1
|
Estimation of Lewis Blood Group Status by Fluorescence Melting Curve Analysis in Simultaneous Genotyping of c.385A>T and Fusion Gene in FUT2 and c.59T>G and c.314C>T in FUT3. Diagnostics (Basel) 2023; 13:diagnostics13050931. [PMID: 36900072 PMCID: PMC10000471 DOI: 10.3390/diagnostics13050931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 02/15/2023] [Accepted: 02/28/2023] [Indexed: 03/06/2023] Open
Abstract
Lewis blood group status is determined by two fucosyltransferase activities: those of FUT2-encoded fucosyltransferase (Se enzyme) and FUT3-encoded fucosyltransferase (Le enzyme). In Japanese populations, c.385A>T in FUT2 and a fusion gene between FUT2 and its pseudogene SEC1P are the cause of most Se enzyme-deficient alleles (Sew and sefus), and c.59T>G and c.314C>T in FUT3 are tag SNPs for almost all nonfunctional FUT3 alleles (le59, le59,508, le59,1067, and le202,314). In this study, we first conducted a single-probe fluorescence melting curve analysis (FMCA) to determine c.385A>T and sefus using a pair of primers that collectively amplify FUT2, sefus, and SEC1P. Then, to estimate Lewis blood group status, a triplex FMCA was performed with a c.385A>T and sefus assay system by adding primers and probes to detect c.59T>G and c.314C>T in FUT3. We also validated these methods by analyzing the genotypes of 96 selected Japanese people whose FUT2 and FUT3 genotypes were already determined. The single-probe FMCA was able to identify six genotype combinations: 385A/A, 385T/T, sefus/sefus, 385A/T, 385A/sefus, and 385T/sefus. In addition, the triplex FMCA successfully identified both FUT2 and FUT3 genotypes, although the resolutions of the analysis of c.385A>T and sefus were somewhat reduced compared to that of the analysis of FUT2 alone. The estimation of the secretor status and Lewis blood group status using the form of FMCA used in this study may be useful for large-scale association studies in Japanese populations.
Collapse
|
2
|
Tang X, Yang Z, Dai K, Liu G, Chang YF, Tang X, Wang K, Zhang Y, Hu B, Cao S, Huang X, Yan Q, Wu R, Zhao Q, Du S, Lang Y, Han X, Huang Y, Wen X, Wen Y. The molecular diversity of transcriptional factor TfoX is a determinant in natural transformation in Glaesserella parasuis. Front Microbiol 2022; 13:948633. [PMID: 35966685 PMCID: PMC9372613 DOI: 10.3389/fmicb.2022.948633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 07/12/2022] [Indexed: 11/13/2022] Open
Abstract
Natural transformation is a mechanism by which a particular bacterial species takes up foreign DNA and integrates it into its genome. The swine pathogen Glaesserella parasuis (G. parasuis) is a naturally transformable bacterium. The regulation of competence, however, is not fully understood. In this study, the natural transformability of 99 strains was investigated. Only 44% of the strains were transformable under laboratory conditions. Through a high-resolution melting curve and phylogenetic analysis, we found that genetic differences in the core regulator of natural transformation, the tfoX gene, leads to two distinct natural transformation phenotypes. In the absence of the tfoX gene, the highly transformable strain SC1401 lost its natural transformability. In addition, when the SC1401 tfoX gene was replaced by the tfoX of SH0165, which has no natural transformability, competence was also lost. These results suggest that TfoX is a core regulator of natural transformation in G. parasuis, and that differences in tfoX can be used as a molecular indicator of natural transformability. Transcriptomic and proteomic analyses of the SC1401 wildtype strain, and a tfoX gene deletion strain showed that differential gene expression and protein synthesis is mainly centered on pathways related to glucose metabolism. The results suggest that tfoX may mediate natural transformation by regulating the metabolism of carbon sources. Our study provides evidence that tfoX plays an important role in the natural transformation of G. parasuis.
Collapse
Affiliation(s)
- Xiaoyu Tang
- Research Center of Swine Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Zhen Yang
- Research Center of Swine Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Ke Dai
- Research Center of Swine Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Geyan Liu
- Research Center of Swine Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Yung-Fu Chang
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, United States
| | - Xinwei Tang
- Research Center of Swine Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Kang Wang
- Research Center of Swine Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Yiwen Zhang
- Research Center of Swine Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Bangdi Hu
- Research Center of Swine Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Sanjie Cao
- Research Center of Swine Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Xiaobo Huang
- Research Center of Swine Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Qigui Yan
- Research Center of Swine Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Rui Wu
- Research Center of Swine Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Qin Zhao
- Research Center of Swine Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Senyan Du
- Research Center of Swine Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Yifei Lang
- Research Center of Swine Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Xinfeng Han
- Research Center of Swine Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Yong Huang
- Research Center of Swine Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Xintian Wen
- Research Center of Swine Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Yiping Wen
- Research Center of Swine Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- *Correspondence: Yiping Wen,
| |
Collapse
|
3
|
Soejima M, Koda Y. Simultaneous genotyping of three major Se enzyme inactivating SNPs of FUT2 based on a triplex probe-based fluorescence melting-curve analysis. Clin Chim Acta 2022; 530:50-54. [PMID: 35271838 DOI: 10.1016/j.cca.2022.03.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 03/04/2022] [Indexed: 11/03/2022]
Abstract
BACKGROUND The ABO(H) secretor status is controlled by FUT2-encoded α(1,2)fucosyltransferase (Se enzyme) activity. Three SNPs of FUT2, 302C>T (rs200157007), 385A>T (rs1047781), and 428G>A (rs601338), cause three major variants of nonsecretor (se) or weak-secretor (Sew) alleles. Evidence has been accumulating that suggests the secretor status is associated with various conditions including infectious diseases but a robust multiplex method for assaying relatively large-scale samples to determine the genotype of these three SNPs simultaneously has not been developed yet. METHODS By combined usage of two Eprobes and a dual-labeled fluorescence probe, we developed a real-time PCR, followed by triplex probe-based fluorescent melting-curve analysis (FMCA) for genotyping of 302C>T, 385A>T, and 428G>A of FUT2 in a single tube. RESULTS Three genotypes of each of three variants of FUT2 were accurately determined by the triplex probe-based FMCA. We then validated this method using genomic DNA samples of 47 Bangladeshis, and the results obtained by using this method were fully concordant with those by previous Sanger sequencing. CONCLUSIONS Since the present single triplex probe-based FMCA is robust, fast, and cost-effective, we are able to effectively estimate the secretor status of subjects on a large scale in many populations around the world.
Collapse
Affiliation(s)
- Mikiko Soejima
- Department of Forensic Medicine, Kurume University School of Medicine, Kurume 830-0011, Japan
| | - Yoshiro Koda
- Department of Forensic Medicine, Kurume University School of Medicine, Kurume 830-0011, Japan.
| |
Collapse
|
4
|
Soejima M, Koda Y. Real-time PCR-based detection of the Alu-mediated deletion of FUT2 (se del2). Leg Med (Tokyo) 2021; 54:101986. [PMID: 34736142 DOI: 10.1016/j.legalmed.2021.101986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 09/16/2021] [Accepted: 10/25/2021] [Indexed: 10/19/2022]
Abstract
Secretor status of the ABH(O) histoblood group antigens is regulated by secretor type α(1,2)fucosyltransferase encoded by FUT2. The sedel2 allele is a complete deletion of the FUT2 coding region generated by Alu-mediated homologous recombination. This deletion seems to be exclusively encountered in certain Oceanian populations. From the perspective of forensic science, sedel2 is considered to be one of ancestry informative markers for these populations. Real-time PCR followed by melting curve analysis was employed to find primer set to specifically amplify sedel2. We designed primers which produced a 231-bp amplicon specific to sedel2. The specificity of these primers was also confirmed by gel electrophoresis and sequencing of the PCR product. Then, two real-time PCR methods based on melting curve analysis and a hydrolysis probe were designed to determine sedel2 zygosity by adding FUT2-specific primers. These two methods were validated by analyzing 24 Samoan subjects. The results obtained from 24 Samoan subjects by the two methods were fully in accordance with those obtained by a previous conventional PCR method that amplified a 2.7-kb fragment of sedel2. Therefore, these two methods seemed to accurately determine the zygosity of sedel2 and were useful for investigation of the distribution and origin of this deletion.
Collapse
Affiliation(s)
- Mikiko Soejima
- Department of Forensic Medicine, Kurume University School of Medicine, Kurume 830-0011, Japan
| | - Yoshiro Koda
- Department of Forensic Medicine, Kurume University School of Medicine, Kurume 830-0011, Japan.
| |
Collapse
|
5
|
Soejima M, Koda Y. Rapid detection of phenotypes Bombay se del and nonsecretor rs200157007 SNP (302C > T) by real-time PCR-based methods. Sci Rep 2021; 11:14996. [PMID: 34294843 PMCID: PMC8298435 DOI: 10.1038/s41598-021-94659-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 07/14/2021] [Indexed: 11/12/2022] Open
Abstract
The sedel allele is one of the nonsecretor alleles (se) of FUT2 generated by an Alu-mediated recombination event and was first found in Indian Bombay phenotype individuals who have anti-H, anti-A, and anti-B antibodies in their serum. As well as anti-A, and anti-B antibodies, anti-H is clinically significant because it causes sever hemolytic transfusion reactions. Like sedel, se302 having a missense single nucleotide polymorphism (SNP), 302C > T, is characteristic of South Asians with a frequency of 10-30%. We developed a real-time PCR melting curve analysis for detection of sedel using a 127-bp amplicon encompassing the breakpoint junction. In addition, by performing duplex PCR by amplifying a 65-bp amplicon of the FUT2 coding region at the same time, we could determine the zygosity of sedel in a single tube. We also developed an Eprobe-mediated PCR assay (Eprobe-PCR) for detection of 302C > T of FUT2. These methods were validated by analyzing 58 Tamils and 54 Sinhalese in Sri Lanka. Both the duplex PCR melting curve analysis for determination of sedel zygosity and the Eprobe-PCR assay for detection of 302C > T exactly determined three genotypes. In addition, the results of the present methods were in complete agreement with those obtained by previously established methods. The two present methods were reliable and seem to be advantageous for large-scale association studies of FUT2 polymorphisms in South Asian populations.
Collapse
Affiliation(s)
- Mikiko Soejima
- Department of Forensic Medicine, Kurume University School of Medicine, Kurume, 830-0011, Japan
| | - Yoshiro Koda
- Department of Forensic Medicine, Kurume University School of Medicine, Kurume, 830-0011, Japan.
| |
Collapse
|
6
|
Soejima M, Koda Y. Detection of the weak-secretor rs1047781 (385A>T) single nucleotide polymorphism using an unlabeled probe high-resolution melting-based method. Electrophoresis 2021; 42:1362-1365. [PMID: 33835481 DOI: 10.1002/elps.202000386] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Revised: 02/22/2021] [Accepted: 03/31/2021] [Indexed: 12/17/2022]
Abstract
FUT2 encodes galactoside 2-α-l-fucosyltransferase 2 which determines the secretor status of ABO(H) blood group antigens. Secretors have at least one functional FUT2 allele (Se), while nonsecretors or weak secretors are homozygous for nonfunctional (non- or weak secretor) FUT2 alleles (se or Sew ). The Sew having the 385A>T missense SNP (rs1047781) is the prevalent nonfunctional allele in East and Southeast Asians. In this study, we developed an unlabeled-probe high-resolution melting (HRM) analysis for genotyping of 385A>T and validated the method by analyzing 72 Japanese whose 385A>T genotypes were confirmed by DNA sequencing. The unlabeled-probe HRM analysis clearly discriminated three genotypes of 385A>T. In addition, the results obtained for the 72 Japanese by this method were fully concordant with previous ones. Estimation of secretor status using this cost-effective method may be useful in East and Southeast Asian populations.
Collapse
Affiliation(s)
- Mikiko Soejima
- Department of Forensic Medicine, Kurume University School of Medicine, Kurume, Japan
| | - Yoshiro Koda
- Department of Forensic Medicine, Kurume University School of Medicine, Kurume, Japan
| |
Collapse
|