STAG2 mutations fine-tune the ALK-driven oncogenic program in ALK-positive anaplastic large cell lymphoma

Abstract

ALK-positive Anaplastic Large Cell Lymphoma (ALK+ ALCL) is a rare yet aggressive T-cell lymphoma, most often characterized by the NPM1::ALK fusion. Because few somatic variants have been identified in ALK+ ALCL, we conducted paired whole-exome sequencing of patient tumors with matched normal tissue. Compared with previous studies, we identified a higher frequency of mutations in cohesin complex genes, mostly STAG2 variants (6/16) predicted to impair protein function. Immunohistochemistry confirmed loss of STAG2 in additional patient tumor samples. Using an original model of NPM1::ALK-driven lymphomagenesis that recapitulates early steps of ALK-driven transformation initiated in primary T lymphocytes, we demonstrated that STAG2 defect accelerates oncogenesis, enhancing early cell proliferation of ALK-positive cells. Single-cell RNA-seq revealed that STAG2 depletion accelerates the early acquisition of the major ALK+ ALCL hallmarks and concomitantly reduces the oncogene-induced senescence signature. Despite higher ALK expression and robust cell transformation, STAG2 depletion resulted in the attenuation of the global ALK+ ALCL transcriptional program. Importantly, STAG2 expression was found decreased upon NPM1::ALK induction, indicating intrinsic downregulation during transformation even without genomic mutations. We also successfully identified STAG2-low/ALK-high cells in both patient-derived tumors and PDX models. Functionally, STAG2-depleted cells exhibit increased cell adhesion and migration, alongside constitutive YAP1 activation and upregulation of adhesion molecule such as ALCAM and CD44 but also increased PD-L1. Overall, our findings reveal that STAG2 loss plays a key role during the earliest stages of ALK+ ALCL lymphomagenesis by promoting cell tolerance to NPM1::ALK expression and increasing permissiveness to malignant transformation while also impacting cell adhesion, migration.