Exome Sequencing of Plasma DNA Portrays the Mutation Landscape of Colorectal Cancer and Discovers Mutated VEGFR2 Receptors as Modulators of Antiangiogenic Therapies.

Abstract

Purpose: Despite the wide use of antiangiogenic drugs in the clinical setting, predictive biomarkers of response to these drugs are still unknown.Experimental Design: We applied whole-exome sequencing of matched germline and basal plasma cell-free DNA samples (WES-cfDNA) on a RAS/BRAF/PIK3CA wild-type metastatic colorectal cancer patient with primary resistance to standard treatment regimens, including inhibitors to the VEGF:VEGFR2 pathway. We performed extensive functional experiments, including ectopic expression of VEGFR2 mutants in different cell lines, kinase and drug sensitivity assays, and cell- and patient-derived xenografts.Results: WES-cfDNA yielded a 77% concordance rate with tumor exome sequencing and enabled the identification of the KDR/VEGFR2 L840F clonal, somatic mutation as the cause of therapy refractoriness in our patient. In addition, we found that 1% to 3% of samples from cancer sequencing projects harbor KDR somatic mutations located in protein residues frequently mutated in other cancer-relevant kinases, such as EGFR, ABL1, and ALK. Our in vitro and in vivo functional assays confirmed that L840F causes strong resistance to antiangiogenic drugs, whereas the KDR hot-spot mutant R1032Q confers sensitivity to strong VEGFR2 inhibitors. Moreover, we showed that the D717V, G800D, G800R, L840F, G843D, S925F, R1022Q, R1032Q, and S1100F VEGFR2 mutants promote tumor growth in mice.Conclusions: Our study supports WES-cfDNA as a powerful platform for portraying the somatic mutation landscape of cancer and discovery of new resistance mechanisms to cancer therapies. Importantly, we discovered that VEGFR2 is somatically mutated across tumor types and that VEGFR2 mutants can be oncogenic and control sensitivity/resistance to antiangiogenic drugs. Clin Cancer Res; 24(15); 3550-9. ©2018 AACR.

• Authors: Rodrigo A Toledo, Elena Garralda, Maria Mitsi, Tirso Pons, Jorge Monsech, Estela Vega, Álvaro Otero, Maria I Albarran, Natalia Baños, Yolanda Durán, Victoria Bonilla, Francesca Sarno, Marta Camacho-Artacho, Tania Sanchez-Perez, Sofia Perea, Rafael Álvarez, Alba De Martino, Daniel Lietha, Carmen Blanco-Aparicio, Antonio Cubillo, Orlando Domínguez, Jorge L Martínez-Torrecuadrada, Manuel Hidalgo
• Journal: Clinical cancer research : an official journal of the American Association for Cancer Research (Clin Cancer Res) Vol. 24 Issue 15 Pg. 3550-3559 (08 01 2018) ISSN: 1557-3265 [Electronic] United States
• PMID: 29588308 (Publication Type: Journal Article, Research Support, Non-U.S. Gov't)
• Copyright: ©2018 American Association for Cancer Research.

Chemical References

• Angiogenesis Inhibitors
• Biomarkers, Tumor
• Cell-Free Nucleic Acids
• VEGFA protein, human
• Vascular Endothelial Growth Factor A
• Class I Phosphatidylinositol 3-Kinases
• PIK3CA protein, human
• ALK protein, human
• Anaplastic Lymphoma Kinase
• EGFR protein, human
• ErbB Receptors
• KDR protein, human
• Vascular Endothelial Growth Factor Receptor-2
• ABL1 protein, human
• Proto-Oncogene Proteins c-abl

Topics

• Anaplastic Lymphoma Kinase (genetics)
• Angiogenesis Inhibitors (administration & dosage, adverse effects)
• Animals
• Biomarkers, Tumor (genetics)
• Cell Line, Tumor
• Cell Proliferation (genetics)
• Cell-Free Nucleic Acids (blood, genetics)
• Class I Phosphatidylinositol 3-Kinases (genetics)
• Colorectal Neoplasms (blood, drug therapy, genetics, pathology)
• ErbB Receptors (genetics)
• Exome (genetics)
• Female
• Heterografts
• Humans
• Mice
• Mutation
• Neovascularization, Pathologic (blood, drug therapy, genetics, pathology)
• Protein Conformation (drug effects)
• Proto-Oncogene Proteins c-abl (genetics)
• Vascular Endothelial Growth Factor A (genetics)
• Vascular Endothelial Growth Factor Receptor-2 (blood, chemistry, genetics)
• Exome Sequencing