RNA expression-based hypoxia score as a prognostic and predictive biomarker in hepatocellular carcinoma.
Authors: Connor Ashton , Krause Harris Benjamin , Price Brandee A. , Elliott Andrew , Khushman Moh'd M. , Lou Emil , Antonarakis Emmanuel S. , Goel Sanjay , Abdelrahim Maen , Kodali Sudha , Saharia Ashish , Ghobrial Rafik Mark , Sledge George W. , Barbas Andrew 
Published: June 2024

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Background: Hepatocellular carcinoma (HCC) has rising incidence and mortality rates. Tumor hypoxia is important in HCC pathogenesis but has not been effectively translated into practice. We studied whether an RNA expression-based hypoxia score (HS) can serve as a prognostic and predictive biomarker in HCC. Methods: Solid tumors across a range of tissues (N=91516) were tested at Caris Life Sciences (Phoenix, AZ) with NextGen Sequencing of DNA (592-gene or whole exome) and RNA (whole transcriptome), including 432 HCC. Mutation prevalence (Mt) was calculated for pathogenic SNVs/indels. PD-L1 expression (SP142; +: ≥2+, ≥5%) was tested by IHC. HS based on RNA expression of 15 genes and normalized across a range of solid tumors was implemented as previously described (Bhandari et al, 2019). Tumors were defined as HS high (-H), medium (-M) and low (-L) by hierarchical clustering. A transcriptomic signature associated with immunotherapy response (T-cell inflamed score) was applied. Fisher’s Exact/χ2 tests were applied as appropriate with p-values adjusted for multiple comparisons ( p < 0.05). Real-world overall survival (OS) data was obtained from insurance claims and log-rank estimates were calculated for molecularly defined subpopulations. Results: Of 432 HCC, 5% were classified as HS-H, 36% HS-M and 59% HS-L. Median age was 67 years (HS-H:70, -M:67, -L:67, p = 0.45), and 77% were male (HS-H: 68%, -M: 75, -L: 79, p= 0.43). The proportion of metastatic tumors did not significantly differ across the three HS groups (%; -H: 36, -M: 29, -L: 23, p= 0.16) nor did the score vary across metastatic sites (% HS-L; Adrenal gland: 46, Bone: 66, Lymph: 52, Misc.: 46, p= 0.49). Prevalence of TP53-Mt in HS-H (72.7%) was higher than in -M (39.5%) and -L (29.1%, p< 0.01). HS-H had higher prevalence of PD-L1+ and T cell-inflamed tumors as compared to -M and -L (PD-L1+ (%): 28.6 v 6.2 v 3.9, p< 0.01; T cell-inflamed (%): 86 v 46 v 17, p< 0.001). HS-H tumors had significantly shorter OS from date of collection (166 days [D]) v -M (396.5 D) and -L (513 D, p< 0.001). Yet, no significant difference in survival since start of treatment (SSOT) was observed in the patient subset that received Atezolizumab (Atezo) (-H: 210 D, -M: 355 D, -L: 386 D, p= 0.54). In HS-M tumors alone, SSOT was similar across investigated therapeutics (Atezo 322 D, Lenvatinib (Lenvat) 366.5 D, Sorafenib (Soraf) 289 D, p= 0.34). In HS-L tumors, patients treated with Soraf (1341 D) had significantly longer SSOT than with Lenvat (444 D) or with Atezo (281.5 D, p= 0.002). Conclusions: In HCC, RNA expression-based HS is associated with TP53 mutations and an immunosuppressive microenvironment. HS-H tumors has worse OS that may be improved with Atezo, whereas HS-L tumors may respond better to Soraf. HS is a potential prognostic and predictive biomarker in HCC that deserves validation in orthogonal data sets and prospective studies.