Biology subjects

Farina-Morillas, M.

Publications and source records attributed to Farina-Morillas, M..

2 recordsLinked to original sources

bioRxiv2026

Pairwise genomic alterations identify prognostic tumor states in multiple cancer types

Genomic models of cancer prognosis usually rely on individual genomic alterations, potentially overlooking clinically meaningful combinations of events. We analyzed genomic and clinical data from nearly 10,000 primary tumors across major cancer types to identify prognostic genomic interactions (PGIs), defined as pairs of genomic alterations whose joint status was associated with patient outcome beyond either alteration alone. By systematically integrating survival associations with pairwise combinations of recurrent copy-number alterations and frequently mutated driver genes, we identified 57 PGIs. These PGIs refined prognostic stratification and were linked to distinct transcriptomic programs representing immune-response, epithelial-mesenchymal transition, and proliferation-related themes. Gene-level mapping highlighted dosage-sensitive candidate genes within recurrent copy-number regions, and gene essentiality profiles supported subsets of PGI-derived gene pairs. Two PGIs were validated in independent datasets. Together, these results establish a framework for identifying prognostic combinations of genomic alterations and connecting them to pathway programs, candidate genes, and functional dependencies in human tumors.

cancer biology↗

bioRxiv2026

Mutational signatures in cancer genomes alter protein sequence motifs in cellular signaling networks

Somatic mutations in cancer genomes arise from distinct, context-specific mutational processes, yet their functional consequences at the protein and network level remain incompletely understood. Here, we show that mutational processes of single-nucleotide variants (SNVs) can systematically rewire signaling networks by inducing amino acid substitutions in short linear motifs (SLiMs) that mediate interactions with kinases and other signaling proteins. By analysing 11,000 cancer genomes and 144 classes of SLiMs, we identify motif-rewiring SNVs (rwSNVs) that create or disrupt SLiMs or remove phosphorylated residues. Mutational processes of methylcytosine deamination, APOBEC activity, and ultraviolet light exposure emerge as major contributors to motif rewiring. rwSNVs are enriched in cancer driver genes and pathways, linking mutation etiology to functional consequences. rwSNVs at the BRAF V600E hotspot associated with UV-related mutagenesis are predicted to generate a phosphorylation motif recognized by PLK1 kinase. Together, these findings reveal how mutational processes shape oncogenic signaling and tumor heterogeneity.

cancer biology↗