Spatial Architecture and Functional Characterization of Super Enhancer Associated Transcriptional Circuits in Aggressive Lymphomas
by Nazli Serin née Nazli
Date of Examination:2023-08-31
Date of issue:2023-10-19
Advisor:Dr. Björn Chapuy
Referee:Prof. Dr. Argyris Papantonis
Referee:PD Dr. Elisabeth Heßmann
Referee:Prof. Dr. Uwe Kornak
Referee:Prof. Dr. Dieter Kube
Referee:Prof. Dr. Tim Beißbart
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EnglishAggressive lymphomas are clinically and biologically heterogenous entities, reflecting a diverse cell of-origins with multiple means of malignant transformation. With chemoimmunotherapy, a majority of patients suffering from diffuse large B-cell lymphoma (DLBCL) achieve long-term remission and are considered cured, while the remaining patients succumb to their disease. In other lymphoma subtypes, such as the heterogenous group of T-cell lymphomas, patients have a more dismal prognosis when treated with chemotherapy, highlighting the unmet medical need to identify novel treatments. The clinical heterogeneity prompted the search for the underlying molecular bases and facilitated molecular-driven classifications with the hope of identifying rational and actionable alterations. Over the last two decades, many large-scale studies, including transcriptional and genomic efforts targeting the coding genome, have identified several key-essential signaling pathways in aggressive lymphomas, resulting in the identification and exploration of new potential therapeutic targets. However, the non-coding genome, which comprises 98% of the genome, remains largely unexplored despite the growing understanding thatm gene regulation is to a large extent, controlled by non-coding regions. Notably, the various genetic alterations that gave rise to the lymphoma are integrated at the level of chromatin, providing the hope that common dependencies can be found by studying chromatin and transcriptional regulation. This raises the intriguing question of whether the complex machinery governing transcription and spatial rearrangement of enhancers provides insight into a better understanding of the underlying biology and could reveal novel cancer cell dependencies. Prior studies have highlighted that enhancers harbor a highly asymmetric loading with certain coactivators, such as BRD4 and the mediator complex, which resulted in the discovery of super enhancers (SEs). The SEs are clusters of constituent enhancers closely associated with maintaining oncogenic and lineage-specific transcriptional circuits. As such, cancer cells are often dependent on the transcriptional programs driven by SE, providing the rationale for this thesis that aims to discover unrecognized cancer dependencies by characterizing SEs in a panel of hard to treat lymphoma subtypes. Combined with the understanding that cancer is caused by derailed gene expression control, I hypothesize that a full map of the essential gene regulatory machinery controlling transcription will identify new dependencies in cancer cells. In this PhD study, I mapped SEs in aggressive lymphomas across 42 lymphoma cell lines using a combination of genome-wide H3K27 acetylation ChIP-Seq and the chromatin accessibility assay, ATAC-Seq. This allowed the identification of the global SE architecture and transcriptional circuitry of the characterized lymphomas. Targeted 3C technology based on the SE-relevant H3K27ac mark, HiChIP-Seq, were then used to map the 3D architecture of all SEs and their controlled target genes. Next, I validated the strength of this approach in identifying cancer cell dependencies by leveraging publicly available CRISPR screen data. Moreover, I validated experimentally in model systems of primary mediastinal large B-cell lymphomas (PMBLs), the finding of a selective acquisition of the PIM3-SE in PMBL, dissected the molecular circuits of PIM3-SE and demonstrated the dependency of this in the model systems of clinical grade PIM inhibitors. Importantly, I also found that the predominant female subtype of lymphoma, PMBL, is regulated by estrogen receptor providing unanticipated insights into the biology of the disease.
Keywords: super-enhancers; aggressive lymphomas