Identification Of Familial Wilms Tumor Predisposition Genes Using Whole Genome Sequencing

Author

Timothy B. Palculict, The University of Texas Graduate School of Biomedical Sciences at HoustonFollow

Date of Graduation

8-2015

Document Type

Dissertation (PhD)

Program Affiliation

Genes and Development

Degree Name

Doctor of Philosophy (PhD)

Advisor/Committee Chair

Vicki Huff

Committee Member

Russell Broaddus

Committee Member

Sharon Plon

Committee Member

Xiaoping Su

Committee Member

Jessica Tyler

Abstract

Wilms tumor, a childhood tumor arising from undifferentiated renal mesenchyme, is diagnosed in North America at a frequency of 1 in 10,000 live births and accounts for 5% of all pediatric cancers. The etiology of Wilms tumor is heterogeneous with multiple genes known to have an effect on Wilms tumor development; however, these genes are rarely associated with familial Wilms tumor. Gene mutations in WT1, WTX, CTNNB1 and TP53 are observed in a third of sporadic tumors, while the causative gene(s) responsible for familial Wilms tumor are largely unknown. Approximately 2% of Wilms tumor patients have a family history of Wilms tumor. Familial predisposition is inherited in an autosomal dominant manner and demonstrates incomplete penetrance, estimated to be 30%.

Whole genome sequencing of eleven individuals in three Wilms tumor families was performed to identify the gene(s) responsible for genetic predisposition to Wilms tumor in these families, and to increase our understanding of a genetically heterogeneous cancer. Variant calling was performed by GATK, FamSeq and CASAVA to detect single nucleotide variations (SNVs), insertions/deletions (indels) and structural variants. Shared variants within each family were identified and prioritized based on expression in fetal kidney, minor allele frequency less than 1%, and the predicted functional significance of the alteration on protein structure. Candidate mutations were then assessed in each family for cosegregation with the affected/obligate carrier status. To examine the sequence integrity and frequency of candidate gene mutations in Wilms tumor, a comprehensive mutation analysis of each candidate gene, including Sanger sequencing of the entire coding region and quantitative PCR (qPCR) to detect exonic insertions/deletions, was performed using genomic DNA from 47 additional Wilms tumor families and tumor DNA from 175 sporadic Wilms tumors. As a result, a recurrent 570kb germline duplication including NBAS, DDX1, MYCN and MYCNOS was identified in 4% of families, as well as germline missense mutations in DICER1 (4% of families) and SPHK2. Functional studies demonstrate that the missense mutation identified in SPHK2 does not have an effect on apoptosis or proliferation, but instead alters SPHK2 subcellular localization and expression of target genes.

Our analysis resulted in the successful identification of Wilms tumor predisposition genes in each family, and provided support for the involvement of DICER1 and DDX1/MYCN in Wilms tumor development. Additionally, our identification of SPHK2 as the 19q familial Wilms tumor predisposition gene has opened up new avenues of research into the role of sphingolipid signaling in nephrogenesis and cancer development. Significantly, the communication of these results directly to patients within each family allows for the continued monitoring of new family members for the potential early detection of not only Wilms tumor, but other phenotypes associated with the specific gene mutations.

Keywords

cancer genetics, Wilms tumor, DICER1, SPHK2, MYCN, DDX1