Abstract When preclinical research fails to replicate human biology, scientific progress stalls, clinical trials falter, and patients continue to suffer. While many factors contribute to these failures, lack of attention to pre-analytic variability is a seminal issue. We recently reported that even short-term exposure to ambient air is sufficient to trigger signaling changes in tumor and non-malignant biospecimens. Those changes in turn alter their biology and responsiveness to targeted therapies. Thus, characterization of tumors collected and processed under physioxia (3% O2) instead of current practice of collection and processing under ambient air (21% O2) will help to identify clinically relevant biomarkers that are affected by O2 tensions. This approach may help to reduce clinical trial failure rates and increase clinical translation of preclinical studies. Towards this goal, we collected human specimens (biopsies, ascites and pleural effusions from 94 donors) under physioxia, then divided the same specimen into two groups; one group maintained under physioxia, the other group exposed to ambient air. Both were for 45-60 minutes before fixing/processing. Samples were subjected to various biomarker analysis using IHC/IF, Western blotting to measure proteins, and nanopore sequencing for DNA methylation. We found the levels of pAKT, a clinically used biomarker of targeted therapy, were constantly higher in clinical samples under physioxia compared to ambient air. Similar effects of O2 tension on pERK and MDM4 levels occurred in cells isolated from ascites or pleural effusion in a time-dependent manner. A significant decrease in pEGFR and p53 levels were observed in cells under physioxia. Moreover, O2 tension-dependent differences extended to key epigenetic regulators including TET2. TET2 levels were lower under physioxia compared to ambient air. Consistently, nanopore sequencing revealed distinct differences in DNA methylation patterns under physioxia and ambient air. The observed differences in signaling pathways extended to cultured cells from ascites fluids and pleural effusions. However, there is a specificity in the effects of O2 tensions on biomarkers as we did not observe significant differences in pPDGFRβ, ATE1 and many other biomarkers under two O2 conditions. These results imply that the O2 tension affects specific biomarkers and epigenome. Collectively, O2 tension could result in dynamic and extensive changes in cell membrane, cytoplasmic and nuclear biomarkers. Observable changes of biomarkers could occur within an hour following exposure to ambient O2, and some changes could last for prolonged period. Thus, our current study lays out a new physiologically relevant biomarker validation/discovery platform, which may accelerate evaluation of physiologically relevant signaling networks, new drug discovery, and enhance clinical translation of preclinical observations. Citation Format: Ruizhong Wang, Adedeji Adebayo, Stephanie Adama, Steven M. Westphal, Hala Fatima, Carla S. Fisher, Hongyu Gao, Yunlong Liu, Ryla G. House, GEORGE SANDUSKY, Sean D. McCabe, Zhongping He, Jamunabai M. Prakash, Amber Roberts, Matt E. Thomas, Mohammad Al-Haddad, Sujani Yadlapati, Pam Rockey, William Berry, Mary B. James, Rana German, Emily M. Nelson, April M. Giron, Troy Moeller, Noah Xique, Kathy D. Miller, Harikrishna Nakshatri. The impact of oxygen exposure on clinical biomarkers - an underrecognized source of pre-analytic variability abstract. In: Proceedings of the American Association for Cancer Research Annual Meeting 2026; Part 1 (Regular Abstracts); 2026 Apr 17-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86(7 Suppl):Abstract nr 7293.
Wang et al. (Fri,) studied this question.