A non-invasive blood test for multi-cancer detection and determination of tissue of origin preceding overt cancer diagnosis - PROJECT SUMMARY In the United States, it is estimated there are ~730,000 new cases of prostate cancer, lung cancer, colorectal cancer (CRC), and ovarian cancer annually. Advances in therapies during the past decades have significantly improved clinical outcomes. For many common cancers, however, treatment options are limited when the cancer is diagnosed with distant metastasis at later stages. Although early detection may reduce cancer mortality, systematic screening programs are available only for a limited number of cancers (e.g., CRC), which also faces challenges such as patient compliance and potential complications. Therefore, minimally-invasive blood-based tools that could detect these common cancers at earlier stages are likely to be paradigm-shifting in cancer control and care. The Prostate, Lung, Colorectal and Ovarian (PLCO) Cancer Screening Trial offers a unique opportunity and resource to investigate the possibility of applying our established 5hmC-Seal assay to: 1) explore cancer-specific early epigenetic marks, specifically 5-hydroxymethylcytosines (5hmC) in circulating cell-free DNA (cfDNA), when the cancer is not “overt”; and 2) develop a multi-cancer detection (MCD) tool that is minimally-invasive and possesses high sensitivity and specificity. Current MCD tests, e.g., Grail’s blood test, are not suitable to exploit the PLCO samples (e.g., that contain very limited amounts of DNA). In contrast, the 5hmC-Seal assay, only requiring nanograms amounts of DNA, together with the next-generation sequencing (NGS) holds the promise to address the challenge as a highly sensitive approach for PLCO biospecimens. Of note, our compelling preliminary results demonstrated: 1) the feasibility of applying the 5hmC-Seal assay to PLCO biospecimens (~200 µL plasma/sample); 2) analysis of genome-wide 5hmC from PLCO samples successfully identified a 5hmC-based model that detected CRC cases months or even years prior to overt disease; 3) altered 5hmC signatures associated with “overt” cases, such as CRC, gastric cancer, lung cancer, liver cancer, and brain cancer showed the biomarker potential of 5hmC in cfDNA for early cancer detection; 4) genome-wide 5hmC shows tissue-specificity and is associated with tissue-specific gene expression; and 5) the possibility of expanding the 5hmC-Seal protocol to PLCO samples stored under different conditions. The primary goal of this U01 is to investigate early epigenetic signatures for common cancers, specifically Prostate Cancer, Lung Cancer, CRC, and Ovarian Cancer, which were targeted by the PLCO Trial. In Aim 1, we will train and validate individual models for common cancers in PLCO samples. In Aim 2, we will develop an MCD algorithm for identifying “pre-clinical” cases in PLCO samples. In Aim 3, we will evaluate the PLCO-trained algorithm for early detection of multiple cancers in prospectively collected samples. This U01 leverages the PLCO biospecimens and our clinical resources as well as our previous studies of biomarker discovery using our highly sensitive 5hmC-Seal assay to fill a critical gap in knowledge required to improve our understanding of epigenetic signals associated with early cancer detection.
