Mutational analysis of the tyrosine kinome in serous and clear cell endometrial cancer uncovers rare somatic mutations in TNK2 and DDR1

Abstract

BackgroundEndometrial cancer (EC) is the 8th leading cause of cancer death amongst American women. Most ECs are endometrioid, serous, or clear cell carcinomas, or an admixture of histologies. Serous and clear ECs are clinically aggressive tumors for which alternative therapeutic approaches are needed. The purpose of this study was to search for somatic mutations in the tyrosine kinome of serous and clear cell ECs, because mutated kinases can point to potential therapeutic targets.MethodsIn a mutation discovery screen, we PCR amplified and Sanger sequenced the exons encoding the catalytic domains of 86 tyrosine kinases from 24 serous, 11 clear cell, and 5 mixed histology ECs. For somatically mutated genes, we next sequenced the remaining coding exons from the 40 discovery screen tumors and sequenced all coding exons from another 72 ECs (10 clear cell, 21 serous, 41 endometrioid). We assessed the copy number of mutated kinases in this cohort of 112 tumors using quantitative real time PCR, and we used immunoblotting to measure expression of these kinases in endometrial cancer cell lines.ResultsOverall, we identified somatic mutations in TNK2 (tyrosine kinase non-receptor, 2) and DDR1 (discoidin domain receptor tyrosine kinase 1) in 5.3% (6 of 112) and 2.7% (3 of 112) of ECs. Copy number gains of TNK2 and DDR1 were identified in another 4.5% and 0.9% of 112 cases respectively. Immunoblotting confirmed TNK2 and DDR1 expression in endometrial cancer cell lines. Three of five missense mutations in TNK2 and one of two missense mutations in DDR1 are predicted to impact protein function by two or more in silico algorithms. The TNK2P761Rfs*72 frameshift mutation was recurrent in EC, and the DDR1R570Q missense mutation was recurrent across tumor types.ConclusionsThis is the first study to systematically search for mutations in the tyrosine kinome in clear cell endometrial tumors. Our findings indicate that high-frequency somatic mutations in the catalytic domains of the tyrosine kinome are rare in clear cell ECs. We uncovered ten new mutations in TNK2 and DDR1 within serous and endometrioid ECs, thus providing novel insights into the mutation spectrum of each gene in EC.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2407-14-884) contains supplementary material, which is available to authorized users.

The prognostic effects of somatic mutations in ER-positive breast cancer

“…DDR1 is a collagen-binding receptor expressed in epithelial cells that stabilizes E-cadherin-mediated intracellular adhesion 27 . DDR1 mutations also occur in endometrial cancer 28 , acute leukemia 29 , and lung cancer 30 . Loss of DDR1 (DDR1-null mice) produces hyper-proliferation and abnormal branching of mammary ducts, suggesting DDR1 is a breast tumor suppressor 31 .…”

Somatic mutation profiles of clear cell endometrial tumors revealed by whole exome and targeted gene sequencing

“…Likewise, the rate of MSI is higher in EECs than SECs 12, 26 . We previously assessed MSI and Sanger sequenced all seven genes in 45 SECs 7, 15, 16 and five of the seven genes in 40 EECs 7, 15, 16, 27 ; here we Sanger sequenced TP53 and ARID1A in EECs (Supplementary Table 6). Overall, 66.7% of CCECs, 82.2% of SECs, and 97.5% of EECs had at least one detectable alteration across the seven genes and MSI.…”

“…Somatic mutations (yellow) and MSI (gray) are indicated. Genes for which a subset of cases (23 tumors) were analyzed previously for mutations and MSI as reported elsewhere 7,15,16,27 are denoted by a pound sign (#).…”

The prognostic effects of somatic mutations in ER-positive breast cancer

“…DDR1 is a collagen-binding receptor expressed in epithelial cells that stabilizes E-cadherin–mediated intracellular adhesion 22 . DDR1 mutations also occur in endometrial cancer 23 , acute leukemia 24 and lung cancer 25 . Loss of DDR1 (DDR1-null mice) produces hyper-proliferation and abnormal branching of mammary ducts, suggesting DDR1 is a breast tumor suppressor 26 .…”