Non-invasive multi-cancer diagnosis using DNA hypomethylation of LINE-1 retrotransposons

The detection of circulating tumor DNA, which allows non-invasive tumor molecular profiling and disease follow-up, promises optimal and individualized management of patients with cancer. However, detecting small fractions of tumor DNA released when the tumor burden is reduced remains a challenge. We implemented a new highly sensitive strategy to detect base-pair resolution methylation patterns from plasma DNA and assessed the potential of hypomethylation of LINE-1 retrotransposons as a non-invasive multi-cancer detection biomarker. Resulting machine learning-based classifiers showed powerful correct classification rates discriminating healthy and tumor plasmas from 6 types of cancers in two independent cohorts (AUC = 88% to 100%, N = 747). This should lead to the development of more efficient non-invasive diagnostic tests adapted to all cancer patients, based on the universality of these factors. One-Sentence Summary LINE-1 retrotransposons hypomethylation is a sensitive and specific biomarker to detect multiple forms of cancer non-invasively. ### Competing Interest Statement CP, MM, MH, and CAA have an ongoing patent application relating to circulating tumor DNA analysis. ### Funding Statement The NGS facility was supported by ANR-10-EQPX-03 (Equipex) and ANR-10-INBS-09-08 (France Genomique Consortium) grants and by the Canceropole Ile-de-France. This research was supported by grants, of which C.P. was recipient, from: The European Research Council (ERC-StG EpiDetect), The Ligue contre le cancer (RS17-75-75), The prematuration program of the Centre National pour la Recherche Scientifique (CNRS), The SiRIC 2 Curie program (INCa-DGOS-Inserm_12554) The DEEP Strive funding (LABEX DEEP 11-LBX0044). CAA research was supported in part by the French government under management of Agence Nationale de la Recherche as part of the Investissements d avenir program, reference ANR-19-P3IA-0001 (PRAIRIE 3IA Institute). ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: Healthy white blood cells and healthy plasma were collected from blood of healthy donors through the French blood establishment (agreement #16/EFS/031) under French and European ethical practices. Blood samples from patients treated at the Institut Curie (Paris, France) were collected, after written informed consent, as part of the following studies: resectable metastatic colorectal cancers from the Prodige14 trial (approved by a French Personal Protection Committee : 'Comite de Protection des Personnes' (CPP) and registered in ClinicalTrials.gov under [NCT01442935][1]); non-small cell lung cancer and metastatic HR+ HER2- breast cancer from the ALCINA study (approved by a French Personal Protection Committee and registered in ClinicalTrials.gov under [NCT02866149][2]; treatment-naive ovarian cancer or triple-negative breast cancer patients eligible for surgery or neoadjuvant chemotherapy from the SCANDARE study (approved by the French National Agency for the Safety of Medicines and Health Products : 'Agence National de Securite du Medicament' (ANSM), a French Personal Protection Committee and registered in ClinicalTrials.gov under [NCT03017573][3]); multiple-types of metastatic cancers from the SHIVA02 study (approved by the French National Agency for the Safety of Medicines and Health Products : 'Agence National de Securite du Medicament' (ANSM), a French Personal Protection Committee and registered in ClinicalTrials.gov under [NCT03084757][4]), non-metastatic operable gastric cancers and advanced uveal melanoma from CTC-CEC-ADN study (approved by a French Personal Protection Committee and registered in [ClinicalTrials.gov][5] under [NCT02220556][6]). Additional archived samples were also retrieved from the biobank of the Institut Curie, patients having provided informed consent for research use. All samples were obtained in accordance with the ethical guidelines, with the principles of Good Clinical Practice and the Declaration of Helsinki. This study was approved by the Internal Review Board and Clinical Research Committee of the Institut Curie. I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as [ClinicalTrials.gov][5]. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes All data produced in the present study are available upon reasonable request to the authors and will soon be deposited and available at the Gene Expression Omnibus database. [1]: /lookup/external-ref?link_type=CLINTRIALGOV&access_num=NCT01442935&atom=%2Fmedrxiv%2Fearly%2F2024%2F01%2F23%2F2024.01.20.23288905.atom [2]: /lookup/external-ref?link_type=CLINTRIALGOV&access_num=NCT02866149&atom=%2Fmedrxiv%2Fearly%2F2024%2F01%2F23%2F2024.01.20.23288905.atom [3]: /lookup/external-ref?link_type=CLINTRIALGOV&access_num=NCT03017573&atom=%2Fmedrxiv%2Fearly%2F2024%2F01%2F23%2F2024.01.20.23288905.atom [4]: /lookup/external-ref?link_type=CLINTRIALGOV&access_num=NCT03084757&atom=%2Fmedrxiv%2Fearly%2F2024%2F01%2F23%2F2024.01.20.23288905.atom [5]: https://ClinicalTrials.gov [6]: /lookup/external-ref?link_type=CLINTRIALGOV&access_num=NCT02220556&atom=%2Fmedrxiv%2Fearly%2F2024%2F01%2F23%2F2024.01.20.23288905.atom