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Zhu Z, Geng Y, Ma L, Yao K, Chang R, Ma Y, Li J. Association between CBS gene T833C, G919A and 844ins68 polymorphisms in the 8th exon region and coronary artery disease: a meta-analysis. Clin Exp Hypertens 2024; 46:2328147. [PMID: 38488417 DOI: 10.1080/10641963.2024.2328147] [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: 06/02/2023] [Accepted: 03/01/2024] [Indexed: 03/19/2024]
Abstract
BACKGROUND Several studies indicate that the cystathionine β-synthase (CBS) gene T833C, G919A and 844ins68 polymorphisms in the 8th exon region may be correlated with coronary artery disease (CAD) susceptibility, but the results have been inconsistent and inconclusive. Thus, a meta-analysis was conducted to provide a comprehensive estimate of these associations. METHODS On the basis of searches in the PubMed, EMBASE, Cochrane Library, Wanfang, VIP, and CNKI databases, we selected 14 case - control studies including 2123 cases and 2368 controls for this meta-analysis. Pooled odds ratios (ORs) with 95% confidence intervals (CIs) were calculated accordingly using a fixed-effect or random-effect model. RESULTS The results indicated an increased risk between the CBS T833C gene polymorphisms and susceptibility to CAD under the dominant model (CC+CT vs. TT: OR = 1.92, 95% CI: 1.11 ~ 3.32), recessive model (CC vs. CT+TT: OR = 1.88, 95% CI: 1.17 ~ 3.03), and homozygous model (CC vs. TT: OR = 2.46, 95% CI: 1.04 ~ 5.83). In these three genetic models, no significant association was identified for CBS G919A (AA+AG vs. GG: OR = 1.48, 95% CI: 0.45 ~ 4.82),(AA vs. AG+GG: OR = 1.58, 95% CI: 0.93 ~ 2.70),(AA vs. GG: OR = 1.66, 95% CI: 0.40 ~ 6.92) or CBS 844ins68 (II+ID vs. DD: OR = 1.04, 95% CI: 0.80 ~ 1.35),(II vs. ID+DD: OR = 1.09, 95% CI: 0.51 ~ 2.36),(II vs. DD: OR = 1.10, 95% CI: 0.51 ~ 2.39). CONCLUSIONS This meta-analysis suggests that the CBS T833C gene polymorphism is significantly associated with the risk of CAD and it shows a stronger association in Asian populations. Individuals with the C allele of the CBS gene T833C polymorphism might be particularly susceptible to CAD.
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Affiliation(s)
- Zijiang Zhu
- Department of thoracic surgery, Gansu Provincial Central Hospital (Gansu Provincial Maternity and Child-care Hospital), Lanzhou, China
| | - Yuhan Geng
- School of Clinical Medicine, Ningxia Medical University, Yinchuan, China
| | - Long Ma
- Department of thoracic surgery, Gansu Provincial Central Hospital (Gansu Provincial Maternity and Child-care Hospital), Lanzhou, China
- Department of thoracic surgery, Gansu University of Chinese Medicine, Lanzhou, China
| | - Keying Yao
- School of Second Clinical Medical, Lanzhou University, Lanzhou, China
| | - Ruitong Chang
- Department of thoracic surgery, Gansu Provincial Central Hospital (Gansu Provincial Maternity and Child-care Hospital), Lanzhou, China
| | - Yongming Ma
- Department of thoracic surgery, Gansu Provincial Central Hospital (Gansu Provincial Maternity and Child-care Hospital), Lanzhou, China
- Department of thoracic surgery, Gansu University of Chinese Medicine, Lanzhou, China
| | - Jialong Li
- Department of thoracic surgery, Gansu Provincial Central Hospital (Gansu Provincial Maternity and Child-care Hospital), Lanzhou, China
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Li X, Li P, Tang W, Zheng J, Fan F, Jiang X, Li Z, Fang Y. Simultaneous determination of subspecies and geographic origins of 110 rice cultivars by microsatellite markers. Food Chem 2024; 445:138657. [PMID: 38354640 DOI: 10.1016/j.foodchem.2024.138657] [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: 11/28/2023] [Revised: 01/23/2024] [Accepted: 01/30/2024] [Indexed: 02/16/2024]
Abstract
Rice varieties of different subspecies types (indica rice and japonica rice) across various geographical origins (Hunan, Jiangsu, and Northeast China) were monitored using microsatellite markers (simple sequence repeats, SSR). 110 representative rice cultivars were collected from the main crop areas. Multiple methods including clustering analysis (neighbor-joining (NJ) method, unweighted pair-group method with arithmetic mean (UPGMA) method), principal component analysis (PCA) and model-based grouping were applied. The study revealed that 25 pairs of SSR markers exhibited a broad range of polymorphism information content (PIC) values, ranging from 0.240 to 0.830. Furthermore, our study successfully achieved a higher overall mean correct rate of 99.09% in determining the geographical origin of rice. Simultaneously, it accurately classified indica rice and japonica rice. These findings are significant as they provide an SSR fingerprint of 110 high-quality rice cultivars, serving as a valuable scientific resource for the detection of rice adulteration and traceability of its origin.
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Affiliation(s)
- Xinyue Li
- College of Food Science and Engineering, Nanjing University of Finance and Economics/Collaborative Innovation Center for Modern Grain Circulation and Safety, Nanjing 210023, China
| | - Peng Li
- College of Food Science and Engineering, Nanjing University of Finance and Economics/Collaborative Innovation Center for Modern Grain Circulation and Safety, Nanjing 210023, China
| | - Wenqian Tang
- College of Food Science and Engineering, Nanjing University of Finance and Economics/Collaborative Innovation Center for Modern Grain Circulation and Safety, Nanjing 210023, China
| | - Jiayu Zheng
- College of Food Science and Engineering, Nanjing University of Finance and Economics/Collaborative Innovation Center for Modern Grain Circulation and Safety, Nanjing 210023, China
| | - Fengjiao Fan
- College of Food Science and Engineering, Nanjing University of Finance and Economics/Collaborative Innovation Center for Modern Grain Circulation and Safety, Nanjing 210023, China
| | - Xiaoyi Jiang
- College of Food Science and Engineering, Nanjing University of Finance and Economics/Collaborative Innovation Center for Modern Grain Circulation and Safety, Nanjing 210023, China
| | - Ziqian Li
- College of Food Science and Engineering, Nanjing University of Finance and Economics/Collaborative Innovation Center for Modern Grain Circulation and Safety, Nanjing 210023, China
| | - Yong Fang
- College of Food Science and Engineering, Nanjing University of Finance and Economics/Collaborative Innovation Center for Modern Grain Circulation and Safety, Nanjing 210023, China.
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Imani MM, Akbari S, Shalchi M, Sadeghi E, Sadeghi M. Relationship between ERCC1 and XPC polymorphisms and the susceptibility to head and neck carcinoma: A systematic review, meta-analysis, and trial sequential analysis. Arch Oral Biol 2024; 162:105955. [PMID: 38479279 DOI: 10.1016/j.archoralbio.2024.105955] [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: 01/24/2024] [Revised: 02/29/2024] [Accepted: 03/07/2024] [Indexed: 04/17/2024]
Abstract
OBJECTIVE This meta-analysis was conducted to investigate the relationship between ERCC1 and XPC polymorphisms and the risk of head and neck cancer (HNC), incorporating more studies and additional analyses. DESIGN An exhaustive search of various databases, including PubMed/Medline, Web of Science, Scopus, and Cochrane Library was carried out, up until November 18, 2023, to identify pertinent studies. The Review Manager 5.3 software was employed to calculate the effect sizes, which were presented as the odds ratio (OR) along with a 95% confidence interval (CI). RESULTS The study found that the T allele (OR = 1.11; p-value = 0.02; 95%CI: 1.02, 1.22) and the TT genotype rs2228000 polymorphism in both the homozygous model (OR = 1.61, p-value = 0.02; 95%CI: 1.07, 2.42) and the recessive model (OR = 1.53; p-value = 0.02; 95%CI: 1.06, 2.22) had statistically significant associations. However, no significant associations were found for rs11615, rs3212986, rs735482, rs2228001, and PAT polymorphisms in any genetic models. CONCLUSIONS The meta-analysis revealed significant associations for the T allele and TT genotype rs2228000 polymorphism, but not for rs11615, rs3212986, rs735482, rs2228001, and PAT polymorphisms. The results highlight the impact of factors such as ethnicity, cancer subtype, and control source on these associations, emphasizing the intricate nature of genetic interactions in disease risk.
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Affiliation(s)
- Mohammad Moslem Imani
- Department of Orthodontics, School of Dentistry, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Sattar Akbari
- Department of Orthodontics, School of Dentistry, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Majid Shalchi
- Department of Orthodontics, School of Dentistry, Guilan University of Medical Sciences, Rasht, Iran
| | - Edris Sadeghi
- Medical Biology Research Centre, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Masoud Sadeghi
- Medical Biology Research Centre, Kermanshah University of Medical Sciences, Kermanshah, Iran.
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Silva IMD, Vacario BGL, Okuyama NCM, Barcelos GRM, Fuganti PE, Guembarovski RL, Cólus IMDS, Serpeloni JM. Polymorphisms in drug-metabolizing genes and urinary bladder cancer susceptibility and prognosis: Possible impacts and future management. Gene 2024; 907:148252. [PMID: 38350514 DOI: 10.1016/j.gene.2024.148252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 01/22/2024] [Accepted: 02/05/2024] [Indexed: 02/15/2024]
Abstract
Epidemiological studies have shown the association of genetic variants with risks of occupational and environmentally induced cancers, including bladder (BC). The current review summarizes the effects of variants in genes encoding phase I and II enzymes in well-designed studies to highlight their contribution to BC susceptibility and prognosis. Polymorphisms in genes codifying drug-metabolizing proteins are of particular interest because of their involvement in the metabolism of exogenous genotoxic compounds, such as tobacco and agrochemicals. The prognosis between muscle-invasive and non-muscle-invasive diseases is very different, and it is difficult to predict which will progress worse. Web of Science, PubMed, and Medline were searched to identify studies published between January 1, 2010, and February 2023. We included 73 eligible studies, more than 300 polymorphisms, and 46 genes/loci. The most studied candidate genes/loci of phase I metabolism were CYP1B1, CYP1A1, CYP1A2, CYP3A4, CYP2D6, CYP2A6, CYP3E1, and ALDH2, and those in phase II were GSTM1, GSTT1, NAT2, GSTP1, GSTA1, GSTO1, and UGT1A1. We used the 46 genes to construct a network of proteins and to evaluate their biological functions based on the Reactome and KEGG databases. Lastly, we assessed their expression in different tissues, including normal bladder and BC samples. The drug-metabolizing pathway plays a relevant role in BC, and our review discusses a list of genes that could provide clues for further exploration of susceptibility and prognostic biomarkers.
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Affiliation(s)
- Isabely Mayara da Silva
- Department of General Biology, Center of Biological Sciences, State University of Londrina (UEL), Londrina 86057-970, Brazil.
| | - Beatriz Geovana Leite Vacario
- Department of General Biology, Center of Biological Sciences, State University of Londrina (UEL), Londrina 86057-970, Brazil; Center of Health Sciences, State University of West Paraná (UNIOESTE), Francisco Beltrão-Paraná, 85605-010, Brazil.
| | - Nádia Calvo Martins Okuyama
- Department of General Biology, Center of Biological Sciences, State University of Londrina (UEL), Londrina 86057-970, Brazil.
| | - Gustavo Rafael Mazzaron Barcelos
- Department of Biosciences, Institute for Health and Society, Federal University of São Paulo (UNIFESP), Santos 11.060-001, Brazil.
| | | | - Roberta Losi Guembarovski
- Department of General Biology, Center of Biological Sciences, State University of Londrina (UEL), Londrina 86057-970, Brazil.
| | - Ilce Mara de Syllos Cólus
- Department of General Biology, Center of Biological Sciences, State University of Londrina (UEL), Londrina 86057-970, Brazil.
| | - Juliana Mara Serpeloni
- Department of General Biology, Center of Biological Sciences, State University of Londrina (UEL), Londrina 86057-970, Brazil.
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Dobrijević Z, Stevanović J, Robajac D, Penezić A, Četić D, Baralić M, Nedić O. Association between nitric oxide synthase (NOS3) gene polymorphisms and diabetic nephropathy: An updated meta-analysis. Mol Cell Endocrinol 2024; 586:112197. [PMID: 38462124 DOI: 10.1016/j.mce.2024.112197] [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: 01/29/2024] [Revised: 02/29/2024] [Accepted: 03/01/2024] [Indexed: 03/12/2024]
Abstract
Polymorphisms located within NOS3 gene have been investigated as susceptibility variants for diabetic nephropathy (DN) in type 2 diabetes mellitus (T2DM) in a large number of studies. However, these previous articles yielded inconsistent results and we aimed at elucidating the impact of NOS3 variants on DN risk in T2DM by conducting an updated systematic data synthesis. A total of 36 studies (12,807 participants) were selected for qualitative data synthesis, while 33 records with 11,649 subjects were included in the meta-analysis. The pooled analysis demonstrated the association of minor alleles of rs2070744 and rs1799983 with an increased susceptibility to DN (P < 0.001 and P = 0.015 for allelic model, respectively). For both of these variants, a significant effect of subgrouping according to ethnicity was found. Rs869109213 displayed an association with DN susceptibility, with pooled effect measures indicating a predisposing effect of the minor allele a (Prec = 0.002, ORrec = 1.960, 95%CI 1.288-2.983; Paavs. bb = 0.001, ORaavs. bb = 2.014, 95%CI 1.316-3.083). These findings support the effects of NOS3 variants on the risk of developing DN in T2DM.
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Affiliation(s)
- Zorana Dobrijević
- University of Belgrade - Institute for the Application of Nuclear Energy, Belgrade, Serbia.
| | - Jovana Stevanović
- University of Belgrade - Institute for the Application of Nuclear Energy, Belgrade, Serbia
| | - Dragana Robajac
- University of Belgrade - Institute for the Application of Nuclear Energy, Belgrade, Serbia
| | - Ana Penezić
- University of Belgrade - Institute for the Application of Nuclear Energy, Belgrade, Serbia
| | - Danilo Četić
- University of Belgrade - Institute for the Application of Nuclear Energy, Belgrade, Serbia
| | - Marko Baralić
- University of Belgrade - School of Medicine, Belgrade, Serbia; Department of Nephrology, University Clinical Centre of Serbia, Belgrade, Serbia
| | - Olgica Nedić
- University of Belgrade - Institute for the Application of Nuclear Energy, Belgrade, Serbia
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Aguilar P, Pérez I de Lanuza G, Carneiro M, Andrade P, Pinho C. The role of historical biogeography in shaping colour morph diversity in the common wall lizard. Mol Ecol 2024; 33:e17338. [PMID: 38572696 DOI: 10.1111/mec.17338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 03/20/2024] [Accepted: 03/22/2024] [Indexed: 04/05/2024]
Abstract
The maintenance of polymorphisms often depends on multiple selective forces, but less is known on the role of stochastic or historical processes in maintaining variation. The common wall lizard (Podarcis muralis) is a colour polymorphic species in which local colour morph frequencies are thought to be modulated by natural and sexual selection. Here, we used genome-wide single-nucleotide polymorphism data to investigate the relationships between morph composition and population biogeography at a regional scale, by comparing morph composition with patterns of genetic variation of 54 populations sampled across the Pyrenees. We found that genetic divergence was explained by geographic distance but not by environmental features. Differences in morph composition were associated with genetic and environmental differentiation, as well as differences in sex ratio. Thus, variation in colour morph frequencies could have arisen via historical events and/or differences in the permeability to gene flow, possibly shaped by the complex topography and environment. In agreement with this hypothesis, colour morph diversity was positively correlated with genetic diversity and rates of gene flow and inversely correlated with the likelihood of the occurrence of bottlenecks. Concurrently, we did not find conclusive evidence for selection in the two colour loci. As an illustration of these effects, we observed that populations with higher proportions of the rarer yellow and yellow-orange morphs had higher genetic diversity. Our results suggest that processes involving a decay in overall genetic diversity, such as reduced gene flow and/or bottleneck events have an important role in shaping population-specific morph composition via non-selective processes.
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Affiliation(s)
- Prem Aguilar
- Research Centre in Biodiversity and Genetic Resources, InBIO, CIBIO, Universidade do Porto, Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal
| | - Guillem Pérez I de Lanuza
- Research Centre in Biodiversity and Genetic Resources, InBIO, CIBIO, Universidade do Porto, Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
- Ethology Lab, Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, València, Spain
| | - Miguel Carneiro
- Research Centre in Biodiversity and Genetic Resources, InBIO, CIBIO, Universidade do Porto, Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
| | - Pedro Andrade
- Research Centre in Biodiversity and Genetic Resources, InBIO, CIBIO, Universidade do Porto, Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
| | - Catarina Pinho
- Research Centre in Biodiversity and Genetic Resources, InBIO, CIBIO, Universidade do Porto, Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
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Miaskowski C, Conley YP, Cooper BA, Paul SM, Smoot BJ, Hammer MJ, Fu M, Levine JD. Identification Of A Higher Risk Lymphedema Phenotype And Associations With Cytokine Gene Polymorphisms. J Pain Symptom Manage 2024; 67:375-383.e3. [PMID: 38307372 DOI: 10.1016/j.jpainsymman.2024.01.033] [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: 10/25/2023] [Revised: 01/21/2024] [Accepted: 01/24/2024] [Indexed: 02/04/2024]
Abstract
CONTEXT Breast cancer-related lymphedema (BCRL) is chronic condition that occurs in 5% to 75% of women following treatment for breast cancer. However, little is known about the risk factors and mechanisms associated with a worse BCRL profile. OBJECTIVES Identify distinct BCRL profiles in women with the condition (i.e., lower vs. higher risk phenotype) and evaluate for associations with pro- and anti-inflammatory genes. METHODS Latent class profile analysis (LCPA) was used to identify the BCRL profiles using phenotypic characteristics evaluated prior to surgery. Candidate gene analyses were done to identify cytokine genes associated with the two BCRL profiles. RESULTS Of the 155 patients evaluated, 35.5% (n = 55) were in the Lower and 64.5% (n = 100) were in the Higher Risk classes. Risk factors for membership in the Higher class included: lower functional status, having sentinel lymph node biopsy, axillary lymph node dissection, mastectomy, higher number of positive lymph nodes, and receipt of chemotherapy. Polymorphisms for interleukin (IL)1-beta and IL6 were associated with membership in the Higher Risk class. CONCLUSION The readily available and clinically relevant phenotypic characteristics associated with a worse BCRL profile can be used by clinicians to identify higher risk patients. If confirmed, these characteristics can be tested in predictive risk models. In addition, the candidate gene findings may guide the development of mechanistically-based interventions to decrease the risk of BCRL.
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Affiliation(s)
- Christine Miaskowski
- School of Nursing, University of California, San Francisco, CA, USA; School of Medicine, University of California, San Francisco, CA, USA.
| | | | - Bruce A Cooper
- School of Nursing, University of California, San Francisco, CA, USA
| | - Steven M Paul
- School of Nursing, University of California, San Francisco, CA, USA
| | - Betty J Smoot
- School of Medicine, University of California, San Francisco, CA, USA
| | | | - Mei Fu
- School of Nursing and Health Studies, University of Missouri, Kansas City, MO, USA
| | - Jon D Levine
- School of Medicine, University of California, San Francisco, CA, USA
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Huang Y, Wang M, Liu C, He G. Comprehensive landscape of non-CODIS STRs in global populations provides new insights into challenging DNA profiles. Forensic Sci Int Genet 2024; 70:103010. [PMID: 38271830 DOI: 10.1016/j.fsigen.2024.103010] [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: 11/27/2023] [Revised: 01/13/2024] [Accepted: 01/14/2024] [Indexed: 01/27/2024]
Abstract
The worldwide implementation of short tandem repeats (STR) profiles in forensic genetics necessitated establishing and expanding the CODIS core loci set to facilitated efficient data management and exchange. Currently, the mainstay CODIS STRs are adopted in most general-purpose forensic kits. However, relying solely on these loci failed to yield satisfactory results for challenging tasks, such as bio-geographical ancestry inference, complex DNA mixture profile interpretation, and distant kinship analysis. In this context, non-CODIS STRs are potent supplements to enhance the systematic discriminating power, particularly when combined with the high-throughput next-generation sequencing (NGS) technique. Nevertheless, comprehensive evaluation on non-CODIS STRs in diverse populations was scarce, hindering their further application in routine caseworks. To address this gap, we investigated genetic variations of 178 historically available non-CODIS STRs from ethnolinguistically different worldwide populations and studied their characteristics and forensic potentials via high-coverage whole genome sequencing (WGS) data. Initially, we delineated the genomic properties of these non-CODIS markers through sequence searching, repeat structure scanning, and manual inspection. Subsequent population genetics analysis suggested that these non-CODIS STRs had comparable polymorphism levels and forensic utility to CODIS STRs. Furthermore, we constructed a theoretical next-generation sequencing (NGS) panel comprising 108 STRs (20 CODIS STRs and 88 non-CODIS STRs), and evaluated its performance in inferring bio-geographical ancestry origins, deconvoluting complex DNA mixtures, and differentiating distant kinships using real and simulated datasets. Our findings demonstrated that incorporating supplementary non-CODIS STRs enabled the extrapolation of multidimensional information from a single STR profile, thereby facilitating the analysis of challenging forensic tasks. In conclusion, this study presents an extensive genomic landscape of forensic non-CODIS STRs among global populations, and emphasized the imperative inclusion of additional polymorphic non-CODIS STRs in future NGS-based forensic systems.
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Affiliation(s)
- Yuguo Huang
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu 610041, China.
| | - Mengge Wang
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu 610041, China
| | - Chao Liu
- Anti-Drug Technology Center of Guangdong Province, Guangzhou 510230, China; Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou 510515, China.
| | - Guanglin He
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu 610041, China; Center for Archaeological Science, Sichuan University, Chengdu 610000, China.
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Tiongco RE, Cayanan ND, Catacata M, Dominguez MJ. Ile105Val polymorphism in the GSTP1 gene is associated with susceptibility to acute myeloid leukemia: an updated systematic review and meta-analysis. Biomarkers 2024; 29:134-142. [PMID: 38428950 DOI: 10.1080/1354750x.2024.2326538] [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: 01/05/2024] [Accepted: 02/28/2024] [Indexed: 03/03/2024]
Abstract
BACKGROUND AND OBJECTIVE Several genetic variations are associated with acute myeloid leukemia (AML) susceptibility, including the GSTP1 Ile105Val polymorphism. Even with the existing meta-analysis conducted on the topic, no consensus has been reached since none of the studies available performed in-depth data analysis. Hence, we performed an updated systematic review and meta-analysis in this paper to obtain more precise estimates. MATERIALS AND METHODS We searched various databases and calculated the odds ratio (OR) and 95% confidence interval (CI) to examine whether the GSTP1 Ile105Val polymorphism is associated with AML susceptibility. Further statistical analysis was also done to obtain more accurate and reliable findings. RESULTS A total of 15 studies are included in the systematic review, but only 9 were included in the meta-analysis due to the studies deviating from the Hardy-Weinberg equilibrium. The analysis showed significantly increased susceptibility to AML in the allelic, co-dominant, and recessive models. Furthermore, subgroup analysis noted increased AML susceptibility in the non-Asian population. Comparing the proportions of the genotypes and alleles showed a significantly higher proportion of the Val/Val genotype and Val allele in the non-Asian cohort. CONCLUSION The GSTP1 Ile105Val polymorphism is significantly associated with AML susceptibility, especially among non-Asians. Further investigation should be performed to strengthen the current results.
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Affiliation(s)
- Raphael Enrique Tiongco
- Department of Medical Technology, College of Allied Medical Professions, Angeles University Foundation, Angeles City, Philippines
| | - Neil David Cayanan
- Department of Medical Technology, College of Allied Medical Professions, Angeles University Foundation, Angeles City, Philippines
| | - Miljun Catacata
- Department of Medical Technology, College of Allied Medical Professions, Angeles University Foundation, Angeles City, Philippines
| | - Michael John Dominguez
- Department of Medical Technology, College of Allied Medical Professions, Angeles University Foundation, Angeles City, Philippines
- School of Medicine, Angeles University Foundation, Angeles City, Philippines
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Breno Zampieri Lima M, Giovana Pereira Daniel T, Tayaná Oliveira Bitencourt H, Carlos Junior Alcantara L, Haddad R, Kashima S, Carolina Elias M, Giovanetti M, Coccuzzo Sampaio S, Nanev Slavov S. Molecular frequency of human gemycircularvirus (GCYV) dna among blood donors from the Brazilian Amazon. Transfus Clin Biol 2024; 31:123-126. [PMID: 38280666 DOI: 10.1016/j.tracli.2024.01.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 01/22/2024] [Accepted: 01/23/2024] [Indexed: 01/29/2024]
Affiliation(s)
- Marlon Breno Zampieri Lima
- Blood Center of Ribeirão Preto, Faculty of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Thuany Giovana Pereira Daniel
- Blood Center of Ribeirão Preto, Faculty of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | | | - Luiz Carlos Junior Alcantara
- Instituto Rene Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Minas Gerais, Brazil; Climate Amplified Diseases And Epidemics (CLIMADE), Americas, Brazil
| | - Rodrigo Haddad
- Campus Ceilandia, University of Brasília, Brasília, Federal District, Brazil
| | - Simone Kashima
- Blood Center of Ribeirão Preto, Faculty of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | | | - Marta Giovanetti
- Instituto Rene Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Minas Gerais, Brazil; Sciences and Technologies for Sustainable Development and One Health, Universitá Campus Bio-Medico di Roma, Rome, Italy
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Huang X, Yin T, Song M, Pan J. Association of estrogen receptor and progesterone receptor genetic polymorphisms with recurrent pregnancy loss: A systematic review and meta-analysis. Eur J Obstet Gynecol Reprod Biol 2024; 296:65-75. [PMID: 38402782 DOI: 10.1016/j.ejogrb.2024.01.008] [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: 09/07/2023] [Revised: 01/02/2024] [Accepted: 01/06/2024] [Indexed: 02/27/2024]
Abstract
OBJECTIVE Estrogen and progesterone play key roles in the maintenance of pregnancy, and their function is mediated via estrogen receptor 1 (ESR1)/estrogen receptor 2 (ESR2) and progesterone receptor (PGR), respectively. It has been suggested the genetic variations in ESR1, ESR2, and PGR may contribute to recurrent pregnancy loss (RPL); however, the available evidence remains controversial. This meta-analysis aimed to explore the relation of various polymorphisms in ESR1, ESR2, and PGR genes to the risk of RPL. METHODS A systematic literature search was conducted using PubMed and Scopus up to August 2023 to obtain relevant studies. The odds ratios (ORs) with 95% confidence intervals (95% CIs) were computed and pooled with the use of random-effects models to test the associations. RESULTS A total of 31 studies with 12 different polymorphisms, including 5 polymorphisms for ESR1, 3 polymorphisms for ESR2, and 4 polymorphisms for PGR, were analyzed in this meta-analysis. Overall, no significant relationship was found between various polymorphisms of ESR1 and ESR2 with RPL in any of the genetic analysis models. PGR rs590688 (C > G) polymorphism was significantly related to the elevated risk of RPL under the dominant (OR = 1.67; 95 %CI: 1.15-2.44), allelic (OR = 1.55; 95 %CI: 1.13-2.12), and GC vs. CC (OR = 1.55; 95 %CI: 1.07-2.23) models. No significant association was identified for other variants of PGR gene. CONCLUSION Unlike estrogen receptors, variations in PGR rs590688 (C > G) may be linked to the increased risk of RPL. More studies are required to confirm this finding.
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Affiliation(s)
- Xiaoge Huang
- Department of Obstetrics, Jinan Maternal and Child Health Care Hospital, Shandong First Medical University, No.2, Jianguo Xiaojingsan Road, Jinan 250001, Shandong, PR China
| | - Ting Yin
- Department of Obstetrics, Jinan Maternal and Child Health Care Hospital, Shandong First Medical University, No.2, Jianguo Xiaojingsan Road, Jinan 250001, Shandong, PR China
| | - Min Song
- Department of Obstetrics, Jinan Maternal and Child Health Care Hospital, Shandong First Medical University, No.2, Jianguo Xiaojingsan Road, Jinan 250001, Shandong, PR China
| | - Jing Pan
- Department of Obstetrics, Jinan Maternal and Child Health Care Hospital, Shandong First Medical University, No.2, Jianguo Xiaojingsan Road, Jinan 250001, Shandong, PR China.
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12
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Lin J, Wu X, Liu Z, Yang H, Chen Y, Li H, Yu Y, Tu Q, Chen Y. Identification, expression and molecular polymorphism of T-cell receptors α and β from the glacial relict Hucho bleekeri. Fish & Shellfish Immunology 2024; 148:109475. [PMID: 38447781 DOI: 10.1016/j.fsi.2024.109475] [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: 01/05/2024] [Revised: 03/01/2024] [Accepted: 03/03/2024] [Indexed: 03/08/2024]
Abstract
The T-cell receptor (TCR) is a specific molecule on the surface of all T cells that mediates cellular adaptive immune responses to antigens. Hucho bleekeri is a critically endangered species and is regarded as a glacial relict that has the lowest-latitude distribution compared with any Eurasian salmonid. In the present study, two TCR genes, namely, TCR α and β, were identified and characterized in H. bleekeri. Both TCR α and TCR β have typical TCR structures, including the IgV domain, IgC domain, connecting peptide, transmembrane and cytoplasmic domains. The two TCR genes were constitutionally expressed in various tissues, with the highest expression found in the spleen for TCR α and in the trunk kidney for TCR β. Challenge of H. bleekeri with LPS or poly(I:C) resulted in significant upregulation of both TCR α and β expression in headkidney and spleen primary cells, indicating their potential roles in the immune response. Molecular polymorphism analysis of the whole ORF regions of TCR α and β in different individuals revealed high diversity of IgV domains of these two genes, especially in complementarity-determining region (CDR) 3. The ratio of nonsynonymous substitution occurred at a significantly higher frequency than synonymous substitution in the CDR of TCR α and β, demonstrating the existence of positive selection. The results obtained in the present study enhance our understanding of TCR roles in regulating immune mechanisms and provide new information for the study of TCR lineage diversity in fish.
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Affiliation(s)
- Jue Lin
- The Fishery Institute of the Sichuan Academy of Agricultural Sciences, Chengdu, 611730, China; Fish Resources and Environment in the Upper Reaches of the Yangtze River Observation and Research Station of Sichuan Province, Chengdu, 611730, China
| | - Xiaoyun Wu
- The Fishery Institute of the Sichuan Academy of Agricultural Sciences, Chengdu, 611730, China; Fish Resources and Environment in the Upper Reaches of the Yangtze River Observation and Research Station of Sichuan Province, Chengdu, 611730, China
| | - Zhao Liu
- The Fishery Institute of the Sichuan Academy of Agricultural Sciences, Chengdu, 611730, China; Fish Resources and Environment in the Upper Reaches of the Yangtze River Observation and Research Station of Sichuan Province, Chengdu, 611730, China
| | - Huanchao Yang
- The Fishery Institute of the Sichuan Academy of Agricultural Sciences, Chengdu, 611730, China; Fish Resources and Environment in the Upper Reaches of the Yangtze River Observation and Research Station of Sichuan Province, Chengdu, 611730, China
| | - Yanling Chen
- The Fishery Institute of the Sichuan Academy of Agricultural Sciences, Chengdu, 611730, China; Fish Resources and Environment in the Upper Reaches of the Yangtze River Observation and Research Station of Sichuan Province, Chengdu, 611730, China
| | - Hua Li
- The Fishery Institute of the Sichuan Academy of Agricultural Sciences, Chengdu, 611730, China; Fish Resources and Environment in the Upper Reaches of the Yangtze River Observation and Research Station of Sichuan Province, Chengdu, 611730, China
| | - Yi Yu
- The Fishery Institute of the Sichuan Academy of Agricultural Sciences, Chengdu, 611730, China; Fish Resources and Environment in the Upper Reaches of the Yangtze River Observation and Research Station of Sichuan Province, Chengdu, 611730, China
| | - Quanyu Tu
- The Fishery Institute of the Sichuan Academy of Agricultural Sciences, Chengdu, 611730, China; Fish Resources and Environment in the Upper Reaches of the Yangtze River Observation and Research Station of Sichuan Province, Chengdu, 611730, China
| | - Yeyu Chen
- The Fishery Institute of the Sichuan Academy of Agricultural Sciences, Chengdu, 611730, China; Fish Resources and Environment in the Upper Reaches of the Yangtze River Observation and Research Station of Sichuan Province, Chengdu, 611730, China.
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Bettim CA, da Silva AV, Kahmann A, Dorn M, Alho CS, Avila E. MC1R and age heteroclassification of face phenotypes in the Rio Grande do Sul population. Int J Legal Med 2024; 138:859-872. [PMID: 38087053 DOI: 10.1007/s00414-023-03143-6] [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: 06/01/2023] [Accepted: 11/22/2023] [Indexed: 04/11/2024]
Abstract
BACKGROUND Forensic DNA phenotyping (FDP) consists of the use of methodologies for predicting externally visible characteristics (EVCs) from the genetic material of biological samples found in crime scenes and has proven to be a promising tool in aiding human identification in police activities. Currently, methods based on multiplex assays and statistical models of prediction of EVCs related to hair, skin, and iris pigmentation using panels of SNP and INDEL biomarkers have already been developed and validated by the forensic scientific community. As well as traces of pigmentation, an individual's perceived age (PA) can also be considered an EVC and its estimation in unknown individuals can be useful for the progress of investigations. Liu and colleagues (2016) were pioneers in evidencing that, in addition to lifestyle and environmental factors, the presence of SNP and INDEL variants in the MC1R gene - which encodes a transmembrane receptor responsible for regulating melanin production - seems to contribute to an individual's PA. The group highlighted the association between these MC1R gene polymorphisms and the PA in the European population, where carriers of risk haplotypes appeared to be up to 2 years older in comparison to their chronological age (CA). PURPOSE Understanding that genotype-phenotype relationships cannot be extrapolated between different population groups, this study aimed to test this hypothesis and verify the applicability of this variant panel in the Rio Grande do Sul admixed population. METHODS Based on genomic data from a sample of 261 volunteers representative of gaucho population and using a multiple linear regression (MLR) model, our group was able to verify a significant association among nine intronic variants in loci adjacent to MC1R (e.g., AFG3L1P, TUBB3, FANCA) and facial age appearance, whose PA was defined after age heteroclassification of standard frontal face images through 11 assessors. RESULTS Different from that observed in European populations, our results show that the presence of effect alleles (R) of the selected variants in our sample influenced both younger and older face phenotypes. The influence of each variant on PA is expressed as β values. CONCLUSIONS There are important molecular mechanisms behind the effects of MC1R locus on PA, and the genomic background of each population seems to be crucial to determine this influence.
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Affiliation(s)
- Cássio Augusto Bettim
- Structural Bioinformatics and Computational Biology Lab, Institute of Informatics, Federal University of Rio Grande Do Sul, Porto Alegre, RS, Brazil
- National Science and Technology Institute for Forensic Science, Porto Alegre, RS, Brazil
| | - Alexsandro Vasconcellos da Silva
- National Science and Technology Institute for Forensic Science, Porto Alegre, RS, Brazil
- Technical Scientific and Identification Sections, Superintendency of Federal Police in Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Alessandro Kahmann
- National Science and Technology Institute for Forensic Science, Porto Alegre, RS, Brazil.
- National Science and Technology Institute for Children Cancer Biology and Pediatric Oncology, Porto Alegre, RS, Brazil.
- Interdisciplinary Department, Federal University of Rio Grande Do Sul, Tramandaí, RS, Brazil.
| | - Márcio Dorn
- Structural Bioinformatics and Computational Biology Lab, Institute of Informatics, Federal University of Rio Grande Do Sul, Porto Alegre, RS, Brazil
- National Science and Technology Institute for Forensic Science, Porto Alegre, RS, Brazil
- National Science and Technology Institute for Children Cancer Biology and Pediatric Oncology, Porto Alegre, RS, Brazil
| | - Clarice Sampaio Alho
- National Science and Technology Institute for Forensic Science, Porto Alegre, RS, Brazil
- National Science and Technology Institute for Children Cancer Biology and Pediatric Oncology, Porto Alegre, RS, Brazil
| | - Eduardo Avila
- National Science and Technology Institute for Forensic Science, Porto Alegre, RS, Brazil
- Technical Scientific and Identification Sections, Superintendency of Federal Police in Rio Grande do Sul, Porto Alegre, RS, Brazil
- National Science and Technology Institute for Children Cancer Biology and Pediatric Oncology, Porto Alegre, RS, Brazil
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Li X, Mao C, He J, Bin X, Liu G, Dong Z, Zhao R, Wan X, Li X. The first chromosome-level genome of the stag beetle Dorcus hopei Saunders, 1854 (Coleoptera: Lucanidae). Sci Data 2024; 11:396. [PMID: 38637640 PMCID: PMC11026507 DOI: 10.1038/s41597-024-03251-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 04/10/2024] [Indexed: 04/20/2024] Open
Abstract
Stag beetles (Coleoptera: Lucanidae) represent a significant saproxylic assemblage in forest ecosystems and are noted for their enlarged mandibles and male polymorphism. Despite their relevance as ideal models for the study of exaggerated mandibles that aid in attracting mates, the regulatory mechanisms associated with these traits remain understudied, and restricted by the lack of high-quality reference genomes for stag beetles. To address this limitation, we successfully assembled the first chromosome-level genome of a representative species Dorcus hopei. The genome was 496.58 Mb in length, with a scaffold N50 size of 54.61 Mb, BUSCO values of 99.8%, and 96.8% of scaffolds anchored to nine pairs of chromosomes. We identified 285.27 Mb (57.45%) of repeat sequences and annotated 11,231 protein-coding genes. This genome will be a valuable resource for further understanding the evolution and ecology of stag beetles, and provides a basis for studying the mechanisms of exaggerated mandibles through comparative analysis.
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Affiliation(s)
- Xiaolu Li
- Department of Ecology, School of Resources and Environmental Engineering, Anhui University, Hefei, 230601, China
| | - Chuyang Mao
- Key Laboratory of Genetic Evolution & Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming, Yunnan, 650223, China
- Yunnan Key Laboratory of Biodiversity Information, Kunming, Yunnan, 650223, China
| | - Jinwu He
- Key Laboratory of Genetic Evolution & Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming, Yunnan, 650223, China
- Yunnan Key Laboratory of Biodiversity Information, Kunming, Yunnan, 650223, China
| | - Xiaoyan Bin
- Department of Ecology, School of Resources and Environmental Engineering, Anhui University, Hefei, 230601, China
| | - Guichun Liu
- Key Laboratory of Genetic Evolution & Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming, Yunnan, 650223, China
- Yunnan Key Laboratory of Biodiversity Information, Kunming, Yunnan, 650223, China
| | - Zhiwei Dong
- Key Laboratory of Genetic Evolution & Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming, Yunnan, 650223, China
- Yunnan Key Laboratory of Biodiversity Information, Kunming, Yunnan, 650223, China
| | - Ruoping Zhao
- Key Laboratory of Genetic Evolution & Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming, Yunnan, 650223, China
- Yunnan Key Laboratory of Biodiversity Information, Kunming, Yunnan, 650223, China
| | - Xia Wan
- Department of Ecology, School of Resources and Environmental Engineering, Anhui University, Hefei, 230601, China.
| | - Xueyan Li
- Key Laboratory of Genetic Evolution & Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming, Yunnan, 650223, China.
- Yunnan Key Laboratory of Biodiversity Information, Kunming, Yunnan, 650223, China.
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15
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Tran DC, Le LHG, Thai TT, Van Hoang S, Do MD, Truong BQ. Effect of AGTR1 A1166C genetic polymorphism on coronary artery lesions and mortality in patients with acute myocardial infarction. PLoS One 2024; 19:e0300273. [PMID: 38635772 PMCID: PMC11026145 DOI: 10.1371/journal.pone.0300273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 02/25/2024] [Indexed: 04/20/2024] Open
Abstract
The pathogenesis and prognosis of patients with acute myocardial infarction (AMI) may be influenced by both genetic and environmental factors. Findings on the relationship of polymorphisms in various genes encoding the renin-angiotensin-aldosterone system with coronary artery lesions and mortality in AMI patients are inconsistent. The aim of this study was to determine whether the AGTR1 A1166C genetic polymorphism affects coronary artery lesions and 1-year mortality in post-AMI patients. Patients with their first AMI admitted to Cho Ray Hospital, Vietnam, from January 2020 to August 2021 were enrolled in this prospective clinical study. All participants underwent invasive coronary angiography and were identified as having the genotypes of AGTR1 A1166C by way of a polymerase chain reaction method. All patients were followed up for all-cause mortality 12 months after AMI. The association of the AGTR1 A1166C polymorphism with coronary artery lesions and 1-year mortality was evaluated using logistic regression and Cox regression analysis, respectively. Five hundred and thirty-one AMI patients were recruited. The mean age was 63.9 ± 11.6 years, and 71.6% of the patients were male. There were no significant differences in the location and number of diseased coronary artery branches between the AA and AC+CC genotypes. The AC and CC genotypes were independently associated with ≥ 90% diameter stenosis of the left anterior descending (LAD) artery (odds ratio = 1.940; 95% confidence interval (CI): 1.059-3.552, p = 0.032). The 1-year all-cause mortality rate difference between patients with the AC and CC genotypes versus those with the AA genotype was not statistically significant (hazard ratio = 1.000, 95% CI: 0.429-2.328, p = 1.000). The AGTR1 A1166C genetic polymorphism is associated with very severe luminal stenosis of the LAD but not with mortality in AMI patients.
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Affiliation(s)
- Duy Cong Tran
- Department of Internal Medicine, University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam
- Department of Cardiology, Cho Ray Hospital, Ho Chi Minh City, Vietnam
- Cardiovascular Center, University Medical Center Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Linh Hoang Gia Le
- Center for Molecular Biomedicine, University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Truc Thanh Thai
- Faculty of Public Health, University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Sy Van Hoang
- Department of Internal Medicine, University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam
- Department of Cardiology, Cho Ray Hospital, Ho Chi Minh City, Vietnam
| | - Minh Duc Do
- Center for Molecular Biomedicine, University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Binh Quang Truong
- Department of Internal Medicine, University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam
- Cardiovascular Center, University Medical Center Ho Chi Minh City, Ho Chi Minh City, Vietnam
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16
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Nelson CW, Poon LLM, Gu H. Reply to: Population genetic considerations regarding the interpretation of within-patient SARS-CoV-2 polymorphism data. Nat Commun 2024; 15:3239. [PMID: 38627383 PMCID: PMC11021549 DOI: 10.1038/s41467-024-46262-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 02/21/2024] [Indexed: 04/19/2024] Open
Affiliation(s)
- Chase W Nelson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, 20850, USA
- Institute for Comparative Genomics, American Museum of Natural History, New York, NY, 10024, USA
| | - Leo L M Poon
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China.
- Centre for Immunology & Infection, Hong Kong Science and Technology Park, Hong Kong SAR, China.
- HKU- Pasteur Research Pole, School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China.
| | - Haogao Gu
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
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17
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Soni V, Terbot JW, Jensen JD. Population genetic considerations regarding the interpretation of within-patient SARS-CoV-2 polymorphism data. Nat Commun 2024; 15:3240. [PMID: 38627371 PMCID: PMC11021480 DOI: 10.1038/s41467-024-46261-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 01/29/2024] [Indexed: 04/19/2024] Open
Affiliation(s)
- Vivak Soni
- Center for Evolution & Medicine, Arizona State University, School of Life Sciences, Tempe, AZ, USA
| | - John W Terbot
- Center for Evolution & Medicine, Arizona State University, School of Life Sciences, Tempe, AZ, USA
- Division of Biological Sciences, University of Montana, Missoula, MT, USA
| | - Jeffrey D Jensen
- Center for Evolution & Medicine, Arizona State University, School of Life Sciences, Tempe, AZ, USA.
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18
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Maleka MF, Spies JJ. Polymorphisms in two key anthocyanic genes of clivia (Clivia miniata L.) reveal evidence of selection and possible association with flower pigmentation. J Evol Biol 2024; 37:429-441. [PMID: 38452247 DOI: 10.1093/jeb/voae025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 01/26/2024] [Accepted: 03/06/2024] [Indexed: 03/09/2024]
Abstract
Members of the genus Clivia show considerable variation in flower pigmentation and morphology. Such variation is affected by mutations that emerge in candidate flower development genes over time. Besides population history, mutations can further illuminate the effects of demographic events in populations in addition to population genetic parameters including selection, recombination, and linkage disequilibrium (LD). The current study aimed to find sequence variants in 2 anthocyanin biosynthetic genes (DFR and bHLH) of Clivia miniata and use the data to assess population genetic factors from a random collection of orange/red- and yellow-flowered specimens. Overall, average nucleotide diversity in the 2 anthocyanin genes was moderate (π = 0.00646), whereas haplotypes differed significantly (Hd ≥ 0.9). Gene evolution was seemingly driven by mutations (CmiDFR) or recombinations (CmibHLH001). LD decayed swiftly within the analyzed gene regions and supported the feasibility of assessing trait-variant associations via the association/linkage mapping approach. In the end, most associations were found to be spurious, but 1 haplotype in CmibHLH001 showed a promising correlation to the orange/red flower phenotype in Clivia specimens. In all, the present study is the first to measure gene-level diversity in C. miniata-data that had never been reported so far. Furthermore, the study also identified allelic and haplotypic variants that may be beneficial in future association genetic studies of Clivia. Such studies, however, consider large diverse populations to control for statistical bias intrinsic to the analysis of small datasets.
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Affiliation(s)
- Mathabatha F Maleka
- Department of Genetics, University of the Free State, Bloemfontein, Republic of South Africa
| | - Johan J Spies
- Department of Genetics, University of the Free State, Bloemfontein, Republic of South Africa
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19
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Zhao HL, You Y, Tian Y, Wang L, An Y, Zhang G, Shu C, Yu M, Zhu Y, Li Q, Zhang Y, Sun N, Hu S, Liu G. Impact of LDLR polymorphisms on lipid levels and atorvastatin's efficacy in a northern Chinese adult Han cohort with dyslipidemia. Lipids Health Dis 2024; 23:106. [PMID: 38616260 PMCID: PMC11016223 DOI: 10.1186/s12944-024-02101-4] [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: 11/21/2023] [Accepted: 04/04/2024] [Indexed: 04/16/2024] Open
Abstract
BACKGROUND Dyslipidemia, a significant risk factor for atherosclerotic cardiovascular disease (ASCVD), is influenced by genetic variations, particularly those in the low-density lipoprotein receptor (LDLR) gene. This study aimed to elucidate the effects of LDLR polymorphisms on baseline serum lipid levels and the therapeutic efficacy of atorvastatin in an adult Han population in northern China with dyslipidemia. METHODS In this study, 255 Han Chinese adults receiving atorvastatin therapy were examined and followed up. The 3' untranslated region (UTR) of the LDLR gene was sequenced to identify polymorphisms. The associations between gene polymorphisms and serum lipid levels, as well as changes in lipid levels after intervention, were evaluated using the Wilcoxon rank sum test, with a P < 0.05 indicating statistical significance. Assessment of linkage disequilibrium patterns and haplotype structures was conducted utilizing Haploview. RESULTS Eleven distinct polymorphisms at LDLR 3' UTR were identified. Seven polymorphisms (rs1433099, rs14158, rs2738466, rs5742911, rs17249057, rs55971831, and rs568219285) were correlated with the baseline serum lipid levels (P < 0.05). In particular, four polymorphisms (rs14158, rs2738466, rs5742911, and rs17249057) were in strong linkage disequilibrium (r2 = 1), and patients with the AGGC haplotype had higher TC and LDL-C levels at baseline. Three polymorphisms (rs1433099, rs2738467, and rs7254521) were correlated with the therapeutic efficacy of atorvastatin (P < 0.05). Furthermore, carriers of the rs2738467 T allele demonstrated a significantly greater reduction in low-density lipoprotein cholesterol (LDL-C) levels post-atorvastatin treatment (P = 0.03), indicating a potentially crucial genetic influence on therapeutic outcomes. Two polymorphisms (rs751672818 and rs566918949) were neither correlated with the baseline serum lipid levels nor atorvastatin's efficacy. CONCLUSIONS This research outlined the complex genetic architecture surrounding LDLR 3' UTR polymorphisms and their role in lipid metabolism and the response to atorvastatin treatment in adult Han Chinese patients with dyslipidemia, highlighting the importance of genetic profiling in enhancing tailored therapeutic strategies. Furthermore, this investigation advocates for the integration of genetic testing into the management of dyslipidemia, paving the way for customized therapeutic approaches that could significantly improve patient care. TRIAL REGISTRATION This multicenter study was approved by the Ethics Committee of Xiangya Hospital Central South University (ethics number K22144). It was a general ethic. In addition, this study was approved by The First Hospital of Hebei Medical University (ethics number 20220418).
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Affiliation(s)
- Hong-Liang Zhao
- Department of Cardiology, The First Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Yang You
- Department of Cardiology, The First Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Yan Tian
- Beijing E-Seq Medical Technology Co. Ltd, Beijing, China
| | - Luyan Wang
- Institute of Hypertension, People's Hospital, Peking University, Beijing, China
| | - Yongqiang An
- Department of Cardiology, The First Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Guoqiang Zhang
- Beijing E-Seq Medical Technology Co. Ltd, Beijing, China
| | - Chang Shu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Mingxin Yu
- Beijing E-Seq Medical Technology Co. Ltd, Beijing, China
| | - Yihua Zhu
- Beijing E-Seq Medical Technology Co. Ltd, Beijing, China
- College of Information Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu Province, China
| | - Qian Li
- Beijing E-Seq Medical Technology Co. Ltd, Beijing, China
| | - Yanwei Zhang
- Beijing E-Seq Medical Technology Co. Ltd, Beijing, China
| | - Ningling Sun
- Institute of Hypertension, People's Hospital, Peking University, Beijing, China.
| | - Songnian Hu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
| | - Gang Liu
- Department of Cardiology, The First Hospital of Hebei Medical University, Shijiazhuang, Hebei, China.
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20
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Horvath R, Minadakis N, Bourgeois Y, Roulin AC. The evolution of transposable elements in Brachypodium distachyon is governed by purifying selection, while neutral and adaptive processes play a minor role. eLife 2024; 12:RP93284. [PMID: 38606833 PMCID: PMC11014726 DOI: 10.7554/elife.93284] [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] [Indexed: 04/13/2024] Open
Abstract
Understanding how plants adapt to changing environments and the potential contribution of transposable elements (TEs) to this process is a key question in evolutionary genomics. While TEs have recently been put forward as active players in the context of adaptation, few studies have thoroughly investigated their precise role in plant evolution. Here, we used the wild Mediterranean grass Brachypodium distachyon as a model species to identify and quantify the forces acting on TEs during the adaptation of this species to various conditions, across its entire geographic range. Using sequencing data from more than 320 natural B. distachyon accessions and a suite of population genomics approaches, we reveal that putatively adaptive TE polymorphisms are rare in wild B. distachyon populations. After accounting for changes in past TE activity, we show that only a small proportion of TE polymorphisms evolved neutrally (<10%), while the vast majority of them are under moderate purifying selection regardless of their distance to genes. TE polymorphisms should not be ignored when conducting evolutionary studies, as they can be linked to adaptation. However, our study clearly shows that while they have a large potential to cause phenotypic variation in B. distachyon, they are not favored during evolution and adaptation over other types of mutations (such as point mutations) in this species.
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Affiliation(s)
- Robert Horvath
- Department of Plant and Microbial Biology, University of ZurichZurichSwitzerland
| | - Nikolaos Minadakis
- Department of Plant and Microbial Biology, University of ZurichZurichSwitzerland
| | - Yann Bourgeois
- DIADE, University of Montpellier, CIRAD, IRDMontpellierFrance
- University of PortsmouthPortsmouthUnited Kingdom
| | - Anne C Roulin
- Department of Plant and Microbial Biology, University of ZurichZurichSwitzerland
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21
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Shahroudi MJ, Rezaei M, Mirzaeipour M, Saravani M, Shahraki-Ghadimi H, Arab S. Association between miR-202, miR-211, and miR-1238 gene polymorphisms and risk of vitiligo. Arch Dermatol Res 2024; 316:118. [PMID: 38597990 DOI: 10.1007/s00403-024-02847-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 02/04/2024] [Accepted: 02/09/2024] [Indexed: 04/11/2024]
Abstract
Vitiligo, as a common pigment defect in the skin, hair, and mucous membranes, results from the destruction of melanocytes. Recent investigations have shown that miRNA dysregulation contributes in the pathogenesis of vitiligo. Therefore, in this research, our aim is to explore the relationship between miR-202 rs12355840, miR-211 rs8039189, and miR-1238 rs12973308 polymorphisms and susceptibility to vitiligo. A total number of 136 vitiligo patients and 129 healthy individuals as a control group were included in this research. The salting out approach was implemented to extraction genomic DNA. The genetic polymorphisms of miR-202 rs12355840, miR-211 rs8039189, and miR-1238 rs12973308 were determined using PCR-RFLP approach. The findings revealed that miR-202 rs12355840 polymorphism under codominant (CT and TT genotypes), dominant, recessive, overdominant, and also allelic models is correlated with increased risk of vitiligo. In addition, codominant, dominant, overdominant, as well as allelic models of miR-211 rs8039189 polymorphism decrease risk of vitiligo. No significant relationship was observed between the miR-1238 rs12973308 polymorphism and susceptibility to vitiligo. The miR-211 rs8039189 polymorphism may serve a protective effect on vitiligo development and miR-202 rs12355840 polymorphism may act as a risk factor for vitiligo susceptibility.
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Affiliation(s)
- Mahdieh Jafari Shahroudi
- Cellular and Molecular Research Center, Research Institute of Cellular and Molecular Sciences in Infectious Diseases, Zahedan University of Medical Sciences, Zahedan, Iran.
- Department of Occupational Health Engineering, School of Health, Shiraz University of Medical Sciences, Shiraz, Iran.
| | - Mahnaz Rezaei
- Cellular and Molecular Research Center, Research Institute of Cellular and Molecular Sciences in Infectious Diseases, Zahedan University of Medical Sciences, Zahedan, Iran
- Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
| | | | - Mohsen Saravani
- Cellular and Molecular Research Center, Research Institute of Cellular and Molecular Sciences in Infectious Diseases, Zahedan University of Medical Sciences, Zahedan, Iran
- Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Hossein Shahraki-Ghadimi
- Cellular and Molecular Research Center, Research Institute of Cellular and Molecular Sciences in Infectious Diseases, Zahedan University of Medical Sciences, Zahedan, Iran
- Bioinformatics and Computational Omics Lab (BioCOOL), Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Sara Arab
- Khatam Al Anbia Hospital, Zahedan University of Medical Sciences, Zahedan, Iran
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22
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Menezes-Júnior LAAD, Sabião TDS, Moura SSD, Batista AP, Menezes MCD, Carraro JCC, Machado-Coelho GLL, Meireles AL. The role of interaction between vitamin D and VDR FokI gene polymorphism (rs2228570) in sleep quality of adults. Sci Rep 2024; 14:8141. [PMID: 38584183 PMCID: PMC10999418 DOI: 10.1038/s41598-024-58561-2] [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: 07/18/2023] [Accepted: 04/01/2024] [Indexed: 04/09/2024] Open
Abstract
To evaluate association of vitamin D with sleep quality in adults and the influence of VDR-gene polymorphism FokI (rs2228570;A > G). Cross-sectional population-based study in adults, conducted in Brazil. The outcome was sleep-quality, evaluated by the Pittsburgh Sleep Quality Index. Vitamin D was determined by indirect electrochemiluminescence and classified as deficiency (VDD), 25(OH)D < 20 ng/mL in a healthy population or 25(OH)D < 30 ng/mL for groups at risk for VDD. FokI polymorphism in the VDR-gene was genotyped by qPCR and classified as homozygous wild (FF or AA), heterozygous (Ff or AG), or homozygous mutant (ff or GG). Multivariate logistic analysis was used to estimate the association between vitamin D and FokI polymorphism with sleep-quality. In a total of 1674 individuals evaluated, 53.6% had poor-sleep-quality, 31.5% had VDD, and the genotype frequency of the FokI polymorphism was 9.9% FF, 44.6% Ff, and 45.5% ff. In multivariate analysis, individuals with VDD had 1.51 times the chance of poor-sleep-quality, and individuals with the ff genotype had 1.49 times the chance of poor-sleep-quality (OR:1.49;95%CI:1.05-2.12) when compared to individuals with the FF or Ff genotype. In the combined analysis, individuals with VDD and ff genotype had more chance of poor-sleep-quality than individuals with sufficient vitamin D and genotype Ff or FF (OR:2.19;95%CI:1.27-3.76). Our data suggest that VDD and VDR FokI gene polymorphism are associated with poor-sleep-quality, and combining the two factors increases the chance of poor-sleep-quality compared to separate groups.
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Affiliation(s)
- Luiz Antônio Alves de Menezes-Júnior
- Postgraduate Program in Health and Nutrition, School of Nutrition, Federal University of Ouro Preto, R. Diogo de Vasconcelos, 122, Ouro Preto, MG, Brazil.
- Research and Study Group On Nutrition and Public Health (GPENSC), Federal University of Ouro Preto, Ouro Preto, Brazil.
- Department of Clinical and Social Nutrition, School of Nutrition, Federal University of Ouro Preto, Ouro Preto, MG, Brazil.
| | - Thais da Silva Sabião
- Postgraduate Program in Health and Nutrition, School of Nutrition, Federal University of Ouro Preto, R. Diogo de Vasconcelos, 122, Ouro Preto, MG, Brazil
- Research and Study Group On Nutrition and Public Health (GPENSC), Federal University of Ouro Preto, Ouro Preto, Brazil
| | - Samara Silva de Moura
- Postgraduate Program in Health and Nutrition, School of Nutrition, Federal University of Ouro Preto, R. Diogo de Vasconcelos, 122, Ouro Preto, MG, Brazil
- Research and Study Group On Nutrition and Public Health (GPENSC), Federal University of Ouro Preto, Ouro Preto, Brazil
| | - Aline Priscila Batista
- Postgraduate Programs in Biological Sciences, Institute of Biological Sciences, Federal University of Ouro Preto, Ouro Preto, MG, Brazil
- School of Medicine, Federal University of Ouro Preto, Ouro Preto, MG, Brazil
| | - Mariana Carvalho de Menezes
- Postgraduate Program in Health and Nutrition, School of Nutrition, Federal University of Ouro Preto, R. Diogo de Vasconcelos, 122, Ouro Preto, MG, Brazil
- Research and Study Group On Nutrition and Public Health (GPENSC), Federal University of Ouro Preto, Ouro Preto, Brazil
- Department of Clinical and Social Nutrition, School of Nutrition, Federal University of Ouro Preto, Ouro Preto, MG, Brazil
| | - Júlia Cristina Cardoso Carraro
- Postgraduate Program in Health and Nutrition, School of Nutrition, Federal University of Ouro Preto, R. Diogo de Vasconcelos, 122, Ouro Preto, MG, Brazil
- Research and Study Group On Nutrition and Public Health (GPENSC), Federal University of Ouro Preto, Ouro Preto, Brazil
- Department of Clinical and Social Nutrition, School of Nutrition, Federal University of Ouro Preto, Ouro Preto, MG, Brazil
| | - George Luiz Lins Machado-Coelho
- Postgraduate Program in Health and Nutrition, School of Nutrition, Federal University of Ouro Preto, R. Diogo de Vasconcelos, 122, Ouro Preto, MG, Brazil
- Postgraduate Programs in Biological Sciences, Institute of Biological Sciences, Federal University of Ouro Preto, Ouro Preto, MG, Brazil
- School of Medicine, Federal University of Ouro Preto, Ouro Preto, MG, Brazil
| | - Adriana Lúcia Meireles
- Postgraduate Program in Health and Nutrition, School of Nutrition, Federal University of Ouro Preto, R. Diogo de Vasconcelos, 122, Ouro Preto, MG, Brazil
- Research and Study Group On Nutrition and Public Health (GPENSC), Federal University of Ouro Preto, Ouro Preto, Brazil
- Department of Clinical and Social Nutrition, School of Nutrition, Federal University of Ouro Preto, Ouro Preto, MG, Brazil
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23
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Tchalova K, Lydon JE, Atkinson L, Fleming AS, Kennedy J, Lecompte V, Meaney MJ, Moss E, O'Donnell KA, O'Donnell KJ, Silveira PP, Sokolowski MB, Steiner M, Bartz JA. Variation in the mu-opioid receptor gene (OPRM1) moderates the influence of maternal sensitivity on child attachment. Transl Psychiatry 2024; 14:181. [PMID: 38580654 PMCID: PMC10997775 DOI: 10.1038/s41398-024-02888-x] [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: 10/25/2022] [Revised: 03/15/2024] [Accepted: 03/20/2024] [Indexed: 04/07/2024] Open
Abstract
The endogenous opioid system is thought to play an important role in mother-infant attachment. In infant rhesus macaques, variation in the μ-opioid receptor gene (OPRM1) is related to differences in attachment behavior that emerges following repeated separation from the mother; specifically, infants carrying at least one copy of the minor G allele of the OPRM1 C77G polymorphism show heightened and more persistent separation distress, as well as a pattern of increased contact-seeking behavior directed towards the mother during reunions (at the expense of affiliation with other group members). Research in adult humans has also linked the minor G allele of the analogous OPRM1 A118G polymorphism with greater interpersonal sensitivity. Adopting an interactionist approach, we examined whether OPRM1 A118G genotype and maternal (in)sensitivity are associated with child attachment style, predicting that children carrying the G allele may be more likely to develop an ambivalent attachment pattern in response to less sensitive maternal care. The sample consisted of 191 mothers participating with their children (n = 223) in the Maternal Adversity, Vulnerability and Neurodevelopment (MAVAN) project, a community-based, birth cohort study of Canadian mothers and their children assessed longitudinally across the child's development. Maternal sensitivity was coded from at-home mother-child interactions videotaped when the child was 18 months of age. Child attachment was assessed at 36 months using the Strange Situation paradigm. As predicted, G allele carriers, but not AA homozygotes, showed increasing odds of being classified as ambivalently attached with decreasing levels of maternal sensitivity. Paralleling earlier non-human animal research, this work provides support for the theory that endogenous opioids contribute to the expression of attachment behaviors in humans.
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Affiliation(s)
- K Tchalova
- Department of Psychology, McGill University, Montréal, QC, Canada
| | - J E Lydon
- Department of Psychology, McGill University, Montréal, QC, Canada
| | - L Atkinson
- Department of Psychology, Toronto Metropolitan University, Toronto, ON, Canada
| | - A S Fleming
- Department of Psychology, University of Toronto Mississauga, Toronto, ON, Canada
| | - J Kennedy
- Department of Psychiatry, University of Toronto, Toronto, ON, Canada
| | - V Lecompte
- L'Université du Québec à Montréal, Montréal, QC, Canada
| | - M J Meaney
- Department of Psychology, McGill University, Montréal, QC, Canada
- Douglas Research Centre, Montréal, QC, Canada
- Singapore Institute for Clinical Sciences, A*STAR, Singapore, Singapore
| | - E Moss
- L'Université du Québec à Montréal, Montréal, QC, Canada
| | - K A O'Donnell
- Yale School of Medicine, Yale University, New Haven, CT, USA
| | - K J O'Donnell
- Department of Psychology, Simon Fraser University, Burnaby, BC, Canada
| | - P P Silveira
- Department of Psychiatry, McGill University, Montréal, QC, Canada
| | - M B Sokolowski
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - M Steiner
- Department of Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton, ON, Canada
| | - J A Bartz
- Department of Psychology, McGill University, Montréal, QC, Canada.
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24
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Cruciat G, Florian AR, Chaikh-Sulaiman MS, Staicu A, Caracostea GV, Procopciuc LM, Stamatian F, Muresan D. TCF7L2 Polymorphism rs7903146 (C/T) and Gestational Diabetes Influence on Obstetric Outcome: A Romanian Case-Control Study. Int J Mol Sci 2024; 25:4039. [PMID: 38612849 PMCID: PMC11012241 DOI: 10.3390/ijms25074039] [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: 02/16/2024] [Revised: 03/25/2024] [Accepted: 04/02/2024] [Indexed: 04/14/2024] Open
Abstract
Gestational diabetes mellitus (GDM) is one of the most frequent predictors of obstetric outcome among Romanian pregnant women. Thus, we aimed to investigate the role of rs7903146 (C/T) TCF7L2 gene polymorphism in the presence of GDM and to evaluate the influence on maternal-fetal outcomes in a cohort of pregnant women from Northern Transylvania. Our prospective case-control study was performed in a tertiary maternity center on 61 patients diagnosed with GDM and 55 normal pregnant patients. The patients were genotyped for rs7903146 (C/T) polymorphism of the TCF7L2 gene using the PCR-RFLP method between 24 and 28 weeks of gestation. The minor T allele was associated with a high risk of developing GDM (OR 1.71 [95% CI 0.82-3.59]) if both heterozygote and homozygote types were considered. Also, a higher risk of developing GDM was observed in homozygous carriers (OR 3.26 [95% CI 1.10-9.68]). Women with the TT genotype were more likely to require insulin therapy during pregnancy than other genotypes with a 5.67-fold increased risk ([1.61-19.97], p = 0.015). TT homozygote type was significantly associated with fetal macrosomia for birth weights greater than the 95th percentile (p = 0.034). The homozygous TT genotype is associated with an increased risk of developing GDM. Also, rs7903146 (C/T) TCF7L2 variant is accompanied by a high probability of developing insulin-dependent gestational diabetes mellitus (ID-GDM). The presence of at least one minor T allele was associated with a higher risk of fetal macrosomia.
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Affiliation(s)
- Gheorghe Cruciat
- Mother and Child Department, Obstetrics and Gynecology I, “Iuliu Haţieganu” University of Medicine and Pharmacy Cluj-Napoca, 400347 Cluj-Napoca, Romania; (G.C.); (A.R.F.); (M.-S.C.-S.); (A.S.); (G.V.C.); (D.M.)
| | - Andreea Roxana Florian
- Mother and Child Department, Obstetrics and Gynecology I, “Iuliu Haţieganu” University of Medicine and Pharmacy Cluj-Napoca, 400347 Cluj-Napoca, Romania; (G.C.); (A.R.F.); (M.-S.C.-S.); (A.S.); (G.V.C.); (D.M.)
| | - Mariam-Suzana Chaikh-Sulaiman
- Mother and Child Department, Obstetrics and Gynecology I, “Iuliu Haţieganu” University of Medicine and Pharmacy Cluj-Napoca, 400347 Cluj-Napoca, Romania; (G.C.); (A.R.F.); (M.-S.C.-S.); (A.S.); (G.V.C.); (D.M.)
| | - Adelina Staicu
- Mother and Child Department, Obstetrics and Gynecology I, “Iuliu Haţieganu” University of Medicine and Pharmacy Cluj-Napoca, 400347 Cluj-Napoca, Romania; (G.C.); (A.R.F.); (M.-S.C.-S.); (A.S.); (G.V.C.); (D.M.)
| | - Gabriela Valentina Caracostea
- Mother and Child Department, Obstetrics and Gynecology I, “Iuliu Haţieganu” University of Medicine and Pharmacy Cluj-Napoca, 400347 Cluj-Napoca, Romania; (G.C.); (A.R.F.); (M.-S.C.-S.); (A.S.); (G.V.C.); (D.M.)
| | - Lucia Maria Procopciuc
- Department of Medical Biochemistry, “Iuliu Haţieganu” University of Medicine and Pharmacy Cluj-Napoca, 400347 Cluj-Napoca, Romania
| | | | - Daniel Muresan
- Mother and Child Department, Obstetrics and Gynecology I, “Iuliu Haţieganu” University of Medicine and Pharmacy Cluj-Napoca, 400347 Cluj-Napoca, Romania; (G.C.); (A.R.F.); (M.-S.C.-S.); (A.S.); (G.V.C.); (D.M.)
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25
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Srithawong S, Muisuk K, Prakhun N, Tungpairojwong N, Kutanan W. Forensic efficiency and genetic polymorphisms of 12 X-chromosomal STR loci in Northeastern Thai populations. Mol Genet Genomics 2024; 299:42. [PMID: 38568251 DOI: 10.1007/s00438-024-02134-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Accepted: 03/07/2024] [Indexed: 04/05/2024]
Abstract
Northeastern Thailand comprises one-third of the country and is home to various populations, with Lao Isan constituting the majority, while others are considered minority groups. Previous studies on forensic short tandem repeats (STRs) in Thailand predominantly focused on autosomal STRs but there was a paucity of X-STRs, exclusively reported from the North and Central regions of the country. In this study, we have newly established a 12 X-STRs from a total of 896 samples from Northeastern Thailand, encompassing Lao Isan as the major group in the region, alongside nine minor populations (Khmer, Mon, Nyahkur, Bru, Kuy, Phutai, Kalueang, Nyaw, and Saek). Across all ten populations, the combined powers of discrimination in both genders were high and the combined mean exclusion chance (MEC) indices calculated for deficiency, normal trio and duo cases were also high (> 0.99999). DXS10148 emerged as the most informative marker, while DXS7423 was identified as the least informative. Genetic comparison based on X-STRs frequency supported genetic distinction of cerain minor groups such as Kuy, Saek and Nyahkur from other northeastern Thai groups as well as genetic differences according to the geographic region of Thai groups (Northeast, North and Central). In sum, the overall results on population genetics are in agreement with earlier reports on other genetic systems, indicating the informativeness of X-STRs for use in anthropological genetics studies. From a forensic perspective, despite the limitations of small sample sizes for minority groups, the present results contribute to filling the gap in the reference X-STRs database of the major group Lao Isan, providing valuable frequency data for forensic applications in Thailand and neighboring countries.
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Affiliation(s)
- Suparat Srithawong
- Department of Biology, Faculty of Science, Khon Kaen University, Khon Kaen, Thailand
| | - Kanha Muisuk
- Department of Forensic Medicine, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Nonglak Prakhun
- Department of Biology, Faculty of Science, Khon Kaen University, Khon Kaen, Thailand
| | | | - Wibhu Kutanan
- Department of Biology, Faculty of Science, Khon Kaen University, Khon Kaen, Thailand.
- Department of Biology, Faculty of Science, Naresuan University, Pitsanulok, Thailand.
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26
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Pandey RK, Srivastava A, Mishra RK, Singh PP, Chaubey G. Novel genetic association of the Furin gene polymorphism rs1981458 with COVID-19 severity among Indian populations. Sci Rep 2024; 14:7822. [PMID: 38570613 PMCID: PMC10991378 DOI: 10.1038/s41598-024-54607-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 02/14/2024] [Indexed: 04/05/2024] Open
Abstract
SARS CoV-2, the causative agent for the ongoing COVID-19 pandemic, it enters the host cell by activating the ACE2 receptor with the help of two proteasesi.e., Furin and TMPRSS2. Therefore, variations in these genes may account for differential susceptibility and severity between populations. Previous studies have shown that the role of ACE2 and TMPRSS2 gene variants in understanding COVID-19 susceptibility among Indian populations. Nevertheless, a knowledge gap exists concerning the COVID-19 susceptibility of Furin gene variants among diverse South Asian ethnic groups. Investigating the role of Furin gene variants and their global phylogeographic structure is essential to comprehensively understanding COVID-19 susceptibility in these populations. We have used 450 samples from diverse Indian states and performed linear regression to analyse the Furin gene variant's with COVID-19 Case Fatality Rate (CFR) that could be epidemiologically associated with disease severity outcomes. Associated genetic variants were further evaluated for their expression and regulatory potential through various Insilco analyses. Additionally, we examined the Furin gene using next-generation sequencing (NGS) data from 393 diverse global samples, with a particular emphasis on South Asia, to investigate its Phylogeographic structure among diverse world populations. We found a significant positive association for the SNP rs1981458 with COVID-19 CFR (p < 0.05) among diverse Indian populations at different timelines of the first and second waves. Further, QTL and other regulatory analyses showed various significant associations for positive regulatory roles of rs1981458 and Furin gene, mainly in Immune cells and virus infection process, highlighting their role in host immunity and viral assembly and processing. The Furin protein-protein interaction suggested that COVID-19 may contribute to Pulmonary arterial hypertension via a typical inflammation mechanism. The phylogeographic architecture of the Furin gene demonstrated a closer genetic affinity of South Asia with West Eurasian populations. Therefore, it is worth proposing that for the Furin gene, the COVID-19 susceptibility of South Asians will be more similar to the West Eurasian population. Our previous studies on the ACE2 and TMPRSS2 genes showed genetic affinity of South Asian with East Eurasians and West Eurasians, respectively. Therefore, with the collective information from these three important genes (ACE2, TMPRSS2 and Furin) we modelled COVID-19 susceptibilityof South Asia in between these two major ancestries with an inclination towards West Eurasia. In conclusion, this study, for the first time, concluded the role of rs1981458 in COVID-19 severity among the Indian population and outlined its regulatory potential.This study also highlights that the genetic structure for COVID-19 susceptibilityof South Asia is distinct, however, inclined to the West Eurasian population. We believe this insight may be utilised as a genetic biomarker to identify vulnerable populations, which might be directly relevant for developing policies and allocating resources more effectively during an epidemic.
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Affiliation(s)
- Rudra Kumar Pandey
- Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi, 221005, India.
| | - Anshika Srivastava
- Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi, 221005, India
| | - Rahul Kumar Mishra
- Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi, 221005, India
| | - Prajjval Pratap Singh
- Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi, 221005, India
| | - Gyaneshwer Chaubey
- Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi, 221005, India.
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27
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Trillo MC, Aisenberg A, Herberstein ME, Bidegaray-Batista L. Amazons Are Back: Absence of Males in a Praying Mantis from Uruguayan Savannas. Neotrop Entomol 2024; 53:323-329. [PMID: 38305945 DOI: 10.1007/s13744-023-01114-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 12/04/2023] [Indexed: 02/03/2024]
Abstract
With a broad distribution throughout South America, Brunneria subaptera (Saussure) (Coptopterygidae) is the most abundant praying mantis species in Uruguay, mostly associated with grassland vegetation. Their body coloration can vary between green or brown sepia. The recent catalog of Uruguayan mantids showed that all specimens of B. subaptera from the collections in Uruguay were females, suggesting an absence of males in natural populations. The aim of this study was to determine the occurrence of female-only populations of B. subaptera in Uruguay. Moreover, we analyzed the genetic variation and estimated the time of the most recent common ancestor of the species. We performed bimonthly samplings in two localities in Uruguay for 1 year and we sexed the individuals. We extracted DNA from the abdominal tissue of adult females and sequenced a fragment of the mitochondrial cox1 gene to assess the genetic diversity and to estimate diversification times. We did not find any males in either of the studied localities. The age estimates revealed a recent origin of the species (2.33 Ma), and there was no genetic differentiation between the individuals from Uruguayan localities. This absence of males of B. subaptera documented in the sampled locations suggests that the species reproduces by thelytokous parthenogenesis. This study opens promising venues for future research into reproductive strategies and polymorphism in South-American praying mantises that inhabit one of the largest areas of grasslands in the world, currently under dramatic deterioration and reduction.
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Affiliation(s)
- Mariana C Trillo
- Depto de Ecología y Biología Evolutiva, Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), Montevideo, Uruguay.
- Depto de Biodiversidad y Genética, Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), Montevideo, Uruguay.
- Sección Entomología, Facultad de Ciencias, Univ de la República, Montevideo, Uruguay.
| | - Anita Aisenberg
- Depto de Ecología y Biología Evolutiva, Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), Montevideo, Uruguay
| | | | - Leticia Bidegaray-Batista
- Depto de Biodiversidad y Genética, Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), Montevideo, Uruguay.
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28
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Rashedi S, Sadeghipour P, Lou J. Aiming for precision: CYP2C19 gene polymorphism and clopidogrel resistance in patients with peripheral artery disease. Thromb Res 2024; 236:240-241. [PMID: 38503672 DOI: 10.1016/j.thromres.2024.03.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 03/06/2024] [Indexed: 03/21/2024]
Affiliation(s)
- Sina Rashedi
- Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Parham Sadeghipour
- Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran; Clinical Trial Center, Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Junyang Lou
- Cardiovascular Medicine Division, Brigham and Women's Hospital, Harvard Medical School, MA, USA.
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29
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Daba G, Daelemans R, Berecha G, Geerinck MWJ, Verreth C, Crauwels S, Lievens B, Honnay O. Genetic diversity and structure of the coffee leaf rust fungus Hemileia vastatrix across different coffee management systems in Ethiopia. Int Microbiol 2024; 27:525-534. [PMID: 37507629 DOI: 10.1007/s10123-023-00409-2] [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: 02/12/2023] [Revised: 07/07/2023] [Accepted: 07/21/2023] [Indexed: 07/30/2023]
Abstract
Although coffee leaf rust (CLR), caused by Hemileia vastatrix, poses an increasing threat to coffee production in Ethiopia, little is known regarding its genetic diversity and structure and how these are affected by coffee management. Here, we used genetic fingerprinting based on sequence-related amplified polymorphism (SRAP) markers to genotype H. vastatrix samples from different coffee shrubs, across 40 sites, covering four coffee production systems (forest coffee, semi plantation coffee, home garden coffee, and plantation coffee) and different altitudes in Ethiopia. In total, 96 H. vastatrix samples were successfully genotyped with three primer combinations, producing a total of 79 scorable bands. We found 35.44% of amplified bands to be polymorphic, and the polymorphic information content (PIC) was 0.45, suggesting high genetic diversity among our CLR isolates. We also found significant isolation-by-distance across the samples investigated and detected significant differences in fungal genetic composition among plantation coffee and home garden coffee and a marginally significant difference among plantation coffee and forest coffee. Furthermore, we found a significant effect of altitude on CLR genetic composition in the forest coffee and plantation systems. Our results suggest that both spore dispersal and different selection pressures in the different coffee management systems are likely responsible for the observed high genetic diversity and genetic structure of CLR isolates in Ethiopia. When selecting Ethiopian coffee genotypes for crop improvement, it is important that these genotypes carry some resistance against CLR. Because our study shows large variation in genetic composition across relatively short geographical distances, a broad selection of rust isolates must be used for coffee resistance screening.
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Affiliation(s)
- Gerba Daba
- Division of Ecology, Evolution and Biodiversity Conservation, Biology Department, KU Leuven, Kasteelpark Arenberg 31, B-3001, Leuven, Belgium.
- College of Agriculture and Veterinary Medicine, Department of Horticulture and Plant Sciences, Jimma University, PO Box 307, Jimma, Ethiopia.
- KU Leuven Plant Institute (LPI), B-3001, Louvain, Belgium.
| | - Robin Daelemans
- Division of Ecology, Evolution and Biodiversity Conservation, Biology Department, KU Leuven, Kasteelpark Arenberg 31, B-3001, Leuven, Belgium
- KU Leuven Plant Institute (LPI), B-3001, Louvain, Belgium
| | - Gezahegn Berecha
- College of Agriculture and Veterinary Medicine, Department of Horticulture and Plant Sciences, Jimma University, PO Box 307, Jimma, Ethiopia
| | - Margot W J Geerinck
- KU Leuven Plant Institute (LPI), B-3001, Louvain, Belgium
- Laboratory for Process Microbial Ecology and Bioinspirational Management, Department of Microbial and Molecular Systems, KU Leuven, Willem De Croylaan 46, B-3001, Louvain, Belgium
| | - Christel Verreth
- Laboratory for Process Microbial Ecology and Bioinspirational Management, Department of Microbial and Molecular Systems, KU Leuven, Willem De Croylaan 46, B-3001, Louvain, Belgium
| | - Sam Crauwels
- KU Leuven Plant Institute (LPI), B-3001, Louvain, Belgium
- Laboratory for Process Microbial Ecology and Bioinspirational Management, Department of Microbial and Molecular Systems, KU Leuven, Willem De Croylaan 46, B-3001, Louvain, Belgium
| | - Bart Lievens
- KU Leuven Plant Institute (LPI), B-3001, Louvain, Belgium
- Laboratory for Process Microbial Ecology and Bioinspirational Management, Department of Microbial and Molecular Systems, KU Leuven, Willem De Croylaan 46, B-3001, Louvain, Belgium
| | - Olivier Honnay
- Division of Ecology, Evolution and Biodiversity Conservation, Biology Department, KU Leuven, Kasteelpark Arenberg 31, B-3001, Leuven, Belgium
- KU Leuven Plant Institute (LPI), B-3001, Louvain, Belgium
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Konuma T, Hamatani-Asakura M, Monna-Oiwa M, Kato S, Isobe M, Yokoyama K, Nannya Y, Takahashi S. Donor NKG2D rs1049174 polymorphism predicts hematopoietic recovery and event-free survival after single-unit cord blood transplantation in adults. Bone Marrow Transplant 2024; 59:566-568. [PMID: 38267584 DOI: 10.1038/s41409-024-02217-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Revised: 01/11/2024] [Accepted: 01/15/2024] [Indexed: 01/26/2024]
Affiliation(s)
- Takaaki Konuma
- Department of Hematology/Oncology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
| | - Megumi Hamatani-Asakura
- Department of Hematology/Oncology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Maki Monna-Oiwa
- Department of Hematology/Oncology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Seiko Kato
- Department of Hematology/Oncology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Masamichi Isobe
- Department of Hematology/Oncology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Kazuaki Yokoyama
- Department of Hematology/Oncology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Yasuhito Nannya
- Department of Hematology/Oncology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Satoshi Takahashi
- Division of Clinical Precision Research Platform, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
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Abdelwahab NR, Mabrouk RR, Zakaria NM, Abdel Nasser A, Mostafa AA, Wahba NS. Vitamin D receptor gene polymorphism in Egyptian multiple sclerosis patients. Egypt J Immunol 2024; 31:44-54. [PMID: 38615234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/15/2024]
Abstract
One of the most common neurological illnesses in the world is multiple sclerosis (MS), a chronic autoimmune demyelinating disease of the central nervous system (CNS). MS has both a genetic and an environmental origin. In terms of environmental factors, vitamin D deficiency is one of the most important risk factors and closely connected with gene polymorphisms involved in vitamin D metabolism, transport, or activity. Since vitamin D activity requires a receptor-mediated response, any changes to the vitamin D receptor (VDR) may have an effect on the pathophysiology of the disease. In this study, we aimed to identify the relationship between VDR gene polymorphisms, FokI A>G (rs2228570), ApaI A>C (rs7975232) and BsmI C>T (rs1544410) and MS. FokI, ApaI and BsmI genotypes were determined in 50 patients with relapsing remitting MS (RRMS) and in 50 control subjects. DNA was isolated from blood samples, and then FokI, ApaI and BsmI gene polymorphisms were identified using allelic discrimination real time polymerase chain reaction (PCR) assay. The distribution of FokI, ApaI and BsmI polymorphisms did not show any significant differences between MS patients and controls. Thus, we concluded that there is no association between the studied VDR gene polymorphisms and MS.
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Affiliation(s)
- Nermin R Abdelwahab
- Department of Clinical Pathology, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Randa R Mabrouk
- Department of Clinical Pathology, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Nahla M Zakaria
- Department of Clinical Pathology, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Azza Abdel Nasser
- Department of Neurology, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Afaf A Mostafa
- Department of Clinical Pathology, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Nancy S Wahba
- Department of Clinical Pathology, Faculty of Medicine, Ain Shams University, Cairo, Egypt
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Li J, Qiao X, Shang J. Association analysis between CD14 gene polymorphisms and peri-implantitis susceptibility in a Chinese population. Immun Inflamm Dis 2024; 12:e1230. [PMID: 38629742 PMCID: PMC11022617 DOI: 10.1002/iid3.1230] [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: 06/14/2023] [Revised: 03/05/2024] [Accepted: 03/08/2024] [Indexed: 04/19/2024] Open
Abstract
OBJECTIVE The goal of the study was to examine the genetic correlation of cluster of differentiation 14 (CD14) gene polymorphisms with peri-implantitis (PI) predisposition in a Chinese Han population. METHODS In the case-control study, blood samples were collected from PI patients and healthy individuals (n = 120/group), who were admitted to the Affiliated Hospital of Yangzhou University from 2021 to 2023. One-way analysis of variance (ANOVA) was applied to compare differences of continuous variables among different groups. Genotype and allele distributions of CD14 gene rs2569190 and rs2915863 polymorphisms were analyzed between groups via χ2 test. RESULTS A high percentage of rs2569190 GG genotype or G allele carriers were identified in PI group compared with control group (p < .01). Rs2569190 GG genotype carriers had high risk to develop PI (odds ratio: 2.545, 95% confidence interval: 1.257-5.156, p = .009). The rs2569190 AA genotype carriers had the lowest values of gingival index, plaque index, calculus index, peri-implant pocket depth, and clinical attachment level, which were the highest in cases with GG genotype. CONCLUSION Rs2569190 polymorphism of CD14 gene was significantly associated with PI predisposition in the Chinese Han population, and the GG genotype and G allele were risk factors for the development of PI.
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Affiliation(s)
- Jie Li
- Department of StomatologyYangzhou Hospital of TCMYangzhouChina
| | - Xiao Qiao
- Department of Oral and Maxillofacial SurgeryTaizhou Stomatological HospitalTaizhouChina
| | - Jin Shang
- Department of StomatologyAffiliated Hospital of Yangzhou UniversityYangzhouChina
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El-Menyar A, Khan NA, Asim M, Rizoli S, Al-Thani H. Beta-Adrenergic Receptor Polymorphism and Patho-Genetics of Trauma: A Transformational Frontier of Personalized Medicine in Neurotrauma. J Neurotrauma 2024; 41:771-788. [PMID: 38117124 DOI: 10.1089/neu.2023.0432] [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: 12/21/2023] Open
Abstract
Trauma is a serious public health issue, and remains a major cause of mortality and disability worldwide. The notion that genetic factors contribute to an individual's response to traumatic injury has advanced significantly. Genetic variations in severely injured patients have been linked to mortality, morbidity, and psychological outcomes. We conducted a comprehensive review of beta-adrenergic receptor polymorphisms and their impact on the pathogenetics of traumatic injuries, which could pave the way for a transformational frontier of personalized medicine in neurotrauma. It remains unclear why some individuals are vulnerable to worse outcomes, whereas others are resilient. Although genetic factors may be significant, the intricate interplay between environmental and genetic factors may be responsible for variations in the presentation and outcome after injury. Recent advancements in genetic analysis and molecular physiology have helped to shed light on the causes of such variability. Although exposure to trauma can initiate a cascade of stress-related responses, these responses alone are insufficient to explain etiopathogenesis. Therefore, gaining insights into how trauma and genetic predispositions to adrenergic variations interact at the molecular level to affect an individual's susceptibility and recuperation could provide an essential understanding of the molecular pathogenesis of traumatic injuries. Therefore, it is imperative to identify potential genetic and physiological markers to guide early management and prognosis of trauma. Such knowledge could pave the way for the discovery of novel biomarkers that can identify a transdiagnostic subgroup that is at high risk and requires early intervention. This could lead to the adoption of personalized medical approaches in neurotrauma care.
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Affiliation(s)
- Ayman El-Menyar
- Trauma and Vascular Surgery, Clinical Research, and Hamad Medical Corporation, Doha, Qatar
- Clinical Medicine, Weill Cornell Medicine, Doha, Qatar
| | - Naushad Ahmad Khan
- Trauma and Vascular Surgery, Clinical Research, and Hamad Medical Corporation, Doha, Qatar
| | - Mohammad Asim
- Trauma and Vascular Surgery, Clinical Research, and Hamad Medical Corporation, Doha, Qatar
| | - Sandro Rizoli
- Trauma Surgery, Hamad Medical Corporation, Doha, Qatar
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Teshnizi SH, Mirzazadeh S, Mashhadi N, Meri S, Kabelitz D, Kalantar K. Association study between killer immunoglobulin-like receptor polymorphisms and susceptibility to COVID-19 disease: a systematic review and meta-analysis. Immunol Res 2024; 72:175-184. [PMID: 37874432 DOI: 10.1007/s12026-023-09428-7] [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: 04/13/2023] [Accepted: 10/12/2023] [Indexed: 10/25/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a known virus that leads to a respiratory disease called coronavirus disease 19 (COVID-19). Natural killer (NK) cells, as members of innate immunity, possess crucial roles in restricting viral infections, including COVID-19. Their functions and development depend on receiving signals through various receptors, of which killer cell immunoglobulin-like receptors (KIRs) belong to the most effective ones. Different studies investigated the association between KIR gene content and susceptibility to COVID-19. Since previous studies have yielded contradictory results, we designed this meta-analysis study to draw comprehensive conclusions about COVID-19 risk and KIR gene association. According to PRISMA guidelines, a systematic search was performed in the electronic databases to find all studies investigating KIR gene contents in COVID-19 patients before March 2023. Any association between KIR genes and COVID-19 risk was determined by calculating pooled odds ratio (OR) and 95% confidence interval (CI). After applying the inclusion and exclusion criteria, 1673 COVID-19 patients and 1526 healthy controls from eight studies were included in this meta-analysis. As the main results, we observed a positive association between the 2DL3 (OR = 1.48, 95% CI = 1.17-1.88, P < 0.001) and susceptibility to COVID-19 and a negative association between the 2DP1 and the risk for COVID-19 (OR = 0.48, 95% CI = 0.23-0.99, P = 0.049). This meta-analysis demonstrated that KIR2DL3, as a member of iKIRs, might be associated with an increased risk of COVID-19 disease.
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Affiliation(s)
| | - Sara Mirzazadeh
- Department of Immunology, School of Medicine, Shiraz University of Medical Sciences, PO Box: 71345-1798, Shiraz, Iran
| | - Niloofar Mashhadi
- Department of Immunology, School of Medicine, Shiraz University of Medical Sciences, PO Box: 71345-1798, Shiraz, Iran
| | - Seppo Meri
- Department of Bacteriology and Immunology and the Translational Immunology Research Program (TRIMM), The University of Helsinki and HUSLAB, Helsinki University Hospital, Helsinki, Finland
| | - Dieter Kabelitz
- Institute of Immunology, Christian-Albrechts University of Kiel and University Hospital Schleswig, Holstein Campus Kiel, 24105, Kiel, Germany
| | - Kurosh Kalantar
- Department of Immunology, School of Medicine, Shiraz University of Medical Sciences, PO Box: 71345-1798, Shiraz, Iran.
- Department of Bacteriology and Immunology and the Translational Immunology Research Program (TRIMM), The University of Helsinki and HUSLAB, Helsinki University Hospital, Helsinki, Finland.
- Autoimmune Diseases Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.
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Lin L, Wang B, Zhang X, Deng C, Zhou C, Zhu J, Wu H, He J. Functional TET2 gene polymorphisms increase the risk of neuroblastoma in Chinese children. IUBMB Life 2024; 76:200-211. [PMID: 38014648 DOI: 10.1002/iub.2791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Accepted: 10/09/2023] [Indexed: 11/29/2023]
Abstract
The 5-methylcytosine (m5C) is the key chemical modification in RNAs. As one of the demethylases in m5C, TET2 has been shown as a tumor suppressor. However, the impact of TET2 gene polymorphisms on neuroblastoma has not been elucidated. 402 neuroblastoma patients and 473 controls were genotyped for TET2 gene polymorphisms using the TaqMan method. The impact of TET2 gene polymorphisms on neuroblastoma susceptibility was determined using multivariate logistic regression analysis. We also adopted genotype-tissue expression database to explore the impact of TET2 gene polymorphisms on the expression of host and nearby genes. We used the R2 platform and Sangerbox tool to analyze the relationship between gene expression and neuroblastoma risk and prognosis through non-parametric testing and Kaplan-Meier analysis, respectively. We found the TET2 gene polymorphisms (rs10007915 G > C and rs7670522 A > C) and the combined 2-5 risk genotypes can significantly increase neuroblastoma risk. Stratification analysis showed that these significant associations were more prominent in certain subgroups. TET2 rs10007915 G > C and rs7670522 A > C are significantly associated with reduced expression of TET2 mRNA. Moreover, lower expression of TET2 gene is associated with high risk, MYCN amplification, and poor prognosis of neuroblastoma. The rs10007915 G > C and rs7670522 A > C are significantly related to the increased expression of inorganic pyrophosphatase 2 mRNA, and higher expression of PPA2 gene is associated with high risk, MYCN amplification, and poor prognosis of neuroblastomas. In summary, TET2 rs10007915 G > C and rs7670522 A > C significantly confer neuroblastoma susceptibility, and further research is needed to investigate the underlying mechanisms.
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Affiliation(s)
- Lei Lin
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, Guangdong, China
| | - Bo Wang
- Department of Clinical Laboratory, Qingdao Eighth People's Hospital, Qingdao, Shandong, China
| | - Xinxin Zhang
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, Guangdong, China
| | - Changmi Deng
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, Guangdong, China
| | - Chunlei Zhou
- Department of Pathology, Children's Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Jinhong Zhu
- Department of Clinical Laboratory, Biobank, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang, China
| | - Haiyan Wu
- Department of Pathology, Children's Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Jing He
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, Guangdong, China
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Zong W, Zhao R, Wang X, Zhou C, Wang J, Chen C, Niu N, Zheng Y, Chen L, Liu X, Hou X, Zhao F, Wang L, Wang L, Song C, Zhang L. Population genetic analysis based on the polymorphisms mediated by transposons in the genomes of pig. DNA Res 2024; 31:dsae008. [PMID: 38447059 DOI: 10.1093/dnares/dsae008] [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: 12/23/2023] [Revised: 02/28/2024] [Accepted: 03/05/2024] [Indexed: 03/08/2024] Open
Abstract
Transposable elements (TEs) mobility is capable of generating a large number of structural variants (SVs), which can have considerable potential as molecular markers for genetic analysis and molecular breeding in livestock. Our results showed that the pig genome contains mainly TE-SVs generated by short interspersed nuclear elements (51,873/76.49%), followed by long interspersed nuclear elements (11,131/16.41%), and more than 84% of the common TE-SVs (Minor allele frequency, MAF > 0.10) were validated to be polymorphic. Subsequently, we utilized the identified TE-SVs to gain insights into the population structure, resulting in clear differentiation among the three pig groups and facilitating the identification of relationships within Chinese local pig breeds. In addition, we investigated the frequencies of TEs in the gene coding regions of different pig groups and annotated the respective TE types, related genes, and functional pathways. Through genome-wide comparisons of Large White pigs and Chinese local pigs utilizing the Beijing Black pigs, we identified TE-mediated SVs associated with quantitative trait loci and observed that they were mainly involved in carcass traits and meat quality traits. Lastly, we present the first documented evidence of TE transduction in the pig genome.
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Affiliation(s)
- Wencheng Zong
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Runze Zhao
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
- College of Animal Science, Shanxi Agricultural University, Jinzhong, China
| | - Xiaoyan Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Chenyu Zhou
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Jinbu Wang
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Cai Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Naiqi Niu
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Yao Zheng
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Li Chen
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
- Chongqing Academy of Animal Science, Chongqing, China
| | - Xin Liu
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Xinhua Hou
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Fuping Zhao
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Ligang Wang
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Lixian Wang
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Chengyi Song
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Longchao Zhang
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
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Fujikawa T, Ito T, Okada R, Sawada M, Mohri K, Tateishi Y, Takahashi R, Asakage T, Tsutsumi T. Combined genetic polymorphisms of the GSTT1 and NRF2 genes increase susceptibility to cisplatin-induced ototoxicity: A preliminary study. Hear Res 2024; 445:108995. [PMID: 38518393 DOI: 10.1016/j.heares.2024.108995] [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: 12/01/2023] [Revised: 03/01/2024] [Accepted: 03/19/2024] [Indexed: 03/24/2024]
Abstract
OBJECTIVE The genotype-phenotype relationship in cisplatin-induced ototoxicity remains unclear. By assessing early shifts in distortion product otoacoustic emission (DPOAE) levels after initial cisplatin administration, we aimed to discriminate patients' susceptibility to cisplatin-induced ototoxicity and elucidate their genetic background. STUDY DESIGN A prospective cross-sectional study. SETTING Tertiary referral hospital in Japan. PATIENTS Twenty-six patients with head and neck cancer were undergoing chemoradiotherapy with three cycles of 100 mg/m2 cisplatin. INTERVENTIONS Repetitive pure-tone audiometry and DPOAE measurements, and blood sampling for DNA extraction were performed. Patients were grouped into early ototoxicity presence or absence based on whether DPOAE level shifts exceeded the corresponding reference limits of the 21-day test interval. MAIN OUTCOME MEASURES Hearing thresholds after each cisplatin cycle, severity of other adverse events, and polymorphisms in cisplatin-induced ototoxicity-associated genes were compared. RESULTS Early ototoxicity was present in 14 and absent in 12 patients. Ototoxicity presence on DPOAEs was associated with greater progression of hearing loss in frequencies ≥2 kHz throughout therapy and with higher ototoxicity grades compared with ototoxicity absence. Ototoxicity was further associated with grade ≥2 nausea. Ototoxicity presence was genetically associated with the GSTT1 null genotype and G-allele of NFE2L2 rs6721961, whereas ototoxicity absence was associated with the GSTM1 null genotype. Dose-dependent progression of hearing loss was the greatest in the combined genotype pattern of GSTT1 null and the T/G or G/G variants of rs6721961. CONCLUSION Early DPOAE changes reflected genetic vulnerability to cisplatin-induced ototoxicity. Hereditary insufficiency of the antioxidant defense system causes severe cisplatin-induced hearing loss and nausea.
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Affiliation(s)
- Taro Fujikawa
- Department of Otolaryngology, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo, Tokyo, 113-8510 Japan.
| | - Taku Ito
- Department of Otolaryngology, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo, Tokyo, 113-8510 Japan
| | - Ryuhei Okada
- Department of Head and Neck Surgery, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo, Tokyo, 113-8510 Japan
| | - Mitsutaka Sawada
- Department of Otolaryngology, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo, Tokyo, 113-8510 Japan
| | - Kaori Mohri
- Department of Otolaryngology, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo, Tokyo, 113-8510 Japan
| | - Yumiko Tateishi
- Department of Head and Neck Surgery, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo, Tokyo, 113-8510 Japan
| | - Ryosuke Takahashi
- Department of Head and Neck Surgery, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo, Tokyo, 113-8510 Japan
| | - Takahiro Asakage
- Department of Head and Neck Surgery, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo, Tokyo, 113-8510 Japan
| | - Takeshi Tsutsumi
- Department of Otolaryngology, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo, Tokyo, 113-8510 Japan
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Surarak T, Chumnumwat S, Nosoongnoen W, Tragulpiankit P. Efficacy, safety, and pharmacokinetics of isoniazid affected by NAT2 polymorphisms in patients with tuberculosis: A systematic review. Clin Transl Sci 2024; 17:e13795. [PMID: 38629592 PMCID: PMC11022300 DOI: 10.1111/cts.13795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 03/22/2024] [Accepted: 03/30/2024] [Indexed: 04/19/2024] Open
Abstract
N-acetyltransferase 2 (NAT2) genetic polymorphisms might alter isoniazid metabolism leading to toxicity. We reviewed the impact of NAT2 genotype status on the pharmacokinetics, efficacy, and safety of isoniazid, a treatment for tuberculosis (TB). A systematic search for research articles published in Scopus, PubMed, and Embase until August 31, 2023, was conducted without filters or limits on the following search terms and Boolean operators: "isoniazid" AND "NAT2." Studies were selected if NAT2 phenotypes with pharmacokinetics or efficacy or safety of isoniazid in patients with TB were reported. Patient characteristics, NAT2 status, isoniazid pharmacokinetic parameters, early treatment failure, and the prevalence of drug-induced liver injury were extracted. If the data were given as a median, these values were standardized to the mean. Forty-one pharmacokinetics and 53 safety studies were included, but only one efficacy study was identified. The average maximum concentrations of isoniazid were expressed as supratherapeutic concentrations in adults (7.16 ± 4.85 μg/mL) and children (6.43 ± 3.87 μg/mL) in slow acetylators. The mean prevalence of drug-induced liver injury was 36.23 ± 19.84 in slow acetylators, which was significantly different from the intermediate (19.49 ± 18.20) and rapid (20.47 ± 20.68) acetylators. Subgroup analysis by continent showed that the highest mean drug-induced liver injury prevalence was in Asian slow acetylators (42.83 ± 27.61). The incidence of early treatment failure was decreased by genotype-guided isoniazid dosing in one study. Traditional weight-based dosing of isoniazid in most children and adults yielded therapeutic isoniazid levels (except for slow acetylators). Drug-induced liver injury was more commonly observed in slow acetylators. Genotype-guided dosing may prevent early treatment failure.
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Kumari N, Ahirwar R, Yadav A, Ramakrishnan L, Sagar SK, Mondal PR. ACE Gene I/D Polymorphism and Cardiometabolic Risk Factors: A Cross Sectional Study of Rural Population. Biochem Genet 2024; 62:1008-1020. [PMID: 37507644 DOI: 10.1007/s10528-023-10462-1] [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: 04/02/2023] [Accepted: 07/18/2023] [Indexed: 07/30/2023]
Abstract
The D allele has been identified as being linked to cardiovascular disease since the discovery of an insertion/deletion (I/D) polymorphism in the ACE gene, this polymorphism has been found to have significant associations with a variety of cardiovascular risk factors. Recent findings indicate a rising prevalence of metabolic disorders among rural populations in developing nations. Research on health matters has been predominantly focused on urban populations, with relatively less attention given to their rural counterparts Hence, the present study attempts to estimate the prevalence of ACE gene I/D polymorphism and explore its association with various cardiovascular risk factors among Rural Yadav population from India. In the present study, 207 (Male 47, Female 160) members of the Yadav community participated in the cross-sectional study. All the socio-demographic factors, somatometric (anthropometric) variables, and the intravenous blood was collected and Physiological (blood pressure), and biochemical (fasting glucose and lipid profile) parameters were measured as recommended by the American Heart Association, allele-specific PCR of the ACE gene I/D polymorphism was carried out, the PCR products were genotyped on 2% agarose gel Electrophoresis and ACE gene polymorphism was analysed for its association with various cardiovascular risk factors. Among the analysed individuals, 34 (16.4%) were found to have the II genotype, 58 (28.0%) had the ID genotype, and 115 (55.6%) had the DD genotype. The allele frequency of the I allele was found to be 0.31, and the frequency of the D allele was 0.69. The frequency of the DD genotype was found to be significantly higher among individuals with high TC, high TG, and low non-HDL levels (p value < 0.05). When considered collectively, the findings of this study are consistent with the hypothesis that the DD genotype of ACE polymorphism represents a correlation with cardiovascular disease risk factors in this population.
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Affiliation(s)
- Neha Kumari
- Department of Anthropology, University of Delhi, Delhi, 110007, India
| | - Rajeev Ahirwar
- Department of Anthropology, University of Delhi, Delhi, 110007, India
| | - Amarjeet Yadav
- Department of Anthropology, University of Delhi, Delhi, 110007, India
| | - Lakshmy Ramakrishnan
- Cardiac Biochemistry, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Surender Kumar Sagar
- Department of Zoology, Swami Shraddhanand College, University of Delhi, Delhi, 110036, India
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Habib CA, El-Sebai AA, Fouad MM, El-Mohamdy MA, Abdel Ghani AM, Bawady SA. Assessment of Stx-1A gene polymorphism (rs1569061) in relation to the development of multiple sclerosis in Egyptian patients. Egypt J Immunol 2024; 31:18-27. [PMID: 38615201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/15/2024]
Abstract
Multiple sclerosis (MS) is a multifactorial polygenic disease; results from autoimmune and neurodegenerative processes which lead to multifocal lesions of the central nervous system. Axonal degeneration was found to be prominent in the inflammation period of MS and contribute to the progression of disability. Soluble N-ethylmaleimide sensitive factor attachment receptor (SNARE) complex plays a vital role in the release of neurotransmitter by synaptic vesicle fusion. Stx-1A protein (Stx-1A), a major component of the SNARE complex, is widely expressed in brain tissue. This study intended to evaluate the prevalence of the Stx-1A gene polymorphism (rs1569061) in the Egyptian population with MS and to investigate its association with various clinical factors. This study included 65 adult Egyptian MS patients and 35 age- and sex-matched normal control subjects. Diagnosis of MS was made by an experienced neurologist according to revised McDonald criteria. All Patients underwent full history taking, included Age of onset of MS, disease duration, disease course and degree of disability according to the Expanded Disability Status Scale (EDSS) and family history of neurological diseases. Stx-1A gene polymorphism (rs1569061) genotyping was performed by TaqMan assay based quantitative real time (qPCR) and verified by sanger sequencer. Genotype and allele frequencies of (rs1569061) did not differ significantly between case and control groups. No difference was detected when comparing the genotype frequency and the allele frequency to different disease parameters. Discrepancy of the minor allele frequency (MAF) of Stx-1A gene (rs1569061) between different populations was noted. In conclusion, our study in Stx-1A gene polymorphism (rs1569061) and MS showed that no difference between the patient and control as regards gene frequency and allele frequency. Predicting no association between the studied polymorphism and MS in the Egyptian population. However, discrepancy between different population was noted as regards the MAF for Stx-1A gene (rs1569061).
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Affiliation(s)
- Christine A Habib
- Department of Clinical and Chemical Pathology, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Aziza A El-Sebai
- Department of Clinical and Chemical Pathology, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Mohamed M Fouad
- Department of Neurology, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Marwa A El-Mohamdy
- Department of Clinical and Chemical Pathology, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Amani M Abdel Ghani
- Department of Clinical and Chemical Pathology, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Somia A Bawady
- Department of Clinical and Chemical Pathology, Faculty of Medicine, Ain Shams University, Cairo, Egypt
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Perera SD, Hegele RA. Genetic variation in apolipoprotein A-V in hypertriglyceridemia. Curr Opin Lipidol 2024; 35:66-77. [PMID: 38117614 PMCID: PMC10919278 DOI: 10.1097/mol.0000000000000916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/22/2023]
Abstract
PURPOSE OF REVIEW While biallelic rare APOA5 pathogenic loss-of-function (LOF) variants cause familial chylomicronemia syndrome, heterozygosity for such variants is associated with highly variable triglyceride phenotypes ranging from normal to severe hypertriglyceridemia, often in the same individual at different time points. Here we provide an updated overview of rare APOA5 variants in hypertriglyceridemia. RECENT FINDINGS Currently, most variants in APOA5 that are considered to be pathogenic according to guidelines of the American College of Medical Genetics and Genomics are those resulting in premature termination codons. There are minimal high quality functional data on the impact of most rare APOA5 missense variants; many are considered as variants of unknown or uncertain significance. Furthermore, particular common polymorphisms of APOA5 , such as p.Ser19Trp and p.Gly185Cys in Caucasian and Asian populations, respectively, are statistically overrepresented in hypertriglyceridemia cohorts and are sometimes misattributed as being causal for chylomicronemia, when they are merely risk alleles for hypertriglyceridemia. SUMMARY Both biallelic and monoallelic LOF variants in APOA5 are associated with severe hypertriglyceridemia, although the biochemical phenotype in the monoallelic state is highly variable and is often exacerbated by secondary factors. Currently, with few exceptions, the principal definitive mechanism for APOA5 pathogenicity is through premature truncation. The pathogenic mechanisms of most missense variants in APOA5 remain unclear and require additional functional experiments or family studies.
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Affiliation(s)
- Shehan D Perera
- Departments of Biochemistry and Medicine, Schulich School of Medicine and Dentistry, Western University, 1151 Richmond Street North, London, Ontario, Canada
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Imani MM, Moradi MM, Rezaei F, Mozaffari HR, Sharifi R, Safaei M, Azizi F, Basamtabar M, Sohrabi Z, Shalchi M, Sadeghi M. Association between alcohol dehydrogenase polymorphisms (rs1229984, rs1573496, rs1154460, and rs284787) and susceptibility to head and neck cancers: A systematic review and meta-analysis. Arch Oral Biol 2024; 160:105898. [PMID: 38278126 DOI: 10.1016/j.archoralbio.2024.105898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 12/25/2023] [Accepted: 01/19/2024] [Indexed: 01/28/2024]
Abstract
OBJECTIVE Head and neck cancer (HNC) is a prevalent and complex group of malignancies with increasing incidence globally. Alcohol dehydrogenases (ADHs) play a crucial role in alcohol metabolism, and their polymorphisms have been linked to HNC risk. This systematic review and meta-analysis aims to evaluate the association between ADH polymorphisms and susceptibility to HNCs, incorporating additional analyses and adding more studies to increase power and accuracy of the results. DESIGN Subgroup analysis, meta-regression analysis, and sensitivity analyses were conducted to explore potential differences within the data and assess the stability of pooled odds ratios (ORs). To mitigate the risk of false conclusions from meta-analyses, a trial sequential analysis was performed. RESULTS For ADH1B rs1229984, the pooled OR (95 % confidence interval (CI)) was 0.73 (0.65, 0.82), 0.42 (0.35, 0.50), 0.57 (0.44, 0.73), 0.56 (0.50, 0.62), and 0.80 (0.73, 0.88), as well as for ADH7 rs1573496, the pooled OR was 0.72 (0.62, 0.85), 0.36 (0.17, 0.74), 0.76 (0.64, 0.91), 0.80 (0.71, 0.91), and 0.38 (0.18, 0.78) with a p < 0.05 in all allelic, homozygous, heterozygous, recessive, and dominant models, respectively. However, no significant association was found between the ADH7 rs1154460 and rs284787 polymorphisms and the risk of HNC with pooled ORs of 1.11 (p = 0.19) and 1.09 (p = 0.24) for the recessive model, respectively. The ethnicities, tumor subsites, control sources, sample sizes, quality scores, and Hardy-Weinberg equilibrium statuses were confounding factors. CONCLUSION The ADH1B rs1229984 and ADH7 rs1573496 polymorphisms are significantly associated with a reduced risk of HNC.
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Affiliation(s)
- Mohammad Moslem Imani
- Department of Orthodontics, School of Dentistry, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Mohamad Mehdi Moradi
- Students Research Committee, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Farzad Rezaei
- Department of Oral and Maxillofacial Surgery, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Hamid Reza Mozaffari
- Department of Oral and Maxillofacial Medicine, School of Dentistry, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Roohollah Sharifi
- Department of Endodontics, School of Dentistry, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Mohsen Safaei
- Advanced Dental Sciences Research Center, School of Dentistry, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Fatemeh Azizi
- Department of Orthodontics, School of Dentistry, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Masoumeh Basamtabar
- Department of Orthodontics, School of Dentistry, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Zahra Sohrabi
- Department of periodontology, School of Dentistry, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Majid Shalchi
- Orthodontic Department, Guilan University of Medical Sciences, School of Dentistry, Rasht, Iran
| | - Masoud Sadeghi
- Medical Biology Research Centre, Kermanshah University of Medical Sciences, Kermanshah, Iran.
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Budi T, Singchat W, Tanglertpaibul N, Thong T, Panthum T, Noito K, Wattanadilokchatkun P, Jehangir M, Chaiyes A, Wongloet W, Vangnai K, Yokthongwattana C, Sinthuvanich C, Ahmad SF, Muangmai N, Han K, Nunome M, Supnithi T, Koga A, Duengkae P, Matsuda Y, Srikulnath K. Research Note: Possible influence of thermal selection on patterns of HSP70 and HSP90 gene polymorphisms in Thai indigenous and local chicken breeds and red junglefowls. Poult Sci 2024; 103:103503. [PMID: 38330888 PMCID: PMC10864794 DOI: 10.1016/j.psj.2024.103503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 01/06/2024] [Accepted: 01/22/2024] [Indexed: 02/10/2024] Open
Abstract
The thermal stress caused by global climate change adversely affects the welfare, productivity, and reproductive performance of farm animals, including chickens, and causes substantial economic losses. However, the understanding of the genetic basis of the indigenous chicken adaptation to high ambient temperatures is limited. Hence, to reveal the genetic basis of thermal stress adaptation in chickens, this study investigated polymorphisms in the heat shock protein 70 (HSP70) and HSP90 genes, known mechanisms of cellular defense against thermal stress in indigenous and local chicken breeds and red junglefowls in Thailand. The result revealed seven alleles of the HSP70 gene. One allele exhibited a missense mutation, where an amino acid changed from Asn to His in the substrate-binding and peptide-binding domains, which is exclusive to the Lao Pa Koi chicken breed. Twenty new alleles with silent mutations in the HSP90 gene highlighted its greater complexity. Despite this diversity, distinct population structures were not found for either HSP70 or HSP90, which suggests incomplete impact on the domestication process and selection. The low genetic diversity, shown by the sharing of alleles between red junglefowls and Thai indigenous and local chicken breeds, aligns with the hypothesis that these alleles have undergone selection in tropical regions, such as Thailand. Selection signature analysis suggests the purifying selection of HSP70 for thermotolerance. This study provides valuable insights for enhancing the conservation of genetic resources with thermotolerant traits, which are essential for developing breeding programs to increase poultry production in the context of global climate change.
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Affiliation(s)
- Trifan Budi
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand; Interdisciplinary Graduate Program in Bioscience, Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
| | - Worapong Singchat
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand; Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
| | - Nivit Tanglertpaibul
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand; Interdisciplinary Graduate Program in Bioscience, Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
| | - Thanyapat Thong
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
| | - Thitipong Panthum
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand; Interdisciplinary Graduate Program in Bioscience, Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
| | - Kantika Noito
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
| | - Pish Wattanadilokchatkun
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
| | - Maryam Jehangir
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
| | - Aingorn Chaiyes
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand; School of Agriculture and Cooperatives, Sukhothai Thammathirat Open University, Nonthaburi 11120, Thailand
| | - Wongsathit Wongloet
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand; Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
| | - Kanithaporn Vangnai
- Department of Food Science and Technology, Faculty of Agro-Industry, Kasetsart University, Bangkok, 10900, Thailand
| | - Chotika Yokthongwattana
- Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Chomdao Sinthuvanich
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand; Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Syed Farhan Ahmad
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand; Interdisciplinary Graduate Program in Bioscience, Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand; Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
| | - Narongrit Muangmai
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand; Department of Fishery Biology, Faculty of Fisheries, Kasetsart University, Bangkok 10900, Thailand
| | - Kyudong Han
- Department of Microbiology, Dankook University, Cheonan 31116, Republic of Korea; Bio-Medical Engineering Core Facility Research Center, Dankook University, Cheonan 31116, Republic of Korea; Smart Animal Bio institute, Dankook University, Cheonan 31116, Republic of Korea
| | - Mitsuo Nunome
- Department of Zoology, Faculty of Science, Okayama University of Science, Kita-ku, Okayama 700-0005, Japan
| | - Thepchai Supnithi
- National Electronics and Computer Technology Center (NECTEC), Khlong Luang, Pathum Thani 12120, Thailand
| | - Akihiko Koga
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
| | - Prateep Duengkae
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand; Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
| | - Yoichi Matsuda
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
| | - Kornsorn Srikulnath
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand; Interdisciplinary Graduate Program in Bioscience, Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand; Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Chatuchak, Bangkok 10900, Thailand; Center for Advanced Studies in Tropical Natural Resources, National Research University-Kasetsart University (CASTNAR, NRU-KU), Kasetsart University, Bangkok 10900, Thailand.
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Sanyal S, Rajput S, Sadhukhan S, Rajender S, Mithal A, Chattopadhyay N. Polymorphisms in the Runx2 and osteocalcin genes affect BMD in postmenopausal women: a systematic review and meta-analysis. Endocrine 2024; 84:63-75. [PMID: 38055125 DOI: 10.1007/s12020-023-03621-2] [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: 09/17/2023] [Accepted: 11/17/2023] [Indexed: 12/07/2023]
Abstract
PURPOSE Runx2 and osteocalcin have pivotal roles in bone homeostasis. Polymorphism of these two genes could alter the function of osteoblasts and consequently bone mineral density (BMD). Attempts to understand the relationship between these polymorphisms and BMD in postmenopausal women across a variety of populations have yielded inconsistent results. This meta-analysis seeks to define the relationship between these polymorphisms with BMD in postmenopausal women. METHODS Eligible studies were identified from three electronic databases. Data were extracted from the eligible studies (4 studies on Runx2 and 6 studies on osteocalcin), and associations of Runx2 T > C and osteocalcin HindIII polymorphisms with BMD in postmenopausal women were assessed using standard difference in means (SDM) and 95% confidence intervals (CI) as statistical measures. RESULTS A significant difference in the lumbar spine (LS) BMD in postmenopausal women was observed between the TT and CC homozygotes for the Runx2 T > C (SDM = -0.445, p-value = 0.034). The mutant genotypes (CC) showed significantly lower LS BMD in comparison to wild type genotypes under recessive model of genetic analysis (TC + TT vs. CC: SDM = -0.451, p-value = 0.032). For osteocalcin, HindIII polymorphism, the mutant genotypes (HH) was associated with significantly higher BMD for both LS and femoral neck (FN) than the wild type (hh) homozygotes (SDM = 0.152, p-value = 0.008 and SDM = 0.139, p-value = 0.016 for LS and FN, respectively). There was no association between total hip (TH) BMD and the osteocalcin HindIII polymorphism. CONCLUSIONS Runx2 T > C and osteocalcin HindIII polymorphisms influence the level of BMD in postmenopausal women and may be used as predictive markers of osteoporosis.
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Affiliation(s)
- Somali Sanyal
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow Campus, Lucknow, Uttar Pradesh, 226018, India.
| | - Swati Rajput
- Division of Endocrinology and Centre for Research in Anabolic Skeletal Targets in Health and Illness (ASTHI), CSIR-Central Drug Research Institute, Lucknow, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Sreyanko Sadhukhan
- Division of Endocrinology and Centre for Research in Anabolic Skeletal Targets in Health and Illness (ASTHI), CSIR-Central Drug Research Institute, Lucknow, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Singh Rajender
- Division of Endocrinology and Centre for Research in Anabolic Skeletal Targets in Health and Illness (ASTHI), CSIR-Central Drug Research Institute, Lucknow, India
| | - Ambrish Mithal
- Institute of Endocrinology and Diabetes, Max Healthcare, Institutional Area, Press Enclave Road, Saket, New Delhi, India.
| | - Naibedya Chattopadhyay
- Division of Endocrinology and Centre for Research in Anabolic Skeletal Targets in Health and Illness (ASTHI), CSIR-Central Drug Research Institute, Lucknow, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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Zhu L, Zhang X, Guan Y, Zhu Y, Zhou Q, Liu B, Ren H, Yang X. Meta-analysis of the association of prosaposin polymorphisms rs4747203 and rs885828 with risk of Parkinson's disease. Acta Neurol Belg 2024; 124:573-580. [PMID: 38206457 DOI: 10.1007/s13760-023-02446-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 11/27/2023] [Indexed: 01/12/2024]
Abstract
BACKGROUND Previous research has established a connection between polymorphisms rs4747203 and rs885828 in the prosaposin (PSAP) gene and an increased risk of Parkinson's disease (PD). However, other studies have found no significant difference in risk compared to the general population. METHODS To evaluate the current evidence linking rs4747203 and rs885828 to PD risk, we conducted a comprehensive search of PubMed, the Web of Science, Embase, and the Cochrane Library for relevant studies up until May 2023. In addition, we analyzed data from the publicly available "PD Variant Browser". We performed a meta-analysis using Stata 17.0 to synthesize the findings from the selected studies. RESULTS Our meta-analysis, which included data from six published studies and the public database, revealed no significant association between PD risk and either rs4747203 [OR (95% CI) = 0.99 (0.93-1.05), I2 = 90.3%, P = 0.635] or rs885828 [OR (95% CI) = 1.01 (0.95-1.07), I2 = 90.7%, P = 0.773]. These results remained consistent when examining subgroups of individuals within or outside of Asia. CONCLUSION The available evidence does not support an association between the genotype at rs4747203 or rs885828 and the risk of PD.
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Affiliation(s)
- Liuhui Zhu
- Department of Geriatric Neurology, First Affiliated Hospital of Kunming Medical University, Kunming, 650032, Yunnan, People's Republic of China
- Joint Institute of Smoking and Health, Kunming, 650106, Yunnan, China
| | - Xinyue Zhang
- Department of Geriatric Neurology, First Affiliated Hospital of Kunming Medical University, Kunming, 650032, Yunnan, People's Republic of China
| | - Ying Guan
- Joint Institute of Smoking and Health, Kunming, 650106, Yunnan, China
| | - Yongyun Zhu
- Department of Geriatric Neurology, First Affiliated Hospital of Kunming Medical University, Kunming, 650032, Yunnan, People's Republic of China
| | - Qian Zhou
- Department of Geriatric Neurology, First Affiliated Hospital of Kunming Medical University, Kunming, 650032, Yunnan, People's Republic of China
| | - Bin Liu
- Department of Geriatric Neurology, First Affiliated Hospital of Kunming Medical University, Kunming, 650032, Yunnan, People's Republic of China
| | - Hui Ren
- Department of Geriatric Neurology, First Affiliated Hospital of Kunming Medical University, Kunming, 650032, Yunnan, People's Republic of China
| | - Xinglong Yang
- Department of Geriatric Neurology, First Affiliated Hospital of Kunming Medical University, Kunming, 650032, Yunnan, People's Republic of China.
- Joint Institute of Smoking and Health, Kunming, 650106, Yunnan, China.
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Ragkousis A, Kazantzis D, Georgalas I, Theodossiadis P, Kroupis C, Chatziralli I. Association of PON1, APOE and SDF-1 Gene Polymorphisms with Treatment Response to Intravitreal Anti-VEGF Treatment in Patients with Retinal Vein Occlusion. Semin Ophthalmol 2024; 39:201-208. [PMID: 37997789 DOI: 10.1080/08820538.2023.2283028] [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: 06/27/2023] [Accepted: 11/09/2023] [Indexed: 11/25/2023]
Abstract
PURPOSE The purpose of this study was to determine whether specific genetic polymorphisms affect the response to intravitreal anti-vascular endothelial growth factor (anti-VEGF) treatment in patients with macular oedema secondary to retinal vein occlusion (RVO). METHODS Participants in this prospective study were 50 patients with macular oedema secondary to RVO, who were treated with intravitreal ranibizumab or aflibercept, and were followed-up for 12 months after initiation of treatment. Five single nucleotide polymorphisms (SNPs) from three different genes (APOE, PON1, SDF-1) were examined as potential predictors for treatment response to intravitreal anti-VEGF agents. RESULTS Patients with the LL genotype of the PON1 L55M SNP had significantly higher reduction in central subfield thickness (CST) at month 12 after initiation of intravitreal anti-VEGF treatment (101.63 ± 56.80 μm in LL vs. 72.44 ± 39.41 μm in LM vs. 40.25 ± 19.33 μm in MM, p = .026). Patients with the M allele of the PON1 L55M SNP were significantly associated with lower reduction in CST compared to non-carriers (68.29 ± 38.77 μm in LM + MM vs. 101.63 ± 56.80 μm in LL, p = .032). CONCLUSION PON1 L55M SNP may serve as a promising genetic biomarker for predicting response to intravitreal anti-VEGF treatment in patients with macular oedema due to RVO.
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Affiliation(s)
- Antonios Ragkousis
- 2nd Department of Ophthalmology, Attikon University Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Dimitrios Kazantzis
- 2nd Department of Ophthalmology, Attikon University Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Ilias Georgalas
- 1st Department of Ophthalmology, "G. Gennimatas" General Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Panagiotis Theodossiadis
- 2nd Department of Ophthalmology, Attikon University Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Christos Kroupis
- Department of Clinical Biochemistry, Attikon University Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Irini Chatziralli
- 2nd Department of Ophthalmology, Attikon University Hospital, National and Kapodistrian University of Athens, Athens, Greece
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Du S, Huang X, He X, Mao M, Chen M, Zhang R, Shao H, Lv Z, Liu X, Chuan J. Association of NUDT15 gene polymorphism with adverse reaction, treatment efficacy, and dose of 6-mercaptopurine in patients with acute lymphoblastic leukemia: a systematic review and meta-analysis. Haematologica 2024; 109:1053-1068. [PMID: 37794799 PMCID: PMC10985454 DOI: 10.3324/haematol.2023.282761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 10/26/2023] [Indexed: 10/06/2023] Open
Abstract
6-mercaptopurine (6-MP) serves as the backbone in the maintenance regimens of acute lymphoblastic leukemia (ALL). We aimed to evaluate the influence of NUDT15 gene polymorphism on the risk of myelosupression, hepatotoxicity and interruption of 6-MP, as well as treatment efficacy and dose of 6-MP in ALL patients. A total of 24 studies with 3,374 patients were included in this meta-analysis. We found 9-fold higher risk of 6-MP induced leukopenia (odds ratio [OR] =9.00, 95% confidence interval [CI]: 3.73-21.74) and 2.5-fold higher risk of 6-MP-induced neutropenia (OR=2.52, 95% CI: 1.72-3.69) for NUDT15 c.415C>T variant carriers in the dominant model. Moreover, we found that the dose intensity of 6-MP in ALL patients with one NUDT15 c.415C>T variant alleles (CT) was 19% less than that in wild-type patients (CC) (mean differences: 19.43%, 95% CI: -25.36 to -13.51). The tolerable dose intensity of 6-MP in NUDT15 c.415C>T homozygote variant (TT) and heterozygote variant (CT) carriers was 49% and 15% less than that in wild-type patients, respectively. The NUDT15 c.415C>T variant group (CT+TT) had seven times (OR=6.98, 95% CI: 2.83-17.22) higher risk of developing 6-MP intolerance than the CC group. However, NUDT15 c.415C>T polymorphism did not appear significantly associated with hepatotoxicity, treatment interruption or relapse incidence. We concluded that NUDT15 c.415C>T was a good predictor for 6-MP-induced myelosuppression in ALL patients. The dose intensity of 6-MP in ALL patients with NUDT15 c.415C>T variants was significantly lower than that in wild-type patients. This research provided a basis for further investigation into relations between NUDT15 gene and adverse reaction, treatment efficacy and dose intensity of 6-MP.
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Affiliation(s)
- Shan Du
- Department of Pharmacy, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, China; Personalized Drug Therapy Key Laboratory of Sichuan Province, School of Medicine, University of Electronic Science and Technology of China, Chengdu
| | - Xuefei Huang
- Department of Pharmacy, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, China; Personalized Drug Therapy Key Laboratory of Sichuan Province, School of Medicine, University of Electronic Science and Technology of China, Chengdu
| | - Xia He
- Department of Pharmacy, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, China; Personalized Drug Therapy Key Laboratory of Sichuan Province, School of Medicine, University of Electronic Science and Technology of China, Chengdu
| | - Mian Mao
- Department of Pharmacy, Sichuan Cancer Hospital, Chengdu
| | - Min Chen
- Department of Pharmacy, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, China; Personalized Drug Therapy Key Laboratory of Sichuan Province, School of Medicine, University of Electronic Science and Technology of China, Chengdu
| | - Rong Zhang
- Department of Pediatrics, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu
| | - Huikai Shao
- Department of Pharmacy, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, China; Personalized Drug Therapy Key Laboratory of Sichuan Province, School of Medicine, University of Electronic Science and Technology of China, Chengdu
| | - Ziyan Lv
- Department of Pharmacy, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, China; Personalized Drug Therapy Key Laboratory of Sichuan Province, School of Medicine, University of Electronic Science and Technology of China, Chengdu
| | - Xinxia Liu
- Department of Pharmacy, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, China; Personalized Drug Therapy Key Laboratory of Sichuan Province, School of Medicine, University of Electronic Science and Technology of China, Chengdu.
| | - Junlan Chuan
- Department of Pharmacy, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, China; Personalized Drug Therapy Key Laboratory of Sichuan Province, School of Medicine, University of Electronic Science and Technology of China, Chengdu.
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Tellini N, De Chiara M, Mozzachiodi S, Tattini L, Vischioni C, Naumova ES, Warringer J, Bergström A, Liti G. Ancient and recent origins of shared polymorphisms in yeast. Nat Ecol Evol 2024; 8:761-776. [PMID: 38472432 DOI: 10.1038/s41559-024-02352-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 01/30/2024] [Indexed: 03/14/2024]
Abstract
Shared genetic polymorphisms between populations and species can be ascribed to ancestral variation or to more recent gene flow. Here, we mapped shared polymorphisms in Saccharomyces cerevisiae and its sister species Saccharomyces paradoxus, which diverged 4-6 million years ago. We used a dense map of single-nucleotide diagnostic markers (mean distance 15.6 base pairs) in 1,673 sequenced S. cerevisiae isolates to catalogue 3,852 sequence blocks (≥5 consecutive markers) introgressed from S. paradoxus, with most being recent and clade-specific. The highly diverged wild Chinese S. cerevisiae lineages were depleted of introgressed blocks but retained an excess of individual ancestral polymorphisms derived from incomplete lineage sorting, perhaps due to less dramatic population bottlenecks. In the non-Chinese S. cerevisiae lineages, we inferred major hybridization events and detected cases of overlapping introgressed blocks across distinct clades due to either shared histories or convergent evolution. We experimentally engineered, in otherwise isogenic backgrounds, the introgressed PAD1-FDC1 gene pair that independently arose in two S. cerevisiae clades and revealed that it increases resistance against diverse antifungal drugs. Overall, our study retraces the histories of divergence and secondary contacts across S. cerevisiae and S. paradoxus populations and unveils a functional outcome.
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Affiliation(s)
- Nicolò Tellini
- CNRS, INSERM, IRCAN, Côte d'Azur University, Nice, France
| | | | | | | | | | - Elena S Naumova
- Kurchatov Complex for Genetic Research (GosNIIgenetika), National Research Center 'Kurchatov Institute', Moscow, Russia
| | - Jonas Warringer
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Anders Bergström
- Ancient Genomics Laboratory, The Francis Crick Institute, London, UK
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Gianni Liti
- CNRS, INSERM, IRCAN, Côte d'Azur University, Nice, France.
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Armatussolikha HR, Winarni TI, Maharani N, Dewantiningrum J, Muniroh M. Impact of GSTT1 AND GSTM1 variants and hair mercury concentration in maternal blood pressure among coastal pregnant women in Central Java, Indonesia. Reprod Toxicol 2024; 125:108574. [PMID: 38462212 DOI: 10.1016/j.reprotox.2024.108574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 03/06/2024] [Accepted: 03/07/2024] [Indexed: 03/12/2024]
Abstract
The GSTT1 and GSTM1 genes have a role in mercury metabolism and excretion, as well as blood pressure response, impacting birth outcomes. The present study assesses whether GSTT1 and GSTM1 deletion variants and maternal hair Hg concentration are associated with blood pressure and birth outcomes among the Indonesian coastal pregnant mother population. A cross-sectional study was conducted on 139 pregnant women in the Jepara coastal area of Central Java, Indonesia. Maternal characteristics during pregnancy, including blood pressure and birth outcomes, were collected. GSTT1 and GSTM1 gene variants were detected using polymerase chain reaction (PCR). Hair Hg levels were measured using the reducing-vaporization mercury analyzer. The mean maternal hair Hg concentration was 0.727±0.558 μg/g. GSTT1 genotype homozygous deletion was found in 41.7% of subjects, while no GSTM1 deletion was found. No statistically significant difference was found between deletion and non-deletion groups for hair Hg. GSTT1 deletion genotype shows protection but is inconclusive toward diastolic hypertension (p=0.048, OR 0.285, CI 0.077-1.052) and insignificant with birth outcomes (all p>0.05). High hair Hg concentration and positive history of cardiovascular diseases increase the risk of systolic and diastolic hypertension during pregnancy with OR 6.871 (CI 95% 1.445-32.660) and 8.518 (CI 95% 2.126-34.125), respectively, while not in birth outcomes. Maternal Hg exposure and history of cardiovascular diseases are independent risk factors for pregnant hypertension, whereas the GSTT1 homozygous deletion genotype has no role in diastolic hypertension and birth outcomes among the Indonesian coastal pregnant mother population.
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Affiliation(s)
- Herna Rizkia Armatussolikha
- Magister Program of Biomedical Science, Faculty of Medicine Universitas Diponegoro, Semarang 50275, Indonesia
| | - Tri Indah Winarni
- Department of Anatomy, Faculty of Medicine, Universitas Diponegoro, Semarang, Central Java 50275, Indonesia; Center for Biomedical Research (CEBIOR), Faculty of Medicine, Universitas Diponegoro, Semarang, Central Java 50275, Indonesia
| | - Nani Maharani
- Center for Biomedical Research (CEBIOR), Faculty of Medicine, Universitas Diponegoro, Semarang, Central Java 50275, Indonesia; Department of Pharmacology and Therapy, Faculty of Medicine, Universitas Diponegoro, Semarang, Central Java 50275, Indonesia
| | - Julian Dewantiningrum
- Department of Obstetrics and Gynecology, Faculty of Medicine, Universitas Diponegoro, Semarang 50275, Indonesia
| | - Muflihatul Muniroh
- Department of Physiology, Faculty of Medicine, Universitas Diponegoro, Semarang 50275, Indonesia.
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Khorrami M, Saneipour M, Moridnia A, Shaygannejad V, Sadeghi E, Kassani A, Sarmadi A, Mirmosayyeb O. Interdependency of NINJ2 gene expression and polymorphism with susceptibility and response to interferon beta in patients with multiple sclerosis. Int J Neurosci 2024; 134:347-352. [PMID: 35912872 DOI: 10.1080/00207454.2022.2102979] [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: 02/27/2022] [Accepted: 06/30/2022] [Indexed: 10/24/2022]
Abstract
OBJECTIVE Multiple sclerosis (MS) is a multifactorial inflammatory and autoimmune condition that lead to chronic neurodegeneration and central nervous system (CNS) demyelination that mainly affects young adults. The incidence and prevalence rate of MS considerably vary in ethnicities and geographic regions and affecting women more than men. Interferon-β (IFN-β) is the first-line disease management for MS, while the majority of affected members does not respond to the IFN-β. Numerous recent studies shown a significant relationship between genetic variations and responsiveness to the IFN-β. Therefore, determining the genetic differences in the drug response could help determine precise treatment strategies. METHODS The genotyping of the rs7298096 polymorphism (SNP) and NINJ2 gene expression were assessed in 99 responders and 106 non-responder patients with IFN-β treated RRMS. RESULTS The distribution of rs7298096 SNP was significantly different in the responders and non-responder patients and the NINJ2 gene expression considerably increased in the non-responder patients compare to the responders. The NINJ2 gene expression level in the AA genotype of the non-responder group was higher than to the other genotypes of both groups. CONCLUSION Our results showed that the NINJ2 gene expression level and rs7298096 genotype possibly affect the response to the IFN-β in patients with RRMS.
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Affiliation(s)
- Mehdi Khorrami
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Maryam Saneipour
- Department of Genetics and Molecular Biology, School of Medicine, Dezful University of Medical Sciences, Dezful, Iran
| | - Abbas Moridnia
- Department of Genetics and Molecular Biology, School of Medicine, Dezful University of Medical Sciences, Dezful, Iran
| | - Vahid Shaygannejad
- Isfahan Neuroscience Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Erfan Sadeghi
- Department of Biostatistics and Epidemiology, Faculty of Health, Isfahan University of Medical Sciences Isfahan Iran, Isfahan, Iran
| | - Aziz Kassani
- Department of Community Medicine, School of Medicine, Dezful University of Medical Sciences, Dezful, Iran
| | - Akram Sarmadi
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Omid Mirmosayyeb
- Isfahan Neuroscience Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
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