Comprehensive profiling of clock genes expression in hepatocellular carcinoma (HCC).
Authors: Battaglin Francesca , Baca Yasmine , Xiu Joanne , Soni Shivani , Algaze Sandra , Jayachandran Priya , Roussos Torres Evanthia T. , Mumenthaler Shannon M. , Lo Jae Ho , Mittal Pooja , Zhang Wu , Goldberg Richard M. , Weinberg Benjamin Adam , Lou Emil , Shields Anthony F. , Marshall John , Goel Sanjay , El-Khoueiry Anthony B. , Kay Steve A. , Lenz Heinz-Josef 
Published: June 2023

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Background: The circadian clock mechanism controls the physiological homeostasis of the liver and plays a key role in hepatocarcinogenesis. Recent evidence unveiled core clock proteins as novel therapeutic targets in cancer. Our group showed that clock regulators BMAL1 and CLOCK can promote proliferation of liver cancer cells by modulating the cell cycle checkpoint kinase Wee1. Here we further evaluated the molecular landscape of clock pathway alterations in HCC leveraging multi-platform profiling of patient tumor samples. Methods: 780 HCC 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). Significance was determined as P-values and adjusted for multiple testing ( q) of < .05. Gene expression profiles were analyzed for transcriptional signatures predictive of response to immunotherapy including the T cell inflamed score (TIS) and IFG score. Real world survival was obtained from insurance claims data and Kaplan-Meier estimates were calculated for comparison. Results: CS was higher in metastatic sites than primary tumors (median transcripts per million [TPM]: 0.81 vs 0.37, P < .05). No significant differences in patient age and sex were observed between CS Q1 (lowest) and Q4 (highest) cohorts, although a trend towards a higher frequency of males was observed in Q4 (76% vs 68%, Q4 vs Q1, P = .07). CS was positively associated with telomerase subunit TERT mutations (64% vs 52%, Q4 vs Q1, P = .04) and negatively correlated with FGF3 copy number amplification (2% vs 6%, P = .04) and WEE1 gene expression (median TPM: 15 vs 28, q < .05). No dMMR/MSI-H tumors were observed in our series and there were no significant associations with tumor mutational burden and PD-L1 protein expression. Expression of immune related genes was lower in tumors with high CS, including IDO1, CD80, PD-L1, LAG3, CD86, TIM3, PD-1 and PD-L2 (fold change: 0.57-0.67 q < .05). NK cell infiltration in the TME and the TIS score were also significantly lower in CS-high HCC ( q < .05). Individually, lower CLOCK and CRY1 tumor mRNA expression were associated with longer OS (Q1 vs Q4: CLOCK HR 0.71, 95%CI [0.51-0.98], P = .04 and CRY1 HR 0.70 [0.51-0.95], P = .02, respectively). Conclusions: This is the most extensive profiling study to investigate the expression of clock genes in HCC. Our data show that clock genes expression impacts patient survival and is associated with alterations in immune-related gene expression and TIS score which suggest a role in the modulation of anti-tumor immunity. These results support the clock pathway role as a oncogenic driver and its potential as a therapeutic target in HCC.