By Joshua Wu
Cancer, often described as the emperor of all maladies, is a disease characterized by uncontrolled cell growth and proliferation. Cancer is expected to cause the death of 606,520 Americans this year, according to the American Cancer Society’s 2020 Facts & Figures. Due to the variety of cell types from which cancers can arise, as well as current technological limits in effective early cancer detection, cancer diagnosis is highly correlated with mortality. However, despite the unpredictability of cancer, researchers have identified several hallmarks of cancer, which are recurrent, essential events during the development of different types of cancer that contribute to cancer growth. One such hallmark is the abnormal activation of oncogenes.
Oncogenes are genes that can transform a normal cell into a cancer cell when mutated or expressed at high levels. A common mechanism employed by cancer to induce increased expression of oncogenes is oncogene amplification, which occurs when DNA sequences encoding oncogenes are duplicated multiple times in the genome. These duplications can be found either on the same chromosome as the original oncogene locus through tandem oncogene amplification, or on different chromosomes through subsequent recombination events. They can be detected through sequencing and other molecular techniques such as fluorescent in situ hybridization, or FISH.
However, it was only recently understood that cancers often employ other previously unidentified types of abnormal chromosomal structures to increase oncogene expression. One such mysterious structure is called extrachromosomal DNA (ecDNA), which, as the name suggests, is composed of chromatin fibers that are not part of the normal chromosomes. ecDNAs are pieces of genetic materials specifically employed by cancer to promote its development. Therefore, understanding how they contribute to cancer development has important biomedical values.
The recent findings reported by Sihan Wu and colleagues have shed light on how the unique topology of ecDNAs drives elevated oncogene expression.
Through super-resolution microscopy, Wu et al. have elucidated that the physical structure of ecDNAs is circular. This circular configuration has key implications for DNA transcription, as it allows DNA transcriptional machinery, consisting of all proteins necessary for transcription, to be closer to distal DNA sequences compared to regular, linear chromosomal DNA. In other words, not only can the expression of nearby DNA sequences be increased, but also more distal ones. Because cancer has taken advantage of the system of ecDNA such that oncogenes are specifically hyper-amplified, this increase in transcriptional efficiency of more distal DNA sequences allows more cancer-promoting mRNAs to be transcribed, leading to greater synthesis rate of cancer-promoting proteins. As these cancer-promoting proteins are often growth hormones or other proliferative signals, the circular structure of ecDNAs triggers a vicious cycle of uncontrolled cell growth and proliferation in various body tissues, thus increasing the chance of cancer spread.
Besides the observation that ecDNAs are circular through immunofluorescent analysis (IF) and chromatin immunoprecipitation assay (ChIP-seq), an assay for transposase-accessible chromatin using sequencing (ATAC-seq), the investigators have discovered that the chromatin that makes up the ecDNAs is in a less compact state, which allows DNA transcriptional machinery to easily bind to the chromatin and initiate transcription. This greater chromatin accessibility is exemplified by the elevation in histone acetylation marks, which loosen the nucleosomes made of histone proteins that normally prevent RNA polymerase from binding the chromatin.
Importantly, despite the foreseeable difficulty in globally treating ecDNAs in cancer patients due to their high genetic heterogeneity, the authors have indicated structural commonalities between these circular ecDNAs and circular bacterial plasmids. As a result, the authors speculate that current molecular biology techniques that target bacterial plasmids may lay the groundwork to generate therapeutic strategies targeting ecDNA. The findings of this paper on the physical structure of ecDNAs add another layer of complexity to our understanding of how cancer drives aberrant oncogene expression, which ultimately can help us in devising more comprehensive cancer therapies.
Cancer Facts & Figures 2020. (n.d.). American Cancer SocietyRetrieved from https://www.cancer.org/content/dam/cancer-org/research/cancer-facts-and-statistics/annual-cancer-facts-and-figures/2020/cancer-facts-and-figures-2020.pdf
Hanahan, D., & Weinberg, R. A. (2011). Hallmarks of Cancer: The Next Generation. Cell, 144(5), 646–674. doi: 10.1016/j.cell.2011.02.013
Wu, S., Turner, K. M., Nguyen, N., Raviram, R., Erb, M., Santini, J., … Mischel, P. S. (2019). Circular ecDNA promotes accessible chromatin and high oncogene expression. Nature, 575(7784), 699–703. doi: 10.1038/s41586-019-1763-5