Enhanced dependency of KRAS-mutant colorectal cancer cells on RAD51-dependent homologous recombination repair identified from genetic interactions in Saccharomyces cerevisiae

Murugan Kalimutho, Amanda L. Bain, Bipasha Mukherjee, Purba Nag, Devathri M. Nanayakkara, Sarah K. Harten, Janelle L. Harris, Goutham N. Subramanian, Debottam Sinha, Senji Shirasawa, Sriganesh Srihari, Sandeep Burma, Kum Kum Khanna

Research output: Contribution to journalArticle

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Abstract

Activating KRAS mutations drive colorectal cancer tumorigenesis and influence response to anti-EGFR-targeted therapy. Despite recent advances in understanding Ras signaling biology and the revolution in therapies for melanoma using BRAF inhibitors, no targeted agents have been effective in KRAS-mutant cancers, mainly due to activation of compensatory pathways. Here, by leveraging the largest synthetic lethal genetic interactome in yeast, we identify that KRAS-mutated colorectal cancer cells have augmented homologous recombination repair (HRR) signaling. We found that KRAS mutation resulted in slowing and stalling of the replication fork and accumulation of DNA damage. Moreover, we found that KRAS-mutant HCT116 cells have an increase in MYC-mediated RAD51 expression with a corresponding increase in RAD51 recruitment to irradiation-induced DNA double-strand breaks (DSBs) compared to genetically complemented isogenic cells. MYC depletion using RNA interference significantly reduced IR-induced RAD51 foci formation and HRR. On the contrary, overexpression of either HA-tagged wild-type (WT) MYC or phospho-mutant S62A increased RAD51 protein levels and hence IR-induced RAD51 foci. Likewise, depletion of RAD51 selectively induced apoptosis in HCT116-mutant cells by increasing DSBs. Pharmacological inhibition targeting HRR signaling combined with PARP inhibition selectivity killed KRAS-mutant cells. Interestingly, these differences were not seen in a second isogenic pair of KRAS WT and mutant cells (DLD-1), likely due to their nondependency on the KRAS mutation for survival. Our data thus highlight a possible mechanism by which KRAS-mutant-dependent cells drive HRR in vitro by upregulating MYC-RAD51 expression. These data may offer a promising therapeutic vulnerability in colorectal cancer cells harboring otherwise nondruggable KRAS mutations, which warrants further investigation in vivo.

Original languageEnglish (US)
Pages (from-to)470-490
Number of pages21
JournalMolecular Oncology
Volume11
Issue number5
DOIs
StatePublished - May 1 2017

Fingerprint

Recombinational DNA Repair
Saccharomyces cerevisiae
Colorectal Neoplasms
HCT116 Cells
Mutation
Rad51 Recombinase
Double-Stranded DNA Breaks
RNA Interference
DNA Damage
Melanoma
Carcinogenesis
Therapeutics
Yeasts
Pharmacology
Apoptosis
Neoplasms

Keywords

  • KRAS
  • RAD51
  • colorectal cancer
  • DNA damage response
  • homologous recombination repair
  • therapeutic vulnerability

ASJC Scopus subject areas

  • Molecular Medicine
  • Genetics
  • Cancer Research

Cite this

Enhanced dependency of KRAS-mutant colorectal cancer cells on RAD51-dependent homologous recombination repair identified from genetic interactions in Saccharomyces cerevisiae. / Kalimutho, Murugan; Bain, Amanda L.; Mukherjee, Bipasha; Nag, Purba; Nanayakkara, Devathri M.; Harten, Sarah K.; Harris, Janelle L.; Subramanian, Goutham N.; Sinha, Debottam; Shirasawa, Senji; Srihari, Sriganesh; Burma, Sandeep; Khanna, Kum Kum.

In: Molecular Oncology, Vol. 11, No. 5, 01.05.2017, p. 470-490.

Research output: Contribution to journalArticle

Kalimutho, M, Bain, AL, Mukherjee, B, Nag, P, Nanayakkara, DM, Harten, SK, Harris, JL, Subramanian, GN, Sinha, D, Shirasawa, S, Srihari, S, Burma, S & Khanna, KK 2017, 'Enhanced dependency of KRAS-mutant colorectal cancer cells on RAD51-dependent homologous recombination repair identified from genetic interactions in Saccharomyces cerevisiae', Molecular Oncology, vol. 11, no. 5, pp. 470-490. https://doi.org/10.1002/1878-0261.12040
Kalimutho, Murugan ; Bain, Amanda L. ; Mukherjee, Bipasha ; Nag, Purba ; Nanayakkara, Devathri M. ; Harten, Sarah K. ; Harris, Janelle L. ; Subramanian, Goutham N. ; Sinha, Debottam ; Shirasawa, Senji ; Srihari, Sriganesh ; Burma, Sandeep ; Khanna, Kum Kum. / Enhanced dependency of KRAS-mutant colorectal cancer cells on RAD51-dependent homologous recombination repair identified from genetic interactions in Saccharomyces cerevisiae. In: Molecular Oncology. 2017 ; Vol. 11, No. 5. pp. 470-490.
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