Fig. 1

A cytotoxicity signature is associated with clonal persistence during in vitro expansion. A Timeline of sample collection. At the recurrence timepoint, orange cells represent T cells derived from the ACT product (based on TcR matching), while pink cells represent endogenous T cells. Bloods at baseline and recurrence were drawn at the time of tumor harvest. B Alluvial plot displaying the frequency in onset blood, onset tumor and ACT product of all clonal groups found in at least two of the three samples. Thresholds of expansions are as follows: singleton = only one cell in the clonal group; rare = the clonal group includes more than 1 cell and occupies less than 0.25% of the sample-specific repertoire; expanded = the clonal group occupies between 0.25% and 0.75% of the sample-specific repertoire, highly expanded = the clonal group occupies more than 0.75% of the sample-specific repertoire. Clonal groups that are highly expanded in the onset tumor and remain highly expanded in culture are classified as preserved. Clonal groups that are highly expanded in the onset tumor and became rare, singletons ore were not found in culture are classified as contracted. For ease of comparison, supplemental Fig. 1 includes the same panel without the middle column. C Table listing the absolute number of cells with the indicated clonotype, as well as the percentage of the repertoire occupied by each clonal group (in parentheses). D Heatmap of differentially expressed genes between expanded TILs belonging to a clonal group that was preserved vs contracted during the ACT culture. Rows represent genes ordered by fold changes. Columns represent individual cells grouped by identity class as indicated on the horizontal bars. Values are scaled and mean-centered log2-transformed gene counts. Arrowheads indicate genes that were also returned by the analysis in F. E Scatter plot of UMAP embeddings of onset TILs, colored by belonging to a clonal group that was preserved or contracted in culture. F Violin plots of genes identify by feature selection using stochastic gates as discriminating between the region occupied by the cells belonging to the preserved vs. contracted clonal groups