Tousinas, Georgios

Abstract Mutations in non-coding regulatory elements are increasingly recognized as critical drivers of cancer development and progression. Among these, structural alterations such as duplications of super-enhancers (SEs), large clusters of enhancers that regulate key oncogenes, have emerged as significant contributors to oncogenesis. In T-cell acute lymphoblastic leukemia (T-ALL), a particularly aggressive hematologic malignancy, SE duplications have been identified in approximately 5% of human cases. These duplications frequently involve a non-coding region located approximately 1.3 megabases downstream of the Myc oncogene, a region known as N-Me. Despite the growing recognition of the role of SE duplications in T-ALL, functional studies to determine their molecular origins and contributions to leukemogenesis have been limited, largely due to the absence of suitable and genetically tractable preclinical models. This gap in knowledge hinders both our understanding of disease pathogenesis and our ability to design targeted therapeutic interventions. Here, we report the generation and characterization of a novel genetically engineered mouse model of T-ALL that spontaneously develops oncogenic SE duplications at the Myc locus. This model offers the first spontaneous in vivo system to investigate the origin, regulation, and oncogenic function of SE duplications. This model was created by conditionally stabilizing β-catenin in CD4⁺CD8⁺ double-positive (DP) thymocytes in combination with targeted deletion of the transcription factor HEB. This combination is sufficient to drive the development of aggressive T-cell leukemias that consistently harbor duplications of the N-Me super-enhancer. This finding recapitulates the genomic alteration observed in a subset of human T-ALL and provides a unique platform for mechanistic studies. We further demonstrate that the molecular events leading to SE duplication and oncogenic Myc activation unfold in a stepwise manner. At the preleukemic stage, stabilization of β-catenin alone is sufficient to enhance recruitment of HEB to the N-Me region. The simultaneous loss of HEB greatly increased chromatin accessibility at the N-Me enhancer. This altered chromatin landscape permits aberrant binding of transcription factors including TCF-1, which plays a critical role in T-cell development and leads to N-Me SE activation associated with significant three-dimensional chromatin reorganization. Chromosome conformation analyses in the leukemic cells reveal the formation of a novel chromatin loop that brings the activated N-Me SE into close spatial proximity with the Myc promoter, enabling oncogenic Myc transcription. These findings uncover a novel mechanistic pathway by which β-catenin and HEB interact to reshape the enhancer landscape and three-dimensional chromatin architecture, ultimately promoting SE duplication and aberrant Myc expression in T-ALL. β-catenin appears to play a dual role, first facilitating HEB recruitment under physiological conditions and then, upon HEB loss, permitting the reprogramming of enhancer activity through chromatin opening and ectopic transcription factor binding. Our data suggest that the cooperative interplay between signaling pathways and transcriptional regulators at enhancer elements can initiate structural genomic changes that drive malignancy. This work provides a long-sought preclinical model that faithfully mirrors key features of human T-ALL. Our findings open new avenues for understanding how non-coding regulatory mutations arise and exert oncogenic effects and have the potential to provide insights that may extend beyond T-ALL to other cancers driven by enhancer dysregulation. Moreover, by revealing molecular intermediates such as β-catenin, HEB, and TCF-1 in the regulation of enhancer activity, our findings identify potential therapeutic targets to disrupt the oncogenic enhancer-promoter interactions that underlie Myc-driven leukemogenesis.

Abstract Activation of β-catenin in CD4+CD8+ double-positive (DP) thymocytes halts development before the thymic selection stage and predisposes to transformation. Leukemogenesis, but not the developmental block, depends on TCF-1, β-catenin’s DNA-binding partner. In this study, we show that β-catenin activation directs the DNA-binding protein HEB to block DP thymocyte development. Conditional loss of HEB in DP thymocytes with stabilized β-catenin restores the frequencies of postselection TCRβhi/CCR7+ and TCRβhi/CD69+ DPs and their cell-cycle profile. This recovery is associated with significant reversal of β-catenin-induced expression changes, particularly those related to the CD69+ DP cell signature and to cell-cycle pathways. Stabilizing β-catenin in DP thymocytes directs HEB binding to ≈11,000 novel DNA sites throughout the genome. Novel HEB sites mark most CD69+ DP cell signature genes that change expression upon activation of β-catenin and then revert after loss of HEB. Moreover, many of the novel HEB sites occupy promoter regions of genes enriched in mitotic cell cycle pathways. HEB binding to those regions correlates with downregulation of the associated genes, and HEB inactivation restores expression to physiologic levels. These findings highlight a molecular interplay between HEB and β-catenin that can impair thymic development.

Abstract Colorectal cancer (CRC) is one of the most common cancers in the world, yet it remains one of the most difficult to treat. Immunotherapy of CRC using checkpoint inhibitors is only efficacious in approximately 4% of patients with high microsatellite instability (MSI-H). In earlier studies we showed that in patients with inflammatory bowel diseases (IBD) and CRC as well as in the APCΔ468 murine polyposis model, Tregs overexpress β-catenin. Furthermore, we demonstrated that expression of a dominant active β-catenin in Tregs induces RORγt, compromising suppressive activity and promoting TH17-like properties. This results in a scurfy-like phenotype. By contrast loss of TCF-1 upregulated RORγt, but only compromised Treg anti-inflammatory functions. These observations suggested cooperation of β-catenin and TCF-1 in regulating Treg plasticity. We show here that in healthy mice, β-catenin expression is significantly higher in Tregs as compared to conventional CD4+ T-cells. In Tregs that express a dominant active β-catenin, ablation of TCF-1 or HEB provide partial rescue, while ablation of both TCF-1 and HEB recovers Treg numbers and prevents the scurfy-like phenotype. These observations suggest that TCF-1, HEB and β-catenin cooperate to determine Treg functions. In search for additional partners, we show that loss of TCF-1 upregulates SATB-1, a chromatin modifier that is known to determine T-cell development and function. Upregulation of SATB-1 is enhanced with the loss of both TCF-1 and HEB. All three transcription factors upregulate RORγt suggesting that they cooperatively determine Treg function and plasticity. Elucidating this cooperation will enhance our ability to control Treg plasticity in health and disease. NIH/NIAID - R01 AI108682-0A1

Abstract T-cell Acute lymphoblastic leukemia (T-ALL) is an aggressive disease with only a 10% 5-year survival rate for patients over 60, due to genomic instability. We have shown that β-catenin and TCF-1 cooperate in DP thymocytes to promote genomic instability leading to lymphomagenesis. We have also established that TCF-1 and HEB cooperate in the DP stage. Now, we aim to determine the molecular underpinnings of T-ALL and thymic development, by elucidating the interplay of all three factors, β-catenin, TCF-1, and HEB. Aberrant activation of β-catenin promotes the development of Lymphoma/Leukemia equivalent to the human disease T-ALL and blocks thymocyte development in the early DP stage. Ablation of TCF-1 in thymocytes with activated β-catenin rescues from lymphomagenesis, but the developmental block persists. Antithetically, developmental progression is achieved only when HEB is conditionally knocked out. In an effort to explain this phenomenon, we found that genes associated with the transition of DP thymocytes from DPsmall to CD69+ are downregulated by activating β-catenin (e.g. Runx-3, Ccr-7, TOX-2, etc.) and revert upon deletion of HEB. This is associated with changes in the binding of TCF-1 to DNA. Genomic sites that acquire TCF-1 binding upon β-catenin activation forfeit this binding when HEB is deleted, while at the same time novel TCF-1 binding sites emerge. These new binding sites are significantly more enriched for the conserved TCF-1 motif than TCF-1-bound sites in WT thymocytes. This observation promotes the notion that HEB guides TCF-1 towards alternative binding sites, thus altering gene expression. These findings highlight the complex interactive relationship of TCF-1 and HEB in both normal development and disease. NIH/NIAID R01 AI147652-01A1