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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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George L, Alex R, Gowane G, Vohra V, Joshi P, Kumar R, Verma A. Weighted single step GWAS reveals genomic regions associated with economic traits in Murrah buffaloes. Anim Biotechnol 2024; 35:2319622. [PMID: 38437001 DOI: 10.1080/10495398.2024.2319622] [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: 03/05/2024]
Abstract
The objective of the present study was to identify genomic regions influencing economic traits in Murrah buffaloes using weighted single step Genome Wide Association Analysis (WssGWAS). Data on 2000 animals, out of which 120 were genotyped using a double digest Restriction site Associated DNA (ddRAD) sequencing approach. The phenotypic data were collected from NDRI, India, on growth traits, viz., body weight at 6M (month), 12M, 18M and 24M, production traits like 305D (day) milk yield, lactation length (LL) and dry period (DP) and reproduction traits like age at first calving (AFC), calving interval (CI) and first service period (FSP). The biallelic genotypic data consisted of 49353 markers post-quality check. The heritability estimates were moderate to high, low to moderate, low for growth, production, reproduction traits, respectively. Important genomic regions explaining more than 0.5% of the total additive genetic variance explained by 30 adjacent SNPs were selected for further analysis of candidate genes. In this study, 105 genomic regions were associated with growth, 35 genomic regions with production and 42 window regions with reproduction traits. Different candidate genes were identified in these genomic regions, of which important are OSBPL8, NAP1L1 for growth, CNTNAP2 for production and ILDR2, TADA1 and POGK for reproduction traits.
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Affiliation(s)
- Linda George
- National Dairy Research Institute, Karnal, India
| | - Rani Alex
- National Dairy Research Institute, Karnal, India
| | - Gopal Gowane
- National Dairy Research Institute, Karnal, India
| | - Vikas Vohra
- National Dairy Research Institute, Karnal, India
| | - Pooja Joshi
- National Dairy Research Institute, Karnal, India
| | - Ravi Kumar
- National Dairy Research Institute, Karnal, India
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Sukhija N, Malik AA, Devadasan JM, Dash A, Bidyalaxmi K, Ravi Kumar D, Kousalaya Devi M, Choudhary A, Kanaka KK, Sharma R, Tripathi SB, Niranjan SK, Sivalingam J, Verma A. Genome-wide selection signatures address trait specific candidate genes in cattle indigenous to arid regions of India. Anim Biotechnol 2024; 35:2290521. [PMID: 38088885 DOI: 10.1080/10495398.2023.2290521] [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: 02/22/2024]
Abstract
The peculiarity of Indian cattle lies in milk quality, resistance to diseases and stressors as well as adaptability. The investigation addressed selection signatures in Gir and Tharparkar cattle, belonging to arid ecotypes of India. Double digest restriction-site associated DNA sequencing (ddRAD-seq) yielded nearly 26 million high-quality reads from unrelated seven Gir and seven Tharparkar cows. In all, 19,127 high-quality SNPs were processed for selection signature analysis. An approach involving within-population composite likelihood ratio (CLR) statistics and between-population FST statistics was used to capture selection signatures within and between the breeds, respectively. A total of 191 selection signatures were addressed using CLR and FST approaches. Selection signatures overlapping 86 and 73 genes were detected as Gir- and Tharparkar-specific, respectively. Notably, genes related to production (CACNA1D, GHRHR), reproduction (ESR1, RBMS3), immunity (NOSTRIN, IL12B) and adaptation (ADAM22, ASL) were annotated to selection signatures. Gene pathway analysis revealed genes in insulin/IGF pathway for milk production, gonadotropin releasing hormone pathway for reproduction, Wnt signalling pathway and chemokine and cytokine signalling pathway for adaptation. This is the first study where selection signatures are identified using ddRAD-seq in indicine cattle breeds. The study shall help in conservation and leveraging genetic improvements in Gir and Tharparkar cattle.
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Affiliation(s)
- Nidhi Sukhija
- ICAR-National Dairy Research Institute, Karnal, India
| | - Anoop Anand Malik
- TERI School of Advanced Studies, Delhi, India
- The Energy and Resources Institute, North Eastern Regional Centre, Guwahati, India
| | | | | | - Kangabam Bidyalaxmi
- ICAR-National Dairy Research Institute, Karnal, India
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - D Ravi Kumar
- ICAR-National Dairy Research Institute, Karnal, India
| | | | | | - K K Kanaka
- ICAR-National Dairy Research Institute, Karnal, India
- ICAR- Indian Institute of Agricultural Biotechnology, Ranchi, India
| | - Rekha Sharma
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | | | | | | | - Archana Verma
- ICAR-National Dairy Research Institute, Karnal, India
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Bayraktar M. Analysing the genetic diversity of three sheep breeds in Turkey and nearby countries using 50 K SNPs data. Anim Biotechnol 2024; 35:2329106. [PMID: 38497403 DOI: 10.1080/10495398.2024.2329106] [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: 03/19/2024]
Abstract
This study analysed the genetic diversity and population structure of eight sheep breeds in Turkey and nearby countries. Moderate genetic diversity was observed, with the Sakiz (SKZ) exhibiting the highest diversity based on heterozygosity and allelic richness (AR) values. Genetic distances revealed differentiation between the populations, with the most significant divergence between the Cyprus Fat Tail (CFT) and SKZ breeds. PCA demonstrated SKZ and Chios (CHI) clustering together, indicating genetic similarity. Karakas (KRS), Norduz (NDZ), Afshari (AFS), Moghani (MOG) and others showed overlap, reflecting genetic relationships. Ancestry analysis found that KRS was predominantly inherited from the second ancestral population, while SKZ and NDZ were primarily derived from the first and second ancestral lineages. This illustrated the populations' diverse origins. Most genetic variation (96.84%) was within, not between, populations. The phi-statistic (PhiPT) indicated moderate differentiation overall. Phylogenetic analysis further demonstrated the genetic distinctiveness of the SKZ breed. ROH and FROH analyses showed that SKZ exhibited the highest homozygosity and inbreeding, while KRS displayed the lowest. This study elucidates these breeds' genetic diversity, structure and relationships. Key findings include moderate diversity, evidence of differentiation between breeds, diverse ancestral origins and distinct ROH patterns. This provides insights into the population's genetic characteristics and conservation requirements.
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Affiliation(s)
- Mervan Bayraktar
- Department of Animal Science, Faculty of Agriculture, Çukurova University, Adana, Turkey
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Abeygunawardana DI, Ranasinghe RMSBK, De Silva SNT, Deshapriya RMC, Gamika PA, Rajapakse J. Prevalence of growth hormone receptor gene polymorphisms and their association with milk production and fertility-related traits of cross-bred dairy cows in Sri Lanka. Anim Biotechnol 2024; 35:2307012. [PMID: 38305036 DOI: 10.1080/10495398.2024.2307012] [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: 02/03/2024]
Abstract
This study investigated the association of selected growth hormone receptor (GHR) gene SNPs with selected fertility and milk production-related phenotypes of cross-bred dairy cows (n = 153) reared on three National Livestock Development Board farms in Sri Lanka. Selected cows were genetically screened for SNPs in the exon 08 (n = 153) and 5' upstream (n = 118) regions of the GHR gene using the target sequencing method. The relationships between different genotypes and fertility traits (average calving interval, average number of services per conception, and age at first calving) and milk production-related traits (average total lactation yield, average lactation length, and average milk yield) were analyzed using the General Linear Model in SPSS. Among the identified Four GHR SNPs, rs1099014416 was significantly associated with average calving interval and age at first calving. Cows with GG genotype exhibited younger age at first calving (918.51 ± 113.42 days) and longer calving intervals (543.41 ± 43.29 days) compared to cows with GT (1275.18 ± 38.31, 515.09 ± 24.49 days) and TT (1212.89 ± 88.22, 364.52 ± 54.01 days) genotypes. Other SNPs did not show associations with the studied traits. SNP rs109014416 has the potential to be used as a genetic marker for fertility-related traits in the selection of cross-bred dairy cows in Sri Lanka which should be validated with a larger population.
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Affiliation(s)
- Dameesha Indeewari Abeygunawardana
- Department of Basic Veterinary Sciences, Faculty of Veterinary Medicine and Animal Science, University of Peradeniya, Peradeniya, Sri Lanka
- Department of Livestock and Avian Sciences, Faculty of Livestock, Fisheries and Nutrition, Wayamba University of Sri Lanka, Makandura, Gonawila (NWP), Sri Lanka
| | | | | | | | - Prathapasinghe Arachchige Gamika
- Department of Livestock and Avian Sciences, Faculty of Livestock, Fisheries and Nutrition, Wayamba University of Sri Lanka, Makandura, Gonawila (NWP), Sri Lanka
| | - Jayanthe Rajapakse
- Department of Veterinary Pathobiology, Faculty of Veterinary Medicine and Animal Science, University of Peradeniya, Peradeniya, Sri Lanka
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Liu J, Zheng W, Wang W, Yang X, Huang Y, Cui P, Ma Z, Zeng X, Zhai R, Weng X, Wu W, Zhang X. Identification of AGO2 and PLEC genes polymorphisms in Hu sheep and their relationship with body size traits. Anim Biotechnol 2024; 35:2295926. [PMID: 38149679 DOI: 10.1080/10495398.2023.2295926] [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: 12/28/2023]
Abstract
The body size traits are major traits in livestock, which intuitively displays the development of the animal's bones and muscles. This study used PCR amplification, Sanger sequencing, KASPar genotyping, and quantitative real-time reverse transcription PCR (qRT-PCR) to analyze the Single-nucleotide polymorphism and expression characteristics of Argonaute RISC catalytic component 2 (AGO2) and Plectin (PLEC) genes in Hu sheep. Two intron mutations were found in Hu sheep, which were AGO2 g.51700 A > C and PLEC g.23157 C > T, respectively. Through association analysis of two mutation sites and body size traits, it was found that AGO2 g.51700 A > C mainly affects the chest and cannon circumference of Hu sheep of while PLEC g.23157 C mainly affects body height and body length. The combined genotypes of AGO2 and PLEC genes with body size traits showed SNPs at the AGO2 g.51700 A > C and PLEC g.23157 C > T loci significantly improved the body size traits of Hu sheep. In addition, the AGO2 gene has the highest expression levels in the heart, rumen, and tail fat, and the PLEC gene is highly expressed in the heart. These two loci can provide new research ideas for improving the body size traits of Hu sheep.
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Affiliation(s)
- Jia Liu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Wenxin Zheng
- Institute of Animal Husbandry Quality Standards, Xinjiang Academy of Animal Sciences, Urumqi, Xinjiang, China
| | - Weimin Wang
- The State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Xiaobin Yang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Yongliang Huang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Panpan Cui
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Zongwu Ma
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Xiwen Zeng
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Rui Zhai
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Xiuxiu Weng
- The State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Weiwei Wu
- Institute of Animal Science, Xinjiang Academy of Animal Sciences, Urumqi, Xinjiang, China
| | - Xiaoxue Zhang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
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Zhu Y, Lin Y, Gong B, Zhang Y, Su G, Yu Y. Dual toeholds regulated CRISPR-Cas12a sensing platform for ApoE single nucleotide polymorphisms genotyping. Biosens Bioelectron 2024; 255:116255. [PMID: 38565025 DOI: 10.1016/j.bios.2024.116255] [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: 12/24/2023] [Revised: 03/13/2024] [Accepted: 03/26/2024] [Indexed: 04/04/2024]
Abstract
Single nucleotide polymorphisms (SNPs) are closely associated with many biological processes, including genetic disease, tumorigenesis, and drug metabolism. Accurate and efficient SNP determination has been proved pivotal in pharmacogenomics and diagnostics. Herein, a universal and high-fidelity genotyping platform is established based on the dual toeholds regulated Cas12a sensing methodology. Different from the conventional single stranded or double stranded activation mode, the dual toeholds regulated mode overcomes protospacer adjacent motif (PAM) limitation via cascade toehold mediated strand displacement reaction, which is highly universal and ultra-specific. To enhance the sensitivity for biological samples analysis, a modified isothermal recombinant polymerase amplification (RPA) strategy is developed via utilizing deoxythymidine substituted primer and uracil-DNA glycosylase (UDG) treatment, designated as RPA-UDG. The dsDNA products containing single stranded toehold domain generated in the RPA-UDG allow further incorporation with dual toeholds regulated Cas12a platform for high-fidelity human sample genotyping. We discriminate all the single-nucleotide polymorphisms of ApoE gene at rs429358 and rs7412 loci with human buccal swab samples with 100% accuracy. Furthermore, we engineer visual readout of genotyping results by exploiting commercial lateral flow strips, which opens new possibilities for field deployable implementation.
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Affiliation(s)
- Yuedong Zhu
- School of Pharmacy, Nantong University, Nantong, Jiangsu, 226001, China
| | - Yanan Lin
- School of Pharmacy, Nantong University, Nantong, Jiangsu, 226001, China
| | - Bin Gong
- School of Pharmacy, Nantong University, Nantong, Jiangsu, 226001, China
| | - Yan Zhang
- School of Pharmacy, Nantong University, Nantong, Jiangsu, 226001, China
| | - Gaoxing Su
- School of Pharmacy, Nantong University, Nantong, Jiangsu, 226001, China.
| | - Yanyan Yu
- School of Pharmacy, Nantong University, Nantong, Jiangsu, 226001, China.
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Wang J, Gu R, Kong X, Luan S, Luo YLL. Genome-wide association studies (GWAS) and post-GWAS analyses of impulsivity: A systematic review. Prog Neuropsychopharmacol Biol Psychiatry 2024; 132:110986. [PMID: 38430953 DOI: 10.1016/j.pnpbp.2024.110986] [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: 09/26/2023] [Revised: 01/30/2024] [Accepted: 02/28/2024] [Indexed: 03/05/2024]
Abstract
Impulsivity is related to a host of mental and behavioral problems. It is a complex construct with many different manifestations, most of which are heritable. The genetic compositions of these impulsivity manifestations, however, remain unclear. A number of genome-wide association studies (GWAS) and post-GWAS analyses have tried to address this issue. We conducted a systematic review of all GWAS and post-GWAS analyses of impulsivity published up to December 2023. Available data suggest that single nucleotide polymorphisms (SNPs) in more than a dozen of genes (e.g., CADM2, CTNNA2, GPM6B) are associated with different measures of impulsivity at genome-wide significant levels. Post-GWAS analyses further show that different measures of impulsivity are subject to different degrees of genetic influence, share few genetic variants, and have divergent genetic overlap with basic personality traits such as extroversion and neuroticism, cognitive ability, psychiatric disorders, substance use, and obesity. These findings shed light on controversies in the conceptualization and measurement of impulsivity, while providing new insights on the underlying mechanisms that yoke impulsivity to psychopathology.
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Affiliation(s)
- Jiaqi Wang
- Key Laboratory of Mental Health, Institute of Psychology, Chinese Academy of Sciences, 16 Lincui Road, Beijing 100101, China; Department of Psychology, University of Chinese Academy of Sciences, 16 Lincui Road, Beijing 100101, China
| | - Ruolei Gu
- Department of Psychology, University of Chinese Academy of Sciences, 16 Lincui Road, Beijing 100101, China; Key Laboratory of Behavioral Science, Institute of Psychology, Chinese Academy of Sciences, 16 Lincui Road, Beijing 100101, China
| | - Xiangzhen Kong
- Department of Psychology and Behavioral Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China; Department of Psychiatry of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, 3 Qingchundong Road, Hangzhou 310016, China
| | - Shenghua Luan
- Department of Psychology, University of Chinese Academy of Sciences, 16 Lincui Road, Beijing 100101, China; Key Laboratory of Behavioral Science, Institute of Psychology, Chinese Academy of Sciences, 16 Lincui Road, Beijing 100101, China
| | - Yu L L Luo
- Key Laboratory of Mental Health, Institute of Psychology, Chinese Academy of Sciences, 16 Lincui Road, Beijing 100101, China; Department of Psychology, University of Chinese Academy of Sciences, 16 Lincui Road, Beijing 100101, China.
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Xiang X, Wang D, Leng J, Li N, Wei C. Association of adiponectin and its receptor gene polymorphisms with the risk of coronary heart disease in northern Guangxi. Cytokine 2024; 178:156567. [PMID: 38489870 DOI: 10.1016/j.cyto.2024.156567] [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: 11/21/2022] [Revised: 02/06/2024] [Accepted: 03/01/2024] [Indexed: 03/17/2024]
Abstract
OBJECTIVE To investigate the association of circulating adiponectin (APN) level and single nucleotide polymorphisms (rs1501299 and rs266729) of the APN gene in the coronary heart disease (CHD) population of Northern Guangxi Province. METHODS Two hundred and sixty-three CHD patients and 235 healthy controls from our hospital from August 2018 to October 2020 were included in this study. ELISA was used to determine the serum APN concentration. PCR-RFLP and direct DNA sequencing were used to analyze the genotypes of APN gene rs1501299 G/T and rs266729 C/G single-nucleotide loci, their distribution differences between the two groups were compared and their correlation with APN concentration was analyzed. RESULTS The serum APN concentration in the CHD group was significantly lower than the control group (14.40(1.42-52.26) μg/mL vs. 29.40 (3.18-90.31) μg/mL, P < 0.001). There were statistically significant differences in the rs266729 genotype of APN single nucleotide locus between the two groups (P < 0.001). The dominant model and recessive model of rs266729 genotype showed that mutant homozygous GG genotype carriers significantly increased the risk of CHD in comparison with C allele carriers (CG + CC) (OR = 2.156, 95 %CI: 1.004-4.631, P = 0.049), and this effect was still significant after adjusting gender and age (OR = 2.695, 95 %CI 1.110-6.540, P = 0.028). In both the dominant and recessive models for rs1501299, ORs before and after adjustment for age and sex revealed no significant association with CHD, with ORs of 0.765 (95 % CI: 0.537-1.091, P = 0.139) and 0.718 (95 % CI: 0.466-1.106, P = 0.133) in the Dominant model, and ORs of 0.960 (95 % CI: 0.442-2.087, P = 0.918) and 0.613 (95 % CI: 0.239-1.570, P = 0.308) in the Recessive model, respectively. No statistically significant differences in APN concentrations across genotypes in both groups (P > 0.05), with chi-square values of 1.633 (control group) and 0.823 (CHD group) for rs1501299, and 1.354 (control group) and 0.618 (CHD group) for rs266729. CONCLUSIONS APN gene of rs266729 C/G single-nucleotide loci gene mutation can significantly increase the risk of CHD. There was no significant correlation between rs1501299 G/T single-nucleotide loci and CHD in Northern Guangxi populations.
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Affiliation(s)
- Xiaohua Xiang
- Department of Laboratory Medicine, Shenzhen Guangming District People's Hospital, Shenzhen 518106, Guangdong Province, China; Department of Laboratory Medicine, The Second Affiliated Hospital of Guilin Medical University, Guilin 541199, Guangxi Province, China.
| | - Di Wang
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guilin Medical University, Guilin 541199, Guangxi Province, China
| | - Jun Leng
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guilin Medical University, Guilin 541199, Guangxi Province, China
| | - Ning Li
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guilin Medical University, Guilin 541199, Guangxi Province, China
| | - Chuandong Wei
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guilin Medical University, Guilin 541199, Guangxi Province, China.
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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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Zhu Y, Zhou X, Jia J, Xue Q. Causal associations between 25-hydroxyvitamin D levels and NMOSD: a two-Sample Mendelian randomization analysis. Neurol Sci 2024; 45:2379-2381. [PMID: 38175315 DOI: 10.1007/s10072-023-07290-x] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 12/22/2023] [Indexed: 01/05/2024]
Affiliation(s)
- Yunfei Zhu
- Department of Neurology, First Affiliated Hospital of Soochow University, Suzhou, 215000, Jiangsu, China
| | - Xiaoling Zhou
- Department of Neurology, Suzhou Municipal Hospital, Suzhou, 215000, Jiangsu, China
| | - Jingjin Jia
- Department of Neurology, First Affiliated Hospital of Soochow University, Suzhou, 215000, Jiangsu, China
| | - Qun Xue
- Department of Neurology, First Affiliated Hospital of Soochow University, Suzhou, 215000, Jiangsu, China.
- Suzhou Clinical Medical Centre, Suzhou, 215000, Jiangsu, China.
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Chang X, Qu H, Liu Y, Glessner J, Hakonarson H. A Protective Role of Low Polygenic Risk Score in Healthy Individuals Carrying Attention-Deficit/Hyperactivity Disorder-Associated Copy Number Variations. Biol Psychiatry 2024; 95:881-887. [PMID: 37865391 DOI: 10.1016/j.biopsych.2023.10.011] [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: 03/30/2023] [Revised: 09/22/2023] [Accepted: 10/11/2023] [Indexed: 10/23/2023]
Abstract
BACKGROUND Previous studies have implicated both rare copy number variations (CNVs) and common variants in liability for attention-deficit/hyperactivity disorder (ADHD). However, how common and rare genetic variants jointly contribute to individual liability requires further investigation in larger cohorts. METHODS This study comprises 9385 participants of European descent and 7810 participants of African American ancestry who were recruited from the greater Philadelphia area by the Children's Hospital of Philadelphia. The polygenic risk score (PRS) of each participant was estimated by linkage disequilibrium pruning and p-value thresholding (P + T) methods using PRSice-2. We investigated whether the risk of ADHD follows a polygenic liability threshold model wherein 1) the risk of ADHD requires less contribution from common variants in the presence of a rare CNV, and 2) control carriers of ADHD-associated CNVs have lower common risk allele burden than noncarriers. RESULTS CNVs previously reported in ADHD cases were significantly associated with ADHD risk in both the European American cohort and the African American cohort. Healthy control participants carrying those same risk CNVs had lower PRSs than those without risk CNVs in the European American cohort. This result was replicated in the African American cohort. However, PRSs were not significantly different in case participants carrying risk CNVs versus those without risk CNVs. CONCLUSIONS These findings provide evidence in support of interactive effects of PRS and ADHD-associated CNVs on disease risk and add novel insights into the genetic basis of ADHD by highlighting a protective role of low PRS in ADHD.
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Affiliation(s)
- Xiao Chang
- College of Artificial Intelligence and Big Data for Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, Shandong, China; Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.
| | - Huiqi Qu
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Yichuan Liu
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Joseph Glessner
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Hakon Hakonarson
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania; Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Division of Human Genetics, Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Faculty of Medicine, University of Iceland, Reykjavik, Iceland.
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13
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Shams SF, Mehrad-Majd H. TNFα-308G>A Polymorphism and Susceptibility to Immune Thrombocytopenia Purpura (ITP): Evidence From a Systematic Review and Meta-analysis. Cytokine 2024; 177:156538. [PMID: 38368694 DOI: 10.1016/j.cyto.2024.156538] [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: 11/18/2023] [Accepted: 02/03/2024] [Indexed: 02/20/2024]
Abstract
BACKGROUND Relation between the emergence of ITP and the presence of TNFα 308G/A polymorphism in the involved individuals has been studied by previous researchers in different ethnicity, but a definite result was not gained. So, this meta-analysis was performed to find an absolute answer to the question whether TNF-α-308G/A polymorphism is a susceptibility factor for ITP or not? METHODS Electronic databases including PubMed, Google scholar, and Science Direct were searched and case control studies compatible to the defined inclusion criteria were selected; their references were also evaluated manually. Pooled OR with 95 % confidence intervals (CIs) as a strength of association between TNF-α-308G/A polymorphism and risk of ITP were calculated using a random-effect model. Funnel plot and Egger's linear regression test were conducted to examine the risk of publication bias. RESULTS Totally, 16 eligible articles were found involving 1470 ITP cases and 2324 healthy controls. The Meta-results revealed that TNFα 308G/A polymorphism is associated with increased risk of ITP under the genetic models of recessive (OR: 1.54, 95 % CI: 1.03-2.29), dominant (OR: 2.29, 95 % CI: 1.44-3.64), and the heterozygote (OR: 2.46, 95 % CI:1.49-4.6). Subgroup analysis suggested a remarkable role for this SNP as a risk factor in the Caucasian ethnicity and the chronic subtype. CONCLUSION TNFα 308G/A polymorphism can be an ITP susceptibility factor in the Caucasian population and the chronic subtype. Although more studies in large scale are needed for clinical decision but this finding can be used in the clinical trials to prevent the ITP consequences in the involved individuals.
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Affiliation(s)
- Seyyede Fatemeh Shams
- Department of Hematology and Blood Banking, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran; Cancer Molecular Pathology Research Centre, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Hassan Mehrad-Majd
- Cancer Molecular Pathology Research Centre, Mashhad University of Medical Sciences, Mashhad, Iran; Clinical Research Development Unit, Ghaem Hospital, Mashhad University of Medical Sciences, Mashhad, Iran.
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14
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Souza-Teodoro LH, Davies NM, Warren HR, Andrade LHSG, Carvalho LA. DHEA and response to antidepressant treatment: A Mendelian Randomization analysis. J Psychiatr Res 2024; 173:151-156. [PMID: 38531145 DOI: 10.1016/j.jpsychires.2024.02.049] [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: 03/09/2023] [Revised: 02/02/2024] [Accepted: 02/21/2024] [Indexed: 03/28/2024]
Abstract
Treatment response is hard to predict and detailed mechanisms unknown. Lower levels of the dehydroepiandrosterone sulphate (DHEA(S)) - a precursor to testosterone and estrogen - have been associated to depression and to response to antidepressant treatment. Previous studies however may have been ridden by confounding and reverse causation. The aim of this study is to evaluate whether higher levels of DHEA(S) are causally linked to response to antidepressants using mendelian randomization (MR). We performed a Two-sample MR analysis using data the largest publicly available GWAS of DHEA(S) levels (n = 14,846) using eight common genetic variants associated to DHEA(S) (seven single nucleotide polymorphisms and one variant rs2497306) and the largest GWAS of antidepressant response (n = 5218) using various MR methods (IVW, MR Egger, Weighted mean, weighted mode, MR-PRESSO) and single SNP analysis. We further investigated for pleiotropy conducting a look up on PhenoScanner and GWAS Catalog. Results show no evidence for DHEA(S) gene risk score from any of MR methods, however, we found a significant association on individual variant analysis for rs11761538, rs17277546, and rs2497306. There was some evidence for heterogeneity and pleiotropy. This is the first paper to show some evidence for a causal association of genetically-predicted DHEA and improvement of depressive symptoms. The effect is not a simple linear effect, and we were unable to dissect whether the effect was direct effect of DHEA(S), mediated by DHEA(S) or on the pathway is not yet clear. Further studies using more refined instrumental variables will help clarify this association.
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Affiliation(s)
- L H Souza-Teodoro
- William Harvey Research Institute, Charterhouse Square, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, EC1M 6BQ, UK; Núcleo de Epidemiologia Psiquiatrica, Instituto de Psiquiatria, Hospital das Clínicas da Faculdade de Medicina da Universidade de Sao Paulo, Brazil
| | - N M Davies
- Division of Psychiatry, University College London, UK; K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, Norwegian University of Science and Technology, Norway; Department of Statistical Sciences, University College London, London, UK
| | - H R Warren
- William Harvey Research Institute, Charterhouse Square, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, EC1M 6BQ, UK; NIHR Cardiovascular Biomedical Research Centre, Barts and the London Faculty of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - L H S G Andrade
- Núcleo de Epidemiologia Psiquiatrica, Instituto de Psiquiatria, Hospital das Clínicas da Faculdade de Medicina da Universidade de Sao Paulo, Brazil
| | - L A Carvalho
- William Harvey Research Institute, Charterhouse Square, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, EC1M 6BQ, UK.
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15
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Johnston KJA, Cote AC, Hicks E, Johnson J, Huckins LM. Genetically Regulated Gene Expression in the Brain Associated With Chronic Pain: Relationships With Clinical Traits and Potential for Drug Repurposing. Biol Psychiatry 2024; 95:745-761. [PMID: 37678542 PMCID: PMC10924073 DOI: 10.1016/j.biopsych.2023.08.023] [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: 12/28/2022] [Revised: 07/20/2023] [Accepted: 08/28/2023] [Indexed: 09/09/2023]
Abstract
BACKGROUND Chronic pain is a common, poorly understood condition. Genetic studies including genome-wide association studies have identified many relevant variants, which have yet to be translated into full understanding of chronic pain. Transcriptome-wide association studies using transcriptomic imputation methods such as S-PrediXcan can help bridge this genotype-phenotype gap. METHODS We carried out transcriptomic imputation using S-PrediXcan to identify genetically regulated gene expression associated with multisite chronic pain in 13 brain tissues and whole blood. Then, we imputed genetically regulated gene expression for over 31,000 Mount Sinai BioMe participants and performed a phenome-wide association study to investigate clinical relationships in chronic pain-associated gene expression changes. RESULTS We identified 95 experiment-wide significant gene-tissue associations (p < 7.97 × 10-7), including 36 unique genes and an additional 134 gene-tissue associations reaching within-tissue significance, including 53 additional unique genes. Of the 89 unique genes in total, 59 were novel for multisite chronic pain and 18 are established drug targets. Chronic pain genetically regulated gene expression for 10 unique genes was significantly associated with cardiac dysrhythmia, metabolic syndrome, disc disorders/dorsopathies, joint/ligament sprain, anemias, and neurologic disorder phecodes. Phenome-wide association study analyses adjusting for mean pain score showed that associations were not driven by mean pain score. CONCLUSIONS We carried out the largest transcriptomic imputation study of any chronic pain trait to date. Results highlight potential causal genes in chronic pain development and tissue and direction of effect. Several gene results were also drug targets. Phenome-wide association study results showed significant associations for phecodes including cardiac dysrhythmia and metabolic syndrome, thereby indicating potential shared mechanisms.
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Affiliation(s)
- Keira J A Johnston
- Department of Psychiatry, Yale University School of Medicine, New Haven, Connecticut.
| | - Alanna C Cote
- Pamela Sklar Division of Psychiatric Genetics, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Emily Hicks
- Pamela Sklar Division of Psychiatric Genetics, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Jessica Johnson
- School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Laura M Huckins
- Department of Psychiatry, Yale University School of Medicine, New Haven, Connecticut.
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16
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Dipta B, Sood S, Mangal V, Bhardwaj V, Thakur AK, Kumar V, Singh B. KASP: a high-throughput genotyping system and its applications in major crop plants for biotic and abiotic stress tolerance. Mol Biol Rep 2024; 51:508. [PMID: 38622474 DOI: 10.1007/s11033-024-09455-z] [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: 12/17/2023] [Accepted: 03/18/2024] [Indexed: 04/17/2024]
Abstract
Advances in plant molecular breeding have resulted in the development of new varieties with superior traits, thus improving the crop germplasm. Breeders can screen a large number of accessions without rigorous and time-consuming phenotyping by marker-assisted selection (MAS). Molecular markers are one of the most imperative tools in plant breeding programmes for MAS to develop new cultivars possessing multiple superior traits. Single nucleotide polymorphisms (SNPs) are ideal for MAS due to their low cost, low genotyping error rates, and reproducibility. Kompetitive Allele Specific PCR (KASP) is a globally recognized technology for SNP genotyping. KASP is an allele-specific oligo extension-based PCR assay that uses fluorescence resonance energy transfer (FRET) to detect genetic variations such as SNPs and insertions/deletions (InDels) at a specific locus. Additionally, KASP allows greater flexibility in assay design, which leads to a higher success rate and the capability to genotype a large population. Its versatility and ease of use make it a valuable tool in various fields, including genetics, agriculture, and medical research. KASP has been extensively used in various plant-breeding applications, such as the identification of germplasm resources, quality control (QC) analysis, allele mining, linkage mapping, quantitative trait locus (QTL) mapping, genetic map construction, trait-specific marker development, and MAS. This review provides an overview of the KASP assay and emphasizes its validation in crop improvement related to various biotic and abiotic stress tolerance and quality traits.
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Affiliation(s)
- Bhawna Dipta
- ICAR-Central Potato Research Institute, Bemloe, Shimla, Himachal Pradesh, 171001, India
| | - Salej Sood
- ICAR-Central Potato Research Institute, Bemloe, Shimla, Himachal Pradesh, 171001, India.
| | - Vikas Mangal
- ICAR-Central Potato Research Institute, Bemloe, Shimla, Himachal Pradesh, 171001, India
| | - Vinay Bhardwaj
- ICAR-National Research Centre on Seed Spices, Tabiji, Ajmer, Rajasthan, 305206, India
| | - Ajay Kumar Thakur
- ICAR-Central Potato Research Institute, Bemloe, Shimla, Himachal Pradesh, 171001, India
| | - Vinod Kumar
- ICAR-Central Potato Research Institute, Bemloe, Shimla, Himachal Pradesh, 171001, India
| | - Brajesh Singh
- ICAR-Central Potato Research Institute, Bemloe, Shimla, Himachal Pradesh, 171001, India
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Jakwerth CA, Weckmann M, Illi S, Charles H, Zissler UM, Oelsner M, Guerth F, Omony J, Nemani SSP, Grychtol R, Dittrich AM, Skevaki C, Foth S, Weber S, Alejandre Alcazar MA, van Koningsbruggen-Rietschel S, Brock R, Blau S, Hansen G, Bahmer T, Rabe KF, Brinkmann F, Kopp MV, Chaker AM, Schaub B, von Mutius E, Schmidt-Weber CB. 17q21 Variants Disturb Mucosal Host Defense in Childhood Asthma. Am J Respir Crit Care Med 2024; 209:947-959. [PMID: 38064241 DOI: 10.1164/rccm.202305-0934oc] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 12/07/2023] [Indexed: 03/13/2024] Open
Abstract
Rationale: The strongest genetic risk factor for childhood-onset asthma, the 17q21 locus, is associated with increased viral susceptibility and disease-promoting processes.Objectives: To identify biological targets underlying the escalated viral susceptibility associated with the clinical phenotype mediated by the 17q21 locus.Methods: Genome-wide transcriptome analysis of nasal brush samples from 261 children (78 healthy, 79 with wheezing at preschool age, 104 asthmatic) within the ALLIANCE (All-Age-Asthma) cohort, with a median age of 10.0 (range, 1.0-20.0) years, was conducted to explore the impact of their 17q21 genotype (SNP rs72163891). Concurrently, nasal secretions from the same patients and visits were collected, and high-sensitivity mesoscale technology was employed to measure IFN protein levels.Measurements and Main Results: This study revealed that the 17q21 risk allele induces a genotype- and asthma/wheeze phenotype-dependent enhancement of mucosal GSDMB expression as the only relevant 17q21-encoded gene in children with preschool wheeze. Increased GSDMB expression correlated with the activation of a type-1 proinflammatory, cell-lytic immune, and natural killer signature, encompassing key genes linked to an IFN type-2-signature (IFNG, CXCL9, CXCL10, KLRC1, CD8A, GZMA). Conversely, there was a reduction in IFN type 1 and type 3 expression signatures at the mRNA and protein levels.Conclusions: This study demonstrates a novel disease-driving mechanism induced by the 17q21 risk allele. Increased mucosal GSDMB expression is associated with a cell-lytic immune response coupled with compromised airway immunocompetence. These findings suggest that GSDMB-related airway cell death and perturbations in the mucosal IFN signature account for the increased vulnerability of 17q21 risk allele carriers to respiratory viral infections during early life, opening new options for future biological interventions.The All-Age-Asthma (ALLIANCE) cohort is registered at www.clinicaltrials.gov (pediatric arm, NCT02496468).
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Affiliation(s)
- Constanze A Jakwerth
- Center of Allergy and Environment (ZAUM), Technical University and Helmholtz Center Munich, Munich, Germany
- Member of the German Center for Lung Research (DZL), Germany
| | - Markus Weckmann
- Member of the German Center for Lung Research (DZL), Germany
- Division of Epigenetics in Chronic Lung Disease, Priority Area Chronic Lung Diseases, Research Center Borstel-Leibniz Lung Center, Borstel, Germany
- Department of Pediatric Pneumology and Allergology, University Medical Center Schleswig-Holstein, Lübeck, Germany
- Airway Research Center North, Borstel, Lübeck, Kiel, Grosshansdorf, Germany
| | - Sabina Illi
- Member of the German Center for Lung Research (DZL), Germany
- Institute for Asthma and Allergy Prevention, Helmholtz Center Munich, German Research Center for Environmental Health, Munich, Germany
- Comprehensive Pneumology Center-Munich, Munich, Germany
| | - Helen Charles
- Center of Allergy and Environment (ZAUM), Technical University and Helmholtz Center Munich, Munich, Germany
- Member of the German Center for Lung Research (DZL), Germany
| | - Ulrich M Zissler
- Center of Allergy and Environment (ZAUM), Technical University and Helmholtz Center Munich, Munich, Germany
- Member of the German Center for Lung Research (DZL), Germany
| | - Madlen Oelsner
- Center of Allergy and Environment (ZAUM), Technical University and Helmholtz Center Munich, Munich, Germany
- Member of the German Center for Lung Research (DZL), Germany
| | - Ferdinand Guerth
- Center of Allergy and Environment (ZAUM), Technical University and Helmholtz Center Munich, Munich, Germany
- Member of the German Center for Lung Research (DZL), Germany
| | - Jimmy Omony
- Member of the German Center for Lung Research (DZL), Germany
- Institute for Asthma and Allergy Prevention, Helmholtz Center Munich, German Research Center for Environmental Health, Munich, Germany
- Comprehensive Pneumology Center-Munich, Munich, Germany
| | - Sai Sneha Priya Nemani
- Member of the German Center for Lung Research (DZL), Germany
- Department of Pediatric Pneumology and Allergology, University Medical Center Schleswig-Holstein, Lübeck, Germany
- Airway Research Center North, Borstel, Lübeck, Kiel, Grosshansdorf, Germany
| | - Ruth Grychtol
- Member of the German Center for Lung Research (DZL), Germany
- Department of Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hanover, Germany
- Biomedical Research in Endstage and Obstructive Lung Disease Hannover, Hanover, Germany
| | - Anna-Maria Dittrich
- Member of the German Center for Lung Research (DZL), Germany
- Department of Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hanover, Germany
- Biomedical Research in Endstage and Obstructive Lung Disease Hannover, Hanover, Germany
| | - Chrysanthi Skevaki
- Member of the German Center for Lung Research (DZL), Germany
- Institute of Laboratory Medicine and Pathobiochemistry, Molecular Diagnostics and
| | - Svenja Foth
- Member of the German Center for Lung Research (DZL), Germany
- Universities of Giessen and Marburg Lung Center, Philipps University Marburg and University Children's Hospital Marburg, University of Marburg, Marburg, Germany
| | - Stefanie Weber
- Member of the German Center for Lung Research (DZL), Germany
- Universities of Giessen and Marburg Lung Center, Philipps University Marburg and University Children's Hospital Marburg, University of Marburg, Marburg, Germany
| | - Miguel A Alejandre Alcazar
- Member of the German Center for Lung Research (DZL), Germany
- Institute for Lung Health and Cardio-Pulmonary Institute, Universities of Giessen and Marburg Lung Center, Giessen, Germany
- Translational Experimental Pediatrics, Experimental Pulmonology, Department of Pediatrics
- Center for Molecular Medicine Cologne and Cologne Excellence Cluster on Stress Responses in Aging-associated Diseases, and
- Pediatric Pulmonology and Allergology, Department of Pediatrics, Faculty of Medicine, University of Cologne and University Hospital Cologne, Cologne, Germany; and
| | - Silke van Koningsbruggen-Rietschel
- Member of the German Center for Lung Research (DZL), Germany
- Pediatric Pulmonology and Allergology, Department of Pediatrics, Faculty of Medicine, University of Cologne and University Hospital Cologne, Cologne, Germany; and
| | - Robert Brock
- Member of the German Center for Lung Research (DZL), Germany
- Pediatric Pulmonology and Allergology, Department of Pediatrics, Faculty of Medicine, University of Cologne and University Hospital Cologne, Cologne, Germany; and
| | - Samira Blau
- Member of the German Center for Lung Research (DZL), Germany
- Pediatric Pulmonology and Allergology, Department of Pediatrics, Faculty of Medicine, University of Cologne and University Hospital Cologne, Cologne, Germany; and
| | - Gesine Hansen
- Member of the German Center for Lung Research (DZL), Germany
- Department of Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hanover, Germany
- Biomedical Research in Endstage and Obstructive Lung Disease Hannover, Hanover, Germany
- Cluster of Excellence 2115 (RESIST), Hannover Medical School, Hanover, Germany
| | - Thomas Bahmer
- Member of the German Center for Lung Research (DZL), Germany
- Airway Research Center North, Borstel, Lübeck, Kiel, Grosshansdorf, Germany
- Internal Medicine Department I, University Hospital Schleswig-Holstein-Campus Kiel, Kiel, Germany
| | - Klaus F Rabe
- Member of the German Center for Lung Research (DZL), Germany
- Airway Research Center North, Borstel, Lübeck, Kiel, Grosshansdorf, Germany
- LungenClinic Grosshansdorf GmbH and Medical Clinics, Christian Albrechts University, Kiel, Germany
| | - Folke Brinkmann
- Member of the German Center for Lung Research (DZL), Germany
- Division of Epigenetics in Chronic Lung Disease, Priority Area Chronic Lung Diseases, Research Center Borstel-Leibniz Lung Center, Borstel, Germany
- Department of Pediatric Pneumology and Allergology, University Medical Center Schleswig-Holstein, Lübeck, Germany
- Airway Research Center North, Borstel, Lübeck, Kiel, Grosshansdorf, Germany
| | - Matthias Volkmar Kopp
- Department of Pediatric Pneumology and Allergology, University Medical Center Schleswig-Holstein, Lübeck, Germany
- Pediatric Respiratory Medicine, Department of Pediatrics, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Airway Research Center North, Borstel, Lübeck, Kiel, Grosshansdorf, Germany
| | - Adam M Chaker
- Center of Allergy and Environment (ZAUM), Technical University and Helmholtz Center Munich, Munich, Germany
- Department of Otorhinolaryngology and Head and Neck Surgery, Medical School, Technical University of Munich, Munich, Germany
| | - Bianca Schaub
- Member of the German Center for Lung Research (DZL), Germany
- Dr. von Hauner Children's Hospital, Ludwig Maximilians University, Munich, Germany
- Comprehensive Pneumology Center-Munich, Munich, Germany
| | - Erika von Mutius
- Member of the German Center for Lung Research (DZL), Germany
- Institute for Asthma and Allergy Prevention, Helmholtz Center Munich, German Research Center for Environmental Health, Munich, Germany
- Dr. von Hauner Children's Hospital, Ludwig Maximilians University, Munich, Germany
| | - Carsten B Schmidt-Weber
- Center of Allergy and Environment (ZAUM), Technical University and Helmholtz Center Munich, Munich, Germany
- Member of the German Center for Lung Research (DZL), Germany
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Parveen A, Batool A, Wajid A, Mukhtar M, Khan KU, Zahid A, Jabeen A, Sahibzada KI. Delving the vitamin D receptor variation and expression profiles in the context of type 2 diabetes among families. Mol Biol Rep 2024; 51:514. [PMID: 38622480 DOI: 10.1007/s11033-024-09387-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Accepted: 02/26/2024] [Indexed: 04/17/2024]
Abstract
BACKGROUND Vitamin D is essential for insulin secretion and sensitivity. Consequently, its inadequacy is linked to higher insulin resistance and Type 2 Diabetes (T2D). The Vitamin D receptor (VDR) gene is one potential candidate for T2D, and multiple polymorphisms in VDR have been examined in various populations, but no conclusive answers have been provided. OBJECTIVES This study was designed to evaluate the susceptibility of VDR gene polymorphism and its expression in diabetic families in Pakistan. METHODOLOGY In this family-based study, twenty diabetic families with a positive family history of T2D and at least three T2D patients were recruited from outpatient clinics and public hospitals. The current study comprised 143 individuals with 55 affected and 88 unaffected individuals. Blood samples of the selected families were collected. DNA was extracted from the collected samples and the PCR-RFLP method was followed to identify the genotyping and RT-qPCR for expression. Phenotypic and genotypic pedigrees of the families were developed by the progeny online tool. The association values of SNPs were determined by TDT and DFAM analysis implemented on Plink software. RESULTS The results explained a significant familial aggregation among phenotypic characters including Age, Gender, BMI (body mass index), age of disease diagnosis, disease duration, and blood pressure in the probands, affected FDRs (First Degree Relatives) and affected SDRs (Second Degree Relatives). A significant association of rs731236 C/T (OR = 1.522), rs2228570 C/T (OR = 1.327) with p < 0.05. Whereas, for rs1544410 G/A (OR = 0.9706) and rs7975232 T/G (OR = 0.7368) no considerable association evidence was seen (p > 0.05) in families. The mRNA expression of VDR increased threefold (p = 0.0204) in patients compared to controls. Variation-based expression analysis exhibited that the rs2228570 genotype influences the expression. CONCLUSION A linkage was found among the FDRs with probands. Variation in the gene VDR at loci rs731236 and rs2228570 was associated with familial T2D. However further research is required to explore more genetic factors that could influence T2D risks in families.
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Affiliation(s)
- Asia Parveen
- Department of Zoology, Government College University, Lahore, Pakistan
| | - Andleeb Batool
- Department of Zoology, Government College University, Lahore, Pakistan.
| | - Abdul Wajid
- Balochistan University of Information Technology Engineering and Management Sciences, Quetta, Pakistan
| | - Maryam Mukhtar
- Department of Zoology, Government College University, Lahore, Pakistan
- Department of Zoology, University of the Punjab, Lahore, Pakistan
| | - Khajid Ullah Khan
- Department of Zoology, Government College University, Lahore, Pakistan
| | - Aqsa Zahid
- Department of Zoology, Government College University, Lahore, Pakistan
| | - Anjum Jabeen
- Department of Zoology, Government College University, Lahore, Pakistan
| | - Kashif Iqbal Sahibzada
- Department of Health Professional Technologies, Faculty of Allied Health Sciences, University of Lahore, Lahore, Pakistan
- School of Bioengineering, Henan University of Technology, Zhengzhou, China
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Choi J, Lee SM, Norwitz ER, Kim JH, Jung YM, Park CW, Jun JK, Lee D, Jin Y, Kim S, Cha B, Park JS, Kim JI. Placental expression quantitative trait loci in an East Asian population. HGG Adv 2024; 5:100276. [PMID: 38310352 PMCID: PMC10883826 DOI: 10.1016/j.xhgg.2024.100276] [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: 08/11/2023] [Revised: 01/29/2024] [Accepted: 01/29/2024] [Indexed: 02/05/2024] Open
Abstract
Expression quantitative trait loci (eQTL) analysis measures the contribution of genetic variation in gene expression on complex traits. Although this methodology has been used to examine gene regulation in numerous human tissues, eQTL research in solid tissues is relatively lacking. We conducted eQTL analysis on placentas collected from an East Asian population in an effort to identify gene regulatory mechanisms in this tissue. Placentas (n = 102) were collected at the time of cesarean delivery. mRNA was extracted, sequenced with NGS, and compared with matched maternal and fetal DNA arrays performed using maternal and neonatal cord blood. Linear regression modeling was performed using tensorQTL. Fine-mapping along with epigenomic annotation was used to select putative functional variants. We identified 2,703 coding genes that contained at least one eQTL with statistical significance (false discovery rate <0.05). After fine-mapping, we found 108 previously unreported eQTL variants with posterior inclusion probability >0.1. Of these, 19% were located in genomic regions with evidence from public placental epigenome suggesting that they may be functionally relevant. For example, variant rs28379289 located in the placenta-specific regulatory region changes the binding affinity of transcription factor leading to higher expression of LGALS3, which is known to affect placental function. This study expands the knowledge base of regulatory elements within the human placenta and identifies 108 previously unreported placenta eQTL signals, which are listed in our publicly available GMI eQTL database. Further studies are needed to identify and characterize genetic regulatory mechanisms that affect placental function in normal pregnancy and placenta-related diseases.
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Affiliation(s)
- Jaeyong Choi
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Korea; Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul, Korea
| | - Seung Mi Lee
- Department of Obstetrics and Gynecology, Seoul National University College of Medicine, Seoul, Korea
| | | | - Ji Hoi Kim
- Department of Obstetrics and Gynecology, Seoul National University College of Medicine, Seoul, Korea
| | - Young Mi Jung
- Department of Obstetrics and Gynecology, Seoul National University College of Medicine, Seoul, Korea
| | - Chan-Wook Park
- Department of Obstetrics and Gynecology, Seoul National University College of Medicine, Seoul, Korea
| | - Jong Kwan Jun
- Department of Obstetrics and Gynecology, Seoul National University College of Medicine, Seoul, Korea
| | - Dakyung Lee
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Korea; Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul, Korea
| | - Yongjoon Jin
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Korea; Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul, Korea
| | - Sookyung Kim
- Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul, Korea
| | - Bukyoung Cha
- Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul, Korea
| | - Joong Shin Park
- Department of Obstetrics and Gynecology, Seoul National University College of Medicine, Seoul, Korea.
| | - Jong-Il Kim
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Korea; Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul, Korea.
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Xiong Z, Thach TQ, Zhang YD, Sham PC. Improved estimation of functional enrichment in SNP heritability using feasible generalized least squares. HGG Adv 2024; 5:100272. [PMID: 38327050 PMCID: PMC10901842 DOI: 10.1016/j.xhgg.2024.100272] [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: 11/06/2023] [Revised: 01/23/2024] [Accepted: 01/23/2024] [Indexed: 02/09/2024] Open
Abstract
Functional enrichment results typically implicate tissue or cell-type-specific biological pathways in disease pathogenesis and as therapeutic targets. We propose generalized linkage disequilibrium score regression (g-LDSC) that requires only genome-wide association studies (GWASs) summary-level data to estimate functional enrichment. The method adopts the same assumptions and regression model formulation as stratified linkage disequilibrium score regression (s-LDSC). Although s-LDSC only partially uses LD information, our method uses the whole LD matrix, which accounts for possible correlated error structure via a feasible generalized least-squares estimation. We demonstrate through simulation studies under various scenarios that g-LDSC provides more precise estimates of functional enrichment than s-LDSC, regardless of model misspecification. In an application to GWAS summary statistics of 15 traits from the UK Biobank, estimates of functional enrichment using g-LDSC were lower and more realistic than those obtained from s-LDSC. In addition, g-LDSC detected more significantly enriched functional annotations among 24 functional annotations for the 15 traits than s-LDSC (118 vs. 51).
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Affiliation(s)
- Zewei Xiong
- Department of Psychiatry, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Thuan-Quoc Thach
- Department of Psychiatry, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Yan Dora Zhang
- Department of Statistics and Actuarial Science, The University of Hong Kong, Hong Kong SAR, China; Centre for PanorOmic Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China.
| | - Pak Chung Sham
- Department of Psychiatry, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China; Centre for PanorOmic Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China; State Key Laboratory of Brain and Cognitive Sciences, The University of Hong Kong, Hong Kong SAR, China.
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21
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Zou X, Zhang J, Wang Y, Zhou D, Deng G, Liu Z. IGF-1 rs6218 polymorphisms modulate the susceptibility to age-related cataract. PeerJ 2024; 12:e17220. [PMID: 38618568 PMCID: PMC11011587 DOI: 10.7717/peerj.17220] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 03/20/2024] [Indexed: 04/16/2024] Open
Abstract
Background Single nucleotide polymorphisms (SNPs), as the most abundant form of DNA variation in the human genome, contribute to age-related cataracts (ARC) development. Apoptosis of lens epithelial cells (LECs) is closely related to ARC formation. Insulin-like growth factor 1 (IGF1) contributes to cell apoptosis regulation. Moreover, IGF1 was indicated to exhibit a close association with cataract formation. Afterward, an investigation was conducted to examine the correlation between polymorphisms in IGF1 and the susceptibility to ARC. Methods The present investigation was a case-control study. Venous blood draws were collected from the participants for DNA genotyping. Lens capsule samples were collected to detect mRNA and apoptosis. TaqMan RT-PCR was used to detect IGF1 polymorphism genotypes and qRT PCR was used to detect IGF1 mRNA levels in LECs. LEC apoptosis was evaluated through flow cytometry. The chi-square test was used to compare differences between ARCs and controls of each SNP. Results We found that the G allele frequency in the IGF1-rs6218 was higher in the ARCs than in the controls. Furthermore, it was observed that the rs6218 GG genotype exhibited a positive correlation to elevated levels of IGF1 mRNA in LECs. The IGF1 mRNA in the LECs and the apoptosis of LECs in nuclear type of ARCs (ARNC) was higher than the controls. Conclusion The susceptibility to ARC was related to IGF1-rs6218 polymorphism, and this polymorphism is associated with IGF1 expression at the mRNA level. Moreover, apoptosis in LECs of ARNCs was found to be increased.
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Affiliation(s)
- Xi Zou
- Changzhou Medical Center, Changzhou, China
- The Third People’s Hospital of Changzhou, Changzhou, China
| | - Jun Zhang
- The Third People’s Hospital of Changzhou, Changzhou, China
| | - Yong Wang
- Nantong First People’s Hospital, Nantong, China
| | - Dong Zhou
- The Third People’s Hospital of Changzhou, Changzhou, China
| | - Guohua Deng
- The Third People’s Hospital of Changzhou, Changzhou, China
| | - Zhinan Liu
- The Third People’s Hospital of Changzhou, Changzhou, China
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Galal ER, Abdelhakam DA, Ahmed LK, Elhusseny Y, Sayed SEP, Eltaweel NH. The association of FSCN1 (rs852479, rs1640233) and HOTAIR (rs920778) polymorphisms with the risk of breast cancer in Egyptian women. Mol Biol Rep 2024; 51:495. [PMID: 38587571 PMCID: PMC11001669 DOI: 10.1007/s11033-024-09459-9] [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: 02/22/2024] [Accepted: 03/19/2024] [Indexed: 04/09/2024]
Abstract
BACKGROUND Breast cancer (BC) is one of the most prevalent cancers that contribute to mortality among women worldwide. Despite contradictory findings, considerable evidence suggests that single nucleotide polymorphisms (SNPs) in the FSCN1 and HOTAIR genes may have a causative impact on the development of BC. This case-control study was conducted to evaluate the association of genotype frequency in FSCN1 rs852479, rs1640233, and HOTAIR rs920778 with susceptibility and prognosis of BC, as well as the impact of clinical stages and hormonal features. METHODS AND RESULTS FSCN1 (rs852479, rs1640233) and HOTAIR (rs920778) were genotyped using TaqMan real-time PCR assay in 200 BC patients and 200 cancer-free controls, all representing Egyptian women. Genotypic analyses in association with clinicopathological factors and disease risk were assessed. As a result, a significant association with BC risk was observed for CC genotype frequency of FSCN1 rs852479 A > C (OR = 0.395, 95% CI 0.204-0.76, p-value = 0.005). However, no significant correlation was detected between the FSCN1 rs1640233 C > T and HOTAIR rs920778 C > T polymorphic variants and susceptibility to BC. Interestingly, CC genotype of FSCN1 rs1640233 was more likely to progress tumor size and lymph node invasion in BC cases (p-value = 0.04 and 0.02, respectively). Moreover, it was revealed that there was a non-significant correlation between the haplotype distributions of FSCN1 rs852479 and rs1640233 and the probability of BC. CONCLUSIONS Based on the sample size and genetic characteristics of the subjects involved in the present study, our findings indicated that FSCN1 rs852479 may contribute to BC susceptibility in a sample of the Egyptian population.
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Affiliation(s)
- Eman Reda Galal
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy (Girls), Al-Azhar University, Cairo, Egypt.
| | - Dina A Abdelhakam
- Department of Clinical Pathology, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Lamiaa Khalaf Ahmed
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy (Girls), Al-Azhar University, Cairo, Egypt
| | - Yasmine Elhusseny
- Medical Biochemistry and Molecular Biology Department, School of Medicine, Newgiza University, Giza, Egypt
| | - Sherif El Prince Sayed
- Department of General Surgery, Faculty of Medicine, Beni-Suef University, Beni Suef, Egypt
| | - Noha H Eltaweel
- Medical Molecular Genetics Department, Human Genetics and Genome Project Institute, National Research Centre, Cairo, Egypt
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Zhang J, Chen W, Chen G, Flannick J, Fikse E, Smerin G, Degner K, Yang Y, Xu C, Li Y, Hanover JA, Simonds WF. Ancestry-specific high-risk gene variant profiling unmasks diabetes-associated genes. Hum Mol Genet 2024; 33:655-666. [PMID: 36255737 PMCID: PMC11000659 DOI: 10.1093/hmg/ddac255] [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: 05/04/2022] [Revised: 09/28/2022] [Accepted: 10/10/2022] [Indexed: 11/15/2022] Open
Abstract
How ancestry-associated genetic variance affects disparities in the risk of polygenic diseases and influences the identification of disease-associated genes warrants a deeper understanding. We hypothesized that the discovery of genes associated with polygenic diseases may be limited by the overreliance on single-nucleotide polymorphism (SNP)-based genomic investigation, as most significant variants identified in genome-wide SNP association studies map to introns and intergenic regions of the genome. To overcome such potential limitations, we developed a gene-constrained, function-based analytical method centered on high-risk variants (hrV) that encode frameshifts, stopgains or splice site disruption. We analyzed the total number of hrV per gene in populations of different ancestry, representing a total of 185 934 subjects. Using this analysis, we developed a quantitative index of hrV (hrVI) across 20 428 genes within each population. We then applied hrVI analysis to the discovery of genes associated with type 2 diabetes mellitus (T2DM), a polygenic disease with ancestry-related disparity. HrVI profiling and gene-to-gene comparisons of ancestry-specific hrV between the case (20 781 subjects) and control (24 440 subjects) populations in the T2DM national repository identified 57 genes associated with T2DM, 40 of which were discoverable only by ancestry-specific analysis. These results illustrate how a function-based, ancestry-specific analysis of genetic variations can accelerate the identification of genes associated with polygenic diseases. Besides T2DM, such analysis may facilitate our understanding of the genetic basis for other polygenic diseases that are also greatly influenced by environmental and behavioral factors, such as obesity, hypertension and Alzheimer's disease.
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Affiliation(s)
- Jianhua Zhang
- Metabolic Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD 20892, United States
| | - Weiping Chen
- Genomic Core, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD 20892, United States
- Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD 20892, United States
| | - Guanjie Chen
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, Bethesda, MD 20892, United States
| | - Jason Flannick
- Metabolism Program, Broad Institute, Cambridge, MA 02142, United States
| | - Emma Fikse
- Metabolic Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD 20892, United States
| | - Glenda Smerin
- Metabolic Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD 20892, United States
| | - Katherine Degner
- Metabolic Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD 20892, United States
| | - Yanqin Yang
- Laboratory of Transplantation Genomics, National Heart Lung and Blood Institute; National Institutes of Health, Bethesda, MD 20892, United States
| | - Catherine Xu
- Genomic Core, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD 20892, United States
| | | | - Yulong Li
- Milton S. Hershey Medical Center, Division of Endocrinology, Diabetes and Metabolism, Penn State University, Hershey, PA 17033, United States
| | - John A Hanover
- Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD 20892, United States
| | - William F Simonds
- Metabolic Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD 20892, United States
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24
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Sun X, Qian Y, Cheng W, Ye D, Liu B, Zhou D, Wen C, Andreassen OA, Mao Y. Characterizing the polygenic overlap and shared loci between rheumatoid arthritis and cardiovascular diseases. BMC Med 2024; 22:152. [PMID: 38589871 PMCID: PMC11003061 DOI: 10.1186/s12916-024-03376-1] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 03/26/2024] [Indexed: 04/10/2024] Open
Abstract
BACKGROUND Despite substantial research revealing that patients with rheumatoid arthritis (RA) have excessive morbidity and mortality of cardiovascular disease (CVD), the mechanism underlying this association has not been fully known. This study aims to systematically investigate the phenotypic and genetic correlation between RA and CVD. METHODS Based on UK Biobank, we conducted two cohort studies to evaluate the phenotypic relationships between RA and CVD, including atrial fibrillation (AF), coronary artery disease (CAD), heart failure (HF), and stroke. Next, we used linkage disequilibrium score regression, Local Analysis of [co]Variant Association, and bivariate causal mixture model (MiXeR) methods to examine the genetic correlation and polygenic overlap between RA and CVD, using genome-wide association summary statistics. Furthermore, we explored specific shared genetic loci by conjunctional false discovery rate analysis and association analysis based on subsets. RESULTS Compared with the general population, RA patients showed a higher incidence of CVD (hazard ratio [HR] = 1.21, 95% confidence interval [CI]: 1.15-1.28). We observed positive genetic correlations of RA with AF and stroke, and a mixture of negative and positive local genetic correlations underlying the global genetic correlation for CAD and HF, with 13 ~ 33% of shared genetic variants for these trait pairs. We further identified 23 pleiotropic loci associated with RA and at least one CVD, including one novel locus (rs7098414, TSPAN14, 10q23.1). Genes mapped to these shared loci were enriched in immune and inflammatory-related pathways, and modifiable risk factors, such as high diastolic blood pressure. CONCLUSIONS This study revealed the shared genetic architecture of RA and CVD, which may facilitate drug target identification and improved clinical management.
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Affiliation(s)
- Xiaohui Sun
- Department of Epidemiology, School of Public Health, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Yu Qian
- Department of Epidemiology, School of Public Health, Zhejiang Chinese Medical University, Hangzhou, 310053, China
- School of Life Sciences, Westlake University, Hangzhou, 310024, China
| | - Weiqiu Cheng
- NORMENT, Institute of Clinical Medicine, University of Oslo, Oslo, 0407, Norway
| | - Ding Ye
- Department of Epidemiology, School of Public Health, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Bin Liu
- Department of Epidemiology, School of Public Health, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Dan Zhou
- School of Public Health and the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Chengping Wen
- College of Basic Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Ole A Andreassen
- NORMENT, Institute of Clinical Medicine, University of Oslo, Oslo, 0407, Norway.
| | - Yingying Mao
- Department of Epidemiology, School of Public Health, Zhejiang Chinese Medical University, Hangzhou, 310053, China.
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Guo M, Deng L, Gu J, Miao J, Yin J, Li Y, Fang Y, Huang B, Sun Z, Qi F, Dong W, Lu Z, Li S, Hu J, Zhang X, Ren L. Genome-wide association study and development of molecular markers for yield and quality traits in peanut (Arachis hypogaea L.). BMC Plant Biol 2024; 24:244. [PMID: 38575936 PMCID: PMC10996145 DOI: 10.1186/s12870-024-04937-5] [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: 05/06/2023] [Accepted: 03/20/2024] [Indexed: 04/06/2024]
Abstract
BACKGROUND This study aims to decipher the genetic basis governing yield components and quality attributes of peanuts, a critical aspect for advancing molecular breeding techniques. Integrating genotype re-sequencing and phenotypic evaluations of seven yield components and two grain quality traits across four distinct environments allowed for the execution of a genome-wide association study (GWAS). RESULTS The nine phenotypic traits were all continuous and followed a normal distribution. The broad heritability ranged from 88.09 to 98.08%, and the genotype-environment interaction effects were all significant. There was a highly significant negative correlation between protein content (PC) and oil content (OC). The 10× genome re-sequencing of 199 peanut accessions yielded a total of 631,988 high-quality single nucleotide polymorphisms (SNPs), with 374 significant SNP loci identified in association with the nine traits of interest. Notably, 66 of these pertinent SNPs were detected in multiple environments, and 48 of them were linked to multiple traits of interest. Five loci situated on chromosome 16 (Chr16) exhibited pleiotropic effects on yield traits, accounting for 17.64-32.61% of the observed phenotypic variation. Two loci on Chr08 were found to be strongly associated with protein and oil contents, accounting for 12.86% and 14.06% of their respective phenotypic variations, respectively. Linkage disequilibrium (LD) block analysis of these seven loci unraveled five nonsynonymous variants, leading to the identification of one yield-related candidate gene and two quality-related candidate genes. The correlation between phenotypic variation and SNP loci in these candidate genes was validated by Kompetitive allele-specific PCR (KASP) marker analysis. CONCLUSIONS Overall, molecular markers were developed for genetic loci associated with yield and quality traits through a GWAS investigation of 199 peanut accessions across four distinct environments. These molecular tools can aid in the development of desirable peanut germplasm with an equilibrium of yield and quality through marker-assisted breeding.
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Affiliation(s)
- Minjie Guo
- Peanut Institute, Kaifeng Academy of Agricultural and Forestry Sciences, Kaifeng, 475004, China
| | - Li Deng
- Peanut Institute, Kaifeng Academy of Agricultural and Forestry Sciences, Kaifeng, 475004, China
| | - Jianzhong Gu
- Peanut Institute, Kaifeng Academy of Agricultural and Forestry Sciences, Kaifeng, 475004, China
| | - Jianli Miao
- Peanut Institute, Kaifeng Academy of Agricultural and Forestry Sciences, Kaifeng, 475004, China
| | - Junhua Yin
- Peanut Institute, Kaifeng Academy of Agricultural and Forestry Sciences, Kaifeng, 475004, China
| | - Yang Li
- Peanut Institute, Kaifeng Academy of Agricultural and Forestry Sciences, Kaifeng, 475004, China
| | - Yuanjin Fang
- Shennong Laboratory, Henan Provincial Key Laboratory for Oil Crops Improvement, Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - Bingyan Huang
- Shennong Laboratory, Henan Provincial Key Laboratory for Oil Crops Improvement, Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - Ziqi Sun
- Shennong Laboratory, Henan Provincial Key Laboratory for Oil Crops Improvement, Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - Feiyan Qi
- Shennong Laboratory, Henan Provincial Key Laboratory for Oil Crops Improvement, Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - Wenzhao Dong
- Shennong Laboratory, Henan Provincial Key Laboratory for Oil Crops Improvement, Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - Zhenhua Lu
- Peanut Institute, Kaifeng Academy of Agricultural and Forestry Sciences, Kaifeng, 475004, China
| | - Shaowei Li
- Peanut Institute, Kaifeng Academy of Agricultural and Forestry Sciences, Kaifeng, 475004, China
| | - Junping Hu
- Peanut Institute, Kaifeng Academy of Agricultural and Forestry Sciences, Kaifeng, 475004, China
| | - Xinyou Zhang
- Shennong Laboratory, Henan Provincial Key Laboratory for Oil Crops Improvement, Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China.
| | - Li Ren
- Peanut Institute, Kaifeng Academy of Agricultural and Forestry Sciences, Kaifeng, 475004, China.
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Asadi-Tarani M, Darashti A, Javadi M, Rezaei M, Saravani M, Salimi S. The effects of ANRIL polymorphisms on colorectal cancer, tumor stage, and tumor grade among Iranian population. Mol Biol Rep 2024; 51:486. [PMID: 38578390 DOI: 10.1007/s11033-024-09420-w] [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: 11/15/2023] [Accepted: 03/05/2024] [Indexed: 04/06/2024]
Abstract
BACKGROUND Colorectal cancer (CRC) is a type of neoplasm, developing in the colon or rectum. The exact etiology of CRC is not well known, but the role of genetic, epigenetic, and environmental factors are established in its pathogenesis. Therefore, the aim of this research was to explore the effects of ANRIL polymorphisms on the CRC and its clinical findings. METHODS AND RESULTS The peripheral blood specimens were collected from 142 CRC patients and 225 controls referred to Milad Hospital, Tehran, Iran. PCR- RFLP method was used to analyze ANRIL rs1333040, rs10757274 rs4977574, and rs1333048 polymorphisms. The ANRIL rs1333040 polymorphism was related to a higher risk of CRC in the co-dominant, dominant, and log-additive models. ANRIL rs10757274, rs4977574, and rs1333048 polymorphisms showed no effect on CRC susceptibility. The CGAA and TGGA haplotypes of ANRIL rs1333040/ rs10757274/ rs4977574/rs1333048 polymorphisms were associated with the higher and the lower risk of CRC respectively. The rs1333040 polymorphism was associated with higher TNM stages (III and IV). The frequency of ANRIL rs10757274 polymorphism was lower in CRC patients over 50 years of age only in the dominant model. In addition, the rs10757274 was associated with well differentiation in CRC patients. CONCLUSION The ANRIL rs1333040 polymorphism was associated with a higher risk of CRC and higher TNM stages. ANRIL rs10757274 polymorphism was associated with the well-differentiated tumor in CRC.
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Affiliation(s)
- Mina Asadi-Tarani
- Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
| | | | | | - Mahnaz Rezaei
- Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
- Cellular and Molecular Research Center, Resistant Tuberculosis Institute, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Mohsen Saravani
- Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
- Cellular and Molecular Research Center, Resistant Tuberculosis Institute, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Saeedeh Salimi
- Cellular and Molecular Research Center, Resistant Tuberculosis Institute, Zahedan University of Medical Sciences, Zahedan, Iran.
- Department of Clinical Biochemistry, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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Zhang L, Xiong Y, Zhang J, Feng Y, Xu A. Systematic proteome-wide Mendelian randomization using the human plasma proteome to identify therapeutic targets for lung adenocarcinoma. J Transl Med 2024; 22:330. [PMID: 38576019 PMCID: PMC10993587 DOI: 10.1186/s12967-024-04919-z] [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: 11/07/2023] [Accepted: 01/21/2024] [Indexed: 04/06/2024] Open
Abstract
BACKGROUND Lung adenocarcinoma (LUAD) is the predominant histological subtype of lung cancer and the leading cause of cancer-related mortality. Identifying effective drug targets is crucial for advancing LUAD treatment strategies. METHODS This study employed proteome-wide Mendelian randomization (MR) and colocalization analyses. We collected data on 1394 plasma proteins from a protein quantitative trait loci (pQTL) study involving 4907 individuals. Genetic associations with LUAD were derived from the Transdisciplinary Research in Cancer of the Lung (TRICL) study, including 11,245 cases and 54,619 controls. We integrated pQTL and LUAD genome-wide association studies (GWASs) data to identify candidate proteins. MR utilizes single nucleotide polymorphisms (SNPs) as genetic instruments to estimate the causal effect of exposure on outcome, while Bayesian colocalization analysis determines the probability of shared causal genetic variants between traits. Our study applied these methods to assess causality between plasma proteins and LUAD. Furthermore, we employed a two-step MR to quantify the proportion of risk factors mediated by proteins on LUAD. Finally, protein-protein interaction (PPI) analysis elucidated potential links between proteins and current LUAD medications. RESULTS We identified nine plasma proteins significantly associated with LUAD. Increased levels of ALAD, FLT1, ICAM5, and VWC2 exhibited protective effects, with odds ratios of 0.79 (95% CI 0.72-0.87), 0.39 (95% CI 0.28-0.55), 0.91 (95% CI 0.72-0.87), and 0.85 (95% CI 0.79-0.92), respectively. Conversely, MDGA2 (OR, 1.13; 95% CI 1.08-1.19), NTM (OR, 1.12; 95% CI 1.09-1.16), PMM2 (OR, 1.35; 95% CI 1.18-1.53), RNASET2 (OR, 1.15; 95% CI 1.08-1.21), and TFPI (OR, 4.58; 95% CI 3.02-6.94) increased LUAD risk. Notably, none of the nine proteins showed evidence of reverse causality. Bayesian colocalization indicated that RNASET2, TFPI, and VWC2 shared the same variant with LUAD. Furthermore, NTM and FLT1 demonstrated interactions with targets of current LUAD medications. Additionally, FLT1 and TFPI are currently under evaluation as therapeutic targets, while NTM, RNASET2, and VWC2 are potentially druggable. These findings shed light on LUAD pathogenesis, highlighting the tumor-promoting effects of RNASET2, TFPI, and NTM, along with the protective effects of VWC2 and FLT1, providing a significant biological foundation for future LUAD therapeutic targets. CONCLUSIONS Our proteome-wide MR analysis highlighted RNASET2, TFPI, VWC2, NTM, and FLT1 as potential drug targets for further clinical investigation in LUAD. However, the specific mechanisms by which these proteins influence LUAD remain elusive. Targeting these proteins in drug development holds the potential for successful clinical trials, providing a pathway to prioritize and reduce costs in LUAD therapeutics.
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Affiliation(s)
- Long Zhang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Yajun Xiong
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Jie Zhang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Yuying Feng
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Aiguo Xu
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China.
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Ping J, Wan J, Luo J, Du B, Liu X, Jiang T, Zhang J. The interaction of RELN-DNMT genes involving in neurotrophin signaling pathway contributes to schizophrenia susceptibility. Int J Dev Neurosci 2024; 84:154-159. [PMID: 38296839 DOI: 10.1002/jdn.10316] [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: 10/17/2023] [Revised: 12/26/2023] [Accepted: 01/11/2024] [Indexed: 02/02/2024] Open
Abstract
OBJECTIVE Schizophrenia belongs to a severe mental illness with complicated clinical presentations, an ill-defined pathogenesis, and no known cause. Many genetic studies imply that polygenic interaction is important in the development of schizophrenia. The main mechanism of the RELN-BDNF-CREB-DNMT signaling pathway in neurodevelopment involves RELN, brain-derived neurotrophic factor (BDNF), transcription factor cyclic adenosine monophosphate response element binding protein (CREB), DNA methyltransferase 1 (DNMT1), as well as DNA methyltransferase 3B (DNMT3B). An early case-control research on 15 polymorphisms in the RELN, CREB, BDNF, DNMT1, and DNMT3B genes was done. A single gene variation has little effect on the pathogenesis of schizophrenia, but the combination of intergenic variation loci has a bigger impact because schizophrenia is a complex polygenic disorder. The objective of the current study sought to explore the impact of genetic interactions between RELN, BDNF, CREB, DNMT1, and DNMT3B on schizophrenia in order to further highlight the genetic factors influencing the risk of schizophrenia. METHODS Taking the case-control study design, with the Diagnostic and Statistical Manual of Mental Disorders-Fifth Edition (DSM-5) to be the evaluation norm, 134 individuals suffering from schizophrenia hospitalized in the Third People's Hospital of Zhongshan City within January 2018 to April 2020 (case group) were selected, and 64 healthy individuals (control group) from the same geographical area had been chosen as well. MassArray identified DNMT1 gene single nucleotide polymorphisms (rs2114724 and rs2228611) and DNMT3B gene SNPs (rs2424932, rs1569686, rs6119954, and rs2424908). Using the generalized multifactor dimensionality reduction (GMDR), the RELN-BDNF-CREB-DNMT pathway's gene interactions were examined for their impact on schizophrenia. RESULTS GMDR analysis showed that the three-order interaction model RELN (rs2073559, rs2229864)-DNMT3B (rs2424908) was the optimal model (p = 0.001), with the consistency of cross-validation of 10/10 and the test accuracy of 0.8711. CONCLUSION The interaction between the RELN (rs2073559, rs2229864)-DNMT3B (rs2424908) may be related to schizophrenia, and large sample sizes should be verified in different population.
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Affiliation(s)
- Junjiao Ping
- Department of Psychiatry, Third People's Hospital of Zhongshan City, Zhongshan, China
- Joint Laboratory of Psychiatric Genetic Research, The Third People's Hospital of Zhongshan, Zhongshan, China
| | - Jing Wan
- Department of Early Intervention, Third People's Hospital of Zhongshan City, Zhongshan, China
| | - Jiali Luo
- Joint Laboratory of Psychiatric Genetic Research, The Third People's Hospital of Zhongshan, Zhongshan, China
| | - Baoguo Du
- Department of Clinical Psychology, The Third People's Hospital of Zhongshan City, Zhongshan, China
| | - Xinxia Liu
- Department of Psychiatry, Third People's Hospital of Zhongshan City, Zhongshan, China
- Joint Laboratory of Psychiatric Genetic Research, The Third People's Hospital of Zhongshan, Zhongshan, China
| | - Tingyun Jiang
- Department of Psychiatry, Third People's Hospital of Zhongshan City, Zhongshan, China
| | - Jie Zhang
- Department of Psychiatry, Third People's Hospital of Zhongshan City, Zhongshan, China
- Joint Laboratory of Psychiatric Genetic Research, The Third People's Hospital of Zhongshan, Zhongshan, China
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Karjalainen MK, Karthikeyan S, Oliver-Williams C, Sliz E, Allara E, Fung WT, Surendran P, Zhang W, Jousilahti P, Kristiansson K, Salomaa V, Goodwin M, Hughes DA, Boehnke M, Fernandes Silva L, Yin X, Mahajan A, Neville MJ, van Zuydam NR, de Mutsert R, Li-Gao R, Mook-Kanamori DO, Demirkan A, Liu J, Noordam R, Trompet S, Chen Z, Kartsonaki C, Li L, Lin K, Hagenbeek FA, Hottenga JJ, Pool R, Ikram MA, van Meurs J, Haller T, Milaneschi Y, Kähönen M, Mishra PP, Joshi PK, Macdonald-Dunlop E, Mangino M, Zierer J, Acar IE, Hoyng CB, Lechanteur YTE, Franke L, Kurilshikov A, Zhernakova A, Beekman M, van den Akker EB, Kolcic I, Polasek O, Rudan I, Gieger C, Waldenberger M, Asselbergs FW, Hayward C, Fu J, den Hollander AI, Menni C, Spector TD, Wilson JF, Lehtimäki T, Raitakari OT, Penninx BWJH, Esko T, Walters RG, Jukema JW, Sattar N, Ghanbari M, Willems van Dijk K, Karpe F, McCarthy MI, Laakso M, Järvelin MR, Timpson NJ, Perola M, Kooner JS, Chambers JC, van Duijn C, Slagboom PE, Boomsma DI, Danesh J, Ala-Korpela M, Butterworth AS, Kettunen J. Genome-wide characterization of circulating metabolic biomarkers. Nature 2024; 628:130-138. [PMID: 38448586 PMCID: PMC10990933 DOI: 10.1038/s41586-024-07148-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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 02/01/2024] [Indexed: 03/08/2024]
Abstract
Genome-wide association analyses using high-throughput metabolomics platforms have led to novel insights into the biology of human metabolism1-7. This detailed knowledge of the genetic determinants of systemic metabolism has been pivotal for uncovering how genetic pathways influence biological mechanisms and complex diseases8-11. Here we present a genome-wide association study for 233 circulating metabolic traits quantified by nuclear magnetic resonance spectroscopy in up to 136,016 participants from 33 cohorts. We identify more than 400 independent loci and assign probable causal genes at two-thirds of these using manual curation of plausible biological candidates. We highlight the importance of sample and participant characteristics that can have significant effects on genetic associations. We use detailed metabolic profiling of lipoprotein- and lipid-associated variants to better characterize how known lipid loci and novel loci affect lipoprotein metabolism at a granular level. We demonstrate the translational utility of comprehensively phenotyped molecular data, characterizing the metabolic associations of intrahepatic cholestasis of pregnancy. Finally, we observe substantial genetic pleiotropy for multiple metabolic pathways and illustrate the importance of careful instrument selection in Mendelian randomization analysis, revealing a putative causal relationship between acetone and hypertension. Our publicly available results provide a foundational resource for the community to examine the role of metabolism across diverse diseases.
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Affiliation(s)
- Minna K Karjalainen
- Systems Epidemiology, Faculty of Medicine, University of Oulu and Biocenter Oulu, Oulu, Finland.
- Research Unit of Population Health, Faculty of Medicine, University of Oulu, Oulu, Finland.
- Northern Finland Birth Cohorts, Arctic Biobank, Infrastructure for Population Studies, Faculty of Medicine, University of Oulu, Oulu, Finland.
| | - Savita Karthikeyan
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Clare Oliver-Williams
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Public Health Specialty Training Programme, Cambridge, UK
| | - Eeva Sliz
- Systems Epidemiology, Faculty of Medicine, University of Oulu and Biocenter Oulu, Oulu, Finland
- Research Unit of Population Health, Faculty of Medicine, University of Oulu, Oulu, Finland
| | - Elias Allara
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- National Institute for Health and Care Research Blood and Transplant Research Unit in Donor Health and Behaviour, University of Cambridge, Cambridge, UK
- Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK
| | - Wing Tung Fung
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK
| | - Praveen Surendran
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Rutherford Fund Fellow, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge, UK
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
| | - Weihua Zhang
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
- Department of Cardiology, Ealing Hospital, London North West University Healthcare NHS Trust, London, UK
| | - Pekka Jousilahti
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Kati Kristiansson
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Veikko Salomaa
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Matt Goodwin
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Science, Bristol Medical School, University of Bristol, Bristol, UK
| | - David A Hughes
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Science, Bristol Medical School, University of Bristol, Bristol, UK
| | - Michael Boehnke
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Lilian Fernandes Silva
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland, Kuopio, Finland
| | - Xianyong Yin
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Jiangsu, China
| | - Anubha Mahajan
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Genentech, South San Francisco, CA, USA
| | - Matt J Neville
- NIHR Oxford Biomedical Research Centre, OUHFT Oxford, Oxford, UK
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Natalie R van Zuydam
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Renée de Mutsert
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Ruifang Li-Gao
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Dennis O Mook-Kanamori
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
- Department of Public Health and Primary Care, Leiden University Medical Center, Leiden, The Netherlands
| | - Ayse Demirkan
- Surrey Institute for People-Centred AI, University of Surrey, Guildford, UK
- Section of Statistical Multi-Omics, Department of Clinical and Experimental Medicine, University of Surrey, Guildford, UK
| | - Jun Liu
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Raymond Noordam
- Department of Internal Medicine, Section of Gerontology and Geriatrics, Leiden University Medical Center, Leiden, The Netherlands
| | - Stella Trompet
- Department of Internal Medicine, Section of Gerontology and Geriatrics, Leiden University Medical Center, Leiden, The Netherlands
- Department of Cardiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Zhengming Chen
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
- MRC Population Health Research Unit, University of Oxford, Oxford, UK
| | - Christiana Kartsonaki
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
- MRC Population Health Research Unit, University of Oxford, Oxford, UK
| | - Liming Li
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
- Peking University Center for Public Health and Epidemic Preparedness and Response, Beijing, China
- Key Laboratory of Epidemiology of Major Diseases, Peking University, Ministry of Education, Beijing, China
| | - Kuang Lin
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Fiona A Hagenbeek
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Jouke Jan Hottenga
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
| | - René Pool
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
| | - M Arfan Ikram
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Joyce van Meurs
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Toomas Haller
- Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Yuri Milaneschi
- Department of Psychiatry, Amsterdam Neuroscience and Amsterdam Public Health, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Mika Kähönen
- Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Department of Clinical Physiology, Tampere University Hospital, Tampere, Finland
| | - Pashupati P Mishra
- Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Department of Clinical Chemistry, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland
| | - Peter K Joshi
- Centre for Global Health, Usher Institute, University of Edinburgh, Edinburgh, Scotland
| | - Erin Macdonald-Dunlop
- Centre for Global Health, Usher Institute, University of Edinburgh, Edinburgh, Scotland
| | - Massimo Mangino
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
- NIHR Biomedical Research Centre at Guy's and St Thomas' Foundation Trust, London, UK
| | - Jonas Zierer
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Ilhan E Acar
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- Department of Ophthalmology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Carel B Hoyng
- Department of Ophthalmology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Yara T E Lechanteur
- Department of Ophthalmology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Lude Franke
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Alexander Kurilshikov
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Alexandra Zhernakova
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Marian Beekman
- Section of Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands
| | - Erik B van den Akker
- Section of Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands
- Center for Computational Biology, Leiden University Medical Center, Leiden, The Netherlands
- The Delft Bioinformatics Lab, Delft University of Technology, Delft, The Netherlands
| | - Ivana Kolcic
- Department of Public Health, School of Medicine, University of Split, Split, Croatia
| | - Ozren Polasek
- Department of Public Health, School of Medicine, University of Split, Split, Croatia
| | - Igor Rudan
- Centre for Global Health, Usher Institute, University of Edinburgh, Edinburgh, Scotland
| | - Christian Gieger
- Research Unit Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
| | - Melanie Waldenberger
- Research Unit Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
| | - Folkert W Asselbergs
- Amsterdam University Medical Centers, Department of Cardiology, University of Amsterdam, Amsterdam, The Netherlands
- Health Data Research UK and Institute of Health Informatics, University College London, London, UK
| | - Caroline Hayward
- Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Jingyuan Fu
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Department of Pediatrics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Anneke I den Hollander
- Department of Ophthalmology, Radboud University Medical Center, Nijmegen, The Netherlands
- Genomics Research Center, Abbvie, Cambridge, MA, USA
| | - Cristina Menni
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Tim D Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - James F Wilson
- Centre for Global Health, Usher Institute, University of Edinburgh, Edinburgh, Scotland
- Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Terho Lehtimäki
- Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Department of Clinical Chemistry, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland
| | - Olli T Raitakari
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland
- Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, Turku, Finland
- Centre for Population Health Research, University of Turku and Turku University Hospital, Turku, Finland
- InFLAMES Research Flagship, University of Turku, Turku, Finland
| | - Brenda W J H Penninx
- Department of Psychiatry, Amsterdam Neuroscience and Amsterdam Public Health, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Tonu Esko
- Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Robin G Walters
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
- MRC Population Health Research Unit, University of Oxford, Oxford, UK
| | - J Wouter Jukema
- Department of Cardiology, Leiden University Medical Center, Leiden, The Netherlands
- Netherlands Heart Institute, Utrecht, The Netherlands
| | - Naveed Sattar
- School of Cardiovascular and Metabolic Health, University of Glasgow, Glasgow, UK
| | - Mohsen Ghanbari
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Ko Willems van Dijk
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
- Department of Internal Medicine, Division Endocrinology, Leiden University Medical Center, Leiden, The Netherlands
- Leiden Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - Fredrik Karpe
- NIHR Oxford Biomedical Research Centre, OUHFT Oxford, Oxford, UK
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Mark I McCarthy
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- Genentech, South San Francisco, CA, USA
| | - Markku Laakso
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland, Kuopio, Finland
- Kuopio University Hospital, Kuopio, Finland
| | - Marjo-Riitta Järvelin
- Research Unit of Population Health, Faculty of Medicine, University of Oulu, Oulu, Finland
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
- Department of Life Sciences, College of Health and Life Sciences, Brunel University London, Uxbridge, UK
- Unit of Primary Health Care, Oulu University Hospital, OYS, Oulu, Finland
| | - Nicholas J Timpson
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Science, Bristol Medical School, University of Bristol, Bristol, UK
| | - Markus Perola
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
- Diabetes and Obesity Research Program, University of Helsinki, Helsinki, Finland
- Estonian Genome Center, University of Tartu, Tartu, Estonia
| | - Jaspal S Kooner
- Department of Cardiology, Ealing Hospital, London North West University Healthcare NHS Trust, London, UK
- Imperial College Healthcare NHS Trust, Imperial College London, London, UK
- MRC-PHE Centre for Environment and Health, Imperial College London, London, UK
- National Heart and Lung Institute, Imperial College London, London, UK
| | - John C Chambers
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
- Department of Cardiology, Ealing Hospital, London North West University Healthcare NHS Trust, London, UK
- Imperial College Healthcare NHS Trust, Imperial College London, London, UK
- MRC-PHE Centre for Environment and Health, Imperial College London, London, UK
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Cornelia van Duijn
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - P Eline Slagboom
- Section of Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands
| | - Dorret I Boomsma
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
- Amsterdam Reproduction and Development (AR&D) Research Institute, Amsterdam, The Netherlands
| | - John Danesh
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- National Institute for Health and Care Research Blood and Transplant Research Unit in Donor Health and Behaviour, University of Cambridge, Cambridge, UK
- Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK
- British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge, UK
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
- Department of Human Genetics, Wellcome Sanger Institute, Hinxton, UK
| | - Mika Ala-Korpela
- Systems Epidemiology, Faculty of Medicine, University of Oulu and Biocenter Oulu, Oulu, Finland
- Research Unit of Population Health, Faculty of Medicine, University of Oulu, Oulu, Finland
- NMR Metabolomics Laboratory, School of Pharmacy, University of Eastern Finland, Kuopio, Finland
| | - Adam S Butterworth
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- National Institute for Health and Care Research Blood and Transplant Research Unit in Donor Health and Behaviour, University of Cambridge, Cambridge, UK
- Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK
- British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge, UK
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
| | - Johannes Kettunen
- Systems Epidemiology, Faculty of Medicine, University of Oulu and Biocenter Oulu, Oulu, Finland
- Research Unit of Population Health, Faculty of Medicine, University of Oulu, Oulu, Finland
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
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30
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Veller C, Coop GM. Interpreting population- and family-based genome-wide association studies in the presence of confounding. PLoS Biol 2024; 22:e3002511. [PMID: 38603516 PMCID: PMC11008796 DOI: 10.1371/journal.pbio.3002511] [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: 03/22/2023] [Accepted: 01/19/2024] [Indexed: 04/13/2024] Open
Abstract
A central aim of genome-wide association studies (GWASs) is to estimate direct genetic effects: the causal effects on an individual's phenotype of the alleles that they carry. However, estimates of direct effects can be subject to genetic and environmental confounding and can also absorb the "indirect" genetic effects of relatives' genotypes. Recently, an important development in controlling for these confounds has been the use of within-family GWASs, which, because of the randomness of mendelian segregation within pedigrees, are often interpreted as producing unbiased estimates of direct effects. Here, we present a general theoretical analysis of the influence of confounding in standard population-based and within-family GWASs. We show that, contrary to common interpretation, family-based estimates of direct effects can be biased by genetic confounding. In humans, such biases will often be small per-locus, but can be compounded when effect-size estimates are used in polygenic scores (PGSs). We illustrate the influence of genetic confounding on population- and family-based estimates of direct effects using models of assortative mating, population stratification, and stabilizing selection on GWAS traits. We further show how family-based estimates of indirect genetic effects, based on comparisons of parentally transmitted and untransmitted alleles, can suffer substantial genetic confounding. We conclude that, while family-based studies have placed GWAS estimation on a more rigorous footing, they carry subtle issues of interpretation that arise from confounding.
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Affiliation(s)
- Carl Veller
- Department of Ecology & Evolution, University of Chicago, Chicago, Illinois, United States of America
| | - Graham M. Coop
- Department of Evolution and Ecology, and Center for Population Biology, University of California, Davis, California, United States of America
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Shokat S, Iqbal R, Riaz S, Yaqub A. Association Between Arsenic Toxicity, AS3MT Gene Polymorphism and Onset of Type 2 Diabetes. Biol Trace Elem Res 2024; 202:1550-1558. [PMID: 37889428 DOI: 10.1007/s12011-023-03919-2] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 10/13/2023] [Indexed: 10/28/2023]
Abstract
Arsenic (As) exposure in drinking water has become a serious public health issue. AS3MT gene is involved in the metabolism of arsenic, so a single nucleotide polymorphism in this gene may lead to the development of type 2 diabetes in arsenic-exposed areas. This study aimed to evaluate the association of the AS3MT gene with the development of type 2 diabetes in highly arsenic-exposed areas of Punjab, Pakistan. Total 200 samples equal in number from high arsenic exposed-areas of Lahore (Nishtar) and Kasur (Mustafa Abad) were collected. rs11191439 was utilized as an influential variable to evaluate the association between arsenic metabolism and diabetes status to find a single nucleotide polymorphism in the AS3MT gene. We observed the arsenic level in drinking water of the arsenic-exposed selected areas 115.54 ± 1.23 µg/L and 96.88 ± 0.48 µg/L, respectively. The As level in the urine of diabetics (98.54 ± 2.63 µg/L and 56.38 ± 12.66 µg/L) was higher as compared to non-diabetics (77.58 ± 1.8 µg/L and 46.9 ± 8.95 µg/L) of both affected areas, respectively. Correspondingly, the As level in the blood of diabetics (6.48 ± 0.08 µg/L and 5.49 ± 1.43 µg/L) and non-diabetics (6.22 ± 0.12 µg/L and 5.26 ± 0.24 µg/L) in the affected areas. Genotyping showed significant differences in the frequencies of alleles among cases and controls. Nevertheless, notable disparities in genotype distribution were observed in SNPs rs11191439 (T/C) (P < 0.05) and when comparing T2D patients and non-diabetic control subjects. The AS3MT gene and clinical parameters show a significant association with the affected people with diabetes living in arsenic-exposed areas.
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Affiliation(s)
- Saima Shokat
- Department of Zoology, Government College University, Lahore, Pakistan.
| | - Riffat Iqbal
- Department of Zoology, Government College University, Lahore, Pakistan
| | - Samreen Riaz
- Institute of Microbiology and Molecular Genetics, University of the Punjab, Lahore, Pakistan
| | - Atif Yaqub
- Department of Zoology, Government College University, Lahore, Pakistan
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Ayari F, Chaaben AB, Abaza H, Mihoub O, Ouni N, Boukouaci W, Kharrat M, Leboyer M, Guemira F, Tamouza R, Mankai A. Association between genetic variants of TLR2, TLR4, TLR9 and schizophrenia. Encephale 2024; 50:178-184. [PMID: 37718198 DOI: 10.1016/j.encep.2023.05.004] [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: 02/20/2023] [Revised: 05/23/2023] [Accepted: 05/23/2023] [Indexed: 09/19/2023]
Abstract
BACKGROUND AND STUDY AIM Schizophrenia (SZ) is a multifactorial disorder involving complex interactions between genetic and environmental factors, where immune dysfunction plays a key etiopathogenic role. In order to explore the control of innate immune responses in SZ, we aimed to investigate the potential association between twelve TLR2, TLR4 and TLR9 variants (TLR2: rs4696480T>A, rs3804099T>C, rs3804100T>C; TLR4: rs1927914G>A, rs10759932T>C, rs4986790A>G, rs4986791T>C, rs11536889G>C, rs11536891T>C; TLR9: rs187084A>G, rs352139T>C and rs352140C>T) and SZ susceptibility in a Tunisian population. PATIENTS AND METHODS This study included 150 patients and 201 healthy controls with no history of psychiatric illness. Genotyping was done using a TaqMan SNP genotyping assay. We also assessed a haplotype analysis for TLR2, TLR4 and TLR9 variants with SZ using Haploview 4.2 Software. RESULTS We found that the AA genotype of the TLR2 rs4696480T>A variant was significantly associated with an increased risk of SZ (46% vs. 31%, P=4.7×10-3, OR=1.87 and 95% CI [1.18-2.97]). The frequency of the TA genotype was significantly higher in the control group than in SZ patients (27% vs. 43%, P=2.1×10-3) and may be associated with protection against SZ (OR=0.49 and 95% CI [0.30-0.80]). Whereas, the TLR9 rs187084-GG genotype was higher in the control group compared to patients (16% vs. 5%, P=1.6×10-3) and would present protection against SZ (OR=0.28, CI=[0.10-0.68]). The ACT haplotype of the TLR2 and the ACC haplotype of the TLR9 gene were identified as a risk haplotypes for SZ (P=0.04, OR=9.30, 95% CI=[1.11-77.71]; P=3×10-4, OR=6.05, 95% CI=[2.29-15.98], respectively). CONCLUSION The results indicate that TLR2 and TLR9 genetic diversity may play a role in genetic vulnerability to SZ. However, including more patients and evaluation of TLR2 and TLR9 expression are recommended.
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Affiliation(s)
- Fayza Ayari
- Clinical Biology Department, Salah Azaiz Institute, Tunis, Tunisia; Faculty of Sciences of Tunis, University Tunis El Manar, Tunis, Tunisia.
| | - Arij Ben Chaaben
- Biology Department, Higher School of Health Sciences and Techniques, Tunis El Manar University, Tunis, Tunisia; Human Genetic Laboratory (LR99E510), Faculty of Medicine, University of Tunis El Manar, Tunis, Tunisia
| | - Hajer Abaza
- Research Unit 03/04 Schizophrenia and Department of Psychiatry F, Razi Hospital, Manouba, Tunisia
| | - Ons Mihoub
- Human Genetic Laboratory (LR99E510), Faculty of Medicine, University of Tunis El Manar, Tunis, Tunisia
| | - Nesrine Ouni
- Clinical Biology Department, Salah Azaiz Institute, Tunis, Tunisia; Faculty of Sciences of Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Wahid Boukouaci
- Université Paris Est Creteil (UPEC), INSERM, IMRB, Translational Neuropsychiatry, Fondation FondaMental, 94010 Creteil, France
| | - Maher Kharrat
- Human Genetic Laboratory (LR99E510), Faculty of Medicine, University of Tunis El Manar, Tunis, Tunisia
| | - Marion Leboyer
- Université Paris Est Creteil (UPEC), INSERM, IMRB, Translational Neuropsychiatry, Fondation FondaMental, 94010 Creteil, France
| | - Fethi Guemira
- Clinical Biology Department, Salah Azaiz Institute, Tunis, Tunisia
| | - Ryad Tamouza
- Université Paris Est Creteil (UPEC), INSERM, IMRB, Translational Neuropsychiatry, Fondation FondaMental, 94010 Creteil, France
| | - Amani Mankai
- Biology Department, Higher School of Health Sciences and Techniques, Tunis El Manar University, Tunis, Tunisia; Research Unit "Obesity: etiopathology and treatment, UR18ES01", National Institute of Nutrition and Food Technology, Tunis, Tunisia
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Tsouris A, Brach G, Friedrich A, Hou J, Schacherer J. Diallel panel reveals a significant impact of low-frequency genetic variants on gene expression variation in yeast. Mol Syst Biol 2024; 20:362-373. [PMID: 38355920 PMCID: PMC10987670 DOI: 10.1038/s44320-024-00021-0] [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: 09/15/2023] [Revised: 01/29/2024] [Accepted: 01/30/2024] [Indexed: 02/16/2024] Open
Abstract
Unraveling the genetic sources of gene expression variation is essential to better understand the origins of phenotypic diversity in natural populations. Genome-wide association studies identified thousands of variants involved in gene expression variation, however, variants detected only explain part of the heritability. In fact, variants such as low-frequency and structural variants (SVs) are poorly captured in association studies. To assess the impact of these variants on gene expression variation, we explored a half-diallel panel composed of 323 hybrids originated from pairwise crosses of 26 natural Saccharomyces cerevisiae isolates. Using short- and long-read sequencing strategies, we established an exhaustive catalog of single nucleotide polymorphisms (SNPs) and SVs for this panel. Combining this dataset with the transcriptomes of all hybrids, we comprehensively mapped SNPs and SVs associated with gene expression variation. While SVs impact gene expression variation, SNPs exhibit a higher effect size with an overrepresentation of low-frequency variants compared to common ones. These results reinforce the importance of dissecting the heritability of complex traits with a comprehensive catalog of genetic variants at the population level.
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Affiliation(s)
- Andreas Tsouris
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
| | - Gauthier Brach
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
| | - Anne Friedrich
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
| | - Jing Hou
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France.
| | - Joseph Schacherer
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France.
- Institut Universitaire de France (IUF), Paris, France.
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Pudjihartono M, Golovina E, Fadason T, O'Sullivan JM, Schierding W. Links between melanoma germline risk loci, driver genes and comorbidities: insight from a tissue-specific multi-omic analysis. Mol Oncol 2024; 18:1031-1048. [PMID: 38308491 PMCID: PMC10994230 DOI: 10.1002/1878-0261.13599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 11/15/2023] [Accepted: 01/22/2024] [Indexed: 02/04/2024] Open
Abstract
Genome-wide association studies (GWAS) have associated 76 loci with the risk of developing melanoma. However, understanding the molecular basis of such associations has remained a challenge because most of these loci are in non-coding regions of the genome. Here, we integrated data on epigenomic markers, three-dimensional (3D) genome organization, and expression quantitative trait loci (eQTL) from melanoma-relevant tissues and cell types to gain novel insights into the mechanisms underlying melanoma risk. This integrative approach revealed a total of 151 target genes, both near and far away from the risk loci in linear sequence, with known and novel roles in the etiology of melanoma. Using protein-protein interaction networks, we identified proteins that interact-directly or indirectly-with the products of the target genes. The interacting proteins were enriched for known melanoma driver genes. Further integration of these target genes into tissue-specific gene regulatory networks revealed patterns of gene regulation that connect melanoma to its comorbidities. Our study provides novel insights into the biological implications of genetic variants associated with melanoma risk.
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Affiliation(s)
| | | | | | - Justin M. O'Sullivan
- Liggins InstituteThe University of AucklandNew Zealand
- The Maurice Wilkins CentreThe University of AucklandNew Zealand
- Australian Parkinson's MissionGarvan Institute of Medical ResearchSydneyAustralia
- MRC Lifecourse Epidemiology UnitUniversity of SouthamptonUK
- Singapore Institute for Clinical SciencesAgency for Science, Technology and Research (A*STAR)Singapore CitySingapore
| | - William Schierding
- Liggins InstituteThe University of AucklandNew Zealand
- The Maurice Wilkins CentreThe University of AucklandNew Zealand
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Prunell-Castañé A, Beyer F, Witte V, Sánchez Garre C, Hernán I, Caldú X, Jurado MÁ, Garolera M. From the reward network to whole-brain metrics: structural connectivity in adolescents and young adults according to body mass index and genetic risk of obesity. Int J Obes (Lond) 2024; 48:567-574. [PMID: 38145996 DOI: 10.1038/s41366-023-01451-w] [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] [Received: 08/24/2023] [Revised: 12/05/2023] [Accepted: 12/12/2023] [Indexed: 12/27/2023]
Abstract
BACKGROUND Obesity is a multifactorial condition. Genetic variants, such as the fat mass and obesity related gene (FTO) polymorphism, may increase the vulnerability of developing obesity by disrupting dopamine signaling within the reward network. Yet, the association of obesity, genetic risk of obesity, and structural connectivity of the reward network in adolescents and young adults remains unexplored. We investigate, in adolescents and young adults, the structural connectivity differences in the reward network and at the whole-brain level according to body mass index (BMI) and the FTO rs9939609 polymorphism. METHODS One hundred thirty-two adolescents and young adults (age range: [10, 21] years, BMI z-score range: [-1.76, 2.69]) were included. Genetic risk of obesity was determined by the presence of the FTO A allele. Whole-brain and reward network structural connectivity were analyzed using graph metrics. Hierarchical linear regression was applied to test the association between BMI-z, genetic risk of obesity, and structural connectivity. RESULTS Higher BMI-z was associated with higher (B = 0.76, 95% CI = [0.30, 1.21], P = 0.0015) and lower (B = -0.003, 95% CI = [-0.006, -0.00005], P = 0.048) connectivity strength for fractional anisotropy at the whole-brain level and of the reward network, respectively. The FTO polymorphism was not associated with structural connectivity nor with BMI-z. CONCLUSIONS We provide evidence that, in healthy adolescents and young adults, higher BMI-z is associated with higher connectivity at the whole-brain level and lower connectivity of the reward network. We did not find the FTO polymorphism to correlate with structural connectivity. Future longitudinal studies with larger sample sizes are needed to assess how genetic determinants of obesity change brain structural connectivity and behavior.
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Affiliation(s)
- Anna Prunell-Castañé
- Departament de Psicologia Clínica i Psicobiologia, Facultat de Psicologia, Universitat de Barcelona, Passeig de la Vall d'Hebron, 171, 08035, Barcelona, Spain
- Institut de Neurociències, Universitat de Barcelona, Barcelona, Spain
- Institut de Recerca Sant Joan de Déu, Esplugues de Llobregat, Spain
| | - Frauke Beyer
- Clinic for Cognitive Neurology, University of Leipzig Medical Center, Leipzig, Germany
- Department of Neurology, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany
| | - Veronica Witte
- Clinic for Cognitive Neurology, University of Leipzig Medical Center, Leipzig, Germany
- Department of Neurology, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany
| | - Consuelo Sánchez Garre
- Pediatric Endocrinology Unit, Hospital de Terrassa, Consorci Sanitari de Terrassa, Terrassa, Barcelona, Spain
| | - Imma Hernán
- Molecular Genetics Unit, Consorci Sanitari de Terrassa, Terrassa, Spain
| | - Xavier Caldú
- Departament de Psicologia Clínica i Psicobiologia, Facultat de Psicologia, Universitat de Barcelona, Passeig de la Vall d'Hebron, 171, 08035, Barcelona, Spain
- Institut de Neurociències, Universitat de Barcelona, Barcelona, Spain
- Institut de Recerca Sant Joan de Déu, Esplugues de Llobregat, Spain
| | - María Ángeles Jurado
- Departament de Psicologia Clínica i Psicobiologia, Facultat de Psicologia, Universitat de Barcelona, Passeig de la Vall d'Hebron, 171, 08035, Barcelona, Spain.
- Institut de Neurociències, Universitat de Barcelona, Barcelona, Spain.
- Institut de Recerca Sant Joan de Déu, Esplugues de Llobregat, Spain.
| | - Maite Garolera
- Brain, Cognition and Behavior: Clinical Research, Consorci Sanitari de Terrassa, Terrassa, Barcelona, Spain
- Neuropsychology Unit, Hospital de Terrassa, Consorci Sanitari de Terrassa, Terrassa, Barcelona, Spain
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Maxwell LM, Clark JD, Walsh J, Conway M, Olsen BJ, Kovach AI. Ecological characteristics explain neutral genetic variation of three coastal sparrow species. Mol Ecol 2024; 33:e17316. [PMID: 38481075 DOI: 10.1111/mec.17316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 02/15/2024] [Accepted: 02/23/2024] [Indexed: 04/09/2024]
Abstract
Eco-phylogeographic approaches to comparative population genetic analyses allow for the inclusion of intrinsic influences as drivers of intraspecific genetic structure. This insight into microevolutionary processes, including changes within a species or lineage, provides better mechanistic understanding of species-specific interactions and enables predictions of evolutionary responses to environmental change. In this study, we used single nucleotide polymorphisms (SNPs) identified from reduced representation sequencing to compare neutral population structure, isolation by distance (IBD), genetic diversity and effective population size (Ne) across three closely related and co-distributed saltmarsh sparrow species differing along a specialization gradient-Nelson's (Ammospiza nelsoni subvirgata), saltmarsh (A. caudacuta) and seaside sparrows (A. maritima maritima). Using an eco-phylogeographic lens within a conservation management context, we tested predictions about species' degree of evolutionary history and ecological specialization to tidal marshes, habitat, current distribution and population status on population genetic metrics. Population structure differed among the species consistent with their current distribution and habitat factors, rather than degree of ecological specialization: seaside sparrows were panmictic, saltmarsh sparrows showed hierarchical structure and Nelson's sparrows were differentiated into multiple, genetically distinct populations. Neutral population genetic theory and demographic/evolutionary history predicted patterns of genetic diversity and Ne rather than degree of ecological specialization. Patterns of population variation and evolutionary distinctiveness (Shapely metric) suggest different conservation measures for long-term persistence and evolutionary potential in each species. Our findings contribute to a broader understanding of the complex factors influencing genetic variation, beyond specialist-generalist status and support the role of an eco-phylogeographic approach in population and conservation genetics.
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Affiliation(s)
- Logan M Maxwell
- Department of Natural Resources and the Environment, University of New Hampshire, Durham, New Hampshire, USA
| | - Jonathan D Clark
- Department of Natural Resources and the Environment, University of New Hampshire, Durham, New Hampshire, USA
| | - Jennifer Walsh
- Department of Natural Resources and the Environment, University of New Hampshire, Durham, New Hampshire, USA
- Fuller Evolutionary Biology Program, Cornell Laboratory of Ornithology, Ithaca, New York, USA
| | - Meaghan Conway
- School of Biology and Ecology, University of Maine, Orono, Maine, USA
| | - Brian J Olsen
- School of Biology and Ecology, University of Maine, Orono, Maine, USA
| | - Adrienne I Kovach
- Department of Natural Resources and the Environment, University of New Hampshire, Durham, New Hampshire, USA
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Xu Q, Shen H, Zhu Y, Zhang J, Shen Z, Jiang J, Zhou J. Causal effects of genetically predicted testosterone on Alzheimer's disease: a two-sample mendelian randomization study. Acta Neurol Belg 2024; 124:591-601. [PMID: 38007406 DOI: 10.1007/s13760-023-02426-4] [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: 06/14/2023] [Accepted: 10/30/2023] [Indexed: 11/27/2023]
Abstract
OBJECTIVE Although several studies have reported that testosterone may protect against Alzheimer's disease, no evidence of a causal relationship has been demonstrated. METHODS A Mendelian randomization (MR) study was performed to determine the causal role of testosterone in Alzheimer's disease. The study utilized public databases obtained from separately published genome-wide associationstudies (GWAS). Single-nucleotide polymorphisms (SNPs) for testosterone were extracted from the most recent and largest published GWAS meta-analysis (178,782 participants), and SNPs for Alzheimer's disease were extracted from UK Biobank (954 AD cases and 487,331 controls). The odds ratio (OR) of the inverse variance weighting (IVW) approach was the primary outcome, and the weighted median and MR Egger regression were used for sensitivity analysis. RESULTS Through IVW, we observed a causal association between genetically predicted testosterone and the risk of Alzheimer's disease, with an OR of 0.99 (95% confidence interval [CI] = 0.998-0.999, p = 0.047). In the sensitivity analyses, the weighted median regression showed directionally similar estimates (OR = 0.99, 95% CI = 0.998-0.999, p = 0.048). The MR Egger regression showed similar estimates (OR = 0.99, 95% CI = 0.998-1.00, p = 0.35), but with lower precision. Funnel plots, MR Egger intercepts, and Mendelian randomization pleiotropy residual sum and outlier (MR-PRESSO) analysis indicated the absence of directional pleiotropy effects. CONCLUSION In conclusion, our MR study provides evidence of a causal relationship between testosterone levels and Alzheimer's disease; however, this relationship must be validated in future studies with larger sample sizes. Early testosterone monitoring may enable the prevention of Alzheimer's and related diseases.
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Affiliation(s)
- Qian Xu
- Department of Neurology, Suzhou Wujiang District Hospital of Traditional Chinese Medicine (Suzhou Wujiang District Second People's Hospital), Wujiang District, Suzhou, 215200, China
| | - Hong Shen
- Department of Neurology, Suzhou Wujiang District Hospital of Traditional Chinese Medicine (Suzhou Wujiang District Second People's Hospital), Wujiang District, Suzhou, 215200, China
| | - Yifan Zhu
- Department of Neurology, Suzhou Wujiang District Hospital of Traditional Chinese Medicine (Suzhou Wujiang District Second People's Hospital), Wujiang District, Suzhou, 215200, China
| | - Junlei Zhang
- Department of Neurology, Suzhou Wujiang District Hospital of Traditional Chinese Medicine (Suzhou Wujiang District Second People's Hospital), Wujiang District, Suzhou, 215200, China
| | - Zhongmei Shen
- Department of Neurology, Suzhou Wujiang District Hospital of Traditional Chinese Medicine (Suzhou Wujiang District Second People's Hospital), Wujiang District, Suzhou, 215200, China
| | - Jianming Jiang
- Department of Neurology, Suzhou Wujiang District Hospital of Traditional Chinese Medicine (Suzhou Wujiang District Second People's Hospital), Wujiang District, Suzhou, 215200, China
| | - Jie Zhou
- Department of Neurology, Suzhou Wujiang District Hospital of Traditional Chinese Medicine (Suzhou Wujiang District Second People's Hospital), Wujiang District, Suzhou, 215200, China.
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Huang H, Hsieh Y, Hsiao C, Lin C, Wang S, Ho K, Chang L, Huang H, Yang S, Chien M. MAOB expression correlates with a favourable prognosis in prostate cancer, and its genetic variants are associated with the metastasis of the disease. J Cell Mol Med 2024; 28:e18229. [PMID: 38520217 PMCID: PMC10960177 DOI: 10.1111/jcmm.18229] [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: 01/19/2024] [Revised: 02/21/2024] [Accepted: 02/24/2024] [Indexed: 03/25/2024] Open
Abstract
Monoamine oxidase B (MAOB), a neurotransmitter-degrading enzyme, was reported to reveal conflicting roles in various cancers. However, the functional role of MAOB and impacts of its genetic variants on prostate cancer (PCa) is unknown. Herein, we genotyped four loci of MAOB single-nucleotide polymorphisms (SNPs), including rs1799836 (A/G), rs3027452 (G/A), rs6651806 (A/C) and rs6324 (G/A) in 702 PCa Taiwanese patients. We discovered that PCa patients carrying the MAOB rs6324 A-allele exhibited an increased risk of having a high initial prostate-specific antigen (iPSA) level (>10 ng/mL). Additionally, patients with the rs3027452 A-allele had a higher risk of developing distal metastasis, particularly in the subpopulation with high iPSA levels. In a subpopulation without postoperative biochemical recurrence, patients carrying the rs1799836 G-allele had a higher risk of developing lymph node metastasis and recurrence compared to those carrying the A-allele. Furthermore, genotype screening in PCa cell lines revealed that cells carrying the rs1799836 G-allele expressed lower MAOB levels than those carrying the A-allele. Functionally, overexpression and knockdown of MAOB in PCa cells respectively suppressed and enhanced cell motility and proliferation. In clinical observations, correlations of lower MAOB expression levels with higher Gleason scores, advanced clinical T stages, tumour metastasis, and poorer prognosis in PCa patients were noted. Our findings suggest that MAOB may act as a suppressor of PCa progression, and the rs3027452 and rs1799836 genetic variants of MAOB are linked to PCa metastasis within the Taiwanese population.
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Affiliation(s)
- Hsiang‐Ching Huang
- Graduate Institute of Medical Sciences, College of MedicineTaipei Medical UniversityTaipeiTaiwan
| | - Yi‐Hsien Hsieh
- Institute of MedicineChung Shan Medical UniversityTaichungTaiwan
- Department of Medical ResearchChung Shan Medical University HospitalTaichungTaiwan
| | - Chi‐Hao Hsiao
- Department of Urology, School of Medicine, College of Medicine and TMU Research Center of Urology and Kidney (TMU‐RCUK)Taipei Medical UniversityTaipeiTaiwan
- Department of Urology, Wan Fang HospitalTaipei Medical UniversityTaipeiTaiwan
| | - Chia‐Yen Lin
- Division of Urology, Department of SurgeryTaichung Veterans General HospitalTaichungTaiwan
- School of MedicineChung Shan Medical UniversityTaichungTaiwan
- School of MedicineNational Yang Ming Chiao Tung UniversityTaipeiTaiwan
| | - Shian‐Shiang Wang
- Division of Urology, Department of SurgeryTaichung Veterans General HospitalTaichungTaiwan
- School of MedicineChung Shan Medical UniversityTaichungTaiwan
- Department of Applied ChemistryNational Chi Nan UniversityNantouTaiwan
| | - Kuo‐Hao Ho
- Graduate Institute of Clinical Medicine, College of MedicineTaipei Medical UniversityTaipeiTaiwan
| | - Lun‐Ching Chang
- Department of Mathematical SciencesFlorida Atlantic UniversityBoca RatonFloridaUSA
| | - Huei‐Mei Huang
- Graduate Institute of Medical Sciences, College of MedicineTaipei Medical UniversityTaipeiTaiwan
| | - Shun‐Fa Yang
- Institute of MedicineChung Shan Medical UniversityTaichungTaiwan
- Department of Medical ResearchChung Shan Medical University HospitalTaichungTaiwan
| | - Ming‐Hsien Chien
- Graduate Institute of Clinical Medicine, College of MedicineTaipei Medical UniversityTaipeiTaiwan
- Pulmonary Research CenterWan Fang Hospital, Taipei Medical UniversityTaipeiTaiwan
- Traditional Herbal Medicine Research CenterTaipei Medical University HospitalTaipeiTaiwan
- TMU Research Center of Cancer Translational MedicineTaipei Medical UniversityTaipeiTaiwan
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Alemu A, Åstrand J, Montesinos-López OA, Isidro Y Sánchez J, Fernández-Gónzalez J, Tadesse W, Vetukuri RR, Carlsson AS, Ceplitis A, Crossa J, Ortiz R, Chawade A. Genomic selection in plant breeding: Key factors shaping two decades of progress. Mol Plant 2024; 17:552-578. [PMID: 38475993 DOI: 10.1016/j.molp.2024.03.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 01/22/2024] [Accepted: 03/08/2024] [Indexed: 03/14/2024]
Abstract
Genomic selection, the application of genomic prediction (GP) models to select candidate individuals, has significantly advanced in the past two decades, effectively accelerating genetic gains in plant breeding. This article provides a holistic overview of key factors that have influenced GP in plant breeding during this period. We delved into the pivotal roles of training population size and genetic diversity, and their relationship with the breeding population, in determining GP accuracy. Special emphasis was placed on optimizing training population size. We explored its benefits and the associated diminishing returns beyond an optimum size. This was done while considering the balance between resource allocation and maximizing prediction accuracy through current optimization algorithms. The density and distribution of single-nucleotide polymorphisms, level of linkage disequilibrium, genetic complexity, trait heritability, statistical machine-learning methods, and non-additive effects are the other vital factors. Using wheat, maize, and potato as examples, we summarize the effect of these factors on the accuracy of GP for various traits. The search for high accuracy in GP-theoretically reaching one when using the Pearson's correlation as a metric-is an active research area as yet far from optimal for various traits. We hypothesize that with ultra-high sizes of genotypic and phenotypic datasets, effective training population optimization methods and support from other omics approaches (transcriptomics, metabolomics and proteomics) coupled with deep-learning algorithms could overcome the boundaries of current limitations to achieve the highest possible prediction accuracy, making genomic selection an effective tool in plant breeding.
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Affiliation(s)
- Admas Alemu
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden.
| | - Johanna Åstrand
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden; Lantmännen Lantbruk, Svalöv, Sweden
| | | | - Julio Isidro Y Sánchez
- Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA), Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo-UPM, 28223 Madrid, Spain
| | - Javier Fernández-Gónzalez
- Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA), Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo-UPM, 28223 Madrid, Spain
| | - Wuletaw Tadesse
- International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat, Morocco
| | - Ramesh R Vetukuri
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Anders S Carlsson
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | | | - José Crossa
- International Maize and Wheat Improvement Center (CIMMYT), Km 45, Carretera México-Veracruz, Texcoco, México 52640, Mexico
| | - Rodomiro Ortiz
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden.
| | - Aakash Chawade
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
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da Cunha Agostini L, de Paula W, Melo AS, Silva NNT, Faria Lopes AC, de Almeida Belo V, Coura-Vital W, de Medeiros Teixeira LF, Lima AA, da Silva GN. Single nucleotide polymorphism (SNP) rs4291 of the angiotensin-converting enzyme (ACE) gene is associated with the response to losartan treatment in hypertensive patients. Mol Biol Rep 2024; 51:458. [PMID: 38551694 DOI: 10.1007/s11033-024-09437-1] [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: 02/05/2024] [Accepted: 03/11/2024] [Indexed: 04/02/2024]
Abstract
Arterial hypertension is characterized by systolic pressure ≥ 140 mmHg and/or diastolic pressure ≥ 90 mmHg and its treatment consists of the use of antihypertensive drugs, as losartan and hydrochlorothiazide. Blood pressure is regulated by angiotensin-converting enzyme (ACE) and polymorphisms in the ACE gene are associated to a greater predisposition to hypertension and response to treatment. The aim of this study was to evaluate the association of genetic polymorphisms of ACE rs4363, rs4291 and rs4335 and the response to antihypertensive drugs in hypertensive patients from Ouro Preto/MG, Brazil. A case-control study was carried out with 87 hypertensive patients being treated with losartan and 75 with hydrochlorothiazide, who answered a questionnaire and had blood samples collected. Biochemical analyzes were performed on serum using UV/Vis spectrophotometry and identification of ACE variants rs4363, rs4291 and rs4335 was performed by real-time PCR using the TaqMan® system. Univariate logistic regression test was performed to compare categorical data in STATA 13.0 software. The results showed that there was an influence of ACE polymorphisms on the response to losartan, demonstrating that AT or TT genotypes of rs4291 were more frequent in the group of controlled AH (54.9%), indicating that these individuals are 2.8 times more likely to of being controlled AH (95% CI 1.12-6.80, p. =0.026) compared to those with AA genotype. In contrast, no influence of ACE polymorphisms on the response to hydrochlorothiazide was observed. In conclusion, the presence of the T allele of the rs4291 variant was associated to controled blood pressure when losartan was used as an antihypertensive agent. These results show the importance of pharmacogenetic studies to detect genetic characteristics, enabling therapeutic individuality and reducing costs for the healthcare system.
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Affiliation(s)
- Lívia da Cunha Agostini
- Programa de Pós-Graduação em Ciências Farmacêuticas (CiPharma), Escola de Farmácia, Universidade Federal de Ouro Preto, Ouro Preto, Brazil
| | - Waléria de Paula
- Programa de Pós-Graduação em Ciências Farmacêuticas (CiPharma), Escola de Farmácia, Universidade Federal de Ouro Preto, Ouro Preto, Brazil
| | - André Sacramento Melo
- Departamento de Análises Clínicas (DEACL), Escola de Farmácia, Universidade Federal de Ouro Preto, Ouro Preto, Brazil
| | | | - Ana Cláudia Faria Lopes
- Departamento de Análises Clínicas (DEACL), Escola de Farmácia, Universidade Federal de Ouro Preto, Ouro Preto, Brazil
| | - Vanessa de Almeida Belo
- Programa de Pós-Graduação em Ciências Farmacêuticas (CiPharma), Escola de Farmácia, Universidade Federal de Ouro Preto, Ouro Preto, Brazil
- Departamento de Farmácia (DEFAR), Escola de Farmácia, Universidade Federal de Ouro Preto, Ouro Preto, Brazil
| | - Wendel Coura-Vital
- Programa de Pós-Graduação em Ciências Farmacêuticas (CiPharma), Escola de Farmácia, Universidade Federal de Ouro Preto, Ouro Preto, Brazil
- Departamento de Análises Clínicas (DEACL), Escola de Farmácia, Universidade Federal de Ouro Preto, Ouro Preto, Brazil
| | | | - Angélica Alves Lima
- Programa de Pós-Graduação em Ciências Farmacêuticas (CiPharma), Escola de Farmácia, Universidade Federal de Ouro Preto, Ouro Preto, Brazil
- Departamento de Análises Clínicas (DEACL), Escola de Farmácia, Universidade Federal de Ouro Preto, Ouro Preto, Brazil
| | - Glenda Nicioli da Silva
- Programa de Pós-Graduação em Ciências Farmacêuticas (CiPharma), Escola de Farmácia, Universidade Federal de Ouro Preto, Ouro Preto, Brazil.
- Departamento de Análises Clínicas (DEACL), Escola de Farmácia, Universidade Federal de Ouro Preto, Ouro Preto, Brazil.
- Departamento de Análises Clínicas (DEACL), Escola de Farmácia, Universidade Federal de Ouro Preto, Morro do Cruzeiro, s/n, Ouro Preto, MG, CEP 35402-163, Brazil.
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Hassan SH, Auda IG, Ali EN, Alosami MH, Hussein RH. Role of endoplasmic reticulum aminopeptidase-1 gene polymorphism (rs13167972) in occurrence susceptibility of ankylosing spondylitis in a sample of Iraqi male patients. Mol Biol Rep 2024; 51:462. [PMID: 38551779 DOI: 10.1007/s11033-024-09438-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 03/11/2024] [Indexed: 04/02/2024]
Abstract
BACKGROUND Ankylosing spondylitis (AS) is a chronic and systemic seronegative inflammatory spondyloarthropathy, an autoimmune disease that has been associated with impaired Endoplasmic Reticulum Aminopeptidase (ERAP)-1 activity, which is involved in priming antigenic peptides. The purpose of this study is to investigate the association of 3-UTR of ERAP1 gene polymorphism (rs13167972) with the AS occurrence susceptibility in a sample of Iraqi male patients. METHODS The AS patients were diagnosed clinically and by magnetic resonance imaging (MRI) and other clinical and laboratory criteria like symptoms, increased C-reactive protein (CRP), and erythrocyte sedimentation rate (ESR). The blood grouping and Body Mass Index (BMI) were also investigated to be associated with AS occurrence. The genotyping of the 3-UTR region of the ERAP1 gene (rs13167972) was done by Sanger sequencing. RESULTS The results revealed that the AS occurred significantly in the age group of 20-35 years (p = 0.013). The BMI shows that the AS patients were overweighted males (p = 0.013) and the most predominant blood group in AS patients was O- (p = 0.002). The ESR and serum level of CRP were significantly raised in AS patient sera (< 0.001). The results of the receiver-operating characteristics curve analysis (ROC) revealed that the CRP (AUC: 0.995, cut-off: 2.48 mg/L, had 95% %sensitivity, 100% specificity, p < 0.001) is more discriminative than BMI (AUC: 0.300, cut-off: 46.91 kg, had 0% sensitivity, 100% specificity, p = 0.001), and ESR (AUC: 0.808, cut-off: 7.50 mm/hr, had 60% sensitivity, 88% specificity, p < 0.001) in distinguishing between AS patients and control group. The genotyping of the 3-UTR region of ERAP1 gene (rs13167972) result shows that the AG and GG genotypes are significantly occurring in AS patients (70%, OR: 2.33, 95%CI: 1.02-5.36, p = 0.04). The G allele is significantly occurring in AS patients (47%, OR: 2.07, 95CI%: 1.15-3.71, p = 0.01). CONCLUSION The AS occurred in young overweight males with blood group O-. The AG and GG genotypes are risk factors for AS development while the G allele is a risk factor that increases the chances for disease incidence.
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Affiliation(s)
| | - Ibtesam Ghadban Auda
- Department of Biology, Mustansiriyah University, College of Science, Baghdad, Iraq
| | - Ekhlass N Ali
- Department of Biology, Mustansiriyah University, College of Science, Baghdad, Iraq
| | | | - Ranya H Hussein
- Mustansiriyah University, College of Tourism Sciences, Baghdad, Iraq
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Berkowitz E, Falik Zaccai TC, Irge D, Gur I, Tiosano B, Kesler A. A genetic survey of patients with familial idiopathic intracranial hypertension residing in a Middle Eastern village: genetic association study. Eur J Med Res 2024; 29:194. [PMID: 38528581 DOI: 10.1186/s40001-024-01800-z] [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: 11/07/2022] [Accepted: 03/18/2024] [Indexed: 03/27/2024] Open
Abstract
BACKGROUND The aim of this study was to determine whether genetic variants are associated with idiopathic intracranial hypertension (IIH) in a unique village where many of the IIH patients have familial ties, a homogenous population and a high prevalence of consanguinity. Several autosomal recessive disorders are common in this village and its population is considered at a high risk for genetic disorders. METHODS The samples were genotyped by the Ilumina OmniExpress-24 Kit, and analyzed by the Eagle V2.4 and DASH software package to cluster haplotypes shared between our cohort. Subsequently, we searched for specific haplotypes that were significantly associated with the patient groups. RESULTS Fourteen patients and 30 controls were included. Samples from 22 female participants (11 patients and 11 controls) were evaluated for haplotype clustering and genome-wide association studies (GWAS). A total of 710,000 single nucleotide polymorphisms (SNPs) were evaluated. Candidate areas positively associated with IIH included genes located on chromosomes 16, 8 (including the CA5A and BANP genes, p < 0.01), and negatively associated with genes located on chromosomes 1 and 6 (including PBX1, LMX1A, ESR1 genes, p < 0.01). CONCLUSIONS We discovered new loci possibly associated with IIH by employing a GWAS technique to estimate the associations with haplotypes instead of specific SNPs. This method can in all probability be used in cases where there is a limited amount of samples but strong familial connections. Several loci were identified that might be strong candidates for follow-up studies in other well-phenotypes cohorts.
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Affiliation(s)
- Eran Berkowitz
- Department of Ophthalmology, Hillel Yaffe Medical Center, 1 Ha-Shalom Street, 38100, Hadera, Israel.
- The Adelson School of Medicine, Ariel University, Ariel, Israel.
- The Ruth and Bruce Rappaport Faculty of Medicine, Technion, Haifa, Israel.
| | | | - Dana Irge
- Genetic Institue, Meir Medical center, Kfar Saba, Israel
| | - Inbar Gur
- Department of Ophthalmology, Hillel Yaffe Medical Center, 1 Ha-Shalom Street, 38100, Hadera, Israel
| | - Beatrice Tiosano
- Department of Ophthalmology, Hillel Yaffe Medical Center, 1 Ha-Shalom Street, 38100, Hadera, Israel
| | - Anat Kesler
- Department of Ophthalmology, Hillel Yaffe Medical Center, 1 Ha-Shalom Street, 38100, Hadera, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- The Adelson School of Medicine, Ariel University, Ariel, Israel
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Goljan E, Abouelhoda M, Tahir A, ElKalioby M, Meyer B, Monies D. Large-scale next generation sequencing based analysis of SLCO1B1 pharmacogenetics variants in the Saudi population. Hum Genomics 2024; 18:30. [PMID: 38523294 PMCID: PMC10962151 DOI: 10.1186/s40246-024-00594-9] [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: 10/12/2023] [Accepted: 02/29/2024] [Indexed: 03/26/2024] Open
Abstract
BACKGROUND SLCO1B1 plays an important role in mediating hepatic clearance of many different drugs including statins, angiotensin-converting enzyme inhibitors, chemotherapeutic agents and antibiotics. Several variants in SLCO1B1 have been shown to have a clinically significant impact, in relation to efficacy of these medications. This study provides a comprehensive overview of SLCO1B1 variation in Saudi individuals, one of the largest Arab populations in the Middle East. METHODS The dataset of 11,889 (9,961 exomes and 1,928 pharmacogenetic gene panel) Saudi nationals, was used to determine the presence and frequencies of SLCO1B1 variants, as described by the Clinical Pharmacogenetic Implementation Consortium (CPIC). RESULTS We identified 141 previously described SNPs, of which rs2306283 (50%) and rs4149056 (28%), were the most common. In addition, we observed six alleles [*15 (24.7%) followed by *20 (8.04%), *14 (5.86%), *5 (3.84%), *31 (0.21%) and *9 (0.03%)] predicted to be clinically actionable. Allele diplotype to phenotype conversion revealed 41 OATP1B1 diplotypes. We estimated the burden of rare, and novel predicted deleterious variants, resulting from 17 such alterations. CONCLUSIONS The data we present, from one of the largest Arab cohorts studied to date, provides the most comprehensive overview of SLCO1B1 variants, and the subsequent OATP1B1 activity of this ethnic group, which thus far remains relatively underrepresented in available international genomic databases. We believe that the presented data provides a basis for further clinical investigations and the application of personalized statin drug therapy guidance in Arabs.
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Affiliation(s)
- Ewa Goljan
- Clinical Genomics, Centre for Genomic Medicine, King Faisal Specialist Hospital and Research Centre, P.O. Box 3354, Riyadh, 11211, Saudi Arabia
| | - Mohammed Abouelhoda
- Computational Biosciences, Centre for Genomic Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Asma Tahir
- Computational Biosciences, Centre for Genomic Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Mohamed ElKalioby
- Computational Biosciences, Centre for Genomic Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Brian Meyer
- Clinical Genomics, Centre for Genomic Medicine, King Faisal Specialist Hospital and Research Centre, P.O. Box 3354, Riyadh, 11211, Saudi Arabia
| | - Dorota Monies
- Clinical Genomics, Centre for Genomic Medicine, King Faisal Specialist Hospital and Research Centre, P.O. Box 3354, Riyadh, 11211, Saudi Arabia.
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Li J, Wang F, Li Z, Feng J, Men Y, Han J, Xia J, Zhang C, Han Y, Chen T, Zhao Y, Zhou S, Da Y, Chai G, Hao J. Integrative multi-omics analysis identifies genetically supported druggable targets and immune cell specificity for myasthenia gravis. J Transl Med 2024; 22:302. [PMID: 38521921 PMCID: PMC10960998 DOI: 10.1186/s12967-024-04994-2] [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: 09/28/2023] [Accepted: 02/12/2024] [Indexed: 03/25/2024] Open
Abstract
BACKGROUND Myasthenia gravis (MG) is a chronic autoimmune disorder characterized by fluctuating muscle weakness. Despite the availability of established therapies, the management of MG symptoms remains suboptimal, partially attributed to lack of efficacy or intolerable side-effects. Therefore, new effective drugs are warranted for treatment of MG. METHODS By employing an analytical framework that combines Mendelian randomization (MR) and colocalization analysis, we estimate the causal effects of blood druggable expression quantitative trait loci (eQTLs) and protein quantitative trait loci (pQTLs) on the susceptibility of MG. We subsequently investigated whether potential genetic effects exhibit cell-type specificity by utilizing genetic colocalization analysis to assess the interplay between immune-cell-specific eQTLs and MG risk. RESULTS We identified significant MR results for four genes (CDC42BPB, CD226, PRSS36, and TNFSF12) using cis-eQTL genetic instruments and three proteins (CTSH, PRSS8, and CPN2) using cis-pQTL genetic instruments. Six of these loci demonstrated evidence of colocalization with MG susceptibility (posterior probability > 0.80). We next undertook genetic colocalization to investigate cell-type-specific effects at these loci. Notably, we identified robust evidence of colocalization, with a posterior probability of 0.854, linking CTSH expression in TH2 cells and MG risk. CONCLUSIONS This study provides crucial insights into the genetic and molecular factors associated with MG susceptibility, singling out CTSH as a potential candidate for in-depth investigation and clinical consideration. It additionally sheds light on the immune-cell regulatory mechanisms related to the disease. However, further research is imperative to validate these targets and evaluate their feasibility for drug development.
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Affiliation(s)
- Jiao Li
- Department of Neurology, Xuanwu Hospital, National Center for Neurological Disorders, Capital Medical University, Beijing, 100053, China
- Beijing Municipal Geriatric Medical Research Center, Beijing, China
- Key Laboratory for Neurodegenerative Diseases of Ministry of Education, Beijing, China
| | - Fei Wang
- Department of Neurology, Xuanwu Hospital, National Center for Neurological Disorders, Capital Medical University, Beijing, 100053, China
- Key Laboratory for Neurodegenerative Diseases of Ministry of Education, Beijing, China
| | - Zhen Li
- Department of Neurology, Xuanwu Hospital, National Center for Neurological Disorders, Capital Medical University, Beijing, 100053, China
| | - Jingjing Feng
- Department of Neurology, Xuanwu Hospital, National Center for Neurological Disorders, Capital Medical University, Beijing, 100053, China
| | - Yi Men
- Department of Neurology, Xuanwu Hospital, National Center for Neurological Disorders, Capital Medical University, Beijing, 100053, China
| | - Jinming Han
- Department of Neurology, Xuanwu Hospital, National Center for Neurological Disorders, Capital Medical University, Beijing, 100053, China
| | - Jiangwei Xia
- Department of Neurology, Xuanwu Hospital, National Center for Neurological Disorders, Capital Medical University, Beijing, 100053, China
| | - Chen Zhang
- Department of Neurology, Xuanwu Hospital, National Center for Neurological Disorders, Capital Medical University, Beijing, 100053, China
| | - Yilai Han
- Department of Neurology, Xuanwu Hospital, National Center for Neurological Disorders, Capital Medical University, Beijing, 100053, China
| | - Teng Chen
- Department of Neurology, Xuanwu Hospital, National Center for Neurological Disorders, Capital Medical University, Beijing, 100053, China
| | - Yinan Zhao
- Department of Neurology, Xuanwu Hospital, National Center for Neurological Disorders, Capital Medical University, Beijing, 100053, China
| | - Sirui Zhou
- Department of Human Genetics, McGill University, Montréal, QC, Canada
| | - Yuwei Da
- Department of Neurology, Xuanwu Hospital, National Center for Neurological Disorders, Capital Medical University, Beijing, 100053, China
| | - Guoliang Chai
- Department of Neurology, Xuanwu Hospital, National Center for Neurological Disorders, Capital Medical University, Beijing, 100053, China.
- Beijing Municipal Geriatric Medical Research Center, Beijing, China.
| | - Junwei Hao
- Department of Neurology, Xuanwu Hospital, National Center for Neurological Disorders, Capital Medical University, Beijing, 100053, China.
- Beijing Municipal Geriatric Medical Research Center, Beijing, China.
- Key Laboratory for Neurodegenerative Diseases of Ministry of Education, Beijing, China.
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Bishnoi S, Jyotsana B, Kumar V, Prakash V, Ranjan R, Narnaware SD, Pannu U. Toll like receptor 4 (TLR4) gene polymorphism and its association with somatic cell score and milk production traits in Indian dromedary camels. Anim Biotechnol 2024; 35:2331642. [PMID: 38520296 DOI: 10.1080/10495398.2024.2331642] [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: 03/25/2024]
Abstract
Our study aimed to explore the genetic variation in the Toll-like receptor 4 (TLR4) gene and establish its association with somatic cell score (SCS) and milk production traits in four Indian camel breeds namely Bikaneri, Kachchhi, Jaisalmeri and Mewari. TLR4 gene fragment of 573 bp spanning 5' UTR, exon-1 and partial intron-1 region was amplified and genotyped using the PCR-sequence based typing method. Only one SNP located at position C472T was identified. Genotyping revealed two alleles (C and T) and three genotypes: CC, CT and TT. The genotype frequencies for CC, CT and TT were 0.116, 0.326 and 0.558 and allele frequencies for C and T alleles were 0.279 and 0.721, respectively. Association study inferred that the effect of genotype on SCS, lactation yield (LY) and peak yield (PY) was non-significant however heterozygote (CT) genotypes recorded lower SCS and higher LY and PY. It can be concluded that the TLR4 gene possesses limited genetic variation, depicting polymorphism at a single locus in Indian camel breeds with a predominance of the TT genotype. The association study indicated that heterozygote animals possess better udder health and production performance, the statistical significance of which needs to be established using a large data set.
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Affiliation(s)
- Seema Bishnoi
- CVAS, Rajasthan University of Veterinary & Animal Sciences, Bikaner, Rajasthan, India
| | - Basanti Jyotsana
- ICAR - National Research Centre on Camel, Bikaner, Rajasthan, India
| | - Virendra Kumar
- CVAS, Rajasthan University of Veterinary & Animal Sciences, Bikaner, Rajasthan, India
| | - Ved Prakash
- ICAR - National Research Centre on Camel, Bikaner, Rajasthan, India
| | - Rakesh Ranjan
- ICAR - National Research Centre on Camel, Bikaner, Rajasthan, India
| | | | - Urmila Pannu
- CVAS, Rajasthan University of Veterinary & Animal Sciences, Bikaner, Rajasthan, India
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Fayedeh F, Khorashadizadeh S, Yousefi M, Abbasifar S, Erfanian N, Rafiee M, Ghasemi F. CTLA-4 expression and polymorphisms in Schizophrenia; a systematic review of literature. Mol Biol Rep 2024; 51:431. [PMID: 38520576 DOI: 10.1007/s11033-024-09299-7] [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: 07/08/2023] [Accepted: 01/29/2024] [Indexed: 03/25/2024]
Abstract
Schizophrenia constitutes a severe psychiatric disorder with detrimental impacts on individuals, their support systems, and the broader economy. Extensive research has revealed a notable association between variations in the Cytotoxic T-lymphocyte-associated protein 4 (CTLA-4) gene and an increased susceptibility to schizophrenia.This study represents the first systematic review of the literature investigating the impact of CTLA-4 polymorphisms and expression on the development and progression of schizophrenia.Our investigation involved a comprehensive search strategy, using a combination of title, abstract, and MESH terms in four databases, including PubMed, Scopus, Web of Science, and Google Scholar, until August 29th, 2023. The complete texts of the identified records were obtained and rigorously assessed based on predefined exclusion and inclusion criteria. Out of the numerous records, a total of 88 were identified through the databases. 10 studies met the criteria; therefore, their quality was assessed and included in this systematic study. The records were then categorized into polymorphism and expression groups. Our investigation emphasizes an association between rs3087243, rs231779, rs231777, rs16840252, rs5742909, and rs231775 polymorphisms and the development of schizophrenia. The results demonstrate a correlation between CTLA-4 polymorphisms and schizophrenia, compelling the need for further research to thoroughly examine the role of CTLA-4 in schizophrenia and other psychiatric disorders.
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Affiliation(s)
- Farzad Fayedeh
- Student Research Committee, Birjand University of Medical Sciences, Birjand, Iran
| | | | - Mohammad Yousefi
- Student Research Committee, Birjand University of Medical Sciences, Birjand, Iran
| | - Sara Abbasifar
- Student Research Committee, Birjand University of Medical Sciences, Birjand, Iran
| | - Nafiseh Erfanian
- Student Research Committee, Birjand University of Medical Sciences, Birjand, Iran
| | - Mitra Rafiee
- Cellular and Molecular Research Center, Department of Immunology, Birjand University of Medical Sciences, Birjand, Iran.
| | - Fahimeh Ghasemi
- Cellular and Molecular Research Center, Birjand University of Medical Sciences, Birjand, Iran.
- Department of Medical Biotechnology, School of Medicine, Birjand University of Medical Sciences, Birjand, Iran.
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Shi W, Zhang Q, Lu Y, Liu J, Ma X, Xie Z, Zhang G, Chang M, Tian Y. Association of single nucleotide polymorphisms in ITLN1 gene with ischemic stroke risk in Xi'an population, Shaanxi province. PeerJ 2024; 12:e16934. [PMID: 38529304 PMCID: PMC10962333 DOI: 10.7717/peerj.16934] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 01/22/2024] [Indexed: 03/27/2024] Open
Abstract
Background Ischemic stroke (IS) is the main cause of death and adult disability. However, the pathogenesis of this complicated disease is unknown. The present study aimed to assess the relationship between ITLN1 single nucleotide polymorphisms (SNPs) and the susceptibility to IS in Xi'an population, Shaanxi province. Methods In this study, we designed polymerase chain reaction (PCR) primers located at -3,308 bp upstream of the transcription initiation site within promoter region of the ITLN1 gene. The target fragment was amplified by PCR and identified by agarose gel electrophoresis. Sanger sequencing was then performed in the samples extracted from a cohort comprising 1,272 participants (636 controls and 636 cases), and the obtained sequences were compared with the reference sequences available on the National Center for Biotechnology Information (NCBI) website to detect SNPs in the ITLN1 gene promoter region. Logistic regression analysis was employed to assess the relationship between ITLN1 polymorphisms and IS risk, with adjustments for age and gender. Significant positive results were tested by false-positive report probability (FPRP) and false discovery rate (FDR). The interaction among noteworthy SNPs and their predictive relationship with IS risk were explored using the Multi-Factor Dimensionality Reduction (MDR) software. Results The results of Sanger sequencing were compared with the reference sequences on the NCBI website, and we found 14 SNPs in ITLN1 gene promoter satisfied Hardy-Weinberg equilibrium (HWE). Logistic regression analysis showed that ITLN1 was associated with a decreased risk of IS (rs6427553: Homozygous C/C: adjusted OR: 0.69, 95% CI [0.48-0.97]; Log-additive: adjusted OR: 0.83, 95% CI [0.70-0.98]; rs7411035: Homozygous G/G: adjusted OR: 0.66, 95% CI [0.47-0.94]; Dominant G/T-G/G: adjusted OR: 0.78, 95% CI [0.62-0.98]; Log-additive: adjusted OR: 0.81, 95% CI [0.69-0.96]; rs4656958: Heterozygous G/A: adjusted OR: 0.74, 95% CI [0.59-0.94]; Homozygous A/A: adjusted OR: 0.51, 95% CI [0.31-0.84]; Dominant G/A-A/A: adjusted OR: 0.71, 95% CI [0.57-0.89]; Recessive A/A: adjusted OR: 0.59, 95% CI [0.36-0.96]; Log-additive: adjusted OR: 0.73, 95% CI [0.61-0.88]), especially in people aged less than 60 years and males. Conclusions In short, our study revealed a correlation between ITLN1 variants (rs6427553, rs7411035 and rs4656958) and IS risk in Xi'an population, Shaanxi province, laying a foundation for ITLN1 gene as a potential biomarker for predicting susceptibility to IS.
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Affiliation(s)
- Wenzhen Shi
- Clinical Medical Research Center, Xi’an Key Laboratory of Cardiovascular and Cerebrovascular Diseases, the Affiliated Hospital of Northwest University, Xi’an No.3 Hospital, Xi’an, China
| | - Qi Zhang
- Clinical Medical Research Center, Xi’an Key Laboratory of Cardiovascular and Cerebrovascular Diseases, the Affiliated Hospital of Northwest University, Xi’an No.3 Hospital, Xi’an, China
| | - Ying Lu
- Department of Neurology, the Affiliated Hospital of Northwest University, Xi’an No.3 Hospital, Xi’an, China
| | - Jie Liu
- Clinical Medical Research Center, Xi’an Key Laboratory of Cardiovascular and Cerebrovascular Diseases, the Affiliated Hospital of Northwest University, Xi’an No.3 Hospital, Xi’an, China
| | - Xiaojuan Ma
- Clinical Medical Research Center, Xi’an Key Laboratory of Cardiovascular and Cerebrovascular Diseases, the Affiliated Hospital of Northwest University, Xi’an No.3 Hospital, Xi’an, China
| | - Zhen Xie
- Xi’an Key Laboratory of Cardiovascular and Cerebrovascular Diseases, The College of Life Sciences and Medicine, Northwest University, Xi’an, China
| | - Gejuan Zhang
- Department of Neurology, the Affiliated Hospital of Northwest University, Xi’an No.3 Hospital, Xi’an, China
| | - Mingze Chang
- Department of Neurology, the Affiliated Hospital of Northwest University, Xi’an No.3 Hospital, Xi’an, China
| | - Ye Tian
- Department of Neurology, the Affiliated Hospital of Northwest University, Xi’an No.3 Hospital, Xi’an, China
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Felício D, Alves-Ferreira M, Santos M, Quintas M, Lopes AM, Lemos C, Pinto N, Martins S. Integrating functional scoring and regulatory data to predict the effect of non-coding SNPs in a complex neurological disease. Brief Funct Genomics 2024; 23:138-149. [PMID: 37254524 DOI: 10.1093/bfgp/elad020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 03/13/2023] [Accepted: 05/09/2023] [Indexed: 06/01/2023] Open
Abstract
Most SNPs associated with complex diseases seem to lie in non-coding regions of the genome; however, their contribution to gene expression and disease phenotype remains poorly understood. Here, we established a workflow to provide assistance in prioritising the functional relevance of non-coding SNPs of candidate genes as susceptibility loci in polygenic neurological disorders. To illustrate the applicability of our workflow, we considered the multifactorial disorder migraine as a model to follow our step-by-step approach. We annotated the overlap of selected SNPs with regulatory elements and assessed their potential impact on gene expression based on publicly available prediction algorithms and functional genomics information. Some migraine risk loci have been hypothesised to reside in non-coding regions and to be implicated in the neurotransmission pathway. In this study, we used a set of 22 non-coding SNPs from neurotransmission and synaptic machinery-related genes previously suggested to be involved in migraine susceptibility based on our candidate gene association studies. After prioritising these SNPs, we focused on non-reported ones that demonstrated high regulatory potential: (1) VAMP2_rs1150 (3' UTR) was predicted as a target of hsa-mir-5010-3p miRNA, possibly disrupting its own gene expression; (2) STX1A_rs6951030 (proximal enhancer) may affect the binding affinity of zinc-finger transcription factors (namely ZNF423) and disturb TBL2 gene expression; and (3) SNAP25_rs2327264 (distal enhancer) expected to be in a binding site of ONECUT2 transcription factor. This study demonstrated the applicability of our practical workflow to facilitate the prioritisation of potentially relevant non-coding SNPs and predict their functional impact in multifactorial neurological diseases.
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Affiliation(s)
- Daniela Felício
- Instituto de Investigação e Inovação em Saúde (i3S), Porto 4200-135, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto 4200-135, Portugal
- Instituto Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, Porto 4050-313, Portugal
| | - Miguel Alves-Ferreira
- Instituto de Investigação e Inovação em Saúde (i3S), Porto 4200-135, Portugal
- Instituto Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, Porto 4050-313, Portugal
- Unit for Genetic and Epidemiological Research in Neurological Diseases (UnIGENe), Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto 4200-135, Portugal
- Centre for Predictive and Preventive Genetics (CGPP), Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto 4200-135, Portugal
| | - Mariana Santos
- Instituto de Investigação e Inovação em Saúde (i3S), Porto 4200-135, Portugal
- Unit for Genetic and Epidemiological Research in Neurological Diseases (UnIGENe), Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto 4200-135, Portugal
| | - Marlene Quintas
- Instituto de Investigação e Inovação em Saúde (i3S), Porto 4200-135, Portugal
- Instituto Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, Porto 4050-313, Portugal
- Unit for Genetic and Epidemiological Research in Neurological Diseases (UnIGENe), Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto 4200-135, Portugal
| | - Alexandra M Lopes
- Instituto de Investigação e Inovação em Saúde (i3S), Porto 4200-135, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto 4200-135, Portugal
- Centre for Predictive and Preventive Genetics (CGPP), Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto 4200-135, Portugal
| | - Carolina Lemos
- Instituto de Investigação e Inovação em Saúde (i3S), Porto 4200-135, Portugal
- Instituto Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, Porto 4050-313, Portugal
- Unit for Genetic and Epidemiological Research in Neurological Diseases (UnIGENe), Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto 4200-135, Portugal
| | - Nádia Pinto
- Instituto de Investigação e Inovação em Saúde (i3S), Porto 4200-135, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto 4200-135, Portugal
- Centro de Matemática da Universidade do Porto (CMUP), Porto 4169-007, Portugal
| | - Sandra Martins
- Instituto de Investigação e Inovação em Saúde (i3S), Porto 4200-135, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto 4200-135, Portugal
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Worku D, Verma A. Genetic variation in bovine LAP3 and SIRT1 genes associated with fertility traits in dairy cattle. BMC Genom Data 2024; 25:32. [PMID: 38500063 PMCID: PMC10949778 DOI: 10.1186/s12863-024-01209-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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 02/15/2024] [Indexed: 03/20/2024] Open
Abstract
BACKGROUND The genetic progress of fertility and reproduction traits in dairy cattle has been constrained by the low heritability of these traits. Identifying candidate genes and variants associated with fertility and reproduction could enhance the accuracy of genetic selection and expedite breeding process of dairy cattle with low-heritability traits. While the bovine LAP3 and SIRT1 genes exhibit well-documented associations with milk production traits in dairy cattle, their effect on cow fertility have not yet been explored. Eleven single nucleotide polymorphisms (SNPs), comprising five in the promoter (rs717156555: C > G, rs720373055: T > C, rs516876447: A > G, rs461857269: C > T and rs720349928: G > A), two in 5'UTR (rs722359733: C > T and rs462932574: T > G), two in intron 12 (rs110932626: A > G and rs43702363: C > T), and one in 3'UTR of exon 13 (rs41255599: C > T) in LAP3 and one in SIRT1 (rs718329990:T > C) genes, have previously been reported to be associated with various traits of milk production and clinical mastitis in Sahiwal and Karan Fries dairy cattle. In this study, the analysis primarily aimed to assess the impact of SNPs within LAP3 and SIRT1 genes on fertility traits in Sahiwal and Karan Fries cattle. Association studies were conducted using mixed linear models, involving 125 Sahiwal and 138 Karan Fries animals in each breed. The analysis utilized a designated PCR-RFLP panel. RESULTS In the promoter region of the LAP3 gene, all variants demonstrated significant (P < 0.05) associations with AFC, except for rs722359733: C > T. However, specific variants with the LAP3 gene's promoter region, namely rs722359733: C > T, rs110932626: A > G, rs43702363: C > T, and rs41255599: C > T, showed significant associations with CI and DO in Sahiwal and Karan Fries cows, respectively. The SNP rs718329990: T > C in the promoter region of SIRT1 gene exhibited a significant association with CI and DO in Sahiwal cattle. Haplotype-based association analysis revealed significant associations between haplotype combinations and AFC, CI and DO in the studied dairy cattle population. Animals with H2H3 and H2H4 haplotype combination exhibited higher AFC, CI and DO than other combinations. CONCLUSIONS These results affirm the involvement of the LAP3 and SIRT1 genes in female fertility traits, indicating that polymorphisms within these genes are linked to the studied traits. Overall, the significant SNPs and haplotypes identified in this study could have the potential to enhance herd profitability and ensure long-term sustainability on dairy farms by enabling the selection of animals with early age first calving and enhance reproductive performance in the dairy cattle breeding program.
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Affiliation(s)
- Destaw Worku
- Department of Animal Science, College of Agriculture, Food and Climate Science, Injibara University, Injibara, Ethiopia.
| | - Archana Verma
- Animal Genetics and Breeding Division, ICAR -National Dairy Research Institute, Karnal, India
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Wu J, Yao L, Liu Y, Zhang S, Wang K. Periodontitis and osteoporosis: a two-sample Mendelian randomization analysis. Braz J Med Biol Res 2024; 57:e12951. [PMID: 38511766 PMCID: PMC10946243 DOI: 10.1590/1414-431x2024e12951] [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: 07/10/2023] [Accepted: 01/05/2024] [Indexed: 03/22/2024] Open
Abstract
The incidences of periodontitis and osteoporosis are rising worldwide. Observational studies have shown that periodontitis is associated with increased risk of osteoporosis. We performed a Mendelian randomization (MR) study to genetically investigate the causality of periodontitis on osteoporosis. We explored the causal effect of periodontitis on osteoporosis by MR analysis. A total of 9 single nucleotide polymorphisms (SNP) were related to periodontitis. The primary approach in this MR analysis was the inverse variance-weighted (IVW) method. Simple median, weighted median, and penalized weighted median were used to analyze sensitivity. The fixed-effect IVW model and random-effect IVW model showed no significant causal effect of genetically predicted periodontitis on the risk of osteoporosis (OR=1.032; 95%CI: 0.923-1.153; P=0.574; OR=1.032; 95%CI: 0.920-1.158; P=0.588, respectively). Similar results were observed in simple mode (OR=1.031; 95%CI: 0.780-1.361, P=0.835), weighted mode (OR=1.120; 95%CI: 0.944-1.328, P=0.229), simple median (OR=1.003; 95%CI: 0.839-1.197, P=0.977), weighted median (OR=1.078; 95%CI: 0.921-1.262, P=0.346), penalized weight median (OR 1.078; 95%CI: 0.919-1.264, P=0.351), and MR-Egger method (OR=1.360; 95%CI: 0.998-1.853, P=0.092). There was no heterogeneity in the IVW and MR-Egger analyses (Q=7.454, P=0.489 and Q=3.901, P=0.791, respectively). MR-Egger regression revealed no evidence of a pleiotropic influence through genetic variants (intercept: -0.004; P=0.101). The leave-one-out sensitivity analysis indicated no driven influence of any individual SNP on the association between periodontitis and osteoporosis. The Mendelian randomization analysis did not show a significant detrimental effect of periodontitis on the risk of osteoporosis.
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Affiliation(s)
- Jiale Wu
- Department of Oral and Maxillofacial Surgery, Peking University School of Medicine, Hospital of Stomatology, Beijing, China
| | - Lihui Yao
- Department of Stomatology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Yuchen Liu
- Department of Oral and Maxillofacial Surgery, Peking University School of Medicine, Hospital of Stomatology, Beijing, China
| | - ShuaiShuai Zhang
- Department of Stomatology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Kan Wang
- Department of Oral and Maxillofacial Surgery, Peking University School of Medicine, Hospital of Stomatology, Beijing, China
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