In-depth assessment of BRAF, NRAS, KRAS, EGFR, and PIK3CA mutations on cell-free DNA in the blood of melanoma patients receiving immune checkpoint inhibition
Abstract Introduction Circulating tumor DNA (ctDNA) holds promise for guiding immune checkpoint inhibitor (ICI) therapy and stratifying responders from non-responders. While tumor-informed ctDNA detection approaches are sensitive and mutation-inclusive, they require tumor tissue, which limits applic...
Saved in:
| Main Authors: | , , , , , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2025-07-01
|
| Series: | Journal of Experimental & Clinical Cancer Research |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s13046-025-03457-w |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1849760946112692224 |
|---|---|
| author | Isabel Heidrich Charlotte Rautmann Cedric Ly Robin Khatri Julian Kött Glenn Geidel Alessandra Rünger Antje Andreas Inga Hansen-Abeck Finn Abeck Anne Menz Stefan Bonn Stefan W. Schneider Daniel J. Smit Christoffer Gebhardt Klaus Pantel |
| author_facet | Isabel Heidrich Charlotte Rautmann Cedric Ly Robin Khatri Julian Kött Glenn Geidel Alessandra Rünger Antje Andreas Inga Hansen-Abeck Finn Abeck Anne Menz Stefan Bonn Stefan W. Schneider Daniel J. Smit Christoffer Gebhardt Klaus Pantel |
| author_sort | Isabel Heidrich |
| collection | DOAJ |
| description | Abstract Introduction Circulating tumor DNA (ctDNA) holds promise for guiding immune checkpoint inhibitor (ICI) therapy and stratifying responders from non-responders. While tumor-informed ctDNA detection approaches are sensitive and mutation-inclusive, they require tumor tissue, which limits applicability in real-world settings. Conversely, tumor-agnostic methods often have limited genomic coverage. In this study, we evaluated a tumor-agnostic, broad-panel ctDNA assay in patients with advanced melanoma treated with ICI. Methods We conducted a prospective analysis of 241 longitudinal samples from 39 patients with unresectable stage III/IV melanoma using a SYSMEX targeted NGS panel covering 1,114 COSMIC mutations. Plasma samples were collected at baseline and during ICI therapy. The assay’s sensitivity reached seven mutant molecules, corresponding to a 0.07% mutation allele frequency (MAF). ctDNA profiles were compared with matched tumor tissue and correlated with clinical features and survival. Results At baseline, ctDNA was detected in 64.5% of patients. Common mutations included BRAF V600E (43.8%) and NRAS G12D (36.4%), followed by KRAS, EGFR, and PIK3CA variants. Overall tissue–plasma concordance was 51.6%, with more extended biopsy–plasma intervals associated with discordance (p = 0.0105). Notably, 12.2% of cases exhibited partial concordance, characterized by shared mutations and additional plasma-only alterations, underscoring the complementary value of blood-based profiling. Persistent or re-emerging ctDNA positivity post-therapy correlated with shorter progression-free survival (PFS, p = 0.003), while ctDNA-negative patients showed significantly improved outcomes. Patients that remained ctDNA-negative had significantly longer progression-free survival (median not reached) compared to those with persistent ctDNA positivity (median 3 months) or those converting to positive (median 7.5 months; p = 0.0073). Early NRAS and KRAS ctDNA levels strongly predicted poor response (p = 0.0069 and p = 0.028). The prognostic impact extended beyond canonical drivers, as non-hotspot variants also correlated with the outcome. Notably, even low-level ctDNA persistence (5–10 MM/mL) carried adverse prognostic implications (p = 0.0054). Concerning a shorter PFS, ctDNA positivity was also associated with elevated S100 levels (p = 0.047). Organ-specific mutation enrichment (e.g., KRASG12D in brain, EGFRG719A in lymph nodes) suggested possible metastatic tropism. Conclusion Broad tumor-agnostic ctDNA analysis effectively identified clinically relevant mutations and predicted outcomes in ICI-treated melanoma patients. This approach enables tissue-independent and real-time ctDNA monitoring and may inform patient selection and therapeutic strategies in future interventional trials. |
| format | Article |
| id | doaj-art-fe3fded8f0ed41acac2bd584276a9c59 |
| institution | DOAJ |
| issn | 1756-9966 |
| language | English |
| publishDate | 2025-07-01 |
| publisher | BMC |
| record_format | Article |
| series | Journal of Experimental & Clinical Cancer Research |
| spelling | doaj-art-fe3fded8f0ed41acac2bd584276a9c592025-08-20T03:06:10ZengBMCJournal of Experimental & Clinical Cancer Research1756-99662025-07-0144111810.1186/s13046-025-03457-wIn-depth assessment of BRAF, NRAS, KRAS, EGFR, and PIK3CA mutations on cell-free DNA in the blood of melanoma patients receiving immune checkpoint inhibitionIsabel Heidrich0Charlotte Rautmann1Cedric Ly2Robin Khatri3Julian Kött4Glenn Geidel5Alessandra Rünger6Antje Andreas7Inga Hansen-Abeck8Finn Abeck9Anne Menz10Stefan Bonn11Stefan W. Schneider12Daniel J. Smit13Christoffer Gebhardt14Klaus Pantel15Institute of Tumor Biology, Fleur Hiege Center for Skin Cancer Research, University Medical Center Hamburg-EppendorfInstitute of Tumor Biology, Fleur Hiege Center for Skin Cancer Research, University Medical Center Hamburg-EppendorfInstitute of Systems Immunology, University Medical Center Hamburg-EppendorfInstitute for Medical Systems Bioinformatics, Center for Molecular Neurobiology (ZMBH), University Medical Center Hamburg-EppendorfDepartment of Dermatology and Venereology, Fleur Hiege Center for Skin Cancer Research, University Medical Center Hamburg-EppendorfDepartment of Dermatology and Venereology, Fleur Hiege Center for Skin Cancer Research, University Medical Center Hamburg-EppendorfDepartment of Dermatology and Venereology, Fleur Hiege Center for Skin Cancer Research, University Medical Center Hamburg-EppendorfInstitute of Tumor Biology, Fleur Hiege Center for Skin Cancer Research, University Medical Center Hamburg-EppendorfDepartment of Dermatology and Venereology, Fleur Hiege Center for Skin Cancer Research, University Medical Center Hamburg-EppendorfDepartment of Dermatology and Venereology, Fleur Hiege Center for Skin Cancer Research, University Medical Center Hamburg-EppendorfInstitute of Pathology, University Medical Center Hamburg-EppendorfInstitute for Medical Systems Bioinformatics, Center for Molecular Neurobiology (ZMBH), University Medical Center Hamburg-EppendorfDepartment of Dermatology and Venereology, Fleur Hiege Center for Skin Cancer Research, University Medical Center Hamburg-EppendorfInstitute of Tumor Biology, Fleur Hiege Center for Skin Cancer Research, University Medical Center Hamburg-EppendorfDepartment of Dermatology and Venereology, Fleur Hiege Center for Skin Cancer Research, University Medical Center Hamburg-EppendorfInstitute of Tumor Biology, Fleur Hiege Center for Skin Cancer Research, University Medical Center Hamburg-EppendorfAbstract Introduction Circulating tumor DNA (ctDNA) holds promise for guiding immune checkpoint inhibitor (ICI) therapy and stratifying responders from non-responders. While tumor-informed ctDNA detection approaches are sensitive and mutation-inclusive, they require tumor tissue, which limits applicability in real-world settings. Conversely, tumor-agnostic methods often have limited genomic coverage. In this study, we evaluated a tumor-agnostic, broad-panel ctDNA assay in patients with advanced melanoma treated with ICI. Methods We conducted a prospective analysis of 241 longitudinal samples from 39 patients with unresectable stage III/IV melanoma using a SYSMEX targeted NGS panel covering 1,114 COSMIC mutations. Plasma samples were collected at baseline and during ICI therapy. The assay’s sensitivity reached seven mutant molecules, corresponding to a 0.07% mutation allele frequency (MAF). ctDNA profiles were compared with matched tumor tissue and correlated with clinical features and survival. Results At baseline, ctDNA was detected in 64.5% of patients. Common mutations included BRAF V600E (43.8%) and NRAS G12D (36.4%), followed by KRAS, EGFR, and PIK3CA variants. Overall tissue–plasma concordance was 51.6%, with more extended biopsy–plasma intervals associated with discordance (p = 0.0105). Notably, 12.2% of cases exhibited partial concordance, characterized by shared mutations and additional plasma-only alterations, underscoring the complementary value of blood-based profiling. Persistent or re-emerging ctDNA positivity post-therapy correlated with shorter progression-free survival (PFS, p = 0.003), while ctDNA-negative patients showed significantly improved outcomes. Patients that remained ctDNA-negative had significantly longer progression-free survival (median not reached) compared to those with persistent ctDNA positivity (median 3 months) or those converting to positive (median 7.5 months; p = 0.0073). Early NRAS and KRAS ctDNA levels strongly predicted poor response (p = 0.0069 and p = 0.028). The prognostic impact extended beyond canonical drivers, as non-hotspot variants also correlated with the outcome. Notably, even low-level ctDNA persistence (5–10 MM/mL) carried adverse prognostic implications (p = 0.0054). Concerning a shorter PFS, ctDNA positivity was also associated with elevated S100 levels (p = 0.047). Organ-specific mutation enrichment (e.g., KRASG12D in brain, EGFRG719A in lymph nodes) suggested possible metastatic tropism. Conclusion Broad tumor-agnostic ctDNA analysis effectively identified clinically relevant mutations and predicted outcomes in ICI-treated melanoma patients. This approach enables tissue-independent and real-time ctDNA monitoring and may inform patient selection and therapeutic strategies in future interventional trials.https://doi.org/10.1186/s13046-025-03457-wCtDNALiquid BiopsyMelanomaBRAFNRASKRAS |
| spellingShingle | Isabel Heidrich Charlotte Rautmann Cedric Ly Robin Khatri Julian Kött Glenn Geidel Alessandra Rünger Antje Andreas Inga Hansen-Abeck Finn Abeck Anne Menz Stefan Bonn Stefan W. Schneider Daniel J. Smit Christoffer Gebhardt Klaus Pantel In-depth assessment of BRAF, NRAS, KRAS, EGFR, and PIK3CA mutations on cell-free DNA in the blood of melanoma patients receiving immune checkpoint inhibition Journal of Experimental & Clinical Cancer Research CtDNA Liquid Biopsy Melanoma BRAF NRAS KRAS |
| title | In-depth assessment of BRAF, NRAS, KRAS, EGFR, and PIK3CA mutations on cell-free DNA in the blood of melanoma patients receiving immune checkpoint inhibition |
| title_full | In-depth assessment of BRAF, NRAS, KRAS, EGFR, and PIK3CA mutations on cell-free DNA in the blood of melanoma patients receiving immune checkpoint inhibition |
| title_fullStr | In-depth assessment of BRAF, NRAS, KRAS, EGFR, and PIK3CA mutations on cell-free DNA in the blood of melanoma patients receiving immune checkpoint inhibition |
| title_full_unstemmed | In-depth assessment of BRAF, NRAS, KRAS, EGFR, and PIK3CA mutations on cell-free DNA in the blood of melanoma patients receiving immune checkpoint inhibition |
| title_short | In-depth assessment of BRAF, NRAS, KRAS, EGFR, and PIK3CA mutations on cell-free DNA in the blood of melanoma patients receiving immune checkpoint inhibition |
| title_sort | in depth assessment of braf nras kras egfr and pik3ca mutations on cell free dna in the blood of melanoma patients receiving immune checkpoint inhibition |
| topic | CtDNA Liquid Biopsy Melanoma BRAF NRAS KRAS |
| url | https://doi.org/10.1186/s13046-025-03457-w |
| work_keys_str_mv | AT isabelheidrich indepthassessmentofbrafnraskrasegfrandpik3camutationsoncellfreednainthebloodofmelanomapatientsreceivingimmunecheckpointinhibition AT charlotterautmann indepthassessmentofbrafnraskrasegfrandpik3camutationsoncellfreednainthebloodofmelanomapatientsreceivingimmunecheckpointinhibition AT cedricly indepthassessmentofbrafnraskrasegfrandpik3camutationsoncellfreednainthebloodofmelanomapatientsreceivingimmunecheckpointinhibition AT robinkhatri indepthassessmentofbrafnraskrasegfrandpik3camutationsoncellfreednainthebloodofmelanomapatientsreceivingimmunecheckpointinhibition AT juliankott indepthassessmentofbrafnraskrasegfrandpik3camutationsoncellfreednainthebloodofmelanomapatientsreceivingimmunecheckpointinhibition AT glenngeidel indepthassessmentofbrafnraskrasegfrandpik3camutationsoncellfreednainthebloodofmelanomapatientsreceivingimmunecheckpointinhibition AT alessandrarunger indepthassessmentofbrafnraskrasegfrandpik3camutationsoncellfreednainthebloodofmelanomapatientsreceivingimmunecheckpointinhibition AT antjeandreas indepthassessmentofbrafnraskrasegfrandpik3camutationsoncellfreednainthebloodofmelanomapatientsreceivingimmunecheckpointinhibition AT ingahansenabeck indepthassessmentofbrafnraskrasegfrandpik3camutationsoncellfreednainthebloodofmelanomapatientsreceivingimmunecheckpointinhibition AT finnabeck indepthassessmentofbrafnraskrasegfrandpik3camutationsoncellfreednainthebloodofmelanomapatientsreceivingimmunecheckpointinhibition AT annemenz indepthassessmentofbrafnraskrasegfrandpik3camutationsoncellfreednainthebloodofmelanomapatientsreceivingimmunecheckpointinhibition AT stefanbonn indepthassessmentofbrafnraskrasegfrandpik3camutationsoncellfreednainthebloodofmelanomapatientsreceivingimmunecheckpointinhibition AT stefanwschneider indepthassessmentofbrafnraskrasegfrandpik3camutationsoncellfreednainthebloodofmelanomapatientsreceivingimmunecheckpointinhibition AT danieljsmit indepthassessmentofbrafnraskrasegfrandpik3camutationsoncellfreednainthebloodofmelanomapatientsreceivingimmunecheckpointinhibition AT christoffergebhardt indepthassessmentofbrafnraskrasegfrandpik3camutationsoncellfreednainthebloodofmelanomapatientsreceivingimmunecheckpointinhibition AT klauspantel indepthassessmentofbrafnraskrasegfrandpik3camutationsoncellfreednainthebloodofmelanomapatientsreceivingimmunecheckpointinhibition |