Differential methylation of circulating free DNA assessed through cfMeDiP as a new tool for breast cancer diagnosis and detection of BRCA1/2 mutation
Abstract Background Recent studies have highlighted the importance of the cell-free DNA (cfDNA) methylation profile in detecting breast cancer (BC) and its different subtypes. We investigated whether plasma cfDNA methylation, using cell-free Methylated DNA Immunoprecipitation and High-Throughput Seq...
Saved in:
| Main Authors: | , , , , , , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2024-10-01
|
| Series: | Journal of Translational Medicine |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12967-024-05734-2 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1850275696145858560 |
|---|---|
| author | Piera Grisolia Rossella Tufano Clara Iannarone Antonio De Falco Francesca Carlino Cinzia Graziano Raffaele Addeo Marianna Scrima Francesco Caraglia Anna Ceccarelli Pier Vitale Nuzzo Alessia Maria Cossu Stefano Forte Raffaella Giuffrida Michele Orditura Michele Caraglia Michele Ceccarelli |
| author_facet | Piera Grisolia Rossella Tufano Clara Iannarone Antonio De Falco Francesca Carlino Cinzia Graziano Raffaele Addeo Marianna Scrima Francesco Caraglia Anna Ceccarelli Pier Vitale Nuzzo Alessia Maria Cossu Stefano Forte Raffaella Giuffrida Michele Orditura Michele Caraglia Michele Ceccarelli |
| author_sort | Piera Grisolia |
| collection | DOAJ |
| description | Abstract Background Recent studies have highlighted the importance of the cell-free DNA (cfDNA) methylation profile in detecting breast cancer (BC) and its different subtypes. We investigated whether plasma cfDNA methylation, using cell-free Methylated DNA Immunoprecipitation and High-Throughput Sequencing (cfMeDIP-seq), may be informative in characterizing breast cancer in patients with BRCA1/2 germline mutations for early cancer detection and response to therapy. Methods We enrolled 23 BC patients with germline mutation of BRCA1 and BRCA2 genes, 19 healthy controls without BRCA1/2 mutation, and two healthy individuals who carried BRCA1/2 mutations. Blood samples were collected for all study subjects at the diagnosis, and plasma was isolated by centrifugation. Cell-free DNA was extracted from 1 mL of plasma, and cfMeDIP-seq was performed for each sample. Shallow whole genome sequencing was performed on the immuno-precipitated samples. Then, the differentially methylated 300-bp regions (DMRs) between 25 BRCA germline mutation carriers and 19 non-carriers were identified. DMRs were compared with tumor-specific regions from public datasets to perform an unbiased analysis. Finally, two statistical classifiers were trained based on the GLMnet and random forest model to evaluate if the identified DMRs could discriminate BRCA-positive from healthy samples. Results We identified 7,095 hypermethylated and 212 hypomethylated regions in 25 BRCA germline mutation carriers compared to 19 controls. These regions discriminate tumors from healthy samples with high accuracy and sensitivity. We show that the circulating tumor DNA of BRCA1/2 mutant breast cancers is characterized by the hypomethylation of genes involved in DNA repair and cell cycle. We uncovered the TFs associated with these DRMs and identified that proteins of the Erythroblast Transformation Specific (ETS) family are particularly active in the hypermethylated regions. Finally, we assessed that these regions could discriminate between BRCA positives from healthy samples with an AUC of 0.95, a sensitivity of 88%, and a specificity of 94.74%. Conclusions Our study emphasizes the importance of tumor cell-derived DNA methylation in BC, reporting a different methylation profile between patients carrying mutations in BRCA1, BRCA2, and wild-type controls. Our minimally invasive approach could allow early cancer diagnosis, assessment of minimal residual disease, and monitoring of response to therapy. |
| format | Article |
| id | doaj-art-b4709ad2f11d40968a2b2c09a3828f5f |
| institution | OA Journals |
| issn | 1479-5876 |
| language | English |
| publishDate | 2024-10-01 |
| publisher | BMC |
| record_format | Article |
| series | Journal of Translational Medicine |
| spelling | doaj-art-b4709ad2f11d40968a2b2c09a3828f5f2025-08-20T01:50:38ZengBMCJournal of Translational Medicine1479-58762024-10-0122111210.1186/s12967-024-05734-2Differential methylation of circulating free DNA assessed through cfMeDiP as a new tool for breast cancer diagnosis and detection of BRCA1/2 mutationPiera Grisolia0Rossella Tufano1Clara Iannarone2Antonio De Falco3Francesca Carlino4Cinzia Graziano5Raffaele Addeo6Marianna Scrima7Francesco Caraglia8Anna Ceccarelli9Pier Vitale Nuzzo10Alessia Maria Cossu11Stefano Forte12Raffaella Giuffrida13Michele Orditura14Michele Caraglia15Michele Ceccarelli16Sylvester Comprehensive Cancer Center and Department of Public Health Sciences, Miller School of Medicine, University of MiamiLaboratory of Computational Biology, IRGSLaboratory of Molecular and Precision Oncology, Biogem, IRGSLaboratory of Computational Biology, IRGSDepartment of Precision Medicine, University of Campania “Luigi Vanvitelli”Laboratory of Molecular and Precision Oncology, Biogem, IRGSOncology Unit, S. Giovanni di Dio HospitalLaboratory of Molecular and Precision Oncology, Biogem, IRGSDepartment of Precision Medicine, University of Campania “Luigi Vanvitelli”Medical Oncology, Catholic University of the Sacred HeartDepartment of Pathology and Laboratory Medicine, Weill Cornell MedicineLaboratory of Molecular and Precision Oncology, Biogem, IRGSIOM RicercaIOM RicercaDepartment of Precision Medicine, University of Campania “Luigi Vanvitelli”Laboratory of Molecular and Precision Oncology, Biogem, IRGSSylvester Comprehensive Cancer Center and Department of Public Health Sciences, Miller School of Medicine, University of MiamiAbstract Background Recent studies have highlighted the importance of the cell-free DNA (cfDNA) methylation profile in detecting breast cancer (BC) and its different subtypes. We investigated whether plasma cfDNA methylation, using cell-free Methylated DNA Immunoprecipitation and High-Throughput Sequencing (cfMeDIP-seq), may be informative in characterizing breast cancer in patients with BRCA1/2 germline mutations for early cancer detection and response to therapy. Methods We enrolled 23 BC patients with germline mutation of BRCA1 and BRCA2 genes, 19 healthy controls without BRCA1/2 mutation, and two healthy individuals who carried BRCA1/2 mutations. Blood samples were collected for all study subjects at the diagnosis, and plasma was isolated by centrifugation. Cell-free DNA was extracted from 1 mL of plasma, and cfMeDIP-seq was performed for each sample. Shallow whole genome sequencing was performed on the immuno-precipitated samples. Then, the differentially methylated 300-bp regions (DMRs) between 25 BRCA germline mutation carriers and 19 non-carriers were identified. DMRs were compared with tumor-specific regions from public datasets to perform an unbiased analysis. Finally, two statistical classifiers were trained based on the GLMnet and random forest model to evaluate if the identified DMRs could discriminate BRCA-positive from healthy samples. Results We identified 7,095 hypermethylated and 212 hypomethylated regions in 25 BRCA germline mutation carriers compared to 19 controls. These regions discriminate tumors from healthy samples with high accuracy and sensitivity. We show that the circulating tumor DNA of BRCA1/2 mutant breast cancers is characterized by the hypomethylation of genes involved in DNA repair and cell cycle. We uncovered the TFs associated with these DRMs and identified that proteins of the Erythroblast Transformation Specific (ETS) family are particularly active in the hypermethylated regions. Finally, we assessed that these regions could discriminate between BRCA positives from healthy samples with an AUC of 0.95, a sensitivity of 88%, and a specificity of 94.74%. Conclusions Our study emphasizes the importance of tumor cell-derived DNA methylation in BC, reporting a different methylation profile between patients carrying mutations in BRCA1, BRCA2, and wild-type controls. Our minimally invasive approach could allow early cancer diagnosis, assessment of minimal residual disease, and monitoring of response to therapy.https://doi.org/10.1186/s12967-024-05734-2Breast cancerCell-free DNADMRscfMeDIP-seqBRCA1BRCA2 |
| spellingShingle | Piera Grisolia Rossella Tufano Clara Iannarone Antonio De Falco Francesca Carlino Cinzia Graziano Raffaele Addeo Marianna Scrima Francesco Caraglia Anna Ceccarelli Pier Vitale Nuzzo Alessia Maria Cossu Stefano Forte Raffaella Giuffrida Michele Orditura Michele Caraglia Michele Ceccarelli Differential methylation of circulating free DNA assessed through cfMeDiP as a new tool for breast cancer diagnosis and detection of BRCA1/2 mutation Journal of Translational Medicine Breast cancer Cell-free DNA DMRs cfMeDIP-seq BRCA1 BRCA2 |
| title | Differential methylation of circulating free DNA assessed through cfMeDiP as a new tool for breast cancer diagnosis and detection of BRCA1/2 mutation |
| title_full | Differential methylation of circulating free DNA assessed through cfMeDiP as a new tool for breast cancer diagnosis and detection of BRCA1/2 mutation |
| title_fullStr | Differential methylation of circulating free DNA assessed through cfMeDiP as a new tool for breast cancer diagnosis and detection of BRCA1/2 mutation |
| title_full_unstemmed | Differential methylation of circulating free DNA assessed through cfMeDiP as a new tool for breast cancer diagnosis and detection of BRCA1/2 mutation |
| title_short | Differential methylation of circulating free DNA assessed through cfMeDiP as a new tool for breast cancer diagnosis and detection of BRCA1/2 mutation |
| title_sort | differential methylation of circulating free dna assessed through cfmedip as a new tool for breast cancer diagnosis and detection of brca1 2 mutation |
| topic | Breast cancer Cell-free DNA DMRs cfMeDIP-seq BRCA1 BRCA2 |
| url | https://doi.org/10.1186/s12967-024-05734-2 |
| work_keys_str_mv | AT pieragrisolia differentialmethylationofcirculatingfreednaassessedthroughcfmedipasanewtoolforbreastcancerdiagnosisanddetectionofbrca12mutation AT rossellatufano differentialmethylationofcirculatingfreednaassessedthroughcfmedipasanewtoolforbreastcancerdiagnosisanddetectionofbrca12mutation AT claraiannarone differentialmethylationofcirculatingfreednaassessedthroughcfmedipasanewtoolforbreastcancerdiagnosisanddetectionofbrca12mutation AT antoniodefalco differentialmethylationofcirculatingfreednaassessedthroughcfmedipasanewtoolforbreastcancerdiagnosisanddetectionofbrca12mutation AT francescacarlino differentialmethylationofcirculatingfreednaassessedthroughcfmedipasanewtoolforbreastcancerdiagnosisanddetectionofbrca12mutation AT cinziagraziano differentialmethylationofcirculatingfreednaassessedthroughcfmedipasanewtoolforbreastcancerdiagnosisanddetectionofbrca12mutation AT raffaeleaddeo differentialmethylationofcirculatingfreednaassessedthroughcfmedipasanewtoolforbreastcancerdiagnosisanddetectionofbrca12mutation AT mariannascrima differentialmethylationofcirculatingfreednaassessedthroughcfmedipasanewtoolforbreastcancerdiagnosisanddetectionofbrca12mutation AT francescocaraglia differentialmethylationofcirculatingfreednaassessedthroughcfmedipasanewtoolforbreastcancerdiagnosisanddetectionofbrca12mutation AT annaceccarelli differentialmethylationofcirculatingfreednaassessedthroughcfmedipasanewtoolforbreastcancerdiagnosisanddetectionofbrca12mutation AT piervitalenuzzo differentialmethylationofcirculatingfreednaassessedthroughcfmedipasanewtoolforbreastcancerdiagnosisanddetectionofbrca12mutation AT alessiamariacossu differentialmethylationofcirculatingfreednaassessedthroughcfmedipasanewtoolforbreastcancerdiagnosisanddetectionofbrca12mutation AT stefanoforte differentialmethylationofcirculatingfreednaassessedthroughcfmedipasanewtoolforbreastcancerdiagnosisanddetectionofbrca12mutation AT raffaellagiuffrida differentialmethylationofcirculatingfreednaassessedthroughcfmedipasanewtoolforbreastcancerdiagnosisanddetectionofbrca12mutation AT micheleorditura differentialmethylationofcirculatingfreednaassessedthroughcfmedipasanewtoolforbreastcancerdiagnosisanddetectionofbrca12mutation AT michelecaraglia differentialmethylationofcirculatingfreednaassessedthroughcfmedipasanewtoolforbreastcancerdiagnosisanddetectionofbrca12mutation AT michelececcarelli differentialmethylationofcirculatingfreednaassessedthroughcfmedipasanewtoolforbreastcancerdiagnosisanddetectionofbrca12mutation |