A team of Korean scientists, led by Dr. Seo of Precision Medicine Center, Seoul National University, Korea, used Bionano optical mapping to identify rearrangements and interpret gene amplification mechanisms in a methotrexate (MTX)-resistant colon cancer cell line (HT-29).
Colorectal cancer is the third most commonly occurring cancer in men and the second most commonly occurring cancer in women. MTX is the most widely used chemotherapeutic drug for treating colon cancer. Unfortunately, once the malignant cells develop drug resistance, it limits the outcome of MTX to arrest the progression of the disease. MTX resistance is acquired through different ways. In colon cancer cells and acute lymphoblastic leukemia, DHFR gene amplification on chromosome 5 has been a hallmark of methotrexate (MTX) resistance. Hence, it is important to identify the genetic features and mechanisms that promote amplification in tumors. These mechanisms might serve as therapeutic targets that can prevent drug resistance and overcome a tumor. However, little is known about DHFR gene amplification due to difficulties in quantifying amplification size and accurately identifying the repetitive rearrangements involved in the process.
Bionano optical mapping was used to analyze a tandemly duplicated 2.2 Mbp region on chromosome 5. Current long and short sequencing-based technologies lacked coverage and mapping over this 2.2 Mbp amplified region. However, using Bionano technology that can analyze long genomic regions, the team of scientists identified a novel insertion at the endpoint of the amplified region, which was missed by long read sequencing using a PacBio platform. In addition to the novel insertion, inversions at both the start and endpoints of the amplified region were also uncovered.
The current study shows that optical mapping, a comprehensive and elegant genome analysis technique, is required to interpret repetitive sequences and structural variations in cancers manifested by gene amplifications. This study ultimately aims to identify the crucial therapeutic mechanisms and provide in-depth guidance toward pharmacological targets for anti-cancer drugs as well as personalized medicine.
Curious to know more about this study? Read the entire study on BioRxiv.