Network-based analysis of heterogeneous patient-matched brain and extracranial melanoma metastasis pairs reveals three homogeneous subgroups.
Comput Struct Biotechnol J
; 23: 1036-1050, 2024 Dec.
Article
in En
| MEDLINE
| ID: mdl-38464935
ABSTRACT
Melanoma, the deadliest form of skin cancer, can metastasize to different organs. Molecular differences between brain and extracranial melanoma metastases are poorly understood. Here, promoter methylation and gene expression of 11 heterogeneous patient-matched pairs of brain and extracranial metastases were analyzed using melanoma-specific gene regulatory networks learned from public transcriptome and methylome data followed by network-based impact propagation of patient-specific alterations. This innovative data analysis strategy allowed to predict potential impacts of patient-specific driver candidate genes on other genes and pathways. The patient-matched metastasis pairs clustered into three robust subgroups with specific downstream targets with known roles in cancer, including melanoma (SG1 RBM38, BCL11B, SG2 GATA3, FES, SG3 SLAMF6, PYCARD). Patient subgroups and ranking of target gene candidates were confirmed in a validation cohort. Summarizing, computational network-based impact analyses of heterogeneous metastasis pairs predicted individual regulatory differences in melanoma brain metastases, cumulating into three consistent subgroups with specific downstream target genes.
Full text:
1
Collection:
01-internacional
Database:
MEDLINE
Language:
En
Journal:
Comput Struct Biotechnol J
Year:
2024
Document type:
Article
Affiliation country:
Germany
Country of publication:
Netherlands