Trk gene copy number variations and methylation

CNV – Overview

In this overview we will show a tumor from the COSMIC database with a TRK3 gene amplification. In our search of TRK gene copy number variations, the first study on the list was COSU331. Apparently, only one patient had a copy number increase in the TRK3 gene.

Philosophically, genes have been referred to as blue prints for proteins.  It does not matter how many copies of a blue print a person has, nothing is going to get made unless the blue print is unrolled and read.  So it is true for genes.  It doesn’t matter how many copies a cell has.  Nothing is going to get made unless the DNA is unwound from histones and it gets read.  Promoter methylation prevents transcription of the DNA.

Figure 1. Like blue prints, copy number doesn’t mean a thing unless the gene is unwound from histones and the promoter de-methylated.


The four cases of TRK3 hyper methylation

We found little correlation between TRK3 CNV and and the TrkC mRNA Z-score.  There were four cases of TRK3 promoter hypermethylation.  all of these tumors were from the same study

Cancer Genome Atlas Network.(2012)Comprehensive molecular characterization of human colon and rectal cancer. Nature. 487(7407):330-7. PubMed

Figure 2 An example of a Circos diagram of mutations in a colon adenocarcinoma

We can zoom in on chromosome 15 to see what is going on.


Figure 2 Four cases of TRK3 promoter hypermethylation found in colon cancer patients

The six cases of TRK2 hyper methylation

Like TRK3, there were no examples of TRK2 promoter hypo methylation in the COSMIC database.  There are six carcinomas in which the TRK2 was hypermethylated:  four in the breast and two in the prostate.  Yamada and coworkers (2004) found more promoter CpG island methylation in prostate cancer and prostate cancer cell lines than in normal prostate.

Figure 3. Tumors showing TRK2 hypermethylation


Yamada Y, Toyota M, Hirokawa Y, Suzuki H, Takagi A, Matsuzaki T, Sugimura Y, Yatani R, Shiraishi T, Watanabe M. (2004) Identification of differentially methylated CpG islands in prostate cancer. Int J Cancer.112(5):840-5.  PubMed


The 13 cases of TRK1 hypo methylation

Eleven of the 13 cases of TrkAIII promoter methylation were from The Cancer Genome Atlas (TCGA) for hepatocarcinoma.  There were no cases of TRK1 hypermethylation in the COSMIC database.

Figure 4. Some examples of TRK1 hypo methylation in the promoter of the TrkAIII splice variant.


In another post we have addressed expression of TrkAIII  in neuroblastoma without consideration of promoter hypo methylation.

There are more references in the COSMIC database of Trk promoter hyper, rather than hypo methylation.   In some ways it is disappointing that there was no follow up on whether hypo methylation of the TrkAIII promoter resulted in over expression of the constitutively active TrkAIII.  If there was over expression of TkAIII, were down stream targets of TrkAIII activated?  In such a scenario, one might consider a Trk treatment.  Ge (Gina) Wei presented a poster at the 2015 AACR demonstrating the effectiveness of a trk small molecule at inhibiting the growth of BaF3 cells transfected with various Trk constructs.  Many of these constructs were Trk fusions that we have covered on a separate site.  Tel-TrkC is MASC (mammary analog of secretory carcinoma treatment) for which there is an open clinical trial.  A fairly low dose of this small molecule was able to inhibit the growth  of BaF3 cells.  KM12 cells are a colorectal cell line that naturally express a Trk fusion with tropomyosin 3.

Figure 5. A small molecule inhibits the growth of BaF3 cells transfected with Trk constructs.

It is interesting to note that the Trk small molecule inhibitor did nothing to inhibit the growth of BaF3 cells growing in response to a native growth factor mouse interleukin 3.  Ge Wei and her coauthors concluded in their 2015 AACR poster:

  • BaF3 cells in the presence of their respective ligands.
    • Entrectinib  inhibits the proliferation of cells over expressing fusion and  wild-type Trks.
    • Their data supported exploration of entrectinib in cancers with NTRK
    rearrangements as well as tumors with Trk over expression.

The results for TrkAIII are particularly exciting if promoter hypo methylation is a reoccurring theme in more than just 13 carcinomas in TCGA database.  As for now, the Trk treatment trial is limited to patients with solid tumors driven by Trk, ROS1, and ALK gene rearrangements.