Fig. 2

Mechanism of intratumoral heterogeneity affecting clinical outcome of immunotherapy in tumor neoantigen and microenvironment. a Neoantigen score of top 100 putative neoantigen of each patient between ITH-L group and ITH-H group. b Association between clonal neoantigen and ITH. The proportion of clonal neoantigen in patients of different ITH level is shown at left violin plot and neoantigen score difference between clonal and subclonal neoantigen is shown at right violin plot. c Neoantigen scores of clonal neoantigens differ across ITH groups (left) while neoantigen scores of subclonal neoantigens don’t (right). d Distribution of Neoantigen Fitness of each patient in ITH-H group and ITH-L group. e Immune subtypes proportion of ITH-H and ITH-L group in Liu cohort (left), TCGA-LUAD (middle), TCGA-LUSC (right). f Schematic representation of potential interplay of tumor mutation burden and intratumoral heterogeneity. High TMB is a positive factor to the response of immunotherapy while high ITH is a negative factor to the response of immunotherapy. In the situation when patient had high TMB with low ITH, the major clone in the tumor contained a relatively higher number and higher proportion of immunogenic neoantigens that responded to T cells (Top left). When patient had high TMB but with high ITH, the proportion of clonal immunogenic neoantigens decreased and patient responded less to T cells during ICIs therapy (Bottom left). When patient had low TMB with low ITH, the total number of immunogenic neoantigens decreased though the proportion of clonal immunogenic neoantigens still remained relative higher. Therefore, the clinical outcomes of TMB-L&ITH-L patients might be worse than that of TMB-H&ITH-L (Top right). However, when patient with low TMB and high ITH received the worst clinical outcome due to the small number and low proportion of clonal immunogenic neoantigens (Bottom right)