Homeodomain-driven oncogenic diversion to a γδTCR phenotype in T-cell acute lymphoblastic leukemia

Abstract

Abstract T-cell acute lymphoblastic leukemia (T-ALL) results from the malignant transformation of thymocytes blocked in their differentiation. Surface expression of the γδ T-cell receptor (γδTCR) is surprisingly frequent in T-ALLs, questioning the susceptibility of the γδ-lineage to leukemogenesis. Among 1233 T-ALLs phenotyped in our center, 33% (n = 403) expressed a TCR, of which 47% (n = 191; 113 adults, 78 children) were positive for γδTCR (γδTCR+). Using a comprehensive analysis, we were able to delineate 2 distinct γδTCR+ T-ALL subtypes, with distinct physiological counterparts. The first (75% of cases) was characterized by ectopic expression of homeodomain-containing oncogenes (HD+), Vβ-Jβ rearrangements, and phenotypic (including surface pre-TCRα chain) and transcriptional profiles reminiscent of cortical thymocytes and was, therefore, termed cortical-like γδ T-ALLs. Transduction of murine T-cell progenitors and human CD34+ cells with HOXA9 or TLX3 (HD+ oncogenes) led to a differentiation bias toward γδTCR-expressing thymocytes. The second subtype (25%) exhibited phenotypic and transcriptional profiles reminiscent of γδ thymocytes, and was termed bona fide γδ T-ALLs. These findings were validated in the COGAALL0434 cohort. Although bona fide γδ T-ALLs were enriched for early T-cell progenitor (ETP)–like and KMT2A-rearranged cases, they mostly eluded the phenotypic definition of ETP-ALLs. Similar to the ETP-like subtype, bona fide γδ T-ALLs were associated with a poor initial response to chemotherapy but were sensitive to the BCL2 inhibitor venetoclax. Our results reveal developmental heterogeneity behind γδTCR expression in T-ALLs and suggest that overrepresentation of this subtype reflects αβ-lineage commitment repression by HD+ oncogenes. These trials were registered at www.clinicaltrials.gov as NCT00222027 (GRAALL2003), NCT00327678 (GRAALL2005), NCT03709719 (GRAALL2014), and NCT00408005 (Children's Oncology Group AALL0434 trial).