Nomenclature report 2019: major histocompatibility complex genes and alleles of Great and Small Ape and Old and New World monkey species

Abstract

The major histocompatibility complex (MHC) is central to the innate and adaptive immune responses of jawed vertebrates. Characteristic of the MHC are high gene density, gene copy number variation, and allelic polymorphism. Because apes and monkeys are the closest living relatives of humans, the MHCs of these non-human primates (NHP) are studied in depth in the context of evolution, biomedicine, and conservation biology. The Immuno Polymorphism Database (IPD)-MHC NHP Database (IPD-MHC NHP), which curates MHC data of great and small apes, as well as Old and New World monkeys, has been upgraded. The curators of the database are responsible for providing official designations for newly discovered alleles. This nomenclature report updates the 2012 report, and summarizes important nomenclature issues and relevant novel features of the IPD-MHC NHP Database. Keywords MHC . NHP . Database . Nomenclature . IPD Natasja G. de Groot and Nel Otting contributed equally to this work. This article is part of the Topical Collection on "Nomenclature, databases and bioinformatics in Immunogenetics" Natasja G. de Groot, Nel Otting, and Ronald E. Bontrop are curators of the IPD-MHC NHP database.

Comparative genetics of the major histocompatibility complex in humans and nonhuman primates

“…In rhesus macaques ( Macaca mulatta , Mamu ), for example, a haplotype can contain one to two highly (major) and up to five low (minor) transcribed A genes (Doxiadis et al., 2013;Karl et al, 2013). To differentiate between the paralogous A genes, they are named A1 to A7 (de Groot et al., 2012, 2019). In cynomolgus macaques ( Macaca fascicularis , Mafa ), an A8 gene can also be present (Shiina et al., 2015).…”

“…Currently, for the other paralogous A genes, the function is poorly understood. Figure 2b provides an overview of a few representative Mamu‐A haplotype configurations, which is defined as the unique combination of different types of A genes on a chromosome (for a complete overview of macaque A haplotype configurations, see de Groot et al., 2019). The number of paralogous Mamu‐B genes on a haplotype can reach up to nineteen, although most of these genes are not transcribed (Daza‐Vamenta et al., 2004).…”

“…Patr‐AL has an overlapping peptide‐binding repertoire with HLA‐A2 (Gleimer et al., 2011), and it is suggested that it may fulfil a specialized function, although it is unclear why the gene then never reached fixation. In several macaque species and in the sooty mangabey ( Cercocebus atys ), an MHC‐B‐ like gene, named MHC‐I , can be found, which is characterized by low levels of polymorphism (de Groot et al., 2019;Heimbruch et al., 2015;Urvater et al., 2000). The gene seems to have arisen from a duplication event in the MHC‐B block of OWM and is fixed.…”

“…For chimpanzees, approximately 250 animals were studied for the MHC, but the number of genes studied per animal may vary. The IPD‐MHC NHP database (de Groot et al., 2019;Maccari et al., 2017) archives 46 Patr‐A , 88 Patr‐B , 47 Patr‐C , 10 Patr‐DPA1 , 34 Patr‐DPB1 , 11 Patr‐DQA1 , 13 Patr‐DQB1 , 5 Patr‐DRA and 81 Patr‐DRB alleles (numbers are according release 3.4.0.0). Although there is a considerable discrepancy between the total number of humans and chimpanzees analysed, a thorough population analysis demonstrated that chimpanzees experienced a selective sweep that targeted their MHC class I region (de Groot & Bontrop, 2013;de Groot et al., 2002).…”

“…But other macaque species, such as the cynomolgus macaque (≈ 3,000 individuals) and southern pigtailed macaques ( Macaca nemestrina, Mane ) (≈ 500 individuals), have also been investigated thoroughly, and more than 2,400 and 800 alleles belonging to 33 and 25 genes, respectively, have been assigned. When focussing on the classical MHC class I and II genes encoding the antigen presentation molecules, in rhesus macaques 245 Mamu‐A1 , 588 Mamu‐B , 50 Mamu‐DPA1 , 66 Mamu‐DPB1 , 47 Mamu‐DQA1 , 79 Mamu‐DQB1 , 28 Mamu‐DRA and 261 Mamu‐DRB alleles have been documented (numbers are according release 3.4.0.0) (de Groot et al., 2019;Maccari et al., 2017). The Mamu‐A1 and Mamu‐B alleles have been subject to expansion, form their own monophyletic groups and do not cluster together with human or great ape Mhc class I A and B alleles, respectively (de Groot et al., 2012).…”