standardized sequence and structure analysis of … labels are used in all imgt® databases and...
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Antibody Biology and EngineeringFrom Basic Mechanisms to Antibody-Based Therapeutics
March 7-12, 2010, Ventura, CA
Standardized sequence and structure analysis of antibody
using IMGT®
http://www.imgt.org
Marie-Paule LefrancMontpellier, France
http://www.imgt.org
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http://www.imgt.orgcreated in 1989
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IMGT standards based on IMGT-ONTOLOGY
http://www.imgt.org
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IMGT-ONTOLOGY seven axioms:
To share, reuse and represent knowledgein Immunogenetics and Life Sciences
IMGT-ONTOLOGY
CLASSIFICATION
NUMEROTATION
DESCRIPTION
ORIENTATION
LOCALIZATION
Giudicelli and Lefranc, Bioinformatics (1999)
IDENTIFICATION OBTENTION
http://www.imgt.org
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CLASSIFICATION axiom
group
subgroup
allele
locus
is a member of an instance of
is a member of an instance of
is a variant of an instance of
is ordered in an instance of
IGLV
IGLV2
IGLV2-11
IGLV2-11*02
human IGL(22q11.2)
is ordered in
is a member of
is a variant of
is a member of
gene
« Concepts » « Instances »
http://www.imgt.org
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Concepts of CLASSIFICATION
1. The IMGT-ONTOLOGY main concepts of classification• include ‘group’, ‘subgroup’, ‘gene’, ‘allele’.• have allowed to set up the nomenclature of the
immunoglobulin (IG) and T cell receptor (TR) genes(V, D, J, C genes).
2. IMGT gene names have been approved by the HUGO Nomenclature Committee (HGNC) in 1999.
3. New alleles are validated by the WHO-IUIS/IMGTnomenclature committee and entered in IMGT/GENE-DB.
4. IMGT/GENE-DB is the international reference database for IG and TR genes (direct links from NCBI Entrez Gene) and alleles.
http://www.imgt.org
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Concepts of CLASSIFICATION
1. The IMGT-ONTOLOGY main concepts of classification• include ‘group’, ‘subgroup’, ‘gene’, ‘allele’.• have allowed to set up the nomenclature of the
immunoglobulin (IG) and T cell receptor (TR) genes(V, D, J, C genes).
2. IMGT gene names have been approved by the HUGO Nomenclature Committee (HGNC) in 1999.
3. New alleles are validated by the WHO-IUIS/IMGTnomenclature committee and entered in IMGT/GENE-DB.
4. IMGT/GENE-DB is the international reference database for IG and TR genes (direct links from NCBI Entrez Gene) and alleles.
http://www.imgt.org
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FR1-IMGT
V-GENEV-EXON
FR2-IMGT FR3-IMGT
L-PART1
V-REGION
CC5 ’UTR 3 ’UTR
CD
R3
-IMG
T
DONOR-SPLICE
W
V-GENE V-EXON
FR3-IMGT CDR3-IMGT
L-PART1 DONOR-SPLICE
V-REGION FR1-IMGT
Label 1 Label 2
V-REGION CDR3-IMGT
Relations entre Labels
DESCRIPTION axiom
PROTOTYPE for a V-GENE http://www.imgt.org
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Concepts of DESCRIPTION
1. The IMGT-ONTOLOGY concepts of description:• comprise the standardized IMGT labels and their relations.• have allowed to describe the IG (or antibody) and TR
sequences and structures, whatever the receptor type,the chain type or the species.
2. IMGT labels are used in all IMGT® databases and tools for the description of:
• nucleotide and amino acid sequences (IMGT/LIGM-DB…)• 2D and 3D structures (IMGT/3Dstructure-DB…).
3. Sequence Ontology (SO) includes IMGT labels.
4. IMGT® databases can be queried using labels (a big ‘plus’compared to generalist databases).
http://www.imgt.org
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Concepts of DESCRIPTION
1. The IMGT-ONTOLOGY concepts of description:• comprise the standardized IMGT labels and their relations.• have allowed to describe the IG (or antibody) and TR
sequences and structures, whatever the receptor type, the chain type or the species.
2. IMGT labels are used in all IMGT® databases and tools for the description of:
• nucleotide and amino acid sequences (IMGT/LIGM-DB…)• 2D and 3D structures (IMGT/3Dstructure-DB…).
3. Sequence Ontology (SO) includes IMGT labels.
4. IMGT® databases can be queried using labels (a big ‘plus’compared to generalist databases).
http://www.imgt.org
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DESCRIPTION
IMGT/LIGM-DB
IMGT-ONTOLOGY:277 IMGT labels for sequences
285 IMGT labels for 3D structures
144 069 sequences from 251 species
http://www.imgt.org
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NUMEROTATION axiom
Lefranc et al. Dev. Comp. Immunol. 27, 55-77 (2003)
CDR-IMGT lengths[8.10.12]
Based on the IMGT unique numbering(first one in 1997)
http://www.imgt.org
IMGT Collier de Perles
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NUMEROTATION axiom
Lefranc et al. Dev. Comp. Immunol. 27, 55-77 (2003)
CDR-IMGT lengths[8.10.12]
Based on the IMGT unique numbering(first one in 1997)
- conserved AA (and codons) are always at the same positions:
23 1st-CYS41 CONSERVED-TRP89 hydrophobic
104 2nd-CYS118 J-PHE, J-TRP
- delimitation of the FR-IMGTand CDR-IMGT is standardized
- CDR-IMGT lengths are crucialinformation
http://www.imgt.org
IMGT Collier de Perles
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Concepts of NUMEROTATION
1. The IMGT-ONTOLOGY concepts of numerotation include:• IMGT unique numbering• IMGT Collier de Perles.
2. The concepts bridge the gap between sequences and 3D structures, at the amino acid (and codon) level, for:
• the variable domains (V-DOMAIN) • the constant domains (C-DOMAIN).
4. The concepts are used for:• mutations, polymorphisms• CDR-IMGT lengths• contact analysis, paratope definition.
5. WHO-INN programme requires the CDR-IMGT lengths for antibody.
http://www.imgt.org
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Concepts of NUMEROTATION
1. The IMGT-ONTOLOGY concepts of numerotation include:• IMGT unique numbering• IMGT Collier de Perles.
2. The concepts bridge the gap between sequences and 3D structures, at the amino acid (and codon) level, for:
• the variable domains (V-DOMAIN) • the constant domains (C-DOMAIN).
4. The concepts are used for:• mutations, polymorphisms• CDR-IMGT lengths• contact analysis, paratope definition.
5. WHO-INN programme requires the CDR-IMGT lengths for antibody.
http://www.imgt.org
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View from above the CDR-IMGT Side view of the V-DOMAIN
V-J junctionV-D-J junction
V-DOMAIN: VH and V-KAPPA
CDR: complementarity determining regionCDR3-IMGT (105-117)V-D-J junction (104-118), V-J junction (104-118)
V-KAPPAVH V-KAPPAVHhttp://www.imgt.org
IMGT® http://www.imgt.org
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The 11 IMGT physicochemical AA classes
Pommié et al. J. Mol Recognit. 17, 17-32 (2004)
http://www.imgt.org
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IMGT/JunctionAnalysis
Yousfi Monod et al. Bioinformatics 20, i379-385 (2004)Pommié et al. J. Mol Recognit. 17, 17-32 (2004)
http://www.imgt.org
Analysis of the IG and TR junctions
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Antibody humanization and engineering
humanrat
IMGT® http://www.imgt.org
VH domain[8.10.12]
2 mutations:S31>T, S28>F T
http://www.imgt.orgAlemtuzumab (CAMPATH®)
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Magdelaine-Beuzelin C. et al. Crit. Rev. Oncol. Hemat. 64, 210-225 (2007)
Towards «Potential immunogenicity evaluation»
• Comparison with the closest human germline genes and alleles• Number of different AA in FR-IMGT
VH alemtuzumab 73 % 14 /91
bevacizumab 72.40 % 23
trastuzumab 81.63 % 9
V-KAPPA alemtuzumab 86.32 % 2 /89
bevacizumab 87.40 % 7
trastuzumab 86.32 % 6
FR-IMGTAA
differences
V-REGIONidentitypercent
http://www.imgt.org
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V-REGIONidentity percent
IMGT/DomainGapAlign
http://www.imgt.org
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IMGT/DomainGapAlignhttp://www.imgt.org
14 different AAin FR-IMGT
14/91
11 different AAin CDR1- andCDR2-IMGT
CDR-IMGT lengths
FR-IMGTlengths
Towards «Potential immunogenicity evaluation»
V-REGIONidentitypercent
Ehrenmann et al. Nucl. Acids Res. 38, D301-307 (2010)
Closest human germlineIGHV4-59*01
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IMGT/DomainGapAlignhttp://www.imgt.org
• very similar (+ + +)• similar (+ - +), (+ + -) • dissimilar (+ - -), (- + -), (- - +)• very dissimilar (- - -)
Towards «Potential immunogenicity evaluation»
Characteristics of the AA class changes:
Ehrenmann et al. Nucl. Acids Res. 38, D301-307 (2010)
(Hydropathy Volume Physicochemical)+ : conserved classes - : different classes
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IMGT Collier de Perles
AA that are differentcompared to the closestgermline V and J genes and alleles
(e.g. for alemtuzumab: 11 AA in CDR1- and CDR2-IMGT and 14 AA in the FR-IMGT, compared to Homo sapiens IGHV4-59*01)
IMGT/DomainGapAlign:http://www.imgt.org
Towards «Potential immunogenicity evaluation»
Ehrenmann et al. Nucl. Acids Res. 38, D301-307 (2010)
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IMGT/3Dstructure-DB
Hydrogen bonds
http://www.imgt.org
Lefranc et al. Nucl. Acids Res. 37, D1006-1012 (2009)
V-DOMAIN
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Kaas Q. et al.2004
Contacts VH-(Ligand), V-KAPPA-(Ligand)http://www.imgt.org
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Kaas Q. et al.Nucl. Acids Res. (2004)
Contacts V-KAPPA-(Ligand)http://www.imgt.org
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Kaas Q. et al. Nucl. Acids Res. (2004)
Contacts VH-(Ligand)http://www.imgt.org
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IMGT/2Dstructure-DB
International Nonproprietary Name (INN)
Ehrenmann et al. Nucl. Acids Res. 38, D301-307 (2010)
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Ehrenmann et al. Nucl. Acids Res. 38,D301-307 (2010)
IMGT/2Dstructure-DB
http://www.imgt.org
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Ehrenmann et al. Nucl. Acids Res. 38, D301-307 (2010)
IMGT/2Dstructure-DB
DESCRIPTION
CLASSIFICATION
NUMEROTATION
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Ehrenmann et al. Nucl. Acids Res. 38, D301-307 (2010)
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Ehrenmann et al. Nucl. Acids Res. 38, D301-307 (2010)
IMGT/mAb-DB
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Ehrenmann et al. Nucl. Acids Res. 38, D301-307 (2010)
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Towards «Potential immunogenicity evaluation»using IMGT-ONTOLOGY:
• Standardized analysis of V-DOMAIN- IMGT Collier de Perles - IMGT/DomainGapAlign
- CDR-IMGT and FR-IMGT delimitations- CDR3-IMGT (V-J and V-D-J junctions)- description of AA differences
• Standardized analysis of antibody/antigen contacts- IMGT/3Dstructure-DB
• Bridging the gap between sequences and 3D structures and vice versa
- IMGT/2Dstructure-DB cards (INN)
Conclusions
http://www.imgt.org
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IMGTIMGT®®
• Immunoglobulins (IG)(or antibodies)
• T cell receptors (TR) • MHC• IgSF and MhcSF
• Sequences• Genes• Structures
http://www.imgt.org
• 6 databases• 15 online tools
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Acknowledgements
BioSTIC-LRACI IMPbioGIS AGENAEPlan Pluri-Formation Université Montpellier 2ANR FLAVORES ANR BIOSYS GIS IBiSAGrand Plateau Technique Régional Languedoc-Roussillon GPTR «ImmunoGrid», 6th PCRDT, STREPS IST
http://www.imgt.org
and the companies that support the IMGT efforts of standardization.
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Many thanks to the IMGT® team at Montpellier, France
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