Changes in colorectal carcinoma genomes under anti-EGFR therapy identified by whole-genome plasma DNA sequencing

• Published in: PLoS genetics Vol. 10; no. 3; p. e1004271
• Main Authors: Mohan, Sumitra, Heitzer, Ellen, Ulz, Peter, Lafer, Ingrid, Lax, Sigurd, Auer, Martina, Pichler, Martin, Gerger, Armin, Eisner, Florian, Hoefler, Gerald, Bauernhofer, Thomas, Geigl, Jochen B, Speicher, Michael R
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 01.03.2014; Public Library of Science (PLoS)
• Subjects: Aged; Aged, 80 and over; Antibodies, Monoclonal - administration & dosage; Antibodies, Monoclonal, Humanized - administration & dosage; Biomarkers, Tumor - blood; Cancer; Cetuximab; Colorectal cancer; Colorectal Neoplasms - blood; Colorectal Neoplasms - drug therapy; Colorectal Neoplasms - genetics; Colorectal Neoplasms - pathology; DNA sequencing; Drug Resistance, Neoplasm - genetics; ErbB Receptors - antagonists & inhibitors; ErbB Receptors - immunology; Female; Genes; Genetic aspects; Genetic research; Genome, Human; High-Throughput Nucleotide Sequencing; Humans; Kinases; Male; Medicine and Health Sciences; Middle Aged; Mutation; Nucleotide sequencing; Oncology, Experimental; Panitumumab; Plasma; Proto-Oncogene Proteins c-met - blood; Receptor, ErbB-2 - blood; Austria
• ISSN: 1553-7404; 1553-7390; 1553-7404
• DOI: 10.1371/journal.pgen.1004271

Monoclonal antibodies targeting the Epidermal Growth Factor Receptor (EGFR), such as cetuximab and panitumumab, have evolved to important therapeutic options in metastatic colorectal cancer (CRC). However, almost all patients with clinical response to anti-EGFR therapies show disease progression within a few months and little is known about mechanism and timing of resistance evolution. Here we analyzed plasma DNA from ten patients treated with anti-EGFR therapy by whole genome sequencing (plasma-Seq) and ultra-sensitive deep sequencing of genes associated with resistance to anti-EGFR treatment such as KRAS, BRAF, PIK3CA, and EGFR. Surprisingly, we observed that the development of resistance to anti-EGFR therapies was associated with acquired gains of KRAS in four patients (40%), which occurred either as novel focal amplifications (n = 3) or as high level polysomy of 12p (n = 1). In addition, we observed focal amplifications of other genes recently shown to be involved in acquired resistance to anti-EGFR therapies, such as MET (n = 2) and ERBB2 (n = 1). Overrepresentation of the EGFR gene was associated with a good initial anti-EGFR efficacy. Overall, we identified predictive biomarkers associated with anti-EGFR efficacy in seven patients (70%), which correlated well with treatment response. In contrast, ultra-sensitive deep sequencing of KRAS, BRAF, PIK3CA, and EGFR did not reveal the occurrence of novel, acquired mutations. Thus, plasma-Seq enables the identification of novel mutant clones and may therefore facilitate early adjustments of therapies that may delay or prevent disease progression.