Trk Mutations in Pediatric Glioma

The following is a gleaning of Trk mutations from a very comprehensive whole genome sequencing study of a very devastating childhood disease: pediatric high grade glioma (Wu 2014). This is not meant to be a comprehensive review of the study but rather an introduction to some really intriguing Trk gene rearrangements and other events that occur with them.

Three next generation seqeuncing techniques were used to detect these structural variants (SV): whole genome sequencing, exome sequencing, and transcriptome sequencing.

Wu and coworkers reported structural variants (SV) producing gene fusions in 47% of diffuse intrinsic pontine gliomas (DIPGs) and non brain stem high grade gliomas (NBS-HGGs).  SV specifically involving TRK1, 2, and 3 were found in 40% of infants iwith NBS-HGGs

genomic alterations in pediatric DIPG (diffuse intrinsic pontine gliomas) and NBS-HGG (non brain stem high grade glioma). The arrow marks the TRK gene rearrangements (lime green bars) that are considered structural variations.

Figure 1 Overview of genomic alterations in pediatric DIPG (diffuse intrinsic pontine gliomas) and NBS-HGG (non brain stem high grade glioma).  The arrow marks the TRK gene rearrangements (lime green bars) that are considered structural variations (SV). Note the orange bars for insertions and deletions.

Figure 1, rows from top to bottom

rows 1-3.  Clinical features.  Note the age of the children in which TRK rearrangements are found.

row 4.  ACVR1 is a gene that codes for an activin receptor type-1  serine threonine kinase.  Unlike TRK genes, only missense mutations (deep purple) were found in this gene.

row 5.  Histone H3 is one of four proteins that act as spools for chromosomal DNA.  Mutations in the H3 gene are frequent in childhood gliomas but not as much so in adult gliomas.

green arrow.  Most of the genomic alterations in these genes are rearrangements also called SV by Wu and coworkers.  Note the absence of other genomic alterations in the TRK genes.

Gene fusions by simple rearrangements and by chromothripsis.

Chromothripsis is the catastrophic shattering of one or more chromosomes followed by error prone piecing them back together.  Circos diagrams were used by Wu and coworkers to give an overview of the landscape of select gliomas harboring Trk gene rearrangements.  The simple diagrams give us a view of a genome of chromosomal rearrangements.

Circos diagrams of pediatric gliomas driven by TRK gene rearrangements

Figure 2. Circos diagrams of pediatric gliomas driven by TRK gene rearrangements. The TPM3-NTRK3 and ETV6-NTRK3 gene fusions have been discussed in greater detail on other sites.

 

SJHGG027_D  This gene rearrangement may not drive cancer because of the orientation of TrkB and Bend5.  Stars mark the positions of these two genes.  Note that other intra-chromosomal rearrangements (green lines) in this patient.

SJHGG009_A  Many gene rearrangements seem to be happening in this tumor.  These multiple rearrangements are a hallmark of chromothripsis.  There should be a purple loop connecting chromosome 9 (TRK2) and chromosome 10 (VCL).   Vinculin, like tropomyosin 3, is an actin binding protein.  Unlike tropomyosin 3, vinculin is associated with cell-cell and cell-extracellular matrix adhesion.

SJHGG004_D  Chromosome 15 is at about 9 o’clock in this diagram.  The BTBD1 and TRK3 genes are marked by stars.  Their fusion is a green loop extending into the center of the circle.  Also note the orange bar telling us that gene amplification has also occurred in this region.   Another interesting feature is the purple loop connecting the general neighborhood of these two genes to chromosome 3.  The BTB/POZ domain-containing protein 1 is part of the ubiquitin ligase process.  It is conceivable that this fusion protein can dimerize in absence of ligand.  The BTBD1-trk3 fusion protein in anticipated to be inhibited with a Trk treatment.

SJHGG016_D  This is one of many tropomyosin 3 – TrkA coding gene rearrangements.  Not much else seems to be going wrong in this glioma.

Chromothripsis and a triple gene fusion

Wu and coworkers sought a greater understanding these events in tumor SJHG004_D.  SJHGG004_D is really a triple gene fusion involving non-coding regions called introns.  We only see only two of these three genes in the fusion protein because the middle gene is removed during mRNA splicing.

chromothripsis is pediatric glioma three genes are located on chromosome. Color of the connecting lines indicates how many times the nucleic acids were sequenced with a close up of the region showing the direction of reading frames. The fusion occured in the introns in the DNA of the gene. e. Only coding regions (exons) of TrkA and BTBD1 remained in the mRNA

Figure 3 A closer look at chromothripsis is pediatric glioma a. All three genes in question are located in a region of chromosome 15. b. The region of chromosome 15 where the rearrangements happened. This time the color of the connecting lines indicates how many times the nucleic acids were sequenced. c. A close up of the region shows thedirection of reading frames. d. The fusion occured in the introns in the DNA of the gene. e. Only coding regions (exons) of TrkA and BTBD1 remained in the mRNA

 

 

 

 

 

 

 

 

 

 

 

 

 

Wu G, Diaz AK, Paugh BS, Rankin SL, Ju B, Li Y, Zhu X, Qu C, Chen X, Zhang J, Easton J, Edmonson M, Ma X, Lu C, Nagahawatte P, Hedlund E, Rusch M, Pounds S, Lin T, Onar-Thomas A, Huether R, Kriwacki R, Parker M, Gupta P, Becksfort J, Wei L, Mulder HL, Boggs K, Vadodaria B, Yergeau D, Russell JC, Ochoa K, Fulton RS, Fulton LL, Jones C, Boop FA, Broniscer A, Wetmore C, Gajjar A, Ding L, Mardis ER, Wilson RK, Taylor MR, Downing JR, Ellison DW, Zhang J, Baker SJ. (2014) The genomic landscape of diffuse intrinsic pontine glioma and pediatric non-brainstem high-grade glioma. Nat Genet 46(5):444-450. PubMed

Important Information:

There is an open TRK fusion clinical trial that is actively enrolling any solid tumor patient with TRK fusions (STARTRK-2). For more information go to the NTRK trial website. The compound used in this clinical trial was tested in a cell line expressing the TPM3-NTRK1 fusion.  Entrectinib has been shown to cross the blood brain barrier in a mouse BCAN-TRK1 glioma model.   To learn more about entrectinib, watch this video.

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