FUT2 Variants Confer Susceptibility to Familial Otitis Media

• Published in: American journal of human genetics Vol. 103; no. 5; pp. 679 - 690
• Main Authors: Santos-Cortez, Regie Lyn P., Chiong, Charlotte M., Frank, Daniel N., Ryan, Allen F., Giese, Arnaud P.J., Bootpetch Roberts, Tori, Daly, Kathleen A., Steritz, Matthew J., Szeremeta, Wasyl, Pedro, Melquiadesa, Pine, Harold, Yarza, Talitha Karisse L., Scholes, Melissa A., Llanes, Erasmo Gonzalo d.V., Yousaf, Saira, Friedman, Norman, Tantoco, Ma. Leah C., Wine, Todd M., Labra, Patrick John, Benoit, Jeanne, Ruiz, Amanda G., de la Cruz, Rhodieleen Anne R., Greenlee, Christopher, Yousaf, Ayesha, Cardwell, Jonathan, Nonato, Rachelle Marie A., Ray, Dylan, Ong, Kimberly Mae C., So, Edward, Robertson, Charles E., Dinwiddie, Jordyn, Lagrana-Villagracia, Sheryl Mae, Gubbels, Samuel P., Shaikh, Rehan S., Cass, Stephen P., Einarsdottir, Elisabet, Lee, Nanette R., Schwartz, David A., Gloria-Cruz, Teresa Luisa I., Bamshad, Michael J., Yang, Ivana V., Kere, Juha, Abes, Generoso T., Prager, Jeremy D., Riazuddin, Saima, Chan, Abner L., Yoon, Patricia J., Nickerson, Deborah A., Cutiongco-de la Paz, Eva Maria, Streubel, Sven-Olrik, Reyes-Quintos, Maria Rina T., Jenkins, Herman A., Mattila, Petri, Chan, Kenny H., Mohlke, Karen L., Leal, Suzanne M., Hafrén, Lena, Chonmaitree, Tasnee, Sale, Michele M., Ahmed, Zubair M.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 01.11.2018; Elsevier
• Subjects: 16S rRNA sequencing; A antigen; Animals; Cell Line; Chlorocebus aethiops; COS Cells; Ear, Middle - microbiology; Exome - genetics; Female; fucosyltransferase; Fucosyltransferases - genetics; FUT2; Galactoside 2-alpha-L-fucosyltransferase; Genetic Variation - genetics; HEK293 Cells; Humans; Male; Mice; Mice, Inbred C57BL; microbiome; Microbiota - physiology; middle ear infection; otitis media; Otitis Media - genetics; Otitis Media - microbiology; Pedigree; TDT; transient expression; transmission disequilibrium test; transient expression; middle ear infection; A antigen; otitis media; TDT; 16S rRNA sequencing; fucosyltransferase; transmission disequilibrium test; FUT2; microbiome
• ISSN: 0002-9297; 1537-6605; 1537-6605
• DOI: 10.1016/j.ajhg.2018.09.010

Non-secretor status due to homozygosity for the common FUT2 variant c.461G>A (p.Trp154∗) is associated with either risk for autoimmune diseases or protection against viral diarrhea and HIV. We determined the role of FUT2 in otitis media susceptibility by obtaining DNA samples from 609 multi-ethnic families and simplex case subjects with otitis media. Exome and Sanger sequencing, linkage analysis, and Fisher exact and transmission disequilibrium tests (TDT) were performed. The common FUT2 c.604C>T (p.Arg202∗) variant co-segregates with otitis media in a Filipino pedigree (LOD = 4.0). Additionally, a rare variant, c.412C>T (p.Arg138Cys), is associated with recurrent/chronic otitis media in European-American children (p = 1.2 × 10−5) and US trios (TDT p = 0.01). The c.461G>A (p.Trp154∗) variant was also over-transmitted in US trios (TDT p = 0.01) and was associated with shifts in middle ear microbiota composition (PERMANOVA p < 10−7) and increased biodiversity. When all missense and nonsense variants identified in multi-ethnic US trios with CADD > 20 were combined, FUT2 variants were over-transmitted in trios (TDT p = 0.001). Fut2 is transiently upregulated in mouse middle ear after inoculation with non-typeable Haemophilus influenzae. Four FUT2 variants—namely p.Ala104Val, p.Arg138Cys, p.Trp154∗, and p.Arg202∗—reduced A antigen in mutant-transfected COS-7 cells, while the nonsense variants also reduced FUT2 protein levels. Common and rare FUT2 variants confer susceptibility to otitis media, likely by modifying the middle ear microbiome through regulation of A antigen levels in epithelial cells. Our families demonstrate marked intra-familial genetic heterogeneity, suggesting that multiple combinations of common and rare variants plus environmental factors influence the individual otitis media phenotype as a complex trait.