The Role of Clonal Evolution and Anti- Apoptotic Dependencies in Cancer Progression and Therapy Resistance: Implications for Personalized Medicine
by Paolo Mazzeo
Date of Examination:2025-02-25
Date of issue:2025-04-10
Advisor:PD Dr. Raphael Koch
Referee:PD Dr. Raphael Koch
Referee:Prof. Dr. Elisabeth Heßmann
Persistent Address:
http://dx.doi.org/10.53846/goediss-11158
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Abstract
English
Cancer is characterized by significant heterogeneity, both across and within individual tumors, posing challenges for treatment. This thesis investigates clonal evolution (CE) and its association with apoptotic mechanisms to enhance our understanding of therapy resistance and improve strategies for patient stratification and personalized therapeutic approaches. By integrating genetic and functional profiling, this work focuses on hematologic malignancies, but also provides an example in thymoma to advance personalized treatment approaches. With the identification of distinct mechanisms conferring resistance to apoptotic cell death in cancer and emerging strategies to target these mechanisms, identification of targetable vulnerabilities within the apoptotic machinery is a specific focus of this thesis. In a case series of T-large granular lymphocytic leukemia (T-LGLL), we assessed targetable anti-apoptotic mechanisms of malignant T-LGLL clones versus the same patients’ healthy T-cells by flow-cytometry based selective BH3 profiling. This approach revealed functional heterogeneity across patients and uncovered a dominant dependence on the anti-apoptotic protein MCL-1 in individual cases, independent of the specific genetic background of the disease. The potential therapeutic relevance of this MCL-1 dependence was further corroborated by ex vivo treatment with an MCL-1 specific inhibitor and thus suggests an approach towards personalized treatment in T-LGLL. The second study employed functional apoptosis profiling to assess apoptotic dependencies in thymic epithelial tumors and thus demonstrates the feasibility of applying functional apoptosis profiling in solid malignancies. Our findings revealed heterogeneous reliance on anti-apoptotic proteins such as MCL-1 and BCL-xL. Single-agent therapies were insufficient to induce effective apoptosis, but combination strategies successfully targeted tumor survival mechanisms, underscoring the value of personalized approaches for these chemoresistant tumors. Next, functional apoptosis profiling was used in T-cell prolymphocytic leukemia (T-PLL) to support drug combination strategies and identified synergistic drug combinations, including cladribine and idasanutlin, which was validated in patient-derived xenograft models. Together, these three studies provide examples of successful pre-clinical identification of targetable vulnerabilities across different entities and different genetic backgrounds. Focusing on genetics in myeloid neoplasms, we characterized clonal dynamics (CD) in lower-risk myelodysplastic syndromes (LR-MDS) using comprehensive longitudinal genetic data. We identified diverse patterns of CE, ranging from stable clones to dynamic shifts in clonal architecture. Interestingly, CE did not directly correlate with adverse outcomes in LR-MDS, likely due to the absence of aggressive genetic alterations. Timely application of disease-modifying therapies mitigated the impact of CD, emphasizing the importance of early therapeutic intervention. Ultimately, we analyzed treatment-associated clonal evolution and anti-apoptotic dependencies in patient samples of high-risk myelodysplastic neoplasms and acute myeloid leukemia. In patients treated with the hypomethylating agent azacitidine and the BCL-2 inhibitor venetoclax, we identified a highly significant correlation of pre-treatment BCL-2 dependence by BH3 profiling with molecular response and improved overall survival. Furthermore, this study characterized clonal dynamics during treatment and associated changes in anti-apoptotic dependencies. Importantly, this approach revealed targetable mechanisms of resistance in individual patients. Overall, this thesis highlights the pivotal role of CE and apoptotic dependencies in therapy resistance, emphasizing the need for intensified and development of innovative and more effective personalized diagnostics and treatment strategies. Future studies should focus on expanding these approaches to validate their efficacy in larger, more comprehensive patient cohorts.
Keywords: Clonal Evolution; Therapy Resistance; Personalized Medicine
