Changes in Colorectal Carcinoma Genomes under Anti-EGFR Therapy Identified by Whole-Genome Plasma DNA Sequencing

Abstract

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.

Large extracellular vesicles carry most of the tumour DNA circulating in prostate cancer patient plasma

“…We obtained 83.9 million mapped reads (≥50 bp of length) from L-EV DNA which provides ~1.4× coverage. This is compatible with low-pass sequencing used to call large somatic aberrations in cfDNA [34] and enabled us to call somatic genomic alterations at a genome-wide scale. A strong correlation between the numbers of reads mapping to the human genome in L-EVs and donor cell DNA ( r  = 0.808, Spearman rank correlation, bin size 0.5 Mbp) indicated similar genome coverage in L-EVs and donor cells.…”

Resistance to Anti-EGFR Therapy in Colorectal Cancer: From Heterogeneity to Convergent Evolution

“…ERBB2 or MET gene amplifi cations were described as drivers of acquired resistance to EGFR blockade in cell models and patient samples ( 35 , 38 ). Several reports confi rmed the initial results on the emergence of MET gene amplifi cation in patients who develop acquired resistance to EGFR blockade ( 73,74 ).…”

Neueste technologische Entwicklungen für die Analyse von zirkulierender Tumor-DNA

“…Neben Mutationen in den Genen KRAS oder EGFR zeigen sich unter anderem auch fokale Amplifikationen von KRAS und MET bei progredienten Patienten unter Anti-EGFR-Therapie, die aus dem Plasma nachgewiesen werden können [86]. Diese und viele weitere Daten weisen auf eine äußerst komplexe Dynamik von Tumoren hin und unterstreichen die Notwendigkeit von kontinuierlich erfassten, genetischen Follow-up-Daten.…”