The average distance between genes within a gene family was calculated by taking the mean of all (n(n-1))/2 where n is the number of genes) pairwise Levenshtein distances (computed by python-Levenshtein), excluding self-comparisons

The average distance between genes within a gene family was calculated by taking the mean of all (n(n-1))/2 where n is the number of genes) pairwise Levenshtein distances (computed by python-Levenshtein), excluding self-comparisons. of animals positive with the 5 UTR located multiplex primer sets (U) or 5 leader located primer sets (L). (A) IGHV gene usage box plots, (B) IGHD gene usage box plots and (C) IGHJ gene usage box plots. Image_2.pdf (1.3M) GUID:?7900B540-5E8D-4201-ACDD-0EB4814C1AF8 Supplementary Table?1: The number of sequences left Urapidil hydrochloride at every step of the preprocessing actions. The libraries starting with S are human individuals, while all others are macaques. For the macaque libraries, a _1 suffix indicates the library was sequenced with the leader primer set, while a _100 suffix indicates sequencing with the 5 UTR primer set. Table_1.xlsx (11K) GUID:?C430C75E-C1FE-43D8-A209-6EE78860E675 Supplementary Table?2: Spearman correlation table. The Collapsed Spearman column contains the results when clones are collapsed by identical V allele, J allele, and HCDR3 nucleotide sequence, while the Uncollapsed Spearman is the same calculation for the counts before collapsing by clonotype. Table_2.xlsx (6.1K) GUID:?7C7DD735-5398-439E-8120-0B63AAF52C8A Data Availability StatementThe datasets Urapidil hydrochloride utilized in this study can be found on the European Nucleotide Archive https://www.ebi.ac.uk/ena/. The human data from Gidoni et al. is usually under the project accession PRJEB26509, while the macaque data from Vazquez Bernat et al. is usually under accession number PRJEB38839. Abstract Macaques are frequently used to evaluate candidate vaccines and to study infection-induced antibody responses, requiring an improved understanding of their na?ve immunoglobulin (IG) repertoires. Baseline gene usage frequencies contextualize studies of antigen-specific immune responses, providing information about how easily one may stimulate a response with a particular VDJ recombination. Studies of human IgM repertoires have shown that IG VDJ gene frequencies vary several orders of magnitude between the most and least utilized genes in a manner that is usually consistent across many individuals but to date comparable analyses are lacking for macaque IgM repertoires. Here, we quantified VDJ gene usage levels in unmutated IgM repertoires of 45 macaques, belonging to two species and four commonly used subgroups: Indian and Chinese origin rhesus macaques and Indonesian and Mauritian origin cynomolgus macaques. We show that VDJ gene frequencies differed greatly between the most and least used genes, with comparable overall patterns observed in macaque subgroups and individuals. However, there were also clear differences affecting the use of specific V, D and J genes. Furthermore, in contrast to humans, macaques of both species utilized IGHV4 family genes to a much higher extent and showed evidence of evolutionary growth of genes of this family. Finally, we used the results to inform the analysis of a broadly neutralizing HIV-1 antibody elicited in SHIV-infected rhesus macaques, RHA1.V2.01, which binds the apex of the Env trimer in a manner that mimics the binding mode of PGT145. We discuss the likelihood that comparable antibodies could be elicited in different macaque subgroups. Keywords: immunoglobulin, IgM repertoires, VDJ frequency, macaques, neutralizing antibodies Introduction Na?ve B cells express highly diverse antigen receptors (B cell receptors, BCRs) to allow recognition of a vast range of possible foreign structures. Upon antigen recognition, na?ve B cells proliferate and undergo selection, resulting in the generation of memory B cells and antibody-producing plasma cells. Hundreds of unique B cells may be engaged in the response to a given antigenic target, where each B cell lineage is usually defined by a characteristic VDJ arrangement. Studies of human B cell repertoires demonstrate that VDJ genes are not equally used in na?ve B cell repertoires, but their frequencies can differ by up to two orders of magnitude (1C3). The VDJ gene usage frequency in na?ve human B cell repertoires is largely consistent between different individuals, suggesting preferences for certain gene rearrangements during B cell development that are comparable between individuals. While the characteristics of IgM repertoires are relatively well-studied in humans, macaque IgM repertoires are less well defined. An obstacle to performing such studies has been the lack of a comprehensive Urapidil hydrochloride database of macaque germline VDJ genes. Despite the publication of the first rhesus macaque genome in 2007 (4), more detailed information about macaque IG germline genes and alleles is only now starting to become available. The generation of initial IG VDJ databases by several research groups over the past years has illustrated the challenge of capturing the genetic diversity in macaques (5C13). Like in humans and other outbred species, the macaque IG heavy chain (IGH) locus contains significant structural variation, with frequent deletions and duplications of IGHV genes (13). Our recent study describing the construction of a comprehensive IG heavy CBLC chain (IGH) database from a set of 45 rhesus and cynomolgus macaques, the Karolinska Institutet Macaque Database (KIMDB, http://kimdb.gkhlab.se/), highlighted the high structural and allelic diversity between.