Comprehensive profiling of clock genes expression in colorectal cancer (CRC).
Authors: Battaglin Francesca , Baca Yasmine , Brodskiy Pavel , Xiu Joanne , Jayachandran Priya , Algaze Sandra , Arai Hiroyuki , Soni Shivani , Roussos Torres Evanthia T. , Mumenthaler Shannon M. , Zhang Wu , Goldberg Richard M. , Weinberg Benjamin Adam , Lou Emil , Shields Anthony Frank , Marshall John , Korn Wolfgang Michael , Kay Steve A. , Lenz Heinz-Josef 
Published: June 2022

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Background: Disruption of the circadian clock has been linked to cancer risk, development and progression. Core clock proteins are emerging as novel therapeutic targets in cancer. We previously showed that polymorphisms in clock genes were associated with anti-VEGF treatment outcome in metastatic CRC. Here we further evaluated the molecular landscape of clock pathway alterations in CRC. Methods: 7591 CRC tested at Caris Life Sciences (Phoenix, AZ) with WTS (Illumina NovaSeq) and NextGen DNA sequencing (NextSeq, 592 Genes and NovaSEQ, WES) were analyzed. Clock gene Score (CS) was determined using expression of core clock genes Z scores (positives of CLOCK, ARNTL, RORA/B/C and negatives of repressors CRY1/2, PER1/2/3, REVERBA/B) stratified by quartiles. xCell was used to quantify cell infiltration in the tumor microenvironment (TME). Consensus molecular subtypes (CMS) were assessed by RNAseq. Significance was determined as P-values adjusted for multiple testing ( q) of <.05. Real world survival was obtained from insurance claims data and Kaplan-Meier estimates were calculated for comparison. Results: CS was higher in primary tumors than metastases and in right- than left-sided CRC ( P <.001). Liver metastases were associated with lower CS (23% Q1 vs 19% Q4, P <.001). CS was positively associated with CMS1 and 3 (21 vs 11% and 23 vs 9%, respectively, Q4 vs Q1) and negatively correlated with CMS2 and 4 (22 vs 32% and 34 vs 48%) (all P <.001). These associations were confirmed in mismatch repair proficient (pMMR) tumors. Overall, TMB-H and dMMR/MSI-H were positively associated with CS (11 vs 6% and 8 vs 4%, Q4 vs Q1, q <.0001) and PD-L1 showed a similar trend ( P <.01, q =.06); the association with TMB-H was not significant in pMMR. High CS was associated with alterations of genes in WNT signaling, RAS, PI3K, TGF-β, and NOTCH pathways, while negatively associated with TP53 mutations, HER2 expression and CDX2 copy numbers, confirmed in pMMR (all q <.05). CS negatively correlated with the angiogenesis pathway signature (Q1 vs Q4 Z score: 6.6 vs -4.6, P <.001). B cells, M1 and M2 macrophages, neutrophils, NK, Tregs, CD4+ and CD8+ T cells, and myeloid dendritic cells were more abundant in the TME of tumors with high CS while cancer associated fibroblasts were lower, regardless of MMR status (all q <.001). Individually, ARNTL tumor expression below median was associated with better OS (overall: HR 0.88, 95% CI [0.82-0.94]; pMMR: HR 0.88 [0.81-0.94]) and longer time on treatment of bevacizumab (overall: HR 0.91 [0.83-0.99]; pMMR: HR 0.91 [0.83-0.99]). Conclusions: This is the most extensive profiling study to investigate the expression of clock genes in CRC. Our data show that clock genes expression is strongly associated with distinct molecular features, immune cell infiltration, angiogenesis pathway enrichment and patient outcomes. These findings support the clock pathway as a therapeutic target in CRC, with a major role in CRC biology and TME modulation.