Gliomas are solid
tumors that originate from glial cells in the brain or spine and account for 74.6% of malignant primary
central nervous system tumors worldwide. As patient-derived primary cells are important tools for drug screening and new
therapy development in
glioma, we aim to understand the genomic similarity of the primary cells to their parental
tumors by comparing their whole-genome copy number variations and expression profile of
glioma clinicopathologic factors. We found that the primary cells from grade II/III
gliomas lost most of the gene copy number alterations (CNAs), which were mainly located on chromosome 1p and 19q in their parental
tumors. The
glioblastoma (GBM) primary cells preserved 83.7% of the gene CNAs in the parental GBM
tumors, including chromosome 7 gain and 10q loss. The CNA gains of LINC00226 and ADAM6 and the chromosome 16p11 loss were reconstituted in primary cells from both grade II/III
gliomas and GBMs. Interestingly, we found these CNAs were correlated to overall survival (OS) in
glioma patients using the Merged Cohort LGG and GBM dataset from cBioPortal. The gene CNAs preserved in
glioma primary cells often predicted poor survival, whereas the gene CNAs lost in grade II/III primary cells were mainly associated to better prognosis in
glioma patients.
Glioma prognostic factors that predict better survival, such as IDH mutations and 1p/19q codeletion in grade II/III
gliomas, were lost in their primary cells, whereas methylated MGMT promoters as well as TERT promoter mutations were preserved in GBM primary cells while lost in grade II/III primary cells. Our results suggest that GBM primary cells tend to preserve CNAs in their parental
tumors, and these CNAs are correlated to poor OS and predict worse prognosis in
glioma patients.