Enrichment technique to allow early detection and monitor emergence of KRAS mutation in response to treatment

Sensitivity of cell-free circulating tumour DNA (ctDNA) assays is often hampered by the limited quantity of intact mutant nucleotide fragments. To overcome the issue of substrate limitation in clinical applications, we developed an enrichment method utilizing pyrrole-imidazole (PI) polyamides and th...

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Bibliographic Details
Published in:Scientific reports 2019-08, Vol.9 (1), p.11346-9, Article 11346
Main Authors: Kitagawa, Yoshiyasu, Okumura, Kazuhiro, Watanabe, Takayoshi, Tsukamoto, Kei, Kitano, Shiro, Nankinzan, Rino, Suzuki, Takuto, Hara, Taro, Soda, Hiroaki, Denda, Tadamichi, Yamaguchi, Taketo, Nagase, Hiroki
Format: Article
Language:English
Subjects:
38/22
38/47
631/1647/2217/2018
631/67/2322
692/4020/1503/1504/1885/1393
692/53/2421
Adult
Aged
Aged, 80 and over
Alleles
Cell Line, Tumor
Cell-Free Nucleic Acids - blood
Circulating Tumor DNA - blood
Codon - drug effects
Colorectal cancer
Colorectal carcinoma
Colorectal Neoplasms - blood
Colorectal Neoplasms - diagnosis
Colorectal Neoplasms - drug therapy
Colorectal Neoplasms - genetics
Deoxyribonucleic acid
DNA
DNA structure
DNA, B-Form - drug effects
DNA, B-Form - genetics
Early Detection of Cancer
Female
Humanities and Social Sciences
Humans
Imidazole
Imidazoles - chemistry
Imidazoles - pharmacology
K-Ras protein
Male
Metastases
Metastasis
Middle Aged
multidisciplinary
Mutation
Mutation - genetics
Nylons - chemistry
Nylons - pharmacology
Patients
Polyamides
Proto-Oncogene Proteins p21(ras) - blood
Proto-Oncogene Proteins p21(ras) - genetics
Pyrroles - chemistry
Pyrroles - pharmacology
Science
Science (multidisciplinary)
Therapeutic applications
Tumors
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Summary:Sensitivity of cell-free circulating tumour DNA (ctDNA) assays is often hampered by the limited quantity of intact mutant nucleotide fragments. To overcome the issue of substrate limitation in clinical applications, we developed an enrichment method utilizing pyrrole-imidazole (PI) polyamides and their ability to bind the minor groove of B-DNA. We present here a proof-of-concept experiment to enrich specific mutant KRAS alleles with biotinylated PI polyamides. We investigated the clinical feasibility of incorporating PI polyamides to detect KRAS mutations in ctDNA from 40 colorectal cancer (CRC) patients, of whom 17 carried mutations in KRAS . After enriching ctDNA with those polyamides, we used digital PCR to detect several common KRAS codon 12 mutations. Enrichment by biotinylated PI polyamides improved the sensitivity of ctDNA analysis (88.9% vs. 11.1%, P  
ISSN:2045-2322
2045-2322
DOI:10.1038/s41598-019-47700-9