Jinzhuang Dou

Sample-level cell counts of CD8 clusters

Statistical test for association of lymphocyte cluster proportion with progression

Fig. S1. Patient disposition and characteristics. Fig. S2. Timing of OI biopsy collection did not correlate with response. Fig. S3. Major cell types identified in the tumor immune microenvironment. Fig. S4. CD4+ T cells identified in the tumor immune microenvironment. Fig. S5. Effector Treg cells in the HPV-positive OPC TIME highly express activation markers. Fig. S6. Treatment-induced changes in Treg proportions and clonotype frequencies. Fig. S7. CD8+ T cells in MHRs have different transcriptional programs vs those in nMHRs. Fig. S8. CD8+ T cells identified in the tumor immune microenvironment. Fig. S9. T cell clusters did not vary by anatomic site. Fig. S10. TRM CD8+ T cells had high expression of tumor-reactive, cytotoxic and checkpoint genes. Fig. S11. Fluorescent imaging of antigen-experienced, memory CD8+ T cells in baseline tumors. Fig. S12. Clonality of CD4+ T-cell TCR repertoire. Fig. S13. CD8+ T-cell TCR repertoire clonality and dynamics. Fig. S14. Phenotypes of treatment-altered CD8 clonotypes varied by response. Fig. S15. Predominant phenotypes of treatment-responsive CD8+ T-cell clonotypes. Fig. S16. Identification of HPV-specific TCRs. Fig. S17. NK cells that express Fc gamma receptor IIIa (CD16) are more activated than those that do not. Fig. S18. Increase in proportion of Effector1(IFNG+) cells associated with reduction in tumor viability.

Table S1. Patient and tumor characteristics. Table S2. Representativeness of study participants. Table S3. Clinical and histopathologic characteristics of individual patients. Table S4. Treatment related adverse events that occurred after first dose. Table S5. Adverse events related to immune checkpoint blockade. Table S6. Serious adverse events.

Clinical and single-cell features used in multivariable regression models

Single-cell RNA and TCR sequencing information and metrics

Differentially expressed genes of CD8+ T cells from MHRs vs non-MHRs at baseline

Differentially expressed genes of CD8 clusters

Statistical test for proportions of CD4+ T cell clusters in the tumor immune microenvironment stratified by histological response and timepoint

CD8+ T-cell clonotypes with significant frequency changes in response to treatment