1
|
Sudarma V, Sunardi D, Marzuki NS, Munasir Z, Asmarinah, Hidayat A, Hegar B. Human Milk Oligosaccharide Profiles and the Secretor and Lewis Gene Status of Indonesian Lactating Mothers. Pediatr Gastroenterol Hepatol Nutr 2023; 26:266-276. [PMID: 37736221 PMCID: PMC10509021 DOI: 10.5223/pghn.2023.26.5.266] [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] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 06/22/2023] [Accepted: 07/27/2023] [Indexed: 09/23/2023] Open
Abstract
Purpose Human milk oligosaccharides (HMOs) may be genetically determined based on the secretor and Lewis status of the mother. This study aims to determine the HMO profile and the secretor and Lewis gene status of Indonesian lactating mothers. Methods Baseline data of 120 mother-infant pairs between 0-4 months post-partum obtained from a prospective longitudinal study was used. The concentrations of 2'-fucosyllactose (2'FL), lacto-N-fucopentaose I (LNFP I), lacto-N-tetraose (LNT), lacto-N-neotetraose (LNnT), 3'-sialyllactose (3'SL), and 6'-sialyllactose (6'SL) were measured. Genetic analysis was performed for mothers using targeted next-generation sequencing and Sanger sequencing. Wild-type AA with the rs1047781 (A385T) polymorphism was categorized as secretor positive, while heterozygous mutant AT was classified as a weak secretor. The presence of rs28362459 (T59G) heterozygous mutant AC and rs3745635 (G508A) heterozygous mutant CT genes indicated a Lewis negative status, and the absence of these genes indicated a positive status. Subsequently, breast milk was classified into various groups, namely Group 1: Secretor+Lewis+ (Se+Le+), Group 2: Secretor-Lewis+ (Se-Le+), Group 3: Secretor+Lewis- (Se+Le-), and Group 4: Secretor-Lewis- (Se-Le-). Data were analyzed using the Mann-Whitney and Kruskal-Wallis rank tests, and a p-value of 0.05 indicated statistical significance. Results A total of 58.3% and 41.7% of the samples had positive and weak secretor statuses, respectively. The proportion of those in Group 1 was 85%, while 15% were Group 3. The results showed that only 2'FL significantly differed according to the secretor status (p-value=0.018). Conclusion All Indonesian lactating mothers in this study were secretor positive, and most of them had a Lewis-positive status.
Collapse
Affiliation(s)
- Verawati Sudarma
- Doctorate Program of Nutrition, Faculty of Medicine, Universitas Indonesia – Dr. Cipto Mangunkusumo General Hospital, Jakarta, Indonesia
- Department of Nutrition, Faculty of Medicine, Universitas Trisakti, Jakarta, Indonesia
| | - Diana Sunardi
- Department of Nutrition, Faculty of Medicine, Universitas Indonesia – Dr. Cipto Mangunkusumo General Hospital, Jakarta, Indonesia
| | - Nanis Sacharina Marzuki
- Eijkman Research Center for Molecular Biology, National Research and Innovation Agency, Jakarta, Indonesia
| | - Zakiudin Munasir
- Department of Child Health, Faculty of Medicine, Universitas Indonesia – Dr. Cipto Mangunkusumo General Hospital, Jakarta, Indonesia
| | - Asmarinah
- Department of Medical Biology, Faculty of Medicine, Universitas Indonesia – Dr. Cipto Mangunkusumo General Hospital, Jakarta, Indonesia
| | - Adi Hidayat
- Department of Public Health, Faculty of Medicine, Universitas Trisakti, Jakarta, Indonesia
| | - Badriul Hegar
- Department of Child Health, Faculty of Medicine, Universitas Indonesia – Dr. Cipto Mangunkusumo General Hospital, Jakarta, Indonesia
- Indonesia Medical Education and Research Institute, Faculty of Medicine, Universitas Indonesia – Dr. Cipto Mangunkusumo General Hospital, Jakarta, Indonesia
| |
Collapse
|
2
|
Berry A, Kapelus D, Singh P, Groome M, de Assis Rosa D. ABO blood types, but not Secretor or Lewis blood types, influence strength of antibody response to Hepatitis B vaccine in Black South African children. Vaccine 2023:S0264-410X(23)00465-6. [PMID: 37169653 DOI: 10.1016/j.vaccine.2023.04.051] [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: 11/15/2022] [Revised: 03/24/2023] [Accepted: 04/19/2023] [Indexed: 05/13/2023]
Abstract
Subunit vaccines for the Hepatitis B virus (HBV) have greatly reduced the prevalence of infection and morbidity through HBV-related liver cirrhosis and cancer. However, strength of immune response to vaccination varies considerably. While it is known that ABO blood types may influence HBV infection risk, the role of ABO and related blood types in strength of immune response to HBV vaccine has not been investigated. We examined 16 polymorphisms in the ABO, FUT2, and FUT3 genes and their related phenotypes for associations with strength of antibody response to HBV vaccine in Black South African infants. Anti-HBc and anti-HBs antibody levels were measured by CMIA assay 1-3 months after the last dose of HBV vaccine. Prior infection occurred in 8/207 individuals (3.86%) who were removed from further study. Of the remaining 199 individuals, 83.4% individuals were strong responders (anti-HBs ≥ 100 mIU/ml, median 973 mIU/ml), another 15.6% were weak responders (anti-HBs < 100 mIU/ml, median 50 mIU/ml) and 1% were non-responders (anti-HBs < 10 mIU/ml). The frequency of weak responders to HBV vaccine was not significantly affected by sex, birthweight, use of an additional booster dose of vaccine or cohort of origin. We characterised patterns of genetic variation present at the ABO, FUT2 and FUT3 loci by use of MassArray genotyping and used these data to predict ABO, Secretor and Lewis phenotypes. We observed significant association of ABO blood type with strength of antibody response to HBV vaccine in a Black South African cohort (p = 0.002). In particular, presence of rs8176747G and expression of B antigen (whether in B blood type or AB blood type) was associated with decreased antibody response to HBV vaccine. Secretor and Lewis blood types were not associated with antibody response to HBV vaccine. This work increases our understanding of the impact that host genetic variation may have on vaccine immunogenicity.
Collapse
Affiliation(s)
- Adam Berry
- School of Molecular and Cell Biology, Faculty of Science, University of the Witwatersrand, Jhb, South Africa
| | - Daniel Kapelus
- School of Molecular and Cell Biology, Faculty of Science, University of the Witwatersrand, Jhb, South Africa
| | - Payal Singh
- School of Molecular and Cell Biology, Faculty of Science, University of the Witwatersrand, Jhb, South Africa
| | - Michelle Groome
- Vaccines and Infectious Diseases Analytics (VIDA) Research Unit, SA Medical Research Council and University of the Witwatersrand, Jhb, South Africa; National Institute for Communicable Diseases, Jhb, South Africa
| | - Debra de Assis Rosa
- School of Molecular and Cell Biology, Faculty of Science, University of the Witwatersrand, Jhb, South Africa.
| |
Collapse
|
3
|
Fu C, Xu X, Xie Y, Liu Y, Liu M, Chen A, Blamey JM, Shi J, Zhao S, Sun J. Rational design of GDP‑D‑mannose mannosyl hydrolase for microbial L‑fucose production. Microb Cell Fact 2023; 22:56. [PMID: 36964553 PMCID: PMC10037897 DOI: 10.1186/s12934-023-02060-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 03/11/2023] [Indexed: 03/26/2023] Open
Abstract
BACKGROUND L‑Fucose is a rare sugar that has beneficial biological activities, and its industrial production is mainly achieved with brown algae through acidic/enzymatic fucoidan hydrolysis and a cumbersome purification process. Fucoidan is synthesized through the condensation of a key substance, guanosine 5'‑diphosphate (GDP)‑L‑fucose. Therefore, a more direct approach for biomanufacturing L‑fucose could be the enzymatic degradation of GDP‑L‑fucose. However, no native enzyme is known to efficiently catalyze this reaction. Therefore, it would be a feasible solution to engineering an enzyme with similar function to hydrolyze GDP‑L‑fucose. RESULTS Herein, we constructed a de novo L‑fucose synthetic route in Bacillus subtilis by introducing heterologous GDP‑L‑fucose synthesis pathway and engineering GDP‑mannose mannosyl hydrolase (WcaH). WcaH displays a high binding affinity but low catalytic activity for GDP‑L‑fucose, therefore, a substrate simulation‑based structural analysis of the catalytic center was employed for the rational design and mutagenesis of selected positions on WcaH to enhance its GDP‑L‑fucose‑splitting efficiency. Enzyme mutants were evaluated in vivo by inserting them into an artificial metabolic pathway that enabled B. subtilis to yield L‑fucose. WcaHR36Y/N38R was found to produce 1.6 g/L L‑fucose during shake‑flask growth, which was 67.3% higher than that achieved by wild‑type WcaH. The accumulated L‑fucose concentration in a 5 L bioreactor reached 6.4 g/L. CONCLUSIONS In this study, we established a novel microbial engineering platform for the fermentation production of L‑fucose. Additionally, we found an efficient GDP‑mannose mannosyl hydrolase mutant for L‑fucose biosynthesis that directly hydrolyzes GDP‑L‑fucose. The engineered strain system established in this study is expected to provide new solutions for L‑fucose or its high value‑added derivatives production.
Collapse
Affiliation(s)
- Cong Fu
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xuexia Xu
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
- iHuman Institute, ShanghaiTech University, Shanghai, 201210, China
| | - Yukang Xie
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yufei Liu
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Min Liu
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Ai Chen
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jenny M Blamey
- Fundación Biociencia, José Domingo Cañas, 2280, Ñuñoa, Santiago, Chile
- Facultad de Química Y Biología, Universidad de Santiago de Chile, 3363, Alameda, Estación Central, Santiago, Chile
| | - Jiping Shi
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Suwen Zhao
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
- iHuman Institute, ShanghaiTech University, Shanghai, 201210, China.
| | - Junsong Sun
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, China.
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| |
Collapse
|
4
|
Soejima M, Koda Y. 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. [PMID: 36900072 DOI: 10.3390/diagnostics13050931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [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
|
5
|
Farahmand M, Latifi T, Kachooei A, Jalilvand S, Shoja Z. Circulating rotavirus P[8]-lineage IV, unlike P[8]-lineage III, significantly related to nonsecretors status in Iranian children. J Med Virol 2023; 95:e28160. [PMID: 36123611 DOI: 10.1002/jmv.28160] [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: 06/06/2022] [Revised: 08/20/2022] [Accepted: 09/14/2022] [Indexed: 01/11/2023]
Abstract
Rotavirus (RV) P[8] strains are responsible for the most of the RV infections globally and are significantly associated with the secretor and Lewis positive status. Among the distinct P[8] lineages, different ligand affinities have been detected which can be linked to differences in secretor status associated histo-blood group antigens (HBGAs). Herein, we report the lineages of P[8] strains and their associated secretor and Lewis antigen phenotypes in Iranian children. The phylogenetic tree and sequence analyses showed that the most common detected RV P[8] strain belonged to P[8]-lineage III (92%) and were significantly associated with secretor and Lewis positive status. In contrast, 8% of P[8] strains clustered into the P[8]-lineage IV and were significantly associated with nonsecretor status, implying that lineage IV tends to infect nonsecretor individuals. Furthermore, protein modeling and amino acid analyses of the VP8* glycan binding site of Iranian P[8]-lineage IV strains indicated two residual substitutions (T184V and N216V/I) compared to the P[8]-lineage III strains that might have affected the glycan affinity among P[8]-lineages IV strains. The corresponding residual changes might permit their continued transmission in nonsecretor children in competition with other P[8]-lineages. Although nonsecretors show natural resistant to P[8] strains, but such residual changes might overcome this natural resistance which in turn might indirectly contribute to the decline in the vaccine efficacy in populations where HBGA polymorphism allows their circulation at high frequency.
Collapse
Affiliation(s)
- Mohammad Farahmand
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Tayebeh Latifi
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Atefeh Kachooei
- Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Somayeh Jalilvand
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Zabihollah Shoja
- Department of Virology, Pasteur Institute of Iran, Tehran, Iran.,Research Center for Emerging and Reemerging Infectious Diseases, Pasteur Institute of Iran, Tehran, Iran
| |
Collapse
|
6
|
Kijner S, Kolodny O, Yassour M. Human milk oligosaccharides and the infant gut microbiome from an eco-evolutionary perspective. Curr Opin Microbiol 2022; 68:102156. [DOI: 10.1016/j.mib.2022.102156] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 03/03/2022] [Accepted: 04/14/2022] [Indexed: 12/21/2022]
|
7
|
Kaur P, Gupta M, Sagar V. FUT2 gene as a genetic susceptible marker of infectious diseases: A Review. Int J Mol Epidemiol Genet 2022; 13:1-14. [PMID: 35892094 PMCID: PMC9301175] [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] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 06/13/2022] [Indexed: 06/15/2023]
Abstract
Some blood group antigens are reported as a susceptibility marker for some diseases. For instance, HBGA (Histo-blood group antigen) which is controlled by gene FUT2 also considered as a susceptible marker. The FUT2 gene which exhibits the expression of alpha-1, 2-L-fucosyltransferase enzyme also leads to HBGA expression for the gut, and it provides a composition of the phenotypical profile that exists in some populations with unique histories of evolution and it can be considered as a marker of the genetic population. It is found to have an association with many diseases which is discussed in this review. Polymorphic mutations are known to inhibit and reduce its function which are population specific. Detailed understanding and deeper knowledge of its role in the pathogenesis and prevention of many diseases is required. FUT2 may also have a potential role in the case of COVID-19 as a susceptible marker due to its association with respiratory diseases and the ABO blood group. There is an utmost need for this kind of review knowing its importance and owing to limited collective information.
Collapse
Affiliation(s)
- Paramvir Kaur
- Department of Community Medicine and Public Health, Postgraduate Institute of Medical Education and Research Chandigarh, India
| | - Madhu Gupta
- Department of Community Medicine and Public Health, Postgraduate Institute of Medical Education and Research Chandigarh, India
| | - Vivek Sagar
- Department of Community Medicine and Public Health, Postgraduate Institute of Medical Education and Research Chandigarh, India
| |
Collapse
|
8
|
Glittenberg MT, Kounatidis I, Atilano M, Ligoxygakis P. A genetic screen in Drosophila reveals the role of fucosylation in host susceptibility to Candida infection. Dis Model Mech 2022; 15:dmm049218. [PMID: 35142345 PMCID: PMC9118035 DOI: 10.1242/dmm.049218] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 01/26/2022] [Indexed: 11/20/2022] Open
Abstract
Candida infections constitute a blind spot in global public health as very few new anti-fungal drugs are being developed. Genetic surveys of host susceptibilities to such infections using mammalian models have certain disadvantages in that obtaining results is time-consuming, owing to relatively long lifespans, and these results have low statistical resolution because sample sizes are usually small. Here, we report a targeted genetic screening of 5698 RNAi lines encompassing 4135 Drosophila genes with human homologues, several of which we identify as important for host survival after Candida albicans infection. These include genes in a variety of functional classes encompassing gene expression, intracellular signalling, metabolism and enzymatic regulation. Analysis of one of the screen hits, the infection-induced α-(1,3)-fucosylase FucTA, showed that N-glycan fucosylation has several targets among proteins involved in host defence, which provides multiple avenues of investigation for the mechanistic analysis of host survival to systemic C. albicans infection.
Collapse
Affiliation(s)
- Marcus T. Glittenberg
- Department of Biochemistry, University of Oxford, South Parks Rd, Oxford OX1 3QU, UK
| | - Ilias Kounatidis
- Department of Biochemistry, University of Oxford, South Parks Rd, Oxford OX1 3QU, UK
| | - Magda Atilano
- Department of Biochemistry, University of Oxford, South Parks Rd, Oxford OX1 3QU, UK
| | - Petros Ligoxygakis
- Department of Biochemistry, University of Oxford, South Parks Rd, Oxford OX1 3QU, UK
| |
Collapse
|
9
|
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] [What about the content of this article? (0)] [Affiliation(s)] [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
|
10
|
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] [What about the content of this article? (0)] [Affiliation(s)] [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
|
11
|
Caldwell J, Matson A, Mosha M, Hagadorn JI, Moore J, Brownell E. Maternal H-antigen secretor status is an early biomarker for potential preterm delivery. J Perinatol 2021; 41:2147-55. [PMID: 33235282 DOI: 10.1038/s41372-020-00870-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 10/08/2020] [Accepted: 11/04/2020] [Indexed: 02/05/2023]
Abstract
OBJECTIVE Pre-pregnancy or first trimester biomarkers predicting preterm delivery are lacking. The purpose of this study was to determine whether maternal H-antigen (secretor status) is a potential biomarker for preterm delivery. METHODS This cohort study examined maternal saliva samples and birth data gathered by the National Children's Study Vanguard pilot phase (2009-2014) and included 300 women who were ≥18 years old and provided birth data and saliva samples. The maternal secretor status phenotype was determined by quantifying H-antigen in saliva using enzyme-linked immunoassay. Mothers were stratified by secretor status and multivariable analysis estimated adjusted associations with preterm delivery. RESULTS Maternal lack of H-antigen production was an independent risk factor for preterm delivery after adjusting for known confounders (aOR 4.53; 95% CI: 1.74, 11.81; P = 0.002). CONCLUSIONS Maternal H-antigen may be a biomarker identifying women at-risk for preterm delivery. Prospective cohort studies validating these findings are needed.
Collapse
|
12
|
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] [What about the content of this article? (0)] [Affiliation(s)] [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
|
13
|
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] [What about the content of this article? (0)] [Affiliation(s)] [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
|
14
|
Farahmand M, Jalilvand S, Arashkia A, Shahmahmoodi S, Afchangi A, Mollaei-Kandelous Y, Shoja Z. Association between circulating rotavirus genotypes and histo-blood group antigens in the children hospitalized with acute gastroenteritis in Iran. J Med Virol 2021; 93:4817-4823. [PMID: 33463743 DOI: 10.1002/jmv.26808] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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: 07/08/2020] [Revised: 10/09/2020] [Accepted: 01/17/2021] [Indexed: 12/16/2022]
Abstract
Rotaviruses are the dominant cause of severe acute gastroenteritis in children under 5 years of age. Previous studies showed that some children are less susceptible to rotavirus gastroenteritis. It has been shown that this resistance depends on the rotavirus genotype and also human histo-blood group antigens (HBGAs), which works as a receptor for rotavirus surface protein (VP4). The present study aimed to evaluate the human genetic susceptibility to rotavirus gastroenteritis in Iran and to obtain a comparative analysis between rotavirus gastroenteritis and secretor or Lewis status in case and control groups in the Iranian population. The study was performed on fecal specimens from 108 children with acute rotavirus gastroenteritis from 2015 to 2017. A total of 50 fecal specimens from children with acute gastroenteritis of unknown etiology were also used as a control group. After the genotyping of positive rotavirus cases and human HBGAs by Sanger sequencing, the phylogenetic tree analysis showed that all rotavirus strains from Iran belonged to P[II]. The most common genotype was P[8] (n = 102; 94.4%), while the remaining belonged to P[4] (n = 3; 2.8%) and P[6] (n = 3; 2.8%) genotypes. The P[8] genotype was found to be associated with secretor and Lewis positive status (p < .05).
Collapse
Affiliation(s)
- Mohammad Farahmand
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Somayeh Jalilvand
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Arash Arashkia
- Department of Molecular Virology, Pasteur Institute of Iran, Tehran, Iran
| | - Shohreh Shahmahmoodi
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Atefeh Afchangi
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Zabihollah Shoja
- Department of Molecular Virology, Pasteur Institute of Iran, Tehran, Iran
| |
Collapse
|
15
|
Boniface K, Byars SG, Cowley D, Kirkwood CD, Bines JE. Human Neonatal Rotavirus Vaccine (RV3-BB) Produces Vaccine Take Irrespective of Histo-Blood Group Antigen Status. J Infect Dis 2020; 221:1070-1078. [PMID: 31763671 PMCID: PMC7075413 DOI: 10.1093/infdis/jiz333] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [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: 05/06/2019] [Accepted: 07/03/2019] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND VP4 [P] genotype binding specificities of rotaviruses and differential expression of histo-blood group antigens (HBGAs) between populations may contribute to reduced efficacy against severe rotavirus disease. P[6]-based rotavirus vaccines could broaden protection in such settings, particularly in Africa, where the Lewis-negative phenotype and P[6] rotavirus strains are common. METHODS The association between HBGA status and G3P[6] rotavirus vaccine (RV3-BB) take was investigated in a phase 2A study of RV3-BB vaccine involving 46 individuals in Dunedin, New Zealand, during 2012-2014. FUT2 and FUT3 genotypes were determined from DNA extracted from stool specimens, and frequencies of positive cumulative vaccine take, defined as an RV3-BB serum immune response (either immunoglobulin A or serum neutralizing antibody) and/or stool excretion of the vaccine strain, stratified by HBGA status were determined. RESULTS RV3-BB produced positive cumulative vaccine take in 29 of 32 individuals (91%) who expressed a functional FUT2 enzyme (the secretor group), 13 of 13 (100%) who were FUT2 null (the nonsecretor group), and 1 of 1 with reduced FUT2 activity (i.e., a weak secretor); in 37 of 40 individuals (93%) who expressed a functional FUT3 enzyme (the Lewis-positive group) and 3 of 3 who were FUT3 null (the Lewis-negative group); and in 25 of 28 Lewis-positive secretors (89%), 12 of 12 Lewis-positive nonsecretors (100%), 2 of 2 Lewis-negative secretors, and 1 of 1 Lewis-negative weak secretor. CONCLUSIONS RV3-BB produced positive cumulative vaccine take irrespective of HBGA status. RV3-BB has the potential to provide an improved level of protection in settings where P[6] rotavirus disease is endemic, irrespective of the HBGA profile of the population.
Collapse
Affiliation(s)
- Karen Boniface
- Enteric Diseases Group, Murdoch Children’s Research Institute, Seattle, Washington
| | - Sean G Byars
- Melbourne School of Population and Global Health, Seattle, Washington
| | - Daniel Cowley
- Enteric Diseases Group, Murdoch Children’s Research Institute, Seattle, Washington
- Department of Pediatrics, University of Melbourne, Seattle, Washington
| | - Carl D Kirkwood
- Enteric Diseases Group, Murdoch Children’s Research Institute, Seattle, Washington
- Department of Pediatrics, University of Melbourne, Seattle, Washington
- Bill and Melinda Gates Foundation, Seattle, Washington
| | - Julie E Bines
- Enteric Diseases Group, Murdoch Children’s Research Institute, Seattle, Washington
- Department of Pediatrics, University of Melbourne, Seattle, Washington
- Department of Gastroenterology and Clinical Nutrition, Royal Children’s Hospital, Parkville, Australia
| |
Collapse
|
16
|
Soejima M, Koda Y. Genetic variation of FUT2 in a Peruvian population: identification of a novel LTR-mediated deletion and characterization of 4 nonsynonymous single-nucleotide polymorphisms. Transfusion 2019; 59:2415-2421. [PMID: 30957248 DOI: 10.1111/trf.15298] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2019] [Revised: 03/19/2019] [Accepted: 03/20/2019] [Indexed: 12/17/2023]
Abstract
BACKGROUND The human FUT2 gene, which encodes a secretor type α(1,2)fucosyltransferase, is reported to have several population-specific single-nucleotide polymorphisms (SNPs) and copy number variations. However, little is known about genetic variation of FUT2 in Native Americans. STUDY DESIGN AND METHODS To detect SNPs and copy number variations of the FUT2 gene in Peruvians, direct sequencing and digital polymerase chain reaction were performed. Haplotypes of observed SNPs were estimated by PHASE software or cloning into plasmids. The functional significance of nonsynonymous SNPs was examined by transient transfection assay. RESULTS We identified three novel nonfunctional alleles (se178,357 , se841 , and sedel4 ) due to two nonsynonymous SNPs (178C > T and 841G > A) and a novel long terminal repeat-mediated recombination with a 4.3-kb deletion in 70 Peruvians. The frequency of nonfunctional alleles was relative low (20.7%). Because se841 has a relatively high frequency (5.7%), it might be a suitable genetic marker for Peruvians. CONCLUSION We identified three novel nonfunctional alleles in 70 Peruvians. To our knowledge, this is the first time a long terminal repeat-mediated gene recombination event at the FUT2 locus has been detected.
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
|
17
|
Abstract
Human norovirus is a major human pathogen causing the majority of cases of viral gastroenteritis globally. Viral entry is the first step of the viral life cycle and is a significant determinant of cell tropism, host range, immune interactions, and pathogenesis. Bile salts and histo-blood group antigens are key mediators of norovirus entry; however, the molecular mechanisms by which these molecules promote infection and the identity of a potential human norovirus receptor remain unknown. Recently, there have been several important advances in norovirus entry biology including the identification of CD300lf as the receptor for murine norovirus and of the role of the minor capsid protein VP2 in viral genome release. Here, we will review the current understanding about norovirus attachment and entry and highlight important future directions.
Collapse
Affiliation(s)
- Vincent R Graziano
- Departments of Laboratory Medicine and Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA.
| | - Jin Wei
- Departments of Laboratory Medicine and Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA.
| | - Craig B Wilen
- Departments of Laboratory Medicine and Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA.
| |
Collapse
|
18
|
Barton SJ, Murray R, Lillycrop KA, Inskip HM, Harvey NC, Cooper C, Karnani N, Zolezzi IS, Sprenger N, Godfrey KM, Binia A. FUT2 Genetic Variants and Reported Respiratory and Gastrointestinal Illnesses During Infancy. J Infect Dis 2019; 219:836-843. [PMID: 30376117 PMCID: PMC6687504 DOI: 10.1093/infdis/jiy582] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 10/25/2018] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Fucosyltransferase 2 (FUT2) controls the production of digestive and respiratory epithelia of histo-blood group antigens involved in the attachment of pathogens. The aim of our study was to relate FUT2 variants to reported gastrointestinal and respiratory illnesses in infancy. METHODS In the Southampton Women's Survey, FUT2 genetic variants (single-nucleotide polymorphisms [SNPs] rs601338 and rs602662) were genotyped in 1831 infants and related to infant illnesses, after adjustment for sex, breastfeeding duration, and potential confounders. RESULTS For FUT2 SNP rs601338, the risk ratios for ≥1 bout of diarrhea during ages 6-12 months and ages 12-24 months per additional risk (G) allele were 1.23 (95% confidence interval [CI], 1.08-1.4; P = .002) and 1.41 (95% CI, 1.24-1.61; P = 1.7 × 10-7), respectively; the risk ratio for ≥1 diagnosis of a lower respiratory illness (ie, pneumonia or bronchiolitis) during ages 12-24 months per additional G allele was 2.66 (95% CI, 1.64-4.3; P = .00007). Similar associations were found between rs602662 and gastrointestinal and respiratory illnesses, owing to the high linkage disequilibrium with rs601338 (R2 = 0.92). Longer breastfeeding duration predicted a lower risk of diarrhea, independent of infant FUT2 genotype. CONCLUSIONS We confirmed that FUT2 G alleles are associated with a higher risk of infant gastrointestinal illnesses and identified novel associations with respiratory illnesses. FUT2 locus variants need consideration in future studies of gastrointestinal and respiratory illnesses among infants.
Collapse
Affiliation(s)
| | - Robert Murray
- Human Development and Health Academic Unit, University of Southampton, UK
| | - Karen A. Lillycrop
- Human Development and Health Academic Unit, University of Southampton, UK
- School of Biological Sciences, University of Southampton, Southampton General Hospital, UK SO16 6YD
| | - Hazel M Inskip
- MRC Lifecourse Epidemiology Unit, University of Southampton, UK
- NIHR Southampton Biomedical Research Centre, University of Southampton and University Hospital Southampton NHS Foundation Trust, UK
| | - Nicholas C Harvey
- MRC Lifecourse Epidemiology Unit, University of Southampton, UK
- NIHR Southampton Biomedical Research Centre, University of Southampton and University Hospital Southampton NHS Foundation Trust, UK
| | - Cyrus Cooper
- MRC Lifecourse Epidemiology Unit, University of Southampton, UK
- NIHR Southampton Biomedical Research Centre, University of Southampton and University Hospital Southampton NHS Foundation Trust, UK
| | - Neerja Karnani
- Singapore Institute for Clinical Sciences, A*STAR, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore
| | | | | | - Keith M. Godfrey
- MRC Lifecourse Epidemiology Unit, University of Southampton, UK
- Human Development and Health Academic Unit, University of Southampton, UK
- NIHR Southampton Biomedical Research Centre, University of Southampton and University Hospital Southampton NHS Foundation Trust, UK
| | - Aristea Binia
- Nestlé Research Center, Lausanne, Nestec S.A., Switzerland
| |
Collapse
|
19
|
Ma L, McJarrow P, Jan Mohamed HJB, Liu X, Welman A, Fong BY. Lactational changes in the human milk oligosaccharide concentration in Chinese and Malaysian mothers' milk. Int Dairy J 2018. [DOI: 10.1016/j.idairyj.2018.07.015] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
|
20
|
Ferkingstad E, Oddsson A, Gretarsdottir S, Benonisdottir S, Thorleifsson G, Deaton AM, Jonsson S, Stefansson OA, Norddahl GL, Zink F, Arnadottir GA, Gunnarsson B, Halldorsson GH, Helgadottir A, Jensson BO, Kristjansson RP, Sveinbjornsson G, Sverrisson DA, Masson G, Olafsson I, Eyjolfsson GI, Sigurdardottir O, Holm H, Jonsdottir I, Olafsson S, Steingrimsdottir T, Rafnar T, Bjornsson ES, Thorsteinsdottir U, Gudbjartsson DF, Sulem P, Stefansson K. Genome-wide association meta-analysis yields 20 loci associated with gallstone disease. Nat Commun 2018; 9:5101. [PMID: 30504769 PMCID: PMC6269469 DOI: 10.1038/s41467-018-07460-y] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 11/01/2018] [Indexed: 01/07/2023] Open
Abstract
Gallstones are responsible for one of the most common diseases in the Western world and are commonly treated with cholecystectomy. We perform a meta-analysis of two genome-wide association studies of gallstone disease in Iceland and the UK, totaling 27,174 cases and 736,838 controls, uncovering 21 novel gallstone-associated variants at 20 loci. Two distinct low frequency missense variants in SLC10A2, encoding the apical sodium-dependent bile acid transporter (ASBT), associate with an increased risk of gallstone disease (Pro290Ser: OR = 1.36 [1.25-1.49], P = 2.1 × 10-12, MAF = 1%; Val98Ile: OR = 1.15 [1.10-1.20], P = 1.8 × 10-10, MAF = 4%). We demonstrate that lower bile acid transport by ASBT is accompanied by greater risk of gallstone disease and highlight the role of the intestinal compartment of the enterohepatic circulation of bile acids in gallstone disease susceptibility. Additionally, two low frequency missense variants in SERPINA1 and HNF4A and 17 common variants represent novel associations with gallstone disease.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | - Florian Zink
- deCODE Genetics/Amgen, Inc., Reykjavik, 101, Iceland
| | | | | | | | | | | | | | | | | | - Gisli Masson
- deCODE Genetics/Amgen, Inc., Reykjavik, 101, Iceland
| | - Isleifur Olafsson
- Department of Clinical Biochemistry, Landspítali University Hospital, Reykjavik, 101, Iceland
| | | | - Olof Sigurdardottir
- Department of Clinical Biochemistry, Akureyri Hospital, Akureyri, 600, Iceland
| | - Hilma Holm
- deCODE Genetics/Amgen, Inc., Reykjavik, 101, Iceland
| | - Ingileif Jonsdottir
- deCODE Genetics/Amgen, Inc., Reykjavik, 101, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, 101, Iceland
- Department of Immunology, Landspitali University Hospital, Reykjavik, 101, Iceland
| | - Sigurdur Olafsson
- Department of Internal Medicine, Landspitali University Hospital, Reykjavik, 101, Iceland
| | - Thora Steingrimsdottir
- Faculty of Medicine, University of Iceland, Reykjavik, 101, Iceland
- Department of Obstetrics and Gynecology, Landspitali University Hospital, Reykjavik, 101, Iceland
| | | | - Einar S Bjornsson
- Faculty of Medicine, University of Iceland, Reykjavik, 101, Iceland
- Department of Internal Medicine, Landspitali University Hospital, Reykjavik, 101, Iceland
| | - Unnur Thorsteinsdottir
- deCODE Genetics/Amgen, Inc., Reykjavik, 101, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, 101, Iceland
| | - Daniel F Gudbjartsson
- deCODE Genetics/Amgen, Inc., Reykjavik, 101, Iceland
- School of Engineering and Natural Sciences, University of Iceland, Reykjavik, 101, Iceland
| | - Patrick Sulem
- deCODE Genetics/Amgen, Inc., Reykjavik, 101, Iceland.
| | - Kari Stefansson
- deCODE Genetics/Amgen, Inc., Reykjavik, 101, Iceland.
- Faculty of Medicine, University of Iceland, Reykjavik, 101, Iceland.
| |
Collapse
|
21
|
Velkova A, Diaz JEL, Pangilinan F, Molloy AM, Mills JL, Shane B, Sanchez E, Cunningham C, McNulty H, Cropp CD, Bailey-Wilson JE, Wilson AF, Brody LC. The FUT2 secretor variant p.Trp154Ter influences serum vitamin B12 concentration via holo-haptocorrin, but not holo-transcobalamin, and is associated with haptocorrin glycosylation. Hum Mol Genet 2017; 26:4975-4988. [PMID: 29040465 PMCID: PMC5886113 DOI: 10.1093/hmg/ddx369] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Revised: 09/19/2017] [Accepted: 09/20/2017] [Indexed: 11/14/2022] Open
Abstract
Vitamin B12 deficiency is common in older individuals. Circulating vitamin B12 concentration can be used to diagnose deficiency, but this test has substantial false positive and false negative rates. We conducted genome-wide association studies (GWAS) in which we resolved total serum vitamin B12 into the fractions bound to transcobalamin and haptocorrin: two carrier proteins with very different biological properties. We replicated reported associations between total circulating vitamin B12 concentrations and a common null variant in FUT2. This allele determines the secretor phenotype in which blood group antigens are found in non-blood body fluids. Vitamin B12 bound to haptocorrin (holoHC) remained highly associated with FUT2 rs601338 (p.Trp154Ter). Transcobalamin bound vitamin B12 (holoTC) was not influenced by this variant. HoloTC is the bioactive the form of the vitamin and is taken up by all tissues. In contrast, holoHC is only taken up by the liver. Using holoHC from individuals with known FUT2 genotypes, we demonstrated that FUT2 rs601338 genotype influences the glycosylation of haptocorrin. We then developed an experimental model demonstrating that holoHC is transported into cultured hepatic cells (HepG2) via the asialoglycoprotein receptor (ASGR). Our data challenge current published hypotheses on the influence of genetic variation on this clinically important measure and are consistent with a model in which FUT2 rs601338 influences holoHC by altering haptocorrin glycosylation, whereas B12 bound to non-glycosylated transcobalamin (i.e. holoTC) is not affected. Our findings explain some of the observed disparity between use of total B12 or holoTC as first-line clinical tests of vitamin B12 status.
Collapse
Affiliation(s)
- Aneliya Velkova
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, Bethesda, MD 20892, USA
| | - Jennifer E L Diaz
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, Bethesda, MD 20892, USA
| | - Faith Pangilinan
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, Bethesda, MD 20892, USA
| | - Anne M Molloy
- Department of Clinical Medicine, School of Medicine, Trinity College Dublin, Dublin 2, Ireland
| | - James L Mills
- Division of Intramural Population Health Research, Eunice Kennedy Shriver NICHD, Bethesda, MD 20852, USA
| | - Barry Shane
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, CA 94720, USA
| | - Erica Sanchez
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, Bethesda, MD 20892, USA
| | | | - Helene McNulty
- Northern Ireland Centre for Food and Health, University of Ulster, Coleraine BT52 1SA, Northern Ireland
| | - Cheryl D Cropp
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, MD 21224, USA
| | - Joan E Bailey-Wilson
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, MD 21224, USA
| | - Alexander F Wilson
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, MD 21224, USA
| | - Lawrence C Brody
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, Bethesda, MD 20892, USA
| |
Collapse
|
22
|
Mozzi A, Pontremoli C, Sironi M. Genetic susceptibility to infectious diseases: Current status and future perspectives from genome-wide approaches. Infect Genet Evol 2017; 66:286-307. [PMID: 28951201 PMCID: PMC7106304 DOI: 10.1016/j.meegid.2017.09.028] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 09/20/2017] [Accepted: 09/21/2017] [Indexed: 02/06/2023]
Abstract
Genome-wide association studies (GWASs) have been widely applied to identify genetic factors that affect complex diseases or traits. Presently, the GWAS Catalog includes > 2800 human studies. Of these, only a minority have investigated the susceptibility to infectious diseases or the response to therapies for the treatment or prevention of infections. Despite their limited application in the field, GWASs have provided valuable insights by pinpointing associations to both innate and adaptive immune response loci, as well as novel unexpected risk factors for infection susceptibility. Herein, we discuss some issues and caveats of GWASs for infectious diseases, we review the most recent findings ensuing from these studies, and we provide a brief summary of selected GWASs for infections in non-human mammals. We conclude that, although the general trend in the field of complex traits is to shift from GWAS to next-generation sequencing, important knowledge on infectious disease-related traits can be still gained by GWASs, especially for those conditions that have never been investigated using this approach. We suggest that future studies will benefit from the leveraging of information from the host's and pathogen's genomes, as well as from the exploration of models that incorporate heterogeneity across populations and phenotypes. Interactions within HLA genes or among HLA variants and polymorphisms located outside the major histocompatibility complex may also play an important role in shaping the susceptibility and response to invading pathogens. Relatively few GWASs for infectious diseases were performed. Phenotype heterogeneity and case/control misclassification can affect GWAS power. Adaptive and innate immunity loci were identified in several infectious disease GWASs. Unexpected loci (e.g., lncRNAs) were also associated with infection susceptibility. GWASs should integrate host and pathogen diversity and use complex association models.
Collapse
Affiliation(s)
- Alessandra Mozzi
- Bioinformatics, Scientific Institute IRCCS E.MEDEA, 23842 Bosisio Parini, Italy
| | - Chiara Pontremoli
- Bioinformatics, Scientific Institute IRCCS E.MEDEA, 23842 Bosisio Parini, Italy
| | - Manuela Sironi
- Bioinformatics, Scientific Institute IRCCS E.MEDEA, 23842 Bosisio Parini, Italy.
| |
Collapse
|
23
|
Loebinger M. Sugar coating bronchiectasis. Thorax 2017; 72:300-301. [DOI: 10.1136/thoraxjnl-2016-209274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
|
24
|
Fransen F, Sahasrabudhe NM, Elderman M, Bosveld M, El Aidy S, Hugenholtz F, Borghuis T, Kousemaker B, Winkel S, van der Gaast-de Jongh C, de Jonge MI, Boekschoten MV, Smidt H, Schols HA, de Vos P. β2→1-Fructans Modulate the Immune System In Vivo in a Microbiota-Dependent and -Independent Fashion. Front Immunol 2017; 8:154. [PMID: 28261212 PMCID: PMC5311052 DOI: 10.3389/fimmu.2017.00154] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [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: 11/19/2016] [Accepted: 01/30/2017] [Indexed: 12/15/2022] Open
Abstract
It has been shown in vitro that only specific dietary fibers contribute to immunity, but studies in vivo are not conclusive. Here, we investigated degree of polymerization (DP) dependent effects of β2→1-fructans on immunity via microbiota-dependent and -independent effects. To this end, conventional or germ-free mice received short- or long-chain β2→1-fructan for 5 days. Immune cell populations in the spleen, mesenteric lymph nodes (MLNs), and Peyer’s patches (PPs) were analyzed with flow cytometry, genome-wide gene expression in the ileum was measured with microarray, and gut microbiota composition was analyzed with 16S rRNA sequencing of fecal samples. We found that β2→1-fructans modulated immunity by both microbiota and microbiota-independent effects. Moreover, effects were dependent on the chain-length of the β2→1-fructans type polymer. Both short- and long-chain β2→1-fructans enhanced T-helper 1 cells in PPs, whereas only short-chain β2→1-fructans increased regulatory T cells and CD11b−CD103− dendritic cells (DCs) in the MLN. A common feature after short- and long-chain β2→1-fructan treatment was enhanced 2-alpha-l-fucosyltransferase 2 expression and other IL-22-dependent genes in the ileum of conventional mice. These effects were not associated with shifts in gut microbiota composition, or altered production of short-chain fatty acids. Both short- and long-chain β2→1-fructans also induced immune effects in germ-free animals, demonstrating direct effect independent from the gut microbiota. Also, these effects were dependent on the chain-length of the β2→1-fructans. Short-chain β2→1-fructan induced lower CD80 expression by CD11b−CD103− DCs in PPs, whereas long-chain β2→1-fructan specifically modulated B cell responses in germ-free mice. In conclusion, support of immunity is determined by the chemical structure of β2→1-fructans and is partially microbiota independent.
Collapse
Affiliation(s)
- Floris Fransen
- Top Institute Food and Nutrition, Wageningen, Netherlands; Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Neha M Sahasrabudhe
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen , Groningen , Netherlands
| | - Marlies Elderman
- Top Institute Food and Nutrition, Wageningen, Netherlands; Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Margaret Bosveld
- Laboratory of Food Chemistry, Wageningen University , Wageningen , Netherlands
| | - Sahar El Aidy
- Microbial Physiology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen , Groningen , Netherlands
| | - Floor Hugenholtz
- Top Institute Food and Nutrition, Wageningen, Netherlands; Laboratory of Microbiology, Wageningen University, Wageningen, Netherlands
| | - Theo Borghuis
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen , Groningen , Netherlands
| | - Ben Kousemaker
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen , Groningen , Netherlands
| | - Simon Winkel
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen , Groningen , Netherlands
| | | | - Marien I de Jonge
- Laboratory of Pediatric Infectious Diseases, Radboud University Medical Center , Nijmegen , Netherlands
| | - Mark V Boekschoten
- Top Institute Food and Nutrition, Wageningen, Netherlands; Nutrition, Metabolism and Genomics Group, Division of Human Nutrition, Wageningen University, Wageningen, Netherlands
| | - Hauke Smidt
- Top Institute Food and Nutrition, Wageningen, Netherlands; Laboratory of Microbiology, Wageningen University, Wageningen, Netherlands
| | - Henk A Schols
- Top Institute Food and Nutrition, Wageningen, Netherlands; Laboratory of Food Chemistry, Wageningen University, Wageningen, Netherlands
| | - Paul de Vos
- Top Institute Food and Nutrition, Wageningen, Netherlands; Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| |
Collapse
|
25
|
Zanjani DS, Afzal Aghaee M, Badiei Z, Mehrasa R, Roodsarabi A, Khayyami ME, Shahabi M. Molecular basis of Bombay phenotype in Mashhad, Iran: identification of a novel FUT1 deletion. Vox Sang 2016; 111:88-92. [PMID: 26926997 DOI: 10.1111/vox.12393] [Citation(s) in RCA: 5] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Revised: 01/25/2016] [Accepted: 01/26/2016] [Indexed: 11/28/2022]
Abstract
BACKGROUND AND OBJECTIVES Bombay phenotype is characterized by the lack of H substance both on red blood cell (RBC) surface and in body secretions. Mutations of fucosyltransferase 1 (FUT1) and fucosyltransferase 2 (FUT2) genes are resulted in this rare phenotype. MATERIALS AND METHODS Five unrelated patients were tested by hemagglutination and adsorption/elution techniques for the presence of ABH antigens. The saliva specimens were analysed by hemagglutination inhibition method. The exons 6 and 7 of ABO gene were sequenced to determine ABO genotype. The coding fragments of FUT1 and FUT2 were amplified and sequenced by specific primers. RESULTS Serologic investigation confirmed Bombay phenotype in all individuals. FUT1 molecular analysis revealed a novel large deletion. Also two novel homozygous mutations were detected; one was a missense mutation (392T>C, L131P) and the other a three nucleotide deletion (668_670delACT, Y224del). FUT2 sequencing showed one reported null allele (428G>A, W143X) and one homozygous deletion of FUT2. CONCLUSION Although FUT2 deletion has been reported, this is the first report of FUT1 deletion. Finding two FUT1 novel alleles in Iranian people is indicative of mutation diversity in this gene.
Collapse
Affiliation(s)
| | - M Afzal Aghaee
- Deputy of Research, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Z Badiei
- Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - R Mehrasa
- Blood Transfusion Research Center, High Institute for Research and Education in Transfusion Medicine, Tehran, Iran
| | - A Roodsarabi
- Cord Blood Stem Cell, Iranian Blood Transfusion Organization, Tehran, Iran
| | | | - M Shahabi
- High Institute for Research and Education in Transfusion Medicine, Tehran, Iran
| |
Collapse
|
26
|
Abstract
Fucose is an L-configuration sugar found abundantly in the mammalian gut. It has long been known to be induced there by the presence of bacteria, but only recently have some of the molecular mechanisms behind this process been uncovered. New work suggests that fucose can have a protective role in both gut-centered and systemic infection and inflammation. This review highlights recent studies showing that, in addition to acting as a food source for beneficial gut symbionts, host fucose can suppress the virulence of pathogens and pathobionts. The relevance of gut fucosylation to human diseases also is discussed.
Collapse
Affiliation(s)
- Joseph M Pickard
- Department of Pathology and Committee on Immunology, The University of Chicago, Chicago, IL 60637
| | - Alexander V Chervonsky
- Department of Pathology and Committee on Immunology, The University of Chicago, Chicago, IL 60637
| |
Collapse
|
27
|
Chanzu NM, Mwanda W, Oyugi J, Anzala O. Mucosal Blood Group Antigen Expression Profiles and HIV Infections: A Study among Female Sex Workers in Kenya. PLoS One 2015; 10:e0133049. [PMID: 26186209 DOI: 10.1371/journal.pone.0133049] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 06/22/2015] [Indexed: 11/19/2022] Open
Abstract
Background The ABO blood group antigens are carbohydrate moieties expressed on human red blood cells however; these antigens can also be expressed on some other cells particularly the surface of epithelial cells and may be found in mucosal secretions. In many human populations 80% secrete ABO antigens (termed ‘secretors’) while 20% do not (termed ‘non-secretors’). Furthermore, there are disease conditions that are associated with secretor status. Objective To investigate correlations between secretor status and HIV infection among female sex workers in Nairobi, Kenya. Methodology This cross-sectional study recruited 280 female sex workers aged 18–65 years from the Pumwani Majengo cohort, Kenya. Blood typing was determined by serological techniques using monoclonal antibodies to the ABO blood group antigens. Secretor phenotyping was determined using anti-H specific lectins specific to salivary, vaginal and cervical blood group H antigen using the agglutination inhibition technique and correlated to individual HIV sero-status. Participants were additionally screened for Bacterial vaginosis, Neisseria gonorrhoea and Trichomonas vaginalis. Results Out of the 280 participants, 212 (75.7%) were secretors and 68 (24.3%) were non-secretors. The incidence of all infections: HIV, Bacterial vaginosis, Neisseria gonorrhoea and Trichomonas vaginalis was higher among secretors compared to non-secretors. However, this difference was only statistically significant for HIV infection incidence rates: HIV infected secretors (83.7%) versus HIV un-infected secretors (71.8%) (p = 0.029) Based on ABO phenotype stratification, the incidence of HIV infection was higher among blood group A secretors (26/52 = 50%), in comparison to B (12/39 = 33.3%: p = 0.066), AB (3/9 = 33.3%: p = 0.355), and O secretors (36/112 = 32.1%: p = 0.028). Conclusion This is the first report to document the variable expression of the ABH blood group antigens profiling secretor and non-secretor phenotypes in the female genital tract among a high-risk population in a Kenyan population. These findings suggest the non-secretor phenotype may confer a certain degree of protection against HIV infection.
Collapse
|
28
|
Le Pendu J, Nyström K, Ruvoën-clouet N. Host–pathogen co-evolution and glycan interactions. Curr Opin Virol 2014; 7:88-94. [DOI: 10.1016/j.coviro.2014.06.001] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Accepted: 06/02/2014] [Indexed: 01/22/2023]
|
29
|
Tian L, Song N, Yao ZQ, Li XJ, Zhang R. Sequence analysis of the human fucosyltransferase 1 and 2 genes in Tibetan blood donors: identification of three novel alleles. Transfusion 2014; 54:1847-50. [PMID: 24527852 DOI: 10.1111/trf.12577] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Revised: 11/28/2013] [Accepted: 12/06/2013] [Indexed: 11/27/2022]
Abstract
BACKGROUND The α(1,2)-fucosyltransferase gene 1 (FUT1) and 2 (FUT2), respectively, regulate H antigen synthesis in red blood cells and body fluids. Genetic polymorphisms of FUT1 and FUT2 are ethnically and geographically specific. STUDY DESIGN AND METHODS Healthy unrelated Tibetan blood donors (n = 200) from the Tibet Autonomous Region of China were recruited for this study. The entire FUT1 and FUT2 coding regions were amplified and sequenced. The haplotypes including novel single-nucleotide polymorphisms (SNPs) were determined by clone sequencing. RESULTS In Tibetans, the major FUT1 allele was wild-type allele with a frequency of 97.75%. One novel FUT1 allele was defined by a novel synonymous mutation (846T>G). The two most common FUT2 alleles were functional allele Se(357) with a frequency of 32.75% and nonfunctional allele se(357,385) with a frequency of 55%. Two new FUT2 alleles were found at low frequency. They were characterized by two novel SNPs on the basis of se(357,385) : 617 T>G (V206G) and 841 G>A (G281R). CONCLUSION Three new alleles in FUT1 and FUT2 genes were identified in the study. The allelic polymorphisms of FUT1 and FUT2 in Tibetans show a population-specific manner.
Collapse
Affiliation(s)
- Li Tian
- Department of Blood Immunology, Institute of Blood Transfusion, Chinese Academy of Medical Sciences, Chengdu, Sichuan, China
| | | | | | | | | |
Collapse
|
30
|
Forni D, Cleynen I, Ferrante M, Cassinotti A, Cagliani R, Ardizzone S, Vermeire S, Fichera M, Lombardini M, Maconi G, de Franchis R, Asselta R, Biasin M, Clerici M, Sironi M. ABO histo-blood group might modulate predisposition to Crohn's disease and affect disease behavior. J Crohns Colitis 2014; 8:489-94. [PMID: 24268527 DOI: 10.1016/j.crohns.2013.10.014] [Citation(s) in RCA: 25] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Revised: 10/31/2013] [Accepted: 10/31/2013] [Indexed: 01/18/2023]
Abstract
BACKGROUND AND AIMS ABO encodes a glycosyltranferase which determines the major human histo-blood group. The FUT2 fucosyltransferase allows expression of ABO antigens on the gastrointestinal mucosa and in bodily secretions (secretor phenotype). A nonsense allele in FUT2 represents a susceptibility variant for Crohn's disease, and both the secretor and ABO blood group status affect the composition of the gut microbiota. Thus, we evaluated if variants in ABO might represent good candidates as Crohn's disease susceptibility loci. METHODS We recruited two case-control cohorts, from Italy (n=1301) and Belgium (n=2331). Subjects were genotyped for one SNP in FUT2 and two variants in ABO. RESULTS No effect on Crohn's disease risk was detected for ABO variants, whereas an association was observed between the FUT2 polymorphism and Crohn's disease susceptibility in the Belgian sample, but not in the Italian cohort. The effect of histo-blood groups was evaluated using group O as the reference. Most non-O groups had odds ratios (ORs) higher than 1 in both cohorts, and combined analysis of the two samples indicated a predisposing effect for the A and B groups (OR=1.17, 95% CI: 1.02-1.32 and OR=1.33, 95% CI: 1.09-1.58, respectively). In Crohn's disease patients, the non-O blood group and the non-secretor status were associated with higher risk of developing a stricturing or penetrating disease. CONCLUSIONS ABO histo-blood group might confer susceptibility to Crohn's disease and modulate disease severity.
Collapse
Affiliation(s)
- Diego Forni
- Bioinformatics, Scientific Institute IRCCS E. Medea, 23842 Bosisio Parini, LC, Italy
| | - Isabelle Cleynen
- Department of Gastroenterology, University Hospital Gasthuisberg, Leuven, Belgium
| | - Marc Ferrante
- Department of Gastroenterology, University Hospital Gasthuisberg, Leuven, Belgium
| | - Andrea Cassinotti
- IBD Unit, Chair of Gastroenterology, Luigi Sacco University Hospital, 20157 Milan, Italy
| | - Rachele Cagliani
- Bioinformatics, Scientific Institute IRCCS E. Medea, 23842 Bosisio Parini, LC, Italy
| | - Sandro Ardizzone
- IBD Unit, Chair of Gastroenterology, Luigi Sacco University Hospital, 20157 Milan, Italy
| | - Severine Vermeire
- Department of Gastroenterology, University Hospital Gasthuisberg, Leuven, Belgium
| | - Maria Fichera
- IBD Unit, Chair of Gastroenterology, Luigi Sacco University Hospital, 20157 Milan, Italy
| | - Marta Lombardini
- IBD Unit, Chair of Gastroenterology, Luigi Sacco University Hospital, 20157 Milan, Italy
| | - Giovanni Maconi
- IBD Unit, Chair of Gastroenterology, Luigi Sacco University Hospital, 20157 Milan, Italy
| | - Roberto de Franchis
- IBD Unit, Chair of Gastroenterology, Luigi Sacco University Hospital, 20157 Milan, Italy
| | - Rosanna Asselta
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Milano, Italy
| | - Mara Biasin
- Chair of Immunology, DISC LITA Vialba, University of Milano, Milano, Italy
| | - Mario Clerici
- Chair of Immunology, Department of Physiopathology and Transplantation, University of Milan, 20090 Milano, Italy; Fondazione Don C. Gnocchi, IRCCS, 20148 Milano, Italy
| | - Manuela Sironi
- Bioinformatics, Scientific Institute IRCCS E. Medea, 23842 Bosisio Parini, LC, Italy.
| |
Collapse
|
31
|
Wu CS, Yen CJ, Chou RH, Chen JN, Huang WC, Wu CY, Yu YL. Downregulation of microRNA-15b by hepatitis B virus X enhances hepatocellular carcinoma proliferation via fucosyltransferase 2-induced Globo H expression. Int J Cancer 2014; 134:1638-47. [PMID: 24122375 DOI: 10.1002/ijc.28501] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [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: 03/24/2013] [Revised: 08/21/2013] [Accepted: 09/10/2013] [Indexed: 02/06/2023]
Abstract
Globo H, a cancer-associated carbohydrate antigen, is highly expressed in various types of cancers. However, the role of Globo H in hepatocellular carcinoma (HCC) remains elusive. In our study, we performed glycan microarray analysis of 134 human serum samples to explore anti-Globo H antibody changes and found that Globo H is upregulated in hepatitis B virus (HBV)-positive HCC. Similarly, immunohistochemistry showed that Globo H expression was higher in tumors compared to normal tissues. In addition, fucosyltransferase 2 (FUT2), the main synthetic enzyme of Globo H, was also increased in HCC cells overexpressing HBV X protein (HBX). HBX plays an important role in promoting cell proliferation and may be related to increased levels of FUT2 and Globo H. Furthermore, using microRNA profiling, we observed that microRNA-15b (miR-15b) was downregulated in patients with HCC and confirmed association of FUT2 expression with expression of its product, Globo H. Therefore, our results suggest that HBX suppressed the expression of miR-15b, which directly targeted FUT2 and then increased levels of Globo H to enhance HCC cell proliferation. Additionally, proliferation of HBX-overexpressing HCC cells was significantly inhibited by treatment with Globo H antibody in vitro. In xenograft animal experiments, we found that overexpression of miR-15b effectively suppressed tumor growth. The newly identified HBX/miR-15b/FUT2/Globo H axis suggests one possible molecular mechanism of HCC cell proliferation and represents a new potential therapeutic target for HCC treatment.
Collapse
Affiliation(s)
- Chen-Shiou Wu
- The Ph.D. Program for Cancer Biology and Drug Discovery, China Medical University, Taichung, Taiwan; Graduate Institute of Cancer Biology and Center for Molecular Medicine, China Medical University, Taichung, Taiwan; Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | | | | | | | | | | | | |
Collapse
|
32
|
Vicentini F, Denadai W, Gomes YM, Rose TL, Ferreira MSR, Le Moullac-Vaidye B, Le Pendu J, Leite JPG, Miagostovich MP, Spano LC. Molecular characterization of noroviruses and HBGA from infected Quilombola children in Espirito Santo State, Brazil. PLoS One 2013; 8:e69348. [PMID: 23894453 PMCID: PMC3718680 DOI: 10.1371/journal.pone.0069348] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2013] [Accepted: 06/08/2013] [Indexed: 12/27/2022] Open
Abstract
Noroviruses (NoV) are the main etiological agents of gastroenteritis outbreaks worldwide and susceptibility to NoV infection has been related to the histo-blood group antigen (HBGA). This study aimed to determine the prevalence of NoV strains and to evaluate the HBGA phenotype and genotype of children from semi-isolated Quilombola communities, descendents of black slaves in Brazil. A total of 397 children up to eleven years old, with and without diarrhea, from Quilombola Communities in the Espirito Santo State, Brazil, were investigated for the presence of NoV from August 2007 to September 2009. Feces were collected from all the children, and blood from the NoV positive children. NoV was screened by reverse transcription-PCR with primers for the RNA-dependent RNA polymerase region; genogroup was determined by PCR with primers for the C and D regions and genotyped by sequencing. HBGA phenotype was performed by gel-spinning and FUT2 and FUT3 were analyzed by PCR or sequencing analysis. NoV were detected in 9.2% (12/131) of diarrheic and 1.5% (4/266) of non-diarrheic children (p<0.05, Fisher's exact test). GI and GII genogroups were present in 12.5% and 87.5% of the samples, respectively. The following genotypes were characterized: GII.4 (25%), GII.12 (25%), GII.6 (12.5%) and GI.1 (6.3%), GI.3 (12.5%) and GI.4 (6.3%). Children infected with NoV showed the A (n = 6), O (n = 6), and B (n = 2) HBGA phenotypes, and 13 of them were classified as secretors (Se) and one as a non secretor (se). Mutations of Se (40), (171,216,357,428,739,960) were found for the FUT2 gene and mutations of Le (59, 202, 314) for the FUT3 gene. The only se child was infected by NoV GI, whereas the Se children were indiscriminately infected by GI or GII. This study showed rates of NoV infection in symptomatic and asymptomatic Quilombola children consistent with other studies. However, children under 12 months were seven times more affected than those between 1 and 5 years old. GII.12 was as frequent as GII.4 and GI.1 and GI.4 were described for the first time in Brazil. Owing to the small number of cases studied, no clear pattern of susceptibility and/or HBGA resistance could be inferred.
Collapse
Affiliation(s)
- Fernando Vicentini
- Departamento de Ciências da Saúde, Universidade Federal do Espírito Santo, São Mateus, Espírito Santo, Brazil.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
33
|
Soejima M, Fujimoto R, Agusa T, Iwata H, Fujihara J, Takeshita H, Minh TB, Trang PTK, Viet PH, Nakajima T, Yoshimoto J, Tanabe S, Koda Y. Genetic variation of FUT2 in a Vietnamese population: identification of two novel Se enzyme-inactivating mutations. Transfusion 2012; 52:1268-75. [PMID: 22188519 DOI: 10.1111/j.1537-2995.2011.03485.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
BACKGROUND The human FUT2 gene encodes a secretor-type α(1,2)fucosyltransferase, and many population-specific polymorphisms have been reported in the coding region. STUDY DESIGN AND METHODS Direct sequencing, real-time polymerase chain reaction, and high-resolution melt (HRM) analysis were done to detect single-nucleotide polymorphism (SNPs) and copy number variations (CNVs) in a Vietnamese population. The impacts of two novel mutations on the encoded enzyme were examined by a transient expression study. RESULTS The major nonfunctional allele in the 294 Vietnamese was se(357,385), whereas no CNV was detected. Two novel SNPs, 818C>A (Thr273Asn) and 853G>A (Ala285Thr), distributed at low frequency, were shown to remarkably affect the enzyme activity. CONCLUSION The allelic polymorphism of FUT2 in Vietnamese is similar to that of other East and Southeast Asian populations. This result may reflect the history and gene flow of this population. In addition, HRM analysis seems to be a simple and effective method for screening rare SNPs of FUT2 in a large number of samples. [Correction statement added after online publication 21-Dec-2011: Thr273Ala has been updated to Thr273Asn throughout.]
Collapse
Affiliation(s)
- Mikiko Soejima
- Department of Forensic Medicine and Human Genetics, Kurume University School of Medicine, Kurume, Japan
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
34
|
Abstract
Large numbers of environmental antigens, including commensal bacteria and food-derived antigens, constitutively interact with the epithelial layer of the gastrointestinal (GI) tract. Commensal bacteria peacefully cohabit with the host GI tract and exert multiple beneficial or destructive effects on their host. Intestinal epithelial cells (IECs) constitute the first physical and immunological protective wall against invasive pathogens and a cohabitation niche for commensal bacteria. As the physiological homeostasis of IECs is maintained by multiple biological processes such as apoptosis, autophagy, and the handling of endoplasmic reticulum stress, the aberrant kinetics of these biological events, which have genetic and environmental causes, leads to the development of host intestinal pathogenesis such as inflammatory bowel disease. In addition, IECs recognize and interact with commensal bacteria and give instructions to mucosal immune cells to initiate an immunological balance between active and quiescent conditions, eventually establishing intestinal homeostasis. The mucosal immune system regulates the homeostasis of gut microbiota by producing immunological molecules such as secretory immunoglobulin A, the production of which is mediated by IECs. IECs therefore play a central role in the creation and maintenance of a physiologically and immunologically stable intestinal environment.
Collapse
Affiliation(s)
- Yoshiyuki Goto
- Division of Mucosal Immunology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | | |
Collapse
|
35
|
Nyström K, Le Gall-Reculé G, Grassi P, Abrantes J, Ruvoën-Clouet N, Le Moullac-Vaidye B, Lopes AM, Esteves PJ, Strive T, Marchandeau S, Dell A, Haslam SM, Le Pendu J. Histo-blood group antigens act as attachment factors of rabbit hemorrhagic disease virus infection in a virus strain-dependent manner. PLoS Pathog 2011; 7:e1002188. [PMID: 21901093 PMCID: PMC3161982 DOI: 10.1371/journal.ppat.1002188] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2011] [Accepted: 06/13/2011] [Indexed: 12/20/2022] Open
Abstract
Rabbit Hemorrhagic disease virus (RHDV), a calicivirus of the Lagovirus genus, and responsible for rabbit hemorrhagic disease (RHD), kills rabbits between 48 to 72 hours post infection with mortality rates as high as 50–90%. Caliciviruses, including noroviruses and RHDV, have been shown to bind histo-blood group antigens (HBGA) and human non-secretor individuals lacking ABH antigens in epithelia have been found to be resistant to norovirus infection. RHDV virus-like particles have previously been shown to bind the H type 2 and A antigens. In this study we present a comprehensive assessment of the strain-specific binding patterns of different RHDV isolates to HBGAs. We characterized the HBGA expression in the duodenum of wild and domestic rabbits by mass spectrometry and relative quantification of A, B and H type 2 expression. A detailed binding analysis of a range of RHDV strains, to synthetic sugars and human red blood cells, as well as to rabbit duodenum, a likely gastrointestinal site for viral entrance was performed. Enzymatic cleavage of HBGA epitopes confirmed binding specificity. Binding was observed to blood group B, A and H type 2 epitopes in a strain-dependent manner with slight differences in specificity for A, B or H epitopes allowing RHDV strains to preferentially recognize different subgroups of animals. Strains related to the earliest described RHDV outbreak were not able to bind A, whereas all other genotypes have acquired A binding. In an experimental infection study, rabbits lacking the correct HBGA ligands were resistant to lethal RHDV infection at low challenge doses. Similarly, survivors of outbreaks in wild populations showed increased frequency of weak binding phenotypes, indicating selection for host resistance depending on the strain circulating in the population. HBGAs thus act as attachment factors facilitating infection, while their polymorphism of expression could contribute to generate genetic resistance to RHDV at the population level. Rabbit hemorrhagic disease virus (RHDV), detected as late as 1984, has spread to large parts of the world, threatening rabbit populations and other species dependent on rabbits in many European countries. Mortality has been shown to be as high as 90% and rabbits are killed 48 to 72 hours after infection. Related viruses called noroviruses, infect humans in a manner dependent on the expression of histo-blood group antigens (HBGAs), which are not only expressed on red blood cells, but also on epithelial cells, in saliva and on mucins of the intestinal tract. RHDV also binds to HBGA and in this report we characterize binding of strains of all genetic groups of RHDV to different HBGAs. We also demonstrate HBGAs to function as attachment factors in a challenge experiment. As polymorphisms of genes involved in HBGA synthesis divide the rabbit population into different subgroups, we find selection of low-binding subgroups of wild rabbits in populations recovering from devastating outbreaks of RHDV. This is the first demonstration of differential HBGA specificities of RHDV strains, description of function in infection and demonstration of host selection due to RHDV infection based on HBGA phenotype.
Collapse
Affiliation(s)
| | - Ghislaine Le Gall-Reculé
- Anses, Laboratoire de Ploufragan/Plouzané, Unité de Virologie, Immunologie, Parasitologie Aviaires et Cunicoles, Ploufragan, France
| | - Paola Grassi
- Division of Molecular Biosciences, Faculty of Natural Sciences, Imperial College London, London, United Kingdom
| | - Joana Abrantes
- INSERM, U892, Université de Nantes, Nantes, France
- CIBIO, Centro de Investigacao em Biodiversidade e Recursos Geneticos, Campus Agrario de Vairao, Vairao, Portugal
| | | | | | - Ana M. Lopes
- CIBIO, Centro de Investigacao em Biodiversidade e Recursos Geneticos, Campus Agrario de Vairao, Vairao, Portugal
| | - Pedro J. Esteves
- CIBIO, Centro de Investigacao em Biodiversidade e Recursos Geneticos, Campus Agrario de Vairao, Vairao, Portugal
- CITS, Centro de Investigacao em Tecnologias de Saude, CESPU, Gandra, Portugal
| | - Tanja Strive
- Commonwealth Scientific and Industrial Research Organisation, Canberra, Australian Capital Territory, Australia
- Invasive Animals Cooperative Research Centre, Canberra, Australia
| | - Stéphane Marchandeau
- Office National de la Chasse et de la Faune Sauvage, Direction des Etudes et de la Recherche, Nantes, France
| | - Anne Dell
- Division of Molecular Biosciences, Faculty of Natural Sciences, Imperial College London, London, United Kingdom
| | - Stuart M. Haslam
- Division of Molecular Biosciences, Faculty of Natural Sciences, Imperial College London, London, United Kingdom
| | | |
Collapse
|
36
|
Soejima M, Koda Y. TaqMan-based real-time polymerase chain reaction for detection of FUT2 copy number variations: identification of novel Alu-mediated deletion. Transfusion 2011; 51:762-9. [PMID: 20880207 DOI: 10.1111/j.1537-2995.2010.02895.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
BACKGROUND The human FUT2 locus, which encodes a secretor-type α(1,2)fucosyltransferase, is known to be highly polymorphic. In addition to many single-nucleotide polymorphisms, three recombination alleles with a deletion of complete or partial FUT2 coding region have been reported. STUDY DESIGN AND METHODS To detect copy number variations (CNVs) of the FUT2 gene including three recombinant alleles by a high-throughput system, we developed a triplex TaqMan real-time polymerase chain reaction (PCR) method. The relative number of copies of two regions of the FUT2 gene, the 5' flanking (FUT2-5') and FUT2-promoter (Prom) regions, were determined by comparing the number of threshold cycles (Ct) to those of the albumin gene (ALB) as the internal control (ΔCt). RESULTS The mean 2(-ΔΔCt) values (FUT2-5'/ALB or Prom/ALB) obtained from 237 samples with known FUT2 copy numbers clearly differentiated two nonoverlapping intervals that corresponded to the one-copy-number samples ranging from 0.42 to 0.59 and two-copy-number samples ranging from 0.81 to 1.19; no FUT2-5' signal for recombination alleles was detected in homozygotes. Using this assay, we detected an individual in a Chinese population with a loss of one copy of the FUT2-5' region resulting from a novel Alu-mediated FUT2 deletion (approx. 4 kb). CONCLUSIONS The TaqMan real-time PCR method was able to detect the number of copies of FUT2 and distinguish different kinds of known CNVs. This system is robust, fast, and suitable for high-throughput analysis.
Collapse
Affiliation(s)
- Mikiko Soejima
- Department of Forensic Medicine and Human Genetics, Kurume University School of Medicine, Kurume, Japan
| | | |
Collapse
|
37
|
Abstract
Detecting whether and how natural selection has targeted regions of the human genome represents a complementary strategy for identifying functionally important loci and variants involved in disease resistance and adaptation to the environment. In contrast with most complex diseases or traits, the genetic architecture of most Mendelian traits is relatively well established. Most mutations associated with Mendelian disease-related traits are highly penetrant and kept at low population frequencies because of the effects of purifying selection. However, this is not always the case. Here, we review several examples of Mendelian mutations-associated with various disease conditions or other traits of anthropological interest-that have increased in frequency in the human population as a result of past positive selection. These examples clearly illustrate the value of a population genetics approach to unravel the biological mechanisms that have been central to our past and present survival against the selective pressures imposed by diseases and other environmental factors.
Collapse
Affiliation(s)
- Lluis Quintana-Murci
- Institut Pasteur, Human Evolutionary Genetics, Department of Genomes and Genetics, Paris, France.
| | | |
Collapse
|
38
|
Teresa DB, Santos RA, Takahashi CS, Carrara HH, Moreira HW, Mattos LC, Lia-Neto N, Cunha LA, Bassi CL, Soares EG, Donadi EA, Mello ER, Soares CP. Polymorphisms of Lewis and Secretor genes are related to breast cancer and metastasis in axillary lymph nodes. Tumour Biol 2010; 31:401-9. [PMID: 20514537 DOI: 10.1007/s13277-010-0048-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2009] [Accepted: 04/29/2010] [Indexed: 12/14/2022] Open
Abstract
ABH and Lewis antigen expression has been associated with cancer development and prognosis, tumor differentiation, and metastasis. Considering that invasive ductal breast carcinoma (IDC) presents multiple molecular alterations, the aim of the present study was to determine whether the polymorphism of ABO, Lewis, and Secretor genes, as well as ABO phenotyping, could be associated with tumor differentiation and lymph nodes metastasis. Seventy-six women with IDC and 78 healthy female blood donors were submitted to ABO phenotyping/genotyping and Lewis and Secretor genotyping. Phenotyping was performed by hemagglutination and genotyping by the polymerase chain reaction with sequence-specific primers. ABO, Lewis, and Secretor genes were classified by individual single nucleotide polymorphism at sites 59, 1067, 202, and 314 of the Lewis gene, 428 of the Secretor gene, and 261 (O1 allele), 526 (O2 and B allele), and 703 (B allele). No association was found between breast cancer and ABO antigen expression (P = 0.9323) or genotype (P = 0.9356). Lewis-negative genotype was associated with IDC (P = 0.0126) but not with anatomoclinical parameters. Nonsecretor genotype was associated with axillary lymph node metastasis (P = 0.0149). In conclusion, Lewis and Secretor genotyping could be useful to predict respectively breast cancer susceptibility and axillary lymph nodes metastasis.
Collapse
Affiliation(s)
- Debora Barreto Teresa
- School of Pharmaceutical Sciences, UNESP, University of São Paulo State, Rua Expedicionários do Brasil, 1621, 14 801 902, Araraquara, Sao Paulo, Brazil
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
39
|
Silva LM, Carvalho AS, Guillon P, Seixas S, Azevedo M, Almeida R, Ruvoën-Clouet N, Reis CA, Le Pendu J, Rocha J, David L. Infection-associated FUT2 (Fucosyltransferase 2) genetic variation and impact on functionality assessed by in vivo studies. Glycoconj J 2010; 27:61-8. [PMID: 19757028 DOI: 10.1007/s10719-009-9255-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2009] [Revised: 08/10/2009] [Accepted: 08/11/2009] [Indexed: 10/20/2022]
Abstract
The secretor (Se)/nonsecretor (se) histo-blood group variation depends on the action of the FUT2 enzyme and has major implications for human susceptibility to infections. To characterize the functionality of FUT2 variants, we assessed the correlation between saliva phenotypes and sequence variation at the FUT2 gene in sixty seven individuals from northern Portugal. While most non-secretor haplotypes were found to carry the 428G > A nonsense mutation in association with a 739G > A missense substitution, we have also identified a recombinant haplotype carrying the 739*A allele together with the efficient 428*G variant in individuals with the Se phenotype. This finding suggested, in contrast to previous results, that the 739*A allele encodes an efficient Se allele. To test this hypothesis we evaluated the in vivo enzyme activity of full coding expression constructs in transient transfection of CHO-K1 cells using FACS (fluorescence-activated cell sorting) analysis and expression of type 2 and type 3 chain H structures as read out. We detected FUT2 activity for the 739*A expression construct, demonstrating that the 739G > A substitution is indeed not inactivating. In accordance with the hypothesis that FUT2 is under long standing balancing selection, we estimated that the time depth of FUT2 global genetic variation is as old as 3 million years. Age estimates of specific variants suggest that the 428G > A mutation occurred at least 1.87 million years ago while the 739G > A substitution is about 816,000 years old. The 385A > T missense mutation underlying the non-secretor phenotype in East Asians appears to be more recent and is likely to have occurred about 256,000 years ago.
Collapse
Affiliation(s)
- Lara M Silva
- IPATIMUP, Institute of Molecular Pathology and Immunology, University of Porto, Rua Dr. Roberto Frias s/n, 4200-465, Porto, Portugal
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
40
|
Ferrer-Admetlla A, Sikora M, Laayouni H, Esteve A, Roubinet F, Blancher A, Calafell F, Bertranpetit J, Casals F. A natural history of FUT2 polymorphism in humans. Mol Biol Evol 2009; 26:1993-2003. [PMID: 19487333 DOI: 10.1093/molbev/msp108] [Citation(s) in RCA: 170] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Because pathogens are powerful selective agents, host-cell surface molecules used by pathogens as identification signals can reveal the signature of selection. Most of them are oligosaccharides, synthesized by glycosyltransferases. One known example is balancing selection shaping ABO evolution as a consequence of both, A and B antigens being recognized as receptors by some pathogens, and anti-A and/or anti-B natural antibodies produced by hosts conferring protection against the numerous infectious agents expressing A and B motifs. These antigens can also be found in tissues other than blood if there is activity of another enzyme, FUT2, a fucosyltransferase responsible for ABO biosynthesis in body fluids. Homozygotes for null variants at this locus present the nonsecretor phenotype (se), because they cannot express ABO antigens in secretions. Multiple independent mutations have been shown to be responsible for the nonsecretor phenotype, which is coexisting with the secretor phenotype in most populations. In this study, we have resequenced the coding region of FUT2 in 732 individuals from 39 worldwide human populations. We report a complex pattern of natural selection acting on the gene. Although frequencies of secretor and nonsecretor phenotypes are similar in different populations, the point mutations at the base of the phenotypes are different, with some variants showing a long history of balancing selection among Eurasian and African populations, and one recent variant showing a fast spread in East Asia, likely due to positive selection. Thus, a convergent phenotype composition has been achieved through different mutations with different evolutionary histories.
Collapse
Affiliation(s)
- Anna Ferrer-Admetlla
- Institut de Biologia Evolutiva (CSIC-UPF), CEXS-UPF-PRBB, Barcelona, Catalonia, Spain
| | | | | | | | | | | | | | | | | |
Collapse
|
41
|
Abrantes J, Posada D, Guillon P, Esteves PJ, Le Pendu J. Widespread gene conversion of alpha-2-fucosyltransferase genes in mammals. J Mol Evol 2009; 69:22-31. [PMID: 19533213 PMCID: PMC2706377 DOI: 10.1007/s00239-009-9239-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2008] [Revised: 03/13/2009] [Accepted: 04/15/2009] [Indexed: 11/25/2022]
Abstract
The alpha-2-fucosyltransferases (alpha2FTs) are enzymes involved in the biosynthesis of alpha2fucosylated glycan structures. In mammalian genomes, there are three alpha2FT genes located in tandem-FUT1, FUT2, and Sec1-each contained within a single exon. It has been suggested that these genes originated from two successive duplications, with FUT1 being generated first and FUT2 and Sec1 second. Despite gene conversion being considered the main mechanism of concerted evolution in gene families, previous studies of primates alpha2FTs failed to detect it, although the occurrence of gene conversion between FUT2 and Sec1 was recently reported in a human allele. The primary aim of our work was to initiate a broader study on the molecular evolution of mammalian alpha2FTs. Sequence comparison leads us to confirm that the three genes appeared by two rounds of duplication. In addition, we were able to detect multiple gene-conversion events at the base of primates and within several nonprimate species involving FUT2 and Sec1. Gene conversion involving FUT1 and either FUT2 or Sec1 was also detected in rabbit. The extent of gene conversion between the alpha2FTs genes appears to be species-specific, possibly related to functional differentiation of these genes. With the exception of rabbits, gene conversion was not observed in the region coding the C-terminal part of the catalytic domain. In this region, the number of amino acids that are identical between FUT1 and FUT2, but different in Sec1, is higher than in other parts of the protein. The biologic meaning of this observation may be related to functional constraints.
Collapse
Affiliation(s)
- Joana Abrantes
- CIBIO-UP, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Rua Padre Armando Quintas, Vairao, Portugal
- INSERM, U892, Institut de Biologie, Université de Nantes, 9 Quai Moncousu, 44093 Nantes, Cedex 01, France
- Departamento de Zoologia e Antropologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal
| | - David Posada
- Departamento de Bioquímica, Genética e Inmunología, Facultad de Biología, Campus Lagoas-Marcosende, Universidad de Vigo, Vigo, 36310 Spain
| | - Patrice Guillon
- INSERM, U892, Institut de Biologie, Université de Nantes, 9 Quai Moncousu, 44093 Nantes, Cedex 01, France
| | - Pedro J. Esteves
- CIBIO-UP, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Rua Padre Armando Quintas, Vairao, Portugal
- CITS, Centro de Investigação em Tecnologias da Saúde, IPSN, CESPU, Gandra, Portugal
| | - Jacques Le Pendu
- INSERM, U892, Institut de Biologie, Université de Nantes, 9 Quai Moncousu, 44093 Nantes, Cedex 01, France
| |
Collapse
|
42
|
Fumagalli M, Cagliani R, Pozzoli U, Riva S, Comi GP, Menozzi G, Bresolin N, Sironi M. Widespread balancing selection and pathogen-driven selection at blood group antigen genes. Genes Dev 2009; 19:199-212. [PMID: 18997004 PMCID: PMC2652214 DOI: 10.1101/gr.082768.108] [Citation(s) in RCA: 116] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2008] [Accepted: 11/04/2008] [Indexed: 12/31/2022]
Abstract
Historically, allelic variations in blood group antigen (BGA) genes have been regarded as possible susceptibility factors for infectious diseases. Since host-pathogen interactions are major determinants in evolution, BGAs can be thought of as selection targets. In order to verify this hypothesis, we obtained an estimate of pathogen richness for geographic locations corresponding to 52 populations distributed worldwide; after correction for multiple tests and for variables different from selective forces, significant correlations with pathogen richness were obtained for multiple variants at 11 BGA loci out of 26. In line with this finding, we demonstrate that three BGA genes, namely CD55, CD151, and SLC14A1, have been subjected to balancing selection, a process, rare outside MHC genes, which maintains variability at a locus. Moreover, we identified a gene region immediately upstream the transcription start site of FUT2 which has undergone non-neutral evolution independently from the coding region. Finally, in the case of BSG, we describe the presence of a highly divergent haplotype clade and the possible reasons for its maintenance, including frequency-dependent balancing selection, are discussed. These data indicate that BGAs have been playing a central role in the host-pathogen arms race during human evolutionary history and no other gene category shows similar levels of widespread selection, with the only exception of loci involved in antigen recognition.
Collapse
Affiliation(s)
- Matteo Fumagalli
- Scientific Institute IRCCS E. Medea, Bioinformatic Lab, 23842 Bosisio Parini (LC), Italy
- Bioengineering Department, Politecnico di Milano, 20133 Milan, Italy
| | - Rachele Cagliani
- Scientific Institute IRCCS E. Medea, Bioinformatic Lab, 23842 Bosisio Parini (LC), Italy
| | - Uberto Pozzoli
- Scientific Institute IRCCS E. Medea, Bioinformatic Lab, 23842 Bosisio Parini (LC), Italy
| | - Stefania Riva
- Scientific Institute IRCCS E. Medea, Bioinformatic Lab, 23842 Bosisio Parini (LC), Italy
| | - Giacomo P. Comi
- Dino Ferrari Centre, Department of Neurological Sciences, University of Milan, IRCCS Ospedale Maggiore Policlinico, Mangiagalli and Regina Elena Foundation, 20100 Milan, Italy
| | - Giorgia Menozzi
- Scientific Institute IRCCS E. Medea, Bioinformatic Lab, 23842 Bosisio Parini (LC), Italy
| | - Nereo Bresolin
- Scientific Institute IRCCS E. Medea, Bioinformatic Lab, 23842 Bosisio Parini (LC), Italy
- Dino Ferrari Centre, Department of Neurological Sciences, University of Milan, IRCCS Ospedale Maggiore Policlinico, Mangiagalli and Regina Elena Foundation, 20100 Milan, Italy
| | - Manuela Sironi
- Scientific Institute IRCCS E. Medea, Bioinformatic Lab, 23842 Bosisio Parini (LC), Italy
| |
Collapse
|
43
|
Hazra A, Kraft P, Selhub J, Giovannucci EL, Thomas G, Hoover RN, Chanock SJ, Hunter DJ. Common variants of FUT2 are associated with plasma vitamin B12 levels. Nat Genet 2008; 40:1160-2. [PMID: 18776911 PMCID: PMC2673801 DOI: 10.1038/ng.210] [Citation(s) in RCA: 120] [Impact Index Per Article: 7.5] [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: 03/18/2008] [Accepted: 06/26/2008] [Indexed: 02/06/2023]
Abstract
We identified a strong association (P = 5.36 x 10(-17)) between rs492602 in FUT2 and plasma vitamin B(12) levels in a genome-wide scan (n = 1,658) and an independent replication sample (n = 1,059) from the Nurses' Health Study. Women homozygous for the rs492602[G] allele had higher B(12) levels. This allele is in strong linkage disequilibrium with the FUT2 nonsecretor variant encoding W143X, suggesting a plausible mechanism for altered B(12) absorption and plasma levels.
Collapse
Affiliation(s)
- Aditi Hazra
- Program in Molecular and Genetic Epidemiology, Department of Epidemiology, Harvard School of Public Health, 677 Huntington Avenue, Boston, MA 02115, USA
- Channing Laboratory, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, 181 Longwood Avenue, Boston, MA 02115, USA
| | - Peter Kraft
- Program in Molecular and Genetic Epidemiology, Department of Epidemiology, Harvard School of Public Health, 677 Huntington Avenue, Boston, MA 02115, USA
| | - Jacob Selhub
- Vitamin Metabolism and Aging Laboratory, Jean Mayer US Department of Agriculture Human Nutrition Research Center on Aging, Tufts University, Boston, MA 02111, USA
| | - Edward L. Giovannucci
- Channing Laboratory, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, 181 Longwood Avenue, Boston, MA 02115, USA
- Department of Nutrition, Harvard School of Public Health, 677 Huntington Avenue, Boston, MA 02115, USA
| | - Gilles Thomas
- Division of Cancer Epidemiology and Genetics, National Cancer Institute(NCI), US National Institutes of Health (NIH), Department of Health and Human Services (DHHS), Bethesda, Maryland 20892, USA
| | - Robert N. Hoover
- Division of Cancer Epidemiology and Genetics, National Cancer Institute(NCI), US National Institutes of Health (NIH), Department of Health and Human Services (DHHS), Bethesda, Maryland 20892, USA
| | - Stephen J. Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute(NCI), US National Institutes of Health (NIH), Department of Health and Human Services (DHHS), Bethesda, Maryland 20892, USA
| | - David J. Hunter
- Program in Molecular and Genetic Epidemiology, Department of Epidemiology, Harvard School of Public Health, 677 Huntington Avenue, Boston, MA 02115, USA
- Channing Laboratory, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, 181 Longwood Avenue, Boston, MA 02115, USA
- Department of Nutrition, Harvard School of Public Health, 677 Huntington Avenue, Boston, MA 02115, USA
- Division of Cancer Epidemiology and Genetics, National Cancer Institute(NCI), US National Institutes of Health (NIH), Department of Health and Human Services (DHHS), Bethesda, Maryland 20892, USA
| |
Collapse
|
44
|
Abstract
BACKGROUND Many single-nucleotide polymorphisms (SNPs) have been identified in the coding region of the FUT2 locus, which encodes secretor type alpha(1,2)fucosyltransferase. These SNPs are highly population-specific. STUDY DESIGN AND METHODS The 1121-bp polymerase chain reaction (PCR) product containing the whole FUT2 coding region in three human populations, Ovambos (n = 74), Turks (n = 70), and Mongolians (n = 118), was sequenced. The haplotypes consisting of novel SNPs were determined by sequencing cloned inserts, and the haplotypes consisting of already reported SNPs were inferred by free computer software (PHASE). The functional significance of novel SNPs by transient expression study was also examined. RESULTS Twenty-four SNPs were found including seven novel SNPs (i.e., 4G > A, 244G > A, 442C > A, 489G > A, 569G > A, 665G > A, and 950C > T). A transient expression study suggested that the 244G > A, 569G > A, and 950C > T SNPs are enzyme-inactivating mutations. CONCLUSION This study identified 24 SNPs in the FUT2 gene, of which 7 were novel. The frequencies of alleles and genotypes were determined in Ovambos, Turks, and Mongolians. The allelic composition of each population was similar to those of geographically closer populations.
Collapse
Affiliation(s)
- Mikiko Soejima
- The Department of Forensic Medicine and Human Genetics, Kurume University School of Medicine, Kurume, Fukuoka, Japan
| | | | | | | | | |
Collapse
|
45
|
Abstract
BACKGROUND Many single-nucleotide polymorphisms have been identified in the coding region of the FUT2 locus, which encodes secretor type alpha(1,2)fucosyltransferase. In addition, three recombination alleles have been reported. Of these recombination alleles, a fusion gene generated by an unequal crossing over between Sec1, a pseudogene that locates 23 kb upstream to and has high sequence homology with FUT2 and FUT2, was identified as a Japanese-specific nonsecretor allele (se(fus)). STUDY DESIGN AND METHODS During the screening of the se(fus) in Mongolians (n = 118), a hybrid allele of Sec1-FUT2-Sec1 was found. RESULTS The DNA sequence suggested that the Sec1-FUT2-Sec1 allele contains a 275-bp sequence (between positions 259 and 533) that is identical to the FUT2 sequence including a 54-bp FUT2-specific region (between positions 417 and 470) and that might have been generated by an interlocus gene conversion. CONCLUSION Because the recombination region of se(fus) and the upstream recombination region of Sec1-FUT2-Sec1 are almost identical, this sequence stretch is likely to be the breakpoint for different kinds of recombinations that occur in this family of genes.
Collapse
Affiliation(s)
- Mikiko Soejima
- Department of Forensic Medicine and Human Genetics, Kurume University School of Medicine, Kurume, Japan
| | | | | | | |
Collapse
|
46
|
Soejima M, Koda Y. Distinct single nucleotide polymorphism pattern at the FUT2 promoter among human populations. Ann Hematol 2008; 87:19-25. [PMID: 17805536 DOI: 10.1007/s00277-007-0362-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2007] [Accepted: 07/27/2007] [Indexed: 11/29/2022]
Abstract
Many single nucleotide polymorphisms (SNPs) have been identified in the coding region of the FUT2 locus, which encodes secretor type alpha(1,2)fucosyltransferase. In this study, we analyzed the sequence variations in the proximal promoter region of FUT2 in several human populations. In African populations, we found two SNPs with intermediate frequency that affected the promoter activity in vitro with a cell type-specific pattern. On the other hand, these two African SNPs were rarely detected outside Africa. Linkage disequilibria (LD) were observed between some haplotypes of the promoter and coding regions, although no characteristic promoter haplotype was linked with the se(428) allele of the coding region, which is estimated to be old. The present results suggest that the pattern of variation in the proximal promoter differs between Africans and non-Africans.
Collapse
Affiliation(s)
- Mikiko Soejima
- Department of Forensic Medicine and Human Genetics, Kurume University School of Medicine, Kurume, 830-0011, Japan
| | | |
Collapse
|
47
|
Soejima M, Pang H, Koda Y. Genetic variation of FUT2 in a Ghanaian population: identification of four novel mutations and inference of balancing selection. Ann Hematol 2007; 86:199-204. [PMID: 17089126 DOI: 10.1007/s00277-006-0203-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2006] [Accepted: 09/11/2006] [Indexed: 11/24/2022]
Abstract
The FUT2 is rich in polymorphisms that show population-specific patterns in its coding sequence. In this study, we found four novel substitutions in 121 Ghanaian samples. In addition, statistical tests considering population expansion scenarios suggested that balancing selection might be responsible for the genetic diversity of FUT2 in this population.
Collapse
Affiliation(s)
- Mikiko Soejima
- Department of Forensic Medicine and Human Genetics, Kurume University School of Medicine, Kurume, Japan
| | | | | |
Collapse
|
48
|
Abstract
Analyses of recently acquired genomic sequence data are leading to important insights into the early evolution of anatomically modern humans, as well as into the more recent demographic processes that accompanied the global radiation of Homo sapiens. Some of the new results contradict early, but still influential, conclusions that were based on analyses of gene trees from mitochondrial DNA and Y-chromosome sequences. In this review, we discuss the different genetic and statistical methods that are available for studying human population history, and identify the most plausible models of human evolution that can accommodate the contrasting patterns observed at different loci throughout the genome.
Collapse
Affiliation(s)
- Daniel Garrigan
- Division of Biotechnology, University of Arizona, Tucson, AZ 85721, USA
| | | |
Collapse
|
49
|
Abstract
Noroviruses have emerged as a major cause of acute gastroenteritis in humans of all ages. Despite high infectivity of the virus and lack of long-term immunity, volunteer and authentic studies has suggested the existence of inherited protective factors. Recent studies have shown that histo-blood group antigens (HBGAs) and in particular secretor status controlled by the α1,2fucosyltransferase FUT2 gene determine susceptibility to norovirus infections, with nonsecretors (FUT2−/−), representing 20% of Europeans, being highly resistant to symptomatic infections with major strains of norovirus. Moreover, the capsid protein from distinct strains shows different HBGA specificities, suggesting a host–pathogen co-evolution driven by carbohydrate–protein interactions.
Collapse
Affiliation(s)
- Jacques Le Pendu
- Inserm U601, University of Nantes, Institute of Biology, 9 Quai Moncousu, 44093 Nantes, Cedex 01, France.
| | | | | | | |
Collapse
|
50
|
Soejima M, Tachida H, Tsuneoka M, Takenaka O, Kimura H, Koda Y. Nucleotide Sequence Analyses of Human Complement 6 (C6) Gene Suggest Balancing Selection. Ann Hum Genet 2005. [DOI: 10.1046/j.1469-1809.2005.00165.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|