BMC Cancer. 2025 Dec 05.
OBJECTIVES: Central nervous system (CNS) metastasis is a major driver of morbidity in metastatic breast cancer, yet the molecular determinants of CNS tropism remain incompletely defined. LYN, a Src-family kinase integrating receptor tyrosine kinase and integrin signaling, is a biologically plausible mediator of metastatic traits.
DESIGN: We performed a retrospective, multi-study analysis of publicly available breast cancer cohorts aggregated in cBioPortal. After harmonization and de-duplication, LYN status was determinable in 5,947 invasive carcinoma of no special type (NST) tumors across 29 studies. The primary endpoint was CNS metastasis at any time (Yes/No), harmonized via a prespecified controlled vocabulary (case-insensitive substring mapping). Somatic LYN variants (coding SNVs/indels) were collapsed to patient-level classes (missense-only; truncating if any nonsense/frameshift/splice). Variants with resolvable positions were mapped to Src-family modules (SH4/Unique, SH3, SH2, SH2-kinase linker, kinase). Two-group comparisons used two-sided Fisher's exact tests with exact 95% CIs; domain screens used omnibus χ² and Benjamini-Hochberg FDR control. A prespecified Firth logistic model evaluated truncating vs. missense within LYN-mutant tumors. SETTING: Public cancer genomics repositories (cBioPortal); multi-institutional cohorts.
PARTICIPANTS: 5,947 tumors across multi-study cohorts with LYN status available.
INTERVENTIONS: None.
MAIN OUTCOME MEASURES: Primary: ever-CNS metastasis (yes/no). Secondary: distribution of LYN variant classes and domains (SH4/Unique, SH3, SH2, linker, kinase). RESULTS: CNS metastasis occurred in 5/46 (10.9%) LYN-mutated tumors vs. 110/5,901 (1.9%) LYN wild-type tumors (odds ratio (OR) = 6.42; 95% confidence interval (CI), 2.49-16.56; p = 0.0018). The endpoint was captured as ever vs. never CNS involvement (event dates unavailable), precluding time-to-event inference. Within LYN-mutant cases, an exploratory domain analysis indicated that distributions differed by CNS status (omnibus χ² p ≈ 0.014); a one-versus-rest signal at the SH4/Unique N-terminus was nominally significant and borderline after false discovery rate (FDR) (unadjusted p ≈ 0.010; q ≈ 0.052; small in-domain n = 3). By mutation class, truncating vs. missense showed a higher CNS-positive proportion (28.6% vs. 7.9%) but did not reach significance (Fisher p = 0.166; alternatively framed OR = 4.22; exact 95% CI, 0.58-30.75; p = 0.182). Firth estimates were directionally consistent with wide profile CIs under sparse counts.
CONCLUSIONS: Across pooled cohorts, LYN mutation is associated with increased odds of CNS metastasis, and domain context appears informative, with a small-sample, FDR-borderline enrichment at the SH4/Unique N-terminus. The truncating-class signal is exploratory given limited power. Signals by domain (notably SH4/Unique) are exploratory and require independent validation in larger, uniformly annotated datasets. Given small mutant denominators and ever-CNS endpoint capture, findings are hypothesis-generating and not actionable for risk stratification or treatment selection. Results motivate domain-aware annotation in future validation studies and mechanistic work.
Keywords: Breast cancer; CBioPortal; CNS metastasis; Domain mapping; Firth logistic; Fisher’s exact; LYN; SH4/Unique; Src-family kinase