Mismatch repair deficiency predicts response of solid tumors to PD-1 blockade

Abstract

The genomes of cancers deficient in mismatch repair contain exceptionally high numbers of somatic mutations. In a proof-of-concept study, we previously showed that colorectal cancers with mismatch repair deficiency were sensitive to immune checkpoint blockade with antibodies to programmed death receptor-1 (PD-1). We have now expanded this study to evaluate the efficacy of PD-1 blockade in patients with advanced mismatch repair-deficient cancers across 12 different tumor types. Objective radiographic responses were observed in 53% of patients, and complete responses were achieved in 21% of patients. Responses were durable, with median progression-free survival and overall survival still not reached. Functional analysis in a responding patient demonstrated rapid in vivo expansion of neoantigen-specific T cell clones that were reactive to mutant neopeptides found in the tumor. These data support the hypothesis that the large proportion of mutant neoantigens in mismatch repair-deficient cancers make them sensitive to immune checkpoint blockade, regardless of the cancers' tissue of origin.

Fig. 1. Patient survival and clinical response to Pembrolizumab across 12 different tumor types with mismatch repair deficiency

(A) Tumor types across 86 patients. (B) Waterfall plot of all radiographic responses across 12 different tumor types at 20 weeks. Tumor responses were measured at regular intervals and values show the best fractional change of the sum of longest diameters (SLD) from the baseline measurements of each measurable tumor. (C) Confirmed radiographic objective responses at 20 weeks in blue compared to the best radiographic responses in the same patients in red. The mean time to the best radiographic response was 28 weeks. (D) Swimmer plot showing survival for each patient with mismatch repair deficient tumors, indicating death, progression and time off therapy. (E) Kaplan-Meier estimates of progression-free survival and (F) overall patient survival.

Fig. 2. TCR clonal dynamics and mutation associated neoantigen recognition in patients responding to PD-1 blockade

(A) T cell receptor (TCR) sequencing was performed on serial peripheral T cell samples obtained before and after PD-1 blockade. Tumor tissue with mismatch repair deficiency was obtained from three responding patients. Figures show 15 TCR clones with the highest fold change in frequency after treatment (left panels) that was also found in the original tumor (right panels). (B) Whole exome sequencing was performed on tumor and matched normal tissue from patient 19. Somatic alterations were analyzed using a neo-antigen prediction pipeline to identify putative mutation associated neoantigens (MANAs). Reactivity to 15 candidate MANAs was tested in a 10 day cultured IFNγ ELISpot assay. Data are shown as the mean number of spot forming cells (SFC) per 10⁶ T cells (top) or mean cytokine activity (bottom) of triplicate wells +/− SD. (C) Seven candidate MANAs were selected for TCR analysis based on ELISpot reactivity (D) MANA-specific T cell responses were identified against 3/7 candidate MANAs (MANA1, MANA2 and MANA4) after a 10-day in vitro stimulation (left panels). MANA specific clones were identified by significant expansion in response to the relevant peptide and no significant expansion in response to any other peptide tested (fig. S3). Data are shown as the fold change in TCR clone frequency compared to the frequency of that clone after identical culture without peptide. These T cell clones were also found in the original tumor biopsy (right panels). (E) Frequency of MANA-specific clones, carcinoembryonic antigen (CEA) and radiographic response in the tumor [from (D)] were tracked in the peripheral blood before treatment, and at various times after pembrolizomab treatment. Time is shown in weeks after first pembrolizumab dose. (F) In vitro binding and stability assays demonstrate the affinity kinetics of each relevant MANA and the corresponding WT peptide (when applicable) for their restricting HLA I allele. The A*02:01-restricted Influenza M GILGFVTL epitope was used as a negative control for each assay and known HLA-matched epitopes were used as positive controls when available. Data are shown as counts per second with increasing peptide concentration for binding assays (top panel) or counts per minute over time for stability assays (bottom panel). Data points indicate the mean of two independent experiments +/− SD. *p < 0.05, **p < 0.01, ***p < 0.001.

Fig. 3. Mismatch repair deficiency across 12,019 tumors

Proportion of tumors deficient in mismatch repair in each cancer subtype, expressed as a percentage. Mismatch repair deficient tumors were identified in 24 out of 32 tumor subtypes tested, more often in early stage (defined as stage < IV) disease.