Dissecting mutational mechanisms underpinning signatures caused by replication errors and endogenous DNA damage

Zou, X.; Koh, G. C. C.; Nanda, A. S.; Degasperi, A.; Urgo, K.; Roumeliotis, T.; Agu, C. A.; Side, L.; Brice, G.; Perez-Alonso, V.; Rueda, D.; Badja, C.; Young, J.; Gomez, C.; Bushell, W.; Harris, R.; Choudhary, J.; Jiricny, J. I.; Skarnes, W. C.; Nik-Zainal, S.

doi:10.1101/2020.08.04.234245

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bioRxiv · 10.1101/2020.08.04.234245

Dissecting mutational mechanisms underpinning signatures caused by replication errors and endogenous DNA damage

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Abstract

Mutational signatures are imprints of pathophysiological processes arising through tumorigenesis. Here, we generate isogenic CRISPR-Cas9 knockouts ({Delta}) of 43 genes in human induced pluripotent stem cells, culture them in the absence of added DNA damage, and perform wholegenome sequencing of 173 daughter subclones. {Delta}OGG1, {Delta}UNG, {Delta}EXO1, {Delta}RNF168, {Delta}MLH1, {Delta}MSH2, {Delta}MSH6, {Delta}PMS1, and {Delta}PMS2 produce marked mutational signatures indicative of being critical mitigators of endogenous DNA changes. Detailed analyses reveal that 8-oxo-dG removal by different repair proteins is sequence-context-specific while uracil clearance is sequencecontext-independent. Signatures of mismatch repair (MMR) deficiency show components of C>A transversions due to oxidative damage, T>C and C>T transitions due to differential misincorporation by replicative polymerases, and T>A transversions for which we propose a reverse template slippage model. {Delta}MLH1, {Delta}MSH6, and {Delta}MSH2 signatures are similar to each other but distinct from {Delta}PMS2. We validate these gene-specificities in cells from patients with Constitutive Mismatch Repair Deficiency Syndrome. Based on these experimental insights, we develop a classifier, MMRDetect, for improved clinical detection of MMR-deficient tumors.

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Zou, X., Koh, G. C. C., Nanda, A. S., Degasperi, A., Urgo, K., Roumeliotis, T., Agu, C. A., Side, L., Brice, G., Perez-Alonso, V., Rueda, D., Badja, C., Young, J., Gomez, C., Bushell, W., Harris, R., Choudhary, J., Jiricny, J. I., Skarnes, W. C., Nik-Zainal, S.. 2020-08-06. Dissecting mutational mechanisms underpinning signatures caused by replication errors and endogenous DNA damage. https://doi.org/10.1101/2020.08.04.234245

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