Proteomic signatures of tumorigenicity, immune evasion, and multidrug resistance in a murine T-cell lymphoma with CNS/ocular tropism

Background: The S49 T-cell lymphoma and its derivative sublines provide a powerful model to dissect how T cell lymphomas acquire tumorigenicity, evade immune surveillance, develop multidrug resistance, and disseminate to the CNS and eyes. The malignant suspension growing line T-25 contrasts with three derivatives: an immunogenic non-tumorigenic adherent T-25-Adh cell line, a tumorigenic revertant Rev-2-T-6, and a MDR1 overexpressing HU-1 cell line, which is drug-resistant yet non-tumorigenic in adults (derived from T-25-Adh). Rev-2-T-6 and HU-1 cell lines are capable of CNS/ocular metastasis in neonates. Methods: We used label-free quantitative proteomics to define programs that underlie these divergent phenotypes. Biological triplicates of T-25, T-25-Adh, Rev-2-T-6, and HU-1 cells were analyzed and compared by high-resolution LC-MS/MS, and proteins were quantified using MaxQuant LFQ. We quantified 3,500 proteins across all lines with high reproducibility. Results: Unsupervised clustering and PCA showed tight triplicate clustering, with T-25 clearly separated from the other variants; HU-1 and T-25-Adh clustered together, and Rev-2-T-6 occupied an intermediate position, consistent with its partial revertant phenotype. Compared to T-25 cells, HU-1, Rev-2-T-6, and T-25-Adh showed 17, 19, and 29 significantly regulated proteins, respectively. HU-1 was enriched for cAMP-related, nuclear envelope, and RNA-processing proteins, together with marked MDR1 overexpression. It showed reduced MHC-I heavy chains and ribosomal components. This is consistent with immune evasion and altered mitochondrial function in a multidrug-resistant yet non-tumorigenic background. Rev-2-T-6 up-regulated cAMP and DNA-replication factors down-regulating MHC-I and mitochondrial enzymes, supporting proliferative, glycolysis-shifted “revertant” state. T-25-Adh displayed down-regulation of cell-cycle and oxidative phosphorylation proteins, defining an adherent, immunogenic, non-tumorigenic program. Conclusions: The present proteomic atlas of S49-derived lymphoma lines reveals shared and lineage-specific signatures of malignancy, immune escape, and drug resistance. Loss of antigen presentation and mitochondrial metabolism, together with activation of cAMP and proliferative programs, characterizes tumorigenic cells, whereas the immunogenic adherent phenotype is associated with reduced proliferation, metabolic down-shifting, and enhanced adhesion/immune pathways. MDR1 up-regulation in HU-1 decouples drug resistance from tumorigenicity while preserving CNS/ocular tropism. These data nominate antigen-processing machinery, cAMP signaling, mitochondrial metabolism, and ABC transporters as biomarkers and therapeutic targets in CNS-tropic lymphomas and provide a framework for comparative analyses with human T-cell malignancies.