Using The MACHETE Method, Scientists Can Now Analyze Copy Number Alterations In Cancer Genomes
Using the MACHETE method, scientists can now analyze copy number alterations in cancer genomes. Poorer survival was shown in mouse models of pancreatic cancer and melanoma when researchers used MACHETE to discover that a significant deletion often destroys a cluster of interferon genes. Possible biomarker of immunotherapy success: intact tumor interferons.
Francisco "Pancho" Barriga and Kaloyan Tsanov of the Sloan Kettering Institute don't want the name of their new research method to take away from their findings, which give new information about a genetic change that causes about 15% of all cancers and may help doctors find patients who are likely to respond to immunotherapies.
The two researchers have come up with a method based on CRISPR that they call MACHETE to study copy number alterations (CNAs). CNAs are common large-scale genomic changes seen in cancer. Molecular Alteration of Chromosomes by Means of Engineered Tandem Elements (MACHTE) describes this kind of chromosome manipulation. As with cancer and other human diseases, this new method involves taking out large, specific pieces of genetic material.
This is important because it gives the first easy and effective way to study CNA deletions in lab models, like the mouse models of pancreatic cancer and melanoma they used in their work, which was published in Nature Cancer on November 7, 2022.
At first, we didn't even want to mention MACHETE in the title of our work so we could focus more on the interesting biology we saw.
- Dr. Barriga, Memorial Sloan Kettering Cancer Center
COPYRIGHT_WI: Published on https://washingtonindependent.com/using-the-machete-method-scientists-can-now-analyze-copy-number-alterations-in-cancer-genomes/ by William Willis on 2022-11-10T08:39:40.482Z
Even yet, when he initially presented the findings, a labmate taped a picture of Danny Trejo's character Machete on his desk. Nor did it prevent another researcher from tweeting a link to the preprint of the study to the actor's account.
Cancer Caused By Multiple Mutations In The Same Gene
To understand how the research broke new ground about one of the most prevalent copy number abnormalities in human tumors and what it can entail for patients, one must understand the underlying biology. Cancer mutations are often seen as "typos" in the genetic code that switch on or off a specific gene. For decades, experts have focused on these little flaws that cause cancer.
Copy number changes may duplicate or delete significant parts of individual chromosomes. A typical tumor has 24 CNAs that affect 30% of its genome, researchers say. Dr. Tsanov, like Dr. Barriga, is a postdoc in the lab of senior author and Cancer Biology & Genetics Program Chair Scott Lowe. "CNAs are just as vital, but more complicated."
CNA-laden tumors are related to recurrence and poorer outcomes in breast, prostate, endometrial, renal clear cell, thyroid, and colorectal cancer. The breadth and diversity of the modifications — impacting hundreds or millions of DNA base pairs rather than a single letter — makes them challenging to re-create in laboratory animals for careful examination.
I wondered: 'How can we select cells with the intended deletions even if they are very rare? I got an idea and drew up the initial concept for what would be the general strategy that evening. When we tried it, it just worked. I may never have something come together that smoothly for the rest of my career.
- Dr. Barriga
The pair recognized they were onto something when genetic modifications produced with MACHETE in a mouse model of pancreatic ductal adenocarcinoma had the same results as a comparable naturally occurring mutation in a different animal model Dr. Tsanov was examining for a separate project.
Dr. Tsanov says the team worked closely from then on. More than a dozen experts from MSK, the Ontario Institute for Cancer Research, NYU Grossman School of Medicine, and the Princess Margaret Cancer Centre in Toronto also participated.
Somatic Copy Number Alterations in Cancer
Research May Identify Immunotherapy Patients
Mice in the lab developed tumors after having genetically "engineered" cells transplanted into their pancreases. The CDKN2A gene, which is known to be a tumor-suppressor gene, was eliminated by the genetic modifications that destroyed a chunk of chromosome 9. Because of this, the cells' natural defenses against tumor development were disabled.
Scientists sought to determine how important a group of proteins called interferons were in stimulating immune cells to attack foreign invaders like cancer cells, so they cut out the genes for all of them in one fell swoop. About half of individuals with 9 p21.3 CNAs, the most common CNA in humans, develop malignancies in which these interferons are also absent.
"We have known about CDKN2A mutations for a long time, and it was already astonishing how they functioned," says Dr. Lowe, who is also an investigator at the Howard Hughes Medical Institute. This research shows that there is much more going on, and it has significant therapeutic implications.
Researchers found that not having enough interferons is bad for cancer because it makes tumors invisible to the cells that protect the immune system and helps them spread.
Dr. Lowe notes that studying interferons has been challenging since they are encoded by a cluster of 16 genes. The use of MACHETE showed a major way that growing cancer cells hide from the immune system and may also contribute to resistance to immunotherapies that try to get the immune system working again so it can fight the cancer.
Dr. Lowe said that co-author Dana Pe'er, a computational biologist at the Sloan Kettering Institute, helped the team understand how the mutation of interferon genes affected immune cells and helped the disease avoid the immune system. The results matched a mouse model of both melanoma and pancreatic cancer.
Therefore, the study results imply that individuals with a functional interferon area may be more suitable for immunotherapy. Even though immunotherapies have a lot of promise, it has been hard to tell which tumors in which people would respond to treatment.
The cluster of interferon genes is not routinely collected even by state-of-the-art genomic assays like MSK-IMPACT®. Dr. Lowe suggests further research is needed to see whether including it in sequencing testing will improve the ability to identify individuals who will have the greatest chance of success with immunotherapy.
Meanwhile, people have been found to have chromosomal deletion syndromes, which include many conditions linked to CNA deletions.