TRAV gene segments further away from the TRAJ gene segment cluster appear more commonly in human tumor and blood samples

• Published in: Molecular immunology 2019-12, Vol.116, p.174-179
• Main Authors: Pakasticali, Nagehan, Gill, Tommy, Chobrutskiy, Boris I., Tong, Wei Lue, Ramsamooj, Michael, Blanck, George
• Format: Article
• Language: English
• Subjects: Genomic distance; Humans; Immune receptor recombinations; Lymphocytes, Tumor-Infiltrating - immunology; Multigene Family - genetics; Multigene Family - immunology; Neoplasms - genetics; Neoplasms - immunology; Receptors, Antigen, T-Cell, alpha-beta - genetics; Receptors, Antigen, T-Cell, alpha-beta - immunology; V and J usage
• ISSN: 0161-5890; 1872-9142
• DOI: 10.1016/j.molimm.2019.10.010

•Over 10,000 TRA immune receptor gene recombinations were evaluated.•The TRA recombinations represent tumor and blood samples.•The analyses indicated that there is increased usage of distal TRAV segments.•Data are consistent with mouse analyses and extend TRAV usage bias to a human disease setting. We considered the possibility that the greater the distance between an immune receptor V and J, the more likely the V usage. Such a hypothesis is supported by results from mouse experiments. And, such a hypothesis is consistent with the fundamental nature of recombination and genomic distance: the further the distance, the greater the chance of a DNA break. Thus, we exploited the vast dataset of V and J recombination reads available for the human TRA gene, particularly from cancer and blood specimens, to assess the frequency of TRAV usage with respect to distance from the TRAJ cluster. Results indicated that, indeed, over the entire TRAV cluster, there is a greater chance of V usage the further the distance from the J cluster. These results do not address causation, and are not consistent for certain individual V gene segments, but the results do indicate that overall, the larger the distance between the V and J gene segment cluster, the more likely the appearance of at least a subset of TRAV segments, particularly among tumor infiltrating lymphocytes. With a similar approach, the distal TRAV gene segments were also found to be more commonly associated with a subset of distal TRAJ segments. These results have implications for restrictions on the apparent TRA repertoire in disease settings.