In silico learning of tumor evolution through mutational time series
| العنوان: | In silico learning of tumor evolution through mutational time series |
|---|---|
| المؤلفون: | Eugene V. Koonin, Noam Auslander, Yuri I. Wolf |
| المصدر: | Proceedings of the National Academy of Sciences of the United States of America |
| بيانات النشر: | Proceedings of the National Academy of Sciences, 2019. |
| سنة النشر: | 2019 |
| مصطلحات موضوعية: | driver mutations, In silico, passenger mutations, Computational biology, Biology, medicine.disease_cause, Evolution, Molecular, Neoplasms, Databases, Genetic, Genetics, medicine, Humans, Computer Simulation, Gene, Sequence (medicine), Mutation, Multidisciplinary, Models, Genetic, Artificial neural network, Cancer, Biological Sciences, neural networks, medicine.disease, cancer progression, machine learning, Recurrent neural network, PNAS Plus, Tumor progression, Neural Networks, Computer, human activities, Algorithms |
| الوصف: | Significance Cancer is caused by the effects of somatic mutations known as drivers. Although a number of major cancer drivers have been identified, it is suspected that many more comparatively rare and conditional drivers exist, and the interactions between different cancer-associated mutations that might be relevant for tumor progression are not well understood. We applied an advanced neural network approach to learn the sequence of mutations and the mutational burden in colon and lung cancers and to identify mutations that are associated with individual drivers. A significant ordering of driver mutations is demonstrated, and numerous, previously undetected conditional drivers are identified. These findings broaden the existing understanding of the mechanisms of tumor progression and have implications for therapeutic strategies. Cancer arises through the accumulation of somatic mutations over time. Understanding the sequence of mutation occurrence during cancer progression can assist early and accurate diagnosis and improve clinical decision-making. Here we employ long short-term memory (LSTM) networks, a class of recurrent neural network, to learn the evolution of a tumor through an ordered sequence of mutations. We demonstrate the capacity of LSTMs to learn complex dynamics of the mutational time series governing tumor progression, allowing accurate prediction of the mutational burden and the occurrence of mutations in the sequence. Using the probabilities learned by the LSTM, we simulate mutational data and show that the simulation results are statistically indistinguishable from the empirical data. We identify passenger mutations that are significantly associated with established cancer drivers in the sequence and demonstrate that the genes carrying these mutations are substantially enriched in interactions with the corresponding driver genes. Breaking the network into modules consisting of driver genes and their interactors, we show that these interactions are associated with poor patient prognosis, thus likely conferring growth advantage for tumor progression. Thus, application of LSTM provides for prediction of numerous additional conditional drivers and reveals hitherto unknown aspects of cancer evolution. |
| تدمد: | 1091-6490 0027-8424 |
| الوصول الحر: | https://explore.openaire.eu/search/publication?articleId=doi_dedup___::e695ca23c7551821fa393e7261e29048Test https://doi.org/10.1073/pnas.1901695116Test |
| حقوق: | OPEN |
| رقم الانضمام: | edsair.doi.dedup.....e695ca23c7551821fa393e7261e29048 |
| قاعدة البيانات: | OpenAIRE |
| تدمد: | 10916490 00278424 |
|---|