Discovery of Red-Shifting Mutations in Firefly Luciferase Using High-Throughput Biochemistry

Photinus pyralis luciferase (FLuc) has proven a valuable tool for bioluminescence imaging, but much of the light emitted from the native enzyme is absorbed by endogenous biomolecules. Thus, luciferases displaying red-shifted emission enable higher resolution during deep-tissue imaging. A robust model of how protein structure determines emission color would greatly aid the engineering of red-shifted mutants, but no consensus has been reached to date. In this work, we applied deep mutational scanning to systematically assess 20 functionally important amino acid positions on FLuc for red-shifting mutations, predicting that an unbiased approach would enable novel contributions to this debate. We report dozens of red-shifting mutations as a result, a large majority of which have not been previously identified. Further characterization revealed that mutations N229T and T352M, in particular, bring about unimodal emission with the majority of photons being >600 nm. The red-shifting mutations identified by this high-throughput approach provide strong biochemical evidence for the multiple-emitter mechanism of color determination and point to the importance of a water network in the enzyme binding pocket for altering the emitter ratio. This work provides a broadly applicable mutational data set tying FLuc structure to emission color that contributes to our mechanistic understanding of emission color determination and should facilitate further engineering of improved probes for deep-tissue imaging.

Circular extrachromosomal DNA promotes tumor heterogeneity in high-risk medulloblastoma

Circular extrachromosomal DNA (ecDNA) in patient tumors is an important driver of oncogenic gene expression, evolution of drug resistance and poor patient outcomes. Applying computational methods for the detection and reconstruction of ecDNA across a retrospective cohort of 481 medulloblastoma tumors from 465 patients, we identify circular ecDNA in 82 patients (18%). Patients with ecDNA-positive medulloblastoma were more than twice as likely to relapse and three times as likely to die within 5 years of diagnosis. A subset of tumors harbored multiple ecDNA lineages, each containing distinct amplified oncogenes. Multimodal sequencing, imaging and CRISPR inhibition experiments in medulloblastoma models reveal intratumoral heterogeneity of ecDNA copy number per cell and frequent putative 'enhancer rewiring' events on ecDNA. This study reveals the frequency and diversity of ecDNA in medulloblastoma, stratified into molecular subgroups, and suggests copy number heterogeneity and enhancer rewiring as oncogenic features of ecDNA.

Abstract 95: The landscape of extrachromosomal circular DNA in medulloblastoma subgroups

Extrachromosomal circular DNA (ecDNA) has been shown to be an important driver of particularly aggressive human cancers. However, it remains unknown to what extent and by which molecular mechanisms ecDNA promotes tumor development and progression in the different molecular subgroups of medulloblastoma (MB), the most common malignant pediatric brain tumor. To answer these questions, we have assembled a multi-institutional retrospective cohort of 472 MB patient samples with available whole genome sequencing (WGS) data, drawing from three non-overlapping public cancer genomic data repositories and covering all four MB subgroups (i.e. WNT, SHH, Group 3 and Group 4). Using genomic cloud computing platforms, local computing resources and recent computational methods for the detection and reconstruction of ecDNA, we find ecDNA in 66 patients (14%) and observe that the presence of ecDNA is associated with significantly poorer outcomes. By subgroup, ecDNA was found in 0/13 WNT (0%), 18/69 SHH (26%), 12/76 G3 (16%) and 14/123 G4 (11%) patients. Affected genomic loci harbor up to hundredfold amplification of oncogenes including MYC, MYCN, and TERT; as well as amplifications of novel putative driver genes involved in chromatin remodeling, DNA repair, and kinase signaling pathways. To investigate the frequency and properties of ecDNA in model systems of MB tumors, we further analyzed WGS data from 24 patient-derived xenografts (PDX) and four cell lines. ecDNA was substantially more frequent in these patient-derived models (17 of 29, 59%) than in our patient cohort. To elucidate the functional regulatory landscapes of ecDNAs in MB, we generated transcriptional (RNA-seq), accessible chromatin (ATAC-seq), and chromatin interaction (Hi-C) profiles from 6 MB tumor samples. In each case, we identify regulatory interactions that cross fusion breakpoints on the ecDNA, representing potential “enhancer rewiring” events that are likely to contribute to transcriptional activation of co-amplified oncogenes. To test this hypothesis, we are currently conducting in-vitro CRISPRi screens targeting regulatory regions on the ecDNA with the aim of testing whether enhancer-rewiring increases the transcription of co-amplified oncogenes and promotes proliferation and cell line growth. In summary, our study analyzes the frequency, diversity and functional relevance of regulatory enhancers co-amplified with oncogenes on ecDNA across MB subgroups and provides strong scientific justification for continued mechanistic studies of ecDNA in MB tumors and tumor models with the potential to uncover new therapeutic approaches.

Citation Format: Owen S. Chapman, Shanqing Wang, Jens Luebeck, Alexandra Garancher, Jon D. Larson, Joshua Lange, John Crawford, Scott L. Pomeroy, Paul Mischel, Ernest Fraenkel, Robert J. Wechsler-Reya, Vineet Bafna, Jill P. Mesirov, Lukas Chavez. The landscape of extrachromosomal circular DNA in medulloblastoma subgroups [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 95.

Abstract 447: Integrated omics modeling of transcriptional regulation in medulloblastoma subtypes

Medulloblastoma (MB) is one of the most common pediatric brain tumors. Current treatment options carry substantial risk for lifelong cognitive and neurological impairment. Consequently, there is a pressing need to elucidate molecular mechanisms with the ultimate goal of developing targeted tumor-specific therapies. In a recent study on proteomes and phospho-proteomes of primary MB tumors, we identified proteomic MB subtypes that were not apparent from transcriptional or methylation data. To identify gene regulatory circuitries that drive these MB subtypes, we have now mapped accessible chromatin and 3D chromosome conformation in 23 and 13 MB tumors from the same cohort, using ATAC-seq and Hi-C respectively. We identify subtype-specific accessible regulatory chromatin regions, including a subset of regions not identifiable by the enhancer mark H3K27ac. We associate regulatory regions to their target gene promoters by correlating transcription with ATAC-seq signal strength, and confirm these relationships using the newly generated Hi-C data. Using an unpublished adaptation of the GSEA algorithm, which we tailored for an enrichment analysis of non-coding regulatory elements instead of genes, we identify transcription factors and master regulators with binding sites specific to an MB subtype. By associating these master regulators with their transcriptional targets, we have derived models of regulatory circuitry in MB which implicate central mechanisms of MB pathogenesis and may inform future therapeutic targeting.

Citation Format: Owen S. Chapman, Tobias Ehrenberger, Tenley C. Archer, Maxwell P. Gold, Filip Mundt, Miriam Adam, Clarence K. Mah, Karsten Krug, Sahaana Chandran, Jesse R. Dixon, Scot L. Pomeroy, Ernest Fraenkel, Jill P. Mesirov, Lukas Chavez. Integrated omics modeling of transcriptional regulation in medulloblastoma subtypes [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 447.