IMGT ( standardization. and tools for the analysis of immunoglobulin and T cell receptor repertoires and 3D structures

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1 IMGT () standardization and tools for the analysis of immunoglobulin and T cell receptor repertoires and 3D structures Marie-Paule Lefranc Laboratoire d ImmunoGénétique Moléculaire Université Montpellier, UPR CNRS 1142, IGH Institut Universitaire de France Tutorial ESF MARIE NETWORK on: «BIOINFORMATICS AND AUTOIMMUNITY», October 11, 2006, Budapest, Hungary Organizers: Vladimir Brusic, Marie-Paule Lefranc and Paolo Riccio The international ImMunoGeneTics information system Coordinator: M.-P. Lefranc, Montpellier, France

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3 IMGT domain: the adaptive immune response Vertebrate s Immunoglobulin (IG) T lymphocyte B lymphocyte peptide T cell receptor (TR) Trimolecular complex MHC

4 cdna (in databases: mrna!)..gagga aggtgtccag gtccctgaga ggtccgccag ttacatatac gaattcactg tgcgagagat cctggtcacc cagcacccag ggagccactc acccagccag cacacagtgc ccaggatgtg tccacctacc cgaggacctg tgcctcgggt acctgagcgt gccatggaac gctaaccgcc gccgccgtcg cttcagcccc gaagtacctg gaccagcata ggtgggccac taaacccacc ttcaccatgg tgtgaggtgc ctctcctgtg gctccaggga tatagagact tatctgcaaa tcttgtaatg gtctcctcag ccagatggga agtgtgacct gatgcctccg ctagccggca actgtgccct ccatctccct ctcttaggtt gtcaccttca gacctctgtg catgggaaga accctctcaa gaggagctgg aaggacgtgc acttgggcat ctgcgcgtgg gaggccctgc catgtcaatg aactggggct aactggtgga cagcctctgg aggggctgga cagtgaaggg tgaatagcct gtgctatatg catccccgac acgtggtcat ggagcgaaag gggacctgta agtccgtgac gcccagttcc catgctgcca cagaagcgaa cctggacgcc gctgctacag ccttcacttg aatccggaaa ccctgaacga tggttcgctg cccggcagga cagccgagga cgctggcctt tgtctgttgt ccgctgggtt gtctggggga attaagcttc atgggtctca ccgattcacc gagagtcgac ttatggtttc cagccccaag cgcctgcctg cggacagggc caccacgagc atgccacgtg ctcaactcca cccccgactg cctcacgtgc ctcaagtggg cgtgtccagt cactgctgcc cacattccgg gctggtgacg gctgcagggg gcccagccag ctggaagaag cacacagaag catggcggag ttccttgttg ggcctggtca agtacctatg agtattagta atctccagag gacacggctg agtccctggg gtcttcccgc gtccagggct gtgaccgcca agccagctga aagcactaca cctaccccat tcactgcacc acactgaccg aagagcgctg gtcctgccgg taccccgagt cccgaggtcc ctgacgtgcc tcacaggagc ggcaccacca ggggacacct accatcgacc gtggacggca cttttttaga 120 agccgggggg 180 ccatgaactg 240 gtagaagtga 300 acaacgccaa 360 tctattactg 420 gccagggaac 480 tgagcctctg 540 tcttccccca 600 gaaacttccc 660 ccctgccggc 720 cgaatcccag 780 ctccctcaac 840 gaccggccct 900 gcctgagaga 960 ttcaaggacc 1020 gctgtgccga 1080 ccaagacccc 1140 acctgctgcc 1200 tggcacgtgg 1260 tgccccgcga 1320 ccttcgctgt 1380 tctcctgcat 1440 gcttggcggg 1500 cctgctactga

5 Spacefill 3D representation of an IgG The Immunoglobulin FactsBook, 2001

6 Immunoglobulin IgG IMGT Repertoire,

7 cdna..gagga aggtgtccag gtccctgaga ggtccgccag ttacatatac gaattcactg t tgcgagagat cctggtcacc cagcacccag ggagccactc acccagccag cacacagtgc ccaggatgtg tccacctacc cgaggacctg tgcctcgggt acctgagcgt gccatggaac gctaaccgcc gccgccgtcg cttcagcccc gaagtacctg gaccagcata ggtgggccac taaacccacc 5 UTR ttcaccatgg tgtgaggtgc ctctcctgtg gctccaggga tatagagact tatctgcaaa tc tcttgtaatg gtctcctcag ccagatggga agtgtgacct gatgcctccg ctagccggca actgtgccct ccatctccct ctcttaggtt gtcaccttca gacctctgtg catgggaaga accctctcaa gaggagctgg aaggacgtgc acttgggcat ctgcgcgtgg gaggccctgc catgtcaatg FR1-IMGT C L-REGION aactggggct aactggtgga cagcctctgg aggggctgga cagtgaaggg tgaatagcct gtgctatatg catccccgac acgtggtcat ggagcgaaag gggacctgta agtccgtgac gcccagttcc catgctgcca cagaagcgaa cctggacgcc gctgctacag ccttcacttg aatccggaaa ccctgaacga tggttcgctg cccggcagga cagccgagga cgctggcctt tgtctgttgt FR2-IMGT W V-REGION ccgctgggtt gtctggggga attaagcttc atgggtctca ccgattcacc gagagtcgac gtttc ttatggtttc cagccccaag cgcctgcctg cggacagggc caccacgagc atgccacgtg ctcaactcca cccccgactg cctcacgtgc ctcaagtggg cgtgtccagt cactgctgcc cacattccgg gctggtgacg gctgcagggg gcccagccag ctggaagaag cacacagaag catggcggag FR3-IMGT C D-REGION ttccttgttg ggcctggtca agtacctatg agtattagta atctccagag gacacggctg agt agtccctggg gtcttcccgc gtccagggct gtgaccgcca agccagctga aagcactaca cctaccccat tcactgcacc acactgaccg aagagcgctg gtcctgccgg taccccgagt cccgaggtcc ctgacgtgcc tcacaggagc ggcaccacca ggggacacct accatcgacc gtggacggca C-REGION W/F JUNCTION cttttttaga 120 agccgggggg 180 ccatgaactg 240 gtagaagtga 300 acaacgccaa 360 tctattactg 420 gccagggaac 480 tgagcctctg 540 tcttccccca 600 gaaacttccc 660 ccctgccggc 720 cgaatcccag 780 ctccctcaac 840 gaccggccct 900 gcctgagaga 960 ttcaaggacc 1020 gctgtgccga 1080 ccaagacccc 1140 acctgctgcc 1200 tggcacgtgg 1260 tgccccgcga 1320 ccttcgctgt 1380 tctcctgcat 1440 gcttggcggg 1500 cctgctactga J-REGION 3 UTR

8 Immunoglobulin (IG) synthesis genomic DNA (IGH Locus 14q32) V D J C 3' 5 rearranged DNA 5 mrna 3' 2 x 1012 different IG per individual IMGT Repertoire,

9 Immunoglobulin (IG) synthesis 150 FUNCTIONAL IG GENES HEAVY CHAIN V D J C V 5' 3' J C LIGHT CHAIN 3' 5' x 23 x POTENTIAL RECOMBINATIONS x x Kappa Lambda POTENTIAL RECOMBINATIONS N-DIVERSITY SOMATIC MUTATIONS x ' 3' ABOUT 6.3 x 106 POSSIBILITIES 5' 3' ABOUT 3.5 x 105 POSSIBILITIES 2 x 1012 DIFFERENT ANTIBODIES IMGT Repertoire,

10 Genomic DNA in germline configuration V-GENE >X HSVI2 Homo sapiens VI-2 gene for immunoglobulin heavy chain tgagagctcc gttcctcacc atggactgga cctggaggat cctcttcttg gtggcagcag ccacaggtaa gaggctccct agtcccagtg atgagaaaga gattgagtcc agtccaggga gatctcatcc acttctgtgt tctctccaca ggagcccact cccaggtgca gctggtgcag tctggggctg aggtgaagaa gcctggggcc tcagtgaagg tctcctgcaa ggcttctgga tacaccttca ccggctacta tatgcactgg gtgcgacagg cccctggaca agggcttgag tggatgggat ggatcaaccc taacagtggt ggcacaaact atgcacagaa gtttcagggc agggtcacca tgaccaggga cacgtccatc agcacagcct acatggagct gagcaggctg tgaaa agatctgacg acacggccgt gtattactgt gcgagagaca cagtgtgaaa acccacatcc acccacatcc tgagggtgtc agaaacccaa gggaggaggc ag tgagggtg 5' 5'UTR L PART1 INIT CODON V INTRON DONOR SPLICE L PART2 ACCEPTOR SPLICE 1st CYS 23 V REGION V RS 3'UTR 2nd CYS V HEPTAMER V 104 V NONAMER SPACER '

11 Genomic DNA in germline configuration D-GENE >J00256 IGHD7-27*01 Homo sapiens D-GENE c tgagctgaga accactgtgc ac att ccagccgcag ggtttttggc taactgggga cacagtgatt ggcagctct caaaaaccat gctcccccgg g ggcagctcta 5' 5'UTR 5 D RS D REGION 5 D NONAMER 5 D SPACER 5 D HEPTAMER 3 D RS 3'UTR 60 3' 3 D 3 D SPACER HEPTAMER 3 D NONAMER J-GENE >J00256 IGHJ1*01 Homo sapiens J-GENE gcccctgg ctcagggctg actcaccgtg act accccgggct gtgggtttct gtgcccctgg gctgaatact tccagcactg gggccagggc accctggtca ccgtctcctc aggtgagtct gctgtactgg ggatagcggg gagccatgtg tactgggcca agcaagggct ttggcttcag 5' 5'UTR J RS J REGION J TRP J NONAMER J SPACER 118 J HEPTAMER DONOR SPLICE 3'UTR 3'

12 Human IGH locus Chromosome 14q32.33 IMGT Repertoire,

13 Giudicelli V. et al. Nucleic Acids Res. 33, D256-D261

14 "CLASSIFICATION" concept group locus is a member of is a member of an instance of subgroup is a member of an instance of IGLV is ordered in an instance of gene is a variant of an instance of allele «Concepts» IGLV2 is a member of IGLV2-11 is a variant of IGLV2-11*02 «Instances» human IGL (22q11.2) is ordered in

15 1999 Entry of the 630 human IG and TR genes at NCBI Cross-references between Entrez Gene and IMGT/GENE-DB

16 IMGT/V-QUEST V-GENE JUNCTION J-GENE Giudicelli et al. Nucleic Acids Res. 32, W435-W440 (2004)

17 Giudicelli et al. Nucleic Acids Res. 32, W435-W440 (2004)

18 Giudicelli et al. Nucleic Acids Res. 32, W435-W440 (2004)

19 IMGT/V-QUEST Score and nucleotide identity Giudicelli et al. Nucleic Acids Res. 32, W435-W440 (2004)

20 Giudicelli et al. Nucleic Acids Res. 32, W435-W440 (2004)

21 Giudicelli et al. Nucleic Acids Res. 32, W435-W440 (2004)

22 IMGT/V-QUEST Case of complementary reverse sequences Giudicelli et al. Nucleic Acids Res. 32, W435-W440 (2004)

23 IMGT/V-QUEST Links to individual results

24 IMGT/V-QUEST For CDR3-IMGT (and the V-REGION), the number of mutations is shown by comparison with the closest germline V-REGION, up to the 3 end deduced from the junction analysis, and between parentheses, up the 3 end of the complete germline V-REGION.

25 The eleven IMGT amino acid classes according to the physico-chemical properties Pommié et al. J. Mol Recognit. 17, 17-32, 2004

26 IMGT/V-QUEST

27 Immunoglobulin (IG) T cell receptor (TR) Contribution of the V-DOMAIN V-J-REGION Light chain 2 V-DOMAINs to the antigen binding site Alpha Gamma V-DOMAIN - Beta Delta V-D-J-REGION Heavy chain V-DJ-REGION V-J-REGION Membrane IgM T cell receptor The Immunoglobulin FactsBook, 2001

28 Junctions of the V-DOMAINs VH V-KAPPA V-D-J junction V-J junction Side view Mouse(Mus musculus) E5.2Fv VH V-KAPPA View from above CDR3-IMGT= Complementarity determining region ( ) V-J junction ( ) V-D-J junction ( )

29 Generation of the JUNCTION diversity 3 V-REGION tgtgcgaaa ga N-REGION D-REGION tacc agcatattgtg gtggtgactgctat tcc N-REGION gatt JUNCTION C A P Y R G D T Y D Y S Wtgttgtgcgcca gcg cca tac cgg ggggtgactactat ggt gac act tat gat tac tcc tgg 5 J-REGION acaactggttcg actcctgg

30 IMGT/JunctionAnalysis Addition Addition Mutation Délétion Délétion Délétion

31 Yousfi Monod et al. Bioinformatics, 20, I379-I385 (2004)

32 Yousfi Monod et al. Bioinformatics, 20, I379-I385 (2004)

33 IMGT/JunctionAnalysis Yousfi Monod et al. Bioinformatics, 20, I379-I385 (2004)

34 MBP specific T cell junctions from MS patients

35 MBP specific T cell junctions from MS patients

36 r Pommié et al. J. Mol Recognit. 17, 17-32, 2004

37 V-DOMAINs VH V-KAPPA Side view Mouse(Mus musculus) E5.2Fv VH V-KAPPA View from above CDR3-IMGT= Complementarity determining region ( ) V-J junction ( ) V-D-J junction ( )

38 IMGT Collier de Perles IMGT Repertoire,

39 Kaas Q. et al. NAR 32, D208-D210 (2004)

40 Kaas Q. et al. NAR 32, D208-D210 (2004)

41 Contact analysis 41V - TRP (W) chain : 1u8k_B Tot NCo Pol HB NPol Cov SS Total number of atomic pair contacts Number of non covalent atomic Number of polar atomic pair contacts Number of hydrogen bonds Number of non polar atomic pair contacts Number of covalent links (other than chain covalent links) Number of disulfide bridges Kaas Q. et al. NAR 32, D208-D210 (2004)

42 IMGT Collier de Perles Kaas Q. et al. NAR 32, D208-D210 (2004)

43 MHC class I IMGT contact sites H2-K1*01 8 residue peptide (code 1jtr) Lefranc et al. Dev. Comp. Immunol. 29, (2005)

44 IMGT pmhc contact sites H2-K1*01 (code 1jtr) 8 residue peptide Kaas and Lefranc In Silico Biology 2005

45 G-ALPHA (MHC class II) with MBP peptide

46 Contacts of G-ALPHA (MHC class II) with MBP peptide

47 IMGT unique numbering V-DOMAIN (IG,TR) AND C-DOMAIN (IG,TR) AND V-LIKE-DOMAIN C-LIKE-DOMAIN (other than IG,TR) (other than IG,TR) Immunoglobulin superfamily (IgSF) G-DOMAIN (MHC) AND G-LIKE-DOMAIN (other than MHC) MHC superfamily (MhcSF)

48 IMGT Collier de Perles Homo sapiens MOG (P13688) V-LIKE-DOMAIN [9.6.9] Duprat E. et al. Recent Res. Devel. Human Genet. 2, (2004)

49 IMGT Collier de Perles Homo sapiens MOG (P13688) V-LIKE-DOMAIN [9.6.9] Duprat E. et al. Recent Res. Devel. Human Genet. 2, (2004)

50 IMGT Collier de Perles Rattus norvegicus MOG (1pkq_E) V-LIKE-DOMAIN [9.6.9] IMGT/3Dstructure-DB,

51 IMGT Collier de Perles Homo sapiens MPZ (P25189) V-LIKE-DOMAIN [ ] 90 mutations in the V-LIKE-DOMAIN of MPZ (P0) Duprat E. et al.recent Res. Devel. Human Genet. 2, (2004)

52 IMGT Collier de Perles Homo sapiens MPZ (P25189) V-LIKE-DOMAIN [ ] Duprat E. et al. Recent Res. Devel. Human Genet. 2, (2004)

53 Interactions between domains (1e4k) IGHG1 (FC-GAMMA1) CH2 C-DOMAIN FCGR3 B [D2 ] C-LIKEDOMAIN [D1] C-LIKE-DOMAIN

54 The IMGT team at Montpellier