Biology subjects

Martinez-Barnetche, J.

Publications and source records attributed to Martinez-Barnetche, J..

3 recordsLinked to original sources

bioRxiv2023

AIRR-C Human IG Reference Sets: curated sets of immunoglobulin heavy and light chain germline genes

Analysis of an individuals immunoglobulin (IG) gene repertoire requires the use of high-quality germline gene Reference Sets. The Adaptive Immune Receptor Repertoire-Community (AIRR-C) Reference Sets have been developed to include only human IG heavy and light chain alleles that have been confirmed by evidence from multiple high-quality sources. By including only those alleles with a high level of support, including some new sequences that currently lack official names, AIRR-seq analysis will have greater accuracy and studies of the evolution of immunoglobulin genes, their allelic variants and the expressed immune repertoire will be facilitated. Although containing less than half the previously recognised IG alleles (e.g. just 198 IGHV sequences), the Reference Sets eliminated erroneous calls and provided excellent coverage when tested on a set of repertoires from 99 individuals comprising over 4 million V(D)J rearrangements. To improve AIRR-seq analysis, some alleles have been extended to deal with short 3 or 5 truncations that can lead them to be overlooked by alignment utilities. To avoid other challenges for analysis programs, exact paralogs (e.g. IGHV1-69*01 and IGHV1-69D*01) are only represented once in each set, though alternative sequence names are noted in accompanying metadata. The Reference Sets also include novel alleles: 8 IGHV alleles, 2 IGKV alleles and 5 IGLV alleles. The version-tracked AIRR-C Reference Sets are freely available at the OGRDB website (https://ogrdb.airr-community.org/germline_sets/Human) and will be regularly updated to include newly-observed and previously-reported sequences that can be confirmed by new high-quality data.

genomics↗

bioRxiv2022

Subfunctionalization and constrained size of the immunoglobulin loci in Ambystoma mexicanum

BackgroundThe axolotl, Ambystoma mexicanum is a unique biological model for complete tissue regeneration. Is a neotenic endangered species and is highly susceptible to environmental stress, including infectious disease. In contrast to other amphibians, the axolotl is particularly vulnerable to certain viral infections. Like other salamanders, the axolotl genome is one of the largest (32 Gb) and the impact of genome size on Ig loci architecture is unknown. To better understand the immune response in axolotl, we aimed to characterize the immunoglobulin loci of A. mexicanum and compare it with other model tetrapods. MethodsThe most recently published genome sequence of A. mexicanum (V6) was used for alignment-based annotation and manual curation using previously described axolotl Ig sequences or reference sequences from other tetrapods. Gene models were further curated using A. mexicanum spleen RNA-seq data. Human reference genomes, Xenopus tropicalis, and Danio rerio (zebrafish) were used for comparison. ResultsCanonical A. mexicanum Heavy chain (IGH), lambda (IGL), sigma (IGS) and Surrogate light chain (SLC) loci were identified. No kappa locus was found. More than half of the IGHV genes and the IGHF gene are pseudogenes, there are no clan I IGHV genes and CDRH3 diversity is restricted. Although the IGH locus size is proportional to genome size, we found local size restriction in the IGHM gene and in the V gene intergenic distances. In addition, there were V genes with abnormally large V-intron sizes, which correlated with loss of gene functionality. ConclusionThe A. mexicanum immunoglobulin loci share the same general genome architecture as most studied tetrapods. Consistent with its large genome, Ig loci are larger; however, local size restrictions indicate evolutionary constraints likely to be imposed by high transcriptional demand of certain Ig genes, as well as the V(D)J recombination over very long genomic distance ranges. The A. mexicanum has undergone an extensive process of pseudogenization which partially explains a reduced potential repertoire diversity that may contribute to its impaired antibody response.

immunology↗

bioRxiv2018

Non-coding Class Switch Recombination-related transcription in human normal and pathological immune responses

BackgroundAntibody class switch recombination (CSR) to IgG, IgA or IgE is a hallmark of adaptive immunity, allowing antibody function diversification beyond IgM. CSR involves a deletion of the IgM/IgD constant region genes placing a new acceptor Constant (CH) gene, downstream of the VDJH exon. CSR depends on non-coding (CSRnc) transcription of donor I and acceptor IH exons, located 5 upstream of each CH coding gene. Although our knowledge of the role of CSRnc transcription has advanced greatly, its extension and importance in healthy and diseased humans is scarce.\n\nMethodsWe analyzed CSRnc transcription in 70,603 publicly available RNA-seq samples, including GTEx, TCGA and the Sequence Read Archive (SRA) using recount2, an online resource consisting of normalized RNA-seq gene and exon counts, as well as coverage BigWig files that can be programmatically accessed through R. CSRnc transcription was validated with a qRT-PCR assay for I, I{gamma}3 and I{gamma}1 in humans in response to vaccination.\n\nResultsWe mapped IH transcription for the human IgH locus, including the less understood IGHD gene. CSRnc transcription was restricted to B cells and is widely distributed in normal adult tissues, but predominant in blood, spleen, MALT-containing tissues, visceral adipose tissue and some so-called \"immune privileged\" tissues. However, significant I{gamma}4 expression was found even in non-lymphoid fetal tissues. CSRnc expression in cancer tissues mimicked the expression of their normal counterparts, with notable pattern changes in some common cancer subsets. CSRnc transcription in tumors appears to result from tumor infiltration by B cells, since CSRnc transcription was not detected in corresponding tumor-derived immortal cell lines. Additionally, significantly increased I5 transcription in ileal mucosa in Crohns disease with ulceration was found.\n\nConclusionsCSRnc transcription occurs in multiple anatomical locations beyond classical secondary lymphoid organs, representing a potentially useful marker of effector B cell responses in normal and pathological immune responses. The pattern of IH exon expression may reveal clues of the local immune response (i.e. cytokine milieu) in health and disease. This is a great example of how the public recount2 data can be used to further our understanding of transcription, including regions outside the known transcriptome.

immunology↗