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Understanding mutation using genome-wide sequence-based approaches

Final Report Summary - WGEN MUTATION (Understanding mutation using genome-wide sequence-based approaches)


Mutation is the engine of evolution, in that it generates the genetic variation necessary for evolution to occur. The objective of this project is the study of mutation and its input into the evolutionary process, using whole genome approaches. During this project we have revealed many significant insights into mutation and how it contributes to diverse important biological and evolutionary phenomena, from the accumulation of antibiotic resistance within bacterial populations, to cancer development within the human body.

With regards to the evolution of antibiotic resistance, it has been demonstrated that when bacterial colonies are starved, the frequency of antibiotic resistance tends to increase, even in the absence of any antibiotic exposure. This was long-thought to be the result of increases in mutation rates in response to starvation that lead to increases in the frequency with which antibiotic resistance mutations occur. Using a whole-genome sequencing-based approach, we were able to demonstrate that, contrary to this widespread assumption, such starvation-induced increases in antibiotic resistance frequencies were not due to increases in mutagenesis. Rather, it appears that specific resistance mutations to a variety of antibiotics are beneficial to bacterial growth under starvation. We could further demonstrate that one such resistance allele that we identified as adaptive under starvation is alarmingly frequent within natural bacterial populations. This antibiotic resistance allele is particularly frequent within-host environments, where on average ~40% of bacteria carry the allele, independent of expected levels of antibiotic exposure. Our results suggest that the antibiotic-independent fitness effects of resistance alleles may strongly affect the frequency with which resistance segregates within natural bacterial populations. These results are important for a number of reasons. First, from the perspective of studying mutation rates, our results show that the very common practice of using antibiotic resistance as a marker for the study of mutation is extremely problematic. From the human health perspective, our results are important for understanding and one day combating the spread of antibiotic resistance, which is currently considered to be one of the most pressing health threats facing humanity. These results were published in two papers in the journals PLoS Genetics and Genome Biology and Evolution.

With regards to studying mutation in the context of cancer – contrary to most genetic diseases that are driven by hereditary mutations, cancer is a disease that is driven by somatic mutations. We have published three papers regarding the dynamics by which somatic mutational biases and the effects of natural selection on somatic mutations drive the evolution of tumors. In the first of these papers, published in PLoS Genetics, and highlighted in Nature Reviews Genetics, we demonstrated that natural selection affects somatic mutations very differently than it does hereditary mutations. We further demonstrated that there is prevalent positive selection within tumors on somatic mutations occurring within genes that are globally expressed across human tissues. Finally, we showed that such globally expressed genes are enriched for, yet unknown, cancer drivers. Identifying such novel cancer drivers is a major aim of cancer genomics. In the second paper, published in the journal Scientific Reports, we disentangled the effects of mutational biases and natural selection in determining variation in the patterns of KRAS driver mutations within different types of tumors. KRAS is a major oncogene that contributes to the development of a variety of tumor types. Within various tumor types different subtypes of KRAS driver mutations are found at different frequencies. We showed that this variation in the distribution of KRAS driver mutations is contributed to by both variation in mutational biases and variation in natural selection. This allowed us to identify specific KRAS mutations that are over represented within a given tumor type, relative to expectations based on mutational patterns. Such specifically over-represented KRAS mutations likely contribute more strongly to specific tumor types. Indeed, we could show that the presence of such mutations within the tumor type in which they tend to be over-represented correlates with worse clinical outcomes to the patients carrying them. These results may have implications for personalizing treatment of patients. In the third paper, published in the journal Genome Biology and Evolution, we characterized genes contributing to cancer and compared them to genes contributing to other genetic disorders. We could show that cancer genes tended to be more constrained in evolution and more functionally central. We further demonstrated that it is the nature of cancer, as a disease that relies mostly on somatic rather than germline mutations, that allows it to affect such functionally central and important genes. It therefore appears that it is the somatic nature of cancer that allows it to be a disease of the most central and important cellular functions.

In addition, this project led to important insights regarding the causes of the extensive observed variation in bacterial nucleotide content and the contribution of gene loss mutations to the evolution of bacterial pathogens. In total, the project has led to the publication of 11 manuscripts, including nine research papers in such journals as PLoS Genetics, Nucleic Acids Research, Genome Biology and Evolution, Microbiome, and Scientific reports, a review article about mutation and its role as the engine of evolution and a book chapter.

The funding received allowed me to fully integrate into my new position and faculty and establish a vibrant, productive research group. Over the years of the project I have established several collaborations with scientists both within and outside of Europe and have presented my work in many scientific meetings. I have also engaged in outreach activities directed at high school students and separately at outreach activities directed at pathologists, aimed at introducing them to concepts of bioinformatic research that they can integrate into their clinical work. Together with two other female faculty members we have also established an ‘advancing women in science’ forum at our faculty.

My laboratory’s website (which is also the project’s website) can be found at: