P04.85 Molecular characteristics of low grade glioma progression

Abstract

Background

Low grade glioma (LGG), especially oligodendroglioma (ODG), are known for their usually good response to radio- and chemotherapy and relatively good prognosis amongst glioma. LGG can stay indolent after initial surgery for years, however many will eventually progress to higher grade tumor, although the pace of progression can differ greatly. Temozolomide administered after resection has been shown to promote a hypermutated recurrent tumor, however, not all patients receive postoperative chemotherapy. We investigated changes in the molecular profiles of genes involved in glioma development between primary and recurrent tumor.

Material and Methods

Eight pairs of tumors, from 6 males and 2 females diagnosed with LGG, were collected between 2008–2015. Three patients received chemo- or radiotherapy between surgeries. 1p19q co-deletion was assessed by droplet digital PCR and IDH mutations by Sanger sequencing. A glioma tailored HaloPlex NGS panel was created with 24 genes and 7 hotspot mutations (IDH1/2 TERT, ATRX, TP53, NF1/2, EGFR, CDKN2A/2B/2C, PTEN, PIK3CA, PIK3R1, CIC, FUBP1, RB1, MLH1/3, MSH2/3/5/6, PMS1/2, BRAF, H3F3A, LRIG1-3, NRAS). Library preparation was followed by Illumina sequencing on MiSeq. Variants were reported if missense or nonsense change was discovered and population allele frequency below 0.01. Transcriptome microarray data from the samples was used for hierarchical clustering and differential expression analysis.

Results

Three pairs of tumors did not show 1p19q co-deletion, out of which one was IDHwt and excluded. Tumors non-codeleted and IDH mutated were diffuse astrocytoma and IDHmut and codeleted tumors were ODG. The seven pairs of tumors were subjected to targeted resequencing and several variants were found. All IDH1mut were confirmed. SIFT and PolyPhen predicted damaging variants were found in FUBP1, CIC, TP53, EGFR, NF1, RB1, ATRX, TERT, CDKN2A, PIK3CA, MLH1 and MSH5. All variants were shared between primary and recurrent tumors, apart from 2 pairs. Mutations found in FUBP1 and CIC in the primary tumor of one ODG patient were absent at recurrence; both tumors were grade II. In an ODG that progressed from grade II to grade III a mutation in PIK3CA was detected at recurrence while a variant in NF1 was lost. Hierarchical clustering showed a good separation of primary and recurrent tumors and nearly 200 differentially expressed genes with 2-fold change were discovered, including up-regulation of the Rho family GTPase3, CHEK1, CDKN2C, CDKN3 and several others.

Conclusion

LGG are relatively stable in their mutational profile at recurrence in the genes analyzed. Mutations in genes thought to be drivers in ODG, like CIC and FUBP1 are not always retained in the recurrent tumor. Differences in expression profiles of primary and relapsed tumors indicate common changes during progression, however an expanded cohort studies are needed for their elucidation.