Developed through research led by head of VHIO’s Cancer Genome Engineering Group Francisco ‘Pancho’ Barriga during his postdoctoral stay at the Memorial Sloan Kettering Cancer Center (MSKCC) (1), New York, MACHETE is designed as novel tool to generate models for the in-depth study of genomic alterations frequently observed in cancer. This innovative system will help to advance insights into the function of genomic deletions and spur the design of novel therapeutic strategies.
Published online ahead of print as a Protocol article in the journal Nature Protocols (2), co-authors Barriga and Scott W. Lowe at MSKCC, present the two-stage MACHETE system—Molecular Alteration of Chromosomes with Engineered Tandem Elements—to address and overcome the previous limitations of other methodologies in successfully retrieving cells with large deletions.
Genome editing is used to make specific changes to the DNA of a cell or organism by adding, deleting, or altering DNA for research purposes. The concept of genetically modifying individual mammalian genes originated over fifty years ago thanks to the pioneering work of Mario R. Capecchi, Oliver Smithies and Martin J. Evans. Their discoveries of principles for introducing specific gene modifications in mice using embryonic stem cells earned them the 2007 Nobel Prize in Physiology or Medicine.
“Their early work paved the way for transforming our understanding of the roles that many genes have in human health and disease, including cancer. The 2020 Nobel Prize in Chemistry was awarded to Emmanuelle Charpentier and Jennifer Doudna for their discovery of CRISPR/Cas9 gene modifying technology that has had a revolutionary impact on the life sciences and has also helped to accelerate the development of new and targeted anti-cancer therapies,” observed Francisco Barriga, corresponding author of this present article.
Barriga’s group studies the function of large-scale chromosomal changes known as copy number alterations (CNAs), by combining state-of-the-art genome engineering strategies to uncover the mechanisms by which CNAs enable cancer cells to propagate and resist therapies. To better understand the complex biology of CNAs to identify new therapeutic strategies that target cells with these chromosomal aberrations,
they combine in vivo cancer models with MACHETE.
“CRISPR technology alone has its limitations in generating cell models of large-scale chromosomal deletions due to the rarity of these events, coupled with the fact that they are very difficult to find. We have therefore developed new gene editing methodology to specifically retrieve cells presenting these deletions,” said Barriga.
MACHETE is a two-stage CRISPR/Cas9-based system involving the initial insertion of a self-destruct button into the targeted chromosome region for deletion. Using CRISPR/Cas9 to eliminate the region of interest, cells bearing deletion destroy this button and survive, while the cells that did not make the deletion self-destruct.
These cell models of large-scale deletions can be used to investigate why patients presenting chromosome alterations have a worse response to treatment, or a poorer prognosis due to a lower likelihood of response to certain therapies.
“It’s rather like hunting for a needle in a haystack. We could use a metal detector to find the needle, but this would be a laborious, time-consuming task. Using MACHETE, we burn the stack so that only the needle remains, that is, the cells presenting the chromosomal alteration that we want to study,” added Francisco Barriga.
He concluded, “We propose a new conceptual and experimental framework for the study of large-scale chromosomal alterations. We know that these changes are very frequent in cancer, and we aim to achieve the same level of understanding that we have from the study of point mutations. New insights will help to better predict patients’ response and ultimately develop therapies that specifically target cells with these deletions.”
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