Reliance upon ancestral mutations is maintained in colorectal cancers that heterogeneously evolve during targeted therapies

Mariangela Russo,Filippo Pietrantonio,Alberto Bardelli,Alberto Sogari,Simona Lamba,Federica Di Nicolantonio,Benedetta Mussolin,Giorgio Corti,Michael Linnebacher,Monica Montone,Luca Lazzari,Giuseppe Rospo,Salvatore Siena,Andrea Sartore-Bianchi,Annalisa Lorenzato,Sabrina Arena,Daniele Oddo

doi:10.1038/s41467-018-04506-z

Abstract

Attempts at eradicating metastatic cancers with targeted therapies are limited by the emergence of resistant subclones bearing heterogeneous (epi)genetic changes. We used colorectal cancer (CRC) to test the hypothesis that interfering with an ancestral oncogenic event shared by all the malignant cells (such as WNT pathway alterations) could override heterogeneous mechanisms of acquired drug resistance. Here, we report that in CRC-resistant cell populations, phylogenetic analysis uncovers a complex subclonal architecture, indicating parallel evolution of multiple independent cellular lineages. Functional and pharmacological modulation of WNT signalling induces cell death in CRC preclinical models from patients that relapsed during the treatment, regardless of the drug type or resistance mechanisms. Concomitant blockade of WNT and MAPK signalling restrains the emergence of drug-resistant clones. Reliance upon the WNT–APC pathway is preserved throughout the branched genomic drift associated with emergence of treatment relapse, thus offering the possibility of a common therapeutic strategy to overcome secondary drug resistance.

Highlights

Attempts at eradicating metastatic cancers with targeted therapies are limited by the emergence of resistant subclones bearing heterogeneousgenetic changes
To test whether dependency on WNT signalling was maintained in CRC cell populations that developed multiple heterogeneous mechanisms of targeted drug resistance, we first generated populations of cells resistant to the BRAF inhibitor dabrafenib, alone or in combination with the anti-EGFR monoclonal antibody cetuximab (Supplementary Fig. 1a, b; Supplementary Table 1), as combination regimens have shown promising activity in BRAF-mutated metastatic colorectal cancer patients[31]
To extend our findings beyond BRAF-mutant CRC, we characterised a previously established collection of RAS/BRAF WT cell lines, which were made resistant to the blockade of oncogenic kinases including anti EGFR antibodies and the NTRK inhibitor entrectinib (Fig. 1 and Supplementary Table 1)[2,3,5,6,7,32]

Summary

Introduction

Attempts at eradicating metastatic cancers with targeted therapies are limited by the emergence of resistant subclones bearing heterogeneous (epi)genetic changes. We and others have previously found that resistance mechanisms to agents blocking oncogenic proteins can be molecularly heterogeneous, and often include genetic alterations in downstream effectors of the same pathway, and/or activation of parallel bypass pathways[3,5,6,7] This phenomenon has been observed in patients, whereby individual metastatic lesions were shown to independently evolve distinct resistance mechanisms, which translated into lesion-specific response to subsequent lines of therapy and consequent clinical failure[8,9]. Most of cancer-linked APC variants are nonsense mutations, occurring in the mutation cluster region resulting in premature stop codons and a truncated gene product lacking the carboxyterminus of the protein[20,22] Because these truncations cause loss of the domains required for binding to β-catenin, APC inactivation leads to accumulation of nuclear β-catenin, which in turn activates the WNT signalling target transcription factors (T-cell factor or Tcf) and the lymphoid enhancer factor (LEF)[23], resulting in hyperactivation of the pathway

Methods

Results

Conclusion