IMGT®, the international ImMunoGeneTics information system® 25 years on

Lefranc, Marie‐Paule; Giudicelli, Véronique; Duroux, Patrice; Jabado-Michaloud, Joumana; Folch, Géraldine; Aouinti, Safa; Carillon, Emilie; Duvergey, Hugo; Houles, Amélie; Paysan-Lafosse, Typhaine; Hadi-Saljoqi, Saida; Sasorith, Souphatta; Lefranc, Gérard; Kossida, Sofia

doi:10.1093/nar/gku1056

Cited by 522 publications

(450 citation statements)

References 67 publications

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“…1 E and F), in line with D-to-J H rearrangement on both alleles preceding V H -to-DJ H rearrangement in developing pro-B cells (5,26,27). The 129SVE mouse strain IgH locus contains more V H s than the C57BL/6 IgH locus with a somewhat different organization (24). Given that 129SVE mice and cell lines have frequently been used in V(D)J recombination studies, we used the same J H 4 bait primers to also generate HTGTS-Rep-seq libraries from 129SVE bone marrow pro-B cells and splenic B cells (Table S2).…”

Section: Resultsmentioning

confidence: 56%

“…Thus, this assay, or adaptations of it, could be useful for detecting changes in repertoires that occur during development, or during an immune response. However, use of HTGTS-Rep-seq for assaying certain antigen receptor repertoires, most notably TCRα repertoires, would currently be more limited given the very large number of different Jαs (24).…”

Section: Resultsmentioning

confidence: 99%

“…We used IgBLAST (23) using joined reads and unjoined reads against V(D)J gene databases using default parameters. The V(D)J gene sequences were obtained from IMGT (24), manually curated, and used to generate IgBLAST sequence databases. Various stringencies were applied to filter reads that can align to V, D, and J genes (IgBLAST score >150, total alignment length >100, overall mismatch ratio <0.1).…”

Section: Methodsmentioning

confidence: 99%

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Highly sensitive and unbiased approach for elucidating antibody repertoires

Lin

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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Developing B lymphocytes undergo V(D)J recombination to assemble germ-line V, D, and J gene segments into exons that encode the antigen-binding variable region of Ig heavy (H) and light (L) chains. IgH and IgL chains associate to form the B-cell receptor (BCR), which, upon antigen binding, activates B cells to secrete BCR as an antibody. Each of the huge number of clonally independent B cells expresses a unique set of IgH and IgL variable regions. The ability of V(D)J recombination to generate vast primary B-cell repertoires results from a combinatorial assortment of large numbers of different V, D, and J segments, coupled with diversification of the junctions between them to generate the complementary determining region 3 (CDR3) for antigen contact. Approaches to evaluate in depth the content of primary antibody repertoires and, ultimately, to study how they are further molded by secondary mutation and affinity maturation processes are of great importance to the B-cell development, vaccine, and antibody fields. We now describe an unbiased, sensitive, and readily accessible assay, referred to as high-throughput genome-wide translocation sequencing-adapted repertoire sequencing (HTGTS-Repseq), to quantify antibody repertoires. HTGTS-Rep-seq quantitatively identifies the vast majority of IgH and IgL V(D)J exons, including their unique CDR3 sequences, from progenitor and mature mouse B lineage cells via the use of specific J primers. HTGTS-Rep-seq also accurately quantifies DJ H intermediates and V(D)J exons in either productive or nonproductive configurations. HTGTS-Rep-seq should be useful for studies of human samples, including clonal B-cell expansions, and also for following antibody affinity maturation processes. 1). In this process, the V, D, and J coding ends are generated as covalent hairpins that must be opened and that are often further processed, before being joined by classical nonhomologous end joining (2). Processing of V, D, J coding ends can involve generation of deletions or insertions of nucleotides at the junction regions (2), including the frequent de novo addition of nucleotides by the terminal deoxynucleotidyl transferase component of the V(D)J recombination process (3). Notably the V(D)J junctional region encodes a major antigen contact region of the antibody variable region, known as complementarity determining region 3 (CDR3), and thus these junctional diversification processes make a huge contribution to antibody diversity.The mouse IgH locus spans 2.7 megabases (Mb). There are 100s of V H s in the several megabase distal portion of the IgH, with the number varying substantially in certain mouse strains (4). The V H s lie ∼100 kb upstream from a 50-kb region containing 13 D H s, which is followed several kilobases downstream by a 2-kb region containing four J H s. The IgH constant region (C H ) exons lie downstream of the J H s. After assembly of a V H DJ H exon, transcription initiates upstream of the V H and terminates downstream of the C H exons, with V(D)J and C H portions being fused...

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Section: Resultsmentioning

confidence: 56%

Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

Highly sensitive and unbiased approach for elucidating antibody repertoires

Lin

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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“…Human and mouse TRAV1 genes are located at the 5′ end of the TRAV locus (IMGT locus representation, www.imgt.org) (27), close to several conserved markers, such as tox4, sall2, and a number of olfactory receptor genes. The localization of the TRAV1 best BLAST hits within the locus was analyzed in each species and is represented in Fig.…”

Section: Resultsmentioning

confidence: 99%

Restricting nonclassical MHC genes coevolve with TRAV genes used by innate-like T cells in mammals

Boudinot

Mondot

Jouneau

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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Whereas major histocompatibility class-1 (MH1) proteins present peptides to T cells displaying a large T-cell receptor (TR) repertoire, MH1Like proteins, such as CD1D and MR1, present glycolipids and microbial riboflavin precursor derivatives, respectively, to T cells expressing invariant TR-α (iTRA) chains. The groove of such MH1Like, as well as iTRA chains used by mucosal-associated invariant T (MAIT) and natural killer T (NKT) cells, respectively, may result from a coevolution under particular selection pressures. Herein, we investigated the evolutionary patterns of the iTRA of MAIT and NKT cells and restricting MH1Like proteins: MR1 appeared 170 Mya and is highly conserved across mammals, evolving more slowly than other MH1Like. It has been pseudogenized or independently lost three times in carnivores, the armadillo, and lagomorphs. The corresponding TRAV1 gene also evolved slowly and harbors highly conserved complementarity determining regions 1 and 2. TRAV1 is absent exclusively from species in which MR1 is lacking, suggesting that its loss released the purifying selection on MR1. In the rabbit, which has very few NKT and no MAIT cells, a previously unrecognized iTRA was identified by sequencing leukocyte RNA. This iTRA uses TRAV41, which is highly conserved across several groups of mammals. A rabbit MH1Like gene was found that appeared with mammals and is highly conserved. It was independently lost in a few groups in which MR1 is present, like primates and Muridae, illustrating compensatory emergences of new MH1Like/Invariant T-cell combinations during evolution. Deciphering their role is warranted to search similar effector functions in humans.MHC | TCR | MAIT | evolution | mammals

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“…Single bacterial colonies were picked and tested by phage-ELISA. The positive colonies were sequenced and analyzed through compared with the human immunoglobulin sequences (IMGT Database) (Ehrenmann et al, 2010;Lefranc et al, 2015). Positive scFv-phagemids were extracted from E. coli XL1-Blue colonies and transformed into non-suppressor E. coli Top10F'.…”

Section: Panning and Expression Of Anti-znt8 Scfvmentioning

confidence: 99%

Screening and identification of human ZnT8-specific single-chain variable fragment (scFv) from type 1 diabetes phage display library

Wang

et al. 2016

Sci. China Life Sci.

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Zinc transporter 8 (ZnT8) is a major autoantigen and a predictive marker in type 1 diabetes (T1D). To investigate ZnT8-specific antibodies, a phage display library from T1D was constructed and single-chain antibodies against ZnT8 were screened and identified. Human T1D single-chain variable fragment (scFv) phage display library consists of approximately 110 8 clones. After four rounds of bio-panning, seven unique clones were positive by phage ELISA. Among them, C27 and C22, which demonstrated the highest affinity to ZnT8, were expressed in Escherichia coli Top10F' and then purified by affinity chromatography. C27 and C22 specifically bound ZnT8 N/C fusion protein and ZnT8 C terminal dimer with one Arg325Trp mutation. The specificity to human islet cells of these scFvs were further confirmed by immunohistochemistry. In conclusion, we have successfully constructed a T1D phage display antibody library and identified two ZnT8-specific scFv clones, C27 and C22. These ZnT8-specific scFvs are potential agents in immunodiagnostic and immunotherapy of T1D.Zinc transporter 8 (ZnT8), phage display, single-chain variable fragment (scFv), type 1 diabetes (T1D) Citation:Wu, Q., Wang, X., Gu, Y., Zhang, X., Qin, Y., Chen, H., Xu, X., Yang, T., and Zhang, M. (2016). Screening and identification of human ZnT8-specific single-chain variable fragment (scFv) from type 1 diabetes phage display library. Sci China Life Sci 59, 686 -693.

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IMGT®, the international ImMunoGeneTics information system® 25 years on

Cited by 522 publications

References 67 publications

Highly sensitive and unbiased approach for elucidating antibody repertoires

Highly sensitive and unbiased approach for elucidating antibody repertoires

Restricting nonclassical MHC genes coevolve with TRAV genes used by innate-like T cells in mammals

Screening and identification of human ZnT8-specific single-chain variable fragment (scFv) from type 1 diabetes phage display library

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