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Qu D, Schürmann P, Rothämel T, Fleßner J, Rehberg D, Dörk T, Klintschar M. Revisiting the association of sudden infant death syndrome (SIDS) with polymorphisms of NHE3 and IL13. Int J Legal Med 2024; 138:743-749. [PMID: 38091065 PMCID: PMC11003888 DOI: 10.1007/s00414-023-03139-2] [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: 10/04/2023] [Accepted: 11/20/2023] [Indexed: 04/11/2024]
Abstract
OBJECTIVES Disturbances of the central nervous system and immune system are thought to play a role in sudden infant death syndrome (SIDS). Dysregulated expression of sodium (Na+)/hydrogen (H+) exchanger 3 (NHE3) in the brainstem and of interleukin 13 (IL13) in the lungs has been observed in SIDS. An association of single-nucleotide polymorphisms (SNPs) in NHE3 and IL13 with SIDS has been proposed, but controversial results were reported. Therefore, there is a need to revisit the association of SNPs in NHE3 and IL13 with SIDS. METHODS Genotyping of rs71597645 (G1131A) and rs2247114 (C2405T) in NHE3 and rs20541 (+ 4464A/G) in IL13 was performed in 201 SIDS cases and 338 controls. A meta-analysis was performed after merging our data with previously published data (all from European populations). RESULTS Polymorphisms rs2247114 (NHE3) and rs20541 (IL13) were significantly associated with SIDS overall and in multiple subgroups, but no association was found for rs71597645 (NHE3). After combining our data with previously published data, a fixed-effect meta-analysis showed that rs2247114 in NHE3 retained a significant association with SIDS under a recessive model (OR 2.78, 95%CI 1.53 to 5.06; p = 0.0008). CONCLUSION Our findings suggest an association of NHE3 variant rs2247114 (C2405T), though not rs71597645 (NHE3), with SIDS. A potential role of rs20541 (IL13) still has to be elucidated. Especially NHE3 seems to be an interesting topic for future SIDS research.
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Affiliation(s)
- Dong Qu
- Institute of Legal Medicine, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - Peter Schürmann
- Gynaecology Research Unit, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - Thomas Rothämel
- Institute of Legal Medicine, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - Jessica Fleßner
- Institute of Legal Medicine, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - Daniela Rehberg
- Institute of Legal Medicine, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - Thilo Dörk
- Gynaecology Research Unit, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - Michael Klintschar
- Institute of Legal Medicine, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany.
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Zhang R, Liu Y, Li W, Wang P, Liu Z, Wen Y, Chu M, Wang L. A mutation in LPAR2 activates the miR-939-5p-LPAR2-PI3K/AKT axis to regulate the proliferation and apoptosis of granulosa cells in sheep. Theriogenology 2024; 219:1-10. [PMID: 38368704 DOI: 10.1016/j.theriogenology.2024.02.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 02/07/2024] [Accepted: 02/07/2024] [Indexed: 02/20/2024]
Abstract
Lysophosphatidic acid receptor-2 (LPAR2) is a G protein-coupled receptor, which is involved in various physiological processes such as cell development, proliferation, and apoptosis, and is thought to play an important role in follicular development and reproduction. There is evidence that miRNA recognition elements (MRE) in the gene 3'UTR often contain single nucleotide polymorphisms (SNPs) that can alter the binding affinity of the target miRNA, leading to dysregulation of gene expression. In this study, we detected a SNP in LPAR2 3 'UTR (rs410670692, c.*701C > T) in 384 small-tailed Han sheep using Sequenom MassARRAY®SNP genotyping. Association analysis showed that the SNP was significantly associated with litter size. Then, the effect of LPAR2 rs410670692 mutation on gene expression in sheep hosts was studied by molecular biotechnology. The results showed that the expression of LPAR2 in the TT genotype was significantly higher than that in the CC genotype, which confirmed the existence of rs410670692, a functional SNP, in LPAR2 3'UTR. We then used bioinformatics methods and double luciferase reporter gene assay to predict and confirm LPAR2 SNP rs410670692 as the direct targeting regulatory element of miR-939-5p. Cell transfection experiments further found that SNP rs410670692 down-regulated the mRNA and protein levels of LPAR2 by influencing the binding of miR-939-5p. To understand the function and mechanism of miR-939-5p in sheep granulosa cells (GCs), we conducted cell proliferation and apoptosis experiments which showed inhibited GCs proliferation along with promoted GCs apoptosis upon overexpression of miR-939-5p. Moreover, overexpression of miR-939-5p promotes apoptosis of granulosa cells by blocking the LPAR2-dependent PI3K/Akt signaling pathway. In conclusion, these results indicate that the SNP rs410670692 of LPAR2 is related to the litter size of small-tailed cold sheep, and miR-939-5p can act as a regulatory element binding to the C mutation of rs410670692 to regulate the expression of LPAR2, affect the development of GCs, and thus indirectly affect the litter size of sheep. These studies provide evidence for the involvement of LPAR2 polymorphism in sheep reproduction and are expected to provide new insights into the molecular genetic mechanisms of litter size traits in sheep.
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Affiliation(s)
- Runan Zhang
- Key Laboratory of Livestock and Poultry Multiomics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu 611130, China; State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
| | - Yufang Liu
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
| | - Wentao Li
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
| | - Peng Wang
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
| | - Ziyi Liu
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
| | - Yuliang Wen
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Mingxing Chu
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China.
| | - Linjie Wang
- Key Laboratory of Livestock and Poultry Multiomics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu 611130, China.
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Feng H, Wei B, Xie X, Li P, Shen X. The potential up-regulation risk of 3' UTR SNP (rs10787760 G > A) for the VAX1 gene is associated with NSCLP in the northwest Chinese population. Gene 2024:148458. [PMID: 38608796 DOI: 10.1016/j.gene.2024.148458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 02/18/2024] [Accepted: 04/08/2024] [Indexed: 04/14/2024]
Abstract
AIMS To investigate the association between single nucleotide polymorphisms (SNPs) in 3'UTR region of VAX1, SYT14 and PAX7 genes and the risk of non-syndromic cleft palate (NSCLP) in a northwest Chinese population. MAIN METHODS A case-control study was conducted in 406 normal controls and 399 NSCLP patients. Using iMLDRTM genotyping technology, eight SNPs of three genes ((rs10787760, rs7086344 at VAX1), (rs1010113, rs851114, and rs485874 at PAX7), and (rs61820397, rs4609425, rs12133399 at SYT14)) were genotyped to investigate the differences in alleles and genotype distribution frequencies between NSCLP patients and healthy controls. RNA Folding Form software was used to predict RNA secondary structure and expression vectors were constructed to explore the function of the relevant SNP. The effect of SNP polymorphism of gene transcription and translation was assessed using qPCR and Western blot analysis. KEY FINDINGS Among the eight SNPs of three genes, rs10787760 of VAX1 gene was found to be associated with an increased risk of NSCLP (OR = 1.341,CI = 1.004-1.790) and the GA genotype of rs10787760 increased the risk of cleft lip and/or palate (CL/P) about 1.42 times (p < 0.05), and carrying the A allele might increase the risk of NSCL/P in male (OR = 1.356, 95 % CI = 1.010-1.823). But there was no association observed with cleft palate only (CPO). Cell function experiments revealed that the G to A mutation in rs10787760 up-regulated GFP-VAX1 transcriptional level by 2.39 and 3.13 times in two cell lines respectively, and enhance the protein expression of the VAX1 gene further. RNA secondary structure study showed that the rs10787760 (G > A) had two different secondary structures in 3'UTR region. SIGNIFICANCE The rs10787760 variant in the 3'UTR region of VAX1 gene is associated with CL/P in northwest Chinese population. We hypothesize that the machanism of it might be caused by the RNA differenct fold in the 3'UTR region caused by the polymorphism of the gene. LEVEL OF EVIDENCE Original Reports.
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Affiliation(s)
- Huan Feng
- School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Bing Wei
- Donggang Branch of the First Hospital of Lanzhou University, Lanzhou University, Lanzhou 730000, China
| | - Xiaodong Xie
- School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, China
| | - Peiqiang Li
- School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, China
| | - Xi Shen
- School of Life Sciences, Lanzhou University, Lanzhou 730000, China.
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Hu X, Wang W, Luo K, Dai J, Zhang Y, Wan Z, He W, Zhang S, Yang L, Tan Q, Li W, Zhang Q, Gong F, Lu G, Tan YQ, Lin G, Du J. Extended application of PGT-M strategies for small pathogenic CNVs. J Assist Reprod Genet 2024; 41:739-750. [PMID: 38263474 PMCID: PMC10957852 DOI: 10.1007/s10815-024-03028-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 01/04/2024] [Indexed: 01/25/2024] Open
Abstract
PURPOSE The preimplantation genetic testing for aneuploidy (PGT-A) platform is not currently available for small copy-number variants (CNVs), especially those < 1 Mb. Through strategies used in PGT for monogenic disease (PGT-M), this study intended to perform PGT for families with small pathogenic CNVs. METHODS Couples who carried small pathogenic CNVs and underwent PGT at the Reproductive and Genetic Hospital of CITIC-Xiangya (Hunan, China) between November 2019 and April 2023 were included in this study. Haplotype analysis was performed through two platforms (targeted sequencing and whole-genome arrays) to identify the unaffected embryos, which were subjected to transplantation. Prenatal diagnosis using amniotic fluid was performed during 18-20 weeks of pregnancy. RESULTS PGT was successfully performed for 20 small CNVs (15 microdeletions and 5 microduplications) in 20 families. These CNVs distributed on chromosomes 1, 2, 6, 7, 13, 15, 16, and X with sizes ranging from 57 to 2120 kb. Three haplotyping-based PGT-M strategies were applied. A total of 89 embryos were identified in 25 PGT cycles for the 20 families. The diagnostic yield was 98.9% (88/89). Nineteen transfers were performed for 17 women, resulting in a 78.9% (15/19) clinical pregnancy rate after each transplantation. Of the nine women who had healthy babies, eight accepted prenatal diagnosis and the results showed no related pathogenic CNVs. CONCLUSION Our results show that the extended haplotyping-based PGT-M strategy application for small pathogenic CNVs compensated for the insufficient resolution of PGT-A. These three PGT-M strategies could be applied to couples with small pathogenic CNVs.
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Affiliation(s)
- Xiao Hu
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, 410008, China
| | - Weili Wang
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, 410008, China
- Institute of Reproductive and Stem Cell Engineering, NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, School of Basic Medical Sciences, Central South University, Changsha, 410078, China
| | - Keli Luo
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, 410008, China
| | - Jing Dai
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, 410008, China
| | - Yi Zhang
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, 410008, China
| | - Zhenxing Wan
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, 410008, China
| | - Wenbin He
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, 410008, China
- Institute of Reproductive and Stem Cell Engineering, NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, School of Basic Medical Sciences, Central South University, Changsha, 410078, China
- College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Shuoping Zhang
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, 410008, China
| | - Lanlin Yang
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, 410008, China
| | - Qin Tan
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, 410008, China
| | - Wen Li
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, 410008, China
- College of Life Science, Hunan Normal University, Changsha, 410081, China
- Key Laboratory of Stem Cell and Reproduction Engineering, Ministry of Health, Changsha, 410000, China
| | - Qianjun Zhang
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, 410008, China
- Institute of Reproductive and Stem Cell Engineering, NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, School of Basic Medical Sciences, Central South University, Changsha, 410078, China
- College of Life Science, Hunan Normal University, Changsha, 410081, China
- Key Laboratory of Stem Cell and Reproduction Engineering, Ministry of Health, Changsha, 410000, China
| | - Fei Gong
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, 410008, China
- College of Life Science, Hunan Normal University, Changsha, 410081, China
- Key Laboratory of Stem Cell and Reproduction Engineering, Ministry of Health, Changsha, 410000, China
| | - Guangxiu Lu
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, 410008, China
- Key Laboratory of Stem Cell and Reproduction Engineering, Ministry of Health, Changsha, 410000, China
| | - Yue-Qiu Tan
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, 410008, China
- Institute of Reproductive and Stem Cell Engineering, NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, School of Basic Medical Sciences, Central South University, Changsha, 410078, China
- College of Life Science, Hunan Normal University, Changsha, 410081, China
- Key Laboratory of Stem Cell and Reproduction Engineering, Ministry of Health, Changsha, 410000, China
| | - Ge Lin
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, 410008, China.
- Institute of Reproductive and Stem Cell Engineering, NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, School of Basic Medical Sciences, Central South University, Changsha, 410078, China.
- College of Life Science, Hunan Normal University, Changsha, 410081, China.
- Key Laboratory of Stem Cell and Reproduction Engineering, Ministry of Health, Changsha, 410000, China.
| | - Juan Du
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, 410008, China.
- College of Life Science, Hunan Normal University, Changsha, 410081, China.
- Key Laboratory of Stem Cell and Reproduction Engineering, Ministry of Health, Changsha, 410000, China.
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Li J, Wang D, Qi L, Yang Y, Pei J, Dong Y, Wang Y, Yao M, Zhang F, Lei Y, Cheng L, Ye W. Genomic sequencing revealed recombination event between clade 1 and clade 2 occurs in circulating varicella-zoster virus in China. Braz J Microbiol 2024; 55:125-132. [PMID: 38052769 PMCID: PMC10920497 DOI: 10.1007/s42770-023-01206-9] [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: 06/27/2023] [Accepted: 11/29/2023] [Indexed: 12/07/2023] Open
Abstract
Varicella-zoster virus (VZV), a member of the Alphaherpesvirinae subfamily, causes varicella in primary infections and establishing a latent stage in sensory ganglia. Upon reactivation, VZV causes herpes zoster with severe neuralgia, especially in elderly patients. The mutation rate for VZV is comparatively lower than the other members of other alpha herpesviruses. Due to geographic isolation, different genotypes of VZV are circulating on separate continents. Here, we successfully isolated a VZV from the vesicular fluid of a youth zoster patient. Based on the single-nucleotide polymorphism profiles of different open reading frames that define the genotype, this newly isolated VZV primarily represents genotype clade 2 but also has characteristics of genotype clade 1. The next-generation sequencing provided a nearly full-length sequence, and further phylogenetic analysis revealed that this VZV isolate is distinct from clades 1 and 2. The Recombination Detection Program indicates that a possible recombinant event may occur between the VZV isolate and clade 1. In summary, we found that there is a circulating VZV isolate in China that may represent a recombinant between clade 1 and clade 2, providing new concerns that need to be considered in the future VZV vaccination program.
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Affiliation(s)
- Jia Li
- Department of Neurology, Xi'an International Medical Center Hospital, Xi'an, 710100, Shaanxi, China
| | - Dan Wang
- Second Affiliated Hospital, Xi'an Medical University, 167th Textile East Street, Xi'an, China
| | - Libin Qi
- Cadet Brigade, School of Preclinical Medicine, Airforce Medical University: Fourth Military Medical University, Xi'an, 710032, China
| | - Yuewu Yang
- Cadet Brigade, School of Preclinical Medicine, Airforce Medical University: Fourth Military Medical University, Xi'an, 710032, China
| | - Jiawei Pei
- Bone Metabolism Lab, School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi, China
| | - Yangchao Dong
- Department of Microbiology, School of Preclinical Medicine, Airforce Medical University: Fourth Military Medical University, Xi'an, Shaanxi, China
| | - Yuan Wang
- Department of Microbiology, School of Preclinical Medicine, Airforce Medical University: Fourth Military Medical University, Xi'an, Shaanxi, China
| | - Min Yao
- Department of Microbiology, School of Preclinical Medicine, Airforce Medical University: Fourth Military Medical University, Xi'an, Shaanxi, China
| | - Fanglin Zhang
- Department of Microbiology, School of Preclinical Medicine, Airforce Medical University: Fourth Military Medical University, Xi'an, Shaanxi, China
| | - Yingfeng Lei
- Department of Microbiology, School of Preclinical Medicine, Airforce Medical University: Fourth Military Medical University, Xi'an, Shaanxi, China.
| | - Linfeng Cheng
- Department of Microbiology, School of Preclinical Medicine, Airforce Medical University: Fourth Military Medical University, Xi'an, Shaanxi, China.
| | - Wei Ye
- Department of Microbiology, School of Preclinical Medicine, Airforce Medical University: Fourth Military Medical University, Xi'an, Shaanxi, China.
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Chen Y, Kong W, Liu M, Li Q, Wang Y, Zheng Y, Zhou Y. Metabolic syndrome and risk of colorectal cancer: A Mendelian randomization study. Heliyon 2024; 10:e23872. [PMID: 38223733 PMCID: PMC10784169 DOI: 10.1016/j.heliyon.2023.e23872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 12/01/2023] [Accepted: 12/14/2023] [Indexed: 01/16/2024] Open
Abstract
Background Observational studies have previously demonstrated a significant relationship among both metabolic syndrome (Mets) and colorectal cancer (CRC). Whether there is a causal link remains controversial. Objective To clarify whether Mets and their components have a causal effect on colorectal cancer, we have carried out a bidirectional Mendelian randomization analysis (MR). Methods This study started from genome-wide association data for Mets and its 5 components (hypertension, waist circumference, fasting blood glucose, serum triglycerides, and serum high-density lipoprotein cholesterol) and colorectal cancer. Mendelian randomization (MR) techniques were used in the study to examine their associations. Results After Benjamini-Hochberg multiple corrections, genetically predicted significant causal link exists between WC (waist circumference) and CRC. The OR was 1.35 (95 % CI: 1.08-1.69; p = 0.0096). Other Mets components (HBP, FBG, TG, HDL), on the other hand, found no evidence of a genetic link between CRC and Mets. In addition, MR results showed that CRC was not causally related to either Mets or the components. We get the same result in the validated dataset. Conclusion According to the bidirectional MR investigation shows a significant causal relationship among obesity and CRC in the Mets component but no causal relationship in the opposite direction.
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Affiliation(s)
- Yuhua Chen
- The First Clinical Medical College, Lanzhou University, Lanzhou, China
- Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, China
- Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, China
| | - Wanru Kong
- Department of Infection Management, Gansu Provincial Hospital, Lanzhou, 730000, China
| | - Min Liu
- Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, China
- Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, China
| | - Qiang Li
- Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, China
- Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, China
| | - Yuping Wang
- Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, China
- Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, China
| | - Ya Zheng
- Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, China
- Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, China
| | - Yongning Zhou
- Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, China
- Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, China
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Camacho J, Negredo A, Carrilero B, Segovia M, Moreno A, Pozo F, Echevarría JE, Echevarría JM, Sánchez-Seco MP, Tarragó D. Mutations in Coding and Non-Coding Regions in Varicella-Zoster Virus Causing Fatal Hemorrhagic Fever Without Rash in an Immunocompetent Patient: Case Report. Infect Dis Ther 2023; 12:2621-2630. [PMID: 37870692 PMCID: PMC10651560 DOI: 10.1007/s40121-023-00884-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 10/03/2023] [Indexed: 10/24/2023] Open
Abstract
INTRODUCTION We report the case of a fatal hemorrhagic varicella primary infection in an immunocompetent man and whole-genome characterization of the virus for the investigation of biomarkers of virulence. CASE A 38-year-old patient born in Nigeria presented to the emergency department with abdominal pain and subsequently developed fatal hemorrhagic disease without skin rash. Extensive laboratory tests including serology and PCR for arenaviruses, bunyaviruses and ebolaviruses were negative. Varicella-zoster virus (VZV) PCR of sera, liver and spleen tissue samples from autopsy revealed the presence of VZV DNA. Primary infection by varicella-zoster virus with hemorrhagic manifestations was diagnosed after virological testing. The VZV genome was sequenced using a mWGS approach. Bioinformatic analysis showed 53 mutations across the genome, 33 of them producing non-synonymous variants affecting up to 14 genes. Some of them, such as ORF11 and ORF 62, encoded for essential functions related to skin or neurotropism. To our knowledge, the mutations reported here have never been described in a VZV causing such a devastating outcome. DISCUSSION In immunocompetent patients, viral factors should be considered in patients with uncommon symptoms or severe diseases. Some relevant mutations revealed by using whole genome sequencing (WGS) directly from clinical samples may be involved in this case and deserves further investigation. CONCLUSION Differential diagnosis of varicella-zoster virus in immunocompetent adults should be considered among patients with suspected VHF, even if the expected vesicular rash is not present at admission and does not arise thereafter. Whole genome sequencing of strains causing uncommon symptoms and/or mortality is needed for epidemiological surveillance and further characterization of putative markers of virulence. Additionally, this report highlights the recommendation for a VZV vaccination policy in non-immunized migrants from developing countries.
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Affiliation(s)
- Juan Camacho
- National Center for Microbiology, Instituto de Salud Carlos III, Madrid, Spain
| | - Anabel Negredo
- National Center for Microbiology, Instituto de Salud Carlos III, Madrid, Spain
- CIBER Enfermedades Infecciosas, Madrid, Spain
| | | | | | | | - Francisco Pozo
- National Center for Microbiology, Instituto de Salud Carlos III, Madrid, Spain
- CIBER Epidemiología y Salud Pública, Madrid, Spain
| | - Juan-Emilio Echevarría
- National Center for Microbiology, Instituto de Salud Carlos III, Madrid, Spain
- CIBER Epidemiología y Salud Pública, Madrid, Spain
| | | | - M Paz Sánchez-Seco
- National Center for Microbiology, Instituto de Salud Carlos III, Madrid, Spain
- CIBER Enfermedades Infecciosas, Madrid, Spain
| | - David Tarragó
- National Center for Microbiology, Instituto de Salud Carlos III, Madrid, Spain.
- CIBER Epidemiología y Salud Pública, Madrid, Spain.
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Fatima N, Jia L, Liu B, Li L, Bai L, Wang W, Zhao S, Wang R, Liu E. A homozygous missense mutation in the fibroblast growth factor 5 gene is associated with the long-hair trait in Angora rabbits. BMC Genomics 2023; 24:298. [PMID: 37268908 DOI: 10.1186/s12864-023-09405-2] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 05/24/2023] [Indexed: 06/04/2023] Open
Abstract
BACKGROUND Rabbits are well-domesticated animals. As a crucial economic animal, rabbit has been successfully bred into wool-use, meat-use and fur-use breeds. Hair length is one of the most economically important traits affecting profitability in wool rabbits. In this study, to identify selection signatures with the long-hair trait, whole-genomic resequencing of long-haired rabbits (Angora rabbits) and short-haired rabbits (Rex and New Zealand rabbits) was performed. RESULTS By genome-wide selective sweeping analysis based on population comparison, we identified a total of 5.85 Mb regions (containing 174 candidate genes) with strong selection signals. Six of these genes (Dusp1, Ihh, Fam134a, Map3k1, Spata16, and Fgf5) were enriched in the MAPK signalling and Hedgehog signalling pathways, both of which are closely associated with hair growth regulation. Among these genes, Fgf5 encodes the FGF5 protein, which is a well-established regulator of hair growth. There was a nonsynonymous nucleotide substitution (T19234C) in the Fgf5 gene. At this locus, the C allele was present in all of the tested Angora rabbits, while the T allele was dominant in New Zealand and Rex rabbits. We further confirmed that the C allele was conserved in Angora rabbits by screening an additional 135 rabbits. Moreover, the results of functional predictions and co-immunoprecipitation revealed that the T19234C mutation impaired the binding capacity of FGF5 to its receptor FGFR1. CONCLUSIONS We discovered that the homozygous missense mutation T19234C within Fgf5 might contribute to the long-hair trait of Angora rabbits by reducing its receptor binding capacity. This finding will provide new insights into the genetic basis underlying the genetic improvement of Angora rabbits and benefit the improvement of rabbit breeding in the future.
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Affiliation(s)
- Nazira Fatima
- Department of Laboratory Animal Science, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, China
- Laboratory Animal Center, Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, China
| | - Linying Jia
- Department of Laboratory Animal Science, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, China
- Laboratory Animal Center, Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, China
| | - Baoning Liu
- Department of Laboratory Animal Science, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, China
- Laboratory Animal Center, Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, China
| | - Lu Li
- Department of Laboratory Animal Science, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, China
- Laboratory Animal Center, Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, China
| | - Liang Bai
- Department of Laboratory Animal Science, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, China
- Laboratory Animal Center, Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, China
| | - Weirong Wang
- Department of Laboratory Animal Science, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, China
- Laboratory Animal Center, Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, China
| | - Sihai Zhao
- Department of Laboratory Animal Science, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, China
- Laboratory Animal Center, Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, China
| | - Rong Wang
- Department of Laboratory Animal Science, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, China.
- Laboratory Animal Center, Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, China.
| | - Enqi Liu
- Department of Laboratory Animal Science, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, China.
- Laboratory Animal Center, Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, China.
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9
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Sasaguri H. Introduction of Genetic Mutations Into Mice by Base Editor and Target-AID. Methods Mol Biol 2023; 2637:111-124. [PMID: 36773142 DOI: 10.1007/978-1-0716-3016-7_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] [Indexed: 02/12/2023]
Abstract
Generating genetically modified animal models that precisely recapitulate disease characteristics forms an integral and indispensable tool to understanding disease pathophysiology. Recently, important advances in genome editing technologies have enabled us to efficiently create sophisticated animal models in short periods of time. Base editing is a modified CRISPR/Cas system that induces base substitution at targeted genomic regions. Here I describe a basic protocol to introduce disease-relevant pathogenic mutations into mice utilizing two representative base editing tools, Base Editor and Target-AID.
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Affiliation(s)
- Hiroki Sasaguri
- Laboratory for Proteolytic Neuroscience, RIKEN Center for Brain Science, Wako, Saitama, Japan.
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10
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Andreou A, Papakyriakou A, Zervou MI, Goulielmos GN, Eliopoulos EE. Is the Association of the Rare rs35667974 IFIH1 Gene Polymorphism With Autoimmune Diseases a Case of RNA Epigenetics? J Mol Evol 2023; 91:204-213. [PMID: 36651965 PMCID: PMC10082101 DOI: 10.1007/s00239-022-10090-0] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 12/27/2022] [Indexed: 01/19/2023]
Abstract
Interferon induced with helicase C domain-containing protein 1 (IFIH1) gene encodes a cytoplasmic RNA helicase otherwise known as melanoma differentiation-associated 5 (MDA5), a RIG-1-like RNA helicase that recognizes viral RNA and is involved in innate immunity through recognition of viral RNA. Upon binding to double-stranded (ds) RNA, MDA5 forms a filamentous assembly along the length of dsRNA and utilizes molecular signatures to discriminate self, versus non-self on the basis of dsRNA length and methylation. Its missense variant rs35667974 is protective for type 1 diabetes, psoriasis, and psoriatic arthritis, but is also found to be associated with an increased risk for ankylosing spondylitis, Crohn's disease, and ulcerative colitis. To gain insight into the complex role of this variant we performed a structural analysis of MDA5 in complex with dsRNA using molecular dynamics simulations. Our data suggest that while the Ile923Val mutation of the rs35667974 variant does not affect binding to native dsRNA significantly, it displays a destabilizing effect in the presence of 2'-O uridine methylation. Thus, the presence of 2'-O-methylation at the dsRNA introduces a sensing signature that leads to selective reduction of the overall MDA catalytic activity. This study represents an evaluation of the role of the shared rs35667974 variant of autoimmune locus IFIH1, reported to lead to selectively reduced catalytic activity of the modified MDA5 phenotype and, as a consequence, reduced negative feedback on cytokine and chemokine signaling and selectively protection against autoimmunity.
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Affiliation(s)
- Athena Andreou
- Laboratory of Genetics, Department of Biotechnology, Agricultural University of Athens, 11855, Athens, Greece
| | - Athanasios Papakyriakou
- Institute of Biosciences and Applications, National Centre for Scientific Research "Demokritos", 15341, Athens, Greece
| | - Maria I Zervou
- Section of Molecular Pathology and Human Genetics, Department of Internal Medicine, School of Medicine, University of Crete, 71003, Heraklion, Greece
| | - George N Goulielmos
- Section of Molecular Pathology and Human Genetics, Department of Internal Medicine, School of Medicine, University of Crete, 71003, Heraklion, Greece.,Department of Internal Medicine, University Hospital of Heraklion, 71500, Heraklion, Greece
| | - Elias E Eliopoulos
- Laboratory of Genetics, Department of Biotechnology, Agricultural University of Athens, 11855, Athens, Greece.
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11
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Abstract
Chromosome conformation capture techniques are a set of methods used to determine 3D genome organization through the capture and identification of physical contacts between pairs of genomic loci. Among them, 4C-seq (circular chromosome conformation capture coupled to high-throughput sequencing) allows for the identification and quantification of the sequences interacting with a preselected locus of interest. 4C-seq has been widely used in the literature, mainly to study chromatin loops between enhancers and promoters or between CTCF binding sites and to identify chromatin domain boundaries. As 3D-contacts may be established in an allele-specific manner, we describe an up-to-date allele-specific 4C-seq protocol, starting from the selection of allele-specific viewpoints to Illumina sequencing. This protocol has mainly been optimized for cultured mammalian cells, but can be adapted for other cell types with relatively minor changes in initial steps.
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Affiliation(s)
- Mélanie Miranda
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Daan Noordermeer
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France.
| | - Benoit Moindrot
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France.
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12
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Bhat ZI, Naseem A, Kumar B, Ponnusamy K, Tiwari RR, Sharma GD, Rizvi MMA. Association of PARK-2 Non-synonyms Polymorphisms and Their In Silico Validation Among North Indian Colorectal Cancer Patients. J Gastrointest Cancer 2021; 53:674-682. [PMID: 34467515 DOI: 10.1007/s12029-021-00693-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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/12/2021] [Indexed: 11/25/2022]
Abstract
PURPOSE PARK2 is a potential tumour suppressor gene and its genetic alterations (regionic loss) are common across many human cancers. The association of PARK2 germline variations (SNPs) with Parkinson's has been shown, but their association in development and progression of cancer remains elusive. The aim of this study was to identify association of PARK2 polymorphisms (rs1801474, rs1801334) with colorectal cancer in a case control study design. METHODS This case control study included a total of 650 genetically unrelated subjects comprising 300 colorectal cancer cases and 350 healthy controls belonging to North Indian. Both SNPs were analyzed using the PCR-RFLP assay. Statistical analysis for describing risk and association was performed using SPSS-17 software. Structural deviations due to non- synonymous substitutions (S167N and D394N) were analyzed using MD simulations. RESULTS The genotype distributions of both the SNPs were in Hardy-Weinberg equilibrium. For both the polymorphisms, the allelic model showed statistically significant risk with OR ~ 1.3. Many of the associations remained significant even after Bonferroni correction (P < 0.00125). The result suggested that both S167N and D394N were deviated from wild type and structures and were stable after 5 ns. The average value of RMSD for backbone atoms was calculated from 5 to 10 ns molecular dynamics simulation data. CONCLUSION In conclusion, our study revealed a significant association of PARK2 SNPs with colorectal cancer as well as their relations with other clinical parameters highlighting their contribution towards colorectal cancer susceptibility in North Indian population.
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Affiliation(s)
- Zafar Iqbal Bhat
- Genome Biology Laboratory, Department of Biosciences, Jamia Millia Islamia, New Delhi, India
| | - Afreen Naseem
- Genome Biology Laboratory, Department of Biosciences, Jamia Millia Islamia, New Delhi, India
| | - Bhupender Kumar
- Department of Biochemistry, Institute of Home Economics, University of Delhi, Delhi, India
| | - Kalaiarasan Ponnusamy
- Synthetic Biology Lab, School ofBiotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Raj Ranjan Tiwari
- Genome Biology Laboratory, Department of Biosciences, Jamia Millia Islamia, New Delhi, India
| | - G D Sharma
- Department of Zoology, P.M.B Gujarati Science College, Indore, India
| | - M Moshahid Alam Rizvi
- Genome Biology Laboratory, Department of Biosciences, Jamia Millia Islamia, New Delhi, India.
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13
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Herbrechter R, Hube N, Buchholz R, Reiner A. Splicing and editing of ionotropic glutamate receptors: a comprehensive analysis based on human RNA-Seq data. Cell Mol Life Sci 2021; 78:5605-5630. [PMID: 34100982 PMCID: PMC8257547 DOI: 10.1007/s00018-021-03865-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Revised: 05/12/2021] [Accepted: 05/22/2021] [Indexed: 12/11/2022]
Abstract
Ionotropic glutamate receptors (iGluRs) play key roles for signaling in the central nervous system. Alternative splicing and RNA editing are well-known mechanisms to increase iGluR diversity and to provide context-dependent regulation. Earlier work on isoform identification has focused on the analysis of cloned transcripts, mostly from rodents. We here set out to obtain a systematic overview of iGluR splicing and editing in human brain based on RNA-Seq data. Using data from two large-scale transcriptome studies, we established a workflow for the de novo identification and quantification of alternative splice and editing events. We detected all canonical iGluR splice junctions, assessed the abundance of alternative events described in the literature, and identified new splice events in AMPA, kainate, delta, and NMDA receptor subunits. Notable events include an abundant transcript encoding the GluA4 amino-terminal domain, GluA4-ATD, a novel C-terminal GluD1 (delta receptor 1) isoform, GluD1-b, and potentially new GluK4 and GluN2C isoforms. C-terminal GluN1 splicing may be controlled by inclusion of a cassette exon, which shows preference for one of the two acceptor sites in the last exon. Moreover, we identified alternative untranslated regions (UTRs) and species-specific differences in splicing. In contrast, editing in exonic iGluR regions appears to be mostly limited to ten previously described sites, two of which result in silent amino acid changes. Coupling of proximal editing/editing and editing/splice events occurs to variable degree. Overall, this analysis provides the first inventory of alternative splicing and editing in human brain iGluRs and provides the impetus for further transcriptome-based and functional investigations.
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Affiliation(s)
- Robin Herbrechter
- Department of Biology and Biotechnology, Ruhr University Bochum, Universitätsstrasse 150, 44801, Bochum, Germany
| | - Nadine Hube
- Department of Biology and Biotechnology, Ruhr University Bochum, Universitätsstrasse 150, 44801, Bochum, Germany
| | - Raoul Buchholz
- Department of Biology and Biotechnology, Ruhr University Bochum, Universitätsstrasse 150, 44801, Bochum, Germany
| | - Andreas Reiner
- Department of Biology and Biotechnology, Ruhr University Bochum, Universitätsstrasse 150, 44801, Bochum, Germany.
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14
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Li R, Shen X, Chen H, Peng D, Wu R, Sun H. Developmental validation of the MGIEasy Signature Identification Library Prep Kit, an all-in-one multiplex system for forensic applications. Int J Legal Med 2021; 135:739-753. [PMID: 33523251 DOI: 10.1007/s00414-021-02507-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 01/08/2021] [Indexed: 01/23/2023]
Abstract
Analyzing genetic markers in nuclear and mitochondrial genomes is helpful in various forensic applications, such as individual identifications and kinship analyses. However, most commercial kits detect these markers separately, which is time-consuming, laborious, and more error-prone (mislabelling, contamination, ...). The MGIEasy Signature Identification Library Prep Kit (hereinafter "MGIEasy identification system"; MGI Tech, Shenzhen, China) has been designed to provide a simple, fast, and robust way to detect appropriate markers in one multiplex PCR reaction: 52 autosomal STRs, 27 X-chromosomal STRs, 48 Y-chromosomal STRs, 145 identity-informative SNPs, 53 ancestry-informative SNPs, 29 phenotype-informative SNPs, and the hypervariable regions of mitochondrial DNA (mtDNA). Here, we validated the performance of MGIEasy identification system following the guidelines of the Scientific Working Group on DNA Analysis Methods (SWGDAM), assessing species specificity, sensitivity, mixture identification, stability under non-optimal conditions (degraded samples, inhibitor contamination, and various substrates), repeatability, and concordance. Libraries prepared using MGIEasy identification system were sequenced on a MGISEQ-2000 instrument (MGI Tech). MGIEasy-derived STR, SNP, and mtDNA genotypes were highly concordant with CE-based STR genotypes (99.79%), MiSeq FGx-based SNP genotypes (99.78%), and Sanger-based mtDNA genotypes (100%), respectively. This system was strongly human-specific, resistant to four common PCR inhibitors, and reliably amplified both low quantities of DNA (as low as 0.125 ng) and degraded DNA (~ 150 nt). Most of the unique alleles from the minor contributor were detected in 1:10 male-female and male-male mixtures; some minor Y-STR alleles were even detected in 1:1000 male-female mixtures. MGIEasy also successfully directly amplified markers from blood stains on FTA cards, filter papers, and swabs. Thus, our results demonstrated that MGIEasy identification system was suitable for use in forensic analyses due to its robust and reliable performance on samples of varying quality and quantity.
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Affiliation(s)
- Ran Li
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, People's Republic of China.,Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, No. 74 Zhongshan Road II, Guangzhou, 510080, Guangdong, People's Republic of China
| | - Xuefeng Shen
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, People's Republic of China.,Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, No. 74 Zhongshan Road II, Guangzhou, 510080, Guangdong, People's Republic of China
| | - Hui Chen
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, People's Republic of China.,Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, No. 74 Zhongshan Road II, Guangzhou, 510080, Guangdong, People's Republic of China
| | - Dan Peng
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, People's Republic of China.,Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, No. 74 Zhongshan Road II, Guangzhou, 510080, Guangdong, People's Republic of China
| | - Riga Wu
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, People's Republic of China.,Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, No. 74 Zhongshan Road II, Guangzhou, 510080, Guangdong, People's Republic of China
| | - Hongyu Sun
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, People's Republic of China. .,Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, No. 74 Zhongshan Road II, Guangzhou, 510080, Guangdong, People's Republic of China.
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15
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Gill PK, Dron JS, Dilliott AA, McIntyre AD, Cao H, Wang J, Movsesyan IG, Malloy MJ, Pullinger CR, Kane JP, Hegele RA. Ancestry-specific profiles of genetic determinants of severe hypertriglyceridemia. J Clin Lipidol 2020; 15:88-96. [PMID: 33303403 DOI: 10.1016/j.jacl.2020.11.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Revised: 10/31/2020] [Accepted: 11/17/2020] [Indexed: 12/01/2022]
Abstract
BACKGROUND Susceptibility to severe hypertriglyceridemia (HTG), defined as plasma triglyceride (TG) levels ≥10 mmol/L (880 mg/dL), is conferred by both heterozygous rare variants in five genes involved in TG metabolism and numerous common single-nucleotide polymorphisms (SNPs) associated with TG levels. OBJECTIVE To date, these genetic susceptibility factors have been comprehensively assessed primarily in severe HTG patients of European ancestry. Here, we expand our analysis to HTG patients of East Asian and Hispanic ancestry. METHODS The genomic DNA of 336, 63 and 199 severe HTG patients of European, East Asian and Hispanic ancestry, respectively, was evaluated using a targeted next-generation sequencing panel to screen for: 1) rare variants in LPL, APOA5, APOC2, GPIHBP1 and LMF1; 2) common, small-to-moderate effect SNPs, quantified using a polygenic score; and 3) common, large-effect polymorphisms, APOA5 p.G185C and p.S19W. RESULTS While the proportion of individuals with high polygenic scores was similar, frequency of rare variant carriers varied across ancestries. Compared with ancestry-matched controls, Hispanic patients were the most likely to have a rare variant (OR = 5.02; 95% CI 3.07-8.21; p < 0.001), while European patients were the least likely (OR = 2.56; 95% CI 1.58-4.13; p < 0.001). The APOA5 p.G185C polymorphism, exclusive to East Asians, was significantly enriched in patients compared with controls (OR = 10.1; 95% CI 5.6-18.3; p < 0.001), showing the highest enrichment among the measured genetic factors. CONCLUSION While TG-associated rare variants and common SNPs are both found in statistical excess in severe HTG patients of different ancestral backgrounds, the overall genetic profiles of each ancestry group were distinct.
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Affiliation(s)
- Praneet K Gill
- Department of Biochemistry, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada; Blackburn Cardiovascular Genetics Laboratory, Robarts Research Institute, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada
| | - Jacqueline S Dron
- Department of Biochemistry, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada; Blackburn Cardiovascular Genetics Laboratory, Robarts Research Institute, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada
| | - Allison A Dilliott
- Department of Biochemistry, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada; Blackburn Cardiovascular Genetics Laboratory, Robarts Research Institute, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada
| | - Adam D McIntyre
- Blackburn Cardiovascular Genetics Laboratory, Robarts Research Institute, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada
| | - Henian Cao
- Blackburn Cardiovascular Genetics Laboratory, Robarts Research Institute, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada
| | - Jian Wang
- Blackburn Cardiovascular Genetics Laboratory, Robarts Research Institute, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada
| | - Irina G Movsesyan
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
| | - Mary J Malloy
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
| | - Clive R Pullinger
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
| | - John P Kane
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
| | - Robert A Hegele
- Department of Biochemistry, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada; Blackburn Cardiovascular Genetics Laboratory, Robarts Research Institute, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada.
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16
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Abstract
Background Angiotensin-converting enzyme 2 (ACE2) is a metallopeptidase that primarily functions as a negative regulator of renin angiotensin system (RAS) by converting angiotensin II (Ang II) to angiotensin 1-7. Contrary to this, another RAS component, angiotensin-converting enzyme (ACE) catalyzes synthesis of Ang II from angiotensin I (Ang I) that functions as active compound in blood pressure regulation. This indicates importance of ACE/ACE2 level in regulating blood pressure by targeting Ang II. An outbreak of severe acute respiratory syndrome (SARS) highlighted the additional role of ACE2 as a receptor for SARS coronavirus (SARS-CoV) infection. Main body of the abstract ACE2 is a functional receptor for SARS-CoV and SARS-CoV-2. Activation of spike (S)-protein by either type II transmembrane serine proteases (TTSPs) or cathepsin-mediated cleavage initiates receptor binding and viral entry. In addition to TTSPs, ACE2 can also be trimmed by ADAM 17 (a disintegrin and metalloproteinase 17) that competes for the same receptor. Cleavage by TTSPs activates ACE2 receptor for binding, whereas ADAM17 releases extracellular fragment called soluble ACE2 (sACE2). Structural studies of both ACE2 and S-protein have found critical sites involved in binding mechanism. In addition to studies on structural motifs, few single-nucleotide polymorphism (SNPs) studies have been done to find an association between genetic variants and SARS susceptibility. Though no association was found in those reports, but seeing the non-reproducibility of SNP studies among different ethnic groups, screening of ACE2 SNPs in individual population can be undertaken. Short conclusion Thus, screening for novel SNPs focussing on recently identified critical regions of ACE2 can be targeted to monitor susceptibility towards coronavirus disease 2019 (COVID-19).
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Affiliation(s)
- Mayank Chaudhary
- Department of Biotechnology, Maharishi Markandeshwar (Deemed to be University), Mullana, Ambala, Haryana 133207 India
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17
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Miao X, Shen Y, Gong X, Yu H, Li B, Chang L, Wang Y, Fan J, Liang Z, Tan B, Li S, Zhang B. A novel forensic panel of 186-plex SNPs and 123-plex STR loci based on massively parallel sequencing. Int J Legal Med 2020; 135:709-718. [PMID: 32851473 DOI: 10.1007/s00414-020-02403-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 08/21/2020] [Indexed: 01/23/2023]
Abstract
The MiSeq® FGX Forensic system and the HID-Ion AmpliSeq Panel were previously developed for massively parallel sequencing (MPS) for forensic casework. Among the three major sequencing platforms, BGISEQ-500TM, which is based on multiple PCRs, is still lacking in forensics. Here, a novel forensic panel was constructed to detect 186 single-nucleotide polymorphisms (SNPs) and 123 short tandem repeats (STRs) with MPS technology on the BGISEQ-500™ platform. First, the library preparation, sequencing process, and data analysis were performed, focusing on the average depth of coverage and heterozygote balance. We calculated the allelic frequencies and forensic parameters of STR and SNP loci in 73 unrelated Chinese Han individuals. In addition, performance was evaluated with accuracy, uniformity, sensitivity, PCR inhibitor, repeatability and reproducibility, mixtures, degraded samples, case-type samples, and pedigree analyses. The results showed that 100% accurate and concordant genotypes can be obtained, and the loci with an abundance in the interquartile range accounted for 92.90% of the total, suggesting reliable uniformity in this panel. We obtained a locus detection rate that was higher than 98.78% from 78 pg of input DNA, and the optimal amount was 1.25-10 ng. The maximum concentrations of hematin and humic acid were 200 and 100 μM, respectively (the ratios of detected loci were 96.52% and 92.41%), in this panel. As a mixture, compared with those of SNPs, minor-contributor alleles of STRs could be detected at higher levels. For the degraded sample, the ratio of detected loci was 98.41%, and most profiles from case-type samples were not significantly different in abundance in our studies. As a whole, this panel showed high-performance, reliable, robust, repeatable, and reproducible results, which are sufficient for paternity testing, individual identification, and use for potentially degraded samples in forensic science.
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Affiliation(s)
- Xinyao Miao
- College of Forensic Medicine, Health Science Center, Xi'an Jiaotong University, Xi'an, People's Republic of China
| | - Yuesheng Shen
- School of Life Science, Northwest A&F University, Yangling, People's Republic of China
| | - Xiaojuan Gong
- College of Forensic Medicine, Health Science Center, Xi'an Jiaotong University, Xi'an, People's Republic of China
- School of Health Science Center, Xi'an Jiaotong University, Xi'an, People's Republic of China
| | - Huiyun Yu
- School of Life Science, Northwest A&F University, Yangling, People's Republic of China
| | - Bowen Li
- School of Life Science, Sichuan University, Chengdu, People's Republic of China
| | - Liao Chang
- College of Forensic Medicine, Health Science Center, Xi'an Jiaotong University, Xi'an, People's Republic of China
| | - Yinan Wang
- College of Forensic Medicine, Health Science Center, Xi'an Jiaotong University, Xi'an, People's Republic of China
| | - Jingna Fan
- College of Forensic Medicine, Health Science Center, Xi'an Jiaotong University, Xi'an, People's Republic of China
| | - Zuhuan Liang
- Forensic Genomics International, The Beijing Genomics Institute (BGI), Shenzhen, People's Republic of China
| | - Bowen Tan
- School of Computer Science, City University of Hong Kong, Hong Kong, People's Republic of China
| | - Shengbin Li
- College of Forensic Medicine, Health Science Center, Xi'an Jiaotong University, Xi'an, People's Republic of China
| | - Bao Zhang
- College of Forensic Medicine, Health Science Center, Xi'an Jiaotong University, Xi'an, People's Republic of China.
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Chen H, Mo M, Liu GY, Gong YM, Yu KD, Xu GZ. Interaction of two functional genetic variants LOXL1 rs1048661 and VEGFA rs3025039 on the risk of age-related macular degeneration in Chinese women. Ann Transl Med 2020; 8:818. [PMID: 32793663 PMCID: PMC7396242 DOI: 10.21037/atm-20-2447] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Background Cumulative evidence indicates that LOXL1 and VEGF-a play important roles in extracellular matrix formation and angiogenesis, respectively. The disorder of extracellular matrix and angiogenesis are the key factors of pathogenesis of age-related macular degeneration (AMD). We hypothesized that rs1048661 (T>G) in the LOXL1 gene and rs3025039 (C>T) in the VEGFA gene might be associated with risk of AMD. Methods A total of 533 unrelated Chinese subjects, 286 cases (247 with early AMD and 39 with late neovascular AMD) and 247 controls, were included in the study. The gene sequences of LOXL1 rs1048661 and VEGFA rs3025039 were amplified by polymerase chain reaction and genotyped. Interaction between rs1048661 and rs3025039 on AMD risk was also assessed. Results LOXL1 rs1048661 but not VEGFA rs3025039 was associated with a significantly increased risk of AMD. The adjusted odds ratio was 1.6 (95% CI, 1.1-2.5) for rs1048661 TT + GT genotype compared with GG homozygotes in the dominant model analysis. Moreover, there was a significant gene-gene interaction between these two polymorphic loci. In VEGFA rs3025039 CC + CT genotype which indicated sufficient expression of VEGF-a, LOXL1 rs1048661 had odds ratios of 1.7 (95% CI, 1.1-2.7) for early AMD and 3.6 (95% CI, 1.1-12.3) for late neovascular AMD in the dominant model analysis. However, LOXL1 rs1048661 did not confer the risk of AMD in subjects harboring VEGFA rs3025039 TT genotype which indicated decreased expression of VEGF-a. Conclusions Our findings suggest that LOXL1 rs1048661 (T>G) may be involved in the risk of AMD. In addition, LOXL1 rs1048661 and VEGFA rs3025039 interacted to confer the development of AMD, especially for late-stage neovascular AMD. Our data need to be further validated.
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Affiliation(s)
- Han Chen
- Department of Ophthalmology, Eye, Ear, Nose and Throat Hospital, Fudan University, Shanghai, China
| | - Miao Mo
- Department of Cancer Prevention & Clinical Statistics Center, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Guang-Yu Liu
- Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Yang-Ming Gong
- Department of Cancer Control & Prevention, Shanghai Municipal Center for Disease Prevention & Control, Shanghai, China
| | - Ke-Da Yu
- Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Ge-Zhi Xu
- Department of Ophthalmology, Eye, Ear, Nose and Throat Hospital, Fudan University, Shanghai, China
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Shahsavari G, Nouryazdan N, Adibhesami G, Birjandi M. Genetic associations and serum paraoxonase levels with atherosclerosis in western Iranian patients. Mol Biol Rep 2020; 47:5137-44. [PMID: 32567023 DOI: 10.1007/s11033-020-05585-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 06/11/2020] [Indexed: 12/20/2022]
Abstract
The oxidative modification of low-density lipoprotein (LDL) in the arterial wall plays a pivotal role in the initiation and progression of atherosclerosis which is a complex and progressive disorder. Paraoxonase1 (PON1), which is required for lipid metabolism, is believed to protect LDL from oxidation. The relationship between PON1 gene Leusin55Methionin (L55M) and Glutamine192Arginine (Q192R) polymorphisms in western Iranians with atherosclerosis and its association with enzyme activity and oxidized low-density lipoprotein (oxLDL) were examined in the present study. In this study, blood specimens were collected from 145 healthy individuals and 154 patients with atherosclerosis proven by angiography referred to Shahid Madani Hospital, Khorramabad, Iran. Genomic deoxy ribonucleic acid (DNA) was extracted from whole blood. For all the subjects, restriction fragment length polymorphism-polymerase chain reaction (RFLP-PCR) was carried out for the detection of L55M and Q192R polymorphisms. PON1 enzyme activity and the level of oxLDL were also evaluated. There was a 3.114-fold increase in the risk of developing atherosclerosis in the subjects presenting the PON1L55M, MM genotype compared to those with the LL genotype (OR 3.114; 95% CI 1.412-6.870). PON1Q192R polymorphism in the PON1 gene was not associated with atherosclerosis. Patients with atherosclerosis had significantly higher oxLDL and reduced PON1 enzyme activity (P < 0.05) compared to the controls. There was no association between the type of genotype, enzyme activity, and oxLDL level. It has been concluded that PON1L55M polymorphism and MM genotype are associated with an increased risk of coronary artery disease (CAD) in Iranian patients with atherosclerosis. We did not find any relationship between PON1Q192R polymorphism and atherosclerosis.
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Chang HA, Fang WH, Tzeng NS, Liu YP, Shyu JF, Wan FJ, Huang SY, Chang TC, Chang CC. Age-dependent association of polymorphisms in the promoter and 5'-untranslated region of the norepinephrine transporter gene with generalized anxiety disorder. J Affect Disord 2020; 270:124-130. [PMID: 32339102 DOI: 10.1016/j.jad.2020.03.059] [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: 08/12/2019] [Revised: 01/07/2020] [Accepted: 03/22/2020] [Indexed: 11/16/2022]
Abstract
BACKGROUND Norepinephrine transporter (NET), which regulates synaptic norepinephrine for noradrenergic signaling, is involved in the pathogenesis of anxiety, while expression of the NET gene differs at different ages. Here, we examine whether genetic variants in the NET gene are associated, in an age-specific manner, with increased risk of generalized anxiety disorder (GAD), one of the most disabling anxiety disorders. METHODS Three common single-nucleotide polymorphisms (SNPs) in the promoter (rs168924: A/G; rs2242446: T/C) and 5'-untranslated region (5'-UTR) (rs2397771: G/C) of the NET gene were genotyped in 2,317 Han-Chinese participants (791 GAD patients and 1,526 controls; age: 20-65). Potential confounding factors, such as gender, stress levels and psychiatric comorbidities, were included as covariates. RESULTS An interaction between age and NET genotypes and haplotypes was found for the risk of GAD. In the younger participants, rs168924 minor allele G homozygotes had the lowest incidence of GAD; however, older subjects displayed an inverse pattern, with homozygous G/G carriers presenting the highest prevalence of GAD. Additionally, younger individuals carrying 2 copies of the GGT haplotype composed of rs2397771-rs168924-rs2242446 had the lowest rate of GAD. However, those with 2 copies of the same haplotype exhibited the highest risk of GAD in the older groups. LIMITATIONS Only 3 common SNPs in the promoter and 5'-UTR of the NET gene were analyzed. CONCLUSIONS Our findings are the first to demonstrate that potentially functional SNPs in the NET promoter and 5'-UTR are associated with an increased risk of GAD, and that such associations are determined in an age-specific way.
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Affiliation(s)
- Hsin-An Chang
- Department of Psychiatry, Tri-Service General Hospital, National Defense Medical Center, No. 325, Sec. 2, Cheng-Kung Road, Nei-Hu District, Taipei 114, Taiwan
| | - Wen-Hui Fang
- Department of Family and Community Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Nian-Sheng Tzeng
- Department of Psychiatry, Tri-Service General Hospital, National Defense Medical Center, No. 325, Sec. 2, Cheng-Kung Road, Nei-Hu District, Taipei 114, Taiwan
| | - Yia-Ping Liu
- Department of Psychiatry, Tri-Service General Hospital, National Defense Medical Center, No. 325, Sec. 2, Cheng-Kung Road, Nei-Hu District, Taipei 114, Taiwan; Department of Psychiatry, Cheng Hsin General Hospital, Taipei, Taiwan; Department of Physiology, Laboratory of Cognitive Neuroscience, National Defense Medical Center, Taipei, Taiwan
| | - Jia-Fwu Shyu
- Department of Psychiatry, Tri-Service General Hospital, National Defense Medical Center, No. 325, Sec. 2, Cheng-Kung Road, Nei-Hu District, Taipei 114, Taiwan; Department of Biology and Anatomy, National Defense Medical Center, Taipei, Taiwan
| | - Fang-Jung Wan
- Department of Psychiatry, Tri-Service General Hospital, National Defense Medical Center, No. 325, Sec. 2, Cheng-Kung Road, Nei-Hu District, Taipei 114, Taiwan
| | - San-Yuan Huang
- Department of Psychiatry, Tri-Service General Hospital, National Defense Medical Center, No. 325, Sec. 2, Cheng-Kung Road, Nei-Hu District, Taipei 114, Taiwan
| | - Tieh-Ching Chang
- Department of Psychiatry, Tri-Service General Hospital, National Defense Medical Center, No. 325, Sec. 2, Cheng-Kung Road, Nei-Hu District, Taipei 114, Taiwan
| | - Chuan-Chia Chang
- Department of Psychiatry, Tri-Service General Hospital, National Defense Medical Center, No. 325, Sec. 2, Cheng-Kung Road, Nei-Hu District, Taipei 114, Taiwan.
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21
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Wang H, Huang C, Liu Y, Yang P, Liao Y, Gu X, Feng X, Chen B. Lack of association between interleukin-22 gene polymorphisms and cancer risk: a case-control study and a meta-analysis. Int J Clin Oncol 2020; 25:521-530. [PMID: 31832882 DOI: 10.1007/s10147-019-01595-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 12/02/2019] [Indexed: 01/05/2023]
Abstract
BACKGROUND Interleukin-22 (IL22) has been implicated in inflammation and tumorigenesis. The association between IL22 gene polymorphisms and cancer risk has been widely explored. However, the limited sample sizes of previous studies may produce inadequate statistical power and conflicting results, which calls for further investigations. In this study, we recruited a total of 1490 cancer patients (480 liver cancer patients, 550 lung cancer patients, and 460 gastric cancer patients) and 800 normal controls to explore the associations between IL22 gene polymorphisms (rs1179251, rs2227485, rs2227511, and rs2227473) and cancer risk. METHOD The genotyping was performed with polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and Sanger sequencing. RESULTS Our results showed that none of the four IL22 gene polymorphisms was associated with the risk of liver, lung or gastric cancer in Hubei Han Chinese population. To improve the statistical strength, a meta-analysis was further conducted. The results further confirmed our present findings and showed that rs1179251, rs2227485, and rs2227473 were not associated with cancer risk in total or stratified analysis. CONCLUSION Consequently, the rs1179251, rs2227485, rs2227511, and rs2227473 polymorphisms may not be associated with cancer risk. However, further investigations using larger samples in different ethnic populations are required.
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Affiliation(s)
- Huan Wang
- Department of Biological Science and Technology, School of Chemistry, Chemical Engineering and Life Sciences, Wuhan University of Technology, Wuhan, China
| | - Chao Huang
- Department of Biological Science and Technology, School of Chemistry, Chemical Engineering and Life Sciences, Wuhan University of Technology, Wuhan, China
| | - Yuxiao Liu
- Department of Biological Science and Technology, School of Chemistry, Chemical Engineering and Life Sciences, Wuhan University of Technology, Wuhan, China
| | - Puyu Yang
- Department of Biological Science and Technology, School of Chemistry, Chemical Engineering and Life Sciences, Wuhan University of Technology, Wuhan, China
| | - Yuxiao Liao
- Department of Biological Science and Technology, School of Chemistry, Chemical Engineering and Life Sciences, Wuhan University of Technology, Wuhan, China
| | - Xiuli Gu
- Center of Reproductive Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Department of Reproductive Genetics, Wuhan Tongji Reproductive Medicine Hospital, Wuhan, China
| | - Xianhong Feng
- Clinical Laboratory, Wuhan Xinzhou District People's Hospital, Wuhan, China
| | - Bifeng Chen
- Department of Biological Science and Technology, School of Chemistry, Chemical Engineering and Life Sciences, Wuhan University of Technology, Wuhan, China.
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Zhang L, Hu XZ, Yu T, Chen Z, Dohl J, Li X, Benedek DM, Fullerton CS, Wynn G, Barrett JE, Li M, Russell DW, Ursano RJ. Genetic association of FKBP5 with PTSD in US service members deployed to Iraq and Afghanistan. J Psychiatr Res 2020; 122:48-53. [PMID: 31927265 DOI: 10.1016/j.jpsychires.2019.12.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 12/23/2019] [Accepted: 12/24/2019] [Indexed: 01/21/2023]
Abstract
Post-traumatic stress disorder (PTSD) is a debilitating mental disorder with a prevalence of more than 7% in the US population and 12% in the military. An interaction of childhood trauma with FKBP5 (a glucocorticoid-regulated immunophilin) has been reported to be associated with PTSD in the general population. However, there are few reports on the association of FKBP5 with PTSD, particularly in important high-risk population such as the military. Here, we examined the association between four single-nucleotide polymorphisms (SNPs; rs3800373, rs9296158, rs1360780, rs9470080) covering the FKBP5 gene and probable PTSD in US service members deployed to Iraq and Afghanistan, a high-risk military population (n = 3890) (Hines et al., 2014). We found that probable PTSD subjects were significantly more likely to carry the A-allele of rs3800373, G-allele of rs9296158, C-allele of rs1360780, and C-allele of rs9470080. Furthermore, the four SNPs were in one block of strong pairwise linkage disequilibrium (r = 0.91-0.96). Within the block there were two major haplotypes of CATT and AGCC (rs3800373-rs9296158-rs1360780-rs9470080) that account for 99% of haplotype diversity. The distribution of the AGCC haplotype was significantly higher in probable PTSD subjects compared to non-PTSD (p<.05). The diplotype-based analysis indicated that the AGCC carriers tended to be probable PTSD. In this study, we demonstrated the association between FKBP5 and probable PTSD in US service members deployed to Iraq and Afghanistan, indicating that FKBP5 might be a risk factor for PTSD.
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Affiliation(s)
- Lei Zhang
- Center for the Study of Traumatic Stress, Department of Psychiatry, Uniformed Services University of the Health Sciences, Bethesda, MD, 20814, USA.
| | - Xian-Zhang Hu
- Center for the Study of Traumatic Stress, Department of Psychiatry, Uniformed Services University of the Health Sciences, Bethesda, MD, 20814, USA
| | - Tianzheng Yu
- Consortium for Health and Military Performance, Department of Military and Emergency Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, 20814, USA
| | - Ze Chen
- Center for the Study of Traumatic Stress, Department of Psychiatry, Uniformed Services University of the Health Sciences, Bethesda, MD, 20814, USA
| | - Jacob Dohl
- Consortium for Health and Military Performance, Department of Military and Emergency Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, 20814, USA
| | - Xiaoxia Li
- Center for the Study of Traumatic Stress, Department of Psychiatry, Uniformed Services University of the Health Sciences, Bethesda, MD, 20814, USA
| | - David M Benedek
- Center for the Study of Traumatic Stress, Department of Psychiatry, Uniformed Services University of the Health Sciences, Bethesda, MD, 20814, USA
| | - Carol S Fullerton
- Center for the Study of Traumatic Stress, Department of Psychiatry, Uniformed Services University of the Health Sciences, Bethesda, MD, 20814, USA
| | - Gary Wynn
- Center for the Study of Traumatic Stress, Department of Psychiatry, Uniformed Services University of the Health Sciences, Bethesda, MD, 20814, USA
| | - James E Barrett
- Department of Neurology, Drexel University College of Medicine Philadelphia, PA, 19102-1192, USA
| | - Mian Li
- Department of Neurology, Washington DC VA Medical Center, Washington, DC, 20422, USA
| | - Dale W Russell
- Center for the Study of Traumatic Stress, Department of Psychiatry, Uniformed Services University of the Health Sciences, Bethesda, MD, 20814, USA; Consortium for Health and Military Performance, Department of Military and Emergency Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, 20814, USA
| | | | - Robert J Ursano
- Center for the Study of Traumatic Stress, Department of Psychiatry, Uniformed Services University of the Health Sciences, Bethesda, MD, 20814, USA
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Dron JS, Wang J, McIntyre AD, Cao H, Hegele RA. The polygenic nature of mild-to-moderate hypertriglyceridemia. J Clin Lipidol 2020; 14:28-34.e2. [PMID: 32033914 DOI: 10.1016/j.jacl.2020.01.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 01/01/2020] [Accepted: 01/06/2020] [Indexed: 12/21/2022]
Abstract
BACKGROUND Patients with mild-to-moderate hypertriglyceridemia (HTG) are thought to share specific genetic susceptibility factors that are also present in patients with severe HTG, but no data have been reported on this issue. OBJECTIVE The objective of this study was to characterize genetic profiles of patients with mild-to-moderate HTG and compare them to patients with severe HTG. METHODS DNA from patients with mild-to-moderate HTG was sequenced using our targeted sequencing panel, "LipidSeq". For each patient, we assessed 1) rare variants disrupting five TG metabolism genes and 2) the accumulation of 16 common single-nucleotide polymorphisms (SNPs) using a polygenic risk score. The genetic profiles for these patients were then compared with normolipidemic controls from the 1000 Genomes Project and with patients with severe HTG. RESULTS Across 134 patients with mild-to-moderate HTG, 9.0% carried heterozygous rare variants and 26.9% had an excess accumulation of common SNPs. Patients with mild-to-moderate HTG were 2.38 times (95% CI [1.13-4.99]; P = .021) more likely to carry a rare variant and 3.26 times (95% CI [2.02-5.26]; P < .0001) more likely to have an extreme polygenic risk score compared with the 1000 Genomes Project. In addition, patients with severe HTG were 1.86 times (95% CI [0.98-3.51]; P = .032) more likely to carry a rare variant and 1.63 times (95% CI [1.07-2.48]; P = .013) more likely to have an extreme polygenic risk score than patients with mild-to-moderate HTG. CONCLUSIONS We report an increased prevalence of genetic determinants in patients with an increased severity of the HTG phenotype when considering either rare variants disrupting TG metabolism genes or an excess accumulation of common SNPs. As well, the findings confirm that the most prevalent genetic contributor to HTG, regardless of severity, is polygenic SNP accumulation.
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Affiliation(s)
- Jacqueline S Dron
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada; Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Jian Wang
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Adam D McIntyre
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Henian Cao
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Robert A Hegele
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada; Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada; Department of Medicine, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada.
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Wang Z, Lu X, Yao X, Liu X, Zhao L, Chang S, Zhang T, Niu B, Wang L. Relationship between HLA-DPA1 genetic polymorphism and anembryonic pregnancy. Mol Genet Genomic Med 2020; 8:e1046. [PMID: 31785132 PMCID: PMC6978238 DOI: 10.1002/mgg3.1046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 10/05/2019] [Accepted: 10/11/2019] [Indexed: 12/01/2022] Open
Abstract
BACKGROUND Human leukocyte antigen (HLA)-DP is an HLA class II molecule. Overexpression of HLA class II molecules in placental trophoblast cells may induce pregnancy loss. However, the association between HLA-DP and pregnancy loss remains unclear. HLA-DPA1 is an HLA-DP peptide chain. The objective of this study was to assess the association between HLA-DPA1 genetic polymorphism and anembryonic pregnancy, a type of early pregnancy loss, in the Chinese population. METHODS A case-control study was designed to compare the frequencies of HLA-DPA1 gene polymorphisms in an anembryonic pregnancy group and a control group. Sixty-eight cases and 122 controls were recruited. Statistical analysis was performed to assess the correlation between single-nucleotide polymorphisms (SNPs) and anembryonic pregnancy susceptibility. MassARRAY high-throughput DNA analysis was used to analyze 19 HLA-DPA1 SNPs. To explore how HLA-DPA1 polymorphism could affect anembryonic pregnancy, HLA-DPA1 serum levels were analyzed by ELISA. RESULTS Homozygous typing of rs1431403 (CC and TT) significantly increased the risk of anembryonic pregnancy in the case group (ORCC = 3.13, 95% CI: 1.50-6.53; ORTT = 2.96, 95% CI: 1.31-6.66; ORCC+TT = 3.06, 95% CI: 1.62-5.78). In samples with high HLA-DPA1 levels (≥1,500 pg/ml), the homozygous rs1431403 genotypes (nCC = 21, 43.8%; nTT = 20, 57.1%) were observed more frequently than were heterozygous genotypes. CONCLUSION HLA-DPA1 rs1431403 may be a risk factor for anembryonic pregnancy in the Chinese population. Homozygous rs1431403 genotypes (CC and TT) may increase the risk of anembryonic pregnancy by aberrantly increasing the HLA-DPA1 levels.
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Affiliation(s)
- Zhendong Wang
- Laboratory of Biochemistry and Molecular BiologyShanxi Medical UniversityShanxiChina
| | - Xiaolin Lu
- Beijing Municipal Key Laboratory of Child Development and NutriomicsCapital Institute of PediatricsBeijingP.R. China
| | - Xiuying Yao
- Department of Obstetrics and GynecologyPLA General Hospital 263th Clinical DepartmentBeijingChina
| | - Xinli Liu
- Department of Obstetrics and GynecologyPLA General Hospital 263th Clinical DepartmentBeijingChina
| | - Linlin Zhao
- Department of Obstetrics and GynecologyPLA General Hospital 263th Clinical DepartmentBeijingChina
| | - Shaoyan Chang
- Beijing Municipal Key Laboratory of Child Development and NutriomicsCapital Institute of PediatricsBeijingP.R. China
| | - Ting Zhang
- Beijing Municipal Key Laboratory of Child Development and NutriomicsCapital Institute of PediatricsBeijingP.R. China
| | - Bo Niu
- Laboratory of Biochemistry and Molecular BiologyShanxi Medical UniversityShanxiChina
- Beijing Municipal Key Laboratory of Child Development and NutriomicsCapital Institute of PediatricsBeijingP.R. China
| | - Li Wang
- Beijing Municipal Key Laboratory of Child Development and NutriomicsCapital Institute of PediatricsBeijingP.R. China
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Varljen T, Sekulovic G, Rakic O, Maksimovic N, Jekic B, Novakovic I, Damnjanovic T. Genetic variant rs16944 in IL1B gene is a risk factor for early-onset sepsis susceptibility and outcome in preterm infants. Inflamm Res 2019; 69:155-157. [PMID: 31863173 DOI: 10.1007/s00011-019-01301-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 11/25/2019] [Accepted: 11/28/2019] [Indexed: 12/13/2022] Open
Abstract
OBJECTIVE Interleukin-1-B (IL1B) is a proinflammatory cytokine that plays an important role in sepsis. The aim of this study was to evaluate the relationships between IL1B-511G/A polymorphism and susceptibility and outcome of early-onset sepsis (EOS) in preterm infants. METHODS DNA was extracted from the buccal swabs of 471 (285 with EOS and 186 control) preterm infants. Genotypes of rs16944 polymorphism were determined with real-time PCR method. RESULTS We found statistically significant higher frequency of IL1B-511AA genotype in EOS group than in control group (p = 0.012). Also, IL1B-511AA genotype is statistically significantly more frequent in patients with lethal EOS outcome (p = 0.011). CONCLUSION Genotype IL1B-511AA was associated with susceptibility to EOS and it is a significant predictor of lethal outcome in preterm infants with EOS.
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Affiliation(s)
- Tatjana Varljen
- Institute of Legal Medicine, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | | | | | - Nela Maksimovic
- Institute of Human Genetics, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Biljana Jekic
- Institute of Human Genetics, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Ivana Novakovic
- Institute of Human Genetics, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Tatjana Damnjanovic
- Institute of Human Genetics, Faculty of Medicine, University of Belgrade, Belgrade, Serbia.
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Irivboje YI, Sanni MT, Fafiolu AO, Olowofeso O, Ikeobi CON. Genetic polymorphisms in part of intron 7 and exon 8 of HSP90AA1 gene and its association with heat tolerance traits in two exotic layer chicken strains. Trop Anim Health Prod 2019; 52:969-977. [PMID: 31707685 DOI: 10.1007/s11250-019-02079-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 09/11/2019] [Indexed: 12/19/2022]
Abstract
Chickens, like other vertebrates, react to stress conditions through their cultured cells by expressing heat shock proteins (HSPs). Genetic association of single-nucleotide polymorphisms (SNPs) in HSPs with desirable traits will reveal their importance as potential genetic markers. Blood samples were collected from 50 birds per strain for DNA extraction, polymerase chain reaction amplification and sequencing of the HSP90AA1 gene. SNPs were detected using Codoncode Aligner. Association of each SNP with heat tolerance traits was analysed using generalized linear model procedure of SAS. A total of seven SNPs were detected, four SNPs; A7T, A160T, T223A and C134T were detected in part of intron 7 to exon 8 of HSP90AA1 gene of BRD while three A160T, T223A and C134T were detected in HYL. SNPC134T, a synonymous variant, was detected in exon 8. Only SNPA7T was in Hardy-Weinberg equilibrium (X2 = 0.03) but had no association with the traits measured. Polymorphic information content calculated showed SNPA160T to be moderately polymorphic; other SNPs were lowly polymorphic. Heterozygosity for SNPs-A160T and T223A of BRD showed moderate genetic variation while the other SNPs and those in HYL recorded low genetic variation. The study concluded that the SNPs detected were majorly lowly polymorphic and also the SNP locus A7T in intron 7 of HSP90AA1 of BRD had no genetic association with heat tolerance traits.
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Affiliation(s)
- Young I Irivboje
- World Bank Centre of Excellence in Agricultural Development and Sustainable Environment, Federal University of Agriculture, Abeokuta, Nigeria. .,Department of Animal Breeding and genetics, Federal University of Agriculture, Abeokuta, Nigeria.
| | - M T Sanni
- Department of Animal Breeding and genetics, Federal University of Agriculture, Abeokuta, Nigeria
| | - A O Fafiolu
- World Bank Centre of Excellence in Agricultural Development and Sustainable Environment, Federal University of Agriculture, Abeokuta, Nigeria.,Department of Animal Nutrition, Federal University of Agriculture, Abeokuta, Nigeria
| | - O Olowofeso
- World Bank Centre of Excellence in Agricultural Development and Sustainable Environment, Federal University of Agriculture, Abeokuta, Nigeria.,Department of Animal Breeding and genetics, Federal University of Agriculture, Abeokuta, Nigeria
| | - C O N Ikeobi
- World Bank Centre of Excellence in Agricultural Development and Sustainable Environment, Federal University of Agriculture, Abeokuta, Nigeria.,Department of Animal Breeding and genetics, Federal University of Agriculture, Abeokuta, Nigeria
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Xu Y, Peng G, Sun M, Li J, Yan W, Tang J, Pan J, Xu Z. Genomic organization of the molt-inhibiting hormone gene in the red swamp crayfish Procambarus clarkii and characterization of single-nucleotide polymorphisms associated with growth. Comp Biochem Physiol B Biochem Mol Biol 2019; 237:110334. [PMID: 31472239 DOI: 10.1016/j.cbpb.2019.110334] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 08/09/2019] [Accepted: 08/26/2019] [Indexed: 01/28/2023]
Abstract
Molt-inhibiting hormone (MIH), a neuropeptide synthesized in the eyestalk in crustaceans, is mainly responsible for the molting by negatively controlling the ecdysteroids secretion. Although there are several reports of the isolation and protein sequencing of MIH in the red swamp crayfish, little is known about the nucleotide sequence and gene organization of this neuropeptide, even less about the association of MIH polymorphisms and growth traits. Here, a 1237 bp full-length MIH cDNA was obtained from the crayfish eyestalk, which encodes a putative protein of 106 amino acids, with a 191 bp 5'-UTR and a 728 bp 3'-UTR. The MIH genomic DNA sequence is 4205 bp in length, which includes three exons interrupted by two introns, and a 929 bp 5'-flanking region. Potential transcription initiation site and transcription factor binding sites were identified in the 5'-flanking region, implying a potential role in transcriptional regulation. Seventeen SNPs in the 5'-flanking region and 3'-UTR were identified, and the associations between these SNPs and growth traits were evaluated with a two-stage design. A SNPs g. -12C > G that showed a significant association with body weight was identified. Individuals with GG genotype had a significantly higher body weight than those with CC genotype (43.98 ± 9.82 g vs. 34.27 ± 6.87 g; P ﹤ 0.001), indicating a beneficial effect of the G allele on the growth of red swamp crayfish. The obtained MIH gene, as well as the identified SNPs, may serve as targets for molecular marker-aided selection in growth improvement of the red swamp crayfish in future studies.
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Affiliation(s)
- Yu Xu
- Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing 210017, China
| | - Gang Peng
- Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing 210017, China
| | - Mengling Sun
- Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing 210017, China
| | - Jiajia Li
- Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing 210017, China
| | - Weihui Yan
- Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing 210017, China
| | - Jianqing Tang
- Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing 210017, China
| | - Jianlin Pan
- Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing 210017, China; The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing 210014, China
| | - Zhiqiang Xu
- Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing 210017, China; The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing 210014, China.
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Ji D, Xing W, Li F, Huang Z, Zheng W, Hu B, Niu F, Zhu Y, Yang X. Correlation of EYS polymorphisms with lumbar disc herniation risk among Han Chinese population. Mol Genet Genomic Med 2019; 7:e890. [PMID: 31359629 PMCID: PMC6732306 DOI: 10.1002/mgg3.890] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 05/05/2019] [Accepted: 07/08/2019] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Lumbar disc herniation (LDH) is a common spinal disease in clinical practice. Once lumbar disc herniation occurs, it seriously reduces patient's quality of life. The EYS (eyes shut homolog) was discovered in recent years and it may be related to lumbar disc herniation. So we conducted a case-control study to explore the relationship between EYS polymorphism and lumbar disc herniation risk. METHODS We selected 5 single-nucleotide polymorphisms (SNPs) of EYS gene in a case-control study with 508 cases and 508 healthy controls to evaluate the relatedness by using genetic model, haplotype, and stratification analysis. RESULTS We found that the minor alleles of rs62413038 (OR = 1.21, 95%CI: 1.01-1.43, p = .036) and rs9450607 (OR = 1.26, 95% CI: 1.05-1.53, p = .016) were associated with an increased risk of lumbar disc herniation in the allelic model analysis. In the genotypic model analysis, rs62413038 displayed a significantly increased risk of lumbar disc herniation in log-additive models (OR = 1.20, 95% CI: 1.01-1.43, p = .039). While the rs9450607 was also obviously associated with an increased lumbar disc herniation risk in recessive (OR = 1.98, 95% CI: 1.24-3.13, p = .004) and log-additive models (OR = 1.27, 95% CI: 1.05-1.55, p = .014). In addition, in the haplotype analyses of the SNPs, we found that the "CGGA" haplotype of rs1482456, rs9342097, rs9450607, and rs7757884 was associated with lumbar disc herniation. (OR = 0.52, 95% CI: 0.30-0.89, p = .017). CONCLUSION These results suggest that EYS polymorphism may be associated with lumbar disc herniation among Han Chinese population. It also opens up a new exploration direction for the etiology of lumbar disc herniation.
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Affiliation(s)
- Demin Ji
- Inner Mongolia Medical University, Hohhot, China.,The Second Affiliated Hospital of Inner Mongolia Medical University, Hohhot, China
| | - Wenhua Xing
- The Second Affiliated Hospital of Inner Mongolia Medical University, Hohhot, China
| | - Feng Li
- The Second Affiliated Hospital of Inner Mongolia Medical University, Hohhot, China
| | - Zhi Huang
- The Second Affiliated Hospital of Inner Mongolia Medical University, Hohhot, China
| | - Wenkai Zheng
- The Second Affiliated Hospital of Inner Mongolia Medical University, Hohhot, China
| | - Baoyang Hu
- Inner Mongolia Medical University, Hohhot, China.,The Second Affiliated Hospital of Inner Mongolia Medical University, Hohhot, China
| | - FangLin Niu
- Key Laboratory of Resource Biology and Biotechnology in Western China (Northwest University), Ministry of Education, Xi'an, China
| | - Yong Zhu
- The Second Affiliated Hospital of Inner Mongolia Medical University, Hohhot, China
| | - Xuejun Yang
- The Second Affiliated Hospital of Inner Mongolia Medical University, Hohhot, China
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Zhang N, Heruth DP, Wu W, Zhang LQ, Nsumu MN, Shortt K, Li K, Jiang X, Wang B, Friesen C, Li DY, Ye SQ. Functional characterization of SLC26A3 c.392C>G (p.P131R) mutation in intestinal barrier function using CRISPR/CAS9-created cell models. Cell Biosci 2019; 9:40. [PMID: 31114672 PMCID: PMC6518688 DOI: 10.1186/s13578-019-0303-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 05/07/2019] [Indexed: 12/11/2022] Open
Abstract
Background Congenital chloride diarrhea (CCD) in a newborn is a rare autosomal recessive disorder with life-threatening complications, requiring early diagnostics and treatment to prevent severe dehydration and infant mortality. SLC26A3 rs386833481 (c.392C>G; p.P131R) gene polymorphism is an important genetic determinant of CCD. Here, we report the influence of the non-synonymous SLC26A3 variant rs386833481 gene polymorphism on the function of the epithelial barrier and the potential mechanisms of these effects. Results We found that P131R-SLC26A3 increased dysfunction of the epithelial barrier compared with wild type SLC26A3 in human colonic Caco-2 and mouse colonic CMT-93 cells. When P131R-SLC26A3 was subsequently reverted to wild type, the epithelial barrier function was restored similar to wild type cells. Further study demonstrated that variant P131R-SLC26A3 disrupts function of epithelial barrier through two distinct molecular mechanisms: (a) decreasing SLC26A3 expression through a ubiquitination pathway and (b) disrupting a key interaction with its partner ZO-1/CFTR, thereby increasing the epithelial permeability. Conclusion Our study provides an important insight of SLC26A3 SNPs in the regulation of the epithelial permeability and indicates that SLC26A3 rs386833481 is likely a causative mutation in the dysfunction of epithelial barrier of CCD, and correction of this SNP or increasing SLC26A3 function could be therapeutically beneficial for chronic diarrhea diseases.
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Affiliation(s)
- Nini Zhang
- 1Division of Gastroenterology, Department of Pediatrics, Children's Mercy Hospitals and Clinics, Kansas City, MO USA.,2Division of Experimental and Translational Genetics, Department of Pediatrics, Children's Mercy Hospitals and Clinics, Kansas City, MO USA.,3Department of Biomedical and Health Informatics, University of Missouri Kansas City School of Medicine, Kansas City, MO USA.,4Department of Pediatrics, Tangdu Hospital, Fourth Military Medical University, Xi'an, Shaanxi China
| | - Daniel P Heruth
- 2Division of Experimental and Translational Genetics, Department of Pediatrics, Children's Mercy Hospitals and Clinics, Kansas City, MO USA
| | - Weibin Wu
- 2Division of Experimental and Translational Genetics, Department of Pediatrics, Children's Mercy Hospitals and Clinics, Kansas City, MO USA.,3Department of Biomedical and Health Informatics, University of Missouri Kansas City School of Medicine, Kansas City, MO USA.,8Department of Neonatology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Li Qin Zhang
- 2Division of Experimental and Translational Genetics, Department of Pediatrics, Children's Mercy Hospitals and Clinics, Kansas City, MO USA.,5Department of Biomedical Sciences, University of Missouri Kansas City School of Medicine, Kansas City, MO USA
| | - Marianne N Nsumu
- 2Division of Experimental and Translational Genetics, Department of Pediatrics, Children's Mercy Hospitals and Clinics, Kansas City, MO USA.,3Department of Biomedical and Health Informatics, University of Missouri Kansas City School of Medicine, Kansas City, MO USA
| | - Katherine Shortt
- 2Division of Experimental and Translational Genetics, Department of Pediatrics, Children's Mercy Hospitals and Clinics, Kansas City, MO USA.,6Division of Cell Biology & Biophysics, University of Missouri Kansas City School of Biological Sciences, Kansas City, MO USA
| | - Kelvin Li
- 7Department of Global Biostatistics and Data Science, Center for Bioinformatics and Genomics, Tulane University, New Orleans, LA USA
| | - Xun Jiang
- 4Department of Pediatrics, Tangdu Hospital, Fourth Military Medical University, Xi'an, Shaanxi China
| | - Baoxi Wang
- 4Department of Pediatrics, Tangdu Hospital, Fourth Military Medical University, Xi'an, Shaanxi China
| | - Craig Friesen
- 1Division of Gastroenterology, Department of Pediatrics, Children's Mercy Hospitals and Clinics, Kansas City, MO USA
| | - Ding-You Li
- 1Division of Gastroenterology, Department of Pediatrics, Children's Mercy Hospitals and Clinics, Kansas City, MO USA
| | - Shui Qing Ye
- 2Division of Experimental and Translational Genetics, Department of Pediatrics, Children's Mercy Hospitals and Clinics, Kansas City, MO USA.,3Department of Biomedical and Health Informatics, University of Missouri Kansas City School of Medicine, Kansas City, MO USA.,6Division of Cell Biology & Biophysics, University of Missouri Kansas City School of Biological Sciences, Kansas City, MO USA
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Xu Y, Zeng A, Song L, Li J, Yan J. Comparative transcriptomics analysis uncovers alternative splicing events and molecular markers in cabbage (Brassica oleracea L.). Planta 2019; 249:1599-1615. [PMID: 30771045 DOI: 10.1007/s00425-019-03108-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [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: 11/27/2018] [Accepted: 02/07/2019] [Indexed: 05/20/2023]
Abstract
Alternative splicing (AS) events were identified and verified in cabbage by comparative transcriptome analysis. The corresponding markers were developed and the germplasm resources were identified. Alternative splicing (AS) is a central regulatory mechanism that greatly contributes to plant gene expression and transcriptome diversity. A large body of evidence has shown that AS complexity is relevant for plant development, evolution, complexity, and adaptation. Both insertion/deletion (InDel) and single nucleotide polymorphism (SNP) are typically co-dominant inheritance markers and have abundant polymorphisms. These have been widely used for marker-assisted selection, genetic mapping, and germplasm identification in plants. However, little is known about the molecular mechanisms underlying AS events and the development of markers including SNP and InDel from the cabbage transcriptome. In this study, three cabbage transcriptome datasets were collected and aligned to the cabbage reference genome to analyze AS events and marker development. 31,524 AS events were identified from three cabbage genotypes, accounting for 20.8% of the total cabbage genes. Alternative 3' splice site donor (A3SS) was the most frequent type of the four main AS events in cabbage. 70,475 InDels and 706,269 SNPs were identified with average frequencies of 1 InDel/6.9 kb and 1 SNP/0.7 kb, respectively. 71,942 potential SSRs were identified in 53,129 assembled unigenes with a density of 1 SSR/6.8 kb. The ratio of SNPs with synonymous/non-synonymous mutations was 1:0.65. 142 InDels and 36 SNPs were randomly selected and validated via Sanger sequencing and polymorphism was found among 66.2% of the InDels and 78.6% of the SNPs. Furthermore, 35 informative InDel markers were successfully used for genetic diversity analysis on 36 cabbage accessions. These results facilitate understanding of the molecular regulation mechanism underlying AS events in cabbage. They also provide molecular marker resource data for genetic mapping construction and germplasm identification, and facilitate the genetic improvement of cabbage via breeding.
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Affiliation(s)
- Yuanyuan Xu
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, People's Republic of China
| | - Aisong Zeng
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, People's Republic of China.
| | - Lixiao Song
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, People's Republic of China
| | - Jiaqing Li
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100083, People's Republic of China
| | - Jiyong Yan
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, People's Republic of China.
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Hsiung A, Naya FJ, Chen X, Shiang R. A schizophrenia associated CMYA5 allele displays differential binding with desmin. J Psychiatr Res 2019; 111:8-15. [PMID: 30658136 PMCID: PMC6467702 DOI: 10.1016/j.jpsychires.2019.01.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 11/28/2018] [Accepted: 01/07/2019] [Indexed: 11/17/2022]
Abstract
CMYA5 is a candidate gene for schizophrenia because of the genetic association of variant rs10043986 (C > T) to this severe mental disorder. Studies of CMYA5 and its gene product, myospryn, in the brain and neuronal cells have not been previously reported. The SNP rs10043986 changes the 4,063rd amino acid from Pro to Leu, which is likely to alter protein function. To understand its potential role in the brain, we examined the neuronal expression of myospryn and its binding partner, desmin, an intermediate filament (IF) protein, and investigated how the two alleles of myospryn affect its binding to desmin. Myospryn and desmin are shown to be expressed in the brain and myospryn is shown to localize to the cytoplasm and nucleus of myoblast, neuroblastoma, and glioblastoma cell lines. Peripherin and vimentin, known brain IF proteins, have high protein similarity to desmin but were found not to interact with myospryn using yeast two-hybrid (Y2H). Using a quantitative Y2H assay and surface plasmon resonance, the T allele (Leu) of rs10043986 was found to have stronger binding to desmin than the C allele (Pro). Based on findings described in this report, we hypothesize that the interaction between myospryn to IF provides structural support and efficient rearrangement of the cytoskeleton network during early neuritogenesis.
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Affiliation(s)
- Anting Hsiung
- Department of Human and Molecular Genetics, Virginia Commonwealth University, 1101 East Marshall Street, Richmond, VA, 23298-0033, USA.
| | - Francisco J Naya
- Department of Biology, Boston University, 5 Cummington Mall, Boston, MA, 02215, USA.
| | - Xiangning Chen
- Department of Human and Molecular Genetics, Virginia Commonwealth University, 1101 East Marshall Street, Richmond, VA, 23298-0033, USA; Department of Psychiatry, Virginia Commonwealth University, 1200 East Broad Street, Richmond, VA, 23298-0710, USA; Nevada Institute of Personalized Medicine and Department of Psychology, University of Nevada, 4505 S. Maryland Parkway, Las Vegas, NV, 89154-4009, USA.
| | - Rita Shiang
- Department of Human and Molecular Genetics, Virginia Commonwealth University, 1101 East Marshall Street, Richmond, VA, 23298-0033, USA.
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Gu X, Li H, Chen X, Zhang X, Mei F, Jia M, Xiong C. PEX10, SIRPA-SIRPG, and SOX5 gene polymorphisms are strongly associated with nonobstructive azoospermia susceptibility. J Assist Reprod Genet 2019; 36:759-768. [PMID: 30863997 DOI: 10.1007/s10815-019-01417-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 02/01/2019] [Indexed: 11/29/2022] Open
Abstract
PURPOSE Male infertility is a multifactorial syndrome encompassing a wide variety of disorders. A previous Chinese genome-wide single-nucleotide polymorphism (SNP) association studies have identified four SNPs (rs12097821 in PRMT6 gene, rs2477686 in PEX10 gene, rs6080550 in SIRPA-SIRPG, and rs10842262 in SOX5 gene) as being significantly associated with risk factors for nonobstructive azoospermia (NOA). However, the results were not fully repeated in later studies, which calls for further investigations. METHODS We here performed a case-control study in a central Chinese population to explore the association between the four SNPs and male infertility, which included 631 infertile men (NOA and oligozoospermia) and 720 healthy fertile men. The genotyping was performed using the polymerase chain reaction-restriction fragment length polymorphism and confirmed by sequencing. RESULTS The results showed that rs12097821 and rs10842262 were strongly associated with the risk of NOA but not total male infertility or oligozoospermia, while rs2477686 and rs6080550 were not associated with the risk of total male infertility, NOA, or oligozoospermia. To improve the statistical strength, a meta-analysis was conducted. The results suggested that rs2477686, rs6080550, and rs10842262 were significantly associated with male infertility, especially with NOA, while rs12097821 was only found to be associated with total male infertility. CONCLUSIONS Collectively, the rs2477686, rs6080550, and rs10842262 may indeed be the genetic risk factors for NOA, which requires further investigation using larger independent sets of samples in different ethnic populations.
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Affiliation(s)
- Xiuli Gu
- Department of Reproductive Genetics, Center of Reproductive Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430032, China.
| | - Honggang Li
- Family Planning Research Institute, Center of Reproductive Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430032, China
| | - Xi Chen
- Department of Hospital Infection Control, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430032, China
| | - Xue Zhang
- Department of Reproductive Genetics, Center of Reproductive Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430032, China
| | - Fen Mei
- Department of Reproductive Genetics, Center of Reproductive Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430032, China
| | - Mingzhu Jia
- Department of Reproductive Genetics, Center of Reproductive Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430032, China
| | - Chengliang Xiong
- Family Planning Research Institute, Center of Reproductive Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430032, China.
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Xu X, Zhang Y, Zhao S, Bian Y, Ning Y, Qin Y. Mutational analysis of theFAM175A gene in patients with premature ovarian insufficiency. Reprod Biomed Online 2019; 38:943-950. [PMID: 31000350 DOI: 10.1016/j.rbmo.2019.02.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 12/30/2018] [Accepted: 02/01/2019] [Indexed: 01/15/2023]
Abstract
RESEARCH QUESTION The family with sequence similarity 175 member A gene (FAM175A; also known as ABRAXAS1, CCDC98 and ABRA1), a member of the DNA repair family, contributes to the BRCA1 (BRCA1 DNA repair associated)-dependent DNA damage response and is associated with age at natural menopause. However, it remains poorly understood whether sequence variants in FAM175A are causative for premature ovarian insufficiency (POI). The aim of this study was to investigate whether mutations in the gene FAM175A were present in patients with POI. DESIGN A total of 400 women with idiopathic POI and 498 control women with regular menstruation (306 age-matched women and 192 women over 40 years old) were recruited. After Sanger sequencing of FAM175A, functional experiments were carried out to explore the deleterious effects of the identified variation. DNA damage was subsequently induced by mitomycin C (MMC), and DNA repair capacity and G2-M checkpoint activation were evaluated by examining the phosphorylation level of H2AX (H2A histone family, member X) and the percentage of mitotic cells, respectively. RESULTS One rare single-nucleotide polymorphism, rs755187051 in gene FAM175A, c.C727G (p.L243V), was identified in two patients but absent in the 498 controls. The functional experiments demonstrated that overexpression of variant p.L243V in HeLa cells resulted in a similar sensitivity to MMC-induced damage compared with cells transfected with wild-type FAM175A. Moreover, after treatment with MMC, there were no differences in DNA repair capacity and G2-M checkpoint activation between the mutant and wild-type genes. CONCLUSION Our results suggest that the p.L243V variant of FAM175A may not be causative for POI. The contribution of FAM175A to POI needs further exploration.
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Affiliation(s)
- Xiaofei Xu
- Centre for Reproductive Medicine, Shandong University, National Research Center for Assisted Reproductive Technology and Reproductive Genetics, The Key Laboratory of Reproductive Endocrinology (Shandong University), Ministry of Education, Jinan, China; Key Laboratory of Assisted Reproduction, Ministry of Education, Center of Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
| | - Yingxin Zhang
- Department of Obstetrics and Gynecology, The Chinese University of Hong Kong, Hong Kong, China
| | - Shidou Zhao
- Centre for Reproductive Medicine, Shandong University, National Research Center for Assisted Reproductive Technology and Reproductive Genetics, The Key Laboratory of Reproductive Endocrinology (Shandong University), Ministry of Education, Jinan, China
| | - Yuehong Bian
- Centre for Reproductive Medicine, Shandong University, National Research Center for Assisted Reproductive Technology and Reproductive Genetics, The Key Laboratory of Reproductive Endocrinology (Shandong University), Ministry of Education, Jinan, China
| | - Yunna Ning
- Centre for Reproductive Medicine, Shandong University, National Research Center for Assisted Reproductive Technology and Reproductive Genetics, The Key Laboratory of Reproductive Endocrinology (Shandong University), Ministry of Education, Jinan, China
| | - Yingying Qin
- Centre for Reproductive Medicine, Shandong University, National Research Center for Assisted Reproductive Technology and Reproductive Genetics, The Key Laboratory of Reproductive Endocrinology (Shandong University), Ministry of Education, Jinan, China.
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Yang Y, Lan Z, Shu H, Zhou H, Jiang X, Hou L, Gu P. Association between expression levels and growth trait-related SNPs located in promoters of the MC4R and MSTN genes in Spinibarbus hollandi. Genes Genomics 2018; 40:1119-25. [PMID: 30315516 DOI: 10.1007/s13258-018-0666-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2017] [Accepted: 02/04/2018] [Indexed: 10/18/2022]
Abstract
Melanocortin 4 receptor: (MC4R) and Myostatin (MSTN) are two important growth trait-related genes in animals. In this study, we showed that two SNPs, MC4R-719A>G and MSTN-519C>T, found in the promoters of the MC4R and MSTN genes, respectively, are both associated with growth traits in Spinibarbus hollandi. Furthermore, we observed that there were significant associations between the expression levels of the MC4R and MSTN genes and these two growth trait-related SNPs. The expression level of MC4R gene in brain was lower in GG genotype fish with extremely high growth performance than that in AA genotype fish with extremely low growth performance. Expression level of the MSTN gene in muscle was lower in TT genotype fish with extremely high growth performance than that in CC and CT genotype fish with lower growth performance. The results indicated that these SNPs located in the promoters of MC4R and MSTN are associated with growth-related traits through modification of gene expression levels. The MSTN and MC4R SNPs may have useful application in effective marker-assisted selection aimed to increase output in S. hollandi.
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Li N, Rowley SM, Thompson ER, McInerny S, Devereux L, Amarasinghe KC, Zethoven M, Lupat R, Goode D, Li J, Trainer AH, Gorringe KL, James PA, Campbell IG. Evaluating the breast cancer predisposition role of rare variants in genes associated with low-penetrance breast cancer risk SNPs. Breast Cancer Res 2018; 20:3. [PMID: 29316957 PMCID: PMC5761188 DOI: 10.1186/s13058-017-0929-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 12/20/2017] [Indexed: 12/30/2022] Open
Abstract
Background Genome-wide association studies (GWASs) have identified numerous single-nucleotide polymorphisms (SNPs) associated with small increases in breast cancer risk. Studies to date suggest that some SNPs alter the expression of the associated genes, which potentially mediates risk modification. On this basis, we hypothesised that some of these genes may be enriched for rare coding variants associated with a higher breast cancer risk. Methods The coding regions and exon-intron boundaries of 56 genes that have either been proposed by GWASs to be the regulatory targets of the SNPs and/or located < 500 kb from the risk SNPs were sequenced in index cases from 1043 familial breast cancer families that previously had negative test results for BRCA1 and BRCA2 mutations and 944 population-matched cancer-free control participants from an Australian population. Rare (minor allele frequency ≤ 0.001 in the Exome Aggregation Consortium and Exome Variant Server databases) loss-of-function (LoF) and missense variants were studied. Results LoF variants were rare in both the cases and control participants across all the candidate genes, with only 38 different LoF variants observed in a total of 39 carriers. For the majority of genes (n = 36), no LoF variants were detected in either the case or control cohorts. No individual gene showed a significant excess of LoF or missense variants in the cases compared with control participants. Among all candidate genes as a group, the total number of carriers with LoF variants was higher in the cases than in the control participants (26 cases and 13 control participants), as was the total number of carriers with missense variants (406 versus 353), but neither reached statistical significance (p = 0.077 and p = 0.512, respectively). The genes contributing most of the excess of LoF variants in the cases included TET2, NRIP1, RAD51B and SNX32 (12 cases versus 2 control participants), whereas ZNF283 and CASP8 contributed largely to the excess of missense variants (25 cases versus 8 control participants). Conclusions Our data suggest that rare LoF and missense variants in genes associated with low-penetrance breast cancer risk SNPs may contribute some additional risk, but as a group these genes are unlikely to be major contributors to breast cancer heritability. Electronic supplementary material The online version of this article (doi:10.1186/s13058-017-0929-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Na Li
- Cancer Genetics Laboratory, Research Division, Peter MacCallum Cancer Centre, 305 Grattan Street, Melbourne, VIC, 3000, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC, Australia
| | - Simone M Rowley
- Cancer Genetics Laboratory, Research Division, Peter MacCallum Cancer Centre, 305 Grattan Street, Melbourne, VIC, 3000, Australia
| | - Ella R Thompson
- Cancer Genetics Laboratory, Research Division, Peter MacCallum Cancer Centre, 305 Grattan Street, Melbourne, VIC, 3000, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC, Australia.,Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Simone McInerny
- Parkville Familial Cancer Centre, Peter MacCallum Cancer Centre and Royal Melbourne Hospital, Melbourne, VIC, Australia
| | - Lisa Devereux
- Cancer Genetics Laboratory, Research Division, Peter MacCallum Cancer Centre, 305 Grattan Street, Melbourne, VIC, 3000, Australia.,LifePool, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Kaushalya C Amarasinghe
- Bioinformatics & Cancer Genomics Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Magnus Zethoven
- Bioinformatics & Cancer Genomics Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Richard Lupat
- Bioinformatics & Cancer Genomics Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - David Goode
- Cancer Genetics Laboratory, Research Division, Peter MacCallum Cancer Centre, 305 Grattan Street, Melbourne, VIC, 3000, Australia.,Bioinformatics Core Facility, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Jason Li
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC, Australia.,Bioinformatics & Cancer Genomics Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Alison H Trainer
- Cancer Genetics Laboratory, Research Division, Peter MacCallum Cancer Centre, 305 Grattan Street, Melbourne, VIC, 3000, Australia.,Parkville Familial Cancer Centre, Peter MacCallum Cancer Centre and Royal Melbourne Hospital, Melbourne, VIC, Australia.,Department of Pathology, University of Melbourne, Melbourne, VIC, Australia
| | - Kylie L Gorringe
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC, Australia.,Department of Pathology, University of Melbourne, Melbourne, VIC, Australia.,Cancer Genomics Program, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Paul A James
- Cancer Genetics Laboratory, Research Division, Peter MacCallum Cancer Centre, 305 Grattan Street, Melbourne, VIC, 3000, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC, Australia.,Parkville Familial Cancer Centre, Peter MacCallum Cancer Centre and Royal Melbourne Hospital, Melbourne, VIC, Australia.,Department of Pathology, University of Melbourne, Melbourne, VIC, Australia
| | - Ian G Campbell
- Cancer Genetics Laboratory, Research Division, Peter MacCallum Cancer Centre, 305 Grattan Street, Melbourne, VIC, 3000, Australia. .,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC, Australia. .,Department of Pathology, University of Melbourne, Melbourne, VIC, Australia.
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Steele KA, Quinton-Tulloch MJ, Amgai RB, Dhakal R, Khatiwada SP, Vyas D, Heine M, Witcombe JR. Accelerating public sector rice breeding with high-density KASP markers derived from whole genome sequencing of indica rice. Mol Breed 2018; 38:38. [PMID: 29563850 PMCID: PMC5842261 DOI: 10.1007/s11032-018-0777-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 01/15/2018] [Indexed: 05/21/2023]
Abstract
Few public sector rice breeders have the capacity to use NGS-derived markers in their breeding programmes despite rapidly expanding repositories of rice genome sequence data. They rely on > 18,000 mapped microsatellites (SSRs) for marker-assisted selection (MAS) using gel analysis. Lack of knowledge about target SNP and InDel variant loci has hampered the uptake by many breeders of Kompetitive allele-specific PCR (KASP), a proprietary technology of LGC genomics that can distinguish alleles at variant loci. KASP is a cost-effective single-step genotyping technology, cheaper than SSRs and more flexible than genotyping by sequencing (GBS) or array-based genotyping when used in selection programmes. Before this study, there were 2015 rice KASP marker loci in the public domain, mainly identified by array-based screening, leaving large proportions of the rice genome with no KASP coverage. Here we have addressed the urgent need for a wide choice of appropriate rice KASP assays and demonstrated that NGS can detect many more KASP to give full genome coverage. Through re-sequencing of nine indica rice breeding lines or released varieties, this study has identified 2.5 million variant sites. Stringent filtering of variants generated 1.3 million potential KASP assay designs, including 92,500 potential functional markers. This strategy delivers a 650-fold increase in potential selectable KASP markers at a density of 3.1 per 1 kb in the indica crosses analysed and 377,178 polymorphic KASP design sites on average per cross. This knowledge is available to breeders and has been utilised to improve the efficiency of public sector breeding in Nepal, enabling identification of polymorphic KASP at any region or quantitative trait loci in relevant crosses. Validation of 39 new KASP was carried out by genotyping progeny from a range of crosses to show that they detected segregating alleles. The new KASP have replaced SSRs to aid trait selection during marker-assisted backcrossing in these crosses, where target traits include rice blast and BLB resistance loci. Furthermore, we provide the software for plant breeders to generate KASP designs from their own datasets.
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Affiliation(s)
- Katherine A. Steele
- School of the Environment, Natural Resources and Geography, SENRGY, Bangor University, Bangor, Gwynedd LL57 2UW UK
| | - Mark J. Quinton-Tulloch
- School of the Environment, Natural Resources and Geography, SENRGY, Bangor University, Bangor, Gwynedd LL57 2UW UK
| | - Resham B. Amgai
- Biotechnology Division, Nepal Agricultural Research Council, PO Box No. 1135, Kathmandu, Nepal
| | - Rajeev Dhakal
- Anamolbiu Private Ltd., P.O. Box 28, Jagritichok, Bharatpur-11, Chitwan, Nepal
- Present Address: LI-BIRD, PO Box 324, Gairapatan, Kaski, Pokhara, Nepal
| | - Shambhu P. Khatiwada
- Biotechnology Division, Nepal Agricultural Research Council, PO Box No. 1135, Kathmandu, Nepal
| | - Darshna Vyas
- LGC Genomics, Units 1 & 2, Trident Industrial Estate, Pindar Road, Hoddesdon, Herts EN11 0WZ UK
| | - Martin Heine
- LGC Genomics, TGS Haus 8, Ostendstr. 25, 12459 Berlin, Germany
- Present Address: NuGEN Technologies Inc., 201 Industrial Road, Suite 310, San Carlos, CA 94070 USA
| | - John R. Witcombe
- School of the Environment, Natural Resources and Geography, SENRGY, Bangor University, Bangor, Gwynedd LL57 2UW UK
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Li W, Li M, Pu X, Guo Y. Distinguishing the disease-associated SNPs based on composition frequency analysis. Interdiscip Sci 2017; 9:459-467. [PMID: 29143920 DOI: 10.1007/s12539-017-0248-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 06/03/2017] [Accepted: 06/26/2017] [Indexed: 12/22/2022]
Abstract
Single-nucleotide polymorphism (SNP) is a basical variation in genome. When SNPs occur at the binding sites of microRNA, they can influence the binding efficiency, cause a fluctuation of the mRNA in vivo, and thus arouse posttranscriptional level abnormality. Therefore, SNP has a strong correlation with diseases. Although enormous SNPs have been experimentally identified, only a tiny proportion of them are truly disease-associated SNPs (dSNPs) that relate to microRNA modification and then are involved in disease causing process. Therefore, it is important to distinguish dSNPs from the usual SNPs. Analysis here shows that composition is different between sequence segments centered by dSNP and SNP. Inspired by the composition, transition and distribution features which are meaningful and effective in characterizing proteins' sequence information, we improved and applied it to represent the frequency and physicochemical properties of a gene sequence. Binary encoding scheme was also used for further labelling four nucleic acids (A, T, C, and G). First, clustering analysis was performed to gain reasonable negative samples. Then, optimization tests were implemented on different ratios of positive vs negative samples and different feature subsets retrieved by evaluation method of F score. The optimal model constructed by random forest achieves an accuracy of more than 90% on the testing data set. Moreover, the promising results of the external validation also demonstrate the practical applicability of our method. Finally, principal component analysis on the features indicates that all features in our method gain the gross contribution to the prediction model.
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Affiliation(s)
- Wenling Li
- College of Chemistry, Sichuan University, Chengdu, 610064, People's Republic of China
| | - Menglong Li
- College of Chemistry, Sichuan University, Chengdu, 610064, People's Republic of China
| | - Xuemei Pu
- College of Chemistry, Sichuan University, Chengdu, 610064, People's Republic of China
| | - Yanzhi Guo
- College of Chemistry, Sichuan University, Chengdu, 610064, People's Republic of China.
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38
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Higashino T, Matsuo H, Okada Y, Nakashima H, Shimizu S, Sakiyama M, Tadokoro S, Nakayama A, Kawaguchi M, Komatsu M, Hishida A, Nakatochi M, Ooyama H, Imaki J, Shinomiya N. A common variant of MAF/c-MAF, transcriptional factor gene in the kidney, is associated with gout susceptibility. Hum Cell 2017; 31:10-13. [PMID: 29080939 DOI: 10.1007/s13577-017-0186-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [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: 08/23/2017] [Accepted: 10/03/2017] [Indexed: 11/27/2022]
Abstract
Gout is a multifactorial disease characterized by acute inflammatory arthritis, and it is caused as a consequence of hyperuricemia. A recent meta-analysis of genome-wide association studies has newly identified the relationship between serum uric acid (SUA) levels and rs889472, a single nucleotide polymorphism of musculoaponeurotic fibrosarcoma oncogene (MAF/c-MAF). However, it remained unclear whether rs889472 is associated with gout susceptibility. In the present study, we investigate the association between c-MAF rs889472 and gout in Japanese male population. We genotyped 625 male patients who were clinically diagnosed as gout and 1221 male control subjects without hyperuricemia or a history of gout by TaqMan method. As a result, the major allele (C), which reportedly increases SUA levels, had a higher frequency in the gout cases (58.8%) than in the controls (55.0%). A logistic regression analysis showed a significant association between rs889472 and gout (p = 0.029, odds ratio = 1.17; 95% confidence interval 1.02-1.34). C-MAF is reported as a pivotal transcriptional factor in the development and differentiation of renal proximal tubular cells. Because urate is mainly regulated in renal proximal tubular cells, c-MAF may have an important role in urate regulation in the kidney and influence not only SUA but also gout susceptibility. Our finding shows that rs889472 of c-MAF is associated with gout susceptibility.
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Affiliation(s)
- Toshihide Higashino
- Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, 3-2 Namiki, Tokorozawa, Saitama, 359-8513, Japan
| | - Hirotaka Matsuo
- Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, 3-2 Namiki, Tokorozawa, Saitama, 359-8513, Japan.
| | - Yukinori Okada
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Osaka, Japan
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Hiroshi Nakashima
- Department of Preventive Medicine and Public Health, National Defense Medical College, Tokorozawa, Japan
| | - Seiko Shimizu
- Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, 3-2 Namiki, Tokorozawa, Saitama, 359-8513, Japan
| | - Masayuki Sakiyama
- Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, 3-2 Namiki, Tokorozawa, Saitama, 359-8513, Japan
| | - Shin Tadokoro
- Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, 3-2 Namiki, Tokorozawa, Saitama, 359-8513, Japan
| | - Akiyoshi Nakayama
- Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, 3-2 Namiki, Tokorozawa, Saitama, 359-8513, Japan
| | - Makoto Kawaguchi
- Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, 3-2 Namiki, Tokorozawa, Saitama, 359-8513, Japan
| | - Mako Komatsu
- Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, 3-2 Namiki, Tokorozawa, Saitama, 359-8513, Japan
| | - Asahi Hishida
- Department of Preventive Medicine, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Masahiro Nakatochi
- Statistical Analysis Section, Center for Advanced Medicine and Clinical Research, Nagoya University Hospital, Nagoya, Aichi, Japan
| | | | - Junko Imaki
- Department of Developmental Anatomy and Regenerative Biology, National Defense Medical College, Tokorozawa, Saitama, Japan
| | - Nariyoshi Shinomiya
- Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, 3-2 Namiki, Tokorozawa, Saitama, 359-8513, Japan
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Wang Y, Zhu YF, Wang Q, Xu J, Yan N, Xu J, Shi LF, He ST, Zhang JA. The haplotype of UBE2L3 gene is associated with Hashimoto's thyroiditis in a Chinese Han population. BMC Endocr Disord 2016; 16:18. [PMID: 27094594 PMCID: PMC4837539 DOI: 10.1186/s12902-016-0098-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/08/2015] [Accepted: 04/14/2016] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND The ubiquitin conjugating enzyme E2L3 (UBE2L3) gene is associated with susceptibility to many autoimmune diseases. The aim of this study was to investigate the association between UBE2L3 gene and autoimmune thyroid diseases (AITDs) and their clinical phenotypes. METHODS We genotyped five single-nucleotide polymorphisms (SNPs) rs131654, rs5754217, rs2298428, rs140489 and rs5998672 of UBE2L3 gene in case groups including 1028 patients with AITDs [676 cases of Graves' disease (GD) and 352 cases of Hashimoto's thyroiditis (HT)] and control group including 897 healthy individuals. The genotyping was performed with the method of polymerase chain reaction-ligase detection reaction (PCR-LDR). RESULTS The frequencies of allele and genotype of five SNPs in gene UBE2L3 showed no statistically significant difference between case groups and control group, respectively. Moreover, no significant differences in frequencies of allele and genotype of five SNPs of the gene were found between clinical subphenotypes of AITDs and control group. Such subphenotypes included GD, HT, and thyroid associated ophthalmopathy (TAO). The negative results were also found in the frequency of other haplotypes of the gene except the haplotype of TCGGC, which was significantly higher in HT group than in control group (P = 0.031, OR = 1.441). CONCLUSIONS The present findings indicate that TCGGC haplotype is associated with an increased risk of HT and UBE2L3 gene is likely to be a susceptibility factor to HT in a Chinese Han population.
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Affiliation(s)
- Yu Wang
- Department of Endocrinology, The First Affiliated Hospital of Xi'an Jiaotong University Health Science Center, No. 277 West Yanta Road, Xi'an, 710061, China
| | - Yuan-feng Zhu
- Department of Endocrinology, The First Affiliated Hospital of Xi'an Jiaotong University Health Science Center, No. 277 West Yanta Road, Xi'an, 710061, China
| | - Qiong Wang
- Department of Endocrinology, The First Affiliated Hospital of Xi'an Jiaotong University Health Science Center, No. 277 West Yanta Road, Xi'an, 710061, China
| | - Jing Xu
- Department of Endocrinology, The First Affiliated Hospital of Xi'an Jiaotong University Health Science Center, No. 277 West Yanta Road, Xi'an, 710061, China
| | - Ni Yan
- Department of Endocrinology, Jinshan Hospital of Fudan University, No. 1508 Longhang Road, , Jinshan District, Shanghai, 201508, China
| | - Jian Xu
- Department of Endocrinology, Jinshan Hospital of Fudan University, No. 1508 Longhang Road, , Jinshan District, Shanghai, 201508, China
| | - Liang-feng Shi
- Department of Endocrinology, Jinshan Hospital of Fudan University, No. 1508 Longhang Road, , Jinshan District, Shanghai, 201508, China
| | - Shuang-tao He
- Department of Endocrinology, Jinshan Hospital of Fudan University, No. 1508 Longhang Road, , Jinshan District, Shanghai, 201508, China
| | - Jin-an Zhang
- Department of Endocrinology, Jinshan Hospital of Fudan University, No. 1508 Longhang Road, , Jinshan District, Shanghai, 201508, China.
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Huang MC, Chuang TP, Chen CH, Wu JY, Chen YT, Li LH, Yang HC. An integrated analysis tool for analyzing hybridization intensities and genotypes using new-generation population-optimized human arrays. BMC Genomics 2016; 17:266. [PMID: 27029637 PMCID: PMC4815280 DOI: 10.1186/s12864-016-2478-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 02/16/2016] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Affymetrix Axiom single nucleotide polymorphism (SNP) arrays provide a cost-effective, high-density, and high-throughput genotyping solution for population-optimized analyses. However, no public software is available for the integrated genomic analysis of hybridization intensities and genotypes for this new-generation population-optimized genotyping platform. RESULTS A set of statistical methods was developed for an integrated analysis of allele frequency (AF), allelic imbalance (AI), loss of heterozygosity (LOH), long contiguous stretch of homozygosity (LCSH), and copy number variation or alteration (CNV/CNA) on the basis of SNP probe hybridization intensities and genotypes. This study analyzed 3,236 samples that were genotyped using different SNP platforms. The proposed AF adjustment method considerably increased the accuracy of AF estimation. The proposed quick circular binary segmentation algorithm for segmenting copy number reduced the computation time of the original segmentation method by 30-67 %. The proposed CNV/CNA detection, which integrates AI and LOH/LCSH detection, had a promising true positive rate and well-controlled false positive rate in simulation studies. Moreover, our real-time quantitative polymerase chain reaction experiments successfully validated the CNVs/CNAs that were identified in the Axiom data analyses using the proposed methods; some of the validated CNVs/CNAs were not detected in the Affymetrix Array 6.0 data analysis using the Affymetrix Genotyping Console. All the analysis functions are packaged into the ALICE (AF/LOH/LCSH/AI/CNV/CNA Enterprise) software. CONCLUSIONS ALICE and the used genomic reference databases, which can be downloaded from http://hcyang.stat.sinica.edu.tw/software/ALICE.html , are useful resources for analyzing genomic data from the Axiom and other SNP arrays.
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Affiliation(s)
- Mei-Chu Huang
- Bioinformatics Program, Taiwan International Graduate Program, Institute of Information Science, Academia Sinica, Taipei, 115, Taiwan.,Institute of Statistical Science, Academia Sinica, No 128, Academia Rd, Sec 2, Nankang, Taipei, 115, Taiwan.,Institute of Biomedical Informatics, National Yang-Ming University, Taipei, 112, Taiwan
| | - Tzu-Po Chuang
- Taiwan International Graduate Program in Molecular Medicine, National Yang-Ming University and Academia Sinica, Taipei, 115, Taiwan.,Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei, 112, Taiwan
| | - Chien-Hsiun Chen
- Institute of Biomedical Sciences, Academia Sinica, Academia Rd, Sec 2, Nankang, Taipei, 115, Taiwan
| | - Jer-Yuarn Wu
- Institute of Biomedical Sciences, Academia Sinica, Academia Rd, Sec 2, Nankang, Taipei, 115, Taiwan
| | - Yuan-Tsong Chen
- Institute of Biomedical Sciences, Academia Sinica, Academia Rd, Sec 2, Nankang, Taipei, 115, Taiwan
| | - Ling-Hui Li
- Institute of Biomedical Sciences, Academia Sinica, Academia Rd, Sec 2, Nankang, Taipei, 115, Taiwan.
| | - Hsin-Chou Yang
- Bioinformatics Program, Taiwan International Graduate Program, Institute of Information Science, Academia Sinica, Taipei, 115, Taiwan. .,Institute of Statistical Science, Academia Sinica, No 128, Academia Rd, Sec 2, Nankang, Taipei, 115, Taiwan. .,Institute of Public Health, National Yang Ming University, Taipei, 112, Taiwan. .,Department of Statistics, National Cheng Kung University, Tainan, 701, Taiwan. .,Institute of Statistics, National Tsing Hua University, Hsinchu, 300, Taiwan. .,School of Public Health, National Defense Medical Center, Taipei, 114, Taiwan.
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Abstract
Genetic heterogeneity explains variation in predisposition for cancer. Whole-genome analysis allows risk to be quantified, giving better targeted screening and quantification of the personalized risk posed by environmental factors. Array-based approaches to whole-genome analysis are rapidly being overtaken by next-generation sequencing (NGS). In this review the different platforms currently available for NGS are compared and the opportunities and risks of this approach are discussed: including the informatics packages required and the ethical issues. Methods applicable to the personal genome machine (PGM) are given as an example of workflows.
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Affiliation(s)
- Victoria Shaw
- NIHR Pancreatic Biomedical Research Unit, Molecular and Clinical Cancer Medicine, Royal Liverpool University Hospital, 5th Floor UCD Block, Daulby Street, Liverpool, L69 3GA, UK
| | - Katie Bullock
- NIHR Pancreatic Biomedical Research Unit, Molecular and Clinical Cancer Medicine, Royal Liverpool University Hospital, 5th Floor UCD Block, Daulby Street, Liverpool, L69 3GA, UK
| | - William Greenhalf
- NIHR Pancreatic Biomedical Research Unit, Molecular and Clinical Cancer Medicine, Royal Liverpool University Hospital, 5th Floor UCD Block, Daulby Street, Liverpool, L69 3GA, UK.
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Deniskin R, Frame IJ, Sosa Y, Akabas MH. Targeting the Plasmodium vivax equilibrative nucleoside transporter 1 (PvENT1) for antimalarial drug development. Int J Parasitol Drugs Drug Resist 2016; 6:1-11. [PMID: 26862473 DOI: 10.1016/j.ijpddr.2015.11.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Revised: 11/18/2015] [Accepted: 11/25/2015] [Indexed: 11/26/2022]
Abstract
Infection with Plasmodium falciparum and vivax cause most cases of malaria. Emerging resistance to current antimalarial medications makes new drug development imperative. Ideally a new antimalarial drug should treat both falciparum and vivax malaria. Because malaria parasites are purine auxotrophic, they rely on purines imported from the host erythrocyte via Equilibrative Nucleoside Transporters (ENTs). Thus, the purine import transporters represent a potential target for antimalarial drug development. For falciparum parasites the primary purine transporter is the P. falciparum Equilibrative Nucleoside Transporter Type 1 (PfENT1). Recently we identified potent PfENT1 inhibitors with nanomolar IC50 values using a robust, yeast-based high throughput screening assay. In the current work we characterized the Plasmodium vivax ENT1 (PvENT1) homologue and its sensitivity to the PfENT1 inhibitors. We expressed a yeast codon-optimized PvENT1 gene in Saccharomyces cerevisiae. PvENT1-expressing yeast imported both purines ([3H]adenosine) and pyrimidines ([3H]uridine), whereas wild type (fui1Δ) yeast did not. Based on radiolabel substrate uptake inhibition experiments, inosine had the lowest IC50 (3.8 μM), compared to guanosine (14.9 μM) and adenosine (142 μM). For pyrimidines, thymidine had an IC50 of 183 μM (vs. cytidine and uridine; mM range). IC50 values were higher for nucleobases compared to the corresponding nucleosides; hypoxanthine had a 25-fold higher IC50 than inosine. The archetypal human ENT1 inhibitor 4-nitrobenzylthioinosine (NBMPR) had no effect on PvENT1, whereas dipyridamole inhibited PvENT1, albeit with a 40 μM IC50, a 1000-fold less sensitive than human ENT1 (hENT1). The PfENT1 inhibitors blocked transport activity of PvENT1 and the five known naturally occurring non-synonymous single nucleotide polymorphisms (SNPs) with similar IC50 values. Thus, the PfENT1 inhibitors also target PvENT1. This implies that development of novel antimalarial drugs that target both falciparum and vivax ENT1 may be feasible. PvENT1 can be functionally expressed in Saccharomyces cerevisiae. PvENT1 transports purine and pyrimidine nucleosides and nucleobases but does not transport nucleotides. PvENT1 is inhibited by recently described PfENT1 inhibitors with similar potency. Identified PvENT1 non-synonymous SNPs do not change PfENT1 inhibitor potency. Plasmodium ENTs may be feasible target for development of novel antimalarial drugs.
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Key Words
- ACT, Artemisinin-based Combination Therapies
- CQ, chloroquine
- Drug development
- EC50, concentration causing 50% of maximal effect
- ENT, equilibrative nucleoside transporter
- EV, empty vector
- HTS, high throughput screen
- IC50, concentration causing 50% inhibition
- Malaria
- NBMPR, 4-nitrobenzylthioinosine
- Nucleoside/nucleobase transport
- Parasite
- PfENT1, P. falciparum ENT type 1
- Plasmodium vivax
- Purines
- PvENT1, P. vivax ENT type 1
- SDM, synthetic defined media
- SNP, single nucleotide polymorphism
- Single-nucleotide polymorphism (SNP)
- Transporter
- WHO, World Health Organization
- WT, wild type
- hENT1, human ENT type 1
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Toktaş ZO, Ekşi MŞ, Yılmaz B, Demir MK, Özgen S, Kılıç T, Konya D. Association of collagen I, IX and vitamin D receptor gene polymorphisms with radiological severity of intervertebral disc degeneration in Southern European Ancestor. Eur Spine J 2015; 24:2432-41. [PMID: 26342701 DOI: 10.1007/s00586-015-4206-5] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [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: 06/02/2015] [Revised: 08/22/2015] [Accepted: 08/22/2015] [Indexed: 01/07/2023]
Abstract
PURPOSE Several genomic loci have been previously found to be associated with intervertebral disc degeneration, so far. Data are mostly derived from northern European countries whereas data derived from Southern European Ancestor are limited. This study aimed to evaluate the association between radiological disease severity of lumbar disc degeneration and certain genetic loci in a sample of participants from Southern Europe. METHODS Seventy-five patients with mild to severe lumbar disc degeneration and 25 healthy controls were enrolled into the study. In each subject, each lumbar intervertebral disc was separately examined to obtain a total radiological score for disease severity. In addition, single-nucleotide polymorphisms of predefined genetic samples were analyzed in all participants: COL1A1 Sp1, COL9a2 Trp2, COL9a3 Trp3, and VDR TaqI. RESULTS Degeneration scores were significantly worse in cases with COL1A1 Sp1, COL9a3 Trp3, and VDR TaqI mutations; however, COL9a2 Trp2 mutation was not associated with a difference in the severity of disc degeneration. In addition, subjects with mutation in more than one gene sample (n = 20) had significantly worse degeneration scores than the remaining study participants (n = 80) (17.70 ± 2.72 vs. 21.81 ± 1.81, p < 0.001). CONCLUSION Single-nucleotide polymorphisms occurring in COL1A1, COL9a3 and VDR genes seem to be associated with the development of lumbar disc degeneration in this cohort, possibly with even more pronounced association when multiple mutations are present in the same individual. By further prospective twin studies in associated genes and analyses of their relationship with environmental factors in an internationally sampled large cohort will make a more clear-minded conclusion about their association with disc degeneration, which would yield better appreciation and clinical planning of some predisposed people for these pathologies.
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Affiliation(s)
- Zafer Orkun Toktaş
- Department of Neurosurgery, Bahçeşehir University Medical Faculty, Çırağan Caddesi Osmanpaşa Mektebi Sokak No: 4-6, 34353, Beşiktaş, Istanbul, Turkey.
| | - Murat Şakir Ekşi
- Department of Orthopedic Surgery, University of California at San Francisco, San Francisco, CA, USA
| | - Baran Yılmaz
- Department of Neurosurgery, Bahçeşehir University Medical Faculty, Çırağan Caddesi Osmanpaşa Mektebi Sokak No: 4-6, 34353, Beşiktaş, Istanbul, Turkey
| | - Mustafa Kemal Demir
- Department of Radiology, Bahçeşehir University Medical Faculty, Istanbul, Turkey
| | - Serdar Özgen
- Department of Neurosurgery, Acıbadem University Medical Faculty, Istanbul, Turkey
| | - Türker Kılıç
- Department of Neurosurgery, Bahçeşehir University Medical Faculty, Çırağan Caddesi Osmanpaşa Mektebi Sokak No: 4-6, 34353, Beşiktaş, Istanbul, Turkey
| | - Deniz Konya
- Department of Neurosurgery, Bahçeşehir University Medical Faculty, Çırağan Caddesi Osmanpaşa Mektebi Sokak No: 4-6, 34353, Beşiktaş, Istanbul, Turkey
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Starska K, Bryś M, Forma E, Olszewski J, Pietkiewicz P, Lewy-Trenda I, Stasikowska-Kanicka O, Danilewicz M, Krześlak A. Metallothionein 2A core promoter region genetic polymorphism and its impact on the risk, tumor behavior, and recurrences of sinonasal inverted papilloma (Schneiderian papilloma). Tumour Biol 2015; 36:8559-71. [PMID: 26036762 PMCID: PMC4672009 DOI: 10.1007/s13277-015-3616-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Accepted: 05/26/2015] [Indexed: 01/20/2023] Open
Abstract
Inverted papillomas are a unique group of locally aggressive benign epithelial neoplasms in the nasal cavity and paranasal sinuses arising from the Schneiderian mucosa. Metallothioneins are sulfhydryl-rich heavy metal-binding proteins required for metal toxicity protection and regulation of biological mechanisms including proliferation and invasion. The goal of this study was to identify three SNPs at loci −5 A/G (rs28366003) and −209 A/G (rs1610216) in the core promoter region and at locus +838 C/G (rs10636) in 3′UTR region of the MT2A gene with IP risk and with tumor invasiveness according to Krouse staging. Genotyping was performed using the PCR restriction fragment length polymorphism technique in 130 genetically unrelated IP individuals, and 418 randomly selected healthy volunteers. The presence of the rs28366003 SNP was significantly related to the risk of IP within the present population-based case-control study. Compared to homozygous common allele carriers, heterozygosity and homozygosity for the G variant had a significantly increased risk of IP (adjusted odds ratio [OR] = 7.71, 95 % confidence interval [CI]: 4.01–14.91, pdominant < 0.001). Moreover, risk allele carriers demonstrated higher Krouse stage (pT1 vs. pT2-4) (OR = 19.32; 95 % CI, 2.30–173.53; p < 0.0001), diffuse tumor growth (OR = 4.58; 95 % CI, 1.70–12.11; p = 0.0008), bone destruction (OR = 4.13; 95 % CI, 1.50–11.60; p = 0.003), and higher incidence of tumor recurrences (OR = 5.11; 95 % CI, 1.68–15.20; p = 0.001). The findings suggest that MT2A gene variation rs28366003 may be implicated in the etiology of sinonasal inverted papilloma in a Polish population.
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Affiliation(s)
- Katarzyna Starska
- I Department of Otolaryngology and Laryngological Oncology, Medical University of Łódź, Kopcinskiego 22, 90-153, Łódź, Poland.
| | - Magdalena Bryś
- Department of Cytobiochemistry, University of Łódź, Pomorska 142/143, 90-236, Łódź, Poland
| | - Ewa Forma
- Department of Cytobiochemistry, University of Łódź, Pomorska 142/143, 90-236, Łódź, Poland
| | - Jurek Olszewski
- II Department of Otolaryngology and Laryngological Oncology, Medical University of Łódź, Żeromskiego 113, 90-549, Łódź, Poland
| | - Piotr Pietkiewicz
- II Department of Otolaryngology and Laryngological Oncology, Medical University of Łódź, Żeromskiego 113, 90-549, Łódź, Poland
| | - Iwona Lewy-Trenda
- Department of Pathology, Medical University of Łódź, Pomorska 251, 92-213, Łódź, Poland
| | | | - Marian Danilewicz
- Department of Pathology, Medical University of Łódź, Pomorska 251, 92-213, Łódź, Poland
| | - Anna Krześlak
- Department of Cytobiochemistry, University of Łódź, Pomorska 142/143, 90-236, Łódź, Poland
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Starska K, Bryś M, Forma E, Olszewski J, Pietkiewicz P, Lewy-Trenda I, Danilewicz M, Krześlak A. The effect of metallothionein 2A core promoter region single-nucleotide polymorphism on accumulation of toxic metals in sinonasal inverted papilloma tissues. Toxicol Appl Pharmacol 2015; 285:187-97. [PMID: 25900616 DOI: 10.1016/j.taap.2015.04.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Revised: 03/08/2015] [Accepted: 04/09/2015] [Indexed: 12/13/2022]
Abstract
Metallothioneins (MTs) are intracellular thiol-rich heavy metal-binding proteins which join trace metal ions protecting cells against heavy metal toxicity and regulate metal distribution and donation to various enzymes and transcription factors. The goal of this study was to identify the -5 A/G (rs28366003) single-nucleotide polymorphism (SNP) in the core promoter region of the MT2A gene, and to investigate its effect on allele-specific gene expression and Cd, Zn, Cu and Ni content in sinonasal inverted papilloma tissue (IP), with non-cancerous sinonasal mucosa (NCM) as a control. The MT2A promoter region -5 A/G SNP was identified by restriction fragment length polymorphism using 117 IP and 132 NCM. MT2A gene analysis was performed by quantitative real-time PCR. Metal levels were analyzed by flame atomic absorption spectrometry. The frequency of A allele carriage was 99.2% and 100% in IP and NCM, respectively. The G allele carriage was detected in 23.9% of IP and in 12.1% of the NCM samples. As a result, a significant association of -5 A/G SNP in MT2A gene with mRNA expression in both groups was determined. A significant association was identified between the -5 A/G SNP in the MT2A gene with mRNA expression in both groups. A highly significant association was detected between the rs28366003 genotype and Cd and Zn content in IP. Furthermore, significant differences were identified between A/A and A/G genotype with regard to the type of metal contaminant. The Spearman rank correlation results showed the MT2A gene expression and both Cd and Cu levels were negatively correlated. The results obtained in this study suggest that the -5 A/G SNP in the MT2A gene may have an effect on allele-specific gene expression and toxic metal accumulation in sinonasal inverted papilloma.
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Affiliation(s)
- Katarzyna Starska
- I Department of Otolaryngology and Laryngological Oncology, Medical University of Łódź, Kopcinskiego 22, 90-153 Łódź, Poland.
| | - Magdalena Bryś
- Department of Cytobiochemistry, University of Łódź, Pomorska 142/143, 90-236 Łódź, Poland
| | - Ewa Forma
- Department of Cytobiochemistry, University of Łódź, Pomorska 142/143, 90-236 Łódź, Poland
| | - Jurek Olszewski
- II Department of Otolaryngology and Laryngological Oncology, Medical University of Łódź, Żeromskiego 113, 90-549 Łódź, Poland
| | - Piotr Pietkiewicz
- II Department of Otolaryngology and Laryngological Oncology, Medical University of Łódź, Żeromskiego 113, 90-549 Łódź, Poland
| | - Iwona Lewy-Trenda
- Department of Pathology, Medical University of Łódź, Pomorska 251, 92-213 Łódź, Poland
| | - Marian Danilewicz
- Department of Pathology, Medical University of Łódź, Pomorska 251, 92-213 Łódź, Poland
| | - Anna Krześlak
- Department of Cytobiochemistry, University of Łódź, Pomorska 142/143, 90-236 Łódź, Poland
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Karra VK, Gumma PK, Chowdhury SJ, Ruttala R, Polipalli SK, Chakravarti A, Kar P. IL-18 polymorphisms in hepatitis B virus related liver disease. Cytokine 2015; 73:277-82. [PMID: 25802197 DOI: 10.1016/j.cyto.2015.02.015] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [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: 11/19/2014] [Revised: 02/13/2015] [Accepted: 02/14/2015] [Indexed: 12/17/2022]
Abstract
Interleukine-18 (IL-18) was originally called interferon (INF-γ) inducing factor and plays a critical dual role in Th1 polarization and viral clearance. We aimed to explore whether single-nucleotide promoter polymorphisms (SNPs) are associated with the outcome of hepatitis B virus (HBV) infection. 271 HBV infected patients were recruited in this study out of these 109 were spontaneously recovered and 162 were diagnosed to be having persistent HBV infection which includes 48 chronic hepatitis, 84 liver cirrhosis, 30 HCC cases and were compared with 280 healthy controls. IL-18 promoter genotyping was performed with sequence-specific primers. The results demonstrated the significant involvement of genotype AA at position -607 in healthy controls (38.6%) when compared to cases (26.0%) (OR=0.54 (0.385-0.797)) and also associated with spontaneous clearance (37.6%) compared to persistent HBV infections (17.9%) (OR=2.76 (1.582-4.832)). Whereas, genotype CC at position -607 in cases (18.0%) when compared to healthy controls (6.7%) (OR=3.03 (1.734-5.303)) also associated with persistent HBV infections (24.1%) compared to spontaneous clearance (9.2%) (OR=0.31 (0.151-0.67)). And genotype GC at position -137 in cases (49.5%) compared to healthy controls (38.5%) (OR=1.55 (1.11-2.18)). Whereas, genotype GG at position -137 in healthy controls (56.8%) compared to cases (45.4%) (OR=0.63 (0.451-0.885)). No significant difference at position -137 was observed between spontaneous clearance and persistent HBV infections. These polymorphisms of the IL-18 gene promoter region at position -607 and -137 could be associated with different outcomes of HBV infection. The people with allele A at position -607 may be protected against HBV infection; moreover AA genotype is associated with spontaneous clearance.
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Affiliation(s)
- Vijay Kumar Karra
- PCR Hepatitis Lab, Dept. of Medicine, Maulana Azad Medical College, University of Delhi, New Delhi 110002, India
| | - Phani Kumar Gumma
- PCR Hepatitis Lab, Dept. of Medicine, Maulana Azad Medical College, University of Delhi, New Delhi 110002, India
| | - Soumya Jyoti Chowdhury
- PCR Hepatitis Lab, Dept. of Medicine, Maulana Azad Medical College, University of Delhi, New Delhi 110002, India
| | - Rajesh Ruttala
- PCR Hepatitis Lab, Dept. of Medicine, Maulana Azad Medical College, University of Delhi, New Delhi 110002, India
| | - Sunil Kumar Polipalli
- PCR Hepatitis Lab, Dept. of Medicine, Maulana Azad Medical College, University of Delhi, New Delhi 110002, India
| | - Anita Chakravarti
- Department of Medical Microbiology, Maulana Azad Medical College, University of Delhi, New Delhi 110002, India
| | - Premashis Kar
- PCR Hepatitis Lab, Dept. of Medicine, Maulana Azad Medical College, University of Delhi, New Delhi 110002, India.
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Yu F, Fienberg SE, Slavković AB, Uhler C. Scalable privacy-preserving data sharing methodology for genome-wide association studies. J Biomed Inform 2014; 50:133-41. [PMID: 24509073 DOI: 10.1016/j.jbi.2014.01.008] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2013] [Revised: 01/21/2014] [Accepted: 01/23/2014] [Indexed: 11/28/2022]
Abstract
The protection of privacy of individual-level information in genome-wide association study (GWAS) databases has been a major concern of researchers following the publication of "an attack" on GWAS data by Homer et al. (2008). Traditional statistical methods for confidentiality and privacy protection of statistical databases do not scale well to deal with GWAS data, especially in terms of guarantees regarding protection from linkage to external information. The more recent concept of differential privacy, introduced by the cryptographic community, is an approach that provides a rigorous definition of privacy with meaningful privacy guarantees in the presence of arbitrary external information, although the guarantees may come at a serious price in terms of data utility. Building on such notions, Uhler et al. (2013) proposed new methods to release aggregate GWAS data without compromising an individual's privacy. We extend the methods developed in Uhler et al. (2013) for releasing differentially-private χ(2)-statistics by allowing for arbitrary number of cases and controls, and for releasing differentially-private allelic test statistics. We also provide a new interpretation by assuming the controls' data are known, which is a realistic assumption because some GWAS use publicly available data as controls. We assess the performance of the proposed methods through a risk-utility analysis on a real data set consisting of DNA samples collected by the Wellcome Trust Case Control Consortium and compare the methods with the differentially-private release mechanism proposed by Johnson and Shmatikov (2013).
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Affiliation(s)
- Fei Yu
- Department of Statistics, Carnegie Mellon University, Pittsburgh, PA 15213-3890, USA.
| | - Stephen E Fienberg
- Department of Statistics, Heinz College, Machine Learning Department, and Cylab, Carnegie Mellon University, Pittsburgh, PA 15213-3890, USA.
| | - Aleksandra B Slavković
- Department of Statistics, Department of Public Health Sciences, Penn State University, University Park, PA 16802, USA.
| | - Caroline Uhler
- Institute of Science and Technology Austria, Am Campus 1, 3400 Klosterneuburg, Austria.
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Wei L, Xiao M, Hayward A, Fu D. Applications and challenges of next-generation sequencing in Brassica species. Planta 2013; 238:1005-24. [PMID: 24062086 DOI: 10.1007/s00425-013-1961-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [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: 09/07/2013] [Accepted: 09/12/2013] [Indexed: 05/09/2023]
Abstract
Next-generation sequencing (NGS) produces numerous (often millions) short DNA sequence reads, typically varying between 25 and 400 bp in length, at a relatively low cost and in a short time. This revolutionary technology is being increasingly applied in whole-genome, transcriptome, epigenome and small RNA sequencing, molecular marker and gene discovery, comparative and evolutionary genomics, and association studies. The Brassica genus comprises some of the most agro-economically important crops, providing abundant vegetables, condiments, fodder, oil and medicinal products. Many Brassica species have undergone the process of polyploidization, which makes their genomes exceptionally complex and can create difficulties in genomics research. NGS injects new vigor into Brassica research, yet also faces specific challenges in the analysis of complex crop genomes and traits. In this article, we review the advantages and limitations of different NGS technologies and their applications and challenges, using Brassica as an advanced model system for agronomically important, polyploid crops. Specifically, we focus on the use of NGS for genome resequencing, transcriptome sequencing, development of single-nucleotide polymorphism markers, and identification of novel microRNAs and their targets. We present trends and advances in NGS technology in relation to Brassica crop improvement, with wide application for sophisticated genomics research into agronomically important polyploid crops.
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Affiliation(s)
- Lijuan Wei
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Agronomy College, Jiangxi Agricultural University, Nanchang, 330045, China
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
| | - Meili Xiao
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
| | - Alice Hayward
- Centre for Integrative Legume Research, School of Agriculture and Food Sciences, The University of Queensland, St Lucia, 4072, Australia
| | - Donghui Fu
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Agronomy College, Jiangxi Agricultural University, Nanchang, 330045, China.
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Sun C, Chu J, Singh S, Salter RD. Identification and characterization of a novel variant of the human P2X(7) receptor resulting in gain of function. Purinergic Signal 2009; 6:31-45. [PMID: 19838818 DOI: 10.1007/s11302-009-9168-9] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2009] [Accepted: 10/05/2009] [Indexed: 11/30/2022] Open
Abstract
The P2X(7) receptor exhibits significant allelic polymorphism in humans, with both loss and gain of function variants potentially impacting on a variety of infectious and inflammatory disorders. At least five loss-of-function polymorphisms (G150R, R307Q, T357S, E496A, and I568N) and two gain-of-function polymorphisms (H155Y and Q460R) have been identified and characterized to date. In this study, we used RT-PCR cloning to isolate and characterize P2X(7) cDNA clones from human PBMCs and THP-1 cells. A previously unreported variant with substitutions of V80M and A166G was identified. When expressed in HEK293 cells, this variant exhibited heightened sensitivity to the P2X(7) agonist (BzATP) relative to the most frequent allele, as shown by pore formation measured by fluorescent dye uptake into cells. Mutational analyses showed that A166G alteration was critical for the gain-of-function change, while V80M was not. Full-length variants with multiple previously identified nonsynonymous SNPs (H155Y, H270R, A348T, and E496A) were also identified. Distinct functional phenotypes of the P2X(7) variants or mutants constructed with multiple polymorphisms were observed. Gain-of-function variations (A166G or H155Y) could not rescue the loss-of-function E496A polymorphism. Synergistic effects of the gain-of-function variations were also observed. We also identified the A348T alteration as a weak gain-of-function variant. Thus, these results identify the new gain-of-function variant A166G and demonstrate that multiple-gene polymorphisms contribute to functional phenotypes of the human P2X(7) receptor. Furthermore, the results demonstrate that the C-terminal of the cysteine-rich domain 1 of P2X(7) is critical for regulation of P2X(7)-mediated pore formation.
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Affiliation(s)
- Chengqun Sun
- Department of Immunology, University of Pittsburgh School of Medicine, E1052 Biomedical Science Tower, Pittsburgh, PA 15261 USA
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