New insight into the genomic structure of dog T cell receptor beta (TRB) locus inferred from expression analysis

Mineccia, Micaela; Massari, Serafina; Linguiti, Giovanna; Ceci, Luigi; Ciccarese, Salvatrice; Antonacci, Rachele

doi:10.1016/j.dci.2012.03.010

Cited by 26 publications

(65 citation statements)

References 48 publications

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“…1) is similar to that of the dog (see Ref. (Mineccia et al 2012) for the locus of Canis lupus familiaris). Like in the dog, the ferret TRB locus spans about 300 Kb, which is much less than the 650 Kb long locus of humans.…”

Section: Resultssupporting

confidence: 59%

“…We combined HTS and genome analysis to describe the (expressed) T cell receptor genes in the TRB locus of the ferret. The genomic organization of the ferret TRB locus is very similar to that described in other mammals such as human, mouse, dog, and rabbit (Mineccia et al 2012;Antonacci et al 2014): the locus is flanked by MOXD2 and EPHB6 at the 5′ and 3′ ends, respectively, and consists of a library of V genes followed by two D-J-C clusters, followed by a V gene, which is nonfunctional in the ferret, with an inverted transcriptional orientation. Thus, the ferret confirms the strong organizational conservation of mammalian TRB loci.…”

Section: Discussionmentioning

confidence: 74%

“…In this study, we annotate the expressed V, D, J, and C genes in the ferret TRB locus by combining genomic information from the locus with HTS of the ferret TRB repertoire. We find that the TRB locus of the ferret has a similar structure to that of other mammalian TRB loci, such as mouse and human (Glusman et al 2001), bovine (Connelley et al 2009), dog (Mineccia et al 2012), and rabbit (Antonacci et al 2014): a library of V genes, followed by two (or three in bovine) D-J-C clusters. Each cluster consists of one D gene, six or seven (six in ferret) J genes, and a single C gene.…”

Section: Introductionmentioning

confidence: 76%

“…Electronic supplementary material The online version of this article (https://doi.org/10.1007/s00251-019-01142-9) contains supplementary material, which is available to authorized users. are much more common than γδ T cells in both human and dog (Mineccia et al 2012). The β chain (at least in humans) tends to interact more closely with the peptide antigen than the α chain (Glanville et al 2017), making the TRB locus the most interesting first candidate to annotate in detail.…”

Section: Introductionmentioning

confidence: 99%

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Characterization of the ferret TRB locus guided by V, D, J, and C gene expression analysis

et al. 2019

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The domestic ferret, Mustela putorius furo, is an important mammalian animal model to study human respiratory infection. However, insufficient genomic annotation hampers detailed studies of ferret T cell responses. In this study, we analyzed the published T cell receptor beta (TRB) locus and performed high-throughput sequencing (HTS) of peripheral blood of four healthy adult ferrets to identify expressed V, D, J, and C genes. The HTS data is used as a guide to manually curate the expressed V, D, J, and C genes. The ferret locus appears to be most similar to that of the dog. Like other mammalian TRB loci, the ferret TRB locus contains a library of variable genes located upstream of two D-J-C gene clusters, followed by a (in the ferret non-functional) V gene with an inverted transcriptional orientation. All TRB genes (expressed or not) reported here have been approved by the IMGT/WHO-IUIS nomenclature committee.

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Section: Resultssupporting

confidence: 59%

Section: Discussionmentioning

confidence: 74%

Section: Introductionmentioning

confidence: 76%

Section: Introductionmentioning

confidence: 99%

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Characterization of the ferret TRB locus guided by V, D, J, and C gene expression analysis

et al. 2019

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“…Several immunoglobulin and T cell receptor loci of veterinary interest have been fully described, and sequence data for some are available through a public database (IMGT). 3,29,34,35 However, most loci comprise a large number of genes requiring more primers than is feasible for multiplexing in a single tube. Knowledge of the V/J usage informs primer design because non-rearranged genes don't have to be considered (Fig.…”

Section: Future Perspectivesmentioning

confidence: 99%

Clonality Testing in Veterinary Medicine

2016

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The accurate distinction of reactive and neoplastic lymphoid proliferations can present challenges. Given the different prognoses and treatment strategies, a correct diagnosis is crucial. Molecular clonality assays assess rearranged lymphocyte antigen receptor gene diversity and can help differentiate reactive from neoplastic lymphoid proliferations. Molecular clonality assays are commonly used to assess atypical, mixed, or mature lymphoid proliferations; small tissue fragments that lack architecture; and fluid samples. In addition, clonality testing can be utilized to track neoplastic clones over time or across anatomic sites. Molecular clonality assays are not stand-alone tests but useful adjuncts that follow clinical, morphologic, and immunophenotypic assessment. Even though clonality testing provides valuable information in a variety of situations, the complexities and pitfalls of this method, as well as its dependency on the experience of the interpreter, are often understated. In addition, a lack of standardized terminology, laboratory practices, and interpretational guidelines hinders the reproducibility of clonality testing across laboratories in veterinary medicine. The objectives of this review are twofold. First, the review is intended to familiarize the diagnostic pathologist or interested clinician with the concepts, potential pitfalls, and limitations of clonality testing. Second, the review strives to provide a basis for future harmonization of clonality testing in veterinary medicine by providing diagnostic guidelines.

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Genomic characteristics of the T cell receptor (TRB) locus in the rabbit (Oryctolagus cuniculus) revealed by comparative and phylogenetic analyses

et al. 2014

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The present study identifies the genomic structure and the gene content of the T cell receptor beta (TRB) locus in the Oryctolagus cuniculus whole genome assembly. The rabbit locus spans less than 600 Kb and the general genomic organization is highly conserved with respect to other mammalian species. A pool of 74 TRB variable (TRBV) genes distributed in 24 subgroups are located upstream of two in tandem-aligned D-J-C gene clusters, each composed of one TRBD, six TRBJ genes, and one TRBC gene, followed by a single TRBV gene with an inverted transcriptional orientation. All TRB genes (functional, ORF, pseudogenes) of this paper have been approved by the IMGT/WHO-IUIS nomenclature committee. Additionally, five potentially functional protease serine (PRSS) trypsinogen or trypsinogen-like genes were identified: two in tandem PRSS-like genes, followed by two PRSS genes with unique traits, lie downstream of the TRBV1 gene and one PRSS gene is located about 400 Kb away downstream of the TRBV genes. Comparative and phylogenetic analyses revealed that multiple duplication events within a few subgroups have generated the germline repertoire of the rabbit TRBV genes, which is substantially larger than those described in humans, mice, and dogs, suggesting that a strong evolutionary pressure has selected the development of a species-specific TRBV repertoire. Hence, the genomic organization of the TRB locus in the genomes appears to be the result of a balance between the maintenance of a core-number of genes essential for the immunological performances and the requirement of newly arisen genes.

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New insight into the genomic structure of dog T cell receptor beta (TRB) locus inferred from expression analysis

Cited by 26 publications

References 48 publications

Characterization of the ferret TRB locus guided by V, D, J, and C gene expression analysis

Characterization of the ferret TRB locus guided by V, D, J, and C gene expression analysis

Clonality Testing in Veterinary Medicine

Genomic characteristics of the T cell receptor (TRB) locus in the rabbit (Oryctolagus cuniculus) revealed by comparative and phylogenetic analyses

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