the wild type, and TNFα stimulation further elevated it. This finding was substantiated by increased luciferase activity of NF-κB p65 with the R59W variant. Modeled structural and binding variation due to R59W change in ANGPTL8 agreed with the observed increase in NF-κB activity. CONCLUSION ANGPTL8 R59W is associated with increased circulatory TNFα, IL7, and NF-κB p65 activity. Weak transient binding of the ANGPTL8 R59W variant explains its regulatory role on the NF-κB pathway and inflammation.
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Affiliation(s)
- Mohamed Abu-Farha
- Department of Biochemistry and Molecular Biology, Dasman Diabetes Institute, Dasman 15462, Kuwait; (M.A.-F.); (D.M.); (A.M.); (S.K.); (N.A.-E.)
| | - Dhanya Madhu
- Department of Biochemistry and Molecular Biology, Dasman Diabetes Institute, Dasman 15462, Kuwait; (M.A.-F.); (D.M.); (A.M.); (S.K.); (N.A.-E.)
| | - Prashantha Hebbar
- Department of Genetics and Bioinformatics, Dasman Diabetes Institute, Dasman 15462, Kuwait; (P.H.); (A.C.); (F.A.-M.)
| | - Anwar Mohammad
- Department of Biochemistry and Molecular Biology, Dasman Diabetes Institute, Dasman 15462, Kuwait; (M.A.-F.); (D.M.); (A.M.); (S.K.); (N.A.-E.)
| | - Arshad Channanath
- Department of Genetics and Bioinformatics, Dasman Diabetes Institute, Dasman 15462, Kuwait; (P.H.); (A.C.); (F.A.-M.)
| | - Sina Kavalakatt
- Department of Biochemistry and Molecular Biology, Dasman Diabetes Institute, Dasman 15462, Kuwait; (M.A.-F.); (D.M.); (A.M.); (S.K.); (N.A.-E.)
| | - Nada Alam-Eldin
- Department of Biochemistry and Molecular Biology, Dasman Diabetes Institute, Dasman 15462, Kuwait; (M.A.-F.); (D.M.); (A.M.); (S.K.); (N.A.-E.)
| | - Fatima Alterki
- Department of internal Medicine, Amiri Hospital, Ministry of Health, Kuwait City 15462, Kuwait;
| | - Ibrahim Taher
- Microbiology Unit, Department of Pathology, College of Medicine, Jouf University, Sakaka P.O. Box 2014, Saudi Arabia;
| | - Osama Alsmadi
- Department of Cell Therapy and Applied Genomics, King Hussein Cancer Center, Amman 1269, Jordan;
| | - Mohammad Shehab
- Division of Gastroenterology, Department of Internal Medicine, Mubarak Alkabeer University Hospital, Kuwait University, Kuwait City 47061, Kuwait;
| | - Hossein Arefanian
- Department of Immunology & Microbiology, Dasman Diabetes Institute, Dasman 15462, Kuwait; (H.A.); (R.A.)
| | - Rasheed Ahmad
- Department of Immunology & Microbiology, Dasman Diabetes Institute, Dasman 15462, Kuwait; (H.A.); (R.A.)
| | - Thangavel Alphonse Thanaraj
- Department of Genetics and Bioinformatics, Dasman Diabetes Institute, Dasman 15462, Kuwait; (P.H.); (A.C.); (F.A.-M.)
| | - Fahd Al-Mulla
- Department of Genetics and Bioinformatics, Dasman Diabetes Institute, Dasman 15462, Kuwait; (P.H.); (A.C.); (F.A.-M.)
| | - Jehad Abubaker
- Department of Biochemistry and Molecular Biology, Dasman Diabetes Institute, Dasman 15462, Kuwait; (M.A.-F.); (D.M.); (A.M.); (S.K.); (N.A.-E.)
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Sang Y, Zhao H, Liu X, Yuan C, Qi G, Li Y, Dong L, Wang Y, Wang D, Wang Y, Dong Y. Genome-wide association study of powdery mildew resistance in cultivated soybean from Northeast China. Front Plant Sci 2023; 14:1268706. [PMID: 38023859 PMCID: PMC10651740 DOI: 10.3389/fpls.2023.1268706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 10/17/2023] [Indexed: 12/01/2023]
Abstract
Powdery mildew (PMD), caused by the pathogen Microsphaera diffusa, leads to substantial yield decreases in susceptible soybean under favorable environmental conditions. Effective prevention of soybean PMD damage can be achieved by identifying resistance genes and developing resistant cultivars. In this study, we genotyped 331 soybean germplasm accessions, primarily from Northeast China, using the SoySNP50K BeadChip, and evaluated their resistance to PMD in a greenhouse setting. To identify marker-trait associations while effectively controlling for population structure, we conducted genome-wide association studies utilizing factored spectrally transformed linear mixed models, mixed linear models, efficient mixed-model association eXpedited, and compressed mixed linear models. The results revealed seven single nucleotide polymorphism (SNP) loci strongly associated with PMD resistance in soybean. Among these, one SNP was localized on chromosome (Chr) 14, and six SNPs with low linkage disequilibrium were localized near or in the region of previously mapped genes on Chr 16. In the reference genome of Williams82, we discovered 96 genes within the candidate region, including 17 resistance (R)-like genes, which were identified as potential candidate genes for PMD resistance. In addition, we performed quantitative real-time reverse transcription polymerase chain reaction analysis to evaluate the gene expression levels in highly resistant and susceptible genotypes, focusing on leaf tissues collected at different times after M. diffusa inoculation. Among the examined genes, three R-like genes, including Glyma.16G210800, Glyma.16G212300, and Glyma.16G213900, were identified as strong candidates associated with PMD resistance. This discovery can significantly enhance our understanding of soybean resistance to PMD. Furthermore, the significant SNPs strongly associated with resistance can serve as valuable markers for genetic improvement in breeding M. diffusa-resistant soybean cultivars.
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Affiliation(s)
- Yongsheng Sang
- College of Agronomy, Jilin Agricultural University, Changchun, Jilin, China
- Soybean Institute, Jilin Academy of Agricultural Sciences, Changchun, Jilin, China
| | - Hongkun Zhao
- Soybean Institute, Jilin Academy of Agricultural Sciences, Changchun, Jilin, China
| | - Xiaodong Liu
- Crop Germplasm Institute, Jilin Academy of Agricultural Sciences, Changchun, Jilin, China
| | - Cuiping Yuan
- Soybean Institute, Jilin Academy of Agricultural Sciences, Changchun, Jilin, China
| | - Guangxun Qi
- Soybean Institute, Jilin Academy of Agricultural Sciences, Changchun, Jilin, China
| | - Yuqiu Li
- Soybean Institute, Jilin Academy of Agricultural Sciences, Changchun, Jilin, China
| | - Lingchao Dong
- Soybean Institute, Jilin Academy of Agricultural Sciences, Changchun, Jilin, China
| | - Yingnan Wang
- Soybean Institute, Jilin Academy of Agricultural Sciences, Changchun, Jilin, China
| | - Dechun Wang
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, United States
| | - Yumin Wang
- Soybean Institute, Jilin Academy of Agricultural Sciences, Changchun, Jilin, China
| | - Yingshan Dong
- College of Agronomy, Jilin Agricultural University, Changchun, Jilin, China
- Soybean Institute, Jilin Academy of Agricultural Sciences, Changchun, Jilin, China
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Ahmed HA, Fahmy EM, Abdelkreem E, Mahmoud EA, Nafady A, Ahmed EH. Frequency of toll-like receptor 4 variants and association with treatment response in children with primary immune thrombocytopenia. Pediatr Blood Cancer 2023; 70:e30646. [PMID: 37638833 DOI: 10.1002/pbc.30646] [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: 02/11/2023] [Revised: 07/25/2023] [Accepted: 08/16/2023] [Indexed: 08/29/2023]
Abstract
OBJECTIVES To investigate the frequency of toll-like receptor 4 (TLR4) variants c.896A>G (p.Asp299Gly) and c.1196C>T (p.Thr399Ile) among Egyptian children with primary immune thrombocytopenia (pITP), and their association with disease course and response to treatment. METHODS A case-control study that included 80 children with pITP and 50 age- and sex-matched healthy controls. TLR4 c.896A>G and c.1196C>T variants were genotyped using polymerase chain reaction-restriction fragment length polymorphism. Patients were classified according to their response to treatment after 3 months as responders and nonresponders. RESULTS Compared with controls, children with pITP had significantly higher minor allele frequencies of TLR4 p.Asp299Gly (16.25% vs. 6%, odds ratio [OR] 3.04, 95% confidence interval [CI]: 1.16-9.36, p = .014) and p.Thr399Ile (20% vs. 4%, OR 6, 95% CI: 2.02-24.01, p < .001). The presence of p.Asp299Gly variant was significantly associated with chronic ITP (OR 7.78, 95% CI: 2.04-35.69, p < .001) and non-response to therapy with steroid (OR 11.67, 95% CI: 1.32-104.08, p = .012), but not thrombopoietin-receptor agonist (OR 1.67, 95% CI: 0.35-8.19, p = .464). Likewise, having p.Thr399Ile variant was significantly associated with chronic ITP (OR 5.14, 95% CI: 1.6-17.4, p = .002) and non-response to therapy with steroid (OR 6.1, 95% CI: 1.01-49.06, p = .046) but not thrombopoietin-receptor agonist (OR 1.57, 95% CI: 0.33-7.58, p = .515). CONCLUSION The presence of TLR4 p.Asp299Gly or p.Thr399Ile variant may be associated with ITP predisposition, chronicity, and non-response to upfront steroid therapy. These findings enhance our understanding of the complex pathophysiology of pITP with potentially important clinical implications.
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Affiliation(s)
- Heba A Ahmed
- Department of Clinical Pathology, Faculty of Medicine, Sohag University, Sohag, Egypt
| | - Eman M Fahmy
- Department of Pediatrics, Faculty of Medicine, Sohag University, Sohag, Egypt
| | - Elsayed Abdelkreem
- Department of Pediatrics, Faculty of Medicine, Sohag University, Sohag, Egypt
| | - Ekram A Mahmoud
- Department of Microbiology & Immunology, Faculty of Medicine, Sohag University, Sohag, Egypt
| | - Asmaa Nafady
- Department of Clinical and Chemical Pathology, Faculty of Medicine, South Valley University, Qena, Egypt
| | - Eman H Ahmed
- Department of Clinical Pathology, South Egypt Cancer Institute, Assiut University, Assiut, Egypt
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Zaki A, Shaheen N, Hosny M, Ramadan A, Nashwan AJ. A rare case of 2q37 deletion syndrome presented with patent foramen ovale. Clin Case Rep 2023; 11:e6970. [PMID: 38028106 PMCID: PMC10658514 DOI: 10.1002/ccr3.6970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 01/23/2023] [Accepted: 02/06/2023] [Indexed: 12/01/2023] Open
Abstract
This case report presents a 3-year-old female child diagnosed with 2q37 deletion syndrome and patent foramen ovale, and the improvement in hypotonia and gross motor delay after 1 year of physical therapy. This case highlights the importance of thorough examination and diagnostic testing in identifying underlying causes of developmental delays.
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Affiliation(s)
- Ahmed Zaki
- Faculty of MedicineCairo UniversityCairoEgypt
| | - Nour Shaheen
- Faculty of MedicineAlexandria UniversityAlexandriaEgypt
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van Pul L, Maurer I, Boeser-Nunnink BD, Harskamp AM, van Dort KA, Kootstra NA. A genetic variation in fucosyltransferase 8 accelerates HIV-1 disease progression indicating a role for N-glycan fucosylation. AIDS 2023; 37:1959-1969. [PMID: 37598360 PMCID: PMC10552802 DOI: 10.1097/qad.0000000000003689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 07/25/2023] [Accepted: 08/07/2023] [Indexed: 08/22/2023]
Abstract
OBJECTIVES Core fucosylation by fucosyltransferase 8 (FUT8) is an important posttranslational modification that impacts components of the immune system. Genetic variations in FUT8 can alter its function and could, therefore, play a role in the antiviral immune response and pathogenesis of HIV-1. This study analysed the effect of a single nucleotide polymorphism (SNP) in FUT8 on the clinical course of HIV-1 infection. DESIGN/METHODS The effect of SNPs in FUT8 on untreated HIV-1 disease outcome were analysed in a cohort of 304 people with HIV-1 (PWH) using survival analysis. Flow-cytometry was used to determine the effect of SNP on T-cell activation, differentiation and exhaustion/senescence. T-cell function was determined by proliferation assay and by measuring intracellular cytokine production. The effect of the SNP on HIV-1 replication was determined by in-vitro HIV-1 infections. Sensitivity of HIV-1 produced in PBMC with or without the SNP to broadly neutralizing antibodies was determined using a TZM-bl based neutralization assay. RESULTS Presence of the minor allele of SNP rs4131564 was associated with accelerated disease progression. The SNP had no effect on T-cell activation and T-cell differentiation in PWH. Additionally, no differences in T-cell functionality as determined by proliferation and cytokine production was observed. HIV-1 replication and neutralization sensitivity was also unaffected by the SNP in FUT8. CONCLUSION SNP rs4131564 in FUT8 showed a major impact on HIV-1 disease course underscoring a role for N-glycan fucosylation even though no clear effect on the immune system or HIV-1 could be determined in vitro .
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Affiliation(s)
- Lisa van Pul
- Amsterdam Institute for Infection and Immunity
- Department of Experimental Immunology, Amsterdam UMC, location University of Amsterdam, Amsterdam, The Netherlands
| | - Irma Maurer
- Amsterdam Institute for Infection and Immunity
- Department of Experimental Immunology, Amsterdam UMC, location University of Amsterdam, Amsterdam, The Netherlands
| | - Brigitte D.M. Boeser-Nunnink
- Amsterdam Institute for Infection and Immunity
- Department of Experimental Immunology, Amsterdam UMC, location University of Amsterdam, Amsterdam, The Netherlands
| | - Agnes M. Harskamp
- Amsterdam Institute for Infection and Immunity
- Department of Experimental Immunology, Amsterdam UMC, location University of Amsterdam, Amsterdam, The Netherlands
| | - Karel A. van Dort
- Amsterdam Institute for Infection and Immunity
- Department of Experimental Immunology, Amsterdam UMC, location University of Amsterdam, Amsterdam, The Netherlands
| | - Neeltje A. Kootstra
- Amsterdam Institute for Infection and Immunity
- Department of Experimental Immunology, Amsterdam UMC, location University of Amsterdam, Amsterdam, The Netherlands
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Asa'ad F, Petrenya N, Jönsson B, Holde GE, Oscarson N, Hadler-Olsen E, Vieira AR, Petzold M, Larsson L. Polymorphism in epigenetic regulating genes in relation to periodontitis, number of teeth, and levels of high-sensitivity C-reactive protein and glycated hemoglobin: The Tromsø Study 2015-2016. J Periodontol 2023; 94:1324-1337. [PMID: 37382343 DOI: 10.1002/jper.23-0108] [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: 02/17/2023] [Revised: 05/25/2023] [Accepted: 05/26/2023] [Indexed: 06/30/2023]
Abstract
BACKGROUND The aim of this study was to investigate the association between periodontitis and four single nucleotide polymorphisms (SNPs) in genes involved in epigenetic regulation of DNA, and between these same SNPs and tooth loss, high-sensitivity C-reactive protein (hs-CRP), and glycated hemoglobin (HbA1c) levels. METHODS We included participants with periodontal examination (n = 3633, aged: 40-93 years) from the Tromsø Study seventh survey (2015-2016), Norway. Periodontitis was defined according to the 2017 AAP/EFP classification system as no periodontitis, grades A, B, or C. Salivary DNA was extracted and genotyping was performed to investigate four SNPs (rs2288349, rs35474715, rs34023346, and rs10010325) in the sequence of the genes DNMT1, IDH2, TET1, and TET2. Association between SNPs and periodontitis was analyzed by logistic regression adjusted for age, sex, and smoking. Subgroup analyses on participants aged 40-49 years were performed. RESULTS In participants aged 40-49 years, homozygous carriage of minor A-allele of rs2288349 (DNMT1) was associated with decreased susceptibility to periodontitis (grade A: odds ratio [OR] 0.55; p = 0.014: grade B/C OR 0.48; p = 0.004). The minor A-allele of rs10010325 (TET2) was associated with increased susceptibility to periodontitis (grade A OR 1.69; p = 0.035: grade B/C OR 1.90; p = 0.014). In the entire sample, homozygous carriage of the G-allele of rs35474715 (IDH2) was associated with having ≤24 teeth (OR 1.31; p = 0.018). Homozygous carriage of the A-allele of TET2 was associated with hs-CRP≥3 mg/L (OR 1.37; p = 0.025) and HbA1c≥6.5% (OR 1.62; p = 0.028). CONCLUSIONS In this Norwegian population, there were associations between polymorphism in genes related to DNA methylation and periodontitis, tooth loss, low-grade inflammation, and hyperglycemia.
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Affiliation(s)
- Farah Asa'ad
- Department of Biomaterials, Institute of Clinical Sciences, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Oral Biochemistry, Institute of Odontology, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Natalia Petrenya
- The Public Dental Health Service Competence Centre of Northern Norway, Tromsø, Norway
| | - Birgitta Jönsson
- The Public Dental Health Service Competence Centre of Northern Norway, Tromsø, Norway
- Department of Periodontology, Institute of Odontology, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Gro Eirin Holde
- The Public Dental Health Service Competence Centre of Northern Norway, Tromsø, Norway
- Department of Clinical Dentistry, Faculty of Health Sciences, UiT the Arctic University of Norway, Tromsø, Norway
| | - Nils Oscarson
- Clinic of Periodontology, The Public Dental Service, Region Västra Götaland, Skövde, Sweden
| | - Elin Hadler-Olsen
- The Public Dental Health Service Competence Centre of Northern Norway, Tromsø, Norway
- Department of Medical Biology, Faculty of Health Sciences, UiT the Artic University of Norway, Tromsø, Norway
| | - Alexandre R Vieira
- Department of Oral and Craniofacial Sciences, School of Dental Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Max Petzold
- School of Public Health and Community Medicine, Institute of Medicine, The Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Lena Larsson
- Department of Periodontology, Institute of Odontology, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
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Villalba A, Coimbra RM, Pampín M, Iglesias D, Costas D, Mariño C, Blanco A, Vera M, Domínguez M, Cacabelos E, Abella E, Incera M, Otero RF, Martínez P. A common garden experiment supports a genetic component underlying the increased resilience of common cockle ( Cerastoderma edule) to the parasite Marteilia cochillia. Evol Appl 2023; 16:1789-1804. [PMID: 38029062 PMCID: PMC10681494 DOI: 10.1111/eva.13601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 08/27/2023] [Accepted: 09/15/2023] [Indexed: 12/01/2023] Open
Abstract
The common cockle is a valuable bivalve species inhabiting the Atlantic European coasts. The parasite Marteilia cochillia has devastated cockle beds in the southern Galician (NW Spain) rias since 2012. Previous data suggested that cockles from Ría de Arousa acquired some resilience to this parasite through natural selection after consecutive annual marteiliosis outbreaks and candidate markers associated with marteiliosis resilience were identified using population genomics and transcriptomics approaches. Here, a common garden experiment was performed using a naïve stock (from Ría de Muros-Noia) and an affected stock (from Ría de Arousa) to test this hypothesis. Breeders from both stocks were used to produce seed cohorts at hatchery, which were pre-grown in a raft (outdoor nursery stage) and deployed in two shellfish beds affected by marteiliosis in Ría de Arousa (growing-out stage). In both beds, the naïve stock showed high marteiliosis prevalence and was fully depleted in a short period, while the affected stock barely showed evidence of marteiliosis. A set of 45 SNPs putatively associated with marteiliosis resilience were fitted for MassARRAY genotyping to check their role in the differential resilience detected between both stocks. Though no significant differentiation was found between the naïve and the affected stocks with neutral markers, 28 SNPs showed significant divergence between them, suggesting that these SNPs were involved in directional selection during eight generations (to the most) of marteiliosis pressure (long-term selection). Furthermore, signals of selection were also detected in the naïve stock along the marteiliosis outbreak in the growing-out stage (short-term selection) and six SNPs, all shared with the long-term evaluation, showed consistent signals of differentiation according to the infection severity. Some of these SNPs were located within immune genes pertaining to families such as proteasome, ubiquitin, tumor necrosis factor, and glutathione S-transferase. These resilience-associated markers will be useful to recover cockle production in Galicia.
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Affiliation(s)
- Antonio Villalba
- Centro de Investigacións Mariñas (CIMA), Consellería do Mar, Xunta de GaliciaVilanova de ArousaSpain
- Departamento de Ciencias de la VidaUniversidad de AlcaláAlcalá de HenaresSpain
- Research Centre for Experimental Marine Biology and Biotechnology (PIE)University of the Basque Country (UPV/EHU)PlentziaSpain
| | - Raquel M. Coimbra
- Departamento de Pesca e AquiculturaUniversidade Federal Rural de PernambucoRecifeBrazil
- Departamento de Zoología, Genética y Antropología Física, Facultad de Veterinaria, Campus TerraUniversidade de Santiago de CompostelaLugoSpain
| | - Marina Pampín
- Departamento de Zoología, Genética y Antropología Física, Facultad de Veterinaria, Campus TerraUniversidade de Santiago de CompostelaLugoSpain
| | - David Iglesias
- Centro de Investigacións Mariñas (CIMA), Consellería do Mar, Xunta de GaliciaVilanova de ArousaSpain
| | - Damián Costas
- Centro de Investigación MariñaUniversidade de Vigo, ECIMATVigoSpain
| | | | - Andrés Blanco
- Departamento de Zoología, Genética y Antropología Física, Facultad de Veterinaria, Campus TerraUniversidade de Santiago de CompostelaLugoSpain
| | - Manuel Vera
- Departamento de Zoología, Genética y Antropología Física, Facultad de Veterinaria, Campus TerraUniversidade de Santiago de CompostelaLugoSpain
| | | | - Eva Cacabelos
- Hydrosphere S. L.VigoSpain
- Instituto de Investigaciones Marinas, Consejo Superior de Investigaciones CientíficasIIM‐CSICVigoSpain
| | - Emilio Abella
- Centro de Investigacións Mariñas (CIMA), Consellería do Mar, Xunta de GaliciaVilanova de ArousaSpain
- Confraría de Pescadores A PastorizaVilanova de ArousaSpain
| | - Mónica Incera
- Centro Tecnolóxico do Mar ‐ Fundación CETMARVigoSpain
| | | | - Paulino Martínez
- Departamento de Zoología, Genética y Antropología Física, Facultad de Veterinaria, Campus TerraUniversidade de Santiago de CompostelaLugoSpain
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Saad MA, Abdul-Sattar AB, Abdelal IT, Baraka A. Shedding Light on the Role of ERAP1 in Axial Spondyloarthritis. Cureus 2023; 15:e48806. [PMID: 38024089 PMCID: PMC10645460 DOI: 10.7759/cureus.48806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/14/2023] [Indexed: 12/01/2023] Open
Abstract
Spondyloarthritis (SpA) is a multifactorial chronic inflammatory disease affecting the axial skeleton (axSpA) and/or peripheral joints (p-SpA) and entheses. The disease's pathogenesis depends on genetic, immunological, mechanical, and environmental factors. Endoplasmic reticulum aminopeptidase 1 (ERAP1) is a multifunctional enzyme that shapes the peptide repertoire presented by major histocompatibility complex (MHC) class I molecules. Genome-wide association studies (GWAS) have identified different single nucleotide polymorphisms (SNPs) in ERAP1 that are associated with several autoimmune diseases, including axSpA. Therefore, a deeper understanding of the ERAP1 role in axSpA could make it a potential therapeutic target for this disease and offer greater insight into its impact on the immune system. Here, we review the biological functions and structure of ERAP1, discuss ERAP1 polymorphisms and their association with axSpA, highlight the interaction between ERAP1 and human leukocyte antigen (HLA)-B27, and review the association between ERAP1 SNPs and axSpA clinical parameters.
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Affiliation(s)
- Mohamed A Saad
- Rheumatology and Rehabilitation, Physical Medicine and Rehabilitation (PMR) Hospital, Kuwait, KWT
| | - Amal B Abdul-Sattar
- Rheumatology and Rehabilitation, Faculty of Medicine, Zagazig University, Zagazig, EGY
| | - Ibrahim T Abdelal
- Rheumatology and Rehabilitation, Faculty of Medicine, Zagazig University, Zagazig, EGY
| | - Ahmed Baraka
- Clinical Pathology, Faculty of Medicine, Zagazig University, Zagazig, EGY
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Park HA, Edelmann D, Canzian F, Seibold P, Harrison TA, Hua X, Shi Q, Silverman A, Benner A, Macauda A, Schneider M, Goldberg RM, Alberts SR, Hoffmeister M, Brenner H, Chan AT, Peters U, Newcomb PA, Chang-Claude J. Genome-wide study of genetic polymorphisms predictive for outcome from first-line oxaliplatin-based chemotherapy in colorectal cancer patients. Int J Cancer 2023; 153:1623-1634. [PMID: 37539667 PMCID: PMC10550047 DOI: 10.1002/ijc.34663] [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: 12/02/2022] [Revised: 04/13/2023] [Accepted: 04/18/2023] [Indexed: 08/05/2023]
Abstract
We conducted the first large genome-wide association study to identify novel genetic variants that predict better (or poorer) prognosis in colorectal cancer patients receiving standard first-line oxaliplatin-based chemotherapy vs chemotherapy without oxaliplatin. We used data from two phase III trials, NCCTG N0147 and NCCTG N9741 and a population-based patient cohort, DACHS. Multivariable Cox proportional hazards models were employed, including an interaction term between each SNP and type of treatment for overall survival (OS) and progression-free survival. The analysis was performed for studies individually, and the results were combined using fixed-effect meta-analyses separately for resected stage III colon cancer (3098 patients from NCCTG N0147 and 549 patients from DACHS) and mCRC (505 patients from NCCTG N9741 and 437 patients from DACHS). We further performed gene-based analysis as well as in silico bioinformatics analysis for CRC-relevant functional genomic annotation of identified loci. In stage III colon cancer patients, a locus on chr22 (rs11912167) was associated with significantly poorer OS after oxaliplatin-based chemotherapy vs chemotherapy without oxaliplatin (Pinteraction < 5 × 10-8 ). For mCRC patients, three loci on chr1 (rs1234556), chr12 (rs11052270) and chr15 (rs11858406) were found to be associated with differential OS (P < 5 × 10-7 ). The locus on chr1 located in the intronic region of RCSD1 was replicated in an independent cohort of 586 mCRC patients from ALGB/SWOG 80405 (Pinteraction = .04). The GWA gene-based analysis yielded for RCSD1 the most significant association with differential OS in mCRC (P = 6.6 × 10-6 ). With further investigation into its biological mechanisms, this finding could potentially be used to individualize first-line treatment and improve clinical outcomes.
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Affiliation(s)
- Hanla A. Park
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Medical Faculty, University of Heidelberg, Heidelberg, Germany
| | - Dominic Edelmann
- Division of Biostatistics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Federico Canzian
- Genomic Epidemiology Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Petra Seibold
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Tabitha A. Harrison
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United State of America
| | - Xinwei Hua
- Department of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, United State of America
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, Massachusetts, United State of America
- Department of Cardiology, Peking University Third Hospital, Peking University, Beijing, China
| | - Qian Shi
- Department of Quantitative Science, Mayo Clinic, Rochester, Minnesota, United State of America
| | - Allison Silverman
- Epidemiology Program, Fred Hutchinson Research Cancer Research Center, Seattle, Washington, United State of America
| | - Axel Benner
- Division of Biostatistics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Angelica Macauda
- Genomic Epidemiology Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Martin Schneider
- Department of General, Visceral and Transplantation Surgery, University of Heidelberg, Heidelberg, Germany
| | | | - Steven R. Alberts
- Division of Medical Oncology, Mayo Clinic, Rochester, Minnesota, United State of America
| | - Michael Hoffmeister
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Division of Preventive Oncology, National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Andrew T. Chan
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts, United State of America
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United State of America
- Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, United State of America
| | - Ulrike Peters
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United State of America
- School of Public Health, University of Washington, Seattle, Washington, United State of America
| | - Polly A. Newcomb
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United State of America
- School of Public Health, University of Washington, Seattle, Washington, United State of America
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Cancer Epidemiology Group, University Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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Li W, Wang X, Zhang X, Li F, Zhang D, Li X, Zhang Y, Zhao Y, Zhao L, Xu D, Cheng J, Wang J, Zhou B, Lin C, Wang W. Polymorphism of sheep PRKAA2 gene and its association with growth traits. Anim Biotechnol 2023; 34:1324-1330. [PMID: 34971343 DOI: 10.1080/10495398.2021.2021215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Small ruminants farming plays an important role in the livelihood of a large part of the population. Herein we aimed to analyze the effects of single nucleotide polymorphisms in PRKAA2 gene on the growth-related traits of Hu sheep and Dorper sheep. The body weight and body type of 1254 sheep were measured at 80, 100, 120, 140, 160 and 180d, and 37620 phenotypic data were collected. RT-qPCR analysis was performed to test PRKAA2 gene expressed in different tissues of sheep, with the highest expression level in spleen, followed by kidney. In the present study, the PRKAA2 gene sequencing revealed one polymorphism located on Chr1 (Oar_rambouillet_v1.0), termed as chr1:32832382 G > A, and were significantly associated with growth traits of sheep (p < 0.05). The body weight, body length, chest circumference, and cannon circumference of individuals with AA genotype were significantly higher than those with the GG and GA genotypes (p < 0.05). Our findings reveal that PRKAA2 gene could be used as a marker-assisted selection to improve the growth-related traits of sheep.
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Affiliation(s)
- Wenxin Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Xiaojuan Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Xiaoxue Zhang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Fadi Li
- The State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
- Engineering Laboratory of Sheep Breeding and Reproduction Biotechnology in Gansu Province, Minqin, China
| | - Deyin Zhang
- The State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Xiaolong Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Yukun Zhang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Yuan Zhao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Liming Zhao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Dan Xu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Jiangbo Cheng
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Jianghui Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Bubo Zhou
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Changchun Lin
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Weimin Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
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128
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Liang X, Jin P, Zhan C, Zhao L, Zi X, Zhi L, Yu K. Glucocorticoid-Induced Transcript 1(GLCCI1) SNP rs37937 Is Associated With the Risk of Developing Allergic Rhinitis and the Response to Intranasal Corticosteroids in a Chinese Han Population. Am J Rhinol Allergy 2023; 37:751-757. [PMID: 37553950 DOI: 10.1177/19458924231193156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/10/2023]
Abstract
BACKGROUND Evidence has shown that glucocorticoid-induced transcript 1 (GLCCI1) single nucleotide polymorphism (SNP) rs37937 is associated with asthma. OBJECTIVES The objective of this study was to investigate whether the GLCCI1 SNP rs37937 is a risk factor for allergic rhinitis (AR) in a Chinese Han population. METHODS A total of 220 individuals including 109 AR patients and 111 healthy subjects were included. The genotyping of GLCCI1 rs37973 was performed by the SNaPshot method. The correlations of rs37973 polymorphism, AR risk, and clinical characteristics were further analyzed, as well as the treatment response to intranasal corticosteroids (INCS) in AR patients of different genotypes. RESULTS Three GLCCI1 rs37973 SNP genotypes were identified in both AR patients and healthy subjects. Significant association between rs37973 polymorphism and AR under allele model, dominant model, heterozygote model, and homozygote model were shown. The A allele frequency of SNP rs37973 in AR was significantly higher than that in controls. The serum total immunoglobulin E (IgE) in AR patients of AA genotype was significantly higher than in patients of GA and GG genotype, and the serum total IgE in GA genotype was significantly higher than in GG genotype. Interestingly, after 4 weeks of INCS treatment for AR patients, the improvement of the nasal itching score, sneezing score, runny nose score, total nasal symptom score, and visual analog scale score of the GG genotype were worse than the AA or GA genotype. CONCLUSION The GLCCI1 rs37937 polymorphism is associated with the risk of developing AR and the response to INCS treatment in the Chinese Han population.
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Affiliation(s)
- Xu Liang
- Department of Otolaryngology, The Second Hospital of Shandong University, Jinan, China
| | - Peng Jin
- Department of Otolaryngology, The Second Hospital of Shandong University, Jinan, China
| | - Changcui Zhan
- Department of Otolaryngology, Dongping County People's Hospital, Taian, China
| | - Li Zhao
- Department of Otolaryngology, The Second Hospital of Shandong University, Jinan, China
| | - Xiaoxue Zi
- Department of Otolaryngology, The Second Hospital of Shandong University, Jinan, China
| | - Lili Zhi
- Department of Allergy, Shandong Provincial Qianfoshan Hospital, The First Affiliated Hospital of Shandong First Medical University, Shandong Institute of Respiratory Diseases, Jinan, China
| | - Kena Yu
- Department of Otolaryngology, The Second Hospital of Shandong University, Jinan, China
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Azarova YE, Klyosova EY, Ivakin VE, Churilin MI, Kolomoets II, Sunyaykina OA, Ragulina VA, Polonikov AV. Polymorphisms of the NCF4 Gene Increase the Risk of Chronic Heart Failure in Patients with Type 2 Diabetes Mellitus. Bull Exp Biol Med 2023; 176:77-81. [PMID: 38085396 DOI: 10.1007/s10517-023-05974-0] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Indexed: 12/19/2023]
Abstract
We showed for the first time that polymorphisms rs2075938 and rs2075938 of the NCF4 gene are associated with the risk of chronic heart failure in patients with type 2 diabetes mellitus (n=1310). In particular, haplotypes ATGTCTAT (OR=1.74, 95%CI=1.23-2.47; p=0.0017) and ATATTCAC (OR=2.83, 95%CI=1.33-6.03; p=0.0072) of NCF4 increase the risk of chronic heart failure in type 2 diabetes mellitus patients. The results show that NADPH oxidase subunit NCF4 is involved in the molecular mechanisms of myocardial damage in type 2 diabetes mellitus.
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Affiliation(s)
- Yu E Azarova
- Kursk State Medical University, Ministry of Health of the Russian Federation, Kursk, Russia.
| | - E Yu Klyosova
- Kursk State Medical University, Ministry of Health of the Russian Federation, Kursk, Russia
| | - V E Ivakin
- Kursk State Medical University, Ministry of Health of the Russian Federation, Kursk, Russia
| | - M I Churilin
- Kursk State Medical University, Ministry of Health of the Russian Federation, Kursk, Russia
| | - I I Kolomoets
- Kursk State Medical University, Ministry of Health of the Russian Federation, Kursk, Russia
| | - O A Sunyaykina
- Kursk State Medical University, Ministry of Health of the Russian Federation, Kursk, Russia
| | - V A Ragulina
- Kursk State Medical University, Ministry of Health of the Russian Federation, Kursk, Russia
| | - A V Polonikov
- Kursk State Medical University, Ministry of Health of the Russian Federation, Kursk, Russia
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130
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Ma M, Zhao J, Xie D, Chen J. Association between GABRG2 Gene Single Nucleotide Polymorphisms and Susceptibility to Ischemic Stroke in a Chinese Population. J Integr Neurosci 2023; 22:151. [PMID: 38176934 DOI: 10.31083/j.jin2206151] [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: 04/18/2023] [Revised: 07/04/2023] [Accepted: 07/20/2023] [Indexed: 01/06/2024] Open
Abstract
BACKGROUND Current evidence suggests that Gamma-aminobutyric acid (GABA) receptors are associated with the occurrence and progression of cerebrovascular diseases. The present study investigated the association between single nucleotide polymorphisms (SNPs) in the Gamma-aminobutyric acid type A receptor gamma2 subunit (GABRG2) gene and ischemic stroke (IS). METHODS A total of 120 healthy volunteers and 187 patients with IS were recruited. Patients underwent complete neurological assessment and classification with the National Institute of Health Stroke Scale (NIHSS) and the Trial of ORG 10172 in Acute Stroke Treatment (TOAST). Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) was used to analyze SNP sites in 4 different regions (rs211037, rs418210, rs211035, and rs424740) of the GABRG2 gene. SHEsis online platform was used to assess SNP allele and genotype frequencies. Multivariate logistic regression analysis was performed to identify the risk factors for IS. RESULTS Univariate analysis showed that the T allele and TT genotype distribution for rs211037 were significantly more frequent in the IS group compared to controls (pallele = 0.01, odds ratio (OR) = 1.673, 95% confidence intervals (CI), 1.119-2.500, pgenotype = 0.03). Furthermore, multivariate logistic regression analysis revealed the TT genotype for rs211037 was an independent risk factor for IS (p = 0.017, OR = 1.925, 95% CI, 1.122-3.303). Age was also found to be an independent risk factor, and the older the age, the higher the risk of IS (p = 0.001, OR = 1.047, 95% CI, 1.020-1.073). Finally, subgroup analysis revealed that patients with the rs211037 TT genotype were associated with a higher NIHSS score (p = 0.03), and that large-artery atherosclerosis (LAA) subtype was predominant in patients with the rs211037 TT genotype (p = 0.042). CONCLUSIONS These findings suggest the rs211037 polymorphism in the GABRG2 gene is an independent risk factor for IS in the Chinese population. GABRG2 could thus be a potential biomarker to assess the risk of IS.
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Affiliation(s)
- Mingming Ma
- Department of Neurology, Hangzhou Red Cross Hospital, 310000 Hangzhou, Zhejiang, China
| | - Jing Zhao
- Department of Neurology, Hangzhou Red Cross Hospital, 310000 Hangzhou, Zhejiang, China
| | - Dandan Xie
- Department of Sports Rehabilitation, Hangzhou Red Cross Hospital, 310000 Hangzhou, Zhejiang, China
| | - Juan Chen
- Experimental Test Center, Children's Hospital of Zhejiang University School of Medicine, 310000 Hangzhou, Zhejiang, China
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Hong JH, Jin EH, Sung JK, Chang IA, Kang H, Lee SI. Association of lncRNA SOX2OT rs9839776 polymorphism with gastric cancer risk in Korean: Case-control study. Medicine (Baltimore) 2023; 102:e35103. [PMID: 37904476 PMCID: PMC10615517 DOI: 10.1097/md.0000000000035103] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 08/16/2023] [Indexed: 11/01/2023] Open
Abstract
Aberrant regulation of the long non-coding RNA SRY-box transcription factor 2 overlapping transcript (SOX2OT) has been reported in various diseases including gastric cancer (GC). However, an association between the well-studied rs9839776 single nucleotide polymorphism in SOX2OT and GC susceptibility has not been reported. This study aimed to evaluate the association between the rs9839776 single nucleotide polymorphism in SOX2OT and GC risk. Genotyping of rs9839776 was conducted using TaqMan genotyping assay for 460 patients with GC and 386 controls. We found that the dominant model (CT+TT) and rs9839776 T allele were significantly associated with decreased GC risk (P = .046, adjusted odds ratio [AOR] = 0.72, 95% confidence interval [CI] = 0.52-1.00 and P = .044, AOR = 0.74, 95% CI = 0.56-0.99, respectively). In addition, stratified analysis revealed that the dominant model (CT+TT) and rs9839776 T allele were significantly associated with decreased risk of lymph node metastasis-negative (P = .039, AOR = 0.67, 95% CI = 0.46-0.98 and P = .049, AOR = 0.71, 95% CI = 0.51-1.00, respectively) and tumor stage I (A+B)/II (A+B+C) (P = .028, AOR = 0.66, 95% CI = 0.50-0.96 and P = .041, AOR = 0.71, 95% CI = 0.52-0.99, respectively) GC. Our findings suggest that the rs9839776 T allele may be a protective factor against GC susceptibility. Further research is needed to clarify whether rs9839776 affects SOX2OT expression.
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Affiliation(s)
- Jang Hee Hong
- Department of Pharmacology, Chungnam National University College of Medicine, Daejeon, Republic of Korea
- Clinical Trials Center, Chungnam National University Hospital, Daejeon, Republic of Korea
| | - Eun-Heui Jin
- Translational Immunology Institute, Chungnam National University College of Medicine, Daejeon, Republic of Korea
| | - Jae Kyu Sung
- Department of Internal Medicine, Chungnam National University Hospital, Chungnam National University College of Medicine, Daejeon, Republic of Korea
| | - In Ae Chang
- Department of Pharmacology, Chungnam National University College of Medicine, Daejeon, Republic of Korea
| | - Hyojin Kang
- Department of Pharmacology, Chungnam National University College of Medicine, Daejeon, Republic of Korea
| | - Sang-Il Lee
- Department of Surgery, Chungnam National University Hospital, Chungnam National University College of Medicine, Daejeon, Republic of Korea
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Andrews JL, Zalesky A, Nair S, Sullivan RP, Green MJ, Pantelis C, Newell KA, Fernandez F. Genetic and Epigenetic Regulation in Lingo-1: Effects on Cognitive Function and White Matter Microstructure in a Case-Control Study for Schizophrenia. Int J Mol Sci 2023; 24:15624. [PMID: 37958608 PMCID: PMC10648795 DOI: 10.3390/ijms242115624] [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: 09/25/2023] [Revised: 10/19/2023] [Accepted: 10/22/2023] [Indexed: 11/15/2023] Open
Abstract
Leucine-rich repeat and immunoglobulin domain-containing protein (Lingo-1) plays a vital role in a large number of neuronal processes underlying learning and memory, which are known to be disrupted in schizophrenia. However, Lingo-1 has never been examined in the context of schizophrenia. The genetic association of a single-nucleotide polymorphism (SNP, rs3144) and methylation (CpG sites) in the Lingo-1 3'-UTR region was examined, with the testing of cognitive dysfunction and white matter (WM) integrity in a schizophrenia case-control cohort (n = 268/group). A large subset of subjects (97 control and 161 schizophrenia subjects) underwent structural magnetic resonance imaging (MRI) brain scans to assess WM integrity. Frequency of the rs3144 minor allele was overrepresented in the schizophrenia population (p = 0.03), with an odds ratio of 1.39 (95% CI 1.016-1.901). CpG sites surrounding rs3144 were hypermethylated in the control population (p = 0.032) compared to the schizophrenia group. rs3144 genotype was predictive of membership to a subclass of schizophrenia subjects with generalized cognitive deficits (p < 0.05), in addition to having associations with WM integrity (p = 0.018). This is the first study reporting a potential implication of genetic and epigenetic risk factors in Lingo-1 in schizophrenia. Both of these genetic and epigenetic alterations may also have associations with cognitive dysfunction and WM integrity in the context of the schizophrenia pathophysiology.
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Affiliation(s)
- Jessica L. Andrews
- School of Medical, Indigenous and Health Sciences, and Molecular Horizons, Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, NSW 2522, Australia (K.A.N.)
| | - Andrew Zalesky
- Melbourne Neuropsychiatry Centre, Department of Psychiatry, The University of Melbourne, Carlton South, VIC 3053, Australia; (A.Z.); (C.P.)
| | - Shalima Nair
- Epigenetics Research Program, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia;
| | - Ryan P. Sullivan
- ARC Centre of Excellence for Electromaterials Science, Intelligent Polymer Research Institute, AIIM Facility, University of Wollongong, Wollongong, NSW 2522, Australia;
| | - Melissa J. Green
- School of Clinical Medicine, Discipline of Psychiatry and Mental Health, UNSW Sydney, Sydney, NSW 2052, Australia;
| | - Christos Pantelis
- Melbourne Neuropsychiatry Centre, Department of Psychiatry, The University of Melbourne, Carlton South, VIC 3053, Australia; (A.Z.); (C.P.)
| | - Kelly A. Newell
- School of Medical, Indigenous and Health Sciences, and Molecular Horizons, Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, NSW 2522, Australia (K.A.N.)
| | - Francesca Fernandez
- School of Medical, Indigenous and Health Sciences, and Molecular Horizons, Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, NSW 2522, Australia (K.A.N.)
- School of Behavioural and Health Sciences, Faculty of Heath Sciences, Australian Catholic University, Banyo, QLD 4014, Australia
- Healthy Brain and Mind Research Centre, Australian Catholic University, Fitzroy, VIC 3065, Australia
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Chang LW, Hung SC, Chou YE, Chen CS, Li JR, Lin CY, Wang SS, Yang SF. The impacts of MACC1 gene polymorphisms on urothelial cell carcinoma susceptibility and clinicopathologic characteristics in Taiwan. J Cancer 2023; 14:3532-3538. [PMID: 38021160 PMCID: PMC10647202 DOI: 10.7150/jca.90130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 10/14/2023] [Indexed: 12/01/2023] Open
Abstract
Urothelial cell carcinoma (UCC) is a common malignancy of the urinary tract in Taiwan. Metastasis-Associated in Colon Cancer 1 (MACC1), a newly identified oncogene and regulator of the HGF/Met signaling pathway, has been shown to play a critical role in the development and progression of several types of cancer. Our study aims to investigate the impact of MACC1 gene polymorphisms on the clinicopathological features of patients with UCC. In this study, we included a total of 719 patients with UCC and 719 healthy controls. The genotyping of five MACC1 gene polymorphisms (rs1990172, rs975263, rs3095007, rs4721888, and rs3735615) was performed using real-time PCR with TaqMan assays. Our findings indicate that urothelial cancer patients with MACC1 rs3095007 A allele had a decreased risk of >T2 stage [Odds ratio (OR)=0.619, 95% CI=0.394-0.971, p=0.036] and lymph node invasion (OR=0.448, 95% CI=0.201-0.998, p=0.044). Additionally, these individuals were associated with longer relapse-free survival (p=0.007) and overall survival (p=0.028). In conclusion, our findings demonstrate that urothelial cancer patients with MACC1 (rs3095007) CA and AA genotypes have a lower risk of advanced T stage and lymph node metastasis. Additionally, these genotypes were associated with longer relapse-free survival and overall survival, highlighting the potential of these biomarkers as predictors of UCC prognosis.
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Affiliation(s)
- Li-Wen Chang
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan
- Division of Urology, Department of Surgery, Taichung Veterans General Hospital, Taichung, Taiwan
- Department of Post-Baccalaureate Medicine, College of Medicine, National Chung Hsing University, Taichung, Taiwan
| | - Sheng-Chun Hung
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan
- Division of Urology, Department of Surgery, Taichung Veterans General Hospital, Taichung, Taiwan
- Department of Post-Baccalaureate Medicine, College of Medicine, National Chung Hsing University, Taichung, Taiwan
| | - Ying-Erh Chou
- School of Medicine, Chung Shan Medical University, Taichung, Taiwan
| | - Chuan-Shu Chen
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan
- Division of Urology, Department of Surgery, Taichung Veterans General Hospital, Taichung, Taiwan
- Department of Post-Baccalaureate Medicine, College of Medicine, National Chung Hsing University, Taichung, Taiwan
| | - Jian-Ri Li
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan
- Division of Urology, Department of Surgery, Taichung Veterans General Hospital, Taichung, Taiwan
- Department of Post-Baccalaureate Medicine, College of Medicine, National Chung Hsing University, Taichung, Taiwan
- Department of Medicine and Nursing, Hungkuang University, Taichung, Taiwan
| | - Chia-Yen Lin
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan
- Division of Urology, Department of Surgery, Taichung Veterans General Hospital, Taichung, Taiwan
- School of Medicine, National Yang Ming University, Taipei, Taiwan
| | - Shian-Shiang Wang
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan
- Division of Urology, Department of Surgery, Taichung Veterans General Hospital, Taichung, Taiwan
- Department of Applied Chemistry, National Chi Nan University, Nantou, Taiwan
| | - Shun-Fa Yang
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan
- Department of Medical Research, Chung Shan Medical University Hospital, Taichung, Taiwan
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134
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Hu X, Lu X. Association between interferon-gamma ( IFN-γ) gene polymorphisms and tuberculosis susceptibility: a systematic review and meta-analysis. Nucleosides Nucleotides Nucleic Acids 2023; 43:472-491. [PMID: 37874649 DOI: 10.1080/15257770.2023.2272641] [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] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Accepted: 10/11/2023] [Indexed: 10/26/2023]
Abstract
Interferon-gamma (IFN-γ) has been established to play a pivotal role in the pathogenesis of tuberculosis (TB). Existing evidence suggests a potential association between the genetic poly-morphisms of IFN-γ and the susceptibility to TB. However, this association remains a topic of controversy. To address this knowledge gap, a meta-analysis was conducted to provide more accurate results regarding their relationship. The pooled odds ratio along with its corresponding 95% confidence interval was calculated using four different gene models. This analytical approach served to evaluate the strength of the association between single nucleotide polymorphisms (SNPs) and TB susceptibility. Additionally, we determined whether a fixed effect model or a random effect model should be applied based on the extent of heterogeneity. Egger's test was used to evaluate publication bias. This study included a total of nine studies, involving 4509 patients with TB and 4378 healthy controls. In non-Asian populations, a C > T mutation at polymorphic variant rs2069705 and a T > C mutation at rs2069718 was associated with an increased risk of TB. Conversely, among Asians, the variants rs2069705, rs2069718, and rs1861494 were not significantly associated with the risk of TB. Importantly, our investigation did not reveal any significant publication bias in the pooled results of the four gene models. In conclusion, this meta-analysis suggests that two SNPs in IFN-γ may be associated with TB susceptibility in non-Asian populations. However, for Asians, there is no evidence to support a conclusive relationship between these SNPs and the risk of TB.
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Affiliation(s)
- Xu Hu
- Department of Respiratory and Critical Care Medicine, The First People's Hospital of Ziyang, Ziyang, Sichuan, China
| | - Xiaoying Lu
- Department of Respiratory and Critical Care Medicine, The First People's Hospital of Ziyang, Ziyang, Sichuan, China
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Zhu P, Schon M, Questa J, Nodine M, Dean C. Causal role of a promoter polymorphism in natural variation of the Arabidopsis floral repressor gene FLC. Curr Biol 2023; 33:4381-4391.e3. [PMID: 37729909 DOI: 10.1016/j.cub.2023.08.079] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 07/06/2023] [Accepted: 08/25/2023] [Indexed: 09/22/2023]
Abstract
Noncoding polymorphism frequently associates with phenotypic variation, but causation and mechanism are rarely established. Noncoding single-nucleotide polymorphisms (SNPs) characterize the major haplotypes of the Arabidopsis thaliana floral repressor gene FLOWERING LOCUS C (FLC). This noncoding polymorphism generates a range of FLC expression levels, determining the requirement for and the response to winter cold. The major adaptive determinant of these FLC haplotypes was shown to be the autumnal levels of FLC expression. Here, we investigate how noncoding SNPs influence FLC transcriptional output. We identify an upstream transcription start site (uTSS) cluster at FLC, whose usage is increased by an A variant at the promoter SNP-230. This variant is present in relatively few Arabidopsis accessions, with the majority containing G at this site. We demonstrate a causal role for the A variant at -230 in reduced FLC transcriptional output. The G variant upregulates FLC expression redundantly with the major transcriptional activator FRIGIDA (FRI). We demonstrate an additive interaction of SNP-230 with an intronic SNP+259, which also differentially influences uTSS usage. Combinatorial interactions between noncoding SNPs and transcriptional activators thus generate quantitative variation in FLC transcription that has facilitated the adaptation of Arabidopsis accessions to distinct climates.
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Affiliation(s)
- Pan Zhu
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Michael Schon
- Laboratory of Molecular Biology, Wageningen University, Wageningen 6708 PB, the Netherlands; Gregor Mendel Institute, Vienna Biocenter, Vienna 1030, Austria
| | - Julia Questa
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Michael Nodine
- Laboratory of Molecular Biology, Wageningen University, Wageningen 6708 PB, the Netherlands; Gregor Mendel Institute, Vienna Biocenter, Vienna 1030, Austria
| | - Caroline Dean
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK.
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Rahman A, Abu-Farha M, Channanath A, Hammad MM, Anoop E, Chandy B, Melhem M, Al-Mulla F, Thanaraj TA, Abubaker J. Single nucleotide polymorphisms in vitamin D binding protein and 25-hydroxylase genes affect vitamin D levels in adolescents of Arab ethnicity in Kuwait. Front Endocrinol (Lausanne) 2023; 14:1257051. [PMID: 37929021 PMCID: PMC10623322 DOI: 10.3389/fendo.2023.1257051] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 10/09/2023] [Indexed: 11/07/2023] Open
Abstract
Vitamin D deficiency (VDD) is widespread in the Arab world despite ample sunshine throughout the year. In our previous study, lifestyle and socio-demographic factors could explain only 45% of variability in vitamin D levels in Kuwaiti adolescents, suggesting that genetics might contribute to VDD in this region. Single nucleotide polymorphisms (SNP) in the 25-hydroxylase (CYP2R1) and the GC globulin (GC) genes have been reported to affect vitamin D levels in various ethnic groups in adults. In this study, we investigated the association of two SNPs from GC (rs4588 and rs7041) and three SNPs from CYP2R1 (rs10741657, rs11023374 and rs12794714) with vitamin D levels and VDD in a nationally representative sample of adolescents of Arab ethnicity from Kuwait. Multivariable linear regression, corrected for age, sex, parental education, governorate, body mass index, and exposure to sun, demonstrated that each of the 5 study variants showed significant associations with plasma 25(OH)D levels in one or more of the additive, recessive, and dominant genetic models - the rs10741657 under all the three models, rs12794714 under both the additive and recessive models, rs7041 under the recessive model; and rs4588 and rs11023374 under the dominant model. Minor alleles at rs4588 (T), rs7041 (A), rs11023374 (C), and rs12794714 (A) led to a decrease in plasma 25(OH)D levels - rs4588:[β (95%CI) = -4.522 (-8.66,-0.38); p=0.033]; rs7041:[β (95%CI) = -6.139 (-11.12,-1.15); p=0.016]; rs11023374:[β (95%CI) = -4.296 (-8.18,-0.40); p=0.031]; and rs12794714:[β (95%CI) = -3.498 (-6.27,-0.72); p=0.014]. Minor allele A at rs10741657 was associated with higher levels of plasma 25(OH)D levels [β (95%CI) = 4.844 (1.62,8.06); p=0.003)] and lower odds of vitamin D deficiency (OR 0.40; p=0.002). These results suggest that the CYP2R1 and GC SNP variants are partly responsible for the high prevalence of VDD in Kuwait. Genotyping these variants may be considered for the prognosis of VDD in Kuwait.
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Affiliation(s)
- Abdur Rahman
- Department of Food Science and Nutrition, College of Life Sciences, Kuwait University, Kuwait City, Kuwait
| | - Mohamed Abu-Farha
- Department of Biochemistry & Molecular Biology, Dasman Diabetes Institute, Kuwait City, Kuwait
| | - Arshad Channanath
- Department of Genetics & Bioinformatics, Dasman Diabetes Institute, Kuwait City, Kuwait
| | - Maha M. Hammad
- Department of Biochemistry & Molecular Biology, Dasman Diabetes Institute, Kuwait City, Kuwait
| | - Emil Anoop
- Special Services Facilities, Dasman Diabetes Institute, Kuwait City, Kuwait
| | - Betty Chandy
- Special Services Facilities, Dasman Diabetes Institute, Kuwait City, Kuwait
| | - Motasem Melhem
- Special Services Facilities, Dasman Diabetes Institute, Kuwait City, Kuwait
| | - Fahd Al-Mulla
- Department of Genetics & Bioinformatics, Dasman Diabetes Institute, Kuwait City, Kuwait
| | | | - Jehad Abubaker
- Department of Biochemistry & Molecular Biology, Dasman Diabetes Institute, Kuwait City, Kuwait
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Chan CC, Yen TH, Tseng HC, Mai B, Ho PK, Chou JL, Wu GJ, Huang YC. A Comprehensive Genetic Study of Microtubule-Associated Gene Clusters for Male Infertility in a Taiwanese Cohort. Int J Mol Sci 2023; 24:15363. [PMID: 37895049 PMCID: PMC10607339 DOI: 10.3390/ijms242015363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 10/14/2023] [Accepted: 10/15/2023] [Indexed: 10/29/2023] Open
Abstract
Advanced reproductive technologies are utilized to identify the genetic mutations that lead to spermatogenic impairment, and allow informed genetic counseling to patients to prevent the transmission of genetic defects to offspring. The purpose of this study was to identify potential single nucleotide polymorphisms (SNPs) associated with male infertility. Genetic variants that may cause infertility are identified by combining the targeted next-generation sequencing (NGS) panel and whole exome sequencing (WES). The validation step of Sanger sequencing adds confidence to the identified variants. Our analysis revealed five distinct affected genes covering seven SNPs based on the targeted NGS panel and WES data: SPATA16 (rs16846616, 1515442, 1515441), CFTR (rs213950), KIF6 (rs2273063), STPG2 (r2903150), and DRC7 (rs3809611). Infertile men have a higher mutation rate than fertile men, especially those with azoospermia. These findings strongly support the hypothesis that the dysfunction of microtubule-related and spermatogenesis-specific genes contributes to idiopathic male infertility. The SPATA16, CFTR, KIF6, STPG2, and DRC7 mutations are associated with male infertility, specifically azoospermia, and a further examination of this genetic function is required.
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Affiliation(s)
- Chying-Chyuan Chan
- Graduate Institute of Medical Sciences, National Defense Medical Center, Taipei 114201, Taiwan; (C.-C.C.)
- Department of Obstetrics and Gynecology, Taipei City Hospital-Renai Branch, Taipei 103212, Taiwan
| | - Te-Hsin Yen
- Department of Obstetrics and Gynecology, Taipei City Hospital-Renai Branch, Taipei 103212, Taiwan
| | - Hao-Chen Tseng
- School of Pharmacy, National Defense Medical Center, Taipei 114201, Taiwan
| | - Brang Mai
- School of Pharmacy, National Defense Medical Center, Taipei 114201, Taiwan
| | - Pin-Kuan Ho
- School of Dentistry, National Defense Medical Center, Taipei 114201, Taiwan
| | - Jian-Liang Chou
- Graduate Institute of Medical Sciences, National Defense Medical Center, Taipei 114201, Taiwan; (C.-C.C.)
- Department of Research and Development, National Defense Medical Center, Taipei 114201, Taiwan
| | - Gwo-Jang Wu
- Graduate Institute of Medical Sciences, National Defense Medical Center, Taipei 114201, Taiwan; (C.-C.C.)
- Reproductive Medical Center, Department of Obstetrics and Gynecology, Tri-Service General Hospital, Taipei 114202, Taiwan
| | - Yu-Chuan Huang
- Graduate Institute of Medical Sciences, National Defense Medical Center, Taipei 114201, Taiwan; (C.-C.C.)
- School of Pharmacy, National Defense Medical Center, Taipei 114201, Taiwan
- Department of Research and Development, National Defense Medical Center, Taipei 114201, Taiwan
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138
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Chen S, Duan Y, Zhang Y, Cheng L, Cai L, Hou X, Li W. Associations Between Single Nucleotide Polymorphisms of Hypoxia-Related Genes and Capsule Formation in Hepatocellular Carcinoma. J Hepatocell Carcinoma 2023; 10:1785-1797. [PMID: 37841371 PMCID: PMC10576505 DOI: 10.2147/jhc.s417830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 08/12/2023] [Indexed: 10/17/2023] Open
Abstract
Purpose Tumor capsule is an independent prognostic factor for patients with hepatocellular carcinoma (HCC) and used increasingly to guide clinical decision-making. Considering the genetic complexity for capsule formation and its potential association with hypoxia, the significance of the polymorphisms of hypoxia-related genes in capsule formation and HCC prognosis remains to be elucidated. Patients and Methods Peripheral blood samples from HCC patients were collected in this study. Single nucleotide polymorphism (SNP) genotyping was conducted by the iPLEX chemistry on a matrix-assisted laser desorption/ionization time-of-flight mass spectrometer (Sequenom, Inc.). The demographic and clinical data for the patients were obtained through medical chart review and/or consultation with the treating physicians. SPSS 25.0, R 4.1.1, and PLINK toolset were used to perform statistical analysis. Results A total of 183 patients were enrolled, including 88 patients assigned to the capsule group and 95 to the non-capsule group. SLC2A1 rs841858 T allele, SLC2A1 rs2297977 T allele, STAT1 rs1547550 C allele, and STAT1 rs34997637 G allele were associated with significantly increased risk of capsule formation. The genotypes of SLC2A1 rs841858, SLC2A1 rs2297977, STAT1 rs34997637, and STAT1 rs1914408 were significantly associated with the formation of HCC capsule. The polymorphisms of STAT1 rs2066802, STAT1 rs12693591, and HIF1A rs2057482 showed close relationship with the prognosis of HCC patients in the capsule group, while the genotype distributions of CTNNB1 rs4135385, IFNG rs1861494, and SERPINE1 rs2227631 were closely related to the survival of patients in the non-capsule group. Further haplotype analysis suggested that SLC2A1 block 1 and STAT1 block 2 were related to the susceptibility of HCC capsule. Conclusion The polymorphisms of the hypoxia-related genes (HIF1A, SERPINE1, IFNG, STAT1, CTNNB1, and SLC2A1) were correlated with the formation of HCC capsule. Several SNPs in these genes also showed association with HCC prognosis except SLC2A1. Further functional studies are warranted to explore the underlying mechanisms.
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Affiliation(s)
- Shanshan Chen
- Cancer Center, Beijing Tongren Hospital, Capital Medical University, Beijing, People’s Republic of China
- Cancer Center, Beijing Ditan Hospital, Capital Medical University, Beijing, People’s Republic of China
| | - Youjia Duan
- Cancer Center, Beijing Ditan Hospital, Capital Medical University, Beijing, People’s Republic of China
| | - Yongchao Zhang
- Cancer Center, Beijing Ditan Hospital, Capital Medical University, Beijing, People’s Republic of China
| | - Long Cheng
- Cancer Center, Beijing Ditan Hospital, Capital Medical University, Beijing, People’s Republic of China
| | - Liang Cai
- Cancer Center, Beijing Ditan Hospital, Capital Medical University, Beijing, People’s Republic of China
| | - Xiaopu Hou
- Cancer Center, Beijing Ditan Hospital, Capital Medical University, Beijing, People’s Republic of China
| | - Wei Li
- Cancer Center, Beijing Tongren Hospital, Capital Medical University, Beijing, People’s Republic of China
- Cancer Center, Beijing Ditan Hospital, Capital Medical University, Beijing, People’s Republic of China
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139
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Thorn V, Xu J. Mitogenome Variations in a Global Population of Aspergillus fumigatus. J Fungi (Basel) 2023; 9:995. [PMID: 37888251 PMCID: PMC10608017 DOI: 10.3390/jof9100995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 10/05/2023] [Accepted: 10/06/2023] [Indexed: 10/28/2023] Open
Abstract
Aspergillus fumigatus is a ubiquitous, critical priority human fungal pathogen. Despite its clinical importance, there is limited knowledge regarding the variations of the genome within mitochondria, the powerhouse organelle within eukaryotic cells. In this study, we leveraged publicly available, raw, whole genome sequence data isolates from 1939 to investigate the variations in the mitochondrial genomes of A. fumigatus. These isolates were isolated from 22 countries on six continents, as well as from outer space and from within the International Space Station. In total, our analysis revealed 39 mitochondrial single nucleotide polymorphisms (mtSNPs) within this global sample, and, together, these 39 mtSNPs grouped the 1939 isolates into 79 mitochondrial multilocus genotypes (MLGs). Among the 79 MLGs, 39 were each distributed in at least two countries and 30 were each shared by at least two continents. The two most frequent MLGs were also broadly distributed: MLG11 represented 420 isolates from 11 countries and four continents and while MLG79 represented 418 isolates from 18 countries and five continents, consistent with long-distance dispersals of mitogenomes. Our population genetic analyses of the mtSNPs revealed limited differentiation among continental populations, but highly variable genetic differences among national populations, largely due to localized clonal expansions of different MLGs. Phylogenetic analysis and Discriminant Analysis of Principal Components of mtSNPs suggested the presence of at least three mitogenome clusters. Linkage disequilibrium, Index of Association, and phylogenetic incompatibility analyses collectively suggested evidence for mitogenome recombination in natural populations of A. fumigatus. In addition, sequence read depth analyses revealed an average ratio of ~20 mitogenomes per nuclear genome in this global population, but the ratios varied among strains within and between certain geographic populations. Together, our results suggest evidence for organelle dynamics, genetic differentiation, recombination, and both widespread and localized clonal expansion of the mitogenomes in the global A. fumigatus population.
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Affiliation(s)
| | - Jianping Xu
- Department of Biology, Institute of Infectious Diseases Research, McMaster University, Hamilton, ON L8S 4K1, Canada;
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140
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Silva MJA, Silva CS, Marinho RL, Cabral JG, Gurrão EPDC, dos Santos PAS, Casseb SMM, Lima KVB, Lima LNGC. Analysis of Epidemiological Factors and SNP rs3804100 of TLR2 for COVID-19 in a Cohort of Professionals Who Worked in the First Pandemic Wave in Belém-PA, Brazil. Genes (Basel) 2023; 14:1907. [PMID: 37895256 PMCID: PMC10606513 DOI: 10.3390/genes14101907] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 09/19/2023] [Accepted: 09/25/2023] [Indexed: 10/29/2023] Open
Abstract
COVID-19 is an infectious disease caused by coronavirus 2 of the severe acute syndrome (SARS-CoV-2). Single nucleotide polymorphisms (SNPs) in genes, such as TLR2, responsible for an effective human immune response, can change the course of infection. The objective of this article was to verify associations between epidemiological factors and TLR2 SNP rs3804100 (Thymine [T] > Cytosine [C]) in professionals from Health Institutions (HI) who worked during the first pandemic wave and COVID-19. A case-control study was conducted with Belém-PA HI workers (Northern Brazil), divided into symptomatology groups (Asymptomatic-AS; n = 91; and Symptomatic-SI; n = 123); and severity groups classified by Chest Computerized Tomography data (symptomatic with pulmonary involvement-SCP; n = 35; symptomatic without pulmonary involvement-SSP; n = 8). Genotyping was performed by Sanger sequencing, and Statistical Analysis was conducted through the SPSS program. Bioinformatics servers predicted the biological functions of the TLR2 SNP. There were associations between the presence of comorbidities and poor prognosis of COVID-19 (especially between symptomatology and severity of COVID-19 and overweight and obesity) and between the sickness in family members and kinship (related to blood relatives). The homozygous recessive (C/C) genotype was not found, and the frequency of the mutant allele (C) was less than 10% in the cohort. No significant associations were found for this SNP in this cohort. The presence of SNP was indicated to be benign and causes a decrease in the stability of the TLR2 protein. These data can help the scientific community and medicine find new forms of COVID-19 containment.
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Affiliation(s)
- Marcos Jessé Abrahão Silva
- Master Program in Epidemiology and Health Surveillance (PPGEVS), Evandro Chagas Institute (IEC), Ananindeua 67030-000, PA, Brazil
| | - Caroliny Soares Silva
- Master and PhD Program in Parasitic Biology in the Amazon (PPGBPA), University of State of Pará (UEPA), Belém 66087-670, PA, Brazil; (C.S.S.); (P.A.S.d.S.)
| | - Rebecca Lobato Marinho
- Evandro Chagas Institute (IEC), Ananindeua 67030-000, PA, Brazil; (R.L.M.); (J.G.C.); (E.P.d.C.G.); (S.M.M.C.); (K.V.B.L.)
| | - Jeanne Gonçalves Cabral
- Evandro Chagas Institute (IEC), Ananindeua 67030-000, PA, Brazil; (R.L.M.); (J.G.C.); (E.P.d.C.G.); (S.M.M.C.); (K.V.B.L.)
| | - Ellen Polyana da Costa Gurrão
- Evandro Chagas Institute (IEC), Ananindeua 67030-000, PA, Brazil; (R.L.M.); (J.G.C.); (E.P.d.C.G.); (S.M.M.C.); (K.V.B.L.)
| | - Pabllo Antonny Silva dos Santos
- Master and PhD Program in Parasitic Biology in the Amazon (PPGBPA), University of State of Pará (UEPA), Belém 66087-670, PA, Brazil; (C.S.S.); (P.A.S.d.S.)
| | - Samir Mansour Moraes Casseb
- Evandro Chagas Institute (IEC), Ananindeua 67030-000, PA, Brazil; (R.L.M.); (J.G.C.); (E.P.d.C.G.); (S.M.M.C.); (K.V.B.L.)
| | - Karla Valéria Batista Lima
- Evandro Chagas Institute (IEC), Ananindeua 67030-000, PA, Brazil; (R.L.M.); (J.G.C.); (E.P.d.C.G.); (S.M.M.C.); (K.V.B.L.)
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141
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Ren H, Guo Z, Qin WJ, Yang ZL. Association of Interleukin-6 Genetic Polymorphisms (rs1800795, -174C > G and rs1800796, -572G > C) With Risk of Essential Hypertension in the Chinese Population. Cureus 2023; 15:e46334. [PMID: 37920615 PMCID: PMC10618844 DOI: 10.7759/cureus.46334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/23/2023] [Indexed: 11/04/2023] Open
Abstract
Background Interleukin-6 (IL-6) plays a critical role in essential hypertension (EH) and cardiovascular disease. Evidence suggests two hotspot single nucleotide polymorphisms (SNPs) of the IL-6 gene (rs1800795, -174C > G and rs1800796, -572G > C) might be associated with the susceptibility of EH. However, no consensus has yet been established. Thus, we aimed to investigate the potential association between IL-6 gene polymorphisms and the risk of EH based on a case-control study in a Chinese population. Materials and methods A total of 479 subjects (272 healthy controls and 207 EH patients) were randomly enrolled in our study. After extracting the genomic DNA, two SNPs of the IL-6 gene (rs1800795, -174C > G and rs1800796, -572G > C) were genotyped to analyze the potential association between these genetic variants and EH risk. Multiple genetic models were performed to investigate the strength of association by calculating the odds ratio (OR) and 95% confidence interval (95% CI). The potential effect of SNPs on gene expression was evaluated using expression quantitative trait loci (eQTL) analysis. Results The genotyping findings of IL-6 rs1800795, -174C > G polymorphism showed three study participants with CG genotype and 204 with GG genotype in the EH patients. The IL-6 -174C > G polymorphism was significantly associated with EH risk (P = 0.046) and conferred a reduced risk of EH development (OR = 0.99, 95%CI = 0.97-1.00). Conversely, no substantial association between IL-6 rs1800796, -572G > C polymorphism and the risk of EH was found in all genetic models (P > 0.05). Moreover, the eQTL analysis indicated that the -174C > G polymorphism was significantly associated with gene expression of IL-6 (P = 0.006), and the G allele corresponded to a reduced IL-6 gene expression (Beta = -0.397). Compared with -174C > G, the -572G > C polymorphism was not found to be significantly associated with IL-6 gene expression (Beta = -0.120, P = 0.560). Conclusions Our findings provide evidence that the rs1800795, -174C > G polymorphism can affect the expression levels of IL-6, and the risk of EH occurrence. However, the rs1800796, -572G > C polymorphism does not regulate the IL-6 gene expression levels and the susceptibility of EH.
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Affiliation(s)
- Huan Ren
- Pharmacy, Hunan Provincial People's Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, CHN
| | - Zhen Guo
- Genetics, Hunan Provincial Key Laboratory of the Fundamental and Clinical Research on Functional Nucleic Acid, Changsha Medical University, Changsha, CHN
| | - Wen-Jie Qin
- Pharmacy, Hunan Provincial People's Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, CHN
| | - Zhi-Ling Yang
- Pharmacy, Hunan Provincial People's Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, CHN
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He J, Ding Y, Lin H, Liu X, Chen X, Shen W, Zhou S, Feng C, Wang M, Xia J, He N. Differential genome-wide associated variants and enriched pathways of ECG parameters among people with versus without HIV. AIDS 2023; 37:1871-1882. [PMID: 37418550 PMCID: PMC10481915 DOI: 10.1097/qad.0000000000003647] [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: 03/02/2023] [Revised: 06/28/2023] [Accepted: 06/30/2023] [Indexed: 07/09/2023]
Abstract
OBJECTIVES People with HIV (PWH) are more likely to develop ECG abnormalities. Substantial evidence exists for genetic contribution to ECG parameters among general population. However, whether and how would host genome associate with ECG parameters among PWH is unclear. Our research aims to analyze and compare genetic variants, mapped genes, and enriched pathways of ECG parameters among PWH and HIV-negative controls. DESIGN A cross-sectional study. METHOD We performed a large original genome-wide association study (GWAS) of ECG parameters among PWH ( n = 1730) and HIV-negative controls ( n = 3746). Genome-wide interaction analyses were also conducted. RESULTS A total of 18 novel variants were detected among PWH, six for PR interval including rs76345397 at ATL2 , 11 for QRS duration including rs10483994 at KCNK10 and rs2478830 at JCAD , and one for QTc interval (rs9815364). Among HIV-negative controls, we identified variants located at previously reported ECG-related genes ( SCN5A , CNOT1 ). Genetic variants had a significant interaction with HIV infection ( P < 5 × 10 -8 ), implying that HIV infection and host genome might jointly influence ECG parameters. Mapped genes for PR interval and QRS duration among PWH were enriched in the biological process of viral genome replication and host response to virus, respectively, whereas enriched pathways for PR interval among HIV-negative controls were in the cellular component of voltage-gated sodium channel complex. CONCLUSION The present GWAS indicated a distinctive impact of host genome on quantitative ECG parameters among PWH. Different from HIV-negative controls, host genome might influence the cardiac electrical activity by interfering with HIV viral infection, production, and latency among PWH.
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Affiliation(s)
- Jiayu He
- Department of Epidemiology, School of Public Health, and Key Laboratory of Public Health Safety of Ministry of Education
- Yi-Wu Research Institute
- Shanghai Institute of Infectious Diseases and Biosecurity, Fudan University, Shanghai
| | - Yingying Ding
- Department of Epidemiology, School of Public Health, and Key Laboratory of Public Health Safety of Ministry of Education
- Yi-Wu Research Institute
| | - Haijiang Lin
- Department of Epidemiology, School of Public Health, and Key Laboratory of Public Health Safety of Ministry of Education
- Taizhou City Center for Disease Control and Prevention, Zhejiang Province, China
| | - Xing Liu
- Department of Epidemiology, School of Public Health, and Key Laboratory of Public Health Safety of Ministry of Education
- Yi-Wu Research Institute
| | - Xiaoxiao Chen
- Department of Epidemiology, School of Public Health, and Key Laboratory of Public Health Safety of Ministry of Education
- Taizhou City Center for Disease Control and Prevention, Zhejiang Province, China
| | - Weiwei Shen
- Taizhou City Center for Disease Control and Prevention, Zhejiang Province, China
| | - Sujuan Zhou
- Department of Epidemiology, School of Public Health, and Key Laboratory of Public Health Safety of Ministry of Education
- Yi-Wu Research Institute
- Shanghai Institute of Infectious Diseases and Biosecurity, Fudan University, Shanghai
| | - Cheng Feng
- Department of Epidemiology, School of Public Health, and Key Laboratory of Public Health Safety of Ministry of Education
- Yi-Wu Research Institute
| | - Miaochen Wang
- Department of Epidemiology, School of Public Health, and Key Laboratory of Public Health Safety of Ministry of Education
- Yi-Wu Research Institute
| | - Jingjing Xia
- Department of Epidemiology, School of Public Health, and Key Laboratory of Public Health Safety of Ministry of Education
- Yi-Wu Research Institute
| | - Na He
- Department of Epidemiology, School of Public Health, and Key Laboratory of Public Health Safety of Ministry of Education
- Yi-Wu Research Institute
- Shanghai Institute of Infectious Diseases and Biosecurity, Fudan University, Shanghai
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Boroujeni PB, Rooney K, Alikhani M, Rahmati S, Feli G, Haratian K, Movaghar B, Meybodi AM. Evaluation of TUBB8 gene alterations in infertile women with oocyte maturation and cleavage arrest referred to Royan Institute. Reprod Biomed Online 2023; 47:103226. [PMID: 37597348 DOI: 10.1016/j.rbmo.2023.04.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 04/25/2023] [Accepted: 04/27/2023] [Indexed: 08/21/2023]
Abstract
RESEARCH QUESTION Are TUBB8 gene variations present in Iranian infertile women with oocyte maturation arrest or embryo cleavage arrest? DESIGN TUBB8 gene variations were investigated by polymerase chain reaction sequencing on blood samples from 16 women with oocyte maturation arrest and 12 women with cleavage arrest, collectively referred to as the experimental cohort, as well as 56 fertile women as the control group. The Exome Sequencing Project and dbSNP databases and the Genome Aggregation Database were used to search the frequency of corresponding variants. PolyPhen and SIFT were used to conduct in-silico analysis of gene variations and Align-GVGD was used to predict the effect of missense variants on proteins. The homology modelling and structure evaluation of variations was also checked. RESULTS Two likely pathogenic variants [c.713C>T (p.Thr238Met), c.1054G>T (p.Ala352Ser)] were identified in patients with oocyte maturation arrest and one likely pathogenic variant [c.G763A, (p.Val255Met)] was identified in a patient with cleavage arrest. These changes were absent in controls. CONCLUSIONS Three deleterious variants in TUBB8 related to oocyte maturation arrest or cleavage arrest and infertility were identified. TUBB8 variant screening for patients with oocyte maturation and cleavage arrest is recommended.
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Affiliation(s)
- Parnaz Borjian Boroujeni
- Department of Genetics, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran
| | - Kathleen Rooney
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, Ontario, Canada; Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada
| | - Mehdi Alikhani
- Department of Molecular Systems Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Saman Rahmati
- Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Ghazaleh Feli
- Department of Genetics, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran
| | - Kaveh Haratian
- Department of Microbiology and Immunology, Medical School, Alborz University of Medical Sciences, Karaj, Iran
| | - Bahar Movaghar
- Department of Embryology, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran.
| | - Anahita Mohseni Meybodi
- Department of Genetics, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran; Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, Ontario, Canada; Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada.
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144
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Barchenger DW, Hsu YM, Liao KJ, Lines CL, Lin SW, Wang YW, Lin TH, Huang SM, Lozada DN, Bosland PW. Rating System for Phytophthora Root Rot Influences Quantitative Trait Locus Detection and Reveals Incomplete Dominance and Duplicative Recessive Epistatic Gene Action in Capsicum annuum. Phytopathology 2023; 113:1959-1966. [PMID: 37246966 DOI: 10.1094/phyto-03-23-0086-r] [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] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Phytophthora capsici is one of the most devastating pathogens facing pepper (Capsicum annuum) producers worldwide. Numerous factors, such as the race of the pathogen, the growing environment, and the source of resistance, have resulted in an overall lack of widely applicable molecular markers associated with resistance. Our objective was to determine the effect of the rating system on quantitative trait locus (QTL) detection and understand inheritance patterns of host resistance that can influence selection and molecular marker accuracy. We evaluated an F2:11 recombinant inbred line population screened against the highly virulent strain (Pc134) and scored using two widely used methods, developed by Bosland and Lindsey and by Black. The rating system developed by Bosland and Lindsey resulted in slightly higher logarithm of odds for the QTL on chromosome 5, and we detected a QTL on chromosome 12 uniquely using this rating system. A QTL on chromosome 10 was detected using both rating systems, but Black resulted in considerably higher logarithm of odds for this QTL compared with the Bosland and Lindsey system. Molecular markers developed were nominally better at accurately predicting the phenotype than previously published molecular markers but did not completely explain resistance in our validation populations. The inheritance pattern of resistance in one of our F2 populations did not significantly deviate from a 7:9 segregation ratio, indicating duplicative recessive epistasis. However, these results could be confounded by the presence of incomplete gene action, which was found through the improved selection accuracy when the phenotypes of heterozygous individuals were grouped with those with susceptible alleles.
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Affiliation(s)
| | - Yu-Ming Hsu
- CNRS, INRAE, Institute of Plant Sciences Paris‑Saclay (IPS2), Univ Evry, Université Paris-Saclay, Orsay, France
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Okuno R, Inoue Y, Hasebe Y, Igarashi T, Kawagishi-Hotta M, Yamada T, Hasegawa S. Genome-wide association studies in the Japanese population identified genetic loci and target gene associated with epidermal turnover. Exp Dermatol 2023; 32:1856-1863. [PMID: 37551986 DOI: 10.1111/exd.14908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 05/10/2023] [Accepted: 07/31/2023] [Indexed: 08/09/2023]
Abstract
The epidermis is an essential organ for life by retaining water and as a protective barrier. The epidermis is maintained through metabolism, in which basal cells produced from epidermal stem cells differentiate into spinous cells, granular cells and corneocytes, and are finally shed from the epidermal surface. This is epidermal turnover, and with aging, there is a decline in epidermis function. Other factors that may affect epidermal turnover include ultraviolet damage and genetic factors. These genetic factors are of particular interest as little is known. Although recent skin-focused genome-wide association studies (GWAS) have been conducted, the genetic regions associated with epidermal turnover are almost uninvestigated. Therefore, we conducted a GWAS on epidermal turnover in the Japanese population, using the corneocyte area, which correlates to the rate of epidermal turnover, as an indicator. As a result, rs2278431 (p = 1.29 × 10-7 ) in 19q13.2 was associated with corneocyte size. Furthermore, eQTL analysis suggested that rs2278431 was related to the SPINT2 gene. In addition, SPINT2 knockdown studies using epidermal keratinocytes revealed that SPINT2 is involved in keratinocyte proliferation and in corneocyte size regulation in reconstructed epidermis. These results suggest that rs2278431 is involved in the expression of SPINT2 and affects epidermal turnover.
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Affiliation(s)
- Ryosuke Okuno
- Research Laboratories, Nippon Menard Cosmetic Co., Ltd., Nagoya, Japan
- Nagoya University-MENARD Collaborative Research Chair, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yu Inoue
- Research Laboratories, Nippon Menard Cosmetic Co., Ltd., Nagoya, Japan
- Nagoya University-MENARD Collaborative Research Chair, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yuichi Hasebe
- Research Laboratories, Nippon Menard Cosmetic Co., Ltd., Nagoya, Japan
- Nagoya University-MENARD Collaborative Research Chair, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Toshio Igarashi
- Research Laboratories, Nippon Menard Cosmetic Co., Ltd., Nagoya, Japan
| | - Mika Kawagishi-Hotta
- Research Laboratories, Nippon Menard Cosmetic Co., Ltd., Nagoya, Japan
- Nagoya University-MENARD Collaborative Research Chair, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Takaaki Yamada
- Research Laboratories, Nippon Menard Cosmetic Co., Ltd., Nagoya, Japan
| | - Seiji Hasegawa
- Research Laboratories, Nippon Menard Cosmetic Co., Ltd., Nagoya, Japan
- Nagoya University-MENARD Collaborative Research Chair, Nagoya University Graduate School of Medicine, Nagoya, Japan
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Xue Y, Sun X, Fu J, Rong L, Zhang H, Zhu Y, Yang X, Hu S, Chen J, Fang Y. PI3K/AKT pathway-related microRNA variants in childhood acute lymphoblastic leukemia. Pediatr Blood Cancer 2023; 70:e30545. [PMID: 37438860 DOI: 10.1002/pbc.30545] [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: 10/23/2022] [Revised: 06/13/2023] [Accepted: 06/16/2023] [Indexed: 07/14/2023]
Abstract
BACKGROUND Dysregulation of microRNAs (miRNAs) targeting genes in the PI3K/Akt pathway has been implicated in the pathogenesis of childhood acute lymphoblastic leukemia (ALL). However, the impact of genetic variants in these miRNAs on ALL susceptibility has not been extensively explored in the Chinese population. METHODS To address this gap, we conducted a case-control study to evaluate the association between genetic variants in five PI3K/AKT pathway-related miRNAs (miR-149, miR-126, miR-492, miR-612, and miR-423) and childhood ALL susceptibility in the Chinese population. Additionally, we investigated the effects of the rs2292832 mutation on ALL cell proliferation and apoptosis. RESULTS Our analyses revealed that the miR-149 rs2292832 mutant heterozygous CT genotype was more frequent in the control group than in the ALL cases, indicating a protective effect against ALL (adjusted odds ratio [OR] = 0.78, 95% confidence interval [CI] = 0.63-0.97, p = .024). Stratification analyses further revealed that the miR-149 rs2292832 CC genotype was associated with an increased risk of childhood ALL in subgroups of older children, females, those with parents who never smoked or drank alcohol, those living in painted houses, those with B-ALL, and those with high-risk ALL. Finally, we observed that the rs2292832 mutation inhibited ALL cell proliferation and induced apoptosis (p = .001), providing a potential mechanism by which this genetic variant may influence ALL susceptibility. CONCLUSION Our study highlights the significant association between the miR-149 rs2292832 genetic variant and childhood ALL susceptibility in the Chinese population. These findings expand our understanding of the complex genetic landscape underlying ALL and have implications for the development of personalized therapeutic strategies.
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Affiliation(s)
- Yao Xue
- Department of Hematology and Oncology, Children's Hospital of Nanjing Medical University, Nanjing, China
- Key Laboratory of Hematology, Nanjing Medical University, Nanjing, China
| | - Xiaoyan Sun
- Department of Hematology and Oncology, Children's Hospital of Nanjing Medical University, Nanjing, China
- Key Laboratory of Hematology, Nanjing Medical University, Nanjing, China
| | - Jinyu Fu
- Department of Hematology and Oncology, Children's Hospital of Nanjing Medical University, Nanjing, China
- Key Laboratory of Hematology, Nanjing Medical University, Nanjing, China
| | - Liucheng Rong
- Department of Hematology and Oncology, Children's Hospital of Nanjing Medical University, Nanjing, China
- Key Laboratory of Hematology, Nanjing Medical University, Nanjing, China
| | - Heng Zhang
- Department of Hematology and Oncology, Children's Hospital of Nanjing Medical University, Nanjing, China
- Key Laboratory of Hematology, Nanjing Medical University, Nanjing, China
| | - Yuting Zhu
- Department of Pediatrics, The Affiliated Huaian No. 1 People's Hospital of Nanjing Medical University, Nanjing, China
| | - Xiaoyun Yang
- Department of Hematology and Oncology, Children's Hospital of Nanjing Medical University, Nanjing, China
- Key Laboratory of Hematology, Nanjing Medical University, Nanjing, China
| | - Shaoyan Hu
- Department of Hematology/Oncology, Children's Hospital of Soochow University, Suzhou, China
| | - Jing Chen
- National Children's Medical Center, Department of Hematology/Oncology, Key Laboratory of Pediatric Hematology and Oncology of China Ministry of Health, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yongjun Fang
- Department of Hematology and Oncology, Children's Hospital of Nanjing Medical University, Nanjing, China
- Key Laboratory of Hematology, Nanjing Medical University, Nanjing, China
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Flore L, Francalacci P, Massidda M, Robledo R, Calò CM. Influence of Different Evolutive Forces on GDF5 Gene Variability. Genes (Basel) 2023; 14:1895. [PMID: 37895244 PMCID: PMC10606091 DOI: 10.3390/genes14101895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 09/26/2023] [Indexed: 10/29/2023] Open
Abstract
The GDF5 gene is involved in the development of skeletal elements, synovial joint formation, tendons, ligaments, and cartilage. Several polymorphisms are present within the gene, and two of them, rs143384 and 143383, were reported to be correlated with osteoarticular disease or muscle flexibility. The aim of this research is to verify if the worldwide distribution of the rs143384 polymorphism among human populations was shaped by selective pressure, or if it was the result of random genetic drift events. Ninety-four individuals of both the male and female sexes, 18-28 years old, from Sardinia were analyzed. We observed the following genotype frequencies: 28.72% of AA homozygotes, 13.83% of GG homozygotes, and 57.45% of AG heterozygotes. The allele frequencies were 0.574 for allele A and 0.426 for allele G. The relationships between the populations were verified via Multidimensional Scaling (MDS). Our data show (i) a clear heterogeneity within the African populations; (ii) a strong differentiation between the African populations and the other populations; and that (iii) the Sardinian population is placed within the European cluster. To reveal possible traces of selective pressure, the Population Branch Statistic (PBS) was calculated; both the rs143384 and 143383 SNPs have low PBS values, suggesting that there are no signals of selective pressure in those areas of the gene.
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Affiliation(s)
- Laura Flore
- Department of Life and Environment Sciences, University of Cagliari, 09042 Cagliari, Italy; (L.F.); (P.F.); (C.M.C.)
| | - Paolo Francalacci
- Department of Life and Environment Sciences, University of Cagliari, 09042 Cagliari, Italy; (L.F.); (P.F.); (C.M.C.)
| | - Myosotis Massidda
- Department of Medical Sciences and Public Health, University of Cagliari, 09042 Cagliari, Italy;
| | - Renato Robledo
- Department of Biomedical Sciences, University of Cagliari, 09042 Cagliari, Italy
| | - Carla Maria Calò
- Department of Life and Environment Sciences, University of Cagliari, 09042 Cagliari, Italy; (L.F.); (P.F.); (C.M.C.)
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Wu M, Du Y, Zhang C, Li Z, Li Q, Qi E, Ruan W, Feng S, Zhou H. Mendelian Randomization Study of Lipid Metabolites Reveals Causal Associations with Heel Bone Mineral Density. Nutrients 2023; 15:4160. [PMID: 37836445 PMCID: PMC10574167 DOI: 10.3390/nu15194160] [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: 09/01/2023] [Revised: 09/22/2023] [Accepted: 09/25/2023] [Indexed: 10/15/2023] Open
Abstract
BACKGROUND Osteoporosis, which is a bone disease, is characterized by low bone mineral density and an increased risk of fractures. The heel bone mineral density is often used as a representative measure of overall bone mineral density. Lipid metabolism, which includes processes such as fatty acid metabolism, glycerol metabolism, inositol metabolism, bile acid metabolism, carnitine metabolism, ketone body metabolism, sterol and steroid metabolism, etc., may have an impact on changes in bone mineral density. While some studies have reported correlations between lipid metabolism and heel bone mineral density, the overall causal relationship between metabolites and heel bone mineral density remains unclear. OBJECTIVE to investigate the causal relationship between lipid metabolites and heel bone mineral density using two-sample Mendelian randomization analysis. METHODS Summary-level data from large-scale genome-wide association studies were extracted to identify genetic variants linked to lipid metabolite levels. These genetic variants were subsequently employed as instrumental variables in Mendelian randomization analysis to estimate the causal effects of each lipid metabolite on heel bone mineral density. Furthermore, metabolites that could potentially be influenced by causal relationships with bone mineral density were extracted from the KEGG and WikiPathways databases. The causal associations between these downstream metabolites and heel bone mineral density were then examined. Lastly, a sensitivity analysis was conducted to evaluate the robustness of the results and address potential sources of bias. RESULTS A total of 130 lipid metabolites were analyzed, and it was found that acetylcarnitine, propionylcarnitine, hexadecanedioate, tetradecanedioate, myo-inositol, 1-arachidonoylglycerophosphorine, 1-linoleoylglycerophoethanolamine, and epiandrosterone sulfate had a causal relationship with heel bone mineral density (p < 0.05). Furthermore, our findings also indicate an absence of causal association between the downstream metabolites associated with the aforementioned metabolites identified in the KEGG and WikiPathways databases and heel bone mineral density. CONCLUSION This work supports the hypothesis that lipid metabolites have an impact on bone health through demonstrating a causal relationship between specific lipid metabolites and heel bone mineral density. This study has significant implications for the development of new strategies to osteoporosis prevention and treatment.
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Affiliation(s)
- Mingxin Wu
- National Spinal Cord Injury International Cooperation Base, Tianjin Key Laboratory of Spine and Spinal Cord Injury, Department of Orthopedics, Tianjin Medical University General Hospital, Tianjin 300070, China
| | - Yufei Du
- Department of Endocrinology and Metabolism, Tianjin Medical University General Hospital, Tianjin 300070, China
| | - Chi Zhang
- Department of Orthopaedics, Qilu Hospital of Shandong University, Shandong University Centre for Orthopaedics, Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong University, Jinan 250013, China
| | - Zhen Li
- National Spinal Cord Injury International Cooperation Base, Tianjin Key Laboratory of Spine and Spinal Cord Injury, Department of Orthopedics, Tianjin Medical University General Hospital, Tianjin 300070, China
| | - Qingyang Li
- Department of Orthopaedics, Qilu Hospital of Shandong University, Shandong University Centre for Orthopaedics, Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong University, Jinan 250013, China
| | - Enlin Qi
- Department of Orthopaedics, Qilu Hospital of Shandong University, Shandong University Centre for Orthopaedics, Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong University, Jinan 250013, China
| | - Wendong Ruan
- National Spinal Cord Injury International Cooperation Base, Tianjin Key Laboratory of Spine and Spinal Cord Injury, Department of Orthopedics, Tianjin Medical University General Hospital, Tianjin 300070, China
| | - Shiqing Feng
- National Spinal Cord Injury International Cooperation Base, Tianjin Key Laboratory of Spine and Spinal Cord Injury, Department of Orthopedics, Tianjin Medical University General Hospital, Tianjin 300070, China
- Department of Orthopaedics, Qilu Hospital of Shandong University, Shandong University Centre for Orthopaedics, Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong University, Jinan 250013, China
| | - Hengxing Zhou
- National Spinal Cord Injury International Cooperation Base, Tianjin Key Laboratory of Spine and Spinal Cord Injury, Department of Orthopedics, Tianjin Medical University General Hospital, Tianjin 300070, China
- Department of Orthopaedics, Qilu Hospital of Shandong University, Shandong University Centre for Orthopaedics, Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong University, Jinan 250013, China
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Avsar O. Identification of the effects of pathogenic genetic variations of human CYP2C9 and CYP2D6: an in silico approach. Nucleosides Nucleotides Nucleic Acids 2023; 43:356-376. [PMID: 37747773 DOI: 10.1080/15257770.2023.2262519] [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] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 09/19/2023] [Indexed: 09/26/2023]
Abstract
Genetic variations in the human cytochrome P450 family 2 subfamily C member 9 (CYP2C9) and cytochrome P450 family 2 subfamily D member 6 (CYP2D6) genes may affect drug metabolism and lead to alterations in phenotypes. Genetic variations are associated with toxicity, adverse drug reactions, inefficient treatment. Various in silico tools were combined to investigate the deleterious effects of missense non-synonymous single nucleotide polymorphisms (nsSNPs) of the human CYP2C9 and CYP2D6. The structural and functional effects of the high-risk non-synonymous SNPs in the human CYP2C9 and CYP2D6 were predicted by numerous computational mutation analysis methods. Out of 24 pathogenic missense SNPs in the CYP2C9, 22 nsSNPs had a decreasing effect on protein stability and 13 SNPs were showed to be located at conserved positions. Out of 27 high-risk deleterious non-synonymous SNPs in the human CYP2D6, 21 SNPs decreased protein stability and 16 nsSNPs were predicted to be positioned at conserved regions. Our present study suggests that the identified functional SNPs may affect drug metabolism associated with CYP2C9 and CYP2D6 enzymes.
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Affiliation(s)
- Orcun Avsar
- Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Hitit University, Corum, Türkiye
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Pessôa R, Clissa PB, Sanabani SS. The Interaction between the Host Genome, Epigenome, and the Gut-Skin Axis Microbiome in Atopic Dermatitis. Int J Mol Sci 2023; 24:14322. [PMID: 37762624 PMCID: PMC10532357 DOI: 10.3390/ijms241814322] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 09/14/2023] [Accepted: 09/15/2023] [Indexed: 09/29/2023] Open
Abstract
Atopic dermatitis (AD) is a chronic inflammatory skin disease that occurs in genetically predisposed individuals. It involves complex interactions among the host immune system, environmental factors (such as skin barrier dysfunction), and microbial dysbiosis. Genome-wide association studies (GWAS) have identified AD risk alleles; however, the associated environmental factors remain largely unknown. Recent evidence suggests that altered microbiota composition (dysbiosis) in the skin and gut may contribute to the pathogenesis of AD. Examples of environmental factors that contribute to skin barrier dysfunction and microbial dysbiosis in AD include allergens, irritants, pollution, and microbial exposure. Studies have reported alterations in the gut microbiome structure in patients with AD compared to control subjects, characterized by increased abundance of Clostridium difficile and decreased abundance of short-chain fatty acid (SCFA)-producing bacteria such as Bifidobacterium. SCFAs play a critical role in maintaining host health, and reduced SCFA production may lead to intestinal inflammation in AD patients. The specific mechanisms through which dysbiotic bacteria and their metabolites interact with the host genome and epigenome to cause autoimmunity in AD are still unknown. By understanding the combination of environmental factors, such as gut microbiota, the genetic and epigenetic determinants that are associated with the development of autoantibodies may help unravel the pathophysiology of the disease. This review aims to elucidate the interactions between the immune system, susceptibility genes, epigenetic factors, and the gut microbiome in the development of AD.
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Affiliation(s)
- Rodrigo Pessôa
- Postgraduate Program in Translational Medicine, Department of Medicine, Federal University of Sao Paulo (UNIFESP), Sao Paulo 04039-002, Brazil;
| | | | - Sabri Saeed Sanabani
- Laboratory of Medical Investigation LIM-56, Division of Dermatology, Medical School, University of Sao Paulo, Sao Paulo 05508-220, Brazil
- Laboratory of Medical Investigation Unit 03, Clinics Hospital, Faculty of Medicine, University of Sao Paulo, Sao Paulo 05403-000, Brazil
- Laboratory of Dermatology and Immunodeficiency LIM56/03, Instituto de Medicina Tropical de Sao Paulo, Faculdade de Medicina, University of Sao Paulo, Av. Dr. Eneas de Carvalho Aguiar, 470 3º Andar, Sao Paulo 05403-000, Brazil
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