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Immunogenetic factors driving formation of ultralong VH CDR3 in Bos taurus antibodies

Cellular & Molecular Immunology 2019年第1期16卷 53-64页

作者： Thaddeus C Deiss Melissa Vadnais Feng Wang Patricia L Chen Ali Torkamani Waithaka Mwangi Marie-Paule Lefranc Michael F Criscitiello Vaughn V Smider comparative immunogenetics laboratory Department of Veterinary PathobiologyCollege of Veterinary Medicine and Biomedical SciencesTexas A&M UniversityCollege StationTX 77843USA Department of Molecular Medicine The Scripps Research InstituteLa JollaCA 92037USA California Institute for Biomedical Research La JollaCA 92037USA Department of Integrative Structural and Computational Biology The Scripps Research InstituteLa JollaCA 92037USA Department of Diagnostic Medicine and Pathobiology College of Veterinary MedicineKansas State UniversityManhattanKS 66506USA IMGT the International ImMunoGeneTics information systemLaboratoire d’ImmunoGénétique MoléculaireInstitut de Génétique HumaineCNRSUniversity of MontpellierMontpellier 34396France Department of Microbial Pathogenesis and Immunology College of MedicineTexas A&M UniversityBryanTX 77807USA Fabrus Inc.La JollaCA 92037USA

The antibody repertoire of Bos taurus is characterized by a subset of variable heavy(VH)chain regions with ultralong third complementarity determining regions(CDR3)which,compared to other species,can provide a potent response to challenging antigens like HIV *** unusual CDR3 can range to over seventy highly diverse amino acids in length and form uniqueβ-ribbon‘stalk’and disulfide bonded‘knob’structures,far from the typical antigen binding *** genetic components and processes for forming these unusual cattle antibody VH CDR3 are not well *** we analyze sequences of Bos taurus antibody VH domains and find that the subset with ultralong CDR3 exclusively uses a single variable gene,IGHV1-7(VHBUL)rearranged to the longest diversity gene,*** eight nucleotide duplication at the 3′end of IGHV1-7 encodes a longer V-region producing an extended Fβ-strand that contributes to the stalk in a rearranged CDR3.A low amino acid variability was observed in CDR1 and CDR2,suggesting that antigen binding for this subset most likely only depends on the *** a novel,potentially AID mediated,deletional diversification mechanism of the *** VH ultralong CDR3 knob was discovered,in which interior codons of the IGHD8-2 region are removed while maintaining integral structural components of the knob and descending strand of the stalk in *** deletions serve to further diversify cysteine positions,and thus disulfide bonded ***,both germline and somatic genetic factors and processes appear to be involved in diversification of this structurally unusual cattle VH ultralong CDR3 repertoire.

关键词： bovine complementarity determining region 3 repertoire diversification deletions immunoglobulin heavy chain

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Antibody upstream sequence diversity and its biological implications revealed by repertoire sequencing

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Journal of Genetics and Genomics 2021年第10期48卷 936-945页

作者： Yan Zhu Xiujia Yang Cuiyu Ma Haipei Tang Qilong Wang Junjie Guan Wenxi Xie Sen Chen Yuan Chen Minhui Wang Chunhong Lan Deqiang Sun Lai Wei Caijun Sun Xueqing Yu Zhenhai Zhang State Key laboratory of Organ Failure Research National Clinical Research Center for Kidney DiseaseDivision of NephrologyNanfang HospitalSouthern Medical UniversityGuangzhou 510515China Department of Bioinformatics School of Basic Medical SciencesSouthern Medical UniversityGuangzhou 510515China Center for Precision Medicine Guangdong Provincial People's HospitalGuangdong Academy of Medical SciencesGuangzhou 510080China Guangdong-Hong Kong Joint laboratory on Immunological and Genetic Kidney Diseases Guangdong Provincial People's HospitalGuangdong Academy of Medical SciencesGuangzhou 510080China Key laboratory of Mental Health of the Ministry of Education Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired IntelligenceSouthern Medical UniversityGuangzhou 510515China Department of Nephrology Hainan Affiliated Hospital of Hainan Medical CollegeHaikou 570311China Department of Nephrology Hainan General HospitalHaikou 570311China Department of Center laboratory The Fifth Affiliated Hospital of Guangzhou Medical UniversityGuangzhou 510700China State Key laboratory of Ophthalmology Zhongshan Ophthalmic CenterSun Yat-sen UniversityGuangzhou 510060China School of Public Health Sun Yat-sen UniversityShenzhen 510006China Division of Nephrology Guangdong Provincial People's HospitalGuangdong Academy of Medical SciencesGuangzhou 510080China

The sequence upstream of the antibody variable region(antibody upstream sequence[AUS])consists of a 5′untranslated region(5′UTR)and a preceding leader *** sequence variations in AUS affect antibody engineering and PCR based antibody quantification and may also be implicated in mRNA transcription and ***,the diversity of AUSs remains *** 5′rapid amplification of cDNA ends and high-throughput antibody repertoire sequencing technique,we acquired full-length AUSs for human,rhesus macaque,cynomolgus macaque,mouse,and *** designed a bioinformatics pipeline and identified 3307 unique AUSs,corresponding to 3026 and 1457 unique sequences for 5′UTR and leader region,*** analysis indicated that 928(63.69%)leader sequences are novel relative to those recorded in the international immunogenetics information ***,leader sequences are more conserved than 5′UTR and seem to coevolve with their downstream V ***,single-nucleotide polymorphisms are position dependent for leader regions and may contribute to the functional reversal of the downstream V ***,the AUGs in AUSs were found to have little impact on gene *** together,our findings can facilitate primer design for capturing antibodies efficiently and provide a valuable resource for antibody engineering and molecule-level antibody studies.

关键词： Antibody upstream sequences 5′UTR Leader sequences Antibody repertoire sequencing Antibody repertoire

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