Figure 6.

Weighted and unweighted measures of entropy demonstrate selection for positively charged amino acids within the CDR3 of HFD TCR repertoires. The median CDR3 length was 14 amino acids, which we analyzed using several sequence entropy methods. A: Shannon entropy reveals enrichment of arginine and depletion of negatively charged amino acids in the CD8⁺ repertoires of HFD-fed mice. B: P-weighted Kullback-Leibler divergence with Hobohm1 clustering reveals that other positively charged amino acids are enriched within HFD CD8⁺ TCR repertoires from AT and that negatively charged amino acids are correspondingly depleted. C and D: Unweighted analyses using Shannon entropy (C) and P-weighted Kullback-Leibler divergence (D) show that these amino acid enrichments are due to clonotypes present at higher frequencies, although there is still enrichment for arginine, lysine, and histidine, all of which carry a positive charge at physiological pH. This indicates that obesity-induced changes in charge and polarity at the repertoire level are driven not only by highly expanded clonotypes but also by clonotypes that are present at lower frequencies.