The role of germline heterozygous LZTR1 variants in pediatric cancer predisposition

Abstract

Cancer is caused by various mutations in the DNA which can occur spontaneously during life, called somatic mutations, or which can already be present in the DNA at birth, called germline mutations. The presence of germline mutations which can cause cancer means that someone has a predisposition to cancer. We can identify whether patients have a cancer predisposition by sequencing the DNA of their healthy cells. In this sequencing data we can look for mutations in well-known cancer predisposition genes, but sometimes interesting mutations appear in genes for which we do not yet know if they result in cancer predisposition. An example of such unknown mutations are mutations in the leucine zipper-like transcription regulator 1 (LZTR1) gene. We have recently identified multiple different mutations in LZTR1 in the germline of children with different types of cancer. We see these germline mutations more often in children with cancer than in healthy people. It is not yet known whether these germline LZTR1 mutations can result in cancer development in children, and thus whether it is a cancer predisposition gene in children. To investigate this, we have created cell lines where the LZTR1 protein is absent, to mimic the presence of a germline LZTR1 mutation in a patient, as well as cell lines where the LZTR1 protein is still present. We performed RNA sequencing on these cell lines and compared the results with each other, to see what the effect of the removal of LZTR1 is on the gene expression. We looked at individual genes as well as whole signaling pathways to see which genes and pathways are higher or lower expressed when LZTR1 is absent, and whether we can link these genes and pathways to cancer development. Thus far, we cannot draw any conclusion from this analysis because the sample size is too small to determine significant changes in gene expression. Besides the cell lines, we have also collected data from children with cancer and a germline mutation in LZTR1. We compared this patient data to a cohort of patients with the same tumor type but without the germline LZTR1 mutation, to see which genes and pathways are higher or lower expressed in the tumors due to the LZTR1 mutation. We have performed this comparison for one tumor sample, which is, again, too small to get significant results from the analysis. Lastly, we wanted to compare the results from the cell lines to the results from the patient data. The aim was to look at the genes that are higher or lower expressed in the cell lines without the LZTR1 protein and see if these specific genes have also changed expression in the tumor samples of the patients. To perform this comparison in the future it is necessary to identify more cell clones with and without the LZTR1 protein and perform RNA sequencing on them, to be able to draw conclusions on significant changes in gene expression caused by the absence of LZTR1.