Examining transcriptional changes to DNA replication and repair factors over uveal melanoma subtypes

Background Uncontrolled replication is a process common to all cancers facilitated by the summation of changes accumulated as tumors progress. The aim of this study was to examine small groups of genes with known biology in replication and repair at the transcriptional and genomic levels, correlating alterations with survival in uveal melanoma tumor progression. Selected components of Pre-Replication, Pre-Initiation, and Replisome Complexes, DNA Damage Response and Mismatch Repair have been observed. Methods Two groups have been generated for selected genes above and below the average alteration level and compared for expression and survival across The Cancer Genome Atlas uveal melanoma subtypes. Significant differences in expression between subtypes monosomic or disomic for chromosome 3 have been identified by Fisher’s exact test. Kaplan Meier survival distribution based on disease specific survival has been compared by Log-rank test. Results Genes with significant alteration include MCM2, MCM4, MCM5, CDC45, MCM10, CIZ1, PCNA, FEN1, LIG1, POLD1, POLE, HUS1, CHECK1, ATRIP, MLH3, and MSH6. Exon 4 skipping in CIZ1 previously identified as a cancer variant, and reportedly used as an early serum biomarker in lung cancer was found. Mismatch Repair protein MLH3 was found to have splicing variations with deletions to both Exon 5 and Exon 7 simultaneously. PCNA, FEN1, and LIG1 had increased relative expression levels not due to mutation or to copy number variation. Conclusion The current study proposes changes in relative and differential expression to replication and repair genes that support the concept their products are causally involved in uveal melanoma. Specific avenues for early biomarker identification and therapeutic approach are suggested.