Utilizing the Dog Genome in the Search for Novel Candidate Genes Involved in Glioma Development—Genome Wide Association Mapping followed by Targeted Massive Parallel Sequencing Identifies a Strongly Associated Locus

Abstract

Gliomas are the most common form of malignant primary brain tumors in humans and second most common in dogs, occurring with similar frequencies in both species. Dogs are valuable spontaneous models of human complex diseases including cancers and may provide insight into disease susceptibility and oncogenesis. Several brachycephalic breeds such as Boxer, Bulldog and Boston Terrier have an elevated risk of developing glioma, but others, including Pug and Pekingese, are not at higher risk. To identify glioma-associated genetic susceptibility factors, an across-breed genome-wide association study (GWAS) was performed on 39 dog glioma cases and 141 controls from 25 dog breeds, identifying a genome-wide significant locus on canine chromosome (CFA) 26 (p = 2.8 x 10−8). Targeted re-sequencing of the 3.4 Mb candidate region was performed, followed by genotyping of the 56 SNVs that best fit the association pattern between the re-sequenced cases and controls. We identified three candidate genes that were highly associated with glioma susceptibility: CAMKK2, P2RX7 and DENR. CAMKK2 showed reduced expression in both canine and human brain tumors, and a non-synonymous variant in P2RX7, previously demonstrated to have a 50% decrease in receptor function, was also associated with disease. Thus, one or more of these genes appear to affect glioma susceptibility.

Probenecid directly impairs activation of the canine P2X7 receptor

“…[1] Activation of this receptor channel allows the rapid flux of Na + , K + and Ca 2+ , and the opening of a pore to allow the movement of organic cations, including fluorescent dyes such as ethidium + , through the plasma membrane. [1] P2X7 is present on canine erythrocytes, lymphocytes and monocytes, [2,3] , as well as brain [4,5] and kidney epithelial cells [6] of dogs. Activation of canine P2X7 leads to pro-inflammatory interleukin-1β (IL-1β) release from monocytes [7] and in whole blood, [8,9] as well as to phosphatidylserine exposure on erythrocytes.…”

Whole-genome genotyping and resequencing reveal the association of a deletion in the complex interferon alpha gene cluster with hypothyroidism in dogs

“…The prioritized variants were breed-specific and potentially causative, thus being instrumental in our fine-mapping approach, as neither the Giant Schnauzer nor any other Schnauzer breed was included in the design of the 170 K Illumina SNPChip. Such high-throughput regenotyping of selected relevant variants has previously been proven as an efficient approach for fine-mapping of genome-wide loci of association [3,37], even though the detection of the actual causative variant(s) has been challenging. The studies that succeeded in identifying causative mutation(s) could employ an additional dog breed sharing the same candidate locus in order to pinpoint the shared minimal haplotype [38].…”

Novel canine isocitrate dehydrogenase 1 mutation Y208C attenuates dimerization ability

“…Since there are more sensitive detection methods, such as allele-specific oligonucleotide–PCR and pyrosequencing ( 29 , 30 ), using these methods may further increase the positive mutation rate. Deep sequencing analysis has been performed in canine glioma cases ( 23 , 31 ), but the Y208C mutation was not detected; therefore, the Y208C mutation may be a unique mutation in CS. Two cases of c.623A>C and p.Y208C mutations in human liver cancer were archived in the Catalog of Somatic Mutations In Cancer (COSMIC; ) database ( 32 ), but the gene function alterations were not described.…”