Ting-Fung Chan1, Kun-Mei Ji2, Aldrin Kay-Yuen Yim3, Xiao-Yu Liu4, Jun-Wei Zhou5, Rui-Qi Li4, Kevin Yi Yang6, Jing Li7, Meng Li4, Patrick Tik-Wan Law1, Yu-Lan Wu4, Ze-Lang Cai4, Hao Qin3, Ying Bao4, Ross Ka-Kit Leung6, Patrick Kwok-Shing Ng5, Ju Zou4, Xiao-Jun Zhong4, Pi-Xin Ran7, Nan-Shan Zhong8, Zhi-Gang Liu9, Stephen Kwok-Wing Tsui10. 1. School of Life Sciences, Chinese University of Hong Kong, Hong Kong, China. 2. State Key Laboratory of Respiratory Disease for Allergy at Shenzhen University, Shenzhen, China. 3. School of Life Sciences, Chinese University of Hong Kong, Hong Kong, China; Hong Kong Bioinformatics Centre, Chinese University of Hong Kong, Hong Kong, China. 4. Shenzhen Key Laboratory of Allergy and Immunology, School of Medicine, Shenzhen University, Shenzhen, China. 5. School of Biomedical Sciences, Chinese University of Hong Kong, Hong Kong, China. 6. Hong Kong Bioinformatics Centre, Chinese University of Hong Kong, Hong Kong, China; School of Biomedical Sciences, Chinese University of Hong Kong, Hong Kong, China. 7. State Key Laboratory of Respiratory Disease, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China. 8. State Key Laboratory of Respiratory Disease, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China. Electronic address: nanshan@vip.163.com. 9. State Key Laboratory of Respiratory Disease for Allergy at Shenzhen University, Shenzhen, China; Shenzhen Key Laboratory of Allergy and Immunology, School of Medicine, Shenzhen University, Shenzhen, China. Electronic address: lzg@szu.edu.cn. 10. Hong Kong Bioinformatics Centre, Chinese University of Hong Kong, Hong Kong, China; School of Biomedical Sciences, Chinese University of Hong Kong, Hong Kong, China. Electronic address: kwtsui@cuhk.edu.hk.
Abstract
BACKGROUND: A sequenced house dust mite (HDM) genome would advance our understanding of HDM allergens, a common cause of human allergies. OBJECTIVE: We sought to produce an annotated Dermatophagoides farinae draft genome and develop a combined genomic-transcriptomic-proteomic approach for elucidation of HDM allergens. METHODS: A D farinae draft genome and transcriptome were assembled with high-throughput sequencing, accommodating microbiome sequences. The allergen gene structures were validated by means of Sanger sequencing. The mite's microbiome composition was determined, and the predominant genus was validated immunohistochemically. The allergenicity of a ubiquinol-cytochrome c reductase binding protein homologue was evaluated with immunoblotting, immunosorbent assays, and skin prick tests. RESULTS: The full gene structures of 20 canonical allergens and 7 noncanonical allergen homologues were produced. A novel major allergen, ubiquinol-cytochrome c reductase binding protein-like protein, was found and designated Der f 24. All 40 sera samples from patients with mite allergy had IgE antibodies against rDer f 24. Of 10 patients tested, 5 had positive skin reactions. The predominant bacterial genus among 100 identified species was Enterobacter (63.4%). An intron was found in the 13.8-kDa D farinae bacteriolytic enzyme gene, indicating that it is of HDM origin. The Kyoto Encyclopedia of Genes and Genomes pathway analysis revealed a phototransduction pathway in D farinae, as well as thiamine and amino acid synthesis pathways, which is suggestive of an endosymbiotic relationship between D farinae and its microbiome. CONCLUSION: An HDM genome draft produced from genomic, transcriptomic, and proteomic experiments revealed allergen genes and a diverse endosymbiotic microbiome, providing a tool for further identification and characterization of HDM allergens and development of diagnostics and immunotherapeutic vaccines.
BACKGROUND: A sequenced house dust mite (HDM) genome would advance our understanding of HDM allergens, a common cause of humanallergies. OBJECTIVE: We sought to produce an annotated Dermatophagoides farinae draft genome and develop a combined genomic-transcriptomic-proteomic approach for elucidation of HDM allergens. METHODS: A D farinae draft genome and transcriptome were assembled with high-throughput sequencing, accommodating microbiome sequences. The allergen gene structures were validated by means of Sanger sequencing. The mite's microbiome composition was determined, and the predominant genus was validated immunohistochemically. The allergenicity of a ubiquinol-cytochrome c reductase binding protein homologue was evaluated with immunoblotting, immunosorbent assays, and skin prick tests. RESULTS: The full gene structures of 20 canonical allergens and 7 noncanonical allergen homologues were produced. A novel major allergen, ubiquinol-cytochrome c reductase binding protein-like protein, was found and designated Der f 24. All 40 sera samples from patients with mite allergy had IgE antibodies against rDer f 24. Of 10 patients tested, 5 had positive skin reactions. The predominant bacterial genus among 100 identified species was Enterobacter (63.4%). An intron was found in the 13.8-kDa D farinae bacteriolytic enzyme gene, indicating that it is of HDM origin. The Kyoto Encyclopedia of Genes and Genomes pathway analysis revealed a phototransduction pathway in D farinae, as well as thiamine and amino acid synthesis pathways, which is suggestive of an endosymbiotic relationship between D farinae and its microbiome. CONCLUSION: An HDM genome draft produced from genomic, transcriptomic, and proteomic experiments revealed allergen genes and a diverse endosymbiotic microbiome, providing a tool for further identification and characterization of HDM allergens and development of diagnostics and immunotherapeutic vaccines.
Keywords:
Der f 24; Enterobacter species; House dust mite; allergen; genome; microbiome; proteome; transcriptome; ubiquinol-cytochrome c reductase binding protein
Authors: Wim Jonckheere; Wannes Dermauw; Vladimir Zhurov; Nicky Wybouw; Jan Van den Bulcke; Carlos A Villarroel; Robert Greenhalgh; Mike Grbić; Rob C Schuurink; Luc Tirry; Geert Baggerman; Richard M Clark; Merijn R Kant; Bartel Vanholme; Gerben Menschaert; Thomas Van Leeuwen Journal: Mol Cell Proteomics Date: 2016-10-04 Impact factor: 5.911
Authors: Robert Greenhalgh; Wannes Dermauw; Joris J Glas; Stephane Rombauts; Nicky Wybouw; Jainy Thomas; Juan M Alba; Ellen J Pritham; Saioa Legarrea; René Feyereisen; Yves Van de Peer; Thomas Van Leeuwen; Richard M Clark; Merijn R Kant Journal: Elife Date: 2020-10-23 Impact factor: 8.140