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

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posted on 2023-03-31, 22:50 authored by Harshabad Singh, Yvonne Y. Li, Liam F. Spurr, Atul B. Shinagare, Ritika Abhyankar, Emma Reilly, Lauren K. Brais, Anwesha Nag, Matthew D. Ducar, Aaron R. Thorner, Geoffrey I. Shapiro, Rachel B. Keller, Cheta Siletti, Jeffrey W. Clark, Anna F. Farago, Jessica J. Lin, George D. Demetri, Rahul Gujrathi, Matthew H. Kulke, Laura E. MacConaill, Azra H. Ligon, Ewa Sicinska, Matthew L. Meyerson, Jeffrey A. Meyerhardt, Andrew D. Cherniack, Brian M. Wolpin, Kimmie Ng, Marios Giannakis, Jason L. Hornick, James M. Cleary

Supplementary Figure 1. Pan-TRK IHC in four cases identified as having NTRK fusions by OncoPanel analysis shows strong cytoplasmic staining confirming the presence of functional TRK fusion protein (40Ã-). Top left image demonstrates the specificity of TRK staining, which is present only in neoplastic cells, whereas adjacent normal crypts are negative. Supplementary Figure 2A. Two cases of ALK fusion in our cohort shared clinical and molecular features but differed in their microsatellite status. Both tumors were APC wild-type (wt) and contained biallelic RNF43 frameshift (fs) mutations. B. Copy number variation by chromosome is color-coded for two ALK fusion-associated colon cancers in our cohort. ALK+MMR-D cancer (top) displays a diploid genome, whereas ALK+MSS cancer (bottom) displays frequent copy number gains and losses. ALK fusion breakpoints are shown in both profiles (arrow). The vertical axis is the ratio of the number of reads for each specimen and a panel of normals in log base 2 scale. A value of 0 denotes no difference from normal (diploid). Supplementary Figure 3A. MMR-D RTK fusion CRC cases display a diploid genome similar to those in other MMR-D cases: BRAF V600E+mutated and Lynch syndrome. Copy number profile plots of RTK fusions or Wnt fusions with MSS CRC show extensive gains and losses and are shown for comparison. 3B. All MMR-D subgroups: BRAF V600E+, Lynch syndrome and RTK fusion show a significantly higher homopolymer indel rate (top) and TMB (bottom) than do MSS tumors with either RTK fusions or Wnt fusions. Supplementary Figure. 4. Histologic analysis with hematoxylin and eosin stained slides for two patients with NTRK1-LMNA fusions. Morphological analysis shows: A. mucinous and B. medullary histology.

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NIH

Damon Runyon Cancer Research Foundation

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ARTICLE ABSTRACT

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. 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. 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. 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.

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    cancer

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