Cell-free DNA methylation of selected genes allows for early detection of the three major cancers in women

Authors and Affiliations:

Sandra P. Nunes ^1,2, Catarina Moreira-Barbosa ¹, Sofia Salta ^1,2, Susana Palma de Sousa ³, Inês Pousa ⁴, Júlio Oliveira ⁴, Marta Soares ⁴, Licínio Rego ⁵, Teresa Dias ⁵, Jéssica Rodrigues ⁶, Luís Antunes ⁶, Rui Henrique ^1,7,8 and Carmen Jerónimo ^1,8,

¹  Cancer Biology & Epigenetics Group—Research Center, Portuguese Oncology Institute of Porto (CI-IPOP), 4200-072 Porto, Portugal;

²  Master in Oncology, Institute of Biomedical Sciences Abel Salazar, University of Porto (ICBAS-UP), 4050-313 Porto, Portugal;

³  Breast Cancer Clinic and Department of Medical Oncology, Portuguese Oncology Institute of Porto, 4200-072 Porto, Portugal;

⁴  Lung Cancer Clinic and Department of Medical Oncology, Portuguese Oncology Institute of Porto, 4200-072 Porto, Portugal;

⁵  Digestive Tract Pathology Clinic and Surgical Oncology, Portuguese Oncology Institute of Porto, 4200-072 Porto, Portugal;

⁶  Department of Epidemiology, Portuguese Oncology Institute of Porto, 4200-072 Porto, Portugal;

⁷  Department of Pathology, Portuguese Oncology Institute of Porto, 4200-072 Porto, Portugal;

⁸  Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar– University of Porto (ICBAS-UP), 4050-313 Porto, Portugal;

Abstract:

Background: Breast (BrC), colorectal (CRC) and lung (LC) cancers are the three most common and deadly cancers in women. Cancer screening entails an increase in early stage disease detection but is hampered by high false-positive rates and overdiagnosis/overtreatment. Aberrant DNA methylation occurs early in cancer and may be detected in circulating cell-free DNA (ccfDNA), constituting a valuable biomarker and enabling non-invasive testing for cancer detection. We aimed to develop a ccfDNA methylation-based test for simultaneous detection of BrC, CRC and LC.

Methods: CcfDNA from BrC, CRC and LC patients and asymptomatic controls were extracted from plasma, sodium-bisulfite modified and whole-genome amplified. APC, FOXA1, MGMT, RARβ2, RASSF1A, SCGB3A1, SEPT9, SHOX2 and SOX17 promoter methylation levels were determined by multiplex quantitative methylation-specific PCR. Associations between methylation and standard clinicopathological parameters were assessed. Biomarkers’ diagnostic performance was also evaluated.

Results: A “PanCancer” panel (APC, FOXA1, RASSF1A) detected the three major cancers with 72% sensitivity and 74% specificity, whereas a “CancerType” panel (SCGB3A1, SEPT9 and SOX17) indicated the most likely cancer topography, with over 80% specificity, although with limited sensitivity.

Conclusions: CcfDNA’s methylation assessment allows for simultaneous screening of BrC, CRC and LC, complementing current modalities, perfecting cancer suspects’ triage, increasing compliance and cost-effectiveness.

Journal: Cancers

Link: https://www.mdpi.com/2072-6694/10/10/357