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Somatic deletions of genes regulating MSH2 protein stability cause DNA mismatch repair deficiency and drug resistance in human leukemia cells

Abstract

DNA mismatch repair enzymes (for example, MSH2) maintain genomic integrity, and their deficiency predisposes to several human cancers and to drug resistance. We found that leukemia cells from a substantial proportion of children (11%) with newly diagnosed acute lymphoblastic leukemia have low or undetectable MSH2 protein levels, despite abundant wild-type MSH2 mRNA. Leukemia cells with low levels of MSH2 contained partial or complete somatic deletions of one to four genes that regulate MSH2 degradation (FRAP1 (also known as MTOR), HERC1, PRKCZ and PIK3C2B); we also found these deletions in individuals with adult acute lymphoblastic leukemia (16%) and sporadic colorectal cancer (13.5%). Knockdown of these genes in human leukemia cells recapitulated the MSH2 protein deficiency by enhancing MSH2 degradation, leading to substantial reduction in DNA mismatch repair and increased resistance to thiopurines. These findings reveal a previously unrecognized mechanism whereby somatic deletions of genes regulating MSH2 degradation result in undetectable levels of MSH2 protein in leukemia cells, DNA mismatch repair deficiency and drug resistance.

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Figure 1: Gene copy number loss and MSH2 protein expression in primary human leukemia cells.
Figure 2: Protein expression in primary leukemia cells with hemizygous deletions, treatment outcome and drug sensitivity according to leukemia cell MSH2 phenotype.
Figure 3: PRKCZ, PIK3C2B, HERC1 and FRAP1 inhibition and MSH2 stability.
Figure 4: Increase in PP2A activity through inhibition or knockdown of FRAP1, HERC1 or PIK3C2B with rescue by okadaic acid (OA) and the effects on MMR activity.

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Acknowledgements

We gratefully acknowledge the subjects and parents who participated in this study and the outstanding technical support of the Hartwell Center for Bioinformatics and Biotechnology at St. Jude Children's Research Hospital. We also thank Y. Wang, T. Brooks, J. Smith, W. Du, S. Mukatira, Y. Chu, M. Needham, P. Hargrove, G. Stocco and S. Paugh for their advice and technical support; J. Groff for preparation of the figures; K. Crews, N. Kornegay and M. Wilkinson for their research database expertise; J.C. Panetta for his modeling expertise; J. Jenkins for his immunohistochemistry expertise; T. Kunkel and A.B. Clark (National Institute of Environmental Health Sciences) for providing the E. coli strains, the wild-type and mutant M13mp2 phage and for their contributions to our MMR experiments; and J. Luis Rosa (Universitat de Barcelona) for providing us with antibodies to HERC1. We thank M. Kastan and D. Green for their critical review and advice. This work was supported in part by grant R37 CA36401 (W.E.E. and M.V.R.), NIH National Institute of General Medical Sciences Pharmacogenomics Research Network grant U01 GM92666 (M.V.R. and W.E.E.), CGM is a Pew Scholar and a St. Baldrick's scholar, and St. Jude is supported by a Cancer Center Support Grant CA 21765 from the National Cancer Institute and by the American Lebanese Syrian Associated Charities (ALSAC). H.G., S.C. and P.H. were funded by the Intramural Research Program of the National Institute of Diabetes and Digestive and Kidney Diseases of the NIH.

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W.E.E. designed and supervised experiments and their analyses and wrote the manuscript with B.D. B.D., Q.C., N.F.K., M.C., E.Y.K., H.G., S.C., P.H., W.E.T. and C.G.M. performed experiments and participated in their analyses. J.R.D., C.G.M. and M.V.R. directed experiments and contributed to the genomic analyses. D.P., Y.F. and C.C. performed the statistical analyses. W.Y. led the genomic analyses in collaboration with other authors. C.-H.P. led the clinical trials and provided the ALL samples. All authors discussed the results and commented on the manuscript.

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Correspondence to William E Evans.

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Diouf, B., Cheng, Q., Krynetskaia, N. et al. Somatic deletions of genes regulating MSH2 protein stability cause DNA mismatch repair deficiency and drug resistance in human leukemia cells. Nat Med 17, 1298–1303 (2011). https://doi.org/10.1038/nm.2430

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