Correlation Between Molecular Genetic Analysis and Nuclear Pleomorphism in Long-Term Recurrent and Metastatic Chordoma

<b>Background/Objectives</b>: Recurrences and metastases occur frequently in chordoma and are the main factors influencing overall survival. However, prognostic biomarkers for recurrence remain limited. This study examines whether quantitative nuclear morphometry can capture recurrence evolution and whether it aligns with immunophenotype and genomic profiling. <b>Methods</b>: A total of 26 specimens from 12 adults (8 patients with non-recurrent tumors and 4 patients with multiple long-term recurrences and metastases over 7 to 16 years) were analyzed using whole-exome sequencing, immunohistochemistry, and nuclear morphometry. <b>Results</b>: Imaging studies and routine histology showed no consistent differences between groups. Morphometry revealed substantial intertumoral variability among non-recurrent tumors and significant longitudinal nuclear remodeling throughout recurrences, dominated by increased nuclear size and asymmetry, as well as altered shape. Primary tumors from patients who later recurred had smaller, more asymmetric, and denser nuclei than non-recurrent tumors. Recurrent samples showed higher proliferation and decreased lamin A/C expression, with focal disruption and detachment from the nuclear envelope in pleomorphic nuclei. The tumor mutational burden was low overall, varied between patients and timepoints, and tended to be higher in recurrent cases. <b>Conclusions</b>: Quantitative nuclear morphometry, integrated with immunophenotyping and genomic profiling, captures recurrence-associated phenotypic remodeling in chordoma and may provide a quantitative framework for future digital pathology or AI approaches, pending validation in larger cohorts.