Using IMGT unique numbering for IG allotypes and Fc-engineered variants of effector properties and half-life of therapeutic antibodies

Abstract

Therapeutic monoclonal antibodies (mAb) are usually of the IgG1, IgG2, and IgG4 classes, and their heavy chains may be modified by amino acid (aa) changes involved in antibody-dependent cellular cytotoxicity (ADCC), antibody-dependent cellular phagocytosis (ADCP), complement-dependent cytotoxicity (CDC), and/or half-life. Allotypes and Fc-engineered variants are classified using IMGT/HGNC gene nomenclature (e.g., Homo sapiens IGHG1). Allotype names follow the WHO/IMGT nomenclature. IMGT-engineered variant names use the IMGT nomenclature (e.g., Homsap G1v1), which comprises species and gene name (both abbreviated) followed by the letter v (for variant) and a number. Both allotypes and engineered variants are defined by their aa changes and positions, based on the IMGT unique numbering for C domain, identified in sequence motifs, referred to as IMGT topological motifs, as their limits and length are standardized and correspond to a structural feature (e.g., strand or loop). One hundred twenty-six variants are displayed with their type, IMGT numbering, Eu-IMGT positions, motifs before and after changes, and their property and function (effector and half-life). Three motifs characterize effector variants, CH2 1.6-3, 23-BC-41, and the FG loop, whereas three different motifs characterize half-life variants, two on CH2 13-AB-18 and 89-96 with H93, and one on CH3 the FG loop with H115.

Keywords: Fc‐engineered variants; allotypes; antibody half‐life; antibody‐dependent cellular cytotoxicity; antibody‐dependent cellular phagocytosis; complement‐dependent cytotoxicity.

FIGURE 1

Concepts of classification for IMGT gene and allele nomenclature (CLASSIFICATION axiom)., , , , , , (A) Hierarchy of the concepts of classification and their relations. The definition of the reciprocal relations between concepts can be read, from one concept to the other, either ascending the hierarchy (solid arrows) or descending the hierarchy (dotted arrows). (B) Examples of concept instances for each concept of classification. The concept instances are associated with an instance of the “Taxon” concept, and more precisely for the “Gene” and “Allele” concepts to an instance of the “Species” concept (here, Homo sapiens). The “Locus” concept is a concept of localization (LOCALIZATION axiom). It is shown with the reciprocal relations to the “Gene” concept. Source: With permission from M‐P. Lefranc and G. Lefranc, LIGM, Founders and Authors of IMGT®, the international ImMunoGeneTics information system®, https://www.imgt.org.

FIGURE 2

IMGT classes of the 20 common amino acids for the “hydropathy,” “volume,” “chemical characteristics” properties (IDENTIFICATION ⁵⁰ ). Three “hydropathy” classes (hydrophobic, neutral, and hydrophilic), five “volume” classes in angstrom3 (A3) ([60–90], [108–117], [138–154], [162–174], and [189–228]) and 11 “chemical characteristics” (aliphatic, sulfur, hydroxyl, acidic, amide, basic, F, W, Y, G, and P) classes were defined. Tyrosine is in the neutral class, although its OH is weakly acidic and polar. Histidine is in the neutral class, although it is weakly basic. Amino acid one‐letter and three‐letter abbreviations: A (Ala), alanine; C (Cys), cysteine; D (Asp), aspartic acid; E (Glu), glutamic acid; F (Phe), phenylalanine; G (Gly), glycine; H (His), histidine; I (Ileu), isoleucine; K (Lys), lysine; L (Leu), leucine; M (Met), methionine; N (Asn), asparagine; P (Pro), proline; Q (Gln), glutamine; R (Arg), arginine; S (Ser), serine; T (Thr), threonine; V (Val), valine; W (Trp), tryptophan; Y (Tyr), tyrosine. Source: With permission from M‐P. Lefranc and G. Lefranc, LIGM, Founders and Authors of IMGT®, the international ImMunoGeneTics information system®, https://www.imgt.org.

FIGURE 3

IMGT Colliers de Perles “On one layer” (left column) and “On two layers” (right column) of CH1, CH2, and CH3 encoded by the four Homo sapiens IGHG genes., , , , , , A, IGHG1*01 (J00228). B, IGHG2*01 (J00230). C, IGHG3*01 (X03604). D, IGHG4*01 (K01316). J00228, J00230, X03604, and K01316 are the GEDI (GenBank/European Nucleotide Archive (ENA)/Database of Japan (DDBJ) and IMGT/LIGM‐DB ¹ , ²⁷ , ²⁸ , ²⁹ , ³⁰ , ³¹ , ³² , ³³ , ³⁴ , ³⁵ , ³⁶ , ³⁷ ) accession numbers of the IMGT/HGNC nucleotide and translation of the IGHG1*01, IGHG2*01, IGHG3*01, and IGHG4*01 IMGT reference sequences. Arrows indicate the direction of the seven beta strands A to G in 3D structures. IMGT anchors are in square. Hatched circles are unoccupied positions according to the IMGT unique numbering for C domain. Amino acids are shown in the one‐letter abbreviation (Figure 2). All proline (P) are in yellow. The hydrophobic amino acids (hydropathy index with positive value: I, V, L, F, C, M, A, and tryptophan W) found at a given position in more than 50% of sequences are shown with a blue background color. Positions with bold letters in red indicate the four conserved aa positions that are common to the V domain and to the C domain: C23 (1st‐CYS), W41 (CONSERVED‐TRP), 89 (hydrophobic), C104 (2nd‐CYS), and the position 118 (diverse in the C domain, in contrast to the highly conserved and hydrophobic J‐REGION F118/W118 in the V domain ¹⁴ ). Source: With permission from M‐P. Lefranc and G. Lefranc, LIGM, Founders and Authors of IMGT®, the international ImMunoGeneTics information system®, https://www.imgt.org.

FIGURE 4

IMGT Protein display of the CH1, CH2, and CH3 of Homo sapiens (Homsap) IGHG1*01 (J00228), IGHG2*01 (J00230), IGHG3*01 (X03604), IGHG4*01 (K01316) genes (G1, G2, G3 and G4), Mus musculus (Musmus) IGHG2A*01 (V00825) and IGHG2B*01 (V00763), Canis lupus familiaris (Canlupfam) IGHG2*01 (IMGT000001) (mG2A, mG2B and cG2, respectively), and the Eu‐IMGT positions (shown vertically on 3 lines, to be read from top to down), based on the IMGT unique numbering for C domain. (Drawn by Marie‐Paule Lefranc and Gérard Lefranc, LIGM, Founders and Authors of IMGT® the international ImMunoGeneTics information system®, https://www.imgt.org).

FIGURE 5

Hinge regions encoded by the hinge exons of the Homo sapiens IGHG1, IGHG2, IGHG3, and IGHG4. The hinge IMGT numbering is shown in bold above the sequences (1–15 for IGHG1, 1–12 for IGHG2, 1–17 (H1), and 1–15 (H2, H3, H4, and H5) for IGHG3, 1–12 for IGHG4). (Drawn by Marie‐Paule Lefranc and Gérard Lefranc, LIGM, Founders and Authors of IMGT® the international ImMunoGeneTics information system®, https://www.imgt.org).