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)


Alexandra Wong, Nishant Gandhi, Joanne Xiu, Sandra Algaze, Priya Jayachandran, Karam Ashouri, Shivani Soni, Wu Zhang, Jae Ho Lo, Pooja Mittal, Lesly Torres-Gonzalez, Benjamin Adam Weinberg, Emil Lou, Sanjay Goel, Jian Yu, Lin Zhang, Francesca Battaglin, Heinz- Josef Lenz

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 (ρ = 0.53, P < 0.05) and were not significantly different in primary vs. metastatic sites. CDK6-Q4 tumors were enriched for mutations in APCHNF1AKRAS and DNMT3A, while CDK6-Q1 was associated with BRAF mutations and PDL1+ tumors (P < 0.05). Mutations in ARID1ACDH1KMT2AFANCLNF2 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.

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