Molecular Characterization and Therapeutic Targeting of Colorectal Cancers Harboring Receptor Tyrosine Kinase Fusions

Abstract

Purpose: Receptor tyrosine kinase fusions in colorectal cancers are rare, but potentially therapeutically relevant. We describe clinical, molecular, and pathologic attributes of RTK fusion-associated colorectal cancer.

Experimental design: We identified all cases with RTK fusions in patients with colorectal cancer seen at Dana-Farber Cancer Institute (Boston, MA) who underwent OncoPanel testing between 2013 and 2018. Clinical, histologic, and molecular features were extracted from the patient charts and molecular testing results.

Results: We identified 12 driver oncogenic fusions in various RTKs. These fusions occurred exclusively in BRAF and RAS wild-type tumors and were enriched in right-sided and mismatch repair-deficient (MMR-D) colorectal cancers. All of the MMR-D colorectal cancers with RTK fusions were found in tumors with acquired MMR-D due to MLH1 promoter hypermethylation and one was associated with a sessile serrated polyp. Molecular profiles of MMR-D colorectal cancer with RTK fusions largely resembled BRAF V600E-mutated MMR-D colorectal cancer, rather than those secondary to Lynch syndrome. We describe two patients with fusion-associated microsatellite stable (MSS) colorectal cancer who derived clinical benefit from therapeutic targeting of their translocation. The first harbored an ALK-CAD fusion and received sequential crizotinib and alectinib therapy for a total of 7.5 months until developing an ALK L1196Q gatekeeper mutation. The second patient, whose tumor contained an ROS1-GOPC fusion, continues to benefit from entrectinib after 9 months of therapy.

Conclusions: RTK fusions in colorectal cancer are a rare, but important disease subgroup that occurs in RAS and BRAF wild-type tumors. Despite enrichment in acquired MMR-D tumors, RTK fusions also occur in MSS colorectal cancer and provide an important therapeutic target.

Figure 1.

Co-mutation plot for RTK and Wnt fusions identified in our study. All cases of RTK fusions are BRAF and KRAS wild-type, whereas all cases of Wnt fusions are wild-type for mutations in canonical Wnt pathway genes including APC, CTNNB1 and RNF43.

Figure 2

A. Tumor mutational burden (TMB), homopolymer indel (HPI) frequency and base change spectrum in our identified groups: MMR-D: BRAF V600E mutated, Lynch syndrome and RTK fusions. MSS: RTK fusions and RSPO fusion. All three MMR-D subgroups have a higher TMB and HPI than MSS tumors with RTK or RSPO fusions. B. Lynch syndrome tumors demonstrate a higher TMB and HPI than MMR-D BRAF V600E tumors. Median TMB and HPI levels of MMR-D RTK fusion tumors are closer to MMR-D BRAF V600E tumors (text) but not significantly (ns) different from Lynch syndrome tumors, probably because of low case numbers. C. Co-mutation plot for the pre-defined groups. D. Varying frequencies of various oncogenes among the three MMR-D cancer subgroups. Q values for each oncogene are listed beneath their identifiers. Oncogenic mutations in KRAS, ERBB2 and CTNNB1 show relative predominance in Lynch syndrome. E. Lynch syndrome-associated MMR-D cancers demonstrate a lower median contribution from signature 15 than do BRAF V600E and RTK fusion-associated MMR-D cancers.

Figure 3

A. Clinical and radiographic correlates of patient treatment history and response. The patient experienced a dramatic albeit short-lived response on alectinib. B. Break-apart FISH probes demonstrated the continued presence of ALK fusion in the alectinib-resistant tumor-derived xenograft. Red and green signals hybridize to the 5’ and 3’ ends of the ALK gene. In the case of an intact ALK gene the two signals map close together, often appearing as a yellow, or fused, signal. Rearranged alleles are scored when at least a two-signal diameter spacing is observed between the red and green ALK signals (Red arrow). In addition to ALK rearrangement the FISH assay shows evidence of ALK gene polysomy as evidenced by 5 copies of ALK gene in the representative image. C. Comparison of SNVs detected in diagnostic and alectinib-resistant samples for this index case. Genetic testing showed a shared TP53 mutation and the continued detection of ALK-CAD fusion. An acquired ALK L1196Q gatekeeper mutation was detected in the alectinib-resistant sample along with several other mutations at low allelic frequency (Suppl. Table 3). RNF43 frameshift (fs) mutation was detected in the alectinib-resistant sample. This gene was not part of the earlier version of the assay performed on the diagnostic sample.

Figure 4

A. Radiographic trajectory of patient with ROS1-GOPC fusion showing consistent growth in retrocrural (A) and left internal iliac lymph nodes (B) between April and December 2019 whilst the patient was being closely observed. Entrectinib was initiated in early January 2020. Scans 8 months into therapy in August 2020 show stable disease with slight reduction in size of adenopathy. Measurements of index retrocrural nodes used for RECIST1.1 measurements are noted. The left internal iliac node is too small for measurements but was FDG avid on a prior PET CT.