uCDR3 number and diversity characterization
The number of unique CDR3 (uCDR3) in
8 samples including both VC and CC samples was determined by CDR3
Nucleic acid sequence, and the number of uCDR3 between PBMC and TIL was
compared. The number of uCDR3 in TIL (mean = 14122.38, median = 8087)
was significantly lower than that of PBMC (mean = 63679.62, median =
56350.5) (Figure 5A, P = 0.00133). In addition, the number of the uCDR3
in each TIL sample was lower than that in its paired PBMC sample (Figure
5B). The accumulate relative abundance of Top10 ranked uCDR3 in every
TIL sample (mean = 50.49, median = 49.83) is higher than that in the
paired PBMC sample (mean = 16.32, median = 13.72). Notably, the
accumulate relative abundance of Top10 uCDR3 is more than 50% in 4 out
of 8 TIL samples. Moreover, we analyzed
the Shannon Entropy in each sample,
which is a quantitative measure of uncertainty that simultaneously takes
both richness and evenness into account. A higher
Shannon entropy indicates that the
TCR sample has more types of uCDR3 or a more even distribution of CDR3
reads. Shannon Entropy of TIL (mean = 4.93, median = 4.96) was
significantly lower than that of PBMC (mean = 9.01, median = 9.31)
(Figure 5D, P = 0.0004). The Shannon Entropy of each TIL sample was
lower than that in its paired PBMC sample (Figure 5E). Collectively, the
comparison of the uCDR3 number, relative abundance distribution of Top10
ranked uCDR3 and Shannon Entropy suggests that TIL samples have more
enriched T cell clones than PBMC.