Dataset Information

A clonality analysis based on T-cell receptor beta and delta loci for high-grade gastrointestinal lymphoma in dogs.

ABSTRACT: Clonality assays based on antigen receptors are used as adjunct examinations in the diagnosis of lymphoproliferative diseases. We investigated the usefulness of the T-cell receptor beta (TRB) and T-cell receptor delta (TRD) loci in clonality assays for high-grade gastrointestinal (GI) lymphoma in dogs. For TRB, we used primers reported previously; for TRD, we designed primers for each of the V and J genes based on genomic sequences. Genomic DNA was extracted from 39 formalin-fixed, paraffin-embedded sections of high-grade GI lymphoma diagnosed histologically. The sensitivity of TRB and TRD primers for GI lymphoma was 41.0% and 38.5%, respectively, which was lower than the 82.1% sensitivity of T-cell receptor gamma (TRG) primers However, some cases that could not be detected using TRG primers had clonality with either TRB or TRD primers. We found the TRG locus to be more suitable as a first choice for the assay of canine lymphoma clonality than the TRB and TRD loci. However, the detection rate of T-cell clonality may be enhanced using TRB and TRD primers for lymphoma cases not detected using TRG primers.

SUBMITTER: Takanosu M

PROVIDER: S-EPMC9597334 | biostudies-literature | 2022 Nov

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

A clonality analysis based on T-cell receptor beta and delta loci for high-grade gastrointestinal lymphoma in dogs.

Takanosu Masamine M Kagawa Yumiko Y

Journal of veterinary diagnostic investigation : official publication of the American Association of Veterinary Laboratory Diagnosticians, Inc 20220802 6

Clonality assays based on antigen receptors are used as adjunct examinations in the diagnosis of lymphoproliferative diseases. We investigated the usefulness of the T-cell receptor beta (TRB) and T-cell receptor delta (TRD) loci in clonality assays for high-grade gastrointestinal (GI) lymphoma in dogs. For TRB, we used primers reported previously; for TRD, we designed primers for each of the V and J genes based on genomic sequences. Genomic DNA was extra ...[more]

PMID: 35918913

Similar Datasets

Project description:The complete germline repertoires of the channel catfish, Ictalurus punctatus, T cell receptor (TR) loci, TRAD, TRB, and TRG were obtained by analyzing genomic data from PacBio sequencing. The catfish TRB locus spans 214 kb, and contains 112 TRBV genes, a single TRBD gene, 31 TRBJ genes and two TRBC genes. In contrast, the TRAD locus is very large, at 1,285 kb. It consists of four TRDD genes, one TRDJ gene followed by the exons for TRDC, 125 TRAJ genes and the exons encoding the TRAC. Downstream of the TRAC, are 140 TRADV genes, and all of them are in the opposite transcriptional orientation. The catfish TRGC locus spans 151 kb and consists of four diverse V-J-C cassettes. Altogether, this locus contains 15 TRGV genes and 10 TRGJ genes. To place our data into context, we also analyzed the zebrafish TR germline gene repertoires. Overall, our findings demonstrated that catfish possesses a more restricted repertoire compared to the zebrafish. For example, the 140 TRADV genes in catfish form eight subgroups based on members sharing 75% nucleotide identity. However, the 149 TRAD genes in zebrafish form 53 subgroups. This difference in subgroup numbers between catfish and zebrafish is best explained by expansions of catfish TRADV subgroups, which likely occurred through multiple, relatively recent gene duplications. Similarly, 112 catfish TRBV genes form 30 subgroups, while the 51 zebrafish TRBV genes are placed into 36 subgroups. Notably, several catfish and zebrafish TRB subgroups share ancestor nodes. In addition, the complete catfish TR gene annotation was used to compile a TR gene segment database, which was applied in clonotype analysis of an available gynogenetic channel catfish transcriptome. Combined, the TR annotation and clonotype analysis suggested that the expressed TRA, TRB, and TRD repertoires were generated by different mechanisms. The diversity of the TRB repertoire depends on the number of TRBV subgroups and TRBJ genes, while TRA diversity relies on the many different TRAJ genes, which appear to be only minimally trimmed. In contrast, TRD diversity relies on nucleotide additions and the utilization of up to four TRDD segments.

Dataset Information

A clonality analysis based on T-cell receptor beta and delta loci for high-grade gastrointestinal lymphoma in dogs.

Publications

A clonality analysis based on T-cell receptor beta and delta loci for high-grade gastrointestinal lymphoma in dogs.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets