Molecular and immune landscape by cyclin dependent kinase (CDK) 4/6 expression and TP53 mutational status in mismatch repair deficient/microsatellite instability high (dMMR/MSI-H) colorectal cancer (CRC).

Background: TP53 mutation (mut) has been reported to be associated with lower anti-tumor immunity and worse response to immune checkpoint inhibition (ICI) in CRC. Recent data suggest that CDK4/6 inhibition may enhance the efficacy of ICI in CRC by modulation of TP53 pathway mediators. We sought to characterize the impact of CDK4/6 expression on mutational profile, tumor microenvironment (TME), and clinical outcomes in patients with dMMR/MSI-H CRC stratified by TP53 mut status. Methods: Tumor profiling was performed for 13,942 samples by NextGen Sequencing on DNA (592-gene panel or WES) and RNA (WTS) at Caris Life Sciences (Phoenix, AZ). Of these, 932 specimens were dMMR/MSI-H. Cohorts were created based on top (Q4) and bottom (Q1) quartiles of CDK4/6 RNA expression (transcripts per million) and further divided based on TP53 mut. Chi-square, Fishers-exact, and Mann Whitney tests were used to determine statistical significance and adjusted for multiple hypothesis testing by Benjamini Hochberg (q, 0.05). Cell infiltration in the TME was estimated by quanTIseq. Insurance claims data was obtained to calculate ICI-survival using Kaplan-Meier estimates from the initiation of treatment to last contact. Results: CDK4 &6 tumor expression levels positively correlated in our dataset (r = 0.53, P, 0.05) and were not significantly different in primary vs. metastatic sites. CDK6-Q4 tumors were enriched for mutations in APC, HNF1A, KRAS and DNMT3A, while CDK6 Q1 was associated with BRAF mutations and PDL1+ tumors (P, 0.05). Mutations in ARID1A, CDH1, KMT2A, FANCL, NF2 and BMPR1A showed opposite trends in CDK6-Q4 compared to Q1 depending on TP53 mut. CDK6-Q4 tumors were associated with higher expression of immune checkpoint genes including CTLA4, CD274, PDCD1LG12, LAG3, CD80, CD86, PDCD1, HAVCR2, IFNG (fold change [FC] Q4 vs Q1: 1.65-3.23, q, 0.05); alongside a TME characterized by higher infiltration rates of B cells, M2 macrophages, and NK cells (FC: 1.19-1.61, q, 0.05), independent of TP53 mut. The T-cell inflamed signature score was also higher in CDK6-Q4 vs Q1 (q, 0.05). Similar results were observed for CDK4. In patients with TP53 mut tumors, CDK6 expression greater than the median was associated with longer ICI survival (HR= 0.46, 95% CI 0.22-0.95, P = 0.032), whereas no difference was observed in patients not stratified by TP53 mut. Conclusions: Our comprehensive analysis is the first to show distinct mutational profiles according to TP53 mut status, and differential expression of immune-related genes and TME cell infiltration independent of TP53 mut in CDK4/6 high vs low dMMR/MSI-H CRC. In our series, CDK6 expression correlated with ICI treatment benefit in TP53 mut tumors, warranting further studies to explore the potential of targeting the CDK4/6 axis to enhance ICI efficacy in CRC. Research Sponsor: Partly supported by National Cancer Institute; Gloria Borges WunderGlo Foundation; Dhont Family Foundation; Gene Gregg Pancreas Research Fund; San Pedro Peninsula Cancer Guild; Daniel Butler Research Fund; V foundation for cancer research; Victoria and Philip Wilson Research Fund; Fong research project; Ming Hsieh research fund.