Ultrasensitive detection of circulating LINE-1 ORF1p as a specific multi-cancer biomarker

Abstract

Improved biomarkers are needed for early cancer detection, risk stratification, treatment selection, and monitoring treatment response. While proteins can be useful blood-based biomarkers, many have limited sensitivity or specificity for these applications. Long INterspersed Element-1 (LINE-1, L1) open reading frame 1 protein (ORF1p) is a transposable element protein overexpressed in carcinomas and high-risk precursors during carcinogenesis with negligible detectable expression in corresponding normal tissues, suggesting ORF1p could be a highly specific cancer biomarker. To explore the potential of ORF1p as a blood-based biomarker, we engineered ultrasensitive digital immunoassays that detect mid-attomolar (10-17 M) ORF1p concentrations in patient plasma samples across multiple cancers with high specificity. Plasma ORF1p shows promise for early detection of ovarian cancer, improves diagnostic performance in a multi-analyte panel, and provides early therapeutic response monitoring in gastric and esophageal cancers. Together, these observations nominate ORF1p as a multi-cancer biomarker with potential utility for disease detection and monitoring.

Competing Interest Statement

MST has received consulting fees from ROME Therapeutics and Tessera Therapeutics that are not related to this work. MST and JL have equity in ROME therapeutics. DTT has received consulting fees from ROME Therapeutics, Tekla Capital, Ikena Oncology, Foundation Medicine, Inc., NanoString Technologies, and Pfizer that are not related to this work. DTT is a founder and has equity in ROME Therapeutics, PanTher Therapeutics and TellBio, Inc., which is not related to this work. DTT receives research support from ACD-Biotechne, PureTech Health LLC, Ribon Therapeutics, and Incyte, which was not used in this work. LMS declares the following relationships: Consultant/advisory board: Novartis, Puma, G1 therapeutics, Daiichi Pharma, Astra Zeneca; Institutional research support: Phillips, Merck, Genentech, Gilead, Eli Lilly. SJK declares Consulting/advisory: Eli Lilly, Merck, BMS, Novartis, Astellas, AstraZeneca, Daiichi-Sankyo, Novartis, Sanofi-Aventis, Natera, Exact Sciences, Mersana. Stock/Equity: Turning Point Therapeutics, Nuvalent. BRR serves on SAB for VincenTech and receives research support from Novartis Institutes for Biomedical Research that are not related to this work. DRW has a financial interest in Quanterix Corporation, a company that develops an ultra-sensitive digital immunoassay platform. He is an inventor of the Simoa technology, a founder of the company and also serves on its Board of Directors. KHB declares relationships with Alamar Biosciences, Genscript, Oncolinea/PrimeFour Therapeutics, ROME Therapeutics, Scaffold Therapeutics, Tessera Therapeutics, and Transposon Therapeutics. MST and KHB receive royalties from sales of ORF1p antibodies and MST, CW, PCF, KRM, BTC, MPR, JL, DRW, and KHB are inventors on a patent related to this work.

Footnotes

* Targeted mass spectrometry data and 3rd generation Simoa assay data