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Nineteen additional groups were found at <3% clonal abundance.
Using a system in which precursor frequency can be manipulated in a murine melanoma model, we demonstrated that the clonal abundance of CD4+ T cells specific for self-tumor antigen positively correlated with antitumor efficacy.
Our findings assert that the differential effects of T cell clonal abundance on phenotypic outcome should be considered during the design of adoptive T cell therapies, including use of engineered T cells.
This approach has led to the discovery of eukaryotic taxa such as the MALV and MAST groups that often dominate the community in terms of clonal abundance.
In addition, analysis of the clonal abundance accounts for over 70% of all Foxp3+ T cells in tumor tissues so it is unlikely that we missed some Treg clones that account for a large fraction of Foxp3+ cells in tumors.
Analysis of the clonal abundance of Treg cells in TCRmini-Foxp3GFP mice bearing B16 melanoma tumors expressing a neoantigen led to the conclusion that Treg cells in tumors are dominated by Foxp3GFP+ cells expressing TCRs shared with effector T cells.
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In the above discussion, clonal abundances were defined by the number of B cells in each clone.
The differences between the results obtained using the weighted and unweighted UniFrac methods most probably reflect the fact that the composition of the phylogroup 3, 4 and 7 treponeme communities present within the two subject groups were relatively similar; however, their respective clonal abundances in the 20 subjects were quite variable.
In addition, of these four samples, two had ⩽20% PCs, suggesting a low abundance of clonal cells for LC amplification.
The differences in relative abundance of clonal complexes were mirrored by F ST values calculated from concatenated nucleotide sequences of the MLST loci, which indicated that the Australian dataset was 3.6% differentiated and the Curaçao set 9.9% differentiated from the Oxfordshire dataset.
Although differences in TCRβ mRNA quantity per cell exist [ 42, 43], clonal rank derived from mRNA abundance correlates well with those quantified from sorted cell population [ 42, 44] or its corresponding gDNA [ 45].
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